[{"intvolume":" 12224","month":"07","alternative_title":["LNCS"],"scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"This paper presents a foundation for refining concurrent programs with structured control flow. The verification problem is decomposed into subproblems that aid interactive program development, proof reuse, and automation. The formalization in this paper is the basis of a new design and implementation of the Civl verifier."}],"related_material":{"record":[{"id":"8332","status":"public","relation":"dissertation_contains"}]},"volume":12224,"language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"8201","success":1,"creator":"dernst","date_updated":"2020-08-06T08:14:54Z","file_size":804237,"date_created":"2020-08-06T08:14:54Z","file_name":"2020_LNCS_Kragl.pdf"}],"publication_status":"published","publication_identifier":{"eisbn":["9783030532888"],"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["9783030532871"]},"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"conference","_id":"8195","department":[{"_id":"ToHe"}],"file_date_updated":"2020-08-06T08:14:54Z","ddc":["000"],"date_updated":"2023-09-07T13:18:00Z","oa":1,"publisher":"Springer Nature","quality_controlled":"1","acknowledgement":"Bernhard Kragl and Thomas A. Henzinger were supported by\r\nthe Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award).","date_created":"2020-08-03T11:45:35Z","doi":"10.1007/978-3-030-53288-8_14","date_published":"2020-07-14T00:00:00Z","page":"275-298","publication":"Computer Aided Verification","day":"14","year":"2020","has_accepted_license":"1","isi":1,"project":[{"grant_number":"Z211","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"title":"Refinement for structured concurrent programs","external_id":{"isi":["000695276000014"]},"article_processing_charge":"No","author":[{"first_name":"Bernhard","id":"320FC952-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7745-9117","full_name":"Kragl, Bernhard","last_name":"Kragl"},{"full_name":"Qadeer, Shaz","last_name":"Qadeer","first_name":"Shaz"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724","last_name":"Henzinger"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Kragl B, Qadeer S, Henzinger TA. 2020. Refinement for structured concurrent programs. Computer Aided Verification. , LNCS, vol. 12224, 275–298.","chicago":"Kragl, Bernhard, Shaz Qadeer, and Thomas A Henzinger. “Refinement for Structured Concurrent Programs.” In Computer Aided Verification, 12224:275–98. Springer Nature, 2020. https://doi.org/10.1007/978-3-030-53288-8_14.","apa":"Kragl, B., Qadeer, S., & Henzinger, T. A. (2020). Refinement for structured concurrent programs. In Computer Aided Verification (Vol. 12224, pp. 275–298). Springer Nature. https://doi.org/10.1007/978-3-030-53288-8_14","ama":"Kragl B, Qadeer S, Henzinger TA. Refinement for structured concurrent programs. In: Computer Aided Verification. Vol 12224. Springer Nature; 2020:275-298. doi:10.1007/978-3-030-53288-8_14","ieee":"B. Kragl, S. Qadeer, and T. A. Henzinger, “Refinement for structured concurrent programs,” in Computer Aided Verification, 2020, vol. 12224, pp. 275–298.","short":"B. Kragl, S. Qadeer, T.A. Henzinger, in:, Computer Aided Verification, Springer Nature, 2020, pp. 275–298.","mla":"Kragl, Bernhard, et al. “Refinement for Structured Concurrent Programs.” Computer Aided Verification, vol. 12224, Springer Nature, 2020, pp. 275–98, doi:10.1007/978-3-030-53288-8_14."}},{"department":[{"_id":"ToHe"}],"date_updated":"2023-09-07T13:18:00Z","status":"public","type":"conference","conference":{"end_date":"2020-06-20","location":"London, United Kingdom","start_date":"2020-06-15","name":"PLDI: Programming Language Design and Implementation"},"_id":"8012","related_material":{"record":[{"relation":"dissertation_contains","id":"8332","status":"public"}]},"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9781450376136"]},"publication_status":"published","month":"06","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1145/3385412.3385980","open_access":"1"}],"oa_version":"Published Version","abstract":[{"text":"Asynchronous programs are notoriously difficult to reason about because they spawn computation tasks which take effect asynchronously in a nondeterministic way. Devising inductive invariants for such programs requires understanding and stating complex relationships between an unbounded number of computation tasks in arbitrarily long executions. In this paper, we introduce inductive sequentialization, a new proof rule that sidesteps this complexity via a sequential reduction, a sequential program that captures every behavior of the original program up to reordering of coarse-grained commutative actions. A sequential reduction of a concurrent program is easy to reason about since it corresponds to a simple execution of the program in an idealized synchronous environment, where processes act in a fixed order and at the same speed. We have implemented and integrated our proof rule in the CIVL verifier, allowing us to provably derive fine-grained implementations of asynchronous programs. We have successfully applied our proof rule to a diverse set of message-passing protocols, including leader election protocols, two-phase commit, and Paxos.","lang":"eng"}],"title":"Inductive sequentialization of asynchronous programs","author":[{"first_name":"Bernhard","id":"320FC952-F248-11E8-B48F-1D18A9856A87","full_name":"Kragl, Bernhard","orcid":"0000-0001-7745-9117","last_name":"Kragl"},{"last_name":"Enea","full_name":"Enea, Constantin","first_name":"Constantin"},{"full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"},{"first_name":"Suha Orhun","full_name":"Mutluergil, Suha Orhun","last_name":"Mutluergil"},{"last_name":"Qadeer","full_name":"Qadeer, Shaz","first_name":"Shaz"}],"external_id":{"isi":["000614622300016"]},"article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Kragl, Bernhard, et al. “Inductive Sequentialization of Asynchronous Programs.” Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation, Association for Computing Machinery, 2020, pp. 227–42, doi:10.1145/3385412.3385980.","short":"B. Kragl, C. Enea, T.A. Henzinger, S.O. Mutluergil, S. Qadeer, in:, Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation, Association for Computing Machinery, 2020, pp. 227–242.","ieee":"B. Kragl, C. Enea, T. A. Henzinger, S. O. Mutluergil, and S. Qadeer, “Inductive sequentialization of asynchronous programs,” in Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation, London, United Kingdom, 2020, pp. 227–242.","apa":"Kragl, B., Enea, C., Henzinger, T. A., Mutluergil, S. O., & Qadeer, S. (2020). Inductive sequentialization of asynchronous programs. In Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation (pp. 227–242). London, United Kingdom: Association for Computing Machinery. https://doi.org/10.1145/3385412.3385980","ama":"Kragl B, Enea C, Henzinger TA, Mutluergil SO, Qadeer S. Inductive sequentialization of asynchronous programs. In: Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation. Association for Computing Machinery; 2020:227-242. doi:10.1145/3385412.3385980","chicago":"Kragl, Bernhard, Constantin Enea, Thomas A Henzinger, Suha Orhun Mutluergil, and Shaz Qadeer. “Inductive Sequentialization of Asynchronous Programs.” In Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation, 227–42. Association for Computing Machinery, 2020. https://doi.org/10.1145/3385412.3385980.","ista":"Kragl B, Enea C, Henzinger TA, Mutluergil SO, Qadeer S. 2020. Inductive sequentialization of asynchronous programs. Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation. PLDI: Programming Language Design and Implementation, 227–242."},"project":[{"name":"The Wittgenstein Prize","grant_number":"Z211","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"doi":"10.1145/3385412.3385980","date_published":"2020-06-01T00:00:00Z","date_created":"2020-06-25T11:40:16Z","page":"227-242","day":"01","publication":"Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation","isi":1,"year":"2020","publisher":"Association for Computing Machinery","quality_controlled":"1","oa":1},{"page":"135","date_created":"2020-09-10T09:26:49Z","date_published":"2020-09-10T00:00:00Z","doi":"10.15479/AT:ISTA:8358","year":"2020","has_accepted_license":"1","day":"10","oa":1,"publisher":"Institute of Science and Technology Austria","acknowledgement":"I should also express my gratitude to the bioimaging facility at IST Austria, for their assistance with the TIRF setup over the years, and especially to Christoph Sommer, who gave me a lot of input when I was starting to dive into programming.","article_processing_charge":"No","author":[{"orcid":"0000-0001-6730-4461","full_name":"Dos Santos Caldas, Paulo R","last_name":"Dos Santos Caldas","id":"38FCDB4C-F248-11E8-B48F-1D18A9856A87","first_name":"Paulo R"}],"title":"Organization and dynamics of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinkers","citation":{"ista":"Dos Santos Caldas PR. 2020. Organization and dynamics of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinkers. Institute of Science and Technology Austria.","chicago":"Dos Santos Caldas, Paulo R. “Organization and Dynamics of Treadmilling Filaments in Cytoskeletal Networks of FtsZ and Its Crosslinkers.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8358.","apa":"Dos Santos Caldas, P. R. (2020). Organization and dynamics of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinkers. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8358","ama":"Dos Santos Caldas PR. Organization and dynamics of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinkers. 2020. doi:10.15479/AT:ISTA:8358","short":"P.R. Dos Santos Caldas, Organization and Dynamics of Treadmilling Filaments in Cytoskeletal Networks of FtsZ and Its Crosslinkers, Institute of Science and Technology Austria, 2020.","ieee":"P. R. Dos Santos Caldas, “Organization and dynamics of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinkers,” Institute of Science and Technology Austria, 2020.","mla":"Dos Santos Caldas, Paulo R. Organization and Dynamics of Treadmilling Filaments in Cytoskeletal Networks of FtsZ and Its Crosslinkers. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8358."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","related_material":{"record":[{"relation":"dissertation_contains","id":"7572","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"7197"}]},"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"isbn":["978-3-99078-009-1"],"issn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"file_size":141602462,"date_updated":"2020-09-10T12:11:29Z","creator":"pcaldas","file_name":"phd_thesis_pcaldas.pdf","date_created":"2020-09-10T12:11:29Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"882f93fe9c351962120e2669b84bf088","file_id":"8364"},{"content_type":"application/x-zip-compressed","relation":"source_file","access_level":"closed","file_id":"8365","checksum":"70cc9e399c4e41e6e6ac445ae55e8558","file_size":450437458,"date_updated":"2020-09-11T07:48:10Z","creator":"pcaldas","file_name":"phd_thesis_latex_pcaldas.zip","date_created":"2020-09-10T12:18:17Z"}],"alternative_title":["ISTA Thesis"],"month":"09","abstract":[{"text":"During bacterial cell division, the tubulin-homolog FtsZ forms a ring-like structure at the center of the cell. This so-called Z-ring acts as a scaffold recruiting several division-related proteins to mid-cell and plays a key role in distributing proteins at the division site, a feature driven by the treadmilling motion of FtsZ filaments around the septum. What regulates the architecture, dynamics and stability of the Z-ring is still poorly understood, but FtsZ-associated proteins (Zaps) are known to play an important role. \r\nAdvances in fluorescence microscopy and in vitro reconstitution experiments have helped to shed light into some of the dynamic properties of these complex systems, but methods that allow to collect and analyze large quantitative data sets of the underlying polymer dynamics are still missing.\r\nHere, using an in vitro reconstitution approach, we studied how different Zaps affect FtsZ filament dynamics and organization into large-scale patterns, giving special emphasis to the role of the well-conserved protein ZapA. For this purpose, we use high-resolution fluorescence microscopy combined with novel image analysis workfows to study pattern organization and polymerization dynamics of active filaments. We quantified the influence of Zaps on FtsZ on three diferent spatial scales: the large-scale organization of the membrane-bound filament network, the underlying\r\npolymerization dynamics and the behavior of single molecules.\r\nWe found that ZapA cooperatively increases the spatial order of the filament network, binds only transiently to FtsZ filaments and has no effect on filament length and treadmilling velocity. Our data provides a model for how FtsZ-associated proteins can increase the precision and stability of the bacterial cell division machinery in a\r\nswitch-like manner, without compromising filament dynamics. Furthermore, we believe that our automated quantitative methods can be used to analyze a large variety of dynamic cytoskeletal systems, using standard time-lapse\r\nmovies of homogeneously labeled proteins obtained from experiments in vitro or even inside the living cell.\r\n","lang":"eng"}],"acknowledged_ssus":[{"_id":"Bio"}],"oa_version":"Published Version","file_date_updated":"2020-09-11T07:48:10Z","department":[{"_id":"MaLo"}],"date_updated":"2023-09-07T13:18:51Z","supervisor":[{"id":"462D4284-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","last_name":"Loose","full_name":"Loose, Martin","orcid":"0000-0001-7309-9724"}],"ddc":["572"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"dissertation","status":"public","_id":"8358"},{"ddc":["000"],"date_updated":"2023-09-07T13:29:00Z","file_date_updated":"2020-10-27T14:31:52Z","department":[{"_id":"HeEd"}],"_id":"8703","status":"public","conference":{"start_date":"2020-09-07","end_date":"2020-09-09","location":"Virtual, Online; Pisa, Italy","name":"ESA: Annual European Symposium on Algorithms"},"tmp":{"short":"CC BY (3.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)"},"type":"conference","language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"8712","checksum":"fe0f7c49a99ed870c671b911e10d5496","success":1,"creator":"cziletti","date_updated":"2020-10-27T14:31:52Z","file_size":733291,"date_created":"2020-10-27T14:31:52Z","file_name":"2020_LIPIcs_Osang.pdf"}],"publication_status":"published","publication_identifier":{"isbn":["9783959771627"],"issn":["18688969"]},"license":"https://creativecommons.org/licenses/by/3.0/","ec_funded":1,"volume":173,"related_material":{"record":[{"relation":"dissertation_contains","id":"9056","status":"public"}]},"oa_version":"Published Version","abstract":[{"text":"Even though Delaunay originally introduced his famous triangulations in the case of infinite point sets with translational periodicity, a software that computes such triangulations in the general case is not yet available, to the best of our knowledge. Combining and generalizing previous work, we present a practical algorithm for computing such triangulations. The algorithm has been implemented and experiments show that its performance is as good as the one of the CGAL package, which is restricted to cubic periodicity. ","lang":"eng"}],"intvolume":" 173","month":"08","scopus_import":"1","alternative_title":["LIPIcs"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Osang GF, Rouxel-Labbé M, Teillaud M. 2020. Generalizing CGAL periodic Delaunay triangulations. 28th Annual European Symposium on Algorithms. ESA: Annual European Symposium on Algorithms, LIPIcs, vol. 173, 75.","chicago":"Osang, Georg F, Mael Rouxel-Labbé, and Monique Teillaud. “Generalizing CGAL Periodic Delaunay Triangulations.” In 28th Annual European Symposium on Algorithms, Vol. 173. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020. https://doi.org/10.4230/LIPIcs.ESA.2020.75.","short":"G.F. Osang, M. Rouxel-Labbé, M. Teillaud, in:, 28th Annual European Symposium on Algorithms, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020.","ieee":"G. F. Osang, M. Rouxel-Labbé, and M. Teillaud, “Generalizing CGAL periodic Delaunay triangulations,” in 28th Annual European Symposium on Algorithms, Virtual, Online; Pisa, Italy, 2020, vol. 173.","apa":"Osang, G. F., Rouxel-Labbé, M., & Teillaud, M. (2020). Generalizing CGAL periodic Delaunay triangulations. In 28th Annual European Symposium on Algorithms (Vol. 173). Virtual, Online; Pisa, Italy: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ESA.2020.75","ama":"Osang GF, Rouxel-Labbé M, Teillaud M. Generalizing CGAL periodic Delaunay triangulations. In: 28th Annual European Symposium on Algorithms. Vol 173. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2020. doi:10.4230/LIPIcs.ESA.2020.75","mla":"Osang, Georg F., et al. “Generalizing CGAL Periodic Delaunay Triangulations.” 28th Annual European Symposium on Algorithms, vol. 173, 75, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020, doi:10.4230/LIPIcs.ESA.2020.75."},"title":"Generalizing CGAL periodic Delaunay triangulations","article_processing_charge":"No","author":[{"full_name":"Osang, Georg F","orcid":"0000-0002-8882-5116","last_name":"Osang","first_name":"Georg F","id":"464B40D6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Mael","last_name":"Rouxel-Labbé","full_name":"Rouxel-Labbé, Mael"},{"first_name":"Monique","last_name":"Teillaud","full_name":"Teillaud, Monique"}],"article_number":"75","project":[{"name":"Alpha Shape Theory Extended","grant_number":"788183","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"publication":"28th Annual European Symposium on Algorithms","day":"26","year":"2020","has_accepted_license":"1","date_created":"2020-10-25T23:01:18Z","date_published":"2020-08-26T00:00:00Z","doi":"10.4230/LIPIcs.ESA.2020.75","oa":1,"quality_controlled":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik"},{"citation":{"ista":"Phuong M, Lampert C. 2020. Functional vs. parametric equivalence of ReLU networks. 8th International Conference on Learning Representations. ICLR: International Conference on Learning Representations.","chicago":"Phuong, Mary, and Christoph Lampert. “Functional vs. Parametric Equivalence of ReLU Networks.” In 8th International Conference on Learning Representations, 2020.","short":"M. Phuong, C. Lampert, in:, 8th International Conference on Learning Representations, 2020.","ieee":"M. Phuong and C. Lampert, “Functional vs. parametric equivalence of ReLU networks,” in 8th International Conference on Learning Representations, Online, 2020.","apa":"Phuong, M., & Lampert, C. (2020). Functional vs. parametric equivalence of ReLU networks. In 8th International Conference on Learning Representations. Online.","ama":"Phuong M, Lampert C. Functional vs. parametric equivalence of ReLU networks. In: 8th International Conference on Learning Representations. ; 2020.","mla":"Phuong, Mary, and Christoph Lampert. “Functional vs. Parametric Equivalence of ReLU Networks.” 8th International Conference on Learning Representations, 2020."},"date_updated":"2023-09-07T13:29:50Z","ddc":["000"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Bui Thi Mai","full_name":"Bui Thi Mai, Phuong","id":"3EC6EE64-F248-11E8-B48F-1D18A9856A87","first_name":"Phuong"},{"last_name":"Lampert","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph"}],"article_processing_charge":"No","department":[{"_id":"ChLa"}],"file_date_updated":"2020-07-14T12:47:59Z","title":"Functional vs. parametric equivalence of ReLU networks","_id":"7481","type":"conference","conference":{"end_date":"2020-04-30","location":"Online","start_date":"2020-04-27","name":"ICLR: International Conference on Learning Representations"},"status":"public","has_accepted_license":"1","year":"2020","publication_status":"published","file":[{"file_name":"main.pdf","date_created":"2020-02-11T09:07:27Z","file_size":405469,"date_updated":"2020-07-14T12:47:59Z","creator":"bphuong","checksum":"8d372ea5defd8cb8fdc430111ed754a9","file_id":"7482","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"day":"26","publication":"8th International Conference on Learning Representations","language":[{"iso":"eng"}],"date_published":"2020-04-26T00:00:00Z","related_material":{"link":[{"relation":"supplementary_material","url":"https://iclr.cc/virtual_2020/poster_Bylx-TNKvH.html"}],"record":[{"status":"public","id":"9418","relation":"dissertation_contains"}]},"date_created":"2020-02-11T09:07:37Z","abstract":[{"text":"We address the following question: How redundant is the parameterisation of ReLU networks? Specifically, we consider transformations of the weight space which leave the function implemented by the network intact. Two such transformations are known for feed-forward architectures: permutation of neurons within a layer, and positive scaling of all incoming weights of a neuron coupled with inverse scaling of its outgoing weights. In this work, we show for architectures with non-increasing widths that permutation and scaling are in fact the only function-preserving weight transformations. For any eligible architecture we give an explicit construction of a neural network such that any other network that implements the same function can be obtained from the original one by the application of permutations and rescaling. The proof relies on a geometric understanding of boundaries between linear regions of ReLU networks, and we hope the developed mathematical tools are of independent interest.","lang":"eng"}],"oa_version":"Published Version","quality_controlled":"1","oa":1,"month":"04"},{"project":[{"_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Analysis of quantum many-body systems","grant_number":"694227"}],"citation":{"apa":"Feliciangeli, D., & Seiringer, R. (2020). Uniqueness and nondegeneracy of minimizers of the Pekar functional on a ball. SIAM Journal on Mathematical Analysis. Society for Industrial & Applied Mathematics . https://doi.org/10.1137/19m126284x","ama":"Feliciangeli D, Seiringer R. Uniqueness and nondegeneracy of minimizers of the Pekar functional on a ball. SIAM Journal on Mathematical Analysis. 2020;52(1):605-622. doi:10.1137/19m126284x","ieee":"D. Feliciangeli and R. Seiringer, “Uniqueness and nondegeneracy of minimizers of the Pekar functional on a ball,” SIAM Journal on Mathematical Analysis, vol. 52, no. 1. Society for Industrial & Applied Mathematics , pp. 605–622, 2020.","short":"D. Feliciangeli, R. Seiringer, SIAM Journal on Mathematical Analysis 52 (2020) 605–622.","mla":"Feliciangeli, Dario, and Robert Seiringer. “Uniqueness and Nondegeneracy of Minimizers of the Pekar Functional on a Ball.” SIAM Journal on Mathematical Analysis, vol. 52, no. 1, Society for Industrial & Applied Mathematics , 2020, pp. 605–22, doi:10.1137/19m126284x.","ista":"Feliciangeli D, Seiringer R. 2020. Uniqueness and nondegeneracy of minimizers of the Pekar functional on a ball. SIAM Journal on Mathematical Analysis. 52(1), 605–622.","chicago":"Feliciangeli, Dario, and Robert Seiringer. “Uniqueness and Nondegeneracy of Minimizers of the Pekar Functional on a Ball.” SIAM Journal on Mathematical Analysis. Society for Industrial & Applied Mathematics , 2020. https://doi.org/10.1137/19m126284x."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"last_name":"Feliciangeli","full_name":"Feliciangeli, Dario","orcid":"0000-0003-0754-8530","id":"41A639AA-F248-11E8-B48F-1D18A9856A87","first_name":"Dario"},{"last_name":"Seiringer","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"isi":["000546967700022"],"arxiv":["1904.08647 "]},"article_processing_charge":"No","title":"Uniqueness and nondegeneracy of minimizers of the Pekar functional on a ball","acknowledgement":"We are grateful for the hospitality at the Mittag-Leffler Institute, where part of this work has been done. The work of the authors was supported by the European Research Council (ERC)under the European Union's Horizon 2020 research and innovation programme grant 694227.","publisher":"Society for Industrial & Applied Mathematics ","quality_controlled":"1","oa":1,"isi":1,"has_accepted_license":"1","year":"2020","day":"12","publication":"SIAM Journal on Mathematical Analysis","page":"605-622","doi":"10.1137/19m126284x","date_published":"2020-02-12T00:00:00Z","date_created":"2021-08-06T07:34:16Z","_id":"9781","article_type":"original","type":"journal_article","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"status":"public","keyword":["Applied Mathematics","Computational Mathematics","Analysis"],"date_updated":"2023-09-07T13:30:11Z","ddc":["510"],"department":[{"_id":"RoSe"}],"abstract":[{"text":"We consider the Pekar functional on a ball in ℝ3. We prove uniqueness of minimizers, and a quadratic lower bound in terms of the distance to the minimizer. The latter follows from nondegeneracy of the Hessian at the minimum.","lang":"eng"}],"oa_version":"Preprint","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1904.08647"}],"month":"02","intvolume":" 52","publication_identifier":{"eissn":["1095-7154"],"issn":["0036-1410"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":52,"related_material":{"record":[{"status":"public","id":"9733","relation":"dissertation_contains"}]},"issue":"1","ec_funded":1},{"abstract":[{"text":"In the present work, we consider the evolution of two fluids separated by a sharp interface in the presence of surface tension—like, for example, the evolution of oil bubbles in water. Our main result is a weak–strong uniqueness principle for the corresponding free boundary problem for the incompressible Navier–Stokes equation: as long as a strong solution exists, any varifold solution must coincide with it. In particular, in the absence of physical singularities, the concept of varifold solutions—whose global in time existence has been shown by Abels (Interfaces Free Bound 9(1):31–65, 2007) for general initial data—does not introduce a mechanism for non-uniqueness. The key ingredient of our approach is the construction of a relative entropy functional capable of controlling the interface error. If the viscosities of the two fluids do not coincide, even for classical (strong) solutions the gradient of the velocity field becomes discontinuous at the interface, introducing the need for a careful additional adaption of the relative entropy.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","month":"05","intvolume":" 236","publication_identifier":{"eissn":["14320673"],"issn":["00039527"]},"publication_status":"published","file":[{"file_name":"2020_ArchRatMechAn_Fischer.pdf","date_created":"2020-11-20T09:14:22Z","creator":"dernst","file_size":1897571,"date_updated":"2020-11-20T09:14:22Z","success":1,"file_id":"8779","checksum":"f107e21b58f5930876f47144be37cf6c","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"volume":236,"related_material":{"record":[{"id":"10007","status":"public","relation":"dissertation_contains"}]},"ec_funded":1,"_id":"7489","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","date_updated":"2023-09-07T13:30:45Z","ddc":["530","532"],"department":[{"_id":"JuFi"}],"file_date_updated":"2020-11-20T09:14:22Z","quality_controlled":"1","publisher":"Springer Nature","oa":1,"has_accepted_license":"1","isi":1,"year":"2020","day":"01","publication":"Archive for Rational Mechanics and Analysis","page":"967-1087","date_published":"2020-05-01T00:00:00Z","doi":"10.1007/s00205-019-01486-2","date_created":"2020-02-16T23:00:50Z","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"665385","name":"International IST Doctoral Program"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"citation":{"mla":"Fischer, Julian L., and Sebastian Hensel. “Weak–Strong Uniqueness for the Navier–Stokes Equation for Two Fluids with Surface Tension.” Archive for Rational Mechanics and Analysis, vol. 236, Springer Nature, 2020, pp. 967–1087, doi:10.1007/s00205-019-01486-2.","apa":"Fischer, J. L., & Hensel, S. (2020). Weak–strong uniqueness for the Navier–Stokes equation for two fluids with surface tension. Archive for Rational Mechanics and Analysis. Springer Nature. https://doi.org/10.1007/s00205-019-01486-2","ama":"Fischer JL, Hensel S. Weak–strong uniqueness for the Navier–Stokes equation for two fluids with surface tension. Archive for Rational Mechanics and Analysis. 2020;236:967-1087. doi:10.1007/s00205-019-01486-2","short":"J.L. Fischer, S. Hensel, Archive for Rational Mechanics and Analysis 236 (2020) 967–1087.","ieee":"J. L. Fischer and S. Hensel, “Weak–strong uniqueness for the Navier–Stokes equation for two fluids with surface tension,” Archive for Rational Mechanics and Analysis, vol. 236. Springer Nature, pp. 967–1087, 2020.","chicago":"Fischer, Julian L, and Sebastian Hensel. “Weak–Strong Uniqueness for the Navier–Stokes Equation for Two Fluids with Surface Tension.” Archive for Rational Mechanics and Analysis. Springer Nature, 2020. https://doi.org/10.1007/s00205-019-01486-2.","ista":"Fischer JL, Hensel S. 2020. Weak–strong uniqueness for the Navier–Stokes equation for two fluids with surface tension. Archive for Rational Mechanics and Analysis. 236, 967–1087."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Julian L","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","full_name":"Fischer, Julian L","orcid":"0000-0002-0479-558X","last_name":"Fischer"},{"full_name":"Hensel, Sebastian","orcid":"0000-0001-7252-8072","last_name":"Hensel","first_name":"Sebastian","id":"4D23B7DA-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"isi":["000511060200001"]},"article_processing_charge":"Yes (via OA deal)","title":"Weak–strong uniqueness for the Navier–Stokes equation for two fluids with surface tension"},{"status":"public","project":[{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program"}],"type":"preprint","article_number":"2003.05478","_id":"10012","department":[{"_id":"JuFi"}],"title":"The local structure of the energy landscape in multiphase mean curvature flow: weak-strong uniqueness and stability of evolutions","author":[{"orcid":"0000-0002-0479-558X","full_name":"Fischer, Julian L","last_name":"Fischer","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","first_name":"Julian L"},{"last_name":"Hensel","orcid":"0000-0001-7252-8072","full_name":"Hensel, Sebastian","first_name":"Sebastian","id":"4D23B7DA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Laux, Tim","last_name":"Laux","first_name":"Tim"},{"first_name":"Thilo","last_name":"Simon","full_name":"Simon, Thilo"}],"external_id":{"arxiv":["2003.05478"]},"article_processing_charge":"No","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"ieee":"J. L. Fischer, S. Hensel, T. Laux, and T. Simon, “The local structure of the energy landscape in multiphase mean curvature flow: weak-strong uniqueness and stability of evolutions,” arXiv. .","short":"J.L. Fischer, S. Hensel, T. Laux, T. Simon, ArXiv (n.d.).","ama":"Fischer JL, Hensel S, Laux T, Simon T. The local structure of the energy landscape in multiphase mean curvature flow: weak-strong uniqueness and stability of evolutions. arXiv.","apa":"Fischer, J. L., Hensel, S., Laux, T., & Simon, T. (n.d.). The local structure of the energy landscape in multiphase mean curvature flow: weak-strong uniqueness and stability of evolutions. arXiv.","mla":"Fischer, Julian L., et al. “The Local Structure of the Energy Landscape in Multiphase Mean Curvature Flow: Weak-Strong Uniqueness and Stability of Evolutions.” ArXiv, 2003.05478.","ista":"Fischer JL, Hensel S, Laux T, Simon T. The local structure of the energy landscape in multiphase mean curvature flow: weak-strong uniqueness and stability of evolutions. arXiv, 2003.05478.","chicago":"Fischer, Julian L, Sebastian Hensel, Tim Laux, and Thilo Simon. “The Local Structure of the Energy Landscape in Multiphase Mean Curvature Flow: Weak-Strong Uniqueness and Stability of Evolutions.” ArXiv, n.d."},"date_updated":"2023-09-07T13:30:45Z","month":"03","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2003.05478"}],"oa":1,"oa_version":"Preprint","acknowledgement":"Parts of the paper were written during the visit of the authors to the Hausdorff Research Institute for Mathematics (HIM), University of Bonn, in the framework of the trimester program “Evolution of Interfaces”. The support and the hospitality of HIM are gratefully acknowledged. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie Grant Agreement No. 665385.","abstract":[{"text":"We prove that in the absence of topological changes, the notion of BV solutions to planar multiphase mean curvature flow does not allow for a mechanism for (unphysical) non-uniqueness. Our approach is based on the local structure of the energy landscape near a classical evolution by mean curvature. Mean curvature flow being the gradient flow of the surface energy functional, we develop a gradient-flow analogue of the notion of calibrations. Just like the existence of a calibration guarantees that one has reached a global minimum in the energy landscape, the existence of a \"gradient flow calibration\" ensures that the route of steepest descent in the energy landscape is unique and stable.","lang":"eng"}],"date_published":"2020-03-11T00:00:00Z","related_material":{"record":[{"id":"10007","status":"public","relation":"dissertation_contains"}]},"date_created":"2021-09-13T12:17:11Z","ec_funded":1,"day":"11","language":[{"iso":"eng"}],"publication":"arXiv","year":"2020","publication_status":"submitted"},{"quality_controlled":"1","publisher":"American Physical Society","oa":1,"acknowledgement":"The authors acknowledge the support from I. Prieto and the IST Nanofabrication Facility. This work was supported by IST Austria and a NOMIS foundation research grant and the Austrian Science Fund (FWF) through BeyondC (F71). MP is the recipient of a P¨ottinger scholarship at IST Austria. JMF acknowledges support from the European Union’s Horizon 2020 research and innovation programs under grant agreement No 732894 (FET Proactive HOT), 862644 (FET Open QUARTET), and the European Research Council under grant agreement\r\nnumber 758053 (ERC StG QUNNECT). ","doi":"10.1103/PhysRevApplied.14.044055","date_published":"2020-10-29T00:00:00Z","date_created":"2020-11-15T23:01:17Z","has_accepted_license":"1","isi":1,"year":"2020","day":"29","publication":"Physical Review Applied","project":[{"name":"Integrating superconducting quantum circuits","grant_number":"F07105","call_identifier":"FWF","_id":"26927A52-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","_id":"257EB838-B435-11E9-9278-68D0E5697425","grant_number":"732894","name":"Hybrid Optomechanical Technologies"},{"grant_number":"862644","name":"Quantum readout techniques and technologies","call_identifier":"H2020","_id":"237CBA6C-32DE-11EA-91FC-C7463DDC885E"},{"grant_number":"758053","name":"A Fiber Optic Transceiver for Superconducting Qubits","_id":"26336814-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"article_number":"044055","author":[{"id":"3F920B30-F248-11E8-B48F-1D18A9856A87","first_name":"Matilda","orcid":"0000-0002-3415-4628","full_name":"Peruzzo, Matilda","last_name":"Peruzzo"},{"last_name":"Trioni","full_name":"Trioni, Andrea","first_name":"Andrea","id":"42F71B44-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Farid","id":"2AED110C-F248-11E8-B48F-1D18A9856A87","full_name":"Hassani, Farid","orcid":"0000-0001-6937-5773","last_name":"Hassani"},{"last_name":"Zemlicka","full_name":"Zemlicka, Martin","first_name":"Martin","id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8112-028X","full_name":"Fink, Johannes M","last_name":"Fink"}],"article_processing_charge":"No","external_id":{"isi":["000582797300003"],"arxiv":["2007.01644"]},"title":"Surpassing the resistance quantum with a geometric superinductor","citation":{"ama":"Peruzzo M, Trioni A, Hassani F, Zemlicka M, Fink JM. 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Surpassing the resistance quantum with a geometric superinductor. Physical Review Applied. 14(4), 044055.","chicago":"Peruzzo, Matilda, Andrea Trioni, Farid Hassani, Martin Zemlicka, and Johannes M Fink. “Surpassing the Resistance Quantum with a Geometric Superinductor.” Physical Review Applied. American Physical Society, 2020. https://doi.org/10.1103/PhysRevApplied.14.044055."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","scopus_import":"1","month":"10","intvolume":" 14","acknowledged_ssus":[{"_id":"NanoFab"}],"abstract":[{"text":"The superconducting circuit community has recently discovered the promising potential of superinductors. These circuit elements have a characteristic impedance exceeding the resistance quantum RQ ≈ 6.45 kΩ which leads to a suppression of ground state charge fluctuations. Applications include the realization of hardware protected qubits for fault tolerant quantum computing, improved coupling to small dipole moment objects and defining a new quantum metrology standard for the ampere. In this work we refute the widespread notion that superinductors can only be implemented based on kinetic inductance, i.e. using disordered superconductors or Josephson junction arrays. We present modeling, fabrication and characterization of 104 planar aluminum coil resonators with a characteristic impedance up to 30.9 kΩ at 5.6 GHz and a capacitance down to ≤ 1 fF, with lowloss and a power handling reaching 108 intra-cavity photons. Geometric superinductors are free of uncontrolled tunneling events and offer high reproducibility, linearity and the ability to couple magnetically - properties that significantly broaden the scope of future quantum circuits. ","lang":"eng"}],"oa_version":"Published Version","issue":"4","volume":14,"related_material":{"record":[{"relation":"research_data","id":"13070","status":"public"},{"relation":"dissertation_contains","id":"9920","status":"public"}]},"ec_funded":1,"publication_identifier":{"eissn":["23317019"]},"publication_status":"published","file":[{"file_name":"2020_PhysReviewApplied_Peruzzo.pdf","date_created":"2021-03-29T11:43:20Z","file_size":2607823,"date_updated":"2021-03-29T11:43:20Z","creator":"dernst","success":1,"file_id":"9300","checksum":"2a634abe75251ae7628cd54c8a4ce2e8","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"article_type":"original","type":"journal_article","status":"public","_id":"8755","file_date_updated":"2021-03-29T11:43:20Z","department":[{"_id":"JoFi"}],"date_updated":"2023-09-07T13:31:22Z","ddc":["530"]},{"project":[{"grant_number":"716117","name":"Optimal Transport and Stochastic Dynamics","call_identifier":"H2020","_id":"256E75B8-B435-11E9-9278-68D0E5697425"},{"_id":"260482E2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":" F06504","name":"Taming Complexity in Partial Di erential Systems"},{"name":"Dissipation and Dispersion in Nonlinear Partial Differential Equations","call_identifier":"FWF","_id":"260788DE-B435-11E9-9278-68D0E5697425"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Gladbach, Peter, et al. “Homogenisation of One-Dimensional Discrete Optimal Transport.” Journal de Mathematiques Pures et Appliquees, vol. 139, no. 7, Elsevier, 2020, pp. 204–34, doi:10.1016/j.matpur.2020.02.008.","ama":"Gladbach P, Kopfer E, Maas J, Portinale L. Homogenisation of one-dimensional discrete optimal transport. Journal de Mathematiques Pures et Appliquees. 2020;139(7):204-234. doi:10.1016/j.matpur.2020.02.008","apa":"Gladbach, P., Kopfer, E., Maas, J., & Portinale, L. (2020). Homogenisation of one-dimensional discrete optimal transport. Journal de Mathematiques Pures et Appliquees. Elsevier. https://doi.org/10.1016/j.matpur.2020.02.008","ieee":"P. Gladbach, E. Kopfer, J. Maas, and L. Portinale, “Homogenisation of one-dimensional discrete optimal transport,” Journal de Mathematiques Pures et Appliquees, vol. 139, no. 7. Elsevier, pp. 204–234, 2020.","short":"P. Gladbach, E. Kopfer, J. Maas, L. Portinale, Journal de Mathematiques Pures et Appliquees 139 (2020) 204–234.","chicago":"Gladbach, Peter, Eva Kopfer, Jan Maas, and Lorenzo Portinale. “Homogenisation of One-Dimensional Discrete Optimal Transport.” Journal de Mathematiques Pures et Appliquees. Elsevier, 2020. https://doi.org/10.1016/j.matpur.2020.02.008.","ista":"Gladbach P, Kopfer E, Maas J, Portinale L. 2020. Homogenisation of one-dimensional discrete optimal transport. Journal de Mathematiques Pures et Appliquees. 139(7), 204–234."},"title":"Homogenisation of one-dimensional discrete optimal transport","author":[{"last_name":"Gladbach","full_name":"Gladbach, Peter","first_name":"Peter"},{"last_name":"Kopfer","full_name":"Kopfer, Eva","first_name":"Eva"},{"id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","orcid":"0000-0002-0845-1338","full_name":"Maas, Jan","last_name":"Maas"},{"last_name":"Portinale","full_name":"Portinale, Lorenzo","id":"30AD2CBC-F248-11E8-B48F-1D18A9856A87","first_name":"Lorenzo"}],"external_id":{"arxiv":["1905.05757"],"isi":["000539439400008"]},"article_processing_charge":"No","acknowledgement":"J.M. gratefully acknowledges support by the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (grant agreement No 716117). J.M. and L.P. also acknowledge support from the Austrian Science Fund (FWF), grants No F65 and W1245. E.K. gratefully acknowledges support by the German Research Foundation through the Hausdorff Center for Mathematics and the Collaborative Research Center 1060. P.G. is partially funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) – 350398276.","quality_controlled":"1","publisher":"Elsevier","oa":1,"day":"01","publication":"Journal de Mathematiques Pures et Appliquees","isi":1,"year":"2020","doi":"10.1016/j.matpur.2020.02.008","date_published":"2020-07-01T00:00:00Z","date_created":"2020-03-08T23:00:47Z","page":"204-234","_id":"7573","status":"public","article_type":"original","type":"journal_article","date_updated":"2023-09-07T13:31:05Z","department":[{"_id":"JaMa"}],"oa_version":"Preprint","abstract":[{"text":"This paper deals with dynamical optimal transport metrics defined by spatial discretisation of the Benamou–Benamou formula for the Kantorovich metric . Such metrics appear naturally in discretisations of -gradient flow formulations for dissipative PDE. However, it has recently been shown that these metrics do not in general converge to , unless strong geometric constraints are imposed on the discrete mesh. In this paper we prove that, in a 1-dimensional periodic setting, discrete transport metrics converge to a limiting transport metric with a non-trivial effective mobility. This mobility depends sensitively on the geometry of the mesh and on the non-local mobility at the discrete level. Our result quantifies to what extent discrete transport can make use of microstructure in the mesh to reduce the cost of transport.","lang":"eng"}],"month":"07","intvolume":" 139","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1905.05757","open_access":"1"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["00217824"]},"publication_status":"published","volume":139,"issue":"7","related_material":{"record":[{"relation":"dissertation_contains","id":"10030","status":"public"}]},"ec_funded":1},{"title":"Evolutionary Γ-convergence of entropic gradient flow structures for Fokker-Planck equations in multiple dimensions","department":[{"_id":"JaMa"}],"external_id":{"arxiv":["2008.10962"]},"article_processing_charge":"No","author":[{"first_name":"Dominik L","id":"35C79D68-F248-11E8-B48F-1D18A9856A87","last_name":"Forkert","full_name":"Forkert, Dominik L"},{"first_name":"Jan","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0845-1338","full_name":"Maas, Jan","last_name":"Maas"},{"first_name":"Lorenzo","id":"30AD2CBC-F248-11E8-B48F-1D18A9856A87","last_name":"Portinale","full_name":"Portinale, Lorenzo"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_updated":"2023-09-07T13:31:05Z","citation":{"apa":"Forkert, D. L., Maas, J., & Portinale, L. (n.d.). Evolutionary Γ-convergence of entropic gradient flow structures for Fokker-Planck equations in multiple dimensions. arXiv.","ama":"Forkert DL, Maas J, Portinale L. Evolutionary Γ-convergence of entropic gradient flow structures for Fokker-Planck equations in multiple dimensions. arXiv.","ieee":"D. L. Forkert, J. Maas, and L. Portinale, “Evolutionary Γ-convergence of entropic gradient flow structures for Fokker-Planck equations in multiple dimensions,” arXiv. .","short":"D.L. Forkert, J. Maas, L. Portinale, ArXiv (n.d.).","mla":"Forkert, Dominik L., et al. “Evolutionary Γ-Convergence of Entropic Gradient Flow Structures for Fokker-Planck Equations in Multiple Dimensions.” ArXiv, 2008.10962.","ista":"Forkert DL, Maas J, Portinale L. Evolutionary Γ-convergence of entropic gradient flow structures for Fokker-Planck equations in multiple dimensions. arXiv, 2008.10962.","chicago":"Forkert, Dominik L, Jan Maas, and Lorenzo Portinale. “Evolutionary Γ-Convergence of Entropic Gradient Flow Structures for Fokker-Planck Equations in Multiple Dimensions.” ArXiv, n.d."},"status":"public","project":[{"grant_number":"716117","name":"Optimal Transport and Stochastic Dynamics","call_identifier":"H2020","_id":"256E75B8-B435-11E9-9278-68D0E5697425"},{"grant_number":"F6504","name":"Taming Complexity in Partial Differential Systems","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2"}],"type":"preprint","article_number":"2008.10962","_id":"10022","date_created":"2021-09-17T10:57:27Z","ec_funded":1,"related_material":{"record":[{"status":"public","id":"11739","relation":"later_version"},{"status":"public","id":"10030","relation":"dissertation_contains"}]},"date_published":"2020-08-25T00:00:00Z","page":"33","language":[{"iso":"eng"}],"publication":"arXiv","day":"25","year":"2020","publication_status":"submitted","month":"08","main_file_link":[{"url":"https://arxiv.org/abs/2008.10962","open_access":"1"}],"oa":1,"acknowledgement":"This work is supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 716117) and by the Austrian Science Fund (FWF), grants No F65 and W1245.","oa_version":"Preprint","abstract":[{"lang":"eng","text":"We consider finite-volume approximations of Fokker-Planck equations on bounded convex domains in R^d and study the corresponding gradient flow structures. We reprove the convergence of the discrete to continuous Fokker-Planck equation via the method of Evolutionary Γ-convergence, i.e., we pass to the limit at the level of the gradient flow structures, generalising the one-dimensional result obtained by Disser and Liero. The proof is of variational nature and relies on a Mosco convergence result for functionals in the discrete-to-continuum limit that is of independent interest. Our results apply to arbitrary regular meshes, even though the associated discrete transport distances may fail to converge to the Wasserstein distance in this generality."}]},{"project":[{"name":"Elastic Coordination for Scalable Machine Learning","grant_number":"805223","call_identifier":"H2020","_id":"268A44D6-B435-11E9-9278-68D0E5697425"}],"author":[{"full_name":"Konstantinov, Nikola H","last_name":"Konstantinov","id":"4B9D76E4-F248-11E8-B48F-1D18A9856A87","first_name":"Nikola H"},{"last_name":"Frantar","full_name":"Frantar, Elias","first_name":"Elias","id":"09a8f98d-ec99-11ea-ae11-c063a7b7fe5f"},{"orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian"},{"first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","last_name":"Lampert"}],"external_id":{"arxiv":["2002.10384"]},"article_processing_charge":"No","title":"On the sample complexity of adversarial multi-source PAC learning","citation":{"chicago":"Konstantinov, Nikola H, Elias Frantar, Dan-Adrian Alistarh, and Christoph Lampert. “On the Sample Complexity of Adversarial Multi-Source PAC Learning.” In Proceedings of the 37th International Conference on Machine Learning, 119:5416–25. ML Research Press, 2020.","ista":"Konstantinov NH, Frantar E, Alistarh D-A, Lampert C. 2020. On the sample complexity of adversarial multi-source PAC learning. Proceedings of the 37th International Conference on Machine Learning. ICML: International Conference on Machine Learning vol. 119, 5416–5425.","mla":"Konstantinov, Nikola H., et al. “On the Sample Complexity of Adversarial Multi-Source PAC Learning.” Proceedings of the 37th International Conference on Machine Learning, vol. 119, ML Research Press, 2020, pp. 5416–25.","short":"N.H. Konstantinov, E. Frantar, D.-A. Alistarh, C. Lampert, in:, Proceedings of the 37th International Conference on Machine Learning, ML Research Press, 2020, pp. 5416–5425.","ieee":"N. H. Konstantinov, E. Frantar, D.-A. Alistarh, and C. Lampert, “On the sample complexity of adversarial multi-source PAC learning,” in Proceedings of the 37th International Conference on Machine Learning, Online, 2020, vol. 119, pp. 5416–5425.","ama":"Konstantinov NH, Frantar E, Alistarh D-A, Lampert C. On the sample complexity of adversarial multi-source PAC learning. In: Proceedings of the 37th International Conference on Machine Learning. Vol 119. ML Research Press; 2020:5416-5425.","apa":"Konstantinov, N. H., Frantar, E., Alistarh, D.-A., & Lampert, C. (2020). On the sample complexity of adversarial multi-source PAC learning. In Proceedings of the 37th International Conference on Machine Learning (Vol. 119, pp. 5416–5425). Online: ML Research Press."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"ML Research Press","quality_controlled":"1","oa":1,"acknowledgement":"Dan Alistarh is supported in part by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 805223 ScaleML). This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing (SciComp).","page":"5416-5425","date_published":"2020-07-12T00:00:00Z","date_created":"2020-11-05T15:25:58Z","has_accepted_license":"1","year":"2020","day":"12","publication":"Proceedings of the 37th International Conference on Machine Learning","type":"conference","conference":{"name":"ICML: International Conference on Machine Learning","location":"Online","end_date":"2020-07-18","start_date":"2020-07-12"},"status":"public","_id":"8724","file_date_updated":"2021-02-15T09:00:01Z","department":[{"_id":"DaAl"},{"_id":"ChLa"}],"date_updated":"2023-09-07T13:42:08Z","ddc":["000"],"scopus_import":"1","month":"07","intvolume":" 119","abstract":[{"text":"We study the problem of learning from multiple untrusted data sources, a scenario of increasing practical relevance given the recent emergence of crowdsourcing and collaborative learning paradigms. Specifically, we analyze the situation in which a learning system obtains datasets from multiple sources, some of which might be biased or even adversarially perturbed. It is\r\nknown that in the single-source case, an adversary with the power to corrupt a fixed fraction of the training data can prevent PAC-learnability, that is, even in the limit of infinitely much training data, no learning system can approach the optimal test error. In this work we show that, surprisingly, the same is not true in the multi-source setting, where the adversary can arbitrarily\r\ncorrupt a fixed fraction of the data sources. Our main results are a generalization bound that provides finite-sample guarantees for this learning setting, as well as corresponding lower bounds. Besides establishing PAC-learnability our results also show that in a cooperative learning setting sharing data with other parties has provable benefits, even if some\r\nparticipants are malicious. ","lang":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"oa_version":"Published Version","volume":119,"related_material":{"link":[{"relation":"supplementary_material","url":"http://proceedings.mlr.press/v119/konstantinov20a/konstantinov20a-supp.pdf"}],"record":[{"relation":"dissertation_contains","status":"public","id":"10799"}]},"ec_funded":1,"publication_identifier":{"issn":["2640-3498"]},"publication_status":"published","file":[{"creator":"dernst","file_size":281286,"date_updated":"2021-02-15T09:00:01Z","file_name":"2020_PMLR_Konstantinov.pdf","date_created":"2021-02-15T09:00:01Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"9120","checksum":"cc755d0054bc4b2be778ea7aa7884d2f"}],"language":[{"iso":"eng"}]},{"_id":"8644","status":"public","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["530"],"date_updated":"2023-09-07T13:44:16Z","file_date_updated":"2020-10-12T12:18:47Z","department":[{"_id":"MiLe"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Determining the phase diagram of systems consisting of smaller subsystems 'connected' via a tunable coupling is a challenging task relevant for a variety of physical settings. A general question is whether new phases, not present in the uncoupled limit, may arise. We use machine learning and a suitable quasidistance between different points of the phase diagram to study layered spin models, in which the spin variables constituting each of the uncoupled systems (to which we refer as layers) are coupled to each other via an interlayer coupling. In such systems, in general, composite order parameters involving spins of different layers may emerge as a consequence of the interlayer coupling. We focus on the layered Ising and Ashkin–Teller models as a paradigmatic case study, determining their phase diagram via the application of a machine learning algorithm to the Monte Carlo data. Remarkably our technique is able to correctly characterize all the system phases also in the case of hidden order parameters, i.e. order parameters whose expression in terms of the microscopic configurations would require additional preprocessing of the data fed to the algorithm. We correctly retrieve the three known phases of the Ashkin–Teller model with ferromagnetic couplings, including the phase described by a composite order parameter. For the bilayer and trilayer Ising models the phases we find are only the ferromagnetic and the paramagnetic ones. Within the approach we introduce, owing to the construction of convolutional neural networks, naturally suitable for layered image-like data with arbitrary number of layers, no preprocessing of the Monte Carlo data is needed, also with regard to its spatial structure. The physical meaning of our results is discussed and compared with analytical data, where available. Yet, the method can be used without any a priori knowledge of the phases one seeks to find and can be applied to other models and structures."}],"month":"09","intvolume":" 22","scopus_import":"1","file":[{"success":1,"checksum":"c9238fff422e7a957c3a0d559f756b3a","file_id":"8650","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2020_NewJournalPhysics_Rzdkowski.pdf","date_created":"2020-10-12T12:18:47Z","creator":"dernst","file_size":2725143,"date_updated":"2020-10-12T12:18:47Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["13672630"]},"publication_status":"published","volume":22,"related_material":{"record":[{"relation":"dissertation_contains","id":"10759","status":"public"}]},"issue":"9","ec_funded":1,"article_number":"093026","project":[{"name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"_id":"05A235A0-7A3F-11EA-A408-12923DDC885E","grant_number":"25681","name":"Analytic and machine learning approaches to composite quantum impurities"},{"call_identifier":"FWF","_id":"26986C82-B435-11E9-9278-68D0E5697425","grant_number":"M02641","name":"A path-integral approach to composite impurities"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"apa":"Rzadkowski, W., Defenu, N., Chiacchiera, S., Trombettoni, A., & Bighin, G. (2020). Detecting composite orders in layered models via machine learning. New Journal of Physics. IOP Publishing. https://doi.org/10.1088/1367-2630/abae44","ama":"Rzadkowski W, Defenu N, Chiacchiera S, Trombettoni A, Bighin G. Detecting composite orders in layered models via machine learning. New Journal of Physics. 2020;22(9). doi:10.1088/1367-2630/abae44","ieee":"W. Rzadkowski, N. Defenu, S. Chiacchiera, A. Trombettoni, and G. Bighin, “Detecting composite orders in layered models via machine learning,” New Journal of Physics, vol. 22, no. 9. IOP Publishing, 2020.","short":"W. Rzadkowski, N. Defenu, S. Chiacchiera, A. Trombettoni, G. Bighin, New Journal of Physics 22 (2020).","mla":"Rzadkowski, Wojciech, et al. “Detecting Composite Orders in Layered Models via Machine Learning.” New Journal of Physics, vol. 22, no. 9, 093026, IOP Publishing, 2020, doi:10.1088/1367-2630/abae44.","ista":"Rzadkowski W, Defenu N, Chiacchiera S, Trombettoni A, Bighin G. 2020. Detecting composite orders in layered models via machine learning. New Journal of Physics. 22(9), 093026.","chicago":"Rzadkowski, Wojciech, N Defenu, S Chiacchiera, A Trombettoni, and Giacomo Bighin. “Detecting Composite Orders in Layered Models via Machine Learning.” New Journal of Physics. IOP Publishing, 2020. https://doi.org/10.1088/1367-2630/abae44."},"title":"Detecting composite orders in layered models via machine learning","author":[{"last_name":"Rzadkowski","full_name":"Rzadkowski, Wojciech","orcid":"0000-0002-1106-4419","id":"48C55298-F248-11E8-B48F-1D18A9856A87","first_name":"Wojciech"},{"last_name":"Defenu","full_name":"Defenu, N","first_name":"N"},{"full_name":"Chiacchiera, S","last_name":"Chiacchiera","first_name":"S"},{"full_name":"Trombettoni, A","last_name":"Trombettoni","first_name":"A"},{"last_name":"Bighin","orcid":"0000-0001-8823-9777","full_name":"Bighin, Giacomo","id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87","first_name":"Giacomo"}],"article_processing_charge":"No","external_id":{"isi":["000573298000001"]},"acknowledgement":"We thank Gesualdo Delfino, Michele Fabrizio, Piero Ferrarese, Robert Konik, Christoph Lampert and Mikhail Lemeshko for stimulating discussions at various stages of this work. WR has received funding from the EU Horizon 2020 program under the Marie Skłodowska-Curie Grant Agreement No. 665385 and is a recipient of a DOC Fellowship of the Austrian Academy of Sciences. GB acknowledges support from the Austrian Science Fund (FWF), under project No. M2641-N27. ND acknowledges support by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) via Collaborative Research Center SFB 1225 (ISOQUANT)--project-id 273811115--and under Germany's Excellence Strategy 'EXC-2181/1-390900948' (the Heidelberg STRUCTURES Excellence Cluster).","publisher":"IOP Publishing","quality_controlled":"1","oa":1,"day":"01","publication":"New Journal of Physics","has_accepted_license":"1","isi":1,"year":"2020","doi":"10.1088/1367-2630/abae44","date_published":"2020-09-01T00:00:00Z","date_created":"2020-10-11T22:01:14Z"},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public","_id":"8705","department":[{"_id":"RoSe"}],"file_date_updated":"2020-10-27T12:49:04Z","date_updated":"2023-09-07T13:43:51Z","ddc":["530"],"scopus_import":"1","intvolume":" 21","month":"12","abstract":[{"text":"We consider the quantum mechanical many-body problem of a single impurity particle immersed in a weakly interacting Bose gas. The impurity interacts with the bosons via a two-body potential. We study the Hamiltonian of this system in the mean-field limit and rigorously show that, at low energies, the problem is well described by the Fröhlich polaron model.","lang":"eng"}],"oa_version":"Published Version","ec_funded":1,"volume":21,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"11473"}]},"issue":"12","publication_status":"published","publication_identifier":{"issn":["1424-0637"]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"8711","checksum":"c12c9c1e6f08def245e42f3cb1d83827","success":1,"date_updated":"2020-10-27T12:49:04Z","file_size":469831,"creator":"cziletti","date_created":"2020-10-27T12:49:04Z","file_name":"2020_Annales_Mysliwy.pdf"}],"project":[{"grant_number":"694227","name":"Analysis of quantum many-body systems","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"},{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385"}],"article_processing_charge":"Yes (via OA deal)","external_id":{"arxiv":["2003.12371"],"isi":["000578111800002"]},"author":[{"last_name":"Mysliwy","full_name":"Mysliwy, Krzysztof","id":"316457FC-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof"},{"orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert"}],"title":"Microscopic derivation of the Fröhlich Hamiltonian for the Bose polaron in the mean-field limit","citation":{"mla":"Mysliwy, Krzysztof, and Robert Seiringer. “Microscopic Derivation of the Fröhlich Hamiltonian for the Bose Polaron in the Mean-Field Limit.” Annales Henri Poincare, vol. 21, no. 12, Springer Nature, 2020, pp. 4003–25, doi:10.1007/s00023-020-00969-3.","ama":"Mysliwy K, Seiringer R. Microscopic derivation of the Fröhlich Hamiltonian for the Bose polaron in the mean-field limit. Annales Henri Poincare. 2020;21(12):4003-4025. doi:10.1007/s00023-020-00969-3","apa":"Mysliwy, K., & Seiringer, R. (2020). Microscopic derivation of the Fröhlich Hamiltonian for the Bose polaron in the mean-field limit. Annales Henri Poincare. Springer Nature. https://doi.org/10.1007/s00023-020-00969-3","ieee":"K. Mysliwy and R. Seiringer, “Microscopic derivation of the Fröhlich Hamiltonian for the Bose polaron in the mean-field limit,” Annales Henri Poincare, vol. 21, no. 12. Springer Nature, pp. 4003–4025, 2020.","short":"K. Mysliwy, R. Seiringer, Annales Henri Poincare 21 (2020) 4003–4025.","chicago":"Mysliwy, Krzysztof, and Robert Seiringer. “Microscopic Derivation of the Fröhlich Hamiltonian for the Bose Polaron in the Mean-Field Limit.” Annales Henri Poincare. Springer Nature, 2020. https://doi.org/10.1007/s00023-020-00969-3.","ista":"Mysliwy K, Seiringer R. 2020. Microscopic derivation of the Fröhlich Hamiltonian for the Bose polaron in the mean-field limit. Annales Henri Poincare. 21(12), 4003–4025."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"publisher":"Springer Nature","quality_controlled":"1","acknowledgement":"Financial support through the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme Grant agreement No. 694227 (R.S.) and the Maria Skłodowska-Curie Grant agreement No. 665386 (K.M.) is gratefully acknowledged. Funding Open access funding provided by Institute of Science and Technology (IST Austria)","page":"4003-4025","date_created":"2020-10-25T23:01:19Z","doi":"10.1007/s00023-020-00969-3","date_published":"2020-12-01T00:00:00Z","year":"2020","isi":1,"has_accepted_license":"1","publication":"Annales Henri Poincare","day":"01"},{"publication_status":"published","publication_identifier":{"issn":["1433-2779"],"eissn":["1433-2787"]},"language":[{"iso":"eng"}],"volume":22,"issue":"6","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"299"}]},"abstract":[{"lang":"eng","text":"We introduce in this paper AMT2.0, a tool for qualitative and quantitative analysis of hybrid continuous and Boolean signals that combine numerical values and discrete events. The evaluation of the signals is based on rich temporal specifications expressed in extended signal temporal logic, which integrates timed regular expressions within signal temporal logic. The tool features qualitative monitoring (property satisfaction checking), trace diagnostics for explaining and justifying property violations and specification-driven measurement of quantitative features of the signal. We demonstrate the tool functionality on several running examples and case studies, and evaluate its performance."}],"oa_version":"None","scopus_import":"1","intvolume":" 22","month":"08","date_updated":"2023-09-08T11:52:02Z","department":[{"_id":"ToHe"}],"_id":"10861","type":"journal_article","article_type":"original","keyword":["Information Systems","Software"],"status":"public","year":"2020","isi":1,"publication":"International Journal on Software Tools for Technology Transfer","day":"03","page":"741-758","date_created":"2022-03-18T10:10:53Z","date_published":"2020-08-03T00:00:00Z","doi":"10.1007/s10009-020-00582-z","quality_controlled":"1","publisher":"Springer Nature","citation":{"chicago":"Nickovic, Dejan, Olivier Lebeltel, Oded Maler, Thomas Ferrere, and Dogan Ulus. “AMT 2.0: Qualitative and Quantitative Trace Analysis with Extended Signal Temporal Logic.” International Journal on Software Tools for Technology Transfer. Springer Nature, 2020. https://doi.org/10.1007/s10009-020-00582-z.","ista":"Nickovic D, Lebeltel O, Maler O, Ferrere T, Ulus D. 2020. AMT 2.0: Qualitative and quantitative trace analysis with extended signal temporal logic. International Journal on Software Tools for Technology Transfer. 22(6), 741–758.","mla":"Nickovic, Dejan, et al. “AMT 2.0: Qualitative and Quantitative Trace Analysis with Extended Signal Temporal Logic.” International Journal on Software Tools for Technology Transfer, vol. 22, no. 6, Springer Nature, 2020, pp. 741–58, doi:10.1007/s10009-020-00582-z.","ieee":"D. Nickovic, O. Lebeltel, O. Maler, T. Ferrere, and D. Ulus, “AMT 2.0: Qualitative and quantitative trace analysis with extended signal temporal logic,” International Journal on Software Tools for Technology Transfer, vol. 22, no. 6. Springer Nature, pp. 741–758, 2020.","short":"D. Nickovic, O. Lebeltel, O. Maler, T. Ferrere, D. Ulus, International Journal on Software Tools for Technology Transfer 22 (2020) 741–758.","apa":"Nickovic, D., Lebeltel, O., Maler, O., Ferrere, T., & Ulus, D. (2020). AMT 2.0: Qualitative and quantitative trace analysis with extended signal temporal logic. International Journal on Software Tools for Technology Transfer. Springer Nature. https://doi.org/10.1007/s10009-020-00582-z","ama":"Nickovic D, Lebeltel O, Maler O, Ferrere T, Ulus D. AMT 2.0: Qualitative and quantitative trace analysis with extended signal temporal logic. International Journal on Software Tools for Technology Transfer. 2020;22(6):741-758. doi:10.1007/s10009-020-00582-z"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000555398600001"]},"article_processing_charge":"No","author":[{"id":"41BCEE5C-F248-11E8-B48F-1D18A9856A87","first_name":"Dejan","last_name":"Nickovic","full_name":"Nickovic, Dejan"},{"first_name":"Olivier","last_name":"Lebeltel","full_name":"Lebeltel, Olivier"},{"full_name":"Maler, Oded","last_name":"Maler","first_name":"Oded"},{"last_name":"Ferrere","orcid":"0000-0001-5199-3143","full_name":"Ferrere, Thomas","first_name":"Thomas","id":"40960E6E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Ulus","full_name":"Ulus, Dogan","first_name":"Dogan"}],"title":"AMT 2.0: Qualitative and quantitative trace analysis with extended signal temporal logic"},{"title":"SCIM: Universal single-cell matching with unpaired feature sets","external_id":{"pmid":["33381818"]},"article_processing_charge":"No","author":[{"first_name":"Stefan G","full_name":"Stark, Stefan G","last_name":"Stark"},{"last_name":"Ficek","full_name":"Ficek, Joanna","first_name":"Joanna"},{"id":"26cfd52f-2483-11ee-8040-88983bcc06d4","first_name":"Francesco","last_name":"Locatello","orcid":"0000-0002-4850-0683","full_name":"Locatello, Francesco"},{"full_name":"Bonilla, Ximena","last_name":"Bonilla","first_name":"Ximena"},{"last_name":"Chevrier","full_name":"Chevrier, Stéphane","first_name":"Stéphane"},{"full_name":"Singer, Franziska","last_name":"Singer","first_name":"Franziska"},{"first_name":"Rudolf","last_name":"Aebersold","full_name":"Aebersold, Rudolf"},{"last_name":"Al-Quaddoomi","full_name":"Al-Quaddoomi, Faisal S","first_name":"Faisal S"},{"first_name":"Jonas","last_name":"Albinus","full_name":"Albinus, Jonas"},{"full_name":"Alborelli, Ilaria","last_name":"Alborelli","first_name":"Ilaria"},{"first_name":"Sonali","last_name":"Andani","full_name":"Andani, Sonali"},{"first_name":"Per-Olof","full_name":"Attinger, Per-Olof","last_name":"Attinger"},{"first_name":"Marina","full_name":"Bacac, Marina","last_name":"Bacac"},{"last_name":"Baumhoer","full_name":"Baumhoer, Daniel","first_name":"Daniel"},{"first_name":"Beatrice","last_name":"Beck-Schimmer","full_name":"Beck-Schimmer, Beatrice"},{"full_name":"Beerenwinkel, Niko","last_name":"Beerenwinkel","first_name":"Niko"},{"first_name":"Christian","last_name":"Beisel","full_name":"Beisel, Christian"},{"first_name":"Lara","last_name":"Bernasconi","full_name":"Bernasconi, Lara"},{"last_name":"Bertolini","full_name":"Bertolini, Anne","first_name":"Anne"},{"first_name":"Bernd","full_name":"Bodenmiller, Bernd","last_name":"Bodenmiller"},{"full_name":"Bonilla, Ximena","last_name":"Bonilla","first_name":"Ximena"},{"last_name":"Casanova","full_name":"Casanova, Ruben","first_name":"Ruben"},{"last_name":"Chevrier","full_name":"Chevrier, Stéphane","first_name":"Stéphane"},{"full_name":"Chicherova, Natalia","last_name":"Chicherova","first_name":"Natalia"},{"first_name":"Maya","last_name":"D'Costa","full_name":"D'Costa, Maya"},{"first_name":"Esther","full_name":"Danenberg, Esther","last_name":"Danenberg"},{"first_name":"Natalie","last_name":"Davidson","full_name":"Davidson, Natalie"},{"full_name":"gan, Monica-Andreea Dră","last_name":"gan","first_name":"Monica-Andreea Dră"},{"first_name":"Reinhard","last_name":"Dummer","full_name":"Dummer, Reinhard"},{"first_name":"Stefanie","last_name":"Engler","full_name":"Engler, Stefanie"},{"full_name":"Erkens, Martin","last_name":"Erkens","first_name":"Martin"},{"first_name":"Katja","full_name":"Eschbach, Katja","last_name":"Eschbach"},{"full_name":"Esposito, Cinzia","last_name":"Esposito","first_name":"Cinzia"},{"first_name":"André","last_name":"Fedier","full_name":"Fedier, 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Rene","last_name":"Holtackers","first_name":"Rene"},{"first_name":"Tamara","last_name":"Huesser","full_name":"Huesser, Tamara"},{"first_name":"Anja","last_name":"Irmisch","full_name":"Irmisch, Anja"},{"first_name":"Francis","full_name":"Jacob, Francis","last_name":"Jacob"},{"first_name":"Andrea","last_name":"Jacobs","full_name":"Jacobs, Andrea"},{"last_name":"Jaeger","full_name":"Jaeger, Tim M","first_name":"Tim M"},{"last_name":"Jahn","full_name":"Jahn, Katharina","first_name":"Katharina"},{"last_name":"James","full_name":"James, Alva R","first_name":"Alva R"},{"first_name":"Philip M","last_name":"Jermann","full_name":"Jermann, Philip M"},{"full_name":"Kahles, André","last_name":"Kahles","first_name":"André"},{"last_name":"Kahraman","full_name":"Kahraman, Abdullah","first_name":"Abdullah"},{"last_name":"Koelzer","full_name":"Koelzer, Viktor H","first_name":"Viktor H"},{"last_name":"Kuebler","full_name":"Kuebler, 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Nicola","last_name":"Miglino","first_name":"Nicola"},{"last_name":"Milani","full_name":"Milani, Emanuela S","first_name":"Emanuela S"},{"first_name":"Holger","last_name":"Moch","full_name":"Moch, Holger"},{"first_name":"Simone","full_name":"Muenst, Simone","last_name":"Muenst"},{"first_name":"Riccardo","full_name":"Murri, Riccardo","last_name":"Murri"},{"first_name":"Charlotte KY","last_name":"Ng","full_name":"Ng, Charlotte KY"},{"full_name":"Nicolet, Stefan","last_name":"Nicolet","first_name":"Stefan"},{"last_name":"Nowak","full_name":"Nowak, Marta","first_name":"Marta"},{"full_name":"Pedrioli, Patrick GA","last_name":"Pedrioli","first_name":"Patrick GA"},{"first_name":"Lucas","last_name":"Pelkmans","full_name":"Pelkmans, Lucas"},{"full_name":"Piscuoglio, Salvatore","last_name":"Piscuoglio","first_name":"Salvatore"},{"full_name":"Prummer, Michael","last_name":"Prummer","first_name":"Michael"},{"last_name":"Ritter","full_name":"Ritter, Mathilde","first_name":"Mathilde"},{"full_name":"Rommel, Christian","last_name":"Rommel","first_name":"Christian"},{"first_name":"María L","full_name":"Rosano-González, María L","last_name":"Rosano-González"},{"first_name":"Gunnar","last_name":"Rätsch","full_name":"Rätsch, Gunnar"},{"first_name":"Natascha","last_name":"Santacroce","full_name":"Santacroce, Natascha"},{"first_name":"Jacobo Sarabia del","last_name":"Castillo","full_name":"Castillo, Jacobo Sarabia del"},{"first_name":"Ramona","full_name":"Schlenker, Ramona","last_name":"Schlenker"},{"last_name":"Schwalie","full_name":"Schwalie, Petra C","first_name":"Petra C"},{"last_name":"Schwan","full_name":"Schwan, Severin","first_name":"Severin"},{"full_name":"Schär, Tobias","last_name":"Schär","first_name":"Tobias"},{"first_name":"Gabriela","last_name":"Senti","full_name":"Senti, Gabriela"},{"first_name":"Franziska","full_name":"Singer, Franziska","last_name":"Singer"},{"full_name":"Sivapatham, Sujana","last_name":"Sivapatham","first_name":"Sujana"},{"last_name":"Snijder","full_name":"Snijder, Berend","first_name":"Berend"},{"last_name":"Sobottka","full_name":"Sobottka, Bettina","first_name":"Bettina"},{"last_name":"Sreedharan","full_name":"Sreedharan, Vipin T","first_name":"Vipin T"},{"first_name":"Stefan","full_name":"Stark, Stefan","last_name":"Stark"},{"first_name":"Daniel J","full_name":"Stekhoven, Daniel J","last_name":"Stekhoven"},{"first_name":"Alexandre PA","full_name":"Theocharides, Alexandre PA","last_name":"Theocharides"},{"first_name":"Tinu M","full_name":"Thomas, Tinu M","last_name":"Thomas"},{"first_name":"Markus","last_name":"Tolnay","full_name":"Tolnay, Markus"},{"first_name":"Vinko","full_name":"Tosevski, Vinko","last_name":"Tosevski"},{"last_name":"Toussaint","full_name":"Toussaint, Nora C","first_name":"Nora C"},{"full_name":"Tuncel, Mustafa A","last_name":"Tuncel","first_name":"Mustafa A"},{"first_name":"Marina","last_name":"Tusup","full_name":"Tusup, Marina"},{"first_name":"Audrey Van","full_name":"Drogen, Audrey Van","last_name":"Drogen"},{"first_name":"Marcus","last_name":"Vetter","full_name":"Vetter, Marcus"},{"last_name":"Vlajnic","full_name":"Vlajnic, Tatjana","first_name":"Tatjana"},{"last_name":"Weber","full_name":"Weber, Sandra","first_name":"Sandra"},{"first_name":"Walter P","last_name":"Weber","full_name":"Weber, Walter P"},{"first_name":"Rebekka","last_name":"Wegmann","full_name":"Wegmann, Rebekka"},{"first_name":"Michael","full_name":"Weller, Michael","last_name":"Weller"},{"full_name":"Wendt, Fabian","last_name":"Wendt","first_name":"Fabian"},{"last_name":"Wey","full_name":"Wey, Norbert","first_name":"Norbert"},{"last_name":"Wicki","full_name":"Wicki, Andreas","first_name":"Andreas"},{"first_name":"Bernd","last_name":"Wollscheid","full_name":"Wollscheid, Bernd"},{"full_name":"Yu, Shuqing","last_name":"Yu","first_name":"Shuqing"},{"first_name":"Johanna","full_name":"Ziegler, Johanna","last_name":"Ziegler"},{"full_name":"Zimmermann, Marc","last_name":"Zimmermann","first_name":"Marc"},{"first_name":"Martin","last_name":"Zoche","full_name":"Zoche, Martin"},{"first_name":"Gregor","full_name":"Zuend, Gregor","last_name":"Zuend"},{"last_name":"Rätsch","full_name":"Rätsch, Gunnar","first_name":"Gunnar"},{"first_name":"Kjong-Van","full_name":"Lehmann, Kjong-Van","last_name":"Lehmann"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Stark, Stefan G., et al. “SCIM: Universal Single-Cell Matching with Unpaired Feature Sets.” Bioinformatics, vol. 36, no. Supplement_2, Oxford University Press, 2020, pp. i919–27, doi:10.1093/bioinformatics/btaa843.","apa":"Stark, S. G., Ficek, J., Locatello, F., Bonilla, X., Chevrier, S., Singer, F., … Lehmann, K.-V. (2020). SCIM: Universal single-cell matching with unpaired feature sets. Bioinformatics. Oxford University Press. https://doi.org/10.1093/bioinformatics/btaa843","ama":"Stark SG, Ficek J, Locatello F, et al. SCIM: Universal single-cell matching with unpaired feature sets. Bioinformatics. 2020;36(Supplement_2):i919-i927. doi:10.1093/bioinformatics/btaa843","ieee":"S. G. Stark et al., “SCIM: Universal single-cell matching with unpaired feature sets,” Bioinformatics, vol. 36, no. Supplement_2. Oxford University Press, pp. i919–i927, 2020.","short":"S.G. Stark, J. Ficek, F. Locatello, X. Bonilla, S. Chevrier, F. Singer, R. Aebersold, F.S. Al-Quaddoomi, J. Albinus, I. Alborelli, S. Andani, P.-O. Attinger, M. Bacac, D. Baumhoer, B. Beck-Schimmer, N. Beerenwinkel, C. Beisel, L. Bernasconi, A. Bertolini, B. Bodenmiller, X. Bonilla, R. Casanova, S. Chevrier, N. Chicherova, M. D’Costa, E. Danenberg, N. Davidson, M.-A.D. gan, R. Dummer, S. Engler, M. Erkens, K. Eschbach, C. Esposito, A. Fedier, P. Ferreira, J. Ficek, A.L. Frei, B. Frey, S. Goetze, L. Grob, G. Gut, D. Günther, M. Haberecker, P. Haeuptle, V. Heinzelmann-Schwarz, S. Herter, R. Holtackers, T. Huesser, A. Irmisch, F. Jacob, A. Jacobs, T.M. Jaeger, K. Jahn, A.R. James, P.M. Jermann, A. Kahles, A. Kahraman, V.H. Koelzer, W. Kuebler, J. Kuipers, C.P. Kunze, C. Kurzeder, K.-V. Lehmann, M. Levesque, S. Lugert, G. Maass, M. Manz, P. Markolin, J. Mena, U. Menzel, J.M. Metzler, N. Miglino, E.S. Milani, H. Moch, S. Muenst, R. Murri, C.K. Ng, S. Nicolet, M. Nowak, P.G. Pedrioli, L. Pelkmans, S. Piscuoglio, M. Prummer, M. Ritter, C. Rommel, M.L. Rosano-González, G. Rätsch, N. Santacroce, J.S. del Castillo, R. Schlenker, P.C. Schwalie, S. Schwan, T. Schär, G. Senti, F. Singer, S. Sivapatham, B. Snijder, B. Sobottka, V.T. Sreedharan, S. Stark, D.J. Stekhoven, A.P. Theocharides, T.M. Thomas, M. Tolnay, V. Tosevski, N.C. Toussaint, M.A. Tuncel, M. Tusup, A.V. Drogen, M. Vetter, T. Vlajnic, S. Weber, W.P. Weber, R. Wegmann, M. Weller, F. Wendt, N. Wey, A. Wicki, B. Wollscheid, S. Yu, J. Ziegler, M. Zimmermann, M. Zoche, G. Zuend, G. Rätsch, K.-V. Lehmann, Bioinformatics 36 (2020) i919–i927.","chicago":"Stark, Stefan G, Joanna Ficek, Francesco Locatello, Ximena Bonilla, Stéphane Chevrier, Franziska Singer, Rudolf Aebersold, et al. “SCIM: Universal Single-Cell Matching with Unpaired Feature Sets.” Bioinformatics. Oxford University Press, 2020. https://doi.org/10.1093/bioinformatics/btaa843.","ista":"Stark SG et al. 2020. SCIM: Universal single-cell matching with unpaired feature sets. Bioinformatics. 36(Supplement_2), i919–i927."},"date_created":"2023-08-21T12:28:20Z","date_published":"2020-12-01T00:00:00Z","doi":"10.1093/bioinformatics/btaa843","page":"i919-i927","publication":"Bioinformatics","day":"01","year":"2020","oa":1,"publisher":"Oxford University Press","quality_controlled":"1","department":[{"_id":"FrLo"}],"extern":"1","date_updated":"2023-09-11T10:21:00Z","keyword":["Computational Mathematics","Computational Theory and Mathematics","Computer Science Applications","Molecular Biology","Biochemistry","Statistics and Probability"],"status":"public","article_type":"original","type":"journal_article","_id":"14125","issue":"Supplement_2","volume":36,"related_material":{"link":[{"url":"https://github.com/ratschlab/scim","relation":"software"}]},"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1367-4811"]},"intvolume":" 36","month":"12","main_file_link":[{"url":"https://doi.org/10.1093/bioinformatics/btaa843","open_access":"1"}],"scopus_import":"1","pmid":1,"oa_version":"Published Version","abstract":[{"text":"Motivation: Recent technological advances have led to an increase in the production and availability of single-cell data. The ability to integrate a set of multi-technology measurements would allow the identification of biologically or clinically meaningful observations through the unification of the perspectives afforded by each technology. In most cases, however, profiling technologies consume the used cells and thus pairwise correspondences between datasets are lost. Due to the sheer size single-cell datasets can acquire, scalable algorithms that are able to universally match single-cell measurements carried out in one cell to its corresponding sibling in another technology are needed.\r\nResults: We propose Single-Cell data Integration via Matching (SCIM), a scalable approach to recover such correspondences in two or more technologies. SCIM assumes that cells share a common (low-dimensional) underlying structure and that the underlying cell distribution is approximately constant across technologies. It constructs a technology-invariant latent space using an autoencoder framework with an adversarial objective. Multi-modal datasets are integrated by pairing cells across technologies using a bipartite matching scheme that operates on the low-dimensional latent representations. We evaluate SCIM on a simulated cellular branching process and show that the cell-to-cell matches derived by SCIM reflect the same pseudotime on the simulated dataset. Moreover, we apply our method to two real-world scenarios, a melanoma tumor sample and a human bone marrow sample, where we pair cells from a scRNA dataset to their sibling cells in a CyTOF dataset achieving 90% and 78% cell-matching accuracy for each one of the samples, respectively.","lang":"eng"}]},{"citation":{"chicago":"Locatello, Francesco, Stefan Bauer, Mario Lucic, Gunnar Rätsch, Sylvain Gelly, Bernhard Schölkopf, and Olivier Bachem. “A Commentary on the Unsupervised Learning of Disentangled Representations.” In The 34th AAAI Conference on Artificial Intelligence, 34:13681–84. Association for the Advancement of Artificial Intelligence, 2020. https://doi.org/10.1609/aaai.v34i09.7120.","ista":"Locatello F, Bauer S, Lucic M, Rätsch G, Gelly S, Schölkopf B, Bachem O. 2020. A commentary on the unsupervised learning of disentangled representations. The 34th AAAI Conference on Artificial Intelligence. AAAI: Conference on Artificial Intelligence vol. 34, 13681–13684.","mla":"Locatello, Francesco, et al. “A Commentary on the Unsupervised Learning of Disentangled Representations.” The 34th AAAI Conference on Artificial Intelligence, vol. 34, no. 9, Association for the Advancement of Artificial Intelligence, 2020, pp. 13681–84, doi:10.1609/aaai.v34i09.7120.","apa":"Locatello, F., Bauer, S., Lucic, M., Rätsch, G., Gelly, S., Schölkopf, B., & Bachem, O. (2020). A commentary on the unsupervised learning of disentangled representations. In The 34th AAAI Conference on Artificial Intelligence (Vol. 34, pp. 13681–13684). New York, NY, United States: Association for the Advancement of Artificial Intelligence. https://doi.org/10.1609/aaai.v34i09.7120","ama":"Locatello F, Bauer S, Lucic M, et al. A commentary on the unsupervised learning of disentangled representations. In: The 34th AAAI Conference on Artificial Intelligence. Vol 34. Association for the Advancement of Artificial Intelligence; 2020:13681-13684. doi:10.1609/aaai.v34i09.7120","ieee":"F. Locatello et al., “A commentary on the unsupervised learning of disentangled representations,” in The 34th AAAI Conference on Artificial Intelligence, New York, NY, United States, 2020, vol. 34, no. 9, pp. 13681–13684.","short":"F. Locatello, S. Bauer, M. Lucic, G. Rätsch, S. Gelly, B. Schölkopf, O. Bachem, in:, The 34th AAAI Conference on Artificial Intelligence, Association for the Advancement of Artificial Intelligence, 2020, pp. 13681–13684."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"26cfd52f-2483-11ee-8040-88983bcc06d4","first_name":"Francesco","last_name":"Locatello","orcid":"0000-0002-4850-0683","full_name":"Locatello, Francesco"},{"full_name":"Bauer, Stefan","last_name":"Bauer","first_name":"Stefan"},{"first_name":"Mario","full_name":"Lucic, Mario","last_name":"Lucic"},{"first_name":"Gunnar","last_name":"Rätsch","full_name":"Rätsch, Gunnar"},{"full_name":"Gelly, Sylvain","last_name":"Gelly","first_name":"Sylvain"},{"first_name":"Bernhard","last_name":"Schölkopf","full_name":"Schölkopf, Bernhard"},{"first_name":"Olivier","last_name":"Bachem","full_name":"Bachem, Olivier"}],"external_id":{"arxiv":["2007.14184"]},"article_processing_charge":"No","title":"A commentary on the unsupervised learning of disentangled representations","quality_controlled":"1","publisher":"Association for the Advancement of Artificial Intelligence","oa":1,"year":"2020","day":"28","publication":"The 34th AAAI Conference on Artificial Intelligence","page":"13681-13684","doi":"10.1609/aaai.v34i09.7120","date_published":"2020-07-28T00:00:00Z","date_created":"2023-08-22T14:07:26Z","_id":"14186","type":"conference","conference":{"start_date":"2020-02-07","location":"New York, NY, United States","end_date":"2020-02-12","name":"AAAI: Conference on Artificial Intelligence"},"status":"public","date_updated":"2023-09-12T07:44:48Z","extern":"1","department":[{"_id":"FrLo"}],"abstract":[{"text":"The goal of the unsupervised learning of disentangled representations is to\r\nseparate the independent explanatory factors of variation in the data without\r\naccess to supervision. In this paper, we summarize the results of Locatello et\r\nal., 2019, and focus on their implications for practitioners. We discuss the\r\ntheoretical result showing that the unsupervised learning of disentangled\r\nrepresentations is fundamentally impossible without inductive biases and the\r\npractical challenges it entails. Finally, we comment on our experimental\r\nfindings, highlighting the limitations of state-of-the-art approaches and\r\ndirections for future research.","lang":"eng"}],"oa_version":"Preprint","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/2007.14184","open_access":"1"}],"month":"07","intvolume":" 34","publication_identifier":{"eissn":["2374-3468"],"isbn":["9781577358350"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":34,"issue":"9"},{"publication_status":"published","language":[{"iso":"eng"}],"volume":119,"abstract":[{"text":"Intelligent agents should be able to learn useful representations by\r\nobserving changes in their environment. We model such observations as pairs of\r\nnon-i.i.d. images sharing at least one of the underlying factors of variation.\r\nFirst, we theoretically show that only knowing how many factors have changed,\r\nbut not which ones, is sufficient to learn disentangled representations.\r\nSecond, we provide practical algorithms that learn disentangled representations\r\nfrom pairs of images without requiring annotation of groups, individual\r\nfactors, or the number of factors that have changed. Third, we perform a\r\nlarge-scale empirical study and show that such pairs of observations are\r\nsufficient to reliably learn disentangled representations on several benchmark\r\ndata sets. Finally, we evaluate our learned representations and find that they\r\nare simultaneously useful on a diverse suite of tasks, including generalization\r\nunder covariate shifts, fairness, and abstract reasoning. Overall, our results\r\ndemonstrate that weak supervision enables learning of useful disentangled\r\nrepresentations in realistic scenarios.","lang":"eng"}],"oa_version":"Preprint","alternative_title":["PMLR"],"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2002.02886"}],"month":"07","intvolume":" 119","date_updated":"2023-09-12T07:59:29Z","extern":"1","department":[{"_id":"FrLo"}],"_id":"14188","type":"conference","conference":{"start_date":"2020-07-13","location":"Virtual","end_date":"2020-07-18","name":"International Conference on Machine Learning"},"status":"public","year":"2020","day":"07","publication":"Proceedings of the 37th International Conference on Machine Learning","page":"6348–6359","date_published":"2020-07-07T00:00:00Z","date_created":"2023-08-22T14:08:14Z","quality_controlled":"1","oa":1,"citation":{"mla":"Locatello, Francesco, et al. “Weakly-Supervised Disentanglement without Compromises.” Proceedings of the 37th International Conference on Machine Learning, vol. 119, 2020, pp. 6348–6359.","ieee":"F. Locatello, B. Poole, G. Rätsch, B. Schölkopf, O. Bachem, and M. Tschannen, “Weakly-supervised disentanglement without compromises,” in Proceedings of the 37th International Conference on Machine Learning, Virtual, 2020, vol. 119, pp. 6348–6359.","short":"F. Locatello, B. Poole, G. Rätsch, B. Schölkopf, O. Bachem, M. Tschannen, in:, Proceedings of the 37th International Conference on Machine Learning, 2020, pp. 6348–6359.","ama":"Locatello F, Poole B, Rätsch G, Schölkopf B, Bachem O, Tschannen M. Weakly-supervised disentanglement without compromises. In: Proceedings of the 37th International Conference on Machine Learning. Vol 119. ; 2020:6348–6359.","apa":"Locatello, F., Poole, B., Rätsch, G., Schölkopf, B., Bachem, O., & Tschannen, M. (2020). Weakly-supervised disentanglement without compromises. In Proceedings of the 37th International Conference on Machine Learning (Vol. 119, pp. 6348–6359). Virtual.","chicago":"Locatello, Francesco, Ben Poole, Gunnar Rätsch, Bernhard Schölkopf, Olivier Bachem, and Michael Tschannen. “Weakly-Supervised Disentanglement without Compromises.” In Proceedings of the 37th International Conference on Machine Learning, 119:6348–6359, 2020.","ista":"Locatello F, Poole B, Rätsch G, Schölkopf B, Bachem O, Tschannen M. 2020. Weakly-supervised disentanglement without compromises. Proceedings of the 37th International Conference on Machine Learning. International Conference on Machine Learning, PMLR, vol. 119, 6348–6359."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"orcid":"0000-0002-4850-0683","full_name":"Locatello, Francesco","last_name":"Locatello","first_name":"Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4"},{"last_name":"Poole","full_name":"Poole, Ben","first_name":"Ben"},{"first_name":"Gunnar","full_name":"Rätsch, Gunnar","last_name":"Rätsch"},{"last_name":"Schölkopf","full_name":"Schölkopf, Bernhard","first_name":"Bernhard"},{"first_name":"Olivier","full_name":"Bachem, Olivier","last_name":"Bachem"},{"first_name":"Michael","last_name":"Tschannen","full_name":"Tschannen, Michael"}],"external_id":{"arxiv":["2002.02886"]},"article_processing_charge":"No","title":"Weakly-supervised disentanglement without compromises"},{"_id":"14187","type":"conference","conference":{"name":"International Conference on Machine Learning","end_date":"2020-07-18","location":"Virtual","start_date":"2020-07-13"},"status":"public","citation":{"mla":"Négiar, Geoffrey, et al. “Stochastic Frank-Wolfe for Constrained Finite-Sum Minimization.” Proceedings of the 37th International Conference on Machine Learning, vol. 119, 2020, pp. 7253–62.","ieee":"G. Négiar et al., “Stochastic Frank-Wolfe for constrained finite-sum minimization,” in Proceedings of the 37th International Conference on Machine Learning, Virtual, 2020, vol. 119, pp. 7253–7262.","short":"G. Négiar, G. Dresdner, A. Tsai, L.E. Ghaoui, F. Locatello, R.M. Freund, F. Pedregosa, in:, Proceedings of the 37th International Conference on Machine Learning, 2020, pp. 7253–7262.","apa":"Négiar, G., Dresdner, G., Tsai, A., Ghaoui, L. E., Locatello, F., Freund, R. M., & Pedregosa, F. (2020). Stochastic Frank-Wolfe for constrained finite-sum minimization. In Proceedings of the 37th International Conference on Machine Learning (Vol. 119, pp. 7253–7262). Virtual.","ama":"Négiar G, Dresdner G, Tsai A, et al. Stochastic Frank-Wolfe for constrained finite-sum minimization. In: Proceedings of the 37th International Conference on Machine Learning. Vol 119. ; 2020:7253-7262.","chicago":"Négiar, Geoffrey, Gideon Dresdner, Alicia Tsai, Laurent El Ghaoui, Francesco Locatello, Robert M. Freund, and Fabian Pedregosa. “Stochastic Frank-Wolfe for Constrained Finite-Sum Minimization.” In Proceedings of the 37th International Conference on Machine Learning, 119:7253–62, 2020.","ista":"Négiar G, Dresdner G, Tsai A, Ghaoui LE, Locatello F, Freund RM, Pedregosa F. 2020. Stochastic Frank-Wolfe for constrained finite-sum minimization. Proceedings of the 37th International Conference on Machine Learning. International Conference on Machine Learning, PMLR, vol. 119, 7253–7262."},"date_updated":"2023-09-12T08:03:40Z","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Négiar, Geoffrey","last_name":"Négiar","first_name":"Geoffrey"},{"first_name":"Gideon","full_name":"Dresdner, Gideon","last_name":"Dresdner"},{"full_name":"Tsai, Alicia","last_name":"Tsai","first_name":"Alicia"},{"first_name":"Laurent El","last_name":"Ghaoui","full_name":"Ghaoui, Laurent El"},{"orcid":"0000-0002-4850-0683","full_name":"Locatello, Francesco","last_name":"Locatello","first_name":"Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4"},{"first_name":"Robert M.","full_name":"Freund, Robert M.","last_name":"Freund"},{"first_name":"Fabian","last_name":"Pedregosa","full_name":"Pedregosa, Fabian"}],"external_id":{"arxiv":["2002.11860"]},"article_processing_charge":"No","title":"Stochastic Frank-Wolfe for constrained finite-sum minimization","department":[{"_id":"FrLo"}],"abstract":[{"text":"We propose a novel Stochastic Frank-Wolfe (a.k.a. conditional gradient)\r\nalgorithm for constrained smooth finite-sum minimization with a generalized\r\nlinear prediction/structure. This class of problems includes empirical risk\r\nminimization with sparse, low-rank, or other structured constraints. The\r\nproposed method is simple to implement, does not require step-size tuning, and\r\nhas a constant per-iteration cost that is independent of the dataset size.\r\nFurthermore, as a byproduct of the method we obtain a stochastic estimator of\r\nthe Frank-Wolfe gap that can be used as a stopping criterion. Depending on the\r\nsetting, the proposed method matches or improves on the best computational\r\nguarantees for Stochastic Frank-Wolfe algorithms. Benchmarks on several\r\ndatasets highlight different regimes in which the proposed method exhibits a\r\nfaster empirical convergence than related methods. Finally, we provide an\r\nimplementation of all considered methods in an open-source package.","lang":"eng"}],"oa_version":"Preprint","quality_controlled":"1","alternative_title":["PMLR"],"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2002.11860"}],"month":"07","intvolume":" 119","publication_status":"published","year":"2020","day":"27","language":[{"iso":"eng"}],"publication":"Proceedings of the 37th International Conference on Machine Learning","page":"7253-7262","volume":119,"date_published":"2020-07-27T00:00:00Z","date_created":"2023-08-22T14:07:52Z"},{"date_published":"2020-09-01T00:00:00Z","date_created":"2023-08-22T14:10:34Z","day":"01","publication":"Journal of Machine Learning Research","has_accepted_license":"1","year":"2020","publisher":"MIT Press","quality_controlled":"1","oa":1,"title":"A sober look at the unsupervised learning of disentangled representations and their evaluation","author":[{"full_name":"Locatello, Francesco","orcid":"0000-0002-4850-0683","last_name":"Locatello","first_name":"Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4"},{"full_name":"Bauer, Stefan","last_name":"Bauer","first_name":"Stefan"},{"first_name":"Mario","full_name":"Lucic, Mario","last_name":"Lucic"},{"full_name":"Rätsch, Gunnar","last_name":"Rätsch","first_name":"Gunnar"},{"first_name":"Sylvain","last_name":"Gelly","full_name":"Gelly, Sylvain"},{"last_name":"Schölkopf","full_name":"Schölkopf, Bernhard","first_name":"Bernhard"},{"first_name":"Olivier","full_name":"Bachem, Olivier","last_name":"Bachem"}],"external_id":{"arxiv":["2010.14766"]},"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Locatello, Francesco, Stefan Bauer, Mario Lucic, Gunnar Rätsch, Sylvain Gelly, Bernhard Schölkopf, and Olivier Bachem. “A Sober Look at the Unsupervised Learning of Disentangled Representations and Their Evaluation.” Journal of Machine Learning Research. MIT Press, 2020.","ista":"Locatello F, Bauer S, Lucic M, Rätsch G, Gelly S, Schölkopf B, Bachem O. 2020. A sober look at the unsupervised learning of disentangled representations and their evaluation. Journal of Machine Learning Research. 21, 209.","mla":"Locatello, Francesco, et al. “A Sober Look at the Unsupervised Learning of Disentangled Representations and Their Evaluation.” Journal of Machine Learning Research, vol. 21, 209, MIT Press, 2020.","apa":"Locatello, F., Bauer, S., Lucic, M., Rätsch, G., Gelly, S., Schölkopf, B., & Bachem, O. (2020). A sober look at the unsupervised learning of disentangled representations and their evaluation. Journal of Machine Learning Research. MIT Press.","ama":"Locatello F, Bauer S, Lucic M, et al. A sober look at the unsupervised learning of disentangled representations and their evaluation. Journal of Machine Learning Research. 2020;21.","ieee":"F. Locatello et al., “A sober look at the unsupervised learning of disentangled representations and their evaluation,” Journal of Machine Learning Research, vol. 21. MIT Press, 2020.","short":"F. Locatello, S. Bauer, M. Lucic, G. Rätsch, S. Gelly, B. Schölkopf, O. Bachem, Journal of Machine Learning Research 21 (2020)."},"article_number":"209","volume":21,"language":[{"iso":"eng"}],"publication_status":"published","month":"09","intvolume":" 21","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://jmlr.csail.mit.edu/papers/v21/19-976.html"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"The idea behind the unsupervised learning of disentangled representations is that real-world data is generated by a few explanatory factors of variation which can be recovered by unsupervised learning algorithms. In this paper, we provide a sober look at recent progress in the field and challenge some common assumptions. We first theoretically show that the unsupervised learning of disentangled representations is fundamentally impossible without inductive biases on both the models and the data. Then, we train over 14000\r\n models covering most prominent methods and evaluation metrics in a reproducible large-scale experimental study on eight data sets. We observe that while the different methods successfully enforce properties “encouraged” by the corresponding losses, well-disentangled models seemingly cannot be identified without supervision. Furthermore, different evaluation metrics do not always agree on what should be considered “disentangled” and exhibit systematic differences in the estimation. Finally, increased disentanglement does not seem to necessarily lead to a decreased sample complexity of learning for downstream tasks. Our results suggest that future work on disentanglement learning should be explicit about the role of inductive biases and (implicit) supervision, investigate concrete benefits of enforcing disentanglement of the learned representations, and consider a reproducible experimental setup covering several data sets."}],"department":[{"_id":"FrLo"}],"extern":"1","ddc":["000"],"date_updated":"2023-09-12T09:23:56Z","status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"14195"},{"article_number":"e1007642","title":"The relation between crosstalk and gene regulation form revisited","article_processing_charge":"No","external_id":{"isi":["000526725200019"]},"author":[{"id":"483E70DE-F248-11E8-B48F-1D18A9856A87","first_name":"Rok","orcid":"0000-0003-2539-3560","full_name":"Grah, Rok","last_name":"Grah"},{"first_name":"Tamar","last_name":"Friedlander","full_name":"Friedlander, Tamar"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ama":"Grah R, Friedlander T. The relation between crosstalk and gene regulation form revisited. PLOS Computational Biology. 2020;16(2). doi:10.1371/journal.pcbi.1007642","apa":"Grah, R., & Friedlander, T. (2020). The relation between crosstalk and gene regulation form revisited. PLOS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1007642","ieee":"R. Grah and T. Friedlander, “The relation between crosstalk and gene regulation form revisited,” PLOS Computational Biology, vol. 16, no. 2. Public Library of Science, 2020.","short":"R. Grah, T. Friedlander, PLOS Computational Biology 16 (2020).","mla":"Grah, Rok, and Tamar Friedlander. “The Relation between Crosstalk and Gene Regulation Form Revisited.” PLOS Computational Biology, vol. 16, no. 2, e1007642, Public Library of Science, 2020, doi:10.1371/journal.pcbi.1007642.","ista":"Grah R, Friedlander T. 2020. The relation between crosstalk and gene regulation form revisited. PLOS Computational Biology. 16(2), e1007642.","chicago":"Grah, Rok, and Tamar Friedlander. “The Relation between Crosstalk and Gene Regulation Form Revisited.” PLOS Computational Biology. Public Library of Science, 2020. https://doi.org/10.1371/journal.pcbi.1007642."},"oa":1,"publisher":"Public Library of Science","quality_controlled":"1","date_created":"2020-03-06T07:39:38Z","doi":"10.1371/journal.pcbi.1007642","date_published":"2020-02-25T00:00:00Z","publication":"PLOS Computational Biology","day":"25","year":"2020","has_accepted_license":"1","isi":1,"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","_id":"7569","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"file_date_updated":"2020-07-14T12:48:00Z","ddc":["000","570"],"date_updated":"2023-09-12T11:02:24Z","intvolume":" 16","month":"02","scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"Genes differ in the frequency at which they are expressed and in the form of regulation used to control their activity. In particular, positive or negative regulation can lead to activation of a gene in response to an external signal. Previous works proposed that the form of regulation of a gene correlates with its frequency of usage: positive regulation when the gene is frequently expressed and negative regulation when infrequently expressed. Such network design means that, in the absence of their regulators, the genes are found in their least required activity state, hence regulatory intervention is often necessary. Due to the multitude of genes and regulators, spurious binding and unbinding events, called “crosstalk”, could occur. To determine how the form of regulation affects the global crosstalk in the network, we used a mathematical model that includes multiple regulators and multiple target genes. We found that crosstalk depends non-monotonically on the availability of regulators. Our analysis showed that excess use of regulation entailed by the formerly suggested network design caused high crosstalk levels in a large part of the parameter space. We therefore considered the opposite ‘idle’ design, where the default unregulated state of genes is their frequently required activity state. We found, that ‘idle’ design minimized the use of regulation and thus minimized crosstalk. In addition, we estimated global crosstalk of S. cerevisiae using transcription factors binding data. We demonstrated that even partial network data could suffice to estimate its global crosstalk, suggesting its applicability to additional organisms. We found that S. cerevisiae estimated crosstalk is lower than that of a random network, suggesting that natural selection reduces crosstalk. In summary, our study highlights a new type of protein production cost which is typically overlooked: that of regulatory interference caused by the presence of excess regulators in the cell. It demonstrates the importance of whole-network descriptions, which could show effects missed by single-gene models.","lang":"eng"}],"issue":"2","volume":16,"related_material":{"record":[{"relation":"research_data","id":"9716","status":"deleted"},{"relation":"research_data","id":"9776","status":"public"},{"id":"9779","status":"public","relation":"used_in_publication"},{"relation":"dissertation_contains","id":"8155","status":"public"},{"id":"9777","status":"public","relation":"research_data"}]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"7579","checksum":"5239dd134dc6e1c71fe7b3ce2953da37","date_updated":"2020-07-14T12:48:00Z","file_size":2209325,"creator":"dernst","date_created":"2020-03-09T15:12:21Z","file_name":"2020_PlosCompBio_Grah.pdf"}],"publication_status":"published","publication_identifier":{"issn":["1553-7358"]}},{"doi":"10.1101/2020.11.03.366948","date_published":"2020-11-05T00:00:00Z","date_created":"2020-11-26T07:17:19Z","year":"2020","publication_status":"submitted","day":"05","publication":"bioRxiv","language":[{"iso":"eng"}],"publisher":"Cold Spring Harbor Laboratory","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2020.11.03.366948"}],"oa":1,"month":"11","abstract":[{"lang":"eng","text":"In mammals, chromatin marks at imprinted genes are asymmetrically inherited to control parentally-biased gene expression. This control is thought predominantly to involve parent-specific differentially methylated regions (DMR) in genomic DNA. However, neither parent-of-origin-specific transcription nor DMRs have been comprehensively mapped. We here address this by integrating transcriptomic and epigenomic approaches in mouse preimplantation embryos (blastocysts). Transcriptome-analysis identified 71 genes expressed with previously unknown parent-of-origin-specific expression in blastocysts (nBiX: novel blastocyst-imprinted expression). Uniparental expression of nBiX genes disappeared soon after implantation. Micro-whole-genome bisulfite sequencing (μWGBS) of individual uniparental blastocysts detected 859 DMRs. Only 18% of nBiXs were associated with a DMR, whereas 60% were associated with parentally-biased H3K27me3. This suggests a major role for Polycomb-mediated imprinting in blastocysts. Five nBiX-clusters contained at least one known imprinted gene, and five novel clusters contained exclusively nBiX-genes. These data suggest a complex program of stage-specific imprinting involving different tiers of regulation."}],"oa_version":"Preprint","pmid":1,"author":[{"full_name":"Santini, Laura","last_name":"Santini","first_name":"Laura"},{"first_name":"Florian","last_name":"Halbritter","full_name":"Halbritter, Florian"},{"full_name":"Titz-Teixeira, Fabian","last_name":"Titz-Teixeira","first_name":"Fabian"},{"first_name":"Toru","last_name":"Suzuki","full_name":"Suzuki, Toru"},{"first_name":"Maki","last_name":"Asami","full_name":"Asami, Maki"},{"first_name":"Julia","full_name":"Ramesmayer, Julia","last_name":"Ramesmayer"},{"full_name":"Ma, Xiaoyan","last_name":"Ma","first_name":"Xiaoyan"},{"first_name":"Andreas","full_name":"Lackner, Andreas","last_name":"Lackner"},{"last_name":"Warr","full_name":"Warr, Nick","first_name":"Nick"},{"id":"48EA0138-F248-11E8-B48F-1D18A9856A87","first_name":"Florian","orcid":"0000-0002-7462-0048","full_name":"Pauler, Florian","last_name":"Pauler"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061"},{"first_name":"Ernest","full_name":"Laue, Ernest","last_name":"Laue"},{"first_name":"Matthias","full_name":"Farlik, Matthias","last_name":"Farlik"},{"first_name":"Christoph","last_name":"Bock","full_name":"Bock, Christoph"},{"full_name":"Beyer, Andreas","last_name":"Beyer","first_name":"Andreas"},{"full_name":"Perry, Anthony C. F.","last_name":"Perry","first_name":"Anthony C. F."},{"first_name":"Martin","last_name":"Leeb","full_name":"Leeb, Martin"}],"external_id":{"pmid":["PPR234457 "]},"article_processing_charge":"No","title":"Novel imprints in mouse blastocysts are predominantly DNA methylation independent","department":[{"_id":"SiHi"}],"citation":{"ama":"Santini L, Halbritter F, Titz-Teixeira F, et al. Novel imprints in mouse blastocysts are predominantly DNA methylation independent. bioRxiv. doi:10.1101/2020.11.03.366948","apa":"Santini, L., Halbritter, F., Titz-Teixeira, F., Suzuki, T., Asami, M., Ramesmayer, J., … Leeb, M. (n.d.). Novel imprints in mouse blastocysts are predominantly DNA methylation independent. bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2020.11.03.366948","short":"L. Santini, F. Halbritter, F. Titz-Teixeira, T. Suzuki, M. Asami, J. Ramesmayer, X. Ma, A. Lackner, N. Warr, F. Pauler, S. Hippenmeyer, E. Laue, M. Farlik, C. Bock, A. Beyer, A.C.F. Perry, M. Leeb, BioRxiv (n.d.).","ieee":"L. Santini et al., “Novel imprints in mouse blastocysts are predominantly DNA methylation independent,” bioRxiv. Cold Spring Harbor Laboratory.","mla":"Santini, Laura, et al. “Novel Imprints in Mouse Blastocysts Are Predominantly DNA Methylation Independent.” BioRxiv, Cold Spring Harbor Laboratory, doi:10.1101/2020.11.03.366948.","ista":"Santini L, Halbritter F, Titz-Teixeira F, Suzuki T, Asami M, Ramesmayer J, Ma X, Lackner A, Warr N, Pauler F, Hippenmeyer S, Laue E, Farlik M, Bock C, Beyer A, Perry ACF, Leeb M. Novel imprints in mouse blastocysts are predominantly DNA methylation independent. bioRxiv, 10.1101/2020.11.03.366948.","chicago":"Santini, Laura, Florian Halbritter, Fabian Titz-Teixeira, Toru Suzuki, Maki Asami, Julia Ramesmayer, Xiaoyan Ma, et al. “Novel Imprints in Mouse Blastocysts Are Predominantly DNA Methylation Independent.” BioRxiv. Cold Spring Harbor Laboratory, n.d. https://doi.org/10.1101/2020.11.03.366948."},"date_updated":"2023-09-12T11:05:28Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"preprint","status":"public","_id":"8813"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-09-12T11:02:25Z","citation":{"ista":"Grah R, Friedlander T. 2020. Maximizing crosstalk, Public Library of Science, 10.1371/journal.pcbi.1007642.s002.","chicago":"Grah, Rok, and Tamar Friedlander. “Maximizing Crosstalk.” Public Library of Science, 2020. https://doi.org/10.1371/journal.pcbi.1007642.s002.","apa":"Grah, R., & Friedlander, T. (2020). Maximizing crosstalk. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1007642.s002","ama":"Grah R, Friedlander T. Maximizing crosstalk. 2020. doi:10.1371/journal.pcbi.1007642.s002","short":"R. Grah, T. Friedlander, (2020).","ieee":"R. Grah and T. Friedlander, “Maximizing crosstalk.” Public Library of Science, 2020.","mla":"Grah, Rok, and Tamar Friedlander. Maximizing Crosstalk. Public Library of Science, 2020, doi:10.1371/journal.pcbi.1007642.s002."},"title":"Maximizing crosstalk","department":[{"_id":"GaTk"}],"author":[{"first_name":"Rok","id":"483E70DE-F248-11E8-B48F-1D18A9856A87","last_name":"Grah","full_name":"Grah, Rok","orcid":"0000-0003-2539-3560"},{"first_name":"Tamar","full_name":"Friedlander, Tamar","last_name":"Friedlander"}],"article_processing_charge":"No","_id":"9777","status":"public","type":"research_data_reference","day":"25","year":"2020","doi":"10.1371/journal.pcbi.1007642.s002","related_material":{"record":[{"status":"public","id":"7569","relation":"used_in_publication"}]},"date_published":"2020-02-25T00:00:00Z","date_created":"2021-08-06T07:21:51Z","oa_version":"None","month":"02","publisher":"Public Library of Science","main_file_link":[{"url":"https://doi.org/10.1371/journal.pcbi.1007642.s002","open_access":"1"}],"oa":1},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ama":"Kragl B. Verifying concurrent programs: Refinement, synchronization, sequentialization. 2020. doi:10.15479/AT:ISTA:8332","apa":"Kragl, B. (2020). Verifying concurrent programs: Refinement, synchronization, sequentialization. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8332","short":"B. Kragl, Verifying Concurrent Programs: Refinement, Synchronization, Sequentialization, Institute of Science and Technology Austria, 2020.","ieee":"B. Kragl, “Verifying concurrent programs: Refinement, synchronization, sequentialization,” Institute of Science and Technology Austria, 2020.","mla":"Kragl, Bernhard. Verifying Concurrent Programs: Refinement, Synchronization, Sequentialization. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8332.","ista":"Kragl B. 2020. Verifying concurrent programs: Refinement, synchronization, sequentialization. Institute of Science and Technology Austria.","chicago":"Kragl, Bernhard. “Verifying Concurrent Programs: Refinement, Synchronization, Sequentialization.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8332."},"title":"Verifying concurrent programs: Refinement, synchronization, sequentialization","article_processing_charge":"No","author":[{"first_name":"Bernhard","id":"320FC952-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7745-9117","full_name":"Kragl, Bernhard","last_name":"Kragl"}],"oa":1,"publisher":"Institute of Science and Technology Austria","day":"03","year":"2020","has_accepted_license":"1","date_created":"2020-09-04T12:24:12Z","date_published":"2020-09-03T00:00:00Z","doi":"10.15479/AT:ISTA:8332","page":"120","_id":"8332","status":"public","type":"dissertation","ddc":["000"],"date_updated":"2023-09-13T08:45:08Z","supervisor":[{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724"}],"department":[{"_id":"ToHe"}],"file_date_updated":"2020-09-04T13:00:17Z","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Designing and verifying concurrent programs is a notoriously challenging, time consuming, and error prone task, even for experts. This is due to the sheer number of possible interleavings of a concurrent program, all of which have to be tracked and accounted for in a formal proof. Inventing an inductive invariant that captures all interleavings of a low-level implementation is theoretically possible, but practically intractable. We develop a refinement-based verification framework that provides mechanisms to simplify proof construction by decomposing the verification task into smaller subtasks.\r\n\r\nIn a first line of work, we present a foundation for refinement reasoning over structured concurrent programs. We introduce layered concurrent programs as a compact notation to represent multi-layer refinement proofs. A layered concurrent program specifies a sequence of connected concurrent programs, from most concrete to most abstract, such that common parts of different programs are written exactly once. Each program in this sequence is expressed as structured concurrent program, i.e., a program over (potentially recursive) procedures, imperative control flow, gated atomic actions, structured parallelism, and asynchronous concurrency. This is in contrast to existing refinement-based verifiers, which represent concurrent systems as flat transition relations. We present a powerful refinement proof rule that decomposes refinement checking over structured programs into modular verification conditions. Refinement checking is supported by a new form of modular, parameterized invariants, called yield invariants, and a linear permission system to enhance local reasoning.\r\n\r\nIn a second line of work, we present two new reduction-based program transformations that target asynchronous programs. These transformations reduce the number of interleavings that need to be considered, thus reducing the complexity of invariants. Synchronization simplifies the verification of asynchronous programs by introducing the fiction, for proof purposes, that asynchronous operations complete synchronously. Synchronization summarizes an asynchronous computation as immediate atomic effect. Inductive sequentialization establishes sequential reductions that captures every behavior of the original program up to reordering of coarse-grained commutative actions. A sequential reduction of a concurrent program is easy to reason about since it corresponds to a simple execution of the program in an idealized synchronous environment, where processes act in a fixed order and at the same speed.\r\n\r\nOur approach is implemented the CIVL verifier, which has been successfully used for the verification of several complex concurrent programs. In our methodology, the overall correctness of a program is established piecemeal by focusing on the invariant required for each refinement step separately. While the programmer does the creative work of specifying the chain of programs and the inductive invariant justifying each link in the chain, the tool automatically constructs the verification conditions underlying each refinement step."}],"month":"09","alternative_title":["ISTA Thesis"],"language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"26fe261550f691280bda4c454bf015c7","file_id":"8333","creator":"bkragl","date_updated":"2020-09-04T12:17:47Z","file_size":1348815,"date_created":"2020-09-04T12:17:47Z","file_name":"kragl-thesis.pdf"},{"access_level":"closed","relation":"source_file","content_type":"application/zip","checksum":"b9694ce092b7c55557122adba8337ebc","file_id":"8335","creator":"bkragl","date_updated":"2020-09-04T13:00:17Z","file_size":372312,"date_created":"2020-09-04T13:00:17Z","file_name":"kragl-thesis.zip"}],"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"related_material":{"record":[{"id":"133","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"8012"},{"id":"8195","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"160"}]}},{"title":"Object-centric learning with slot attention","department":[{"_id":"FrLo"}],"external_id":{"arxiv":["2006.15055"]},"article_processing_charge":"No","author":[{"id":"26cfd52f-2483-11ee-8040-88983bcc06d4","first_name":"Francesco","full_name":"Locatello, Francesco","orcid":"0000-0002-4850-0683","last_name":"Locatello"},{"last_name":"Weissenborn","full_name":"Weissenborn, Dirk","first_name":"Dirk"},{"last_name":"Unterthiner","full_name":"Unterthiner, Thomas","first_name":"Thomas"},{"first_name":"Aravindh","last_name":"Mahendran","full_name":"Mahendran, Aravindh"},{"first_name":"Georg","full_name":"Heigold, Georg","last_name":"Heigold"},{"last_name":"Uszkoreit","full_name":"Uszkoreit, Jakob","first_name":"Jakob"},{"last_name":"Dosovitskiy","full_name":"Dosovitskiy, Alexey","first_name":"Alexey"},{"first_name":"Thomas","last_name":"Kipf","full_name":"Kipf, Thomas"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","citation":{"chicago":"Locatello, Francesco, Dirk Weissenborn, Thomas Unterthiner, Aravindh Mahendran, Georg Heigold, Jakob Uszkoreit, Alexey Dosovitskiy, and Thomas Kipf. “Object-Centric Learning with Slot Attention.” In Advances in Neural Information Processing Systems, 33:11525–38. Curran Associates, 2020.","ista":"Locatello F, Weissenborn D, Unterthiner T, Mahendran A, Heigold G, Uszkoreit J, Dosovitskiy A, Kipf T. 2020. Object-centric learning with slot attention. Advances in Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems vol. 33, 11525–11538.","mla":"Locatello, Francesco, et al. “Object-Centric Learning with Slot Attention.” Advances in Neural Information Processing Systems, vol. 33, Curran Associates, 2020, pp. 11525–38.","short":"F. Locatello, D. Weissenborn, T. Unterthiner, A. Mahendran, G. Heigold, J. Uszkoreit, A. Dosovitskiy, T. Kipf, in:, Advances in Neural Information Processing Systems, Curran Associates, 2020, pp. 11525–11538.","ieee":"F. Locatello et al., “Object-centric learning with slot attention,” in Advances in Neural Information Processing Systems, Virtual, 2020, vol. 33, pp. 11525–11538.","apa":"Locatello, F., Weissenborn, D., Unterthiner, T., Mahendran, A., Heigold, G., Uszkoreit, J., … Kipf, T. (2020). Object-centric learning with slot attention. In Advances in Neural Information Processing Systems (Vol. 33, pp. 11525–11538). Virtual: Curran Associates.","ama":"Locatello F, Weissenborn D, Unterthiner T, et al. Object-centric learning with slot attention. In: Advances in Neural Information Processing Systems. Vol 33. Curran Associates; 2020:11525-11538."},"date_updated":"2023-09-13T12:19:19Z","status":"public","conference":{"name":"NeurIPS: Neural Information Processing Systems","end_date":"2020-12-12","location":"Virtual","start_date":"2020-12-06"},"type":"conference","_id":"14326","date_created":"2023-09-13T12:03:46Z","date_published":"2020-01-01T00:00:00Z","volume":33,"page":"11525-11538","language":[{"iso":"eng"}],"publication":"Advances in Neural Information Processing Systems","year":"2020","publication_status":"published","publication_identifier":{"isbn":["9781713829546"]},"intvolume":" 33","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2006.15055","open_access":"1"}],"oa":1,"quality_controlled":"1","publisher":"Curran Associates","oa_version":"Preprint","abstract":[{"text":"Learning object-centric representations of complex scenes is a promising step towards enabling efficient abstract reasoning from low-level perceptual features. Yet, most deep learning approaches learn distributed representations that do not capture the compositional properties of natural scenes. In this paper, we present the Slot Attention module, an architectural component that interfaces with perceptual representations such as the output of a convolutional neural network and produces a set of task-dependent abstract representations which we call slots. These slots are exchangeable and can bind to any object in the input by specializing through a competitive procedure over multiple rounds of attention. We empirically demonstrate that Slot Attention can extract object-centric representations that enable generalization to unseen compositions when trained on unsupervised object discovery and supervised property prediction tasks.\r\n\r\n","lang":"eng"}]},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Gladbach, Peter, Eva Kopfer, and Jan Maas. “Scaling Limits of Discrete Optimal Transport.” SIAM Journal on Mathematical Analysis. Society for Industrial and Applied Mathematics, 2020. https://doi.org/10.1137/19M1243440.","ista":"Gladbach P, Kopfer E, Maas J. 2020. Scaling limits of discrete optimal transport. SIAM Journal on Mathematical Analysis. 52(3), 2759–2802.","mla":"Gladbach, Peter, et al. “Scaling Limits of Discrete Optimal Transport.” SIAM Journal on Mathematical Analysis, vol. 52, no. 3, Society for Industrial and Applied Mathematics, 2020, pp. 2759–802, doi:10.1137/19M1243440.","short":"P. Gladbach, E. Kopfer, J. Maas, SIAM Journal on Mathematical Analysis 52 (2020) 2759–2802.","ieee":"P. Gladbach, E. Kopfer, and J. Maas, “Scaling limits of discrete optimal transport,” SIAM Journal on Mathematical Analysis, vol. 52, no. 3. Society for Industrial and Applied Mathematics, pp. 2759–2802, 2020.","ama":"Gladbach P, Kopfer E, Maas J. Scaling limits of discrete optimal transport. SIAM Journal on Mathematical Analysis. 2020;52(3):2759-2802. doi:10.1137/19M1243440","apa":"Gladbach, P., Kopfer, E., & Maas, J. (2020). Scaling limits of discrete optimal transport. SIAM Journal on Mathematical Analysis. Society for Industrial and Applied Mathematics. https://doi.org/10.1137/19M1243440"},"title":"Scaling limits of discrete optimal transport","external_id":{"isi":["000546975100017"],"arxiv":["1809.01092"]},"article_processing_charge":"No","publist_id":"7983","author":[{"last_name":"Gladbach","full_name":"Gladbach, Peter","first_name":"Peter"},{"last_name":"Kopfer","full_name":"Kopfer, Eva","first_name":"Eva"},{"orcid":"0000-0002-0845-1338","full_name":"Maas, Jan","last_name":"Maas","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","first_name":"Jan"}],"publication":"SIAM Journal on Mathematical Analysis","day":"01","year":"2020","isi":1,"date_created":"2018-12-11T11:44:28Z","date_published":"2020-10-01T00:00:00Z","doi":"10.1137/19M1243440","page":"2759-2802","oa":1,"publisher":"Society for Industrial and Applied Mathematics","quality_controlled":"1","date_updated":"2023-09-18T08:13:15Z","department":[{"_id":"JaMa"}],"_id":"71","status":"public","article_type":"original","type":"journal_article","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["10957154"],"issn":["00361410"]},"issue":"3","volume":52,"oa_version":"Preprint","abstract":[{"lang":"eng","text":"We consider dynamical transport metrics for probability measures on discretisations of a bounded convex domain in ℝd. These metrics are natural discrete counterparts to the Kantorovich metric 𝕎2, defined using a Benamou-Brenier type formula. Under mild assumptions we prove an asymptotic upper bound for the discrete transport metric Wt in terms of 𝕎2, as the size of the mesh T tends to 0. However, we show that the corresponding lower bound may fail in general, even on certain one-dimensional and symmetric two-dimensional meshes. In addition, we show that the asymptotic lower bound holds under an isotropy assumption on the mesh, which turns out to be essentially necessary. This assumption is satisfied, e.g., for tilings by convex regular polygons, and it implies Gromov-Hausdorff convergence of the transport metric."}],"intvolume":" 52","month":"10","main_file_link":[{"url":"https://arxiv.org/abs/1809.01092","open_access":"1"}],"scopus_import":"1"},{"type":"journal_article","article_type":"original","status":"public","_id":"5681","file_date_updated":"2020-10-08T08:34:53Z","department":[{"_id":"ChWo"}],"date_updated":"2023-09-18T09:30:01Z","ddc":["006"],"scopus_import":"1","intvolume":" 26","month":"06","abstract":[{"lang":"eng","text":"We introduce dynamically warping grids for adaptive liquid simulation. Our primary contributions are a strategy for dynamically deforming regular grids over the course of a simulation and a method for efficiently utilizing these deforming grids for liquid simulation. Prior work has shown that unstructured grids are very effective for adaptive fluid simulations. However, unstructured grids often lead to complicated implementations and a poor cache hit rate due to inconsistent memory access. Regular grids, on the other hand, provide a fast, fixed memory access pattern and straightforward implementation. Our method combines the advantages of both: we leverage the simplicity of regular grids while still achieving practical and controllable spatial adaptivity. We demonstrate that our method enables adaptive simulations that are fast, flexible, and robust to null-space issues. At the same time, our method is simple to implement and takes advantage of existing highly-tuned algorithms."}],"acknowledged_ssus":[{"_id":"ScienComp"}],"oa_version":"Submitted Version","pmid":1,"volume":26,"issue":"6","publication_status":"published","publication_identifier":{"issn":["10772626"],"eissn":["19410506"]},"language":[{"iso":"eng"}],"file":[{"date_created":"2020-10-08T08:34:53Z","file_name":"preprint.pdf","date_updated":"2020-10-08T08:34:53Z","file_size":21910098,"creator":"wojtan","checksum":"8d4c55443a0ee335bb5bb652de503042","file_id":"8626","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"article_processing_charge":"No","external_id":{"isi":["000532295600014"],"pmid":["30507534"]},"author":[{"last_name":"Hikaru","full_name":"Hikaru, Ibayashi","first_name":"Ibayashi"},{"first_name":"Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","last_name":"Wojtan","orcid":"0000-0001-6646-5546","full_name":"Wojtan, Christopher J"},{"first_name":"Nils","full_name":"Thuerey, Nils","last_name":"Thuerey"},{"last_name":"Igarashi","full_name":"Igarashi, Takeo","first_name":"Takeo"},{"first_name":"Ryoichi","last_name":"Ando","full_name":"Ando, Ryoichi"}],"title":"Simulating liquids on dynamically warping grids","citation":{"mla":"Hikaru, Ibayashi, et al. “Simulating Liquids on Dynamically Warping Grids.” IEEE Transactions on Visualization and Computer Graphics, vol. 26, no. 6, IEEE, 2020, pp. 2288–302, doi:10.1109/TVCG.2018.2883628.","apa":"Hikaru, I., Wojtan, C., Thuerey, N., Igarashi, T., & Ando, R. (2020). Simulating liquids on dynamically warping grids. IEEE Transactions on Visualization and Computer Graphics. IEEE. https://doi.org/10.1109/TVCG.2018.2883628","ama":"Hikaru I, Wojtan C, Thuerey N, Igarashi T, Ando R. Simulating liquids on dynamically warping grids. IEEE Transactions on Visualization and Computer Graphics. 2020;26(6):2288-2302. doi:10.1109/TVCG.2018.2883628","short":"I. Hikaru, C. Wojtan, N. Thuerey, T. Igarashi, R. Ando, IEEE Transactions on Visualization and Computer Graphics 26 (2020) 2288–2302.","ieee":"I. Hikaru, C. Wojtan, N. Thuerey, T. Igarashi, and R. Ando, “Simulating liquids on dynamically warping grids,” IEEE Transactions on Visualization and Computer Graphics, vol. 26, no. 6. IEEE, pp. 2288–2302, 2020.","chicago":"Hikaru, Ibayashi, Chris Wojtan, Nils Thuerey, Takeo Igarashi, and Ryoichi Ando. “Simulating Liquids on Dynamically Warping Grids.” IEEE Transactions on Visualization and Computer Graphics. IEEE, 2020. https://doi.org/10.1109/TVCG.2018.2883628.","ista":"Hikaru I, Wojtan C, Thuerey N, Igarashi T, Ando R. 2020. Simulating liquids on dynamically warping grids. IEEE Transactions on Visualization and Computer Graphics. 26(6), 2288–2302."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"quality_controlled":"1","publisher":"IEEE","acknowledgement":"This work was partially supported by JSPS Grant-in-Aid forYoung Scientists (Start-up) 16H07410, the ERC StartingGrantsrealFlow(StG-2015-637014) andBigSplash(StG-2014-638176). This research was supported by the Scientific Ser-vice Units (SSU) of IST Austria through resources providedby Scientific Computing. We would like to express my grati-tude to Nobuyuki Umetani and Tomas Skrivan for insight-ful discussion.","page":"2288-2302","date_created":"2018-12-16T22:59:21Z","date_published":"2020-06-01T00:00:00Z","doi":"10.1109/TVCG.2018.2883628","year":"2020","isi":1,"has_accepted_license":"1","publication":"IEEE Transactions on Visualization and Computer Graphics","day":"01"},{"status":"public","type":"dissertation","_id":"8958","department":[{"_id":"MiLe"}],"file_date_updated":"2020-12-30T07:18:03Z","ddc":["539"],"supervisor":[{"orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail","last_name":"Lemeshko","first_name":"Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-09-20T11:30:58Z","month":"12","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","abstract":[{"text":"The oft-quoted dictum by Arthur Schawlow: ``A diatomic molecule has one atom too many'' has been disavowed. Inspired by the possibility to experimentally manipulate and enhance chemical reactivity in helium nanodroplets, we investigate the rotation of coupled cold molecules in the presence of a many-body environment.\r\nIn this thesis, we introduce new variational approaches to quantum impurities and apply them to the Fröhlich polaron - a quasiparticle formed out of an electron (or other point-like impurity) in a polar medium, and to the angulon - a quasiparticle formed out of a rotating molecule in a bosonic bath.\r\nWith this theoretical toolbox, we reveal the self-localization transition for the angulon quasiparticle. We show that, unlike for polarons, self-localization of angulons occurs at finite impurity-bath coupling already at the mean-field level. The transition is accompanied by the spherical-symmetry breaking of the angulon ground state and a discontinuity in the first derivative of the ground-state energy. Moreover, the type of symmetry breaking is dictated by the symmetry of the microscopic impurity-bath interaction, which leads to a number of distinct self-localized states. \r\nFor the system containing multiple impurities, by analogy with the bipolaron, we introduce the biangulon quasiparticle describing two rotating molecules that align with respect to each other due to the effective attractive interaction mediated by the excitations of the bath. We study this system from the strong-coupling regime to the weak molecule-bath interaction regime. We show that the molecules tend to have a strong alignment in the ground state, the biangulon shows shifted angulon instabilities and an additional spectral instability, where resonant angular momentum transfer between the molecules and the bath takes place. Finally, we introduce a diagonalization scheme that allows us to describe the transition from two separated angulons to a biangulon as a function of the distance between the two molecules.","lang":"eng"}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"5886","status":"public"},{"id":"8587","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"1120","status":"public"}]},"ec_funded":1,"file":[{"success":1,"checksum":"3994c54a1241451d561db1d4f43bad30","file_id":"8967","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"THESIS_Xiang_Li.pdf","date_created":"2020-12-22T10:55:56Z","creator":"xli","file_size":3622305,"date_updated":"2020-12-22T10:55:56Z"},{"content_type":"application/x-zip-compressed","relation":"source_file","access_level":"closed","file_id":"8968","checksum":"0954ecfc5554c05615c14de803341f00","file_size":4018859,"date_updated":"2020-12-30T07:18:03Z","creator":"xli","file_name":"THESIS_Xiang_Li.zip","date_created":"2020-12-22T10:56:03Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","publication_status":"published","project":[{"grant_number":"P29902","name":"Quantum rotations in the presence of a many-body environment","call_identifier":"FWF","_id":"26031614-B435-11E9-9278-68D0E5697425"},{"name":"Angulon: physics and applications of a new quasiparticle","grant_number":"801770","call_identifier":"H2020","_id":"2688CF98-B435-11E9-9278-68D0E5697425"}],"title":"Rotation of coupled cold molecules in the presence of a many-body environment","author":[{"full_name":"Li, Xiang","last_name":"Li","id":"4B7E523C-F248-11E8-B48F-1D18A9856A87","first_name":"Xiang"}],"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Li X. 2020. Rotation of coupled cold molecules in the presence of a many-body environment. Institute of Science and Technology Austria.","chicago":"Li, Xiang. “Rotation of Coupled Cold Molecules in the Presence of a Many-Body Environment.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8958.","ieee":"X. Li, “Rotation of coupled cold molecules in the presence of a many-body environment,” Institute of Science and Technology Austria, 2020.","short":"X. Li, Rotation of Coupled Cold Molecules in the Presence of a Many-Body Environment, Institute of Science and Technology Austria, 2020.","apa":"Li, X. (2020). Rotation of coupled cold molecules in the presence of a many-body environment. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8958","ama":"Li X. Rotation of coupled cold molecules in the presence of a many-body environment. 2020. doi:10.15479/AT:ISTA:8958","mla":"Li, Xiang. Rotation of Coupled Cold Molecules in the Presence of a Many-Body Environment. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8958."},"publisher":"Institute of Science and Technology Austria","oa":1,"date_published":"2020-12-21T00:00:00Z","doi":"10.15479/AT:ISTA:8958","date_created":"2020-12-21T09:44:30Z","page":"125","day":"21","has_accepted_license":"1","year":"2020"},{"has_accepted_license":"1","year":"2020","day":"14","page":"148","doi":"10.15479/AT:ISTA:8386","date_published":"2020-09-14T00:00:00Z","date_created":"2020-09-14T01:04:53Z","acknowledgement":"The research in this thesis has received funding from the European Union’s Horizon 2020 research and innovation programme, under the Marie Skłodowska-Curie grant agreement No 642841 (DISTRO) and the European Research Council grant agreement No 715767 (MATERIALIZABLE). All the research projects in this thesis were also supported by Scientific Service Units (SSUs) at IST Austria.","publisher":"Institute of Science and Technology Austria","oa":1,"citation":{"chicago":"Zhang, Ran. “Structure-Aware Computational Design and Its Application to 3D Printable Volume Scattering, Mechanism, and Multistability.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8386.","ista":"Zhang R. 2020. Structure-aware computational design and its application to 3D printable volume scattering, mechanism, and multistability. Institute of Science and Technology Austria.","mla":"Zhang, Ran. Structure-Aware Computational Design and Its Application to 3D Printable Volume Scattering, Mechanism, and Multistability. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8386.","ama":"Zhang R. Structure-aware computational design and its application to 3D printable volume scattering, mechanism, and multistability. 2020. doi:10.15479/AT:ISTA:8386","apa":"Zhang, R. (2020). Structure-aware computational design and its application to 3D printable volume scattering, mechanism, and multistability. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8386","short":"R. Zhang, Structure-Aware Computational Design and Its Application to 3D Printable Volume Scattering, Mechanism, and Multistability, Institute of Science and Technology Austria, 2020.","ieee":"R. Zhang, “Structure-aware computational design and its application to 3D printable volume scattering, mechanism, and multistability,” Institute of Science and Technology Austria, 2020."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"last_name":"Zhang","full_name":"Zhang, Ran","orcid":"0000-0002-3808-281X","id":"4DDBCEB0-F248-11E8-B48F-1D18A9856A87","first_name":"Ran"}],"article_processing_charge":"No","title":"Structure-aware computational design and its application to 3D printable volume scattering, mechanism, and multistability","project":[{"_id":"2508E324-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"642841","name":"Distributed 3D Object Design"},{"grant_number":"715767","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","call_identifier":"H2020","_id":"24F9549A-B435-11E9-9278-68D0E5697425"}],"publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","publication_status":"published","file":[{"file_id":"8388","checksum":"edcf578b6e1c9b0dd81ff72d319b66ba","content_type":"application/x-zip-compressed","relation":"source_file","access_level":"closed","file_name":"Thesis_Ran.zip","date_created":"2020-09-14T01:02:59Z","file_size":1245800191,"date_updated":"2020-09-14T12:18:43Z","creator":"rzhang"},{"file_id":"8396","checksum":"817e20c33be9247f906925517c56a40d","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2020-09-15T12:51:53Z","file_name":"PhD_thesis_Ran Zhang_20200915.pdf","creator":"rzhang","date_updated":"2020-09-15T12:51:53Z","file_size":161385316}],"language":[{"iso":"eng"}],"related_material":{"record":[{"status":"public","id":"486","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"1002","status":"public"}]},"ec_funded":1,"acknowledged_ssus":[{"_id":"SSU"}],"abstract":[{"text":"Form versus function is a long-standing debate in various design-related fields, such as architecture as well as graphic and industrial design. A good design that balances form and function often requires considerable human effort and collaboration among experts from different professional fields. Computational design tools provide a new paradigm for designing functional objects. In computational design, form and function are represented as mathematical\r\nquantities, with the help of numerical and combinatorial algorithms, they can assist even novice users in designing versatile models that exhibit their desired functionality. This thesis presents three disparate research studies on the computational design of functional objects: The appearance of 3d print—we optimize the volumetric material distribution for faithfully replicating colored surface texture in 3d printing; the dynamic motion of mechanical structures—\r\nour design system helps the novice user to retarget various mechanical templates with different functionality to complex 3d shapes; and a more abstract functionality, multistability—our algorithm automatically generates models that exhibit multiple stable target poses. For each of these cases, our computational design tools not only ensure the functionality of the results but also permit the user aesthetic freedom over the form. Moreover, fabrication constraints\r\nwere taken into account, which allow for the immediate creation of physical realization via 3D printing or laser cutting.","lang":"eng"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"09","supervisor":[{"last_name":"Bickel","orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd","first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-09-22T09:49:31Z","ddc":["003"],"file_date_updated":"2020-09-15T12:51:53Z","department":[{"_id":"BeBi"}],"_id":"8386","type":"dissertation","status":"public"},{"year":"2020","has_accepted_license":"1","day":"22","page":"178","date_created":"2020-06-22T09:22:23Z","doi":"10.15479/AT:ISTA:7996","date_published":"2020-06-22T00:00:00Z","oa":1,"publisher":"Institute of Science and Technology Austria","citation":{"mla":"Kukucka, Josip. Implementation of a Hole Spin Qubit in Ge Hut Wires and Dispersive Spin Sensing. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7996.","ieee":"J. Kukucka, “Implementation of a hole spin qubit in Ge hut wires and dispersive spin sensing,” Institute of Science and Technology Austria, 2020.","short":"J. Kukucka, Implementation of a Hole Spin Qubit in Ge Hut Wires and Dispersive Spin Sensing, Institute of Science and Technology Austria, 2020.","apa":"Kukucka, J. (2020). Implementation of a hole spin qubit in Ge hut wires and dispersive spin sensing. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7996","ama":"Kukucka J. Implementation of a hole spin qubit in Ge hut wires and dispersive spin sensing. 2020. doi:10.15479/AT:ISTA:7996","chicago":"Kukucka, Josip. “Implementation of a Hole Spin Qubit in Ge Hut Wires and Dispersive Spin Sensing.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7996.","ista":"Kukucka J. 2020. Implementation of a hole spin qubit in Ge hut wires and dispersive spin sensing. Institute of Science and Technology Austria."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","author":[{"full_name":"Kukucka, Josip","last_name":"Kukucka","id":"3F5D8856-F248-11E8-B48F-1D18A9856A87","first_name":"Josip"}],"title":"Implementation of a hole spin qubit in Ge hut wires and dispersive spin sensing","publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"date_created":"2020-06-22T09:22:04Z","file_name":"JK_thesis_latex_source_files.zip","date_updated":"2020-07-14T12:48:07Z","file_size":392794743,"creator":"dernst","checksum":"467e52feb3e361ce8cf5fe8d5c254ece","file_id":"7997","content_type":"application/x-zip-compressed","access_level":"closed","relation":"main_file"},{"file_id":"7998","checksum":"1de716bf110dbd77d383e479232bf496","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"PhD_thesis_JK_pdfa.pdf","date_created":"2020-06-22T09:21:29Z","creator":"dernst","file_size":28453247,"date_updated":"2020-07-14T12:48:07Z"}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"1328","status":"public"},{"id":"7541","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"77"},{"id":"23","status":"public","relation":"part_of_dissertation"},{"id":"840","status":"public","relation":"part_of_dissertation"}]},"abstract":[{"lang":"eng","text":"Quantum computation enables the execution of algorithms that have exponential complexity. This might open the path towards the synthesis of new materials or medical drugs, optimization of transport or financial strategies etc., intractable on even the fastest classical computers. A quantum computer consists of interconnected two level quantum systems, called qubits, that satisfy DiVincezo’s criteria. Worldwide, there are ongoing efforts to find the qubit architecture which will unite quantum error correction compatible single and two qubit fidelities, long distance qubit to qubit coupling and \r\n calability. Superconducting qubits have gone the furthest in this race, demonstrating an algorithm running on 53 coupled qubits, but still the fidelities are not even close to those required for realizing a single logical qubit. emiconductor qubits offer extremely good characteristics, but they are currently investigated across different platforms. Uniting those good characteristics into a single platform might be a big step towards the quantum computer realization.\r\nHere we describe the implementation of a hole spin qubit hosted in a Ge hut wire double quantum dot. The high and tunable spin-orbit coupling together with a heavy hole state character is expected to allow fast spin manipulation and long coherence times. Furthermore large lever arms, for hut wire devices, should allow good coupling to superconducting resonators enabling efficient long distance spin to spin coupling and a sensitive gate reflectometry spin readout. The developed cryogenic setup (printed circuit board sample holders, filtering, high-frequency wiring) enabled us to perform low temperature spin dynamics experiments. Indeed, we measured the fastest single spin qubit Rabi frequencies reported so far, reaching 140 MHz, while the dephasing times of 130 ns oppose the long decoherence predictions. In order to further investigate this, a double quantum dot gate was connected directly to a lumped element\r\nresonator which enabled gate reflectometry readout. The vanishing inter-dot transition signal, for increasing external magnetic field, revealed the spin nature of the measured quantity."}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"06","date_updated":"2023-09-26T15:50:22Z","supervisor":[{"id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios","last_name":"Katsaros","orcid":"0000-0001-8342-202X","full_name":"Katsaros, Georgios"}],"ddc":["530"],"file_date_updated":"2020-07-14T12:48:07Z","department":[{"_id":"GeKa"}],"_id":"7996","type":"dissertation","status":"public"},{"title":"Stochastic games with lexicographic reachability-safety objectives","article_processing_charge":"No","external_id":{"arxiv":["2005.04018"],"isi":["000695272500021"]},"author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"last_name":"Katoen","full_name":"Katoen, Joost P","id":"4524F760-F248-11E8-B48F-1D18A9856A87","first_name":"Joost P"},{"first_name":"Maximilian","last_name":"Weininger","full_name":"Weininger, Maximilian"},{"first_name":"Tobias","last_name":"Winkler","full_name":"Winkler, Tobias"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Chatterjee, Krishnendu, Joost P Katoen, Maximilian Weininger, and Tobias Winkler. “Stochastic Games with Lexicographic Reachability-Safety Objectives.” In International Conference on Computer Aided Verification, 12225:398–420. Springer Nature, 2020. https://doi.org/10.1007/978-3-030-53291-8_21.","ista":"Chatterjee K, Katoen JP, Weininger M, Winkler T. 2020. Stochastic games with lexicographic reachability-safety objectives. International Conference on Computer Aided Verification. CAV: Computer Aided Verification, LNCS, vol. 12225, 398–420.","mla":"Chatterjee, Krishnendu, et al. “Stochastic Games with Lexicographic Reachability-Safety Objectives.” International Conference on Computer Aided Verification, vol. 12225, Springer Nature, 2020, pp. 398–420, doi:10.1007/978-3-030-53291-8_21.","apa":"Chatterjee, K., Katoen, J. P., Weininger, M., & Winkler, T. (2020). Stochastic games with lexicographic reachability-safety objectives. In International Conference on Computer Aided Verification (Vol. 12225, pp. 398–420). Springer Nature. https://doi.org/10.1007/978-3-030-53291-8_21","ama":"Chatterjee K, Katoen JP, Weininger M, Winkler T. Stochastic games with lexicographic reachability-safety objectives. In: International Conference on Computer Aided Verification. Vol 12225. Springer Nature; 2020:398-420. doi:10.1007/978-3-030-53291-8_21","ieee":"K. Chatterjee, J. P. Katoen, M. Weininger, and T. Winkler, “Stochastic games with lexicographic reachability-safety objectives,” in International Conference on Computer Aided Verification, 2020, vol. 12225, pp. 398–420.","short":"K. Chatterjee, J.P. Katoen, M. Weininger, T. Winkler, in:, International Conference on Computer Aided Verification, Springer Nature, 2020, pp. 398–420."},"project":[{"call_identifier":"H2020","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818"},{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification"}],"date_created":"2020-08-16T22:00:58Z","date_published":"2020-07-14T00:00:00Z","doi":"10.1007/978-3-030-53291-8_21","page":"398-420","publication":"International Conference on Computer Aided Verification","day":"14","year":"2020","isi":1,"has_accepted_license":"1","oa":1,"publisher":"Springer Nature","quality_controlled":"1","file_date_updated":"2020-08-17T11:32:44Z","department":[{"_id":"KrCh"}],"ddc":["000"],"date_updated":"2023-10-03T11:36:13Z","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"conference":{"name":"CAV: Computer Aided Verification"},"type":"conference","_id":"8272","ec_funded":1,"related_material":{"record":[{"relation":"later_version","status":"public","id":"12738"}]},"volume":12225,"language":[{"iso":"eng"}],"file":[{"file_name":"2020_LNCS_CAV_Chatterjee.pdf","date_created":"2020-08-17T11:32:44Z","file_size":625056,"date_updated":"2020-08-17T11:32:44Z","creator":"dernst","success":1,"checksum":"093d4788d7d5b2ce0ffe64fbe7820043","file_id":"8276","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"publication_status":"published","publication_identifier":{"eissn":["16113349"],"isbn":["9783030532901"],"issn":["03029743"]},"intvolume":" 12225","month":"07","alternative_title":["LNCS"],"scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"We study turn-based stochastic zero-sum games with lexicographic preferences over reachability and safety objectives. Stochastic games are standard models in control, verification, and synthesis of stochastic reactive systems that exhibit both randomness as well as angelic and demonic non-determinism. Lexicographic order allows to consider multiple objectives with a strict preference order over the satisfaction of the objectives. To the best of our knowledge, stochastic games with lexicographic objectives have not been studied before. We establish determinacy of such games and present strategy and computational complexity results. For strategy complexity, we show that lexicographically optimal strategies exist that are deterministic and memory is only required to remember the already satisfied and violated objectives. For a constant number of objectives, we show that the relevant decision problem is in NP∩coNP , matching the current known bound for single objectives; and in general the decision problem is PSPACE -hard and can be solved in NEXPTIME∩coNEXPTIME . We present an algorithm that computes the lexicographically optimal strategies via a reduction to computation of optimal strategies in a sequence of single-objectives games. We have implemented our algorithm and report experimental results on various case studies."}]},{"year":"2020","isi":1,"publication":"Methods in Cell Biology","day":"27","page":"145-161","date_created":"2020-03-08T23:00:47Z","doi":"10.1016/bs.mcb.2020.01.006","date_published":"2020-02-27T00:00:00Z","oa":1,"publisher":"Elsevier","quality_controlled":"1","citation":{"ista":"Dos Santos Caldas PR, Radler P, Sommer CM, Loose M. 2020.Computational analysis of filament polymerization dynamics in cytoskeletal networks. In: Methods in Cell Biology. Methods in Cell Biology, vol. 158, 145–161.","chicago":"Dos Santos Caldas, Paulo R, Philipp Radler, Christoph M Sommer, and Martin Loose. “Computational Analysis of Filament Polymerization Dynamics in Cytoskeletal Networks.” In Methods in Cell Biology, edited by Phong Tran, 158:145–61. Elsevier, 2020. https://doi.org/10.1016/bs.mcb.2020.01.006.","apa":"Dos Santos Caldas, P. R., Radler, P., Sommer, C. M., & Loose, M. (2020). Computational analysis of filament polymerization dynamics in cytoskeletal networks. In P. Tran (Ed.), Methods in Cell Biology (Vol. 158, pp. 145–161). Elsevier. https://doi.org/10.1016/bs.mcb.2020.01.006","ama":"Dos Santos Caldas PR, Radler P, Sommer CM, Loose M. Computational analysis of filament polymerization dynamics in cytoskeletal networks. In: Tran P, ed. Methods in Cell Biology. Vol 158. Elsevier; 2020:145-161. doi:10.1016/bs.mcb.2020.01.006","short":"P.R. Dos Santos Caldas, P. Radler, C.M. Sommer, M. Loose, in:, P. Tran (Ed.), Methods in Cell Biology, Elsevier, 2020, pp. 145–161.","ieee":"P. R. Dos Santos Caldas, P. Radler, C. M. Sommer, and M. Loose, “Computational analysis of filament polymerization dynamics in cytoskeletal networks,” in Methods in Cell Biology, vol. 158, P. Tran, Ed. Elsevier, 2020, pp. 145–161.","mla":"Dos Santos Caldas, Paulo R., et al. “Computational Analysis of Filament Polymerization Dynamics in Cytoskeletal Networks.” Methods in Cell Biology, edited by Phong Tran, vol. 158, Elsevier, 2020, pp. 145–61, doi:10.1016/bs.mcb.2020.01.006."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000611826500008"]},"article_processing_charge":"No","author":[{"id":"38FCDB4C-F248-11E8-B48F-1D18A9856A87","first_name":"Paulo R","last_name":"Dos Santos Caldas","full_name":"Dos Santos Caldas, Paulo R","orcid":"0000-0001-6730-4461"},{"orcid":"0000-0001-9198-2182 ","full_name":"Radler, Philipp","last_name":"Radler","id":"40136C2A-F248-11E8-B48F-1D18A9856A87","first_name":"Philipp"},{"id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph M","full_name":"Sommer, Christoph M","orcid":"0000-0003-1216-9105","last_name":"Sommer"},{"first_name":"Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","full_name":"Loose, Martin","orcid":"0000-0001-7309-9724","last_name":"Loose"}],"title":"Computational analysis of filament polymerization dynamics in cytoskeletal networks","editor":[{"first_name":"Phong ","full_name":"Tran, Phong ","last_name":"Tran"}],"project":[{"grant_number":"679239","name":"Self-Organization of the Bacterial Cell","call_identifier":"H2020","_id":"2595697A-B435-11E9-9278-68D0E5697425"},{"name":"Reconstitution of Bacterial Cell Division Using Purified Components","_id":"260D98C8-B435-11E9-9278-68D0E5697425"}],"publication_status":"published","publication_identifier":{"issn":["0091679X"]},"language":[{"iso":"eng"}],"ec_funded":1,"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"8358"}]},"volume":158,"abstract":[{"lang":"eng","text":"The polymerization–depolymerization dynamics of cytoskeletal proteins play essential roles in the self-organization of cytoskeletal structures, in eukaryotic as well as prokaryotic cells. While advances in fluorescence microscopy and in vitro reconstitution experiments have helped to study the dynamic properties of these complex systems, methods that allow to collect and analyze large quantitative datasets of the underlying polymer dynamics are still missing. Here, we present a novel image analysis workflow to study polymerization dynamics of active filaments in a nonbiased, highly automated manner. Using treadmilling filaments of the bacterial tubulin FtsZ as an example, we demonstrate that our method is able to specifically detect, track and analyze growth and shrinkage of polymers, even in dense networks of filaments. We believe that this automated method can facilitate the analysis of a large variety of dynamic cytoskeletal systems, using standard time-lapse movies obtained from experiments in vitro as well as in the living cell. Moreover, we provide scripts implementing this method as supplementary material."}],"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/839571"}],"scopus_import":"1","alternative_title":["Methods in Cell Biology"],"intvolume":" 158","month":"02","date_updated":"2023-10-04T09:50:24Z","department":[{"_id":"MaLo"}],"_id":"7572","type":"book_chapter","status":"public"},{"month":"01","intvolume":" 5","scopus_import":"1","main_file_link":[{"url":"http://europepmc.org/article/PMC/7048620","open_access":"1"}],"oa_version":"Submitted Version","pmid":1,"abstract":[{"text":"Most bacteria accomplish cell division with the help of a dynamic protein complex called the divisome, which spans the cell envelope in the plane of division. Assembly and activation of this machinery are coordinated by the tubulin-related GTPase FtsZ, which was found to form treadmilling filaments on supported bilayers in vitro1, as well as in live cells, in which filaments circle around the cell division site2,3. Treadmilling of FtsZ is thought to actively move proteins around the division septum, thereby distributing peptidoglycan synthesis and coordinating the inward growth of the septum to form the new poles of the daughter cells4. However, the molecular mechanisms underlying this function are largely unknown. Here, to study how FtsZ polymerization dynamics are coupled to downstream proteins, we reconstituted part of the bacterial cell division machinery using its purified components FtsZ, FtsA and truncated transmembrane proteins essential for cell division. We found that the membrane-bound cytosolic peptides of FtsN and FtsQ co-migrated with treadmilling FtsZ–FtsA filaments, but despite their directed collective behaviour, individual peptides showed random motion and transient confinement. Our work suggests that divisome proteins follow treadmilling FtsZ filaments by a diffusion-and-capture mechanism, which can give rise to a moving zone of signalling activity at the division site.","lang":"eng"}],"volume":5,"related_material":{"record":[{"relation":"dissertation_contains","id":"14280","status":"public"}],"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/little-cell-big-cover-story/","relation":"press_release"}]},"ec_funded":1,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2058-5276"]},"publication_status":"published","status":"public","type":"journal_article","article_type":"letter_note","_id":"7387","department":[{"_id":"MaLo"}],"date_updated":"2023-10-06T12:22:38Z","publisher":"Springer Nature","quality_controlled":"1","oa":1,"acknowledgement":"We acknowledge members of the Loose laboratory at IST Austria for helpful discussions—in particular, P. Caldas for help with the treadmilling analysis, M. Jimenez, A. Raso and N. Ropero for providing Alexa Fluor 488- and Alexa Fluor 647-labelled FtsA for the MST and analytical ultracentrifugation experiments. We thank C. You for providing the DODA-tris-NTA phospholipids, as well as J. Piehler and C. Richter (Department of Biology, University of Osnabruck, Germany) for the SLIMfast single-molecule tracking software and help with the confinement analysis. We thank J. Errington and H. Murray (both at Newcastle University, UK) for critical reading of the manuscript, and J. Brugués (MPI-CBG and MPI-PKS, Dresden, Germany) for help with the MATLAB programming and reading of the manuscript. This work was supported by the European Research Council through grant ERC-2015-StG-679239 to M.L. and grants HFSP LT 000824/2016-L4 and EMBO ALTF 1163-2015 to N.B., a grant from the Ministry of Economy and Competitiveness of the Spanish Government (BFU2016-75471-C2-1-P) to C.A. and G.R., and a Wellcome Trust Senior Investigator award (101824/Z/13/Z) and a grant from the BBSRC (BB/R017409/1) to W.V.","date_published":"2020-01-20T00:00:00Z","doi":"10.1038/s41564-019-0657-5","date_created":"2020-01-28T16:14:41Z","page":"407-417","day":"20","publication":"Nature Microbiology","isi":1,"year":"2020","project":[{"call_identifier":"H2020","_id":"2595697A-B435-11E9-9278-68D0E5697425","name":"Self-Organization of the Bacterial Cell","grant_number":"679239"},{"grant_number":"LT000824/2016","name":"Reconstitution of bacterial cell wall sythesis","_id":"259B655A-B435-11E9-9278-68D0E5697425"},{"_id":"2596EAB6-B435-11E9-9278-68D0E5697425","grant_number":"ALTF 2015-1163","name":"Synthesis of bacterial cell wall"}],"title":"Diffusion and capture permits dynamic coupling between treadmilling FtsZ filaments and cell division proteins","author":[{"last_name":"Baranova","orcid":"0000-0002-3086-9124","full_name":"Baranova, Natalia S.","id":"38661662-F248-11E8-B48F-1D18A9856A87","first_name":"Natalia S."},{"first_name":"Philipp","id":"40136C2A-F248-11E8-B48F-1D18A9856A87","full_name":"Radler, Philipp","orcid":"0000-0001-9198-2182 ","last_name":"Radler"},{"full_name":"Hernández-Rocamora, Víctor M.","last_name":"Hernández-Rocamora","first_name":"Víctor M."},{"full_name":"Alfonso, Carlos","last_name":"Alfonso","first_name":"Carlos"},{"first_name":"Maria D","id":"319AA9CE-F248-11E8-B48F-1D18A9856A87","last_name":"Lopez Pelegrin","full_name":"Lopez Pelegrin, Maria D"},{"first_name":"Germán","full_name":"Rivas, Germán","last_name":"Rivas"},{"first_name":"Waldemar","full_name":"Vollmer, Waldemar","last_name":"Vollmer"},{"id":"462D4284-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","last_name":"Loose","orcid":"0000-0001-7309-9724","full_name":"Loose, Martin"}],"article_processing_charge":"No","external_id":{"pmid":["31959972"],"isi":["000508584700007"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Baranova NS, Radler P, Hernández-Rocamora VM, Alfonso C, Lopez Pelegrin MD, Rivas G, Vollmer W, Loose M. 2020. Diffusion and capture permits dynamic coupling between treadmilling FtsZ filaments and cell division proteins. Nature Microbiology. 5, 407–417.","chicago":"Baranova, Natalia S., Philipp Radler, Víctor M. Hernández-Rocamora, Carlos Alfonso, Maria D Lopez Pelegrin, Germán Rivas, Waldemar Vollmer, and Martin Loose. “Diffusion and Capture Permits Dynamic Coupling between Treadmilling FtsZ Filaments and Cell Division Proteins.” Nature Microbiology. Springer Nature, 2020. https://doi.org/10.1038/s41564-019-0657-5.","ama":"Baranova NS, Radler P, Hernández-Rocamora VM, et al. Diffusion and capture permits dynamic coupling between treadmilling FtsZ filaments and cell division proteins. Nature Microbiology. 2020;5:407-417. doi:10.1038/s41564-019-0657-5","apa":"Baranova, N. S., Radler, P., Hernández-Rocamora, V. M., Alfonso, C., Lopez Pelegrin, M. D., Rivas, G., … Loose, M. (2020). Diffusion and capture permits dynamic coupling between treadmilling FtsZ filaments and cell division proteins. Nature Microbiology. Springer Nature. https://doi.org/10.1038/s41564-019-0657-5","ieee":"N. S. Baranova et al., “Diffusion and capture permits dynamic coupling between treadmilling FtsZ filaments and cell division proteins,” Nature Microbiology, vol. 5. Springer Nature, pp. 407–417, 2020.","short":"N.S. Baranova, P. Radler, V.M. Hernández-Rocamora, C. Alfonso, M.D. Lopez Pelegrin, G. Rivas, W. Vollmer, M. Loose, Nature Microbiology 5 (2020) 407–417.","mla":"Baranova, Natalia S., et al. “Diffusion and Capture Permits Dynamic Coupling between Treadmilling FtsZ Filaments and Cell Division Proteins.” Nature Microbiology, vol. 5, Springer Nature, 2020, pp. 407–17, doi:10.1038/s41564-019-0657-5."}},{"language":[{"iso":"eng"}],"file":[{"file_size":1476072,"date_updated":"2020-07-24T07:09:06Z","creator":"mwintrae","file_name":"57-2-05_4214-1454Vegter-Wintraecken_OpenAccess_CC-BY-NC.pdf","date_created":"2020-07-24T07:09:06Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"8164"}],"publication_status":"published","publication_identifier":{"eissn":["1588-2896"],"issn":["0081-6906"]},"ec_funded":1,"volume":57,"issue":"2","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Fejes Tóth [3] studied approximations of smooth surfaces in three-space by piecewise flat triangular meshes with a given number of vertices on the surface that are optimal with respect to Hausdorff distance. He proves that this Hausdorff distance decreases inversely proportional with the number of vertices of the approximating mesh if the surface is convex. He also claims that this Hausdorff distance is inversely proportional to the square of the number of vertices for a specific non-convex surface, namely a one-sheeted hyperboloid of revolution bounded by two congruent circles. We refute this claim, and show that the asymptotic behavior of the Hausdorff distance is linear, that is the same as for convex surfaces."}],"intvolume":" 57","month":"07","scopus_import":"1","ddc":["510"],"date_updated":"2023-10-10T13:05:27Z","department":[{"_id":"HeEd"}],"file_date_updated":"2020-07-24T07:09:06Z","_id":"8163","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"type":"journal_article","article_type":"original","publication":"Studia Scientiarum Mathematicarum Hungarica","day":"24","year":"2020","isi":1,"has_accepted_license":"1","date_created":"2020-07-24T07:09:18Z","date_published":"2020-07-24T00:00:00Z","doi":"10.1556/012.2020.57.2.1454","page":"193-199","acknowledgement":"The authors are greatly indebted to Dror Atariah, Günther Rote and John Sullivan for discussion and suggestions. The authors also thank Jean-Daniel Boissonnat, Ramsay Dyer, David de Laat and Rien van de Weijgaert for discussion. This work has been supported in part by the European Union’s Seventh Framework Programme for Research of the\r\nEuropean Commission, under FET-Open grant number 255827 (CGL Computational Geometry Learning) and ERC Grant Agreement number 339025 GUDHI (Algorithmic Foundations of Geometry Understanding in Higher Dimensions), the European Union’s Horizon 2020 research and innovation programme under the Marie Sk lodowska-Curie grant agreement number 754411,and the Austrian Science Fund (FWF): Z00342 N31.","oa":1,"quality_controlled":"1","publisher":"Akadémiai Kiadó","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Vegter, Gert, and Mathijs Wintraecken. “Refutation of a Claim Made by Fejes Tóth on the Accuracy of Surface Meshes.” Studia Scientiarum Mathematicarum Hungarica. Akadémiai Kiadó, 2020. https://doi.org/10.1556/012.2020.57.2.1454.","ista":"Vegter G, Wintraecken M. 2020. Refutation of a claim made by Fejes Tóth on the accuracy of surface meshes. Studia Scientiarum Mathematicarum Hungarica. 57(2), 193–199.","mla":"Vegter, Gert, and Mathijs Wintraecken. “Refutation of a Claim Made by Fejes Tóth on the Accuracy of Surface Meshes.” Studia Scientiarum Mathematicarum Hungarica, vol. 57, no. 2, Akadémiai Kiadó, 2020, pp. 193–99, doi:10.1556/012.2020.57.2.1454.","apa":"Vegter, G., & Wintraecken, M. (2020). Refutation of a claim made by Fejes Tóth on the accuracy of surface meshes. Studia Scientiarum Mathematicarum Hungarica. Akadémiai Kiadó. https://doi.org/10.1556/012.2020.57.2.1454","ama":"Vegter G, Wintraecken M. Refutation of a claim made by Fejes Tóth on the accuracy of surface meshes. Studia Scientiarum Mathematicarum Hungarica. 2020;57(2):193-199. doi:10.1556/012.2020.57.2.1454","short":"G. Vegter, M. Wintraecken, Studia Scientiarum Mathematicarum Hungarica 57 (2020) 193–199.","ieee":"G. Vegter and M. Wintraecken, “Refutation of a claim made by Fejes Tóth on the accuracy of surface meshes,” Studia Scientiarum Mathematicarum Hungarica, vol. 57, no. 2. Akadémiai Kiadó, pp. 193–199, 2020."},"title":"Refutation of a claim made by Fejes Tóth on the accuracy of surface meshes","article_processing_charge":"No","external_id":{"isi":["000570978400005"]},"author":[{"full_name":"Vegter, Gert","last_name":"Vegter","first_name":"Gert"},{"first_name":"Mathijs","id":"307CFBC8-F248-11E8-B48F-1D18A9856A87","last_name":"Wintraecken","full_name":"Wintraecken, Mathijs","orcid":"0000-0002-7472-2220"}],"project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"268116B8-B435-11E9-9278-68D0E5697425","grant_number":"Z00342","name":"The Wittgenstein Prize"}]},{"publication_status":"published","publication_identifier":{"issn":["1735-4463"],"eissn":["2008-9473"]},"language":[{"iso":"eng"}],"file":[{"creator":"dernst","file_size":261688,"date_updated":"2020-10-19T11:14:20Z","file_name":"2020_ijmsi_Shakiba_accepted.pdf","date_created":"2020-10-19T11:14:20Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"f299661a6d51cda6d255a76be696f48d","file_id":"8676"}],"volume":15,"issue":"2","abstract":[{"text":"We study relations between evidence theory and S-approximation spaces. Both theories have their roots in the analysis of Dempsterchr('39')s multivalued mappings and lower and upper probabilities, and have close relations to rough sets. We show that an S-approximation space, satisfying a monotonicity condition, can induce a natural belief structure which is a fundamental block in evidence theory. We also demonstrate that one can induce a natural belief structure on one set, given a belief structure on another set, if the two sets are related by a partial monotone S-approximation space. ","lang":"eng"}],"oa_version":"Submitted Version","scopus_import":"1","intvolume":" 15","month":"10","date_updated":"2023-10-16T09:25:00Z","ddc":["000"],"file_date_updated":"2020-10-19T11:14:20Z","department":[{"_id":"KrCh"}],"_id":"8671","type":"journal_article","article_type":"original","status":"public","year":"2020","has_accepted_license":"1","publication":"Iranian Journal of Mathematical Sciences and Informatics","day":"01","page":"117-128","date_created":"2020-10-18T22:01:36Z","date_published":"2020-10-01T00:00:00Z","doi":"10.29252/ijmsi.15.2.117","acknowledgement":"We are very grateful to the anonymous reviewer for detailed comments and suggestions that significantly improved the presentation of this paper. The research was partially supported by a DOC fellowship of the Austrian Academy of Sciences.","oa":1,"publisher":"Iranian Academic Center for Education, Culture and Research","quality_controlled":"1","citation":{"chicago":"Shakiba, A., Amir Kafshdar Goharshady, M.R. Hooshmandasl, and M. Alambardar Meybodi. “A Note on Belief Structures and S-Approximation Spaces.” Iranian Journal of Mathematical Sciences and Informatics. Iranian Academic Center for Education, Culture and Research, 2020. https://doi.org/10.29252/ijmsi.15.2.117.","ista":"Shakiba A, Goharshady AK, Hooshmandasl MR, Alambardar Meybodi M. 2020. A note on belief structures and s-approximation spaces. Iranian Journal of Mathematical Sciences and Informatics. 15(2), 117–128.","mla":"Shakiba, A., et al. “A Note on Belief Structures and S-Approximation Spaces.” Iranian Journal of Mathematical Sciences and Informatics, vol. 15, no. 2, Iranian Academic Center for Education, Culture and Research, 2020, pp. 117–28, doi:10.29252/ijmsi.15.2.117.","apa":"Shakiba, A., Goharshady, A. K., Hooshmandasl, M. R., & Alambardar Meybodi, M. (2020). A note on belief structures and s-approximation spaces. Iranian Journal of Mathematical Sciences and Informatics. Iranian Academic Center for Education, Culture and Research. https://doi.org/10.29252/ijmsi.15.2.117","ama":"Shakiba A, Goharshady AK, Hooshmandasl MR, Alambardar Meybodi M. A note on belief structures and s-approximation spaces. Iranian Journal of Mathematical Sciences and Informatics. 2020;15(2):117-128. doi:10.29252/ijmsi.15.2.117","ieee":"A. Shakiba, A. K. Goharshady, M. R. Hooshmandasl, and M. Alambardar Meybodi, “A note on belief structures and s-approximation spaces,” Iranian Journal of Mathematical Sciences and Informatics, vol. 15, no. 2. Iranian Academic Center for Education, Culture and Research, pp. 117–128, 2020.","short":"A. Shakiba, A.K. Goharshady, M.R. Hooshmandasl, M. Alambardar Meybodi, Iranian Journal of Mathematical Sciences and Informatics 15 (2020) 117–128."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["1805.10672"]},"article_processing_charge":"No","author":[{"last_name":"Shakiba","full_name":"Shakiba, A.","first_name":"A."},{"full_name":"Goharshady, Amir Kafshdar","orcid":"0000-0003-1702-6584","last_name":"Goharshady","first_name":"Amir Kafshdar","id":"391365CE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hooshmandasl","full_name":"Hooshmandasl, M.R.","first_name":"M.R."},{"last_name":"Alambardar Meybodi","full_name":"Alambardar Meybodi, M.","first_name":"M."}],"title":"A note on belief structures and s-approximation spaces","project":[{"_id":"267066CE-B435-11E9-9278-68D0E5697425","name":"Quantitative Analysis of Probablistic Systems with a focus on Crypto-currencies"}]},{"article_number":"82","author":[{"full_name":"Dareiotis, Konstantinos","last_name":"Dareiotis","first_name":"Konstantinos"},{"first_name":"Mate","id":"44ECEDF2-F248-11E8-B48F-1D18A9856A87","full_name":"Gerencser, Mate","last_name":"Gerencser"}],"article_processing_charge":"No","external_id":{"arxiv":["1812.04583"],"isi":["000550150700001"]},"title":"On the regularisation of the noise for the Euler-Maruyama scheme with irregular drift","citation":{"ista":"Dareiotis K, Gerencser M. 2020. On the regularisation of the noise for the Euler-Maruyama scheme with irregular drift. Electronic Journal of Probability. 25, 82.","chicago":"Dareiotis, Konstantinos, and Mate Gerencser. “On the Regularisation of the Noise for the Euler-Maruyama Scheme with Irregular Drift.” Electronic Journal of Probability. Institute of Mathematical Statistics, 2020. https://doi.org/10.1214/20-EJP479.","apa":"Dareiotis, K., & Gerencser, M. (2020). On the regularisation of the noise for the Euler-Maruyama scheme with irregular drift. Electronic Journal of Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/20-EJP479","ama":"Dareiotis K, Gerencser M. On the regularisation of the noise for the Euler-Maruyama scheme with irregular drift. Electronic Journal of Probability. 2020;25. doi:10.1214/20-EJP479","ieee":"K. Dareiotis and M. Gerencser, “On the regularisation of the noise for the Euler-Maruyama scheme with irregular drift,” Electronic Journal of Probability, vol. 25. Institute of Mathematical Statistics, 2020.","short":"K. Dareiotis, M. Gerencser, Electronic Journal of Probability 25 (2020).","mla":"Dareiotis, Konstantinos, and Mate Gerencser. “On the Regularisation of the Noise for the Euler-Maruyama Scheme with Irregular Drift.” Electronic Journal of Probability, vol. 25, 82, Institute of Mathematical Statistics, 2020, doi:10.1214/20-EJP479."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","publisher":"Institute of Mathematical Statistics","oa":1,"date_published":"2020-07-16T00:00:00Z","doi":"10.1214/20-EJP479","date_created":"2019-04-30T07:40:17Z","has_accepted_license":"1","isi":1,"year":"2020","day":"16","publication":"Electronic Journal of Probability","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"6359","department":[{"_id":"JaMa"}],"file_date_updated":"2020-09-21T13:15:02Z","date_updated":"2023-10-16T09:22:50Z","ddc":["510"],"scopus_import":"1","month":"07","intvolume":" 25","abstract":[{"text":"The strong rate of convergence of the Euler-Maruyama scheme for nondegenerate SDEs with irregular drift coefficients is considered. In the case of α-Hölder drift in the recent literature the rate α/2 was proved in many related situations. By exploiting the regularising effect of the noise more efficiently, we show that the rate is in fact arbitrarily close to 1/2 for all α>0. The result extends to Dini continuous coefficients, while in d=1 also to all bounded measurable coefficients.","lang":"eng"}],"oa_version":"Published Version","volume":25,"publication_identifier":{"eissn":["1083-6489"]},"publication_status":"published","file":[{"creator":"dernst","date_updated":"2020-09-21T13:15:02Z","file_size":273042,"date_created":"2020-09-21T13:15:02Z","file_name":"2020_EJournProbab_Dareiotis.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"8549","checksum":"8e7c42e72596f6889d786e8e8b89994f","success":1}],"language":[{"iso":"eng"}]},{"file":[{"creator":"dernst","date_updated":"2020-09-14T13:39:14Z","file_size":30224591,"date_created":"2020-09-14T13:39:14Z","file_name":"2020_Thesis_Royer.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"c914d2f88846032f3d8507734861b6ee","file_id":"8391","success":1},{"file_id":"8392","checksum":"ae98fb35d912cff84a89035ae5794d3c","access_level":"closed","relation":"main_file","content_type":"application/x-zip-compressed","date_created":"2020-09-14T13:39:17Z","file_name":"thesis_sources.zip","creator":"dernst","date_updated":"2020-09-14T13:39:17Z","file_size":74227627}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-007-7"]},"publication_status":"published","degree_awarded":"PhD","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"7936"},{"id":"7937","status":"public","relation":"part_of_dissertation"},{"status":"public","id":"8193","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"8092"},{"id":"911","status":"public","relation":"part_of_dissertation"}]},"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Deep neural networks have established a new standard for data-dependent feature extraction pipelines in the Computer Vision literature. Despite their remarkable performance in the standard supervised learning scenario, i.e. when models are trained with labeled data and tested on samples that follow a similar distribution, neural networks have been shown to struggle with more advanced generalization abilities, such as transferring knowledge across visually different domains, or generalizing to new unseen combinations of known concepts. In this thesis we argue that, in contrast to the usual black-box behavior of neural networks, leveraging more structured internal representations is a promising direction\r\nfor tackling such problems. In particular, we focus on two forms of structure. First, we tackle modularity: We show that (i) compositional architectures are a natural tool for modeling reasoning tasks, in that they efficiently capture their combinatorial nature, which is key for generalizing beyond the compositions seen during training. We investigate how to to learn such models, both formally and experimentally, for the task of abstract visual reasoning. Then, we show that (ii) in some settings, modularity allows us to efficiently break down complex tasks into smaller, easier, modules, thereby improving computational efficiency; We study this behavior in the context of generative models for colorization, as well as for small objects detection. Secondly, we investigate the inherently layered structure of representations learned by neural networks, and analyze its role in the context of transfer learning and domain adaptation across visually\r\ndissimilar domains. "}],"acknowledged_ssus":[{"_id":"CampIT"},{"_id":"ScienComp"}],"month":"09","alternative_title":["ISTA Thesis"],"ddc":["000"],"supervisor":[{"orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph","last_name":"Lampert","first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-10-16T10:04:02Z","file_date_updated":"2020-09-14T13:39:17Z","department":[{"_id":"ChLa"}],"_id":"8390","status":"public","type":"dissertation","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"day":"14","has_accepted_license":"1","year":"2020","doi":"10.15479/AT:ISTA:8390","date_published":"2020-09-14T00:00:00Z","date_created":"2020-09-14T13:42:09Z","page":"197","acknowledgement":"Last but not least, I would like to acknowledge the support of the IST IT and scientific computing team for helping provide a great work environment.","publisher":"Institute of Science and Technology Austria","oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Royer, Amélie. Leveraging Structure in Computer Vision Tasks for Flexible Deep Learning Models. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8390.","ama":"Royer A. Leveraging structure in Computer Vision tasks for flexible Deep Learning models. 2020. doi:10.15479/AT:ISTA:8390","apa":"Royer, A. (2020). Leveraging structure in Computer Vision tasks for flexible Deep Learning models. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8390","short":"A. Royer, Leveraging Structure in Computer Vision Tasks for Flexible Deep Learning Models, Institute of Science and Technology Austria, 2020.","ieee":"A. Royer, “Leveraging structure in Computer Vision tasks for flexible Deep Learning models,” Institute of Science and Technology Austria, 2020.","chicago":"Royer, Amélie. “Leveraging Structure in Computer Vision Tasks for Flexible Deep Learning Models.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8390.","ista":"Royer A. 2020. Leveraging structure in Computer Vision tasks for flexible Deep Learning models. Institute of Science and Technology Austria."},"title":"Leveraging structure in Computer Vision tasks for flexible Deep Learning models","author":[{"last_name":"Royer","orcid":"0000-0002-8407-0705","full_name":"Royer, Amélie","id":"3811D890-F248-11E8-B48F-1D18A9856A87","first_name":"Amélie"}],"article_processing_charge":"No"},{"day":"01","publication":"Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition","has_accepted_license":"1","year":"2020","date_published":"2020-07-01T00:00:00Z","doi":"10.1109/CVPR42600.2020.00752","date_created":"2020-07-31T16:53:49Z","page":"7498-7507","publisher":"IEEE","quality_controlled":"1","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Henderson, Paul M., et al. “Leveraging 2D Data to Learn Textured 3D Mesh Generation.” Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition, IEEE, 2020, pp. 7498–507, doi:10.1109/CVPR42600.2020.00752.","short":"P.M. Henderson, V. Tsiminaki, C. Lampert, in:, Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition, IEEE, 2020, pp. 7498–7507.","ieee":"P. M. Henderson, V. Tsiminaki, and C. Lampert, “Leveraging 2D data to learn textured 3D mesh generation,” in Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition, Virtual, 2020, pp. 7498–7507.","ama":"Henderson PM, Tsiminaki V, Lampert C. Leveraging 2D data to learn textured 3D mesh generation. In: Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition. IEEE; 2020:7498-7507. doi:10.1109/CVPR42600.2020.00752","apa":"Henderson, P. M., Tsiminaki, V., & Lampert, C. (2020). Leveraging 2D data to learn textured 3D mesh generation. In Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition (pp. 7498–7507). Virtual: IEEE. https://doi.org/10.1109/CVPR42600.2020.00752","chicago":"Henderson, Paul M, Vagia Tsiminaki, and Christoph Lampert. “Leveraging 2D Data to Learn Textured 3D Mesh Generation.” In Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition, 7498–7507. IEEE, 2020. https://doi.org/10.1109/CVPR42600.2020.00752.","ista":"Henderson PM, Tsiminaki V, Lampert C. 2020. Leveraging 2D data to learn textured 3D mesh generation. Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition. CVPR: Conference on Computer Vision and Pattern Recognition, 7498–7507."},"title":"Leveraging 2D data to learn textured 3D mesh generation","author":[{"last_name":"Henderson","full_name":"Henderson, Paul M","orcid":"0000-0002-5198-7445","first_name":"Paul M","id":"13C09E74-18D9-11E9-8878-32CFE5697425"},{"first_name":"Vagia","last_name":"Tsiminaki","full_name":"Tsiminaki, Vagia"},{"first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph","last_name":"Lampert"}],"article_processing_charge":"No","external_id":{"arxiv":["2004.04180"]},"file":[{"file_size":10262773,"date_updated":"2020-07-31T16:57:12Z","creator":"phenders","file_name":"paper.pdf","date_created":"2020-07-31T16:57:12Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"8187"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2575-7075"],"eisbn":["9781728171685"]},"publication_status":"published","oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Numerous methods have been proposed for probabilistic generative modelling of\r\n3D objects. However, none of these is able to produce textured objects, which\r\nrenders them of limited use for practical tasks. In this work, we present the\r\nfirst generative model of textured 3D meshes. Training such a model would\r\ntraditionally require a large dataset of textured meshes, but unfortunately,\r\nexisting datasets of meshes lack detailed textures. We instead propose a new\r\ntraining methodology that allows learning from collections of 2D images without\r\nany 3D information. To do so, we train our model to explain a distribution of\r\nimages by modelling each image as a 3D foreground object placed in front of a\r\n2D background. Thus, it learns to generate meshes that when rendered, produce\r\nimages similar to those in its training set.\r\n A well-known problem when generating meshes with deep networks is the\r\nemergence of self-intersections, which are problematic for many use-cases. As a\r\nsecond contribution we therefore introduce a new generation process for 3D\r\nmeshes that guarantees no self-intersections arise, based on the physical\r\nintuition that faces should push one another out of the way as they move.\r\n We conduct extensive experiments on our approach, reporting quantitative and\r\nqualitative results on both synthetic data and natural images. These show our\r\nmethod successfully learns to generate plausible and diverse textured 3D\r\nsamples for five challenging object classes."}],"month":"07","scopus_import":"1","main_file_link":[{"url":"https://openaccess.thecvf.com/content_CVPR_2020/papers/Henderson_Leveraging_2D_Data_to_Learn_Textured_3D_Mesh_Generation_CVPR_2020_paper.pdf","open_access":"1"}],"ddc":["004"],"date_updated":"2023-10-17T07:37:11Z","file_date_updated":"2020-07-31T16:57:12Z","department":[{"_id":"ChLa"}],"_id":"8186","status":"public","type":"conference","conference":{"end_date":"2020-06-19","location":"Virtual","start_date":"2020-06-14","name":"CVPR: Conference on Computer Vision and Pattern Recognition"}},{"publication":"Plant Signaling & Behavior","day":"01","year":"2020","isi":1,"date_created":"2020-01-30T10:12:04Z","date_published":"2020-01-01T00:00:00Z","doi":"10.1080/15592324.2019.1687175","oa":1,"quality_controlled":"1","publisher":"Taylor & Francis","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Sinclair SA, Krämer U. 2020. Generation of effective zinc-deficient agar-solidified media allows identification of root morphology changes in response to zinc limitation. Plant Signaling & Behavior. 15(1), 1687175.","chicago":"Sinclair, Scott A, and U. Krämer. “Generation of Effective Zinc-Deficient Agar-Solidified Media Allows Identification of Root Morphology Changes in Response to Zinc Limitation.” Plant Signaling & Behavior. Taylor & Francis, 2020. https://doi.org/10.1080/15592324.2019.1687175.","apa":"Sinclair, S. A., & Krämer, U. (2020). Generation of effective zinc-deficient agar-solidified media allows identification of root morphology changes in response to zinc limitation. Plant Signaling & Behavior. Taylor & Francis. https://doi.org/10.1080/15592324.2019.1687175","ama":"Sinclair SA, Krämer U. Generation of effective zinc-deficient agar-solidified media allows identification of root morphology changes in response to zinc limitation. Plant Signaling & Behavior. 2020;15(1). doi:10.1080/15592324.2019.1687175","short":"S.A. Sinclair, U. Krämer, Plant Signaling & Behavior 15 (2020).","ieee":"S. A. Sinclair and U. Krämer, “Generation of effective zinc-deficient agar-solidified media allows identification of root morphology changes in response to zinc limitation,” Plant Signaling & Behavior, vol. 15, no. 1. Taylor & Francis, 2020.","mla":"Sinclair, Scott A., and U. Krämer. “Generation of Effective Zinc-Deficient Agar-Solidified Media Allows Identification of Root Morphology Changes in Response to Zinc Limitation.” Plant Signaling & Behavior, vol. 15, no. 1, 1687175, Taylor & Francis, 2020, doi:10.1080/15592324.2019.1687175."},"title":"Generation of effective zinc-deficient agar-solidified media allows identification of root morphology changes in response to zinc limitation","external_id":{"isi":["000494909300001"],"pmid":["31696764"]},"article_processing_charge":"No","author":[{"id":"2D99FE6A-F248-11E8-B48F-1D18A9856A87","first_name":"Scott A","full_name":"Sinclair, Scott A","orcid":"0000-0002-4566-0593","last_name":"Sinclair"},{"full_name":"Krämer, U.","last_name":"Krämer","first_name":"U."}],"article_number":"1687175","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["1559-2324"]},"volume":15,"issue":"1","pmid":1,"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Earlier, we demonstrated that transcript levels of METAL TOLERANCE PROTEIN2 (MTP2) and of HEAVY METAL ATPase2 (HMA2) increase strongly in roots of Arabidopsis upon prolonged zinc (Zn) deficiency and respond to shoot physiological Zn status, and not to the local Zn status in roots. This provided evidence for shoot-to-root communication in the acclimation of plants to Zn deficiency. Zn-deficient soils limit both the yield and quality of agricultural crops and can result in clinically relevant nutritional Zn deficiency in human populations. Implementing Zn deficiency during cultivation of the model plant Arabidopsis thaliana on agar-solidified media is difficult because trace element contaminations are present in almost all commercially available agars. Here, we demonstrate root morphological acclimations to Zn deficiency on agar-solidified medium following the effective removal of contaminants. These advancements allow reproducible phenotyping toward understanding fundamental plant responses to deficiencies of Zn and other essential trace elements."}],"intvolume":" 15","month":"01","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7012054"}],"scopus_import":"1","date_updated":"2023-10-17T09:01:48Z","department":[{"_id":"JiFr"}],"_id":"7416","status":"public","article_type":"original","type":"journal_article"},{"issue":"3","volume":252,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0039-3223"],"eissn":["1730-6337"]},"intvolume":" 252","month":"03","scopus_import":"1","oa_version":"Preprint","abstract":[{"lang":"eng","text":"In order to provide a local description of a regular function in a small neighbourhood of a point x, it is sufficient by Taylor’s theorem to know the value of the function as well as all of its derivatives up to the required order at the point x itself. In other words, one could say that a regular function is locally modelled by the set of polynomials. The theory of regularity structures due to Hairer generalizes this observation and provides an abstract setup, which in the application to singular SPDE extends the set of polynomials by functionals constructed from, e.g., white noise. In this context, the notion of Taylor polynomials is lifted to the notion of so-called modelled distributions. The celebrated reconstruction theorem, which in turn was inspired by Gubinelli’s \\textit {sewing lemma}, is of paramount importance for the theory. It enables one to reconstruct a modelled distribution as a true distribution on Rd which is locally approximated by this extended set of models or “monomials”. In the original work of Hairer, the error is measured by means of Hölder norms. This was then generalized to the whole scale of Besov spaces by Hairer and Labbé. It is the aim of this work to adapt the analytic part of the theory of regularity structures to the scale of Triebel–Lizorkin spaces."}],"department":[{"_id":"JuFi"},{"_id":"GradSch"}],"date_updated":"2023-10-17T09:15:53Z","keyword":["General Mathematics"],"status":"public","article_type":"original","type":"journal_article","_id":"9196","date_created":"2021-02-25T08:55:03Z","doi":"10.4064/sm180411-11-2","date_published":"2020-03-01T00:00:00Z","page":"251-297","publication":"Studia Mathematica","day":"01","year":"2020","isi":1,"quality_controlled":"1","publisher":"Instytut Matematyczny","title":"Modelled distributions of Triebel–Lizorkin type","article_processing_charge":"No","external_id":{"isi":["000558100500002"],"arxiv":["1709.05202"]},"author":[{"full_name":"Hensel, Sebastian","orcid":"0000-0001-7252-8072","last_name":"Hensel","id":"4D23B7DA-F248-11E8-B48F-1D18A9856A87","first_name":"Sebastian"},{"full_name":"Rosati, Tommaso","last_name":"Rosati","first_name":"Tommaso"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Hensel, Sebastian, and Tommaso Rosati. “Modelled Distributions of Triebel–Lizorkin Type.” Studia Mathematica, vol. 252, no. 3, Instytut Matematyczny, 2020, pp. 251–97, doi:10.4064/sm180411-11-2.","short":"S. Hensel, T. Rosati, Studia Mathematica 252 (2020) 251–297.","ieee":"S. Hensel and T. Rosati, “Modelled distributions of Triebel–Lizorkin type,” Studia Mathematica, vol. 252, no. 3. Instytut Matematyczny, pp. 251–297, 2020.","apa":"Hensel, S., & Rosati, T. (2020). Modelled distributions of Triebel–Lizorkin type. Studia Mathematica. Instytut Matematyczny. https://doi.org/10.4064/sm180411-11-2","ama":"Hensel S, Rosati T. Modelled distributions of Triebel–Lizorkin type. Studia Mathematica. 2020;252(3):251-297. doi:10.4064/sm180411-11-2","chicago":"Hensel, Sebastian, and Tommaso Rosati. “Modelled Distributions of Triebel–Lizorkin Type.” Studia Mathematica. Instytut Matematyczny, 2020. https://doi.org/10.4064/sm180411-11-2.","ista":"Hensel S, Rosati T. 2020. Modelled distributions of Triebel–Lizorkin type. Studia Mathematica. 252(3), 251–297."}},{"volume":16,"issue":"1","related_material":{"record":[{"relation":"research_data","id":"9723","status":"deleted"}]},"publication_identifier":{"issn":["1553-7374"]},"publication_status":"published","file":[{"file_name":"2020_PLOSPatho_Dick.pdf","date_created":"2020-02-11T10:07:28Z","file_size":4551246,"date_updated":"2020-07-14T12:47:59Z","creator":"dernst","checksum":"a297f54d1fef0efe4789ca00f37f241e","file_id":"7484","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"01","intvolume":" 16","abstract":[{"lang":"eng","text":"Retrovirus assembly is driven by the multidomain structural protein Gag. Interactions between the capsid domains (CA) of Gag result in Gag multimerization, leading to an immature virus particle that is formed by a protein lattice based on dimeric, trimeric, and hexameric protein contacts. Among retroviruses the inter- and intra-hexamer contacts differ, especially in the N-terminal sub-domain of CA (CANTD). For HIV-1 the cellular molecule inositol hexakisphosphate (IP6) interacts with and stabilizes the immature hexamer, and is required for production of infectious virus particles. We have used in vitro assembly, cryo-electron tomography and subtomogram averaging, atomistic molecular dynamics simulations and mutational analyses to study the HIV-related lentivirus equine infectious anemia virus (EIAV). In particular, we sought to understand the structural conservation of the immature lentivirus lattice and the role of IP6 in EIAV assembly. Similar to HIV-1, IP6 strongly promoted in vitro assembly of EIAV Gag proteins into virus-like particles (VLPs), which took three morphologically highly distinct forms: narrow tubes, wide tubes, and spheres. Structural characterization of these VLPs to sub-4Å resolution unexpectedly showed that all three morphologies are based on an immature lattice with preserved key structural components, highlighting the structural versatility of CA to form immature assemblies. A direct comparison between EIAV and HIV revealed that both lentiviruses maintain similar immature interfaces, which are established by both conserved and non-conserved residues. In both EIAV and HIV-1, IP6 regulates immature assembly via conserved lysine residues within the CACTD and SP. Lastly, we demonstrate that IP6 stimulates in vitro assembly of immature particles of several other retroviruses in the lentivirus genus, suggesting a conserved role for IP6 in lentiviral assembly."}],"acknowledged_ssus":[{"_id":"ScienComp"}],"pmid":1,"oa_version":"Published Version","file_date_updated":"2020-07-14T12:47:59Z","department":[{"_id":"FlSc"}],"date_updated":"2023-10-17T12:29:34Z","ddc":["570"],"article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"7464","doi":"10.1371/journal.ppat.1008277","date_published":"2020-01-27T00:00:00Z","date_created":"2020-02-06T18:47:17Z","isi":1,"has_accepted_license":"1","year":"2020","day":"27","publication":"PLOS Pathogens","quality_controlled":"1","publisher":"Public Library of Science","oa":1,"author":[{"first_name":"Robert A.","last_name":"Dick","full_name":"Dick, Robert A."},{"first_name":"Chaoyi","full_name":"Xu, Chaoyi","last_name":"Xu"},{"last_name":"Morado","full_name":"Morado, Dustin R.","first_name":"Dustin R."},{"full_name":"Kravchuk, Vladyslav","orcid":"0000-0001-9523-9089","last_name":"Kravchuk","first_name":"Vladyslav","id":"4D62F2A6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Clifton L.","full_name":"Ricana, Clifton L.","last_name":"Ricana"},{"last_name":"Lyddon","full_name":"Lyddon, Terri D.","first_name":"Terri D."},{"full_name":"Broad, Arianna M.","last_name":"Broad","first_name":"Arianna M."},{"last_name":"Feathers","full_name":"Feathers, J. Ryan","first_name":"J. Ryan"},{"first_name":"Marc C.","full_name":"Johnson, Marc C.","last_name":"Johnson"},{"first_name":"Volker M.","last_name":"Vogt","full_name":"Vogt, Volker M."},{"full_name":"Perilla, Juan R.","last_name":"Perilla","first_name":"Juan R."},{"last_name":"Briggs","full_name":"Briggs, John A. G.","first_name":"John A. G."},{"orcid":"0000-0003-4790-8078","full_name":"Schur, Florian KM","last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian KM"}],"article_processing_charge":"No","external_id":{"isi":["000510746400010"],"pmid":["31986188"]},"title":"Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly","citation":{"ama":"Dick RA, Xu C, Morado DR, et al. Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly. PLOS Pathogens. 2020;16(1). doi:10.1371/journal.ppat.1008277","apa":"Dick, R. A., Xu, C., Morado, D. R., Kravchuk, V., Ricana, C. L., Lyddon, T. D., … Schur, F. K. (2020). Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly. PLOS Pathogens. Public Library of Science. https://doi.org/10.1371/journal.ppat.1008277","ieee":"R. A. Dick et al., “Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly,” PLOS Pathogens, vol. 16, no. 1. Public Library of Science, 2020.","short":"R.A. Dick, C. Xu, D.R. Morado, V. Kravchuk, C.L. Ricana, T.D. Lyddon, A.M. Broad, J.R. Feathers, M.C. Johnson, V.M. Vogt, J.R. Perilla, J.A.G. Briggs, F.K. Schur, PLOS Pathogens 16 (2020).","mla":"Dick, Robert A., et al. “Structures of Immature EIAV Gag Lattices Reveal a Conserved Role for IP6 in Lentivirus Assembly.” PLOS Pathogens, vol. 16, no. 1, e1008277, Public Library of Science, 2020, doi:10.1371/journal.ppat.1008277.","ista":"Dick RA, Xu C, Morado DR, Kravchuk V, Ricana CL, Lyddon TD, Broad AM, Feathers JR, Johnson MC, Vogt VM, Perilla JR, Briggs JAG, Schur FK. 2020. Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly. PLOS Pathogens. 16(1), e1008277.","chicago":"Dick, Robert A., Chaoyi Xu, Dustin R. Morado, Vladyslav Kravchuk, Clifton L. Ricana, Terri D. Lyddon, Arianna M. Broad, et al. “Structures of Immature EIAV Gag Lattices Reveal a Conserved Role for IP6 in Lentivirus Assembly.” PLOS Pathogens. Public Library of Science, 2020. https://doi.org/10.1371/journal.ppat.1008277."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"grant_number":"P31445","name":"Structural conservation and diversity in retroviral capsid","call_identifier":"FWF","_id":"26736D6A-B435-11E9-9278-68D0E5697425"}],"article_number":"e1008277"},{"file":[{"file_name":"2020_PlosCompBio_Tkadlec.pdf","date_created":"2020-02-03T07:32:42Z","file_size":1817531,"date_updated":"2020-07-14T12:47:53Z","creator":"dernst","file_id":"7441","checksum":"ce32ee2d2f53aed832f78bbd47e882df","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["15537358"]},"publication_status":"published","volume":16,"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"7196"}]},"ec_funded":1,"oa_version":"Published Version","abstract":[{"text":"The fixation probability of a single mutant invading a population of residents is among the most widely-studied quantities in evolutionary dynamics. Amplifiers of natural selection are population structures that increase the fixation probability of advantageous mutants, compared to well-mixed populations. Extensive studies have shown that many amplifiers exist for the Birth-death Moran process, some of them substantially increasing the fixation probability or even guaranteeing fixation in the limit of large population size. On the other hand, no amplifiers are known for the death-Birth Moran process, and computer-assisted exhaustive searches have failed to discover amplification. In this work we resolve this disparity, by showing that any amplification under death-Birth updating is necessarily bounded and transient. Our boundedness result states that even if a population structure does amplify selection, the resulting fixation probability is close to that of the well-mixed population. Our transience result states that for any population structure there exists a threshold r⋆ such that the population structure ceases to amplify selection if the mutant fitness advantage r is larger than r⋆. Finally, we also extend the above results to δ-death-Birth updating, which is a combination of Birth-death and death-Birth updating. On the positive side, we identify population structures that maintain amplification for a wide range of values r and δ. These results demonstrate that amplification of natural selection depends on the specific mechanisms of the evolutionary process.","lang":"eng"}],"month":"01","intvolume":" 16","scopus_import":"1","ddc":["000"],"date_updated":"2023-10-17T12:29:47Z","file_date_updated":"2020-07-14T12:47:53Z","department":[{"_id":"KrCh"}],"_id":"7212","status":"public","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"day":"17","publication":"PLoS computational biology","has_accepted_license":"1","isi":1,"year":"2020","date_published":"2020-01-17T00:00:00Z","doi":"10.1371/journal.pcbi.1007494","date_created":"2019-12-23T13:45:11Z","publisher":"Public Library of Science","quality_controlled":"1","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Tkadlec, Josef, et al. “Limits on Amplifiers of Natural Selection under Death-Birth Updating.” PLoS Computational Biology, vol. 16, e1007494, Public Library of Science, 2020, doi:10.1371/journal.pcbi.1007494.","short":"J. Tkadlec, A. Pavlogiannis, K. Chatterjee, M.A. Nowak, PLoS Computational Biology 16 (2020).","ieee":"J. Tkadlec, A. Pavlogiannis, K. Chatterjee, and M. A. Nowak, “Limits on amplifiers of natural selection under death-Birth updating,” PLoS computational biology, vol. 16. Public Library of Science, 2020.","ama":"Tkadlec J, Pavlogiannis A, Chatterjee K, Nowak MA. Limits on amplifiers of natural selection under death-Birth updating. PLoS computational biology. 2020;16. doi:10.1371/journal.pcbi.1007494","apa":"Tkadlec, J., Pavlogiannis, A., Chatterjee, K., & Nowak, M. A. (2020). Limits on amplifiers of natural selection under death-Birth updating. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1007494","chicago":"Tkadlec, Josef, Andreas Pavlogiannis, Krishnendu Chatterjee, and Martin A. Nowak. “Limits on Amplifiers of Natural Selection under Death-Birth Updating.” PLoS Computational Biology. Public Library of Science, 2020. https://doi.org/10.1371/journal.pcbi.1007494.","ista":"Tkadlec J, Pavlogiannis A, Chatterjee K, Nowak MA. 2020. Limits on amplifiers of natural selection under death-Birth updating. PLoS computational biology. 16, e1007494."},"title":"Limits on amplifiers of natural selection under death-Birth updating","author":[{"first_name":"Josef","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","last_name":"Tkadlec","full_name":"Tkadlec, Josef","orcid":"0000-0002-1097-9684"},{"first_name":"Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","last_name":"Pavlogiannis","full_name":"Pavlogiannis, Andreas","orcid":"0000-0002-8943-0722"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"},{"last_name":"Nowak","full_name":"Nowak, Martin A.","first_name":"Martin A."}],"article_processing_charge":"No","external_id":{"arxiv":["1906.02785"],"isi":["000510916500025"]},"article_number":"e1007494","project":[{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S11407","name":"Game Theory"}]},{"oa":1,"publisher":"Institute of Science and Technology Austria","page":"144","date_created":"2019-12-20T12:26:36Z","date_published":"2020-01-12T00:00:00Z","doi":"10.15479/AT:ISTA:7196","year":"2020","has_accepted_license":"1","day":"12","article_processing_charge":"No","author":[{"id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","first_name":"Josef","orcid":"0000-0002-1097-9684","full_name":"Tkadlec, Josef","last_name":"Tkadlec"}],"title":"A role of graphs in evolutionary processes","citation":{"ista":"Tkadlec J. 2020. A role of graphs in evolutionary processes. Institute of Science and Technology Austria.","chicago":"Tkadlec, Josef. “A Role of Graphs in Evolutionary Processes.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7196.","apa":"Tkadlec, J. (2020). A role of graphs in evolutionary processes. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7196","ama":"Tkadlec J. A role of graphs in evolutionary processes. 2020. doi:10.15479/AT:ISTA:7196","ieee":"J. Tkadlec, “A role of graphs in evolutionary processes,” Institute of Science and Technology Austria, 2020.","short":"J. Tkadlec, A Role of Graphs in Evolutionary Processes, Institute of Science and Technology Austria, 2020.","mla":"Tkadlec, Josef. A Role of Graphs in Evolutionary Processes. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7196."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","alternative_title":["ISTA Thesis"],"month":"01","abstract":[{"lang":"eng","text":"In this thesis we study certain mathematical aspects of evolution. The two primary forces that drive an evolutionary process are mutation and selection. Mutation generates new variants in a population. Selection chooses among the variants depending on the reproductive rates of individuals. Evolutionary processes are intrinsically random – a new mutation that is initially present in the population at low frequency can go extinct, even if it confers a reproductive advantage. The overall rate of evolution is largely determined by two quantities: the probability that an invading advantageous mutation spreads through the population (called fixation probability) and the time until it does so (called fixation time). Both those quantities crucially depend not only on the strength of the invading mutation but also on the population structure. In this thesis, we aim to understand how the underlying population structure affects the overall rate of evolution. Specifically, we study population structures that increase the fixation probability of advantageous mutants (called amplifiers of selection). Broadly speaking, our results are of three different types: We present various strong amplifiers, we identify regimes under which only limited amplification is feasible, and we propose population structures that provide different tradeoffs between high fixation probability and short fixation time."}],"oa_version":"Published Version","related_material":{"record":[{"relation":"dissertation_contains","id":"7210","status":"public"},{"relation":"dissertation_contains","status":"public","id":"5751"},{"status":"public","id":"7212","relation":"dissertation_contains"}]},"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"eissn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"date_updated":"2020-07-14T12:47:52Z","file_size":21100497,"creator":"jtkadlec","date_created":"2020-01-12T11:49:49Z","file_name":"thesis.zip","content_type":"application/zip","access_level":"closed","relation":"source_file","checksum":"451f8e64b0eb26bf297644ac72bfcbe9","file_id":"7255"},{"file_id":"7367","checksum":"d8c44cbc4f939c49a8efc9d4b8bb3985","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2020-01-28T07:32:42Z","file_name":"2020_Tkadlec_Thesis.pdf","creator":"dernst","date_updated":"2020-07-14T12:47:52Z","file_size":11670983}],"type":"dissertation","status":"public","_id":"7196","file_date_updated":"2020-07-14T12:47:52Z","department":[{"_id":"KrCh"},{"_id":"GradSch"}],"date_updated":"2023-10-17T12:29:46Z","supervisor":[{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"}],"ddc":["519"]},{"page":"8773-8784","date_published":"2020-07-13T00:00:00Z","date_created":"2021-02-25T09:36:22Z","has_accepted_license":"1","year":"2020","day":"13","publication":"Proceedings of the 37th International Conference on Machine Learning","quality_controlled":"1","publisher":"ML Research Press","oa":1,"acknowledgement":"M. Mondelli was partially supported by the 2019 LopezLoreta Prize. The authors thank Phan-Minh Nguyen for helpful discussions and the IST Distributed Algorithms and Systems Lab for providing computational resources.","author":[{"full_name":"Shevchenko, Alexander","last_name":"Shevchenko","first_name":"Alexander"},{"id":"27EB676C-8706-11E9-9510-7717E6697425","first_name":"Marco","last_name":"Mondelli","orcid":"0000-0002-3242-7020","full_name":"Mondelli, Marco"}],"external_id":{"arxiv":["1912.10095"]},"article_processing_charge":"No","title":"Landscape connectivity and dropout stability of SGD solutions for over-parameterized neural networks","citation":{"ieee":"A. Shevchenko and M. Mondelli, “Landscape connectivity and dropout stability of SGD solutions for over-parameterized neural networks,” in Proceedings of the 37th International Conference on Machine Learning, 2020, vol. 119, pp. 8773–8784.","short":"A. Shevchenko, M. Mondelli, in:, Proceedings of the 37th International Conference on Machine Learning, ML Research Press, 2020, pp. 8773–8784.","apa":"Shevchenko, A., & Mondelli, M. (2020). Landscape connectivity and dropout stability of SGD solutions for over-parameterized neural networks. In Proceedings of the 37th International Conference on Machine Learning (Vol. 119, pp. 8773–8784). ML Research Press.","ama":"Shevchenko A, Mondelli M. Landscape connectivity and dropout stability of SGD solutions for over-parameterized neural networks. In: Proceedings of the 37th International Conference on Machine Learning. Vol 119. ML Research Press; 2020:8773-8784.","mla":"Shevchenko, Alexander, and Marco Mondelli. “Landscape Connectivity and Dropout Stability of SGD Solutions for Over-Parameterized Neural Networks.” Proceedings of the 37th International Conference on Machine Learning, vol. 119, ML Research Press, 2020, pp. 8773–84.","ista":"Shevchenko A, Mondelli M. 2020. Landscape connectivity and dropout stability of SGD solutions for over-parameterized neural networks. Proceedings of the 37th International Conference on Machine Learning. vol. 119, 8773–8784.","chicago":"Shevchenko, Alexander, and Marco Mondelli. “Landscape Connectivity and Dropout Stability of SGD Solutions for Over-Parameterized Neural Networks.” In Proceedings of the 37th International Conference on Machine Learning, 119:8773–84. ML Research Press, 2020."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"name":"Prix Lopez-Loretta 2019 - Marco Mondelli","_id":"059876FA-7A3F-11EA-A408-12923DDC885E"}],"volume":119,"publication_status":"published","file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"9217","checksum":"f042c8d4316bd87c6361aa76f1fbdbbe","file_size":5336380,"date_updated":"2021-03-02T15:38:14Z","creator":"dernst","file_name":"2020_PMLR_Shevchenko.pdf","date_created":"2021-03-02T15:38:14Z"}],"language":[{"iso":"eng"}],"month":"07","intvolume":" 119","abstract":[{"lang":"eng","text":"The optimization of multilayer neural networks typically leads to a solution\r\nwith zero training error, yet the landscape can exhibit spurious local minima\r\nand the minima can be disconnected. In this paper, we shed light on this\r\nphenomenon: we show that the combination of stochastic gradient descent (SGD)\r\nand over-parameterization makes the landscape of multilayer neural networks\r\napproximately connected and thus more favorable to optimization. More\r\nspecifically, we prove that SGD solutions are connected via a piecewise linear\r\npath, and the increase in loss along this path vanishes as the number of\r\nneurons grows large. This result is a consequence of the fact that the\r\nparameters found by SGD are increasingly dropout stable as the network becomes\r\nwider. We show that, if we remove part of the neurons (and suitably rescale the\r\nremaining ones), the change in loss is independent of the total number of\r\nneurons, and it depends only on how many neurons are left. Our results exhibit\r\na mild dependence on the input dimension: they are dimension-free for two-layer\r\nnetworks and depend linearly on the dimension for multilayer networks. We\r\nvalidate our theoretical findings with numerical experiments for different\r\narchitectures and classification tasks."}],"oa_version":"Published Version","file_date_updated":"2021-03-02T15:38:14Z","department":[{"_id":"MaMo"}],"date_updated":"2023-10-17T12:43:19Z","ddc":["000"],"type":"conference","status":"public","_id":"9198"},{"project":[{"grant_number":"788183","name":"Alpha Shape Theory Extended","call_identifier":"H2020","_id":"266A2E9E-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","name":"Persistence and stability of geometric complexes","grant_number":"I02979-N35"}],"citation":{"short":"A. Akopyan, H. Edelsbrunner, Computational and Mathematical Biophysics 8 (2020) 51–67.","ieee":"A. Akopyan and H. Edelsbrunner, “The weighted mean curvature derivative of a space-filling diagram,” Computational and Mathematical Biophysics, vol. 8, no. 1. De Gruyter, pp. 51–67, 2020.","apa":"Akopyan, A., & Edelsbrunner, H. (2020). The weighted mean curvature derivative of a space-filling diagram. Computational and Mathematical Biophysics. De Gruyter. https://doi.org/10.1515/cmb-2020-0100","ama":"Akopyan A, Edelsbrunner H. The weighted mean curvature derivative of a space-filling diagram. Computational and Mathematical Biophysics. 2020;8(1):51-67. doi:10.1515/cmb-2020-0100","mla":"Akopyan, Arseniy, and Herbert Edelsbrunner. “The Weighted Mean Curvature Derivative of a Space-Filling Diagram.” Computational and Mathematical Biophysics, vol. 8, no. 1, De Gruyter, 2020, pp. 51–67, doi:10.1515/cmb-2020-0100.","ista":"Akopyan A, Edelsbrunner H. 2020. The weighted mean curvature derivative of a space-filling diagram. Computational and Mathematical Biophysics. 8(1), 51–67.","chicago":"Akopyan, Arseniy, and Herbert Edelsbrunner. “The Weighted Mean Curvature Derivative of a Space-Filling Diagram.” Computational and Mathematical Biophysics. De Gruyter, 2020. https://doi.org/10.1515/cmb-2020-0100."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Akopyan","orcid":"0000-0002-2548-617X","full_name":"Akopyan, Arseniy","first_name":"Arseniy","id":"430D2C90-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","title":"The weighted mean curvature derivative of a space-filling diagram","acknowledgement":"The authors of this paper thank Roland Roth for suggesting the analysis of the weighted\r\ncurvature derivatives for the purpose of improving molecular dynamics simulations and for his continued encouragement. They also thank Patrice Koehl for the implementation of the formulas and for his encouragement and advise along the road. Finally, they thank two anonymous reviewers for their constructive criticism.\r\nThis project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 78818 Alpha). It is also partially supported by the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, through grant no. I02979-N35 of the Austrian Science Fund (FWF).","quality_controlled":"1","publisher":"De Gruyter","oa":1,"has_accepted_license":"1","year":"2020","day":"20","publication":"Computational and Mathematical Biophysics","page":"51-67","doi":"10.1515/cmb-2020-0100","date_published":"2020-06-20T00:00:00Z","date_created":"2021-02-17T15:13:01Z","_id":"9157","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","date_updated":"2023-10-17T12:34:51Z","ddc":["510"],"file_date_updated":"2021-02-19T13:56:24Z","department":[{"_id":"HeEd"}],"abstract":[{"lang":"eng","text":"Representing an atom by a solid sphere in 3-dimensional Euclidean space, we get the space-filling diagram of a molecule by taking the union. Molecular dynamics simulates its motion subject to bonds and other forces, including the solvation free energy. The morphometric approach [12, 17] writes the latter as a linear combination of weighted versions of the volume, area, mean curvature, and Gaussian curvature of the space-filling diagram. We give a formula for the derivative of the weighted mean curvature. Together with the derivatives of the weighted volume in [7], the weighted area in [3], and the weighted Gaussian curvature [1], this yields the derivative of the morphometric expression of the solvation free energy."}],"oa_version":"Published Version","month":"06","intvolume":" 8","publication_identifier":{"issn":["2544-7297"]},"publication_status":"published","file":[{"file_id":"9171","checksum":"cea41de9937d07a3b927d71ee8b4e432","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2021-02-19T13:56:24Z","file_name":"2020_CompMathBiophysics_Akopyan2.pdf","date_updated":"2021-02-19T13:56:24Z","file_size":562359,"creator":"dernst"}],"language":[{"iso":"eng"}],"issue":"1","volume":8,"ec_funded":1},{"department":[{"_id":"HeEd"}],"file_date_updated":"2021-02-19T13:33:19Z","date_updated":"2023-10-17T12:35:10Z","ddc":["510"],"article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"9156","volume":8,"issue":"1","ec_funded":1,"publication_identifier":{"issn":["2544-7297"]},"publication_status":"published","file":[{"date_created":"2021-02-19T13:33:19Z","file_name":"2020_CompMathBiophysics_Akopyan.pdf","date_updated":"2021-02-19T13:33:19Z","file_size":707452,"creator":"dernst","checksum":"ca43a7440834eab6bbea29c59b56ef3a","file_id":"9170","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"month":"07","intvolume":" 8","abstract":[{"text":"The morphometric approach [11, 14] writes the solvation free energy as a linear combination of weighted versions of the volume, area, mean curvature, and Gaussian curvature of the space-filling diagram. We give a formula for the derivative of the weighted Gaussian curvature. Together with the derivatives of the weighted volume in [7], the weighted area in [4], and the weighted mean curvature in [1], this yields the derivative of the morphometric expression of solvation free energy.","lang":"eng"}],"oa_version":"Published Version","author":[{"first_name":"Arseniy","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","last_name":"Akopyan","orcid":"0000-0002-2548-617X","full_name":"Akopyan, Arseniy"},{"last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert"}],"external_id":{"arxiv":["1908.06777"]},"article_processing_charge":"No","title":"The weighted Gaussian curvature derivative of a space-filling diagram","citation":{"mla":"Akopyan, Arseniy, and Herbert Edelsbrunner. “The Weighted Gaussian Curvature Derivative of a Space-Filling Diagram.” Computational and Mathematical Biophysics, vol. 8, no. 1, De Gruyter, 2020, pp. 74–88, doi:10.1515/cmb-2020-0101.","ama":"Akopyan A, Edelsbrunner H. The weighted Gaussian curvature derivative of a space-filling diagram. Computational and Mathematical Biophysics. 2020;8(1):74-88. doi:10.1515/cmb-2020-0101","apa":"Akopyan, A., & Edelsbrunner, H. (2020). The weighted Gaussian curvature derivative of a space-filling diagram. Computational and Mathematical Biophysics. De Gruyter. https://doi.org/10.1515/cmb-2020-0101","short":"A. Akopyan, H. Edelsbrunner, Computational and Mathematical Biophysics 8 (2020) 74–88.","ieee":"A. Akopyan and H. Edelsbrunner, “The weighted Gaussian curvature derivative of a space-filling diagram,” Computational and Mathematical Biophysics, vol. 8, no. 1. De Gruyter, pp. 74–88, 2020.","chicago":"Akopyan, Arseniy, and Herbert Edelsbrunner. “The Weighted Gaussian Curvature Derivative of a Space-Filling Diagram.” Computational and Mathematical Biophysics. De Gruyter, 2020. https://doi.org/10.1515/cmb-2020-0101.","ista":"Akopyan A, Edelsbrunner H. 2020. The weighted Gaussian curvature derivative of a space-filling diagram. Computational and Mathematical Biophysics. 8(1), 74–88."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"_id":"266A2E9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Alpha Shape Theory Extended","grant_number":"788183"},{"_id":"2561EBF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"I02979-N35","name":"Persistence and stability of geometric complexes"}],"page":"74-88","date_published":"2020-07-21T00:00:00Z","doi":"10.1515/cmb-2020-0101","date_created":"2021-02-17T15:12:44Z","has_accepted_license":"1","year":"2020","day":"21","publication":"Computational and Mathematical Biophysics","quality_controlled":"1","publisher":"De Gruyter","oa":1,"acknowledgement":"The authors of this paper thank Roland Roth for suggesting the analysis of theweighted\r\ncurvature derivatives for the purpose of improving molecular dynamics simulations. They also thank Patrice Koehl for the implementation of the formulas and for his encouragement and advise along the road. Finally, they thank two anonymous reviewers for their constructive criticism.\r\nThis project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 78818 Alpha). It is also partially supported by the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, through grant no. I02979-N35 of the Austrian Science Fund (FWF)."},{"oa_version":"Published Version","abstract":[{"lang":"eng","text":"We consider the symmetric simple exclusion process in Zd with quenched bounded dynamic random conductances and prove its hydrodynamic limit in path space. The main tool is the connection, due to the self-duality of the process, between the invariance principle for single particles starting from all points and the macroscopic behavior of the density field. While the hydrodynamic limit at fixed macroscopic times is obtained via a generalization to the time-inhomogeneous context of the strategy introduced in [41], in order to prove tightness for the sequence of empirical density fields we develop a new criterion based on the notion of uniform conditional stochastic continuity, following [50]. In conclusion, we show that uniform elliptic dynamic conductances provide an example of environments in which the so-called arbitrary starting point invariance principle may be derived from the invariance principle of a single particle starting from the origin. Therefore, our hydrodynamics result applies to the examples of quenched environments considered in, e.g., [1], [3], [6] in combination with the hypothesis of uniform ellipticity."}],"intvolume":" 25","month":"10","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"8976","checksum":"d75359b9814e78d57c0a481b7cde3751","success":1,"date_updated":"2020-12-28T08:24:08Z","file_size":696653,"creator":"dernst","date_created":"2020-12-28T08:24:08Z","file_name":"2020_ElectronJProbab_Redig.pdf"}],"publication_status":"published","publication_identifier":{"eissn":["1083-6489"]},"ec_funded":1,"volume":25,"_id":"8973","status":"public","article_type":"original","type":"journal_article","ddc":["510"],"date_updated":"2023-10-17T12:51:56Z","file_date_updated":"2020-12-28T08:24:08Z","department":[{"_id":"JaMa"}],"acknowledgement":"We warmly thank S.R.S. Varadhan for many enlightening discussions at an early stage of this work. We are indebted to Francesca Collet for fruitful discussions and constant support all throughout this work. We thank Simone Floreani\r\nand Alberto Chiarini for helpful conversations on the final part of this paper as well as both referees for their careful reading and for raising relevant issues on some weak points contained in a previous version of this manuscript; we believe this helped us to improve it.\r\nPart of this work was done during the authors’ stay at the Institut Henri Poincaré (UMS 5208 CNRS-Sorbonne Université) – Centre Emile Borel during the trimester Stochastic Dynamics Out of Equilibrium. The authors thank this institution for hospitality and support (through LabEx CARMIN, ANR-10-LABX-59-01). F.S. thanks laboratoire\r\nMAP5 of Université de Paris, and E.S. thanks Delft University, for financial support and hospitality. F.S. acknowledges NWO for financial support via the TOP1 grant 613.001.552 as well as funding from the European Union’s Horizon 2020 research and innovation programme under the Marie-Skłodowska-Curie grant agreement No. 754411. This research has been conducted within the FP2M federation (CNRS FR 2036).","oa":1,"publisher":" Institute of Mathematical Statistics","quality_controlled":"1","publication":"Electronic Journal of Probability","day":"21","year":"2020","isi":1,"has_accepted_license":"1","date_created":"2020-12-27T23:01:17Z","date_published":"2020-10-21T00:00:00Z","doi":"10.1214/20-EJP536","article_number":"138","project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Redig, F., Saada, E., & Sau, F. (2020). Symmetric simple exclusion process in dynamic environment: Hydrodynamics. Electronic Journal of Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/20-EJP536","ama":"Redig F, Saada E, Sau F. Symmetric simple exclusion process in dynamic environment: Hydrodynamics. Electronic Journal of Probability. 2020;25. doi:10.1214/20-EJP536","short":"F. Redig, E. Saada, F. Sau, Electronic Journal of Probability 25 (2020).","ieee":"F. Redig, E. Saada, and F. Sau, “Symmetric simple exclusion process in dynamic environment: Hydrodynamics,” Electronic Journal of Probability, vol. 25. Institute of Mathematical Statistics, 2020.","mla":"Redig, Frank, et al. “Symmetric Simple Exclusion Process in Dynamic Environment: Hydrodynamics.” Electronic Journal of Probability, vol. 25, 138, Institute of Mathematical Statistics, 2020, doi:10.1214/20-EJP536.","ista":"Redig F, Saada E, Sau F. 2020. Symmetric simple exclusion process in dynamic environment: Hydrodynamics. Electronic Journal of Probability. 25, 138.","chicago":"Redig, Frank, Ellen Saada, and Federico Sau. “Symmetric Simple Exclusion Process in Dynamic Environment: Hydrodynamics.” Electronic Journal of Probability. Institute of Mathematical Statistics, 2020. https://doi.org/10.1214/20-EJP536."},"title":"Symmetric simple exclusion process in dynamic environment: Hydrodynamics","article_processing_charge":"No","external_id":{"arxiv":["1811.01366"],"isi":["000591737500001"]},"author":[{"last_name":"Redig","full_name":"Redig, Frank","first_name":"Frank"},{"full_name":"Saada, Ellen","last_name":"Saada","first_name":"Ellen"},{"last_name":"Sau","full_name":"Sau, Federico","id":"E1836206-9F16-11E9-8814-AEFDE5697425","first_name":"Federico"}]},{"date_updated":"2023-10-17T12:51:10Z","department":[{"_id":"TiBr"}],"_id":"179","status":"public","type":"journal_article","article_type":"original","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0012-7094"]},"volume":169,"issue":"16","oa_version":"Preprint","abstract":[{"lang":"eng","text":"An asymptotic formula is established for the number of rational points of bounded anticanonical height which lie on a certain Zariski dense subset of the biprojective hypersurface x1y21+⋯+x4y24=0 in ℙ3×ℙ3. This confirms the modified Manin conjecture for this variety, in which the removal of a thin set of rational points is allowed."}],"intvolume":" 169","month":"09","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1805.10715"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Browning, Timothy D, and Roger Heath Brown. “Density of Rational Points on a Quadric Bundle in ℙ3×ℙ3.” Duke Mathematical Journal. Duke University Press, 2020. https://doi.org/10.1215/00127094-2020-0031.","ista":"Browning TD, Heath Brown R. 2020. Density of rational points on a quadric bundle in ℙ3×ℙ3. Duke Mathematical Journal. 169(16), 3099–3165.","mla":"Browning, Timothy D., and Roger Heath Brown. “Density of Rational Points on a Quadric Bundle in ℙ3×ℙ3.” Duke Mathematical Journal, vol. 169, no. 16, Duke University Press, 2020, pp. 3099–165, doi:10.1215/00127094-2020-0031.","ieee":"T. D. Browning and R. Heath Brown, “Density of rational points on a quadric bundle in ℙ3×ℙ3,” Duke Mathematical Journal, vol. 169, no. 16. Duke University Press, pp. 3099–3165, 2020.","short":"T.D. Browning, R. Heath Brown, Duke Mathematical Journal 169 (2020) 3099–3165.","apa":"Browning, T. D., & Heath Brown, R. (2020). Density of rational points on a quadric bundle in ℙ3×ℙ3. Duke Mathematical Journal. Duke University Press. https://doi.org/10.1215/00127094-2020-0031","ama":"Browning TD, Heath Brown R. Density of rational points on a quadric bundle in ℙ3×ℙ3. Duke Mathematical Journal. 2020;169(16):3099-3165. doi:10.1215/00127094-2020-0031"},"title":"Density of rational points on a quadric bundle in ℙ3×ℙ3","external_id":{"isi":["000582676300002"],"arxiv":["1805.10715"]},"article_processing_charge":"No","author":[{"first_name":"Timothy D","id":"35827D50-F248-11E8-B48F-1D18A9856A87","last_name":"Browning","full_name":"Browning, Timothy D","orcid":"0000-0002-8314-0177"},{"full_name":"Heath Brown, Roger","last_name":"Heath Brown","first_name":"Roger"}],"publication":"Duke Mathematical Journal","day":"10","year":"2020","isi":1,"date_created":"2018-12-11T11:45:02Z","doi":"10.1215/00127094-2020-0031","date_published":"2020-09-10T00:00:00Z","page":"3099-3165","oa":1,"publisher":"Duke University Press","quality_controlled":"1"},{"month":"10","publisher":"Royal Society","main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.5973013.v1","open_access":"1"}],"oa":1,"oa_version":"Published Version","abstract":[{"text":"Data and mathematica notebooks for plotting figures from Language learning with communication between learners","lang":"eng"}],"related_material":{"record":[{"relation":"used_in_publication","id":"198","status":"public"}]},"doi":"10.6084/m9.figshare.5973013.v1","date_published":"2020-10-15T00:00:00Z","date_created":"2021-08-06T13:09:57Z","day":"15","year":"2020","status":"public","type":"research_data_reference","_id":"9814","department":[{"_id":"KrCh"}],"title":"Data and mathematica notebooks for plotting figures from language learning with communication between learners from language acquisition with communication between learners","author":[{"first_name":"Rasmus","id":"3B699956-F248-11E8-B48F-1D18A9856A87","last_name":"Ibsen-Jensen","full_name":"Ibsen-Jensen, Rasmus","orcid":"0000-0003-4783-0389"},{"first_name":"Josef","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","last_name":"Tkadlec","full_name":"Tkadlec, Josef","orcid":"0000-0002-1097-9684"},{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Martin","full_name":"Nowak, Martin","last_name":"Nowak"}],"article_processing_charge":"No","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"ista":"Ibsen-Jensen R, Tkadlec J, Chatterjee K, Nowak M. 2020. Data and mathematica notebooks for plotting figures from language learning with communication between learners from language acquisition with communication between learners, Royal Society, 10.6084/m9.figshare.5973013.v1.","chicago":"Ibsen-Jensen, Rasmus, Josef Tkadlec, Krishnendu Chatterjee, and Martin Nowak. “Data and Mathematica Notebooks for Plotting Figures from Language Learning with Communication between Learners from Language Acquisition with Communication between Learners.” Royal Society, 2020. https://doi.org/10.6084/m9.figshare.5973013.v1.","apa":"Ibsen-Jensen, R., Tkadlec, J., Chatterjee, K., & Nowak, M. (2020). Data and mathematica notebooks for plotting figures from language learning with communication between learners from language acquisition with communication between learners. Royal Society. https://doi.org/10.6084/m9.figshare.5973013.v1","ama":"Ibsen-Jensen R, Tkadlec J, Chatterjee K, Nowak M. Data and mathematica notebooks for plotting figures from language learning with communication between learners from language acquisition with communication between learners. 2020. doi:10.6084/m9.figshare.5973013.v1","short":"R. Ibsen-Jensen, J. Tkadlec, K. Chatterjee, M. Nowak, (2020).","ieee":"R. Ibsen-Jensen, J. Tkadlec, K. Chatterjee, and M. Nowak, “Data and mathematica notebooks for plotting figures from language learning with communication between learners from language acquisition with communication between learners.” Royal Society, 2020.","mla":"Ibsen-Jensen, Rasmus, et al. Data and Mathematica Notebooks for Plotting Figures from Language Learning with Communication between Learners from Language Acquisition with Communication between Learners. Royal Society, 2020, doi:10.6084/m9.figshare.5973013.v1."},"date_updated":"2023-10-18T06:36:00Z"},{"acknowledgement":"This work is supported by the Office of Naval Research (N00014-16-1-2927- A00003), Vannevar Bush Faculty Fellowship (N00014-16-1-2812- P00005), Department of Energy (DE-SC0019174- 0001), and Defense Threat Reduction Agency (HDTRA1-15-1-0017- P00005).","quality_controlled":"1","publisher":"American Physical Society","oa":1,"isi":1,"year":"2020","day":"24","publication":"Physical Review Letters","doi":"10.1103/PhysRevLett.125.043202","date_published":"2020-07-24T00:00:00Z","date_created":"2020-08-24T06:24:04Z","article_number":"043202","citation":{"ista":"Malia BK, Martínez-Rincón J, Wu Y, Hosten O, Kasevich MA. 2020. Free space Ramsey spectroscopy in rubidium with noise below the quantum projection limit. Physical Review Letters. 125(4), 043202.","chicago":"Malia, Benjamin K., Julián Martínez-Rincón, Yunfan Wu, Onur Hosten, and Mark A. Kasevich. “Free Space Ramsey Spectroscopy in Rubidium with Noise below the Quantum Projection Limit.” Physical Review Letters. American Physical Society, 2020. https://doi.org/10.1103/PhysRevLett.125.043202.","apa":"Malia, B. K., Martínez-Rincón, J., Wu, Y., Hosten, O., & Kasevich, M. A. (2020). Free space Ramsey spectroscopy in rubidium with noise below the quantum projection limit. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.125.043202","ama":"Malia BK, Martínez-Rincón J, Wu Y, Hosten O, Kasevich MA. Free space Ramsey spectroscopy in rubidium with noise below the quantum projection limit. Physical Review Letters. 2020;125(4). doi:10.1103/PhysRevLett.125.043202","ieee":"B. K. Malia, J. Martínez-Rincón, Y. Wu, O. Hosten, and M. A. Kasevich, “Free space Ramsey spectroscopy in rubidium with noise below the quantum projection limit,” Physical Review Letters, vol. 125, no. 4. American Physical Society, 2020.","short":"B.K. Malia, J. Martínez-Rincón, Y. Wu, O. Hosten, M.A. Kasevich, Physical Review Letters 125 (2020).","mla":"Malia, Benjamin K., et al. “Free Space Ramsey Spectroscopy in Rubidium with Noise below the Quantum Projection Limit.” Physical Review Letters, vol. 125, no. 4, 043202, American Physical Society, 2020, doi:10.1103/PhysRevLett.125.043202."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Benjamin K.","full_name":"Malia, Benjamin K.","last_name":"Malia"},{"first_name":"Julián","last_name":"Martínez-Rincón","full_name":"Martínez-Rincón, Julián"},{"first_name":"Yunfan","last_name":"Wu","full_name":"Wu, Yunfan"},{"id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","first_name":"Onur","last_name":"Hosten","full_name":"Hosten, Onur","orcid":"0000-0002-2031-204X"},{"full_name":"Kasevich, Mark A.","last_name":"Kasevich","first_name":"Mark A."}],"article_processing_charge":"No","external_id":{"arxiv":["1912.10218"],"pmid":["32794788"],"isi":["000552227400008"]},"title":"Free space Ramsey spectroscopy in rubidium with noise below the quantum projection limit","abstract":[{"lang":"eng","text":"We demonstrate the utility of optical cavity generated spin-squeezed states in free space atomic fountain clocks in ensembles of 390 000 87Rb atoms. Fluorescence imaging, correlated to an initial quantum nondemolition measurement, is used for population spectroscopy after the atoms are released from a confining lattice. For a free fall time of 4 milliseconds, we resolve a single-shot phase sensitivity of 814(61) microradians, which is 5.8(0.6) decibels (dB) below the quantum projection limit. We observe that this squeezing is preserved as the cloud expands to a roughly 200 μm radius and falls roughly 300 μm in free space. Ramsey spectroscopy with 240 000 atoms at a 3.6 ms Ramsey time results in a single-shot fractional frequency stability of 8.4(0.2)×10−12, 3.8(0.2) dB below the quantum projection limit. The sensitivity and stability are limited by the technical noise in the fluorescence detection protocol and the microwave system, respectively."}],"oa_version":"Preprint","pmid":1,"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1912.10218"}],"month":"07","intvolume":" 125","publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"publication_status":"published","language":[{"iso":"eng"}],"issue":"4","volume":125,"_id":"8285","article_type":"original","type":"journal_article","status":"public","date_updated":"2023-10-18T08:38:35Z","department":[{"_id":"OnHo"}]},{"publisher":"Optica Publishing Group","quality_controlled":"1","alternative_title":["OSA Technical Digest"],"scopus_import":"1","month":"01","abstract":[{"lang":"eng","text":"We discus noise channels in coherent electro-optic up-conversion between microwave and optical fields, in particular due to optical heating. We also report on a novel configuration, which promises to be flexible and highly efficient."}],"oa_version":"None","date_created":"2021-11-21T23:01:31Z","date_published":"2020-01-01T00:00:00Z","doi":"10.1364/QUANTUM.2020.QTu8A.1","year":"2020","publication_status":"published","publication_identifier":{"isbn":["9-781-5575-2820-9"]},"language":[{"iso":"eng"}],"publication":"OSA Quantum 2.0 Conference","day":"01","conference":{"start_date":"2020-09-14","location":"Washington, DC, United States","end_date":"2020-09-17","name":"OSA: Optical Society of America"},"type":"conference","status":"public","_id":"10328","article_number":"QTu8A.1","article_processing_charge":"No","author":[{"last_name":"Lambert","full_name":"Lambert, Nicholas J.","first_name":"Nicholas J."},{"first_name":"Sonia","last_name":"Mobassem","full_name":"Mobassem, Sonia"},{"id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","first_name":"Alfredo R","orcid":"0000-0001-6249-5860","full_name":"Rueda Sanchez, Alfredo R","last_name":"Rueda Sanchez"},{"first_name":"Harald G.L.","full_name":"Schwefel, Harald G.L.","last_name":"Schwefel"}],"department":[{"_id":"JoFi"}],"title":"New designs and noise channels in electro-optic microwave to optical up-conversion","citation":{"ista":"Lambert NJ, Mobassem S, Rueda Sanchez AR, Schwefel HGL. 2020. New designs and noise channels in electro-optic microwave to optical up-conversion. OSA Quantum 2.0 Conference. OSA: Optical Society of America, OSA Technical Digest, , QTu8A.1.","chicago":"Lambert, Nicholas J., Sonia Mobassem, Alfredo R Rueda Sanchez, and Harald G.L. Schwefel. “New Designs and Noise Channels in Electro-Optic Microwave to Optical up-Conversion.” In OSA Quantum 2.0 Conference. Optica Publishing Group, 2020. https://doi.org/10.1364/QUANTUM.2020.QTu8A.1.","short":"N.J. Lambert, S. Mobassem, A.R. Rueda Sanchez, H.G.L. Schwefel, in:, OSA Quantum 2.0 Conference, Optica Publishing Group, 2020.","ieee":"N. J. Lambert, S. Mobassem, A. R. Rueda Sanchez, and H. G. L. Schwefel, “New designs and noise channels in electro-optic microwave to optical up-conversion,” in OSA Quantum 2.0 Conference, Washington, DC, United States, 2020.","ama":"Lambert NJ, Mobassem S, Rueda Sanchez AR, Schwefel HGL. New designs and noise channels in electro-optic microwave to optical up-conversion. In: OSA Quantum 2.0 Conference. Optica Publishing Group; 2020. doi:10.1364/QUANTUM.2020.QTu8A.1","apa":"Lambert, N. J., Mobassem, S., Rueda Sanchez, A. R., & Schwefel, H. G. L. (2020). New designs and noise channels in electro-optic microwave to optical up-conversion. In OSA Quantum 2.0 Conference. Washington, DC, United States: Optica Publishing Group. https://doi.org/10.1364/QUANTUM.2020.QTu8A.1","mla":"Lambert, Nicholas J., et al. “New Designs and Noise Channels in Electro-Optic Microwave to Optical up-Conversion.” OSA Quantum 2.0 Conference, QTu8A.1, Optica Publishing Group, 2020, doi:10.1364/QUANTUM.2020.QTu8A.1."},"date_updated":"2023-10-18T08:32:34Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"department":[{"_id":"TiVo"}],"date_updated":"2023-10-18T09:20:55Z","type":"conference","conference":{"location":"Vancouver, Canada","end_date":"2020-12-12","start_date":"2020-12-06","name":"NeurIPS: Conference on Neural Information Processing Systems"},"status":"public","_id":"9633","related_material":{"link":[{"url":"https://doi.org/10.1101/2020.10.24.353409","relation":"is_continued_by"}],"record":[{"id":"14422","status":"public","relation":"dissertation_contains"}]},"volume":33,"ec_funded":1,"publication_identifier":{"issn":["1049-5258"]},"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"url":"https://proceedings.neurips.cc/paper/2020/hash/bdbd5ebfde4934142c8a88e7a3796cd5-Abstract.html","open_access":"1"}],"month":"12","intvolume":" 33","abstract":[{"lang":"eng","text":"The search for biologically faithful synaptic plasticity rules has resulted in a large body of models. They are usually inspired by – and fitted to – experimental data, but they rarely produce neural dynamics that serve complex functions. These failures suggest that current plasticity models are still under-constrained by existing data. Here, we present an alternative approach that uses meta-learning to discover plausible synaptic plasticity rules. Instead of experimental data, the rules are constrained by the functions they implement and the structure they are meant to produce. Briefly, we parameterize synaptic plasticity rules by a Volterra expansion and then use supervised learning methods (gradient descent or evolutionary strategies) to minimize a problem-dependent loss function that quantifies how effectively a candidate plasticity rule transforms an initially random network into one with the desired function. We first validate our approach by re-discovering previously described plasticity rules, starting at the single-neuron level and “Oja’s rule”, a simple Hebbian plasticity rule that captures the direction of most variability of inputs to a neuron (i.e., the first principal component). We expand the problem to the network level and ask the framework to find Oja’s rule together with an anti-Hebbian rule such that an initially random two-layer firing-rate network will recover several principal components of the input space after learning. Next, we move to networks of integrate-and-fire neurons with plastic inhibitory afferents. We train for rules that achieve a target firing rate by countering tuned excitation. Our algorithm discovers a specific subset of the manifold of rules that can solve this task. Our work is a proof of principle of an automated and unbiased approach to unveil synaptic plasticity rules that obey biological constraints and can solve complex functions."}],"oa_version":"Published Version","author":[{"first_name":"Basile J","id":"C7610134-B532-11EA-BD9F-F5753DDC885E","last_name":"Confavreux","full_name":"Confavreux, Basile J"},{"full_name":"Zenke, Friedemann","last_name":"Zenke","first_name":"Friedemann"},{"first_name":"Everton J.","full_name":"Agnes, Everton J.","last_name":"Agnes"},{"last_name":"Lillicrap","full_name":"Lillicrap, Timothy","first_name":"Timothy"},{"last_name":"Vogels","full_name":"Vogels, Tim P","orcid":"0000-0003-3295-6181","first_name":"Tim P","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425"}],"article_processing_charge":"No","title":"A meta-learning approach to (re)discover plasticity rules that carve a desired function into a neural network","citation":{"short":"B.J. Confavreux, F. Zenke, E.J. Agnes, T. Lillicrap, T.P. Vogels, in:, Advances in Neural Information Processing Systems, 2020, pp. 16398–16408.","ieee":"B. J. Confavreux, F. Zenke, E. J. Agnes, T. Lillicrap, and T. P. Vogels, “A meta-learning approach to (re)discover plasticity rules that carve a desired function into a neural network,” in Advances in Neural Information Processing Systems, Vancouver, Canada, 2020, vol. 33, pp. 16398–16408.","apa":"Confavreux, B. J., Zenke, F., Agnes, E. J., Lillicrap, T., & Vogels, T. P. (2020). A meta-learning approach to (re)discover plasticity rules that carve a desired function into a neural network. In Advances in Neural Information Processing Systems (Vol. 33, pp. 16398–16408). Vancouver, Canada.","ama":"Confavreux BJ, Zenke F, Agnes EJ, Lillicrap T, Vogels TP. A meta-learning approach to (re)discover plasticity rules that carve a desired function into a neural network. In: Advances in Neural Information Processing Systems. Vol 33. ; 2020:16398-16408.","mla":"Confavreux, Basile J., et al. “A Meta-Learning Approach to (Re)Discover Plasticity Rules That Carve a Desired Function into a Neural Network.” Advances in Neural Information Processing Systems, vol. 33, 2020, pp. 16398–408.","ista":"Confavreux BJ, Zenke F, Agnes EJ, Lillicrap T, Vogels TP. 2020. A meta-learning approach to (re)discover plasticity rules that carve a desired function into a neural network. Advances in Neural Information Processing Systems. NeurIPS: Conference on Neural Information Processing Systems vol. 33, 16398–16408.","chicago":"Confavreux, Basile J, Friedemann Zenke, Everton J. Agnes, Timothy Lillicrap, and Tim P Vogels. “A Meta-Learning Approach to (Re)Discover Plasticity Rules That Carve a Desired Function into a Neural Network.” In Advances in Neural Information Processing Systems, 33:16398–408, 2020."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","project":[{"_id":"c084a126-5a5b-11eb-8a69-d75314a70a87","grant_number":"214316/Z/18/Z","name":"What’s in a memory? Spatiotemporal dynamics in strongly coupled recurrent neuronal networks."},{"_id":"0aacfa84-070f-11eb-9043-d7eb2c709234","call_identifier":"H2020","name":"Learning the shape of synaptic plasticity rules for neuronal architectures and function through machine learning.","grant_number":"819603"}],"page":"16398-16408","date_published":"2020-12-06T00:00:00Z","date_created":"2021-07-04T22:01:27Z","year":"2020","day":"06","publication":"Advances in Neural Information Processing Systems","quality_controlled":"1","oa":1,"acknowledgement":"We would like to thank Chaitanya Chintaluri, Georgia Christodoulou, Bill Podlaski and Merima Šabanovic for useful discussions and comments. This work was supported by a Wellcome Trust ´ Senior Research Fellowship (214316/Z/18/Z), a BBSRC grant (BB/N019512/1), an ERC consolidator Grant (SYNAPSEEK), a Leverhulme Trust Project Grant (RPG-2016-446), and funding from École Polytechnique, Paris."},{"day":"01","publication":"Cell Reports","has_accepted_license":"1","isi":1,"year":"2020","date_published":"2020-12-01T00:00:00Z","doi":"10.1016/j.celrep.2020.108463","date_created":"2020-12-13T23:01:21Z","acknowledgement":"We thank Drs. Sebastian Bednarek (University of Wisconsin-Madison), Niko Geldner (University of Lausanne), and Karin Schumacher (Heidelberg University) for kindly sharing published Arabidopsis lines; Dr. Satoshi Naramoto for the pPIN2::PIN2-GFP; pVHA-a1::VHA-a1-mRFP reporter; the staff at the Life Science Facility and Bioimaging Facility, Monika Hrtyan, and Dorota Jaworska at IST Austria for technical support; and Drs. Su Tang (Texas A&M University),\r\nMelinda Abas (BOKU), Eva Benkova´ (IST Austria), Christian Luschnig (BOKU), Bartel Vanholme (Gent University), and the Friml group for valuable discussions. The research leading to these findings was funded by the European Union’s Horizon 2020 program (ERC grant agreement no. 742985, to J.F.), the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no.\r\n291734, the Swiss National Funds (31003A_165877, to M.G.), the Ministry of Education, Youth, and Sports of the Czech Republic (project no. CZ.02.1.01/0.0/0.0/16_019/0000738, EU Operational Programme ‘‘Research, development and education and Centre for Plant Experimental Biology’’), and the EU Operational Programme Prague - Competitiveness (project no. CZ.2.16/3.1.00/21519). S.T. was funded by a European Molecular Biology Organization (EMBO) long-term postdoctoral fellowship (ALTF 723-2015). X.Z. was partly supported by a PhD scholarship from the China Scholarship Council.","quality_controlled":"1","publisher":"Elsevier","oa":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Tan S, Di Donato M, Glanc M, et al. Non-steroidal anti-inflammatory drugs target TWISTED DWARF1-regulated actin dynamics and auxin transport-mediated plant development. Cell Reports. 2020;33(9). doi:10.1016/j.celrep.2020.108463","apa":"Tan, S., Di Donato, M., Glanc, M., Zhang, X., Klíma, P., Liu, J., … Friml, J. (2020). Non-steroidal anti-inflammatory drugs target TWISTED DWARF1-regulated actin dynamics and auxin transport-mediated plant development. Cell Reports. Elsevier. https://doi.org/10.1016/j.celrep.2020.108463","ieee":"S. Tan et al., “Non-steroidal anti-inflammatory drugs target TWISTED DWARF1-regulated actin dynamics and auxin transport-mediated plant development,” Cell Reports, vol. 33, no. 9. Elsevier, 2020.","short":"S. Tan, M. Di Donato, M. Glanc, X. Zhang, P. Klíma, J. Liu, A. Bailly, N. Ferro, J. Petrášek, M. Geisler, J. Friml, Cell Reports 33 (2020).","mla":"Tan, Shutang, et al. “Non-Steroidal Anti-Inflammatory Drugs Target TWISTED DWARF1-Regulated Actin Dynamics and Auxin Transport-Mediated Plant Development.” Cell Reports, vol. 33, no. 9, 108463, Elsevier, 2020, doi:10.1016/j.celrep.2020.108463.","ista":"Tan S, Di Donato M, Glanc M, Zhang X, Klíma P, Liu J, Bailly A, Ferro N, Petrášek J, Geisler M, Friml J. 2020. Non-steroidal anti-inflammatory drugs target TWISTED DWARF1-regulated actin dynamics and auxin transport-mediated plant development. Cell Reports. 33(9), 108463.","chicago":"Tan, Shutang, Martin Di Donato, Matous Glanc, Xixi Zhang, Petr Klíma, Jie Liu, Aurélien Bailly, et al. “Non-Steroidal Anti-Inflammatory Drugs Target TWISTED DWARF1-Regulated Actin Dynamics and Auxin Transport-Mediated Plant Development.” Cell Reports. Elsevier, 2020. https://doi.org/10.1016/j.celrep.2020.108463."},"title":"Non-steroidal anti-inflammatory drugs target TWISTED DWARF1-regulated actin dynamics and auxin transport-mediated plant development","author":[{"first_name":"Shutang","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","full_name":"Tan, Shutang","orcid":"0000-0002-0471-8285","last_name":"Tan"},{"first_name":"Martin","last_name":"Di Donato","full_name":"Di Donato, Martin"},{"first_name":"Matous","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","orcid":"0000-0003-0619-7783","full_name":"Glanc, Matous","last_name":"Glanc"},{"full_name":"Zhang, Xixi","orcid":"0000-0001-7048-4627","last_name":"Zhang","id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A","first_name":"Xixi"},{"full_name":"Klíma, Petr","last_name":"Klíma","first_name":"Petr"},{"first_name":"Jie","full_name":"Liu, Jie","last_name":"Liu"},{"first_name":"Aurélien","last_name":"Bailly","full_name":"Bailly, Aurélien"},{"first_name":"Noel","last_name":"Ferro","full_name":"Ferro, Noel"},{"last_name":"Petrášek","full_name":"Petrášek, Jan","first_name":"Jan"},{"first_name":"Markus","full_name":"Geisler, Markus","last_name":"Geisler"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří"}],"external_id":{"isi":["000595658100018"],"pmid":["33264621"]},"article_processing_charge":"Yes","article_number":"108463","project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425"},{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"},{"_id":"256FEF10-B435-11E9-9278-68D0E5697425","name":"Long Term Fellowship","grant_number":"723-2015"}],"file":[{"date_created":"2020-12-14T07:33:39Z","file_name":"2020_CellReports_Tan.pdf","creator":"dernst","date_updated":"2020-12-14T07:33:39Z","file_size":8056434,"file_id":"8948","checksum":"ed18cba0fb48ed2e789381a54cc21904","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["22111247"]},"publication_status":"published","volume":33,"related_material":{"link":[{"url":"https://ist.ac.at/en/news/plants-on-aspirin/","relation":"press_release","description":"News on IST Homepage"}]},"issue":"9","ec_funded":1,"oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","text":"The widely used non-steroidal anti-inflammatory drugs (NSAIDs) are derivatives of the phytohormone salicylic acid (SA). SA is well known to regulate plant immunity and development, whereas there have been few reports focusing on the effects of NSAIDs in plants. Our studies here reveal that NSAIDs exhibit largely overlapping physiological activities to SA in the model plant Arabidopsis. NSAID treatments lead to shorter and agravitropic primary roots and inhibited lateral root organogenesis. Notably, in addition to the SA-like action, which in roots involves binding to the protein phosphatase 2A (PP2A), NSAIDs also exhibit PP2A-independent effects. Cell biological and biochemical analyses reveal that many NSAIDs bind directly to and inhibit the chaperone activity of TWISTED DWARF1, thereby regulating actin cytoskeleton dynamics and subsequent endosomal trafficking. Our findings uncover an unexpected bioactivity of human pharmaceuticals in plants and provide insights into the molecular mechanism underlying the cellular action of this class of anti-inflammatory compounds."}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"month":"12","intvolume":" 33","scopus_import":"1","ddc":["580"],"date_updated":"2023-11-16T13:03:31Z","file_date_updated":"2020-12-14T07:33:39Z","department":[{"_id":"JiFr"}],"_id":"8943","status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"}},{"isi":1,"year":"2020","day":"26","publication":"Proceedings of the National Academy of Sciences of the United States of America","page":"11233-11239","doi":"10.1073/pnas.1913716117","date_published":"2020-05-26T00:00:00Z","date_created":"2020-06-07T22:00:51Z","quality_controlled":"1","publisher":"National Academy of Sciences","oa":1,"citation":{"mla":"Xu, Duo, et al. “Nonlinear Hydrodynamic Instability and Turbulence in Pulsatile Flow.” Proceedings of the National Academy of Sciences of the United States of America, vol. 117, no. 21, National Academy of Sciences, 2020, pp. 11233–39, doi:10.1073/pnas.1913716117.","short":"D. Xu, A. Varshney, X. Ma, B. Song, M. Riedl, M. Avila, B. Hof, Proceedings of the National Academy of Sciences of the United States of America 117 (2020) 11233–11239.","ieee":"D. Xu et al., “Nonlinear hydrodynamic instability and turbulence in pulsatile flow,” Proceedings of the National Academy of Sciences of the United States of America, vol. 117, no. 21. National Academy of Sciences, pp. 11233–11239, 2020.","ama":"Xu D, Varshney A, Ma X, et al. Nonlinear hydrodynamic instability and turbulence in pulsatile flow. Proceedings of the National Academy of Sciences of the United States of America. 2020;117(21):11233-11239. doi:10.1073/pnas.1913716117","apa":"Xu, D., Varshney, A., Ma, X., Song, B., Riedl, M., Avila, M., & Hof, B. (2020). Nonlinear hydrodynamic instability and turbulence in pulsatile flow. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.1913716117","chicago":"Xu, Duo, Atul Varshney, Xingyu Ma, Baofang Song, Michael Riedl, Marc Avila, and Björn Hof. “Nonlinear Hydrodynamic Instability and Turbulence in Pulsatile Flow.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2020. https://doi.org/10.1073/pnas.1913716117.","ista":"Xu D, Varshney A, Ma X, Song B, Riedl M, Avila M, Hof B. 2020. Nonlinear hydrodynamic instability and turbulence in pulsatile flow. Proceedings of the National Academy of Sciences of the United States of America. 117(21), 11233–11239."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"last_name":"Xu","full_name":"Xu, Duo","first_name":"Duo","id":"3454D55E-F248-11E8-B48F-1D18A9856A87"},{"id":"2A2006B2-F248-11E8-B48F-1D18A9856A87","first_name":"Atul","last_name":"Varshney","orcid":"0000-0002-3072-5999","full_name":"Varshney, Atul"},{"last_name":"Ma","orcid":"0000-0002-0179-9737","full_name":"Ma, Xingyu","first_name":"Xingyu","id":"34BADBA6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Song","full_name":"Song, Baofang","first_name":"Baofang"},{"first_name":"Michael","id":"3BE60946-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4844-6311","full_name":"Riedl, Michael","last_name":"Riedl"},{"last_name":"Avila","full_name":"Avila, Marc","first_name":"Marc"},{"id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn","last_name":"Hof","orcid":"0000-0003-2057-2754","full_name":"Hof, Björn"}],"external_id":{"arxiv":["2005.11190"],"isi":["000536797100014"]},"article_processing_charge":"No","title":"Nonlinear hydrodynamic instability and turbulence in pulsatile flow","project":[{"call_identifier":"FWF","_id":"238B8092-32DE-11EA-91FC-C7463DDC885E","name":"Instabilities in pulsating pipe flow of Newtonian and complex fluids","grant_number":"I04188"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"}],"publication_identifier":{"eissn":["10916490"],"issn":["00278424"]},"publication_status":"published","language":[{"iso":"eng"}],"issue":"21","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"12726"},{"relation":"dissertation_contains","status":"public","id":"14530"}],"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/blood-flows-more-turbulent-than-previously-expected/","relation":"press_release"}]},"volume":117,"ec_funded":1,"abstract":[{"lang":"eng","text":"Pulsating flows through tubular geometries are laminar provided that velocities are moderate. This in particular is also believed to apply to cardiovascular flows where inertial forces are typically too low to sustain turbulence. On the other hand, flow instabilities and fluctuating shear stresses are held responsible for a variety of cardiovascular diseases. Here we report a nonlinear instability mechanism for pulsating pipe flow that gives rise to bursts of turbulence at low flow rates. Geometrical distortions of small, yet finite, amplitude are found to excite a state consisting of helical vortices during flow deceleration. The resulting flow pattern grows rapidly in magnitude, breaks down into turbulence, and eventually returns to laminar when the flow accelerates. This scenario causes shear stress fluctuations and flow reversal during each pulsation cycle. Such unsteady conditions can adversely affect blood vessels and have been shown to promote inflammation and dysfunction of the shear stress-sensitive endothelial cell layer."}],"oa_version":"Preprint","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2005.11190"}],"month":"05","intvolume":" 117","date_updated":"2023-11-30T10:55:13Z","department":[{"_id":"BjHo"}],"_id":"7932","type":"journal_article","article_type":"original","status":"public"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Alt, Johannes, László Erdös, and Torben H Krüger. “The Dyson Equation with Linear Self-Energy: Spectral Bands, Edges and Cusps.” Documenta Mathematica. EMS Press, 2020. https://doi.org/10.4171/dm/780.","ista":"Alt J, Erdös L, Krüger TH. 2020. The Dyson equation with linear self-energy: Spectral bands, edges and cusps. Documenta Mathematica. 25, 1421–1539.","mla":"Alt, Johannes, et al. “The Dyson Equation with Linear Self-Energy: Spectral Bands, Edges and Cusps.” Documenta Mathematica, vol. 25, EMS Press, 2020, pp. 1421–539, doi:10.4171/dm/780.","ama":"Alt J, Erdös L, Krüger TH. The Dyson equation with linear self-energy: Spectral bands, edges and cusps. Documenta Mathematica. 2020;25:1421-1539. doi:10.4171/dm/780","apa":"Alt, J., Erdös, L., & Krüger, T. H. (2020). The Dyson equation with linear self-energy: Spectral bands, edges and cusps. Documenta Mathematica. EMS Press. https://doi.org/10.4171/dm/780","ieee":"J. Alt, L. Erdös, and T. H. Krüger, “The Dyson equation with linear self-energy: Spectral bands, edges and cusps,” Documenta Mathematica, vol. 25. EMS Press, pp. 1421–1539, 2020.","short":"J. Alt, L. Erdös, T.H. Krüger, Documenta Mathematica 25 (2020) 1421–1539."},"title":"The Dyson equation with linear self-energy: Spectral bands, edges and cusps","author":[{"full_name":"Alt, Johannes","last_name":"Alt","id":"36D3D8B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes"},{"last_name":"Erdös","full_name":"Erdös, László","orcid":"0000-0001-5366-9603","first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Torben H","id":"3020C786-F248-11E8-B48F-1D18A9856A87","last_name":"Krüger","orcid":"0000-0002-4821-3297","full_name":"Krüger, Torben H"}],"external_id":{"arxiv":["1804.07752"]},"article_processing_charge":"Yes","quality_controlled":"1","publisher":"EMS Press","oa":1,"day":"01","publication":"Documenta Mathematica","has_accepted_license":"1","year":"2020","date_published":"2020-09-01T00:00:00Z","doi":"10.4171/dm/780","date_created":"2023-12-18T10:37:43Z","page":"1421-1539","_id":"14694","status":"public","keyword":["General Mathematics"],"article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["510"],"date_updated":"2023-12-18T10:46:09Z","file_date_updated":"2023-12-18T10:42:32Z","department":[{"_id":"LaEr"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"We study the unique solution m of the Dyson equation \\( -m(z)^{-1} = z\\1 - a + S[m(z)] \\) on a von Neumann algebra A with the constraint Imm≥0. Here, z lies in the complex upper half-plane, a is a self-adjoint element of A and S is a positivity-preserving linear operator on A. We show that m is the Stieltjes transform of a compactly supported A-valued measure on R. Under suitable assumptions, we establish that this measure has a uniformly 1/3-Hölder continuous density with respect to the Lebesgue measure, which is supported on finitely many intervals, called bands. In fact, the density is analytic inside the bands with a square-root growth at the edges and internal cubic root cusps whenever the gap between two bands vanishes. The shape of these singularities is universal and no other singularity may occur. We give a precise asymptotic description of m near the singular points. These asymptotics generalize the analysis at the regular edges given in the companion paper on the Tracy-Widom universality for the edge eigenvalue statistics for correlated random matrices [the first author et al., Ann. Probab. 48, No. 2, 963--1001 (2020; Zbl 1434.60017)] and they play a key role in the proof of the Pearcey universality at the cusp for Wigner-type matrices [G. Cipolloni et al., Pure Appl. Anal. 1, No. 4, 615--707 (2019; Zbl 07142203); the second author et al., Commun. Math. Phys. 378, No. 2, 1203--1278 (2020; Zbl 07236118)]. We also extend the finite dimensional band mass formula from [the first author et al., loc. cit.] to the von Neumann algebra setting by showing that the spectral mass of the bands is topologically rigid under deformations and we conclude that these masses are quantized in some important cases."}],"month":"09","intvolume":" 25","file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"12aacc1d63b852ff9a51c1f6b218d4a6","file_id":"14695","success":1,"creator":"dernst","date_updated":"2023-12-18T10:42:32Z","file_size":1374708,"date_created":"2023-12-18T10:42:32Z","file_name":"2020_DocumentaMathematica_Alt.pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1431-0643"],"issn":["1431-0635"]},"publication_status":"published","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"6183"}]},"volume":25},{"alternative_title":["ISTA Thesis"],"month":"07","abstract":[{"lang":"eng","text":"We present solutions to several problems originating from geometry and discrete mathematics: existence of equipartitions, maps without Tverberg multiple points, and inscribing quadrilaterals. Equivariant obstruction theory is the natural topological approach to these type of questions. However, for the specific problems we consider it had yielded only partial or no results. 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Topological methods in geometry and discrete mathematics. Institute of Science and Technology Austria.","mla":"Avvakumov, Sergey. Topological Methods in Geometry and Discrete Mathematics. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8156.","ama":"Avvakumov S. Topological methods in geometry and discrete mathematics. 2020. doi:10.15479/AT:ISTA:8156","apa":"Avvakumov, S. (2020). Topological methods in geometry and discrete mathematics. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8156","short":"S. Avvakumov, Topological Methods in Geometry and Discrete Mathematics, Institute of Science and Technology Austria, 2020.","ieee":"S. Avvakumov, “Topological methods in geometry and discrete mathematics,” Institute of Science and Technology Austria, 2020."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Lewin M, Lieb EH, Seiringer R. 2020. The local density approximation in density functional theory. Pure and Applied Analysis. 2(1), 35–73.","chicago":"Lewin, Mathieu, Elliott H. Lieb, and Robert Seiringer. “ The Local Density Approximation in Density Functional Theory.” Pure and Applied Analysis. Mathematical Sciences Publishers, 2020. https://doi.org/10.2140/paa.2020.2.35.","ama":"Lewin M, Lieb EH, Seiringer R. The local density approximation in density functional theory. Pure and Applied Analysis. 2020;2(1):35-73. doi:10.2140/paa.2020.2.35","apa":"Lewin, M., Lieb, E. H., & Seiringer, R. (2020). The local density approximation in density functional theory. Pure and Applied Analysis. Mathematical Sciences Publishers. https://doi.org/10.2140/paa.2020.2.35","ieee":"M. Lewin, E. H. Lieb, and R. Seiringer, “ The local density approximation in density functional theory,” Pure and Applied Analysis, vol. 2, no. 1. Mathematical Sciences Publishers, pp. 35–73, 2020.","short":"M. Lewin, E.H. Lieb, R. Seiringer, Pure and Applied Analysis 2 (2020) 35–73.","mla":"Lewin, Mathieu, et al. “ The Local Density Approximation in Density Functional Theory.” Pure and Applied Analysis, vol. 2, no. 1, Mathematical Sciences Publishers, 2020, pp. 35–73, doi:10.2140/paa.2020.2.35."},"title":" The local density approximation in density functional theory","author":[{"first_name":"Mathieu","last_name":"Lewin","full_name":"Lewin, Mathieu"},{"first_name":"Elliott H.","full_name":"Lieb, Elliott H.","last_name":"Lieb"},{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","last_name":"Seiringer","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert"}],"article_processing_charge":"No","external_id":{"arxiv":["1903.04046"]},"day":"01","publication":"Pure and Applied Analysis","year":"2020","date_published":"2020-01-01T00:00:00Z","doi":"10.2140/paa.2020.2.35","date_created":"2024-01-28T23:01:44Z","page":"35-73","publisher":"Mathematical Sciences Publishers","quality_controlled":"1","oa":1,"date_updated":"2024-01-29T09:01:12Z","department":[{"_id":"RoSe"}],"_id":"14891","status":"public","type":"journal_article","article_type":"original","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2578-5893"],"eissn":["2578-5885"]},"publication_status":"published","volume":2,"issue":"1","oa_version":"Preprint","abstract":[{"lang":"eng","text":"We give the first mathematically rigorous justification of the local density approximation in density functional theory. We provide a quantitative estimate on the difference between the grand-canonical Levy–Lieb energy of a given density (the lowest possible energy of all quantum states having this density) and the integral over the uniform electron gas energy of this density. The error involves gradient terms and justifies the use of the local density approximation in the situation where the density is very flat on sufficiently large regions in space."}],"month":"01","intvolume":" 2","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.1903.04046"}]},{"status":"public","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"article_type":"original","type":"journal_article","_id":"8914","department":[{"_id":"LoSw"}],"file_date_updated":"2020-12-03T11:45:26Z","ddc":["570"],"date_updated":"2024-01-31T10:15:34Z","intvolume":" 450","month":"12","scopus_import":"1","oa_version":"Published Version","pmid":1,"abstract":[{"text":"Amyotrophic lateral sclerosis (ALS) leads to a loss of specific motor neuron populations in the spinal cord and cortex. Emerging evidence suggests that interneurons may also be affected, but a detailed characterization of interneuron loss and its potential impacts on motor neuron loss and disease progression is lacking. To examine this issue, the fate of V1 inhibitory neurons during ALS was assessed in the ventral spinal cord using the SODG93A mouse model. The V1 population makes up ∼30% of all ventral inhibitory neurons, ∼50% of direct inhibitory synaptic contacts onto motor neuron cell bodies, and is thought to play a key role in modulating motor output, in part through recurrent and reciprocal inhibitory circuits. We find that approximately half of V1 inhibitory neurons are lost in SODG93A mice at late disease stages, but that this loss is delayed relative to the loss of motor neurons and V2a excitatory neurons. We further identify V1 subpopulations based on transcription factor expression that are differentially susceptible to degeneration in SODG93A mice. At an early disease stage, we show that V1 synaptic contacts with motor neuron cell bodies increase, suggesting an upregulation of inhibition before V1 neurons are lost in substantial numbers. These data support a model in which progressive changes in V1 synaptic contacts early in disease, and in select V1 subpopulations at later stages, represent a compensatory upregulation and then deleterious breakdown of specific interneuron circuits within the spinal cord.","lang":"eng"}],"volume":450,"language":[{"iso":"eng"}],"file":[{"success":1,"checksum":"da7413c819e079720669c82451b49294","file_id":"8915","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2020_Neuroscience_Salamatina.pdf","date_created":"2020-12-03T11:45:26Z","creator":"dernst","file_size":4071247,"date_updated":"2020-12-03T11:45:26Z"}],"publication_status":"published","publication_identifier":{"issn":["0306-4522"]},"title":"Differential loss of spinal interneurons in a mouse model of ALS","external_id":{"isi":["000595588700008"],"pmid":["32858144"]},"article_processing_charge":"Yes (via OA deal)","author":[{"first_name":"Alina","full_name":"Salamatina, Alina","last_name":"Salamatina"},{"first_name":"Jerry H","last_name":"Yang","full_name":"Yang, Jerry H"},{"first_name":"Susan","last_name":"Brenner-Morton","full_name":"Brenner-Morton, Susan"},{"first_name":"Jay B ","full_name":"Bikoff, Jay B ","last_name":"Bikoff"},{"first_name":"Linjing","last_name":"Fang","full_name":"Fang, Linjing"},{"first_name":"Christopher R","full_name":"Kintner, Christopher R","last_name":"Kintner"},{"last_name":"Jessell","full_name":"Jessell, Thomas M","first_name":"Thomas M"},{"full_name":"Sweeney, Lora Beatrice Jaeger","orcid":"0000-0001-9242-5601","last_name":"Sweeney","first_name":"Lora Beatrice Jaeger","id":"56BE8254-C4F0-11E9-8E45-0B23E6697425"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Salamatina, Alina, et al. “Differential Loss of Spinal Interneurons in a Mouse Model of ALS.” Neuroscience, vol. 450, Elsevier, 2020, pp. 81–95, doi:10.1016/j.neuroscience.2020.08.011.","ieee":"A. Salamatina et al., “Differential loss of spinal interneurons in a mouse model of ALS,” Neuroscience, vol. 450. Elsevier, pp. 81–95, 2020.","short":"A. Salamatina, J.H. Yang, S. Brenner-Morton, J.B. Bikoff, L. Fang, C.R. Kintner, T.M. Jessell, L.B. Sweeney, Neuroscience 450 (2020) 81–95.","ama":"Salamatina A, Yang JH, Brenner-Morton S, et al. Differential loss of spinal interneurons in a mouse model of ALS. Neuroscience. 2020;450:81-95. doi:10.1016/j.neuroscience.2020.08.011","apa":"Salamatina, A., Yang, J. H., Brenner-Morton, S., Bikoff, J. B., Fang, L., Kintner, C. R., … Sweeney, L. B. (2020). Differential loss of spinal interneurons in a mouse model of ALS. Neuroscience. Elsevier. https://doi.org/10.1016/j.neuroscience.2020.08.011","chicago":"Salamatina, Alina, Jerry H Yang, Susan Brenner-Morton, Jay B Bikoff, Linjing Fang, Christopher R Kintner, Thomas M Jessell, and Lora B. Sweeney. “Differential Loss of Spinal Interneurons in a Mouse Model of ALS.” Neuroscience. Elsevier, 2020. https://doi.org/10.1016/j.neuroscience.2020.08.011.","ista":"Salamatina A, Yang JH, Brenner-Morton S, Bikoff JB, Fang L, Kintner CR, Jessell TM, Sweeney LB. 2020. Differential loss of spinal interneurons in a mouse model of ALS. Neuroscience. 450, 81–95."},"oa":1,"quality_controlled":"1","publisher":"Elsevier","acknowledgement":"This work was made possible by the generous support of Project ALS. Imaging and related analyses were facilitated by The Waitt Advanced Biophotonics Center Core at the Salk Institute, supported by grants from NIH-NCI CCSG (P30 014195) and NINDS Neuroscience Center (NS072031). The authors would like to additionally thank Drs. Jane Dodd, Robert Brownstone, and Laskaro Zagoraiou for helpful comments on the manuscript. This manuscript is dedicated to Tom Jessell, an inspirational scientist, friend and mentor.","date_created":"2020-12-03T11:47:31Z","doi":"10.1016/j.neuroscience.2020.08.011","date_published":"2020-12-01T00:00:00Z","page":"81-95","publication":"Neuroscience","day":"01","year":"2020","has_accepted_license":"1","isi":1},{"_id":"8834","status":"public","type":"research_data","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"ddc":["530"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-02-21T12:41:26Z","citation":{"short":"G. Katsaros, (2020).","ieee":"G. Katsaros, “Enhancement of proximity induced superconductivity in planar Germanium.” Institute of Science and Technology Austria, 2020.","apa":"Katsaros, G. (2020). Enhancement of proximity induced superconductivity in planar Germanium. 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Estimating Inbreeding and Its Effects in a Long-Term Study of Snapdragons (Antirrhinum Majus). Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8254.","ama":"Arathoon LS. Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus). 2020. doi:10.15479/AT:ISTA:8254","apa":"Arathoon, L. S. (2020). Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus). Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8254","ieee":"L. S. Arathoon, “Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus).” Institute of Science and Technology Austria, 2020.","short":"L.S. Arathoon, (2020).","chicago":"Arathoon, Louise S. “Estimating Inbreeding and Its Effects in a Long-Term Study of Snapdragons (Antirrhinum Majus).” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8254.","ista":"Arathoon LS. 2020. Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus), Institute of Science and Technology Austria, 10.15479/AT:ISTA:8254."},"month":"08","publisher":"Institute of Science and Technology Austria","oa":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Here are the research data underlying the publication \"Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus)\". Further information are summed up in the README document.\r\nThe files for this record have been updated and are now found in the linked DOI https://doi.org/10.15479/AT:ISTA:9192."}],"doi":"10.15479/AT:ISTA:8254","related_material":{"record":[{"relation":"later_version","id":"11321","status":"public"},{"status":"public","id":"9192","relation":"later_version"}]},"date_published":"2020-08-18T00:00:00Z","date_created":"2020-08-12T12:49:23Z","contributor":[{"last_name":"Arathoon","first_name":"Louise S","contributor_type":"data_collector","id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87"},{"id":"455235B8-F248-11E8-B48F-1D18A9856A87","first_name":"Parvathy","contributor_type":"project_member","last_name":"Surendranadh"},{"orcid":"0000-0002-8548-5240","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_member","first_name":"Nicholas H"},{"id":"419049E2-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_member","first_name":"David","orcid":"0000-0002-4014-8478","last_name":"Field"},{"first_name":"Melinda","contributor_type":"project_member","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","last_name":"Pickup","orcid":"0000-0001-6118-0541"},{"contributor_type":"project_member","first_name":"Carina","id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87","last_name":"Baskett"}],"day":"18","file":[{"creator":"dernst","file_size":5778420,"date_updated":"2020-08-18T08:03:23Z","file_name":"Data_Rcode_MathematicaNB.zip","date_created":"2020-08-18T08:03:23Z","relation":"main_file","access_level":"open_access","content_type":"application/x-zip-compressed","success":1,"file_id":"8280","checksum":"4f1382ed4384751b6013398c11557bf6"}],"has_accepted_license":"1","year":"2020"},{"year":"2020","isi":1,"has_accepted_license":"1","publication":"Advanced Materials","day":"23","date_created":"2020-02-28T09:47:00Z","date_published":"2020-04-23T00:00:00Z","doi":"10.1002/adma.201906523","acknowledgement":"This work was supported by the National Key R&D Program of China (Grant Nos. 2016YFA0301701 and 2016YFA0300600), the NSFC (Grant Nos. 11574356, 11434010, and 11404252), the Strategic Priority Research Program of CAS (Grant No. XDB30000000), the ERC Starting Grant No. 335497, the FWF P32235 project, and the European Union's Horizon 2020 research and innovation program under Grant Agreement #862046. This research was supported by the Scientific Service Units of IST Austria through resources provided by the MIBA Machine Shop and the nanofabrication facility. F.L. thanks support from DOE (Grant No. DE‐FG02‐04ER46148). H.H. thanks the Startup Funding from Xi'an Jiaotong University.","oa":1,"publisher":"Wiley","quality_controlled":"1","citation":{"chicago":"Gao, Fei, Jian-Huan Wang, Hannes Watzinger, Hao Hu, Marko J. Rančić, Jie-Yin Zhang, Ting Wang, et al. “Site-Controlled Uniform Ge/Si Hut Wires with Electrically Tunable Spin-Orbit Coupling.” Advanced Materials. Wiley, 2020. https://doi.org/10.1002/adma.201906523.","ista":"Gao F, Wang J-H, Watzinger H, Hu H, Rančić MJ, Zhang J-Y, Wang T, Yao Y, Wang G-L, Kukucka J, Vukušić L, Kloeffel C, Loss D, Liu F, Katsaros G, Zhang J-J. 2020. Site-controlled uniform Ge/Si hut wires with electrically tunable spin-orbit coupling. Advanced Materials. 32(16), 1906523.","mla":"Gao, Fei, et al. “Site-Controlled Uniform Ge/Si Hut Wires with Electrically Tunable Spin-Orbit Coupling.” Advanced Materials, vol. 32, no. 16, 1906523, Wiley, 2020, doi:10.1002/adma.201906523.","apa":"Gao, F., Wang, J.-H., Watzinger, H., Hu, H., Rančić, M. J., Zhang, J.-Y., … Zhang, J.-J. (2020). Site-controlled uniform Ge/Si hut wires with electrically tunable spin-orbit coupling. Advanced Materials. Wiley. https://doi.org/10.1002/adma.201906523","ama":"Gao F, Wang J-H, Watzinger H, et al. Site-controlled uniform Ge/Si hut wires with electrically tunable spin-orbit coupling. Advanced Materials. 2020;32(16). doi:10.1002/adma.201906523","short":"F. Gao, J.-H. Wang, H. Watzinger, H. Hu, M.J. Rančić, J.-Y. Zhang, T. Wang, Y. Yao, G.-L. Wang, J. Kukucka, L. Vukušić, C. Kloeffel, D. Loss, F. Liu, G. Katsaros, J.-J. Zhang, Advanced Materials 32 (2020).","ieee":"F. Gao et al., “Site-controlled uniform Ge/Si hut wires with electrically tunable spin-orbit coupling,” Advanced Materials, vol. 32, no. 16. Wiley, 2020."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000516660900001"]},"article_processing_charge":"Yes (via OA deal)","author":[{"first_name":"Fei","last_name":"Gao","full_name":"Gao, Fei"},{"first_name":"Jian-Huan","full_name":"Wang, Jian-Huan","last_name":"Wang"},{"id":"35DF8E50-F248-11E8-B48F-1D18A9856A87","first_name":"Hannes","last_name":"Watzinger","full_name":"Watzinger, Hannes"},{"last_name":"Hu","full_name":"Hu, Hao","first_name":"Hao"},{"last_name":"Rančić","full_name":"Rančić, Marko J.","first_name":"Marko J."},{"first_name":"Jie-Yin","full_name":"Zhang, Jie-Yin","last_name":"Zhang"},{"first_name":"Ting","last_name":"Wang","full_name":"Wang, Ting"},{"full_name":"Yao, Yuan","last_name":"Yao","first_name":"Yuan"},{"first_name":"Gui-Lei","last_name":"Wang","full_name":"Wang, Gui-Lei"},{"last_name":"Kukucka","full_name":"Kukucka, Josip","first_name":"Josip","id":"3F5D8856-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-2424-8636","full_name":"Vukušić, Lada","last_name":"Vukušić","first_name":"Lada","id":"31E9F056-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Christoph","full_name":"Kloeffel, Christoph","last_name":"Kloeffel"},{"first_name":"Daniel","last_name":"Loss","full_name":"Loss, Daniel"},{"last_name":"Liu","full_name":"Liu, Feng","first_name":"Feng"},{"id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios","last_name":"Katsaros","full_name":"Katsaros, Georgios","orcid":"0000-0001-8342-202X"},{"last_name":"Zhang","full_name":"Zhang, Jian-Jun","first_name":"Jian-Jun"}],"title":"Site-controlled uniform Ge/Si hut wires with electrically tunable spin-orbit coupling","article_number":"1906523","project":[{"call_identifier":"FP7","_id":"25517E86-B435-11E9-9278-68D0E5697425","name":"Towards Spin qubits and Majorana fermions in Germanium selfassembled hut-wires","grant_number":"335497"},{"name":"Towards scalable hut wire quantum devices","grant_number":"P32235","call_identifier":"FWF","_id":"237B3DA4-32DE-11EA-91FC-C7463DDC885E"},{"_id":"237E5020-32DE-11EA-91FC-C7463DDC885E","call_identifier":"H2020","grant_number":"862046","name":"TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS"}],"publication_status":"published","publication_identifier":{"issn":["0935-9648"]},"language":[{"iso":"eng"}],"file":[{"date_created":"2020-11-20T10:11:35Z","file_name":"2020_AdvancedMaterials_Gao.pdf","date_updated":"2020-11-20T10:11:35Z","file_size":5242880,"creator":"dernst","checksum":"c622737dc295972065782558337124a2","file_id":"8782","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"ec_funded":1,"volume":32,"issue":"16","related_material":{"record":[{"relation":"dissertation_contains","id":"7996","status":"public"},{"status":"public","id":"9222","relation":"research_data"}]},"acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"abstract":[{"text":"Semiconductor nanowires have been playing a crucial role in the development of nanoscale devices for the realization of spin qubits, Majorana fermions, single photon emitters, nanoprocessors, etc. The monolithic growth of site‐controlled nanowires is a prerequisite toward the next generation of devices that will require addressability and scalability. Here, combining top‐down nanofabrication and bottom‐up self‐assembly, the growth of Ge wires on prepatterned Si (001) substrates with controllable position, distance, length, and structure is reported. This is achieved by a novel growth process that uses a SiGe strain‐relaxation template and can be potentially generalized to other material combinations. Transport measurements show an electrically tunable spin–orbit coupling, with a spin–orbit length similar to that of III–V materials. Also, charge sensing between quantum dots in closely spaced wires is observed, which underlines their potential for the realization of advanced quantum devices. The reported results open a path toward scalable qubit devices using nanowires on silicon.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 32","month":"04","date_updated":"2024-02-21T12:42:12Z","ddc":["530"],"department":[{"_id":"GeKa"}],"file_date_updated":"2020-11-20T10:11:35Z","_id":"7541","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public"},{"_id":"8930","status":"public","keyword":["Escherichia coli","antibiotic combinations","translation","growth laws","drug interactions","bacterial physiology","translation inhibitors"],"type":"research_data","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Kavcic, Bor. Analysis Scripts and Research Data for the Paper “Minimal Biophysical Model of Combined Antibiotic Action.” Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8930.","ieee":"B. Kavcic, “Analysis scripts and research data for the paper ‘Minimal biophysical model of combined antibiotic action.’” Institute of Science and Technology Austria, 2020.","short":"B. Kavcic, (2020).","ama":"Kavcic B. Analysis scripts and research data for the paper “Minimal biophysical model of combined antibiotic action.” 2020. doi:10.15479/AT:ISTA:8930","apa":"Kavcic, B. (2020). Analysis scripts and research data for the paper “Minimal biophysical model of combined antibiotic action.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8930","chicago":"Kavcic, Bor. “Analysis Scripts and Research Data for the Paper ‘Minimal Biophysical Model of Combined Antibiotic Action.’” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8930.","ista":"Kavcic B. 2020. Analysis scripts and research data for the paper ‘Minimal biophysical model of combined antibiotic action’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:8930."},"date_updated":"2024-02-21T12:41:42Z","department":[{"_id":"GaTk"}],"title":"Analysis scripts and research data for the paper \"Minimal biophysical model of combined antibiotic action\"","file_date_updated":"2020-12-09T15:00:19Z","author":[{"first_name":"Bor","id":"350F91D2-F248-11E8-B48F-1D18A9856A87","last_name":"Kavcic","full_name":"Kavcic, Bor","orcid":"0000-0001-6041-254X"}],"article_processing_charge":"No","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Phenomenological relations such as Ohm’s or Fourier’s law have a venerable history in physics but are still scarce in biology. This situation restrains predictive theory. Here, we build on bacterial “growth laws,” which capture physiological feedback between translation and cell growth, to construct a minimal biophysical model for the combined action of ribosome-targeting antibiotics. Our model predicts drug interactions like antagonism or synergy solely from responses to individual drugs. We provide analytical results for limiting cases, which agree well with numerical results. We systematically refine the model by including direct physical interactions of different antibiotics on the ribosome. In a limiting case, our model provides a mechanistic underpinning for recent predictions of higher-order interactions that were derived using entropy maximization. We further refine the model to include the effects of antibiotics that mimic starvation and the presence of resistance genes. We describe the impact of a starvation-mimicking antibiotic on drug interactions analytically and verify it experimentally. Our extended model suggests a change in the type of drug interaction that depends on the strength of resistance, which challenges established rescaling paradigms. We experimentally show that the presence of unregulated resistance genes can lead to altered drug interaction, which agrees with the prediction of the model. While minimal, the model is readily adaptable and opens the door to predicting interactions of second and higher-order in a broad range of biological systems."}],"month":"12","publisher":"Institute of Science and Technology Austria","oa":1,"day":"10","file":[{"creator":"bkavcic","file_size":315494370,"date_updated":"2020-12-09T15:00:19Z","file_name":"PLoSCompBiol2020_datarep.zip","date_created":"2020-12-09T15:00:19Z","relation":"main_file","access_level":"open_access","content_type":"application/zip","success":1,"checksum":"60a818edeffaa7da1ebf5f8fbea9ba18","file_id":"8932"}],"has_accepted_license":"1","year":"2020","doi":"10.15479/AT:ISTA:8930","related_material":{"record":[{"relation":"used_in_publication","id":"8997","status":"public"}]},"date_published":"2020-12-10T00:00:00Z","date_created":"2020-12-09T15:04:02Z","contributor":[{"orcid":"0000-0002-6699-1455","last_name":"Tkačik","contributor_type":"supervisor","first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"},{"id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","contributor_type":"supervisor","first_name":"Tobias","last_name":"Bollenbach"}]},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"date_updated":"2024-02-21T12:41:57Z","citation":{"ista":"Nagy-Staron AA. 2020. Sequences of gene regulatory network permutations for the article ‘Local genetic context shapes the function of a gene regulatory network’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:8951.","chicago":"Nagy-Staron, Anna A. “Sequences of Gene Regulatory Network Permutations for the Article ‘Local Genetic Context Shapes the Function of a Gene Regulatory Network.’” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8951.","ieee":"A. A. Nagy-Staron, “Sequences of gene regulatory network permutations for the article ‘Local genetic context shapes the function of a gene regulatory network.’” Institute of Science and Technology Austria, 2020.","short":"A.A. Nagy-Staron, (2020).","ama":"Nagy-Staron AA. Sequences of gene regulatory network permutations for the article “Local genetic context shapes the function of a gene regulatory network.” 2020. doi:10.15479/AT:ISTA:8951","apa":"Nagy-Staron, A. A. (2020). Sequences of gene regulatory network permutations for the article “Local genetic context shapes the function of a gene regulatory network.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8951","mla":"Nagy-Staron, Anna A. Sequences of Gene Regulatory Network Permutations for the Article “Local Genetic Context Shapes the Function of a Gene Regulatory Network.” Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8951."},"title":"Sequences of gene regulatory network permutations for the article \"Local genetic context shapes the function of a gene regulatory network\"","file_date_updated":"2020-12-20T22:01:44Z","department":[{"_id":"CaGu"}],"article_processing_charge":"No","author":[{"id":"3ABC5BA6-F248-11E8-B48F-1D18A9856A87","first_name":"Anna A","last_name":"Nagy-Staron","orcid":"0000-0002-1391-8377","full_name":"Nagy-Staron, Anna A"}],"_id":"8951","keyword":["Gene regulatory networks","Gene expression","Escherichia coli","Synthetic Biology"],"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"research_data","file":[{"relation":"main_file","access_level":"open_access","content_type":"text/plain","success":1,"file_id":"8952","checksum":"f57862aeee1690c7effd2b1117d40ed1","creator":"bkavcic","file_size":523,"date_updated":"2020-12-20T09:52:52Z","file_name":"readme.txt","date_created":"2020-12-20T09:52:52Z"},{"checksum":"f2c6d5232ec6d551b6993991e8689e9f","file_id":"8954","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/octet-stream","date_created":"2020-12-20T22:01:44Z","file_name":"GRNs Research depository.gb","creator":"bkavcic","date_updated":"2020-12-20T22:01:44Z","file_size":379228}],"day":"21","year":"2020","has_accepted_license":"1","date_created":"2020-12-20T10:00:26Z","contributor":[{"id":"3ABC5BA6-F248-11E8-B48F-1D18A9856A87","first_name":"Anna A","contributor_type":"project_member","last_name":"Nagy-Staron"},{"first_name":"Kathrin","id":"3AEC8556-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_member","last_name":"Tomasek"},{"contributor_type":"project_member","first_name":"Caroline","last_name":"Caruso Carter"},{"last_name":"Sonnleitner","contributor_type":"project_member","first_name":"Elisabeth"},{"first_name":"Bor","id":"350F91D2-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_member","orcid":"0000-0001-6041-254X","last_name":"Kavcic"},{"contributor_type":"project_member","first_name":"Tiago","last_name":"Paixão"},{"contributor_type":"project_manager","first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","last_name":"Guet"}],"date_published":"2020-12-21T00:00:00Z","doi":"10.15479/AT:ISTA:8951","related_material":{"record":[{"status":"public","id":"9283","relation":"used_in_publication"}]},"oa_version":"Published Version","abstract":[{"text":"Gene expression levels are influenced by multiple coexisting molecular mechanisms. Some of these interactions, such as those of transcription factors and promoters have been studied extensively. However, predicting phenotypes of gene regulatory networks remains a major challenge. Here, we use a well-defined synthetic gene regulatory network to study how network phenotypes depend on local genetic context, i.e. the genetic neighborhood of a transcription factor and its relative position. We show that one gene regulatory network with fixed topology can display not only quantitatively but also qualitatively different phenotypes, depending solely on the local genetic context of its components. Our results demonstrate that changes in local genetic context can place a single transcriptional unit within two separate regulons without the need for complex regulatory sequences. We propose that relative order of individual transcriptional units, with its potential for combinatorial complexity, plays an important role in shaping phenotypes of gene regulatory networks.","lang":"eng"}],"month":"12","oa":1,"publisher":"Institute of Science and Technology Austria"},{"abstract":[{"text":"Organisms cope with change by employing transcriptional regulators. However, when faced with rare environments, the evolution of transcriptional regulators and their promoters may be too slow. We ask whether the intrinsic instability of gene duplication and amplification provides a generic alternative to canonical gene regulation. By real-time monitoring of gene copy number mutations in E. coli, we show that gene duplications and amplifications enable adaptation to fluctuating environments by rapidly generating copy number, and hence expression level, polymorphism. This ‘amplification-mediated gene expression tuning’ occurs on timescales similar to canonical gene regulation and can deal with rapid environmental changes. Mathematical modeling shows that amplifications also tune gene expression in stochastic environments where transcription factor-based schemes are hard to evolve or maintain. The fleeting nature of gene amplifications gives rise to a generic population-level mechanism that relies on genetic heterogeneity to rapidly tune expression of any gene, without leaving any genomic signature.","lang":"eng"}],"oa_version":"Published Version","publisher":"Institute of Science and Technology Austria","oa":1,"month":"01","has_accepted_license":"1","year":"2020","day":"28","file":[{"file_id":"7384","checksum":"9d292cf5207b3829225f44c044cdb3fd","content_type":"application/zip","access_level":"open_access","relation":"main_file","date_created":"2020-01-28T10:39:40Z","file_name":"Scripts.zip","date_updated":"2020-07-14T12:47:57Z","file_size":73363365,"creator":"rgrah"},{"date_created":"2020-01-28T10:39:30Z","file_name":"READ_ME_MAIN.txt","creator":"rgrah","date_updated":"2020-07-14T12:47:57Z","file_size":962,"checksum":"4076ceab32ef588cc233802bab24c1ab","file_id":"7385","access_level":"open_access","relation":"main_file","content_type":"text/plain"}],"doi":"10.15479/AT:ISTA:7383","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"7652"}]},"date_published":"2020-01-28T00:00:00Z","date_created":"2020-01-28T10:41:49Z","contributor":[{"last_name":"Guet","orcid":"0000-0001-6220-2052","contributor_type":"project_leader","first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"}],"_id":"7383","type":"research_data","status":"public","keyword":["Matlab scripts","analysis of microfluidics","mathematical model"],"date_updated":"2024-02-21T12:42:31Z","citation":{"ista":"Grah R. 2020. Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation, Institute of Science and Technology Austria, 10.15479/AT:ISTA:7383.","chicago":"Grah, Rok. “Matlab Scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression Regulation.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7383.","short":"R. Grah, (2020).","ieee":"R. Grah, “Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation.” Institute of Science and Technology Austria, 2020.","apa":"Grah, R. (2020). Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7383","ama":"Grah R. Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation. 2020. doi:10.15479/AT:ISTA:7383","mla":"Grah, Rok. Matlab Scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression Regulation. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7383."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Grah, Rok","orcid":"0000-0003-2539-3560","last_name":"Grah","first_name":"Rok","id":"483E70DE-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","title":"Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation","file_date_updated":"2020-07-14T12:47:57Z","department":[{"_id":"CaGu"},{"_id":"GaTk"}]},{"citation":{"chicago":"Katsaros, Georgios. “Transport Data for: Site‐controlled Uniform Ge/Si Hut Wires with Electrically Tunable Spin–Orbit Coupling.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:9222.","ista":"Katsaros G. 2020. Transport data for: Site‐controlled uniform Ge/Si Hut wires with electrically tunable spin–orbit coupling, Institute of Science and Technology Austria, 10.15479/AT:ISTA:9222.","mla":"Katsaros, Georgios. Transport Data for: Site‐controlled Uniform Ge/Si Hut Wires with Electrically Tunable Spin–Orbit Coupling. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:9222.","ieee":"G. Katsaros, “Transport data for: Site‐controlled uniform Ge/Si Hut wires with electrically tunable spin–orbit coupling.” Institute of Science and Technology Austria, 2020.","short":"G. Katsaros, (2020).","apa":"Katsaros, G. (2020). Transport data for: Site‐controlled uniform Ge/Si Hut wires with electrically tunable spin–orbit coupling. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:9222","ama":"Katsaros G. Transport data for: Site‐controlled uniform Ge/Si Hut wires with electrically tunable spin–orbit coupling. 2020. doi:10.15479/AT:ISTA:9222"},"date_updated":"2024-02-21T12:42:13Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["530"],"author":[{"id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios","last_name":"Katsaros","full_name":"Katsaros, Georgios","orcid":"0000-0001-8342-202X"}],"article_processing_charge":"No","file_date_updated":"2021-03-10T07:31:50Z","department":[{"_id":"GeKa"}],"title":"Transport data for: Site‐controlled uniform Ge/Si Hut wires with electrically tunable spin–orbit coupling","_id":"9222","type":"research_data","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"status":"public","has_accepted_license":"1","year":"2020","file":[{"content_type":"application/x-zip-compressed","relation":"main_file","access_level":"open_access","checksum":"41b66e195ed3dbd73077feee77b05652","file_id":"9223","file_size":13317557,"date_updated":"2021-03-05T17:50:45Z","creator":"gkatsaro","file_name":"DOI_SiteControlledHWs.zip","date_created":"2021-03-05T17:50:45Z"},{"file_name":"Readme.txt","date_created":"2021-03-10T07:31:50Z","file_size":3515,"date_updated":"2021-03-10T07:31:50Z","creator":"dernst","success":1,"file_id":"9233","checksum":"a1dc5f710ba4b3bb7f248195ba754ab2","content_type":"text/plain","relation":"main_file","access_level":"open_access"}],"day":"16","doi":"10.15479/AT:ISTA:9222","date_published":"2020-03-16T00:00:00Z","related_material":{"record":[{"relation":"used_in_publication","id":"7541","status":"public"}]},"date_created":"2021-03-05T18:00:47Z","contributor":[{"last_name":"Katsaros","contributor_type":"research_group","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios"}],"oa_version":"Published Version","publisher":"Institute of Science and Technology Austria","oa":1,"month":"03"},{"project":[{"grant_number":"715767","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","call_identifier":"H2020","_id":"24F9549A-B435-11E9-9278-68D0E5697425"}],"citation":{"mla":"Guseinov, Ruslan. Computational Design of Curved Thin Shells: From Glass Façades to Programmable Matter. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8366.","ama":"Guseinov R. Computational design of curved thin shells: From glass façades to programmable matter. 2020. doi:10.15479/AT:ISTA:8366","apa":"Guseinov, R. (2020). Computational design of curved thin shells: From glass façades to programmable matter. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8366","short":"R. Guseinov, Computational Design of Curved Thin Shells: From Glass Façades to Programmable Matter, Institute of Science and Technology Austria, 2020.","ieee":"R. Guseinov, “Computational design of curved thin shells: From glass façades to programmable matter,” Institute of Science and Technology Austria, 2020.","chicago":"Guseinov, Ruslan. “Computational Design of Curved Thin Shells: From Glass Façades to Programmable Matter.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8366.","ista":"Guseinov R. 2020. Computational design of curved thin shells: From glass façades to programmable matter. Institute of Science and Technology Austria."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","author":[{"id":"3AB45EE2-F248-11E8-B48F-1D18A9856A87","first_name":"Ruslan","orcid":"0000-0001-9819-5077","full_name":"Guseinov, Ruslan","last_name":"Guseinov"}],"title":"Computational design of curved thin shells: From glass façades to programmable matter","acknowledgement":"During the work on this thesis, I received substantial support from IST Austria’s scientific service units. A big thank you to Todor Asenov and other Miba Machine Shop team members for their help with fabrication of experimental prototypes. In addition, I would like to thank Scientific Computing team for the support with high performance computing.\r\nFinancial support was provided by the European Research Council (ERC) under grant agreement No 715767 - MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling, which I gratefully acknowledge.","oa":1,"publisher":"Institute of Science and Technology Austria","year":"2020","has_accepted_license":"1","day":"21","page":"118","date_created":"2020-09-10T16:19:55Z","date_published":"2020-09-21T00:00:00Z","doi":"10.15479/AT:ISTA:8366","_id":"8366","type":"dissertation","keyword":["computer-aided design","shape modeling","self-morphing","mechanical engineering"],"status":"public","date_updated":"2024-02-21T12:44:29Z","supervisor":[{"last_name":"Bickel","orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd"}],"ddc":["000"],"department":[{"_id":"BeBi"}],"file_date_updated":"2020-09-16T15:11:01Z","abstract":[{"lang":"eng","text":"Fabrication of curved shells plays an important role in modern design, industry, and science. Among their remarkable properties are, for example, aesthetics of organic shapes, ability to evenly distribute loads, or efficient flow separation. They find applications across vast length scales ranging from sky-scraper architecture to microscopic devices. But, at\r\nthe same time, the design of curved shells and their manufacturing process pose a variety of challenges. In this thesis, they are addressed from several perspectives. In particular, this thesis presents approaches based on the transformation of initially flat sheets into the target curved surfaces. This involves problems of interactive design of shells with nontrivial mechanical constraints, inverse design of complex structural materials, and data-driven modeling of delicate and time-dependent physical properties. At the same time, two newly-developed self-morphing mechanisms targeting flat-to-curved transformation are presented.\r\nIn architecture, doubly curved surfaces can be realized as cold bent glass panelizations. Originally flat glass panels are bent into frames and remain stressed. This is a cost-efficient fabrication approach compared to hot bending, when glass panels are shaped plastically. However such constructions are prone to breaking during bending, and it is highly\r\nnontrivial to navigate the design space, keeping the panels fabricable and aesthetically pleasing at the same time. We introduce an interactive design system for cold bent glass façades, while previously even offline optimization for such scenarios has not been sufficiently developed. Our method is based on a deep learning approach providing quick\r\nand high precision estimation of glass panel shape and stress while handling the shape\r\nmultimodality.\r\nFabrication of smaller objects of scales below 1 m, can also greatly benefit from shaping originally flat sheets. In this respect, we designed new self-morphing shell mechanisms transforming from an initial flat state to a doubly curved state with high precision and detail. Our so-called CurveUps demonstrate the encodement of the geometric information\r\ninto the shell. Furthermore, we explored the frontiers of programmable materials and showed how temporal information can additionally be encoded into a flat shell. This allows prescribing deformation sequences for doubly curved surfaces and, thus, facilitates self-collision avoidance enabling complex shapes and functionalities otherwise impossible.\r\nBoth of these methods include inverse design tools keeping the user in the design loop."}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"ScienComp"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"09","degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-010-7"]},"language":[{"iso":"eng"}],"file":[{"checksum":"f8da89553da36037296b0a80f14ebf50","file_id":"8367","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2020-09-10T16:11:49Z","file_name":"thesis_rguseinov.pdf","date_updated":"2020-09-10T16:11:49Z","file_size":70950442,"creator":"rguseino"},{"date_updated":"2020-09-16T15:11:01Z","file_size":76207597,"creator":"rguseino","date_created":"2020-09-11T09:39:48Z","file_name":"thesis_source.zip","content_type":"application/x-zip-compressed","access_level":"closed","relation":"source_file","checksum":"e8fd944c960c20e0e27e6548af69121d","file_id":"8374"}],"ec_funded":1,"related_material":{"record":[{"status":"deleted","id":"7151","relation":"research_data"},{"relation":"part_of_dissertation","status":"public","id":"7262"},{"id":"8562","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"1001"},{"status":"public","id":"8375","relation":"research_data"}]}},{"acknowledgement":"We thank IST Austria’s Scientific Computing team for their support, Corinna Datsiou and Sophie Pennetier for their expert input on the practical applications of cold bent glass, and Zaha Hadid Architects and Waagner Biro for providing the architectural datasets. Photo of Fondation Louis Vuitton by Francisco Anzola / CC BY 2.0 / cropped.\r\nPhoto of Opus by Danica O. Kus. This project has received funding from the European Union’s\r\nHorizon 2020 research and innovation program under grant agreement No 675789 - Algebraic Representations in Computer-Aided Design for complEx Shapes (ARCADES), from the European Research Council (ERC) under grant agreement No 715767 - MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling, and SFB-Transregio “Discretization in Geometry and Dynamics” through grant I 2978 of the Austrian Science Fund (FWF). F. Rist and K. Gavriil have been partially supported by KAUST baseline funding.","oa":1,"publisher":"Association for Computing Machinery","quality_controlled":"1","year":"2020","isi":1,"has_accepted_license":"1","publication":"ACM Transactions on Graphics","day":"26","date_created":"2020-09-23T11:30:02Z","doi":"10.1145/3414685.3417843","date_published":"2020-11-26T00:00:00Z","article_number":"208","project":[{"grant_number":"715767","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","call_identifier":"H2020","_id":"24F9549A-B435-11E9-9278-68D0E5697425"}],"citation":{"chicago":"Gavriil, Konstantinos, Ruslan Guseinov, Jesus Perez Rodriguez, Davide Pellis, Paul M Henderson, Florian Rist, Helmut Pottmann, and Bernd Bickel. “Computational Design of Cold Bent Glass Façades.” ACM Transactions on Graphics. Association for Computing Machinery, 2020. https://doi.org/10.1145/3414685.3417843.","ista":"Gavriil K, Guseinov R, Perez Rodriguez J, Pellis D, Henderson PM, Rist F, Pottmann H, Bickel B. 2020. Computational design of cold bent glass façades. ACM Transactions on Graphics. 39(6), 208.","mla":"Gavriil, Konstantinos, et al. “Computational Design of Cold Bent Glass Façades.” ACM Transactions on Graphics, vol. 39, no. 6, 208, Association for Computing Machinery, 2020, doi:10.1145/3414685.3417843.","short":"K. Gavriil, R. Guseinov, J. Perez Rodriguez, D. Pellis, P.M. Henderson, F. Rist, H. Pottmann, B. Bickel, ACM Transactions on Graphics 39 (2020).","ieee":"K. Gavriil et al., “Computational design of cold bent glass façades,” ACM Transactions on Graphics, vol. 39, no. 6. Association for Computing Machinery, 2020.","apa":"Gavriil, K., Guseinov, R., Perez Rodriguez, J., Pellis, D., Henderson, P. M., Rist, F., … Bickel, B. (2020). Computational design of cold bent glass façades. ACM Transactions on Graphics. Association for Computing Machinery. https://doi.org/10.1145/3414685.3417843","ama":"Gavriil K, Guseinov R, Perez Rodriguez J, et al. Computational design of cold bent glass façades. ACM Transactions on Graphics. 2020;39(6). doi:10.1145/3414685.3417843"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"arxiv":["2009.03667"],"isi":["000595589100048"]},"article_processing_charge":"No","author":[{"first_name":"Konstantinos","last_name":"Gavriil","full_name":"Gavriil, Konstantinos"},{"id":"3AB45EE2-F248-11E8-B48F-1D18A9856A87","first_name":"Ruslan","full_name":"Guseinov, Ruslan","orcid":"0000-0001-9819-5077","last_name":"Guseinov"},{"full_name":"Perez Rodriguez, Jesus","last_name":"Perez Rodriguez","id":"2DC83906-F248-11E8-B48F-1D18A9856A87","first_name":"Jesus"},{"last_name":"Pellis","full_name":"Pellis, Davide","first_name":"Davide"},{"first_name":"Paul M","id":"13C09E74-18D9-11E9-8878-32CFE5697425","last_name":"Henderson","full_name":"Henderson, Paul M","orcid":"0000-0002-5198-7445"},{"full_name":"Rist, Florian","last_name":"Rist","first_name":"Florian"},{"first_name":"Helmut","full_name":"Pottmann, Helmut","last_name":"Pottmann"},{"first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","last_name":"Bickel","orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd"}],"title":"Computational design of cold bent glass façades","abstract":[{"text":"Cold bent glass is a promising and cost-efficient method for realizing doubly curved glass facades. They are produced by attaching planar glass sheets to curved frames and require keeping the occurring stress within safe limits.\r\nHowever, it is very challenging to navigate the design space of cold bent glass panels due to the fragility of the material, which impedes the form-finding for practically feasible and aesthetically pleasing cold bent glass facades. We propose an interactive, data-driven approach for designing cold bent glass facades that can be seamlessly integrated into a typical architectural design pipeline. Our method allows non-expert users to interactively edit a parametric surface while providing real-time feedback on the deformed shape and maximum stress of cold bent glass panels. Designs are automatically refined to minimize several fairness criteria while maximal stresses are kept within glass limits. We achieve interactive frame rates by using a differentiable Mixture Density Network trained from more than a million simulations. Given a curved boundary, our regression model is capable of handling multistable\r\nconfigurations and accurately predicting the equilibrium shape of the panel and its corresponding maximal stress. We show predictions are highly accurate and validate our results with a physical realization of a cold bent glass surface.","lang":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"oa_version":"Submitted Version","scopus_import":"1","intvolume":" 39","month":"11","publication_status":"published","publication_identifier":{"issn":["0730-0301"],"eissn":["1557-7368"]},"language":[{"iso":"eng"}],"file":[{"creator":"bbickel","date_updated":"2023-05-23T20:54:43Z","file_size":28964641,"date_created":"2023-05-23T20:54:43Z","file_name":"coldglass.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"c7f67717ad74e670b7daeae732abe151","file_id":"13084","success":1}],"ec_funded":1,"volume":39,"issue":"6","related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/bend-dont-break/"}],"record":[{"relation":"dissertation_contains","status":"public","id":"8366"},{"relation":"research_data","id":"8761","status":"public"}]},"_id":"8562","article_type":"original","type":"journal_article","status":"public","date_updated":"2024-02-21T12:43:21Z","ddc":["000"],"file_date_updated":"2023-05-23T20:54:43Z","department":[{"_id":"BeBi"}]},{"year":"2020","has_accepted_license":"1","isi":1,"publication":"Nano Letters","day":"01","page":"5201-5206","date_created":"2020-08-06T09:25:04Z","date_published":"2020-06-01T00:00:00Z","doi":"10.1021/acs.nanolett.0c01466","acknowledgement":"We acknowledge G. Burkard, V. N. Golovach, C. Kloeffel, D.Loss, P. Rabl, and M. Rancič ́ for helpful discussions. We\r\nfurther acknowledge T. Adletzberger, J. Aguilera, T. Asenov, S. Bagiante, T. Menner, L. Shafeek, P. Taus, P. Traunmüller, and D. Waldhausl for their invaluable assistance. This research was supported by the Scientific Service Units of IST Austria through resources provided by the MIBA Machine Shop and the nanofabrication facility, by the FWF-P 32235 project, by the National Key R&D Program of China (2016YFA0301701, 2016YFA0300600), and by the European Union’s Horizon 2020 research and innovation program under grant agreement no. 862046. All data of this publication are available at 10.15479/AT:ISTA:7689.","oa":1,"quality_controlled":"1","publisher":"American Chemical Society","citation":{"mla":"Katsaros, Georgios, et al. “Zero Field Splitting of Heavy-Hole States in Quantum Dots.” Nano Letters, vol. 20, no. 7, American Chemical Society, 2020, pp. 5201–06, doi:10.1021/acs.nanolett.0c01466.","short":"G. Katsaros, J. Kukucka, L. Vukušić, H. Watzinger, F. Gao, T. Wang, J.-J. Zhang, K. Held, Nano Letters 20 (2020) 5201–5206.","ieee":"G. Katsaros et al., “Zero field splitting of heavy-hole states in quantum dots,” Nano Letters, vol. 20, no. 7. American Chemical Society, pp. 5201–5206, 2020.","apa":"Katsaros, G., Kukucka, J., Vukušić, L., Watzinger, H., Gao, F., Wang, T., … Held, K. (2020). Zero field splitting of heavy-hole states in quantum dots. Nano Letters. American Chemical Society. https://doi.org/10.1021/acs.nanolett.0c01466","ama":"Katsaros G, Kukucka J, Vukušić L, et al. Zero field splitting of heavy-hole states in quantum dots. Nano Letters. 2020;20(7):5201-5206. doi:10.1021/acs.nanolett.0c01466","chicago":"Katsaros, Georgios, Josip Kukucka, Lada Vukušić, Hannes Watzinger, Fei Gao, Ting Wang, Jian-Jun Zhang, and Karsten Held. “Zero Field Splitting of Heavy-Hole States in Quantum Dots.” Nano Letters. American Chemical Society, 2020. https://doi.org/10.1021/acs.nanolett.0c01466.","ista":"Katsaros G, Kukucka J, Vukušić L, Watzinger H, Gao F, Wang T, Zhang J-J, Held K. 2020. Zero field splitting of heavy-hole states in quantum dots. Nano Letters. 20(7), 5201–5206."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"Yes (via OA deal)","external_id":{"pmid":["32479090"],"isi":["000548893200066"]},"author":[{"first_name":"Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","last_name":"Katsaros","orcid":"0000-0001-8342-202X","full_name":"Katsaros, Georgios"},{"last_name":"Kukucka","full_name":"Kukucka, Josip","id":"3F5D8856-F248-11E8-B48F-1D18A9856A87","first_name":"Josip"},{"id":"31E9F056-F248-11E8-B48F-1D18A9856A87","first_name":"Lada","orcid":"0000-0003-2424-8636","full_name":"Vukušić, Lada","last_name":"Vukušić"},{"first_name":"Hannes","id":"35DF8E50-F248-11E8-B48F-1D18A9856A87","last_name":"Watzinger","full_name":"Watzinger, Hannes"},{"last_name":"Gao","full_name":"Gao, Fei","first_name":"Fei"},{"first_name":"Ting","full_name":"Wang, Ting","orcid":"0000-0002-4619-9575","last_name":"Wang"},{"first_name":"Jian-Jun","last_name":"Zhang","full_name":"Zhang, Jian-Jun"},{"full_name":"Held, Karsten","last_name":"Held","first_name":"Karsten"}],"title":"Zero field splitting of heavy-hole states in quantum dots","project":[{"grant_number":"P32235","name":"Towards scalable hut wire quantum devices","_id":"237B3DA4-32DE-11EA-91FC-C7463DDC885E","call_identifier":"FWF"},{"grant_number":"862046","name":"TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS","_id":"237E5020-32DE-11EA-91FC-C7463DDC885E","call_identifier":"H2020"}],"publication_status":"published","publication_identifier":{"eissn":["1530-6992"],"issn":["1530-6984"]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"8204","file_size":3308906,"date_updated":"2020-08-06T09:35:37Z","creator":"dernst","file_name":"2020_NanoLetters_Katsaros.pdf","date_created":"2020-08-06T09:35:37Z"}],"ec_funded":1,"related_material":{"record":[{"relation":"research_data","status":"public","id":"7689"}]},"volume":20,"issue":"7","abstract":[{"text":"Using inelastic cotunneling spectroscopy we observe a zero field splitting within the spin triplet manifold of Ge hut wire quantum dots. The states with spin ±1 in the confinement direction are energetically favored by up to 55 μeV compared to the spin 0 triplet state because of the strong spin–orbit coupling. The reported effect should be observable in a broad class of strongly confined hole quantum-dot systems and might need to be considered when operating hole spin qubits.","lang":"eng"}],"acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","intvolume":" 20","month":"06","date_updated":"2024-02-21T12:44:01Z","ddc":["530"],"file_date_updated":"2020-08-06T09:35:37Z","department":[{"_id":"GeKa"}],"_id":"8203","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","status":"public"},{"language":[{"iso":"eng"}],"file":[{"success":1,"file_id":"8749","checksum":"6a7b0543c440f4c000a1864e69377d95","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2020_eLife_Gridchyn.pdf","date_created":"2020-11-09T09:17:40Z","creator":"dernst","file_size":447669,"date_updated":"2020-11-09T09:17:40Z"}],"publication_status":"published","publication_identifier":{"eissn":["2050084X"]},"volume":9,"related_material":{"record":[{"status":"public","id":"8563","relation":"research_data"}]},"oa_version":"Published Version","abstract":[{"lang":"eng","text":"In vitro work revealed that excitatory synaptic inputs to hippocampal inhibitory interneurons could undergo Hebbian, associative, or non-associative plasticity. Both behavioral and learning-dependent reorganization of these connections has also been demonstrated by measuring spike transmission probabilities in pyramidal cell-interneuron spike cross-correlations that indicate monosynaptic connections. Here we investigated the activity-dependent modification of these connections during exploratory behavior in rats by optogenetically inhibiting pyramidal cell and interneuron subpopulations. Light application and associated firing alteration of pyramidal and interneuron populations led to lasting changes in pyramidal-interneuron connection weights as indicated by spike transmission changes. Spike transmission alterations were predicted by the light-mediated changes in the number of pre- and postsynaptic spike pairing events and by firing rate changes of interneurons but not pyramidal cells. This work demonstrates the presence of activity-dependent associative and non-associative reorganization of pyramidal-interneuron connections triggered by the optogenetic modification of the firing rate and spike synchrony of cells."}],"intvolume":" 9","month":"10","scopus_import":"1","ddc":["570"],"date_updated":"2024-02-21T12:43:40Z","department":[{"_id":"JoCs"}],"file_date_updated":"2020-11-09T09:17:40Z","_id":"8740","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","publication":"eLife","day":"05","year":"2020","has_accepted_license":"1","isi":1,"date_created":"2020-11-08T23:01:25Z","doi":"10.7554/eLife.61106","date_published":"2020-10-05T00:00:00Z","acknowledgement":"We thank Michele Nardin and Federico Stella for comments on an earlier version of the manuscript. K Deisseroth for providing the pAAV-CaMKIIα::eNpHR3.0-YFP plasmid through Addgene. E Boyden for providing AAV2/1.CaMKII::ArchT.GFP.WPRE.SV40 plasmid through Penn Vector Core. This work was supported by the Austrian Science Fund (I02072 and I03713) and a Swiss National Science Foundation grant to PS. The authors declare no conflicts of interest.","oa":1,"publisher":"eLife Sciences Publications","quality_controlled":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Gridchyn I, Schönenberger P, O’Neill J, Csicsvari JL. 2020. 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However, most proposed solutions evolve towards a target geometry without considering time-dependent actuation paths. To achieve more complex geometries and avoid self-collisions, it is critical to encode a spatial and temporal shape evolution within the initially flat shell. Recent realizations of time-dependent morphing are limited to the actuation of few, discrete hinges and cannot form doubly curved surfaces. Here, we demonstrate a method for encoding temporal shape evolution in architected shells that assume complex shapes and doubly curved geometries. The shells are non-periodic tessellations of pre-stressed contractile unit cells that soften in water at rates prescribed locally by mesostructure geometry. The ensuing midplane contraction is coupled to the formation of encoded curvatures. We propose an inverse design tool based on a data-driven model for unit cells’ temporal responses.","lang":"eng"}],"oa_version":"Published Version","file_date_updated":"2020-07-14T12:47:55Z","department":[{"_id":"BeBi"}],"date_updated":"2024-02-21T12:45:02Z","ddc":["000"],"article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","keyword":["Design","Synthesis and processing","Mechanical engineering","Polymers"],"_id":"7262"},{"related_material":{"record":[{"relation":"research_data","status":"public","id":"8586"}]},"date_published":"2020-12-01T00:00:00Z","doi":"10.15479/AT:ISTA:14592","date_created":"2023-11-22T15:00:57Z","contributor":[{"contributor_type":"researcher","first_name":"Florian","id":"404F5528-F248-11E8-B48F-1D18A9856A87","last_name":"Fäßler","orcid":"0000-0001-7149-769X"},{"last_name":"Zens","first_name":"Bettina","id":"45FD126C-F248-11E8-B48F-1D18A9856A87","contributor_type":"researcher"},{"contributor_type":"researcher","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","last_name":"Hauschild"},{"contributor_type":"researcher","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian KM","last_name":"Schur","orcid":"0000-0003-4790-8078"}],"has_accepted_license":"1","year":"2020","day":"01","file":[{"file_name":"3Dprint-files_download_v2.zip","date_created":"2023-11-22T14:58:44Z","creator":"fschur","file_size":49297,"date_updated":"2023-11-22T14:58:44Z","success":1,"file_id":"14593","checksum":"0108616e2a59e51879ea51299a29b091","relation":"main_file","access_level":"open_access","content_type":"application/zip"},{"content_type":"text/plain","relation":"main_file","access_level":"open_access","success":1,"file_id":"14637","checksum":"4c66ddedee4d01c1c4a7978208350cfc","file_size":641,"date_updated":"2023-12-01T10:39:59Z","creator":"cchlebak","file_name":"readme.txt","date_created":"2023-12-01T10:39:59Z"}],"publisher":"Institute of Science and Technology Austria","oa":1,"month":"12","abstract":[{"lang":"eng","text":"Cryo-electron microscopy (cryo-EM) of cellular specimens provides insights into biological processes and structures within a native context. However, a major challenge still lies in the efficient and reproducible preparation of adherent cells for subsequent cryo-EM analysis. This is due to the sensitivity of many cellular specimens to the varying seeding and culturing conditions required for EM experiments, the often limited amount of cellular material and also the fragility of EM grids and their substrate. Here, we present low-cost and reusable 3D printed grid holders, designed to improve specimen preparation when culturing challenging cellular samples directly on grids. The described grid holders increase cell culture reproducibility and throughput, and reduce the resources required for cell culturing. We show that grid holders can be integrated into various cryo-EM workflows, including micro-patterning approaches to control cell seeding on grids, and for generating samples for cryo-focused ion beam milling and cryo-electron tomography experiments. Their adaptable design allows for the generation of specialized grid holders customized to a large variety of applications."}],"oa_version":"Published Version","author":[{"full_name":"Schur, Florian KM","orcid":"0000-0003-4790-8078","last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian KM"}],"article_processing_charge":"No","file_date_updated":"2023-12-01T10:39:59Z","title":"STL-files for 3D-printed grid holders described in Fäßler F, Zens B, et al.; 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy","department":[{"_id":"FlSc"}],"citation":{"chicago":"Schur, Florian KM. “STL-Files for 3D-Printed Grid Holders Described in Fäßler F, Zens B, et Al.; 3D Printed Cell Culture Grid Holders for Improved Cellular Specimen Preparation in Cryo-Electron Microscopy.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:14592.","ista":"Schur FK. 2020. STL-files for 3D-printed grid holders described in Fäßler F, Zens B, et al.; 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy, Institute of Science and Technology Austria, 10.15479/AT:ISTA:14592.","mla":"Schur, Florian KM. STL-Files for 3D-Printed Grid Holders Described in Fäßler F, Zens B, et Al.; 3D Printed Cell Culture Grid Holders for Improved Cellular Specimen Preparation in Cryo-Electron Microscopy. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:14592.","ama":"Schur FK. STL-files for 3D-printed grid holders described in Fäßler F, Zens B, et al.; 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy. 2020. doi:10.15479/AT:ISTA:14592","apa":"Schur, F. K. (2020). STL-files for 3D-printed grid holders described in Fäßler F, Zens B, et al.; 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:14592","ieee":"F. K. Schur, “STL-files for 3D-printed grid holders described in Fäßler F, Zens B, et al.; 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy.” Institute of Science and Technology Austria, 2020.","short":"F.K. Schur, (2020)."},"date_updated":"2024-02-21T12:44:48Z","ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"research_data","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"project":[{"grant_number":"P33367","name":"Structure and isoform diversity of the Arp2/3 complex","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A"}],"status":"public","_id":"14592"},{"ec_funded":1,"volume":881,"language":[{"iso":"eng"}],"file":[{"success":1,"checksum":"8951f094c8c7dae9ff8db885199bc296","file_id":"8625","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"main.pdf","date_created":"2020-10-08T08:16:48Z","file_size":310598,"date_updated":"2020-10-08T08:16:48Z","creator":"bchatter"}],"publication_status":"published","publication_identifier":{"eissn":["18609503"],"isbn":["9783030366865"],"issn":["1860949X"]},"intvolume":" 881","month":"01","scopus_import":"1","alternative_title":["SCI"],"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Persistent homology is a powerful tool in Topological Data Analysis (TDA) to capture the topological properties of data succinctly at different spatial resolutions. For graphical data, the shape, and structure of the neighborhood of individual data items (nodes) are an essential means of characterizing their properties. We propose the use of persistent homology methods to capture structural and topological properties of graphs and use it to address the problem of link prediction. We achieve encouraging results on nine different real-world datasets that attest to the potential of persistent homology-based methods for network analysis."}],"department":[{"_id":"DaAl"}],"file_date_updated":"2020-10-08T08:16:48Z","ddc":["004"],"date_updated":"2024-02-22T13:16:06Z","status":"public","conference":{"name":"COMPLEX: International Conference on Complex Networks and their Applications","start_date":"2019-12-10","end_date":"2019-12-12","location":"Lisbon, Portugal"},"type":"conference","_id":"7213","date_created":"2019-12-29T23:00:45Z","doi":"10.1007/978-3-030-36687-2_3","date_published":"2020-01-01T00:00:00Z","page":"27-39","publication":"Complex Networks and their applications VIII","day":"01","year":"2020","isi":1,"has_accepted_license":"1","oa":1,"publisher":"Springer Nature","quality_controlled":"1","title":"A persistent homology perspective to the link prediction problem","external_id":{"isi":["000843927300003"]},"article_processing_charge":"No","author":[{"full_name":"Bhatia, Sumit","last_name":"Bhatia","first_name":"Sumit"},{"last_name":"Chatterjee","orcid":"0000-0002-2742-4028","full_name":"Chatterjee, Bapi","id":"3C41A08A-F248-11E8-B48F-1D18A9856A87","first_name":"Bapi"},{"first_name":"Deepak","last_name":"Nathani","full_name":"Nathani, Deepak"},{"first_name":"Manohar","last_name":"Kaul","full_name":"Kaul, Manohar"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Bhatia, Sumit, Bapi Chatterjee, Deepak Nathani, and Manohar Kaul. “A Persistent Homology Perspective to the Link Prediction Problem.” In Complex Networks and Their Applications VIII, 881:27–39. Springer Nature, 2020. https://doi.org/10.1007/978-3-030-36687-2_3.","ista":"Bhatia S, Chatterjee B, Nathani D, Kaul M. 2020. A persistent homology perspective to the link prediction problem. Complex Networks and their applications VIII. COMPLEX: International Conference on Complex Networks and their Applications, SCI, vol. 881, 27–39.","mla":"Bhatia, Sumit, et al. “A Persistent Homology Perspective to the Link Prediction Problem.” Complex Networks and Their Applications VIII, vol. 881, Springer Nature, 2020, pp. 27–39, doi:10.1007/978-3-030-36687-2_3.","apa":"Bhatia, S., Chatterjee, B., Nathani, D., & Kaul, M. (2020). A persistent homology perspective to the link prediction problem. In Complex Networks and their applications VIII (Vol. 881, pp. 27–39). Lisbon, Portugal: Springer Nature. https://doi.org/10.1007/978-3-030-36687-2_3","ama":"Bhatia S, Chatterjee B, Nathani D, Kaul M. A persistent homology perspective to the link prediction problem. In: Complex Networks and Their Applications VIII. Vol 881. Springer Nature; 2020:27-39. doi:10.1007/978-3-030-36687-2_3","ieee":"S. Bhatia, B. Chatterjee, D. Nathani, and M. Kaul, “A persistent homology perspective to the link prediction problem,” in Complex Networks and their applications VIII, Lisbon, Portugal, 2020, vol. 881, pp. 27–39.","short":"S. Bhatia, B. Chatterjee, D. Nathani, M. Kaul, in:, Complex Networks and Their Applications VIII, Springer Nature, 2020, pp. 27–39."},"project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}]},{"conference":{"end_date":"2020-11-13","location":"Virtual, United States","start_date":"2020-11-09","name":"CCS: Computer and Communications Security"},"type":"conference","status":"public","_id":"10556","department":[{"_id":"ElKo"}],"date_updated":"2024-02-22T13:10:45Z","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2019/1015"}],"scopus_import":"1","month":"10","abstract":[{"text":"In this paper, we present the first Asynchronous Distributed Key Generation (ADKG) algorithm which is also the first distributed key generation algorithm that can generate cryptographic keys with a dual (f,2f+1)-threshold (where f is the number of faulty parties). As a result, using our ADKG we remove the trusted setup assumption that the most scalable consensus algorithms make. In order to create a DKG with a dual (f,2f+1)- threshold we first answer in the affirmative the open question posed by Cachin et al. [7] on how to create an Asynchronous Verifiable Secret Sharing (AVSS) protocol with a reconstruction threshold of f+1Proceedings of the 2020 ACM SIGSAC Conference on Computer and Communications Security. Association for Computing Machinery; 2020:1751–1767. doi:10.1145/3372297.3423364","apa":"Kokoris Kogias, E., Malkhi, D., & Spiegelman, A. (2020). Asynchronous distributed key generation for computationally-secure randomness, consensus, and threshold signatures. In Proceedings of the 2020 ACM SIGSAC Conference on Computer and Communications Security (pp. 1751–1767). Virtual, United States: Association for Computing Machinery. https://doi.org/10.1145/3372297.3423364","short":"E. Kokoris Kogias, D. Malkhi, A. Spiegelman, in:, Proceedings of the 2020 ACM SIGSAC Conference on Computer and Communications Security, Association for Computing Machinery, 2020, pp. 1751–1767.","ieee":"E. Kokoris Kogias, D. Malkhi, and A. Spiegelman, “Asynchronous distributed key generation for computationally-secure randomness, consensus, and threshold signatures,” in Proceedings of the 2020 ACM SIGSAC Conference on Computer and Communications Security, Virtual, United States, 2020, pp. 1751–1767.","mla":"Kokoris Kogias, Eleftherios, et al. “Asynchronous Distributed Key Generation for Computationally-Secure Randomness, Consensus, and Threshold Signatures.” Proceedings of the 2020 ACM SIGSAC Conference on Computer and Communications Security, Association for Computing Machinery, 2020, pp. 1751–1767, doi:10.1145/3372297.3423364.","ista":"Kokoris Kogias E, Malkhi D, Spiegelman A. 2020. Asynchronous distributed key generation for computationally-secure randomness, consensus, and threshold signatures. Proceedings of the 2020 ACM SIGSAC Conference on Computer and Communications Security. CCS: Computer and Communications Security, 1751–1767.","chicago":"Kokoris Kogias, Eleftherios, Dahlia Malkhi, and Alexander Spiegelman. “Asynchronous Distributed Key Generation for Computationally-Secure Randomness, Consensus, and Threshold Signatures.” In Proceedings of the 2020 ACM SIGSAC Conference on Computer and Communications Security, 1751–1767. Association for Computing Machinery, 2020. https://doi.org/10.1145/3372297.3423364."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa":1,"publisher":"Association for Computing Machinery","quality_controlled":"1","acknowledgement":"We would like to thank Ittai Abraham for the discussions and guidance during the initial conception of the project, especially for HAVSS. Furthermore, we would like to thank the anonymous reviewers for pointing out the relevance of this work to MPC protocols.","page":"1751–1767","date_created":"2021-12-16T13:23:27Z","doi":"10.1145/3372297.3423364","date_published":"2020-10-30T00:00:00Z","year":"2020","isi":1,"publication":"Proceedings of the 2020 ACM SIGSAC Conference on Computer and Communications Security","day":"30"},{"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Garcia Soto, Miriam, and Pavithra Prabhakar. “Hybridization for Stability Verification of Nonlinear Switched Systems.” 2020 IEEE Real-Time Systems Symposium, IEEE, 2020, pp. 244–56, doi:10.1109/RTSS49844.2020.00031.","short":"M. Garcia Soto, P. Prabhakar, in:, 2020 IEEE Real-Time Systems Symposium, IEEE, 2020, pp. 244–256.","ieee":"M. Garcia Soto and P. Prabhakar, “Hybridization for stability verification of nonlinear switched systems,” in 2020 IEEE Real-Time Systems Symposium, Houston, TX, USA , 2020, pp. 244–256.","ama":"Garcia Soto M, Prabhakar P. Hybridization for stability verification of nonlinear switched systems. In: 2020 IEEE Real-Time Systems Symposium. IEEE; 2020:244-256. doi:10.1109/RTSS49844.2020.00031","apa":"Garcia Soto, M., & Prabhakar, P. (2020). Hybridization for stability verification of nonlinear switched systems. In 2020 IEEE Real-Time Systems Symposium (pp. 244–256). Houston, TX, USA : IEEE. https://doi.org/10.1109/RTSS49844.2020.00031","chicago":"Garcia Soto, Miriam, and Pavithra Prabhakar. “Hybridization for Stability Verification of Nonlinear Switched Systems.” In 2020 IEEE Real-Time Systems Symposium, 244–56. IEEE, 2020. https://doi.org/10.1109/RTSS49844.2020.00031.","ista":"Garcia Soto M, Prabhakar P. 2020. Hybridization for stability verification of nonlinear switched systems. 2020 IEEE Real-Time Systems Symposium. RTTS: Real-Time Systems Symposium, 244–256."},"title":"Hybridization for stability verification of nonlinear switched systems","author":[{"first_name":"Miriam","id":"4B3207F6-F248-11E8-B48F-1D18A9856A87","full_name":"Garcia Soto, Miriam","orcid":"0000-0003-2936-5719","last_name":"Garcia Soto"},{"first_name":"Pavithra","full_name":"Prabhakar, Pavithra","last_name":"Prabhakar"}],"article_processing_charge":"No","external_id":{"isi":["000680435100021"]},"project":[{"call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","grant_number":"Z211"}],"day":"01","publication":"2020 IEEE Real-Time Systems Symposium","has_accepted_license":"1","isi":1,"year":"2020","doi":"10.1109/RTSS49844.2020.00031","date_published":"2020-12-01T00:00:00Z","date_created":"2021-02-26T16:38:24Z","page":"244-256","acknowledgement":"Miriam Garc´ıa Soto was partially supported by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award). Pavithra Prabhakar was partially supported by NSF CAREER Award No. 1552668, NSF Award No. 2008957 and ONR YIP Award No. N000141712577.","publisher":"IEEE","quality_controlled":"1","oa":1,"ddc":["000"],"date_updated":"2024-02-22T13:25:19Z","file_date_updated":"2021-02-26T16:38:14Z","department":[{"_id":"ToHe"}],"_id":"9202","status":"public","type":"conference","conference":{"start_date":"2020-12-01","end_date":"2020-12-04","location":"Houston, TX, USA ","name":"RTTS: Real-Time Systems Symposium"},"file":[{"date_created":"2021-02-26T16:38:14Z","file_name":"main.pdf","date_updated":"2021-02-26T16:38:14Z","file_size":1125794,"creator":"mgarcias","checksum":"8f97f229316c3b3a6f0cf99297aa0941","file_id":"9203","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"publication_identifier":{"eisbn":["9781728183244"],"eissn":["2576-3172"]},"publication_status":"published","oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"We propose a novel hybridization method for stability analysis that over-approximates nonlinear dynamical systems by switched systems with linear inclusion dynamics. We observe that existing hybridization techniques for safety analysis that over-approximate nonlinear dynamical systems by switched affine inclusion dynamics and provide fixed approximation error, do not suffice for stability analysis. Hence, we propose a hybridization method that provides a state-dependent error which converges to zero as the state tends to the equilibrium point. The crux of our hybridization computation is an elegant recursive algorithm that uses partial derivatives of a given function to obtain upper and lower bound matrices for the over-approximating linear inclusion. We illustrate our method on some examples to demonstrate the application of the theory for stability analysis. In particular, our method is able to establish stability of a nonlinear system which does not admit a polynomial Lyapunov function."}],"month":"12"},{"year":"2020","isi":1,"publication":"Communications in Mathematical Physics","day":"01","page":"1311-1395","date_created":"2019-09-24T17:30:59Z","doi":"10.1007/s00220-019-03555-9","date_published":"2020-06-01T00:00:00Z","acknowledgement":"We would like to thank P. T. Nam and R. Seiringer for several useful discussions and\r\nfor suggesting us to use the localization techniques from [9]. C. Boccato has received funding from the\r\nEuropean Research Council (ERC) under the programme Horizon 2020 (Grant Agreement 694227). B. Schlein gratefully acknowledges support from the NCCR SwissMAP and from the Swiss National Foundation of Science (Grant No. 200020_1726230) through the SNF Grant “Dynamical and energetic properties of Bose–Einstein condensates”.","oa":1,"publisher":"Springer","quality_controlled":"1","citation":{"mla":"Boccato, Chiara, et al. “Optimal Rate for Bose-Einstein Condensation in the Gross-Pitaevskii Regime.” Communications in Mathematical Physics, vol. 376, Springer, 2020, pp. 1311–95, doi:10.1007/s00220-019-03555-9.","ieee":"C. Boccato, C. Brennecke, S. Cenatiempo, and B. Schlein, “Optimal rate for Bose-Einstein condensation in the Gross-Pitaevskii regime,” Communications in Mathematical Physics, vol. 376. Springer, pp. 1311–1395, 2020.","short":"C. Boccato, C. Brennecke, S. Cenatiempo, B. Schlein, Communications in Mathematical Physics 376 (2020) 1311–1395.","ama":"Boccato C, Brennecke C, Cenatiempo S, Schlein B. Optimal rate for Bose-Einstein condensation in the Gross-Pitaevskii regime. Communications in Mathematical Physics. 2020;376:1311-1395. doi:10.1007/s00220-019-03555-9","apa":"Boccato, C., Brennecke, C., Cenatiempo, S., & Schlein, B. (2020). Optimal rate for Bose-Einstein condensation in the Gross-Pitaevskii regime. Communications in Mathematical Physics. Springer. https://doi.org/10.1007/s00220-019-03555-9","chicago":"Boccato, Chiara, Christian Brennecke, Serena Cenatiempo, and Benjamin Schlein. “Optimal Rate for Bose-Einstein Condensation in the Gross-Pitaevskii Regime.” Communications in Mathematical Physics. Springer, 2020. https://doi.org/10.1007/s00220-019-03555-9.","ista":"Boccato C, Brennecke C, Cenatiempo S, Schlein B. 2020. Optimal rate for Bose-Einstein condensation in the Gross-Pitaevskii regime. Communications in Mathematical Physics. 376, 1311–1395."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","external_id":{"arxiv":["1812.03086"],"isi":["000536053300012"]},"author":[{"id":"342E7E22-F248-11E8-B48F-1D18A9856A87","first_name":"Chiara","last_name":"Boccato","full_name":"Boccato, Chiara"},{"first_name":"Christian","last_name":"Brennecke","full_name":"Brennecke, Christian"},{"last_name":"Cenatiempo","full_name":"Cenatiempo, Serena","first_name":"Serena"},{"last_name":"Schlein","full_name":"Schlein, Benjamin","first_name":"Benjamin"}],"title":"Optimal rate for Bose-Einstein condensation in the Gross-Pitaevskii regime","project":[{"name":"Analysis of quantum many-body systems","grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"publication_status":"published","publication_identifier":{"eissn":["1432-0916"],"issn":["0010-3616"]},"language":[{"iso":"eng"}],"ec_funded":1,"volume":376,"abstract":[{"lang":"eng","text":"We consider systems of bosons trapped in a box, in the Gross–Pitaevskii regime. We show that low-energy states exhibit complete Bose–Einstein condensation with an optimal bound on the number of orthogonal excitations. This extends recent results obtained in Boccato et al. (Commun Math Phys 359(3):975–1026, 2018), removing the assumption of small interaction potential."}],"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1812.03086"}],"scopus_import":"1","intvolume":" 376","month":"06","date_updated":"2024-02-22T13:33:02Z","department":[{"_id":"RoSe"}],"_id":"6906","type":"journal_article","article_type":"original","status":"public"},{"publisher":"Elsevier","quality_controlled":"1","publication":"Gastrulation: From Embryonic Pattern to Form","day":"01","year":"2020","isi":1,"date_created":"2020-01-30T09:24:06Z","doi":"10.1016/bs.ctdb.2019.07.001","date_published":"2020-01-01T00:00:00Z","page":"319-341","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"short":"A.E.E. Bruce, C.-P.J. Heisenberg, in:, L. Solnica-Krezel (Ed.), Gastrulation: From Embryonic Pattern to Form, Elsevier, 2020, pp. 319–341.","ieee":"A. E. E. Bruce and C.-P. J. Heisenberg, “Mechanisms of zebrafish epiboly: A current view,” in Gastrulation: From Embryonic Pattern to Form, vol. 136, L. Solnica-Krezel, Ed. Elsevier, 2020, pp. 319–341.","ama":"Bruce AEE, Heisenberg C-PJ. Mechanisms of zebrafish epiboly: A current view. In: Solnica-Krezel L, ed. Gastrulation: From Embryonic Pattern to Form. Vol 136. Current Topics in Developmental Biology. Elsevier; 2020:319-341. doi:10.1016/bs.ctdb.2019.07.001","apa":"Bruce, A. E. E., & Heisenberg, C.-P. J. (2020). Mechanisms of zebrafish epiboly: A current view. In L. Solnica-Krezel (Ed.), Gastrulation: From Embryonic Pattern to Form (Vol. 136, pp. 319–341). Elsevier. https://doi.org/10.1016/bs.ctdb.2019.07.001","mla":"Bruce, Ashley E. E., and Carl-Philipp J. Heisenberg. “Mechanisms of Zebrafish Epiboly: A Current View.” Gastrulation: From Embryonic Pattern to Form, edited by Lilianna Solnica-Krezel, vol. 136, Elsevier, 2020, pp. 319–41, doi:10.1016/bs.ctdb.2019.07.001.","ista":"Bruce AEE, Heisenberg C-PJ. 2020.Mechanisms of zebrafish epiboly: A current view. In: Gastrulation: From Embryonic Pattern to Form. vol. 136, 319–341.","chicago":"Bruce, Ashley E.E., and Carl-Philipp J Heisenberg. “Mechanisms of Zebrafish Epiboly: A Current View.” In Gastrulation: From Embryonic Pattern to Form, edited by Lilianna Solnica-Krezel, 136:319–41. Current Topics in Developmental Biology. Elsevier, 2020. https://doi.org/10.1016/bs.ctdb.2019.07.001."},"editor":[{"first_name":"Lilianna ","full_name":"Solnica-Krezel, Lilianna ","last_name":"Solnica-Krezel"}],"title":"Mechanisms of zebrafish epiboly: A current view","external_id":{"isi":["000611830600012"]},"article_processing_charge":"No","author":[{"first_name":"Ashley E.E.","last_name":"Bruce","full_name":"Bruce, Ashley E.E."},{"last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"None","abstract":[{"text":"Epiboly is a conserved gastrulation movement describing the thinning and spreading of a sheet or multi-layer of cells. The zebrafish embryo has emerged as a vital model system to address the cellular and molecular mechanisms that drive epiboly. In the zebrafish embryo, the blastoderm, consisting of a simple squamous epithelium (the enveloping layer) and an underlying mass of deep cells, as well as a yolk nuclear syncytium (the yolk syncytial layer) undergo epiboly to internalize the yolk cell during gastrulation. The major events during zebrafish epiboly are: expansion of the enveloping layer and the internal yolk syncytial layer, reduction and removal of the yolk membrane ahead of the advancing blastoderm margin and deep cell rearrangements between the enveloping layer and yolk syncytial layer to thin the blastoderm. Here, work addressing the cellular and molecular mechanisms as well as the sources of the mechanical forces that underlie these events is reviewed. The contribution of recent findings to the current model of epiboly as well as open questions and future prospects are also discussed.","lang":"eng"}],"intvolume":" 136","month":"01","scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0070-2153"],"isbn":["9780128127988"]},"volume":136,"_id":"7410","series_title":"Current Topics in Developmental Biology","status":"public","type":"book_chapter","date_updated":"2024-02-22T13:23:09Z","department":[{"_id":"CaHe"}]},{"ec_funded":1,"volume":128,"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"6482"}],"link":[{"url":"https://doi.org/10.1007/s11263-019-01262-5","relation":"erratum"}]},"issue":"4","language":[{"iso":"eng"}],"file":[{"checksum":"155e63edf664dcacb3bdc1c2223e606f","file_id":"7110","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2019-11-26T10:30:02Z","file_name":"2019_IJCV_Sun.pdf","date_updated":"2020-07-14T12:47:45Z","file_size":1715072,"creator":"dernst"}],"publication_status":"published","publication_identifier":{"eissn":["1573-1405"],"issn":["0920-5691"]},"intvolume":" 128","month":"04","scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"We study the problem of automatically detecting if a given multi-class classifier operates outside of its specifications (out-of-specs), i.e. on input data from a different distribution than what it was trained for. This is an important problem to solve on the road towards creating reliable computer vision systems for real-world applications, because the quality of a classifier’s predictions cannot be guaranteed if it operates out-of-specs. Previously proposed methods for out-of-specs detection make decisions on the level of single inputs. This, however, is insufficient to achieve low false positive rate and high false negative rates at the same time. In this work, we describe a new procedure named KS(conf), based on statistical reasoning. Its main component is a classical Kolmogorov–Smirnov test that is applied to the set of predicted confidence values for batches of samples. Working with batches instead of single samples allows increasing the true positive rate without negatively affecting the false positive rate, thereby overcoming a crucial limitation of single sample tests. We show by extensive experiments using a variety of convolutional network architectures and datasets that KS(conf) reliably detects out-of-specs situations even under conditions where other tests fail. It furthermore has a number of properties that make it an excellent candidate for practical deployment: it is easy to implement, adds almost no overhead to the system, works with any classifier that outputs confidence scores, and requires no a priori knowledge about how the data distribution could change.","lang":"eng"}],"file_date_updated":"2020-07-14T12:47:45Z","department":[{"_id":"ChLa"}],"ddc":["004"],"date_updated":"2024-02-22T14:57:30Z","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","_id":"6944","date_created":"2019-10-14T09:14:28Z","date_published":"2020-04-01T00:00:00Z","doi":"10.1007/s11263-019-01232-x","page":"970-995","publication":"International Journal of Computer Vision","day":"01","year":"2020","has_accepted_license":"1","isi":1,"oa":1,"publisher":"Springer Nature","quality_controlled":"1","title":"KS(conf): A light-weight test if a multiclass classifier operates outside of its specifications","external_id":{"isi":["000494406800001"]},"article_processing_charge":"Yes (via OA deal)","author":[{"first_name":"Rémy","last_name":"Sun","full_name":"Sun, Rémy"},{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","last_name":"Lampert","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Sun, Rémy, and Christoph Lampert. “KS(Conf): A Light-Weight Test If a Multiclass Classifier Operates Outside of Its Specifications.” International Journal of Computer Vision. Springer Nature, 2020. https://doi.org/10.1007/s11263-019-01232-x.","ista":"Sun R, Lampert C. 2020. KS(conf): A light-weight test if a multiclass classifier operates outside of its specifications. International Journal of Computer Vision. 128(4), 970–995.","mla":"Sun, Rémy, and Christoph Lampert. “KS(Conf): A Light-Weight Test If a Multiclass Classifier Operates Outside of Its Specifications.” International Journal of Computer Vision, vol. 128, no. 4, Springer Nature, 2020, pp. 970–95, doi:10.1007/s11263-019-01232-x.","ama":"Sun R, Lampert C. KS(conf): A light-weight test if a multiclass classifier operates outside of its specifications. International Journal of Computer Vision. 2020;128(4):970-995. doi:10.1007/s11263-019-01232-x","apa":"Sun, R., & Lampert, C. (2020). KS(conf): A light-weight test if a multiclass classifier operates outside of its specifications. International Journal of Computer Vision. Springer Nature. https://doi.org/10.1007/s11263-019-01232-x","short":"R. Sun, C. Lampert, International Journal of Computer Vision 128 (2020) 970–995.","ieee":"R. Sun and C. Lampert, “KS(conf): A light-weight test if a multiclass classifier operates outside of its specifications,” International Journal of Computer Vision, vol. 128, no. 4. Springer Nature, pp. 970–995, 2020."},"project":[{"_id":"2532554C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Lifelong Learning of Visual Scene Understanding","grant_number":"308036"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}]},{"issue":"POPL","related_material":{"link":[{"relation":"software","url":"https://doi.org/10.5281/zenodo.3533633"}]},"volume":4,"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"8328","checksum":"c6193d109ff4ecb17e7a6513d8eb34c0","success":1,"date_updated":"2020-09-01T11:12:58Z","file_size":564151,"creator":"cziletti","date_created":"2020-09-01T11:12:58Z","file_name":"2019_ACM_POPL_Wang.pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2475-1421"]},"publication_status":"published","month":"01","intvolume":" 4","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"The notion of program sensitivity (aka Lipschitz continuity) specifies that changes in the program input result in proportional changes to the program output. For probabilistic programs the notion is naturally extended to expected sensitivity. A previous approach develops a relational program logic framework for proving expected sensitivity of probabilistic while loops, where the number of iterations is fixed and bounded. In this work, we consider probabilistic while loops where the number of iterations is not fixed, but randomized and depends on the initial input values. We present a sound approach for proving expected sensitivity of such programs. Our sound approach is martingale-based and can be automated through existing martingale-synthesis algorithms. Furthermore, our approach is compositional for sequential composition of while loops under a mild side condition. We demonstrate the effectiveness of our approach on several classical examples from Gambler's Ruin, stochastic hybrid systems and stochastic gradient descent. We also present experimental results showing that our automated approach can handle various probabilistic programs in the literature."}],"file_date_updated":"2020-09-01T11:12:58Z","department":[{"_id":"KrCh"}],"ddc":["004"],"date_updated":"2024-02-22T15:16:45Z","status":"public","type":"conference","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"8324","doi":"10.1145/3371093","date_published":"2020-01-01T00:00:00Z","date_created":"2020-08-30T22:01:12Z","day":"01","publication":"Proceedings of the ACM on Programming Languages","has_accepted_license":"1","year":"2020","publisher":"ACM","quality_controlled":"1","oa":1,"acknowledgement":"We thank anonymous reviewers for helpful comments, especially for pointing to us a scenario of piecewise-linear approximation (Remark5). The research was partially supported by the National Natural Science Foundation of China (NSFC) under Grant No. 61802254, 61672229, 61832015,61772336,11871221 and Austrian Science Fund (FWF) NFN under Grant No. S11407-N23 (RiSE/SHiNE). We thank Prof. Yuxi Fu, director of the BASICS Lab at Shanghai Jiao Tong University, for his support.","title":"Proving expected sensitivity of probabilistic programs with randomized variable-dependent termination time","author":[{"first_name":"Peixin","last_name":"Wang","full_name":"Wang, Peixin"},{"full_name":"Fu, Hongfei","last_name":"Fu","first_name":"Hongfei"},{"last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Yuxin","last_name":"Deng","full_name":"Deng, Yuxin"},{"first_name":"Ming","last_name":"Xu","full_name":"Xu, Ming"}],"article_processing_charge":"No","external_id":{"arxiv":["1902.04744"]},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Wang P, Fu H, Chatterjee K, Deng Y, Xu M. 2020. Proving expected sensitivity of probabilistic programs with randomized variable-dependent termination time. Proceedings of the ACM on Programming Languages. vol. 4, 25.","chicago":"Wang, Peixin, Hongfei Fu, Krishnendu Chatterjee, Yuxin Deng, and Ming Xu. “Proving Expected Sensitivity of Probabilistic Programs with Randomized Variable-Dependent Termination Time.” In Proceedings of the ACM on Programming Languages, Vol. 4. ACM, 2020. https://doi.org/10.1145/3371093.","ieee":"P. Wang, H. Fu, K. Chatterjee, Y. Deng, and M. Xu, “Proving expected sensitivity of probabilistic programs with randomized variable-dependent termination time,” in Proceedings of the ACM on Programming Languages, 2020, vol. 4, no. POPL.","short":"P. Wang, H. Fu, K. Chatterjee, Y. Deng, M. Xu, in:, Proceedings of the ACM on Programming Languages, ACM, 2020.","apa":"Wang, P., Fu, H., Chatterjee, K., Deng, Y., & Xu, M. (2020). Proving expected sensitivity of probabilistic programs with randomized variable-dependent termination time. In Proceedings of the ACM on Programming Languages (Vol. 4). ACM. https://doi.org/10.1145/3371093","ama":"Wang P, Fu H, Chatterjee K, Deng Y, Xu M. Proving expected sensitivity of probabilistic programs with randomized variable-dependent termination time. In: Proceedings of the ACM on Programming Languages. Vol 4. ACM; 2020. doi:10.1145/3371093","mla":"Wang, Peixin, et al. “Proving Expected Sensitivity of Probabilistic Programs with Randomized Variable-Dependent Termination Time.” Proceedings of the ACM on Programming Languages, vol. 4, no. POPL, 25, ACM, 2020, doi:10.1145/3371093."},"project":[{"call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","name":"Game Theory"}],"article_number":"25"},{"publisher":"Karger Publishers","quality_controlled":"1","isi":1,"year":"2020","day":"01","publication":"Brain, Behavior and Evolution","page":"27-36","doi":"10.1159/000504162","date_published":"2020-01-01T00:00:00Z","date_created":"2019-12-09T09:04:13Z","citation":{"ista":"Salazar JE, Severin D, Vega Zuniga TA, Fernández-Aburto P, Deichler A, Sallaberry A. M, Mpodozis J. 2020. Anatomical specializations related to foraging in the visual system of a nocturnal insectivorous bird, the band-winged nightjar (Aves: Caprimulgiformes). Brain, Behavior and Evolution. 94(1–4), 27–36.","chicago":"Salazar, Juan Esteban, Daniel Severin, Tomas A Vega Zuniga, Pedro Fernández-Aburto, Alfonso Deichler, Michel Sallaberry A., and Jorge Mpodozis. “Anatomical Specializations Related to Foraging in the Visual System of a Nocturnal Insectivorous Bird, the Band-Winged Nightjar (Aves: Caprimulgiformes).” Brain, Behavior and Evolution. Karger Publishers, 2020. https://doi.org/10.1159/000504162.","ieee":"J. E. Salazar et al., “Anatomical specializations related to foraging in the visual system of a nocturnal insectivorous bird, the band-winged nightjar (Aves: Caprimulgiformes),” Brain, Behavior and Evolution, vol. 94, no. 1–4. Karger Publishers, pp. 27–36, 2020.","short":"J.E. Salazar, D. Severin, T.A. Vega Zuniga, P. Fernández-Aburto, A. Deichler, M. Sallaberry A., J. Mpodozis, Brain, Behavior and Evolution 94 (2020) 27–36.","ama":"Salazar JE, Severin D, Vega Zuniga TA, et al. Anatomical specializations related to foraging in the visual system of a nocturnal insectivorous bird, the band-winged nightjar (Aves: Caprimulgiformes). Brain, Behavior and Evolution. 2020;94(1-4):27-36. doi:10.1159/000504162","apa":"Salazar, J. E., Severin, D., Vega Zuniga, T. A., Fernández-Aburto, P., Deichler, A., Sallaberry A., M., & Mpodozis, J. (2020). Anatomical specializations related to foraging in the visual system of a nocturnal insectivorous bird, the band-winged nightjar (Aves: Caprimulgiformes). Brain, Behavior and Evolution. Karger Publishers. https://doi.org/10.1159/000504162","mla":"Salazar, Juan Esteban, et al. “Anatomical Specializations Related to Foraging in the Visual System of a Nocturnal Insectivorous Bird, the Band-Winged Nightjar (Aves: Caprimulgiformes).” Brain, Behavior and Evolution, vol. 94, no. 1–4, Karger Publishers, 2020, pp. 27–36, doi:10.1159/000504162."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Salazar, Juan Esteban","last_name":"Salazar","first_name":"Juan Esteban"},{"full_name":"Severin, Daniel","last_name":"Severin","first_name":"Daniel"},{"full_name":"Vega Zuniga, Tomas A","last_name":"Vega Zuniga","id":"2E7C4E78-F248-11E8-B48F-1D18A9856A87","first_name":"Tomas A"},{"first_name":"Pedro","full_name":"Fernández-Aburto, Pedro","last_name":"Fernández-Aburto"},{"last_name":"Deichler","full_name":"Deichler, Alfonso","first_name":"Alfonso"},{"full_name":"Sallaberry A., Michel","last_name":"Sallaberry A.","first_name":"Michel"},{"full_name":"Mpodozis, Jorge","last_name":"Mpodozis","first_name":"Jorge"}],"external_id":{"isi":["000522856600004"],"pmid":["31751995"]},"article_processing_charge":"No","title":"Anatomical specializations related to foraging in the visual system of a nocturnal insectivorous bird, the band-winged nightjar (Aves: Caprimulgiformes)","abstract":[{"text":"Nocturnal animals that rely on their visual system for foraging, mating, and navigation usually exhibit specific traits associated with living in scotopic conditions. Most nocturnal birds have several visual specializations, such as enlarged eyes and an increased orbital convergence. However, the actual role of binocular vision in nocturnal foraging is still debated. Nightjars (Aves: Caprimulgidae) are predators that actively pursue and capture flying insects in crepuscular and nocturnal environments, mainly using a conspicuous “sit-and-wait” tactic on which pursuit begins with an insect flying over the bird that sits on the ground. In this study, we describe the visual system of the band-winged nightjar (Systellura longirostris), with emphasis on anatomical features previously described as relevant for nocturnal birds. Orbit convergence, determined by 3D scanning of the skull, was 73.28°. The visual field, determined by ophthalmoscopic reflex, exhibits an area of maximum binocular overlap of 42°, and it is dorsally oriented. The eyes showed a nocturnal-like normalized corneal aperture/axial length index. Retinal ganglion cells (RGCs) were relatively scant, and distributed in an unusual oblique-band pattern, with higher concentrations in the ventrotemporal quadrant. Together, these results indicate that the band-winged nightjar exhibits a retinal specialization associated with the binocular area of their dorsal visual field, a relevant area for pursuit triggering and prey attacks. The RGC distribution observed is unusual among birds, but similar to that of some visually dependent insectivorous bats, suggesting that those features might be convergent in relation to feeding strategies.","lang":"eng"}],"pmid":1,"oa_version":"None","scopus_import":"1","month":"01","intvolume":" 94","publication_identifier":{"eissn":["1421-9743"],"issn":["0006-8977"]},"publication_status":"published","language":[{"iso":"eng"}],"issue":"1-4","volume":94,"_id":"7160","type":"journal_article","article_type":"original","status":"public","date_updated":"2024-02-22T15:18:34Z","department":[{"_id":"MaJö"}]},{"_id":"6184","status":"public","type":"journal_article","article_type":"original","date_updated":"2024-02-22T14:34:33Z","department":[{"_id":"LaEr"}],"oa_version":"Preprint","abstract":[{"text":"We prove edge universality for a general class of correlated real symmetric or complex Hermitian Wigner matrices with arbitrary expectation. Our theorem also applies to internal edges of the self-consistent density of states. In particular, we establish a strong form of band rigidity which excludes mismatches between location and label of eigenvalues close to internal edges in these general models.","lang":"eng"}],"intvolume":" 48","month":"03","main_file_link":[{"url":"https://arxiv.org/abs/1804.07744","open_access":"1"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0091-1798"]},"ec_funded":1,"related_material":{"record":[{"status":"public","id":"149","relation":"dissertation_contains"},{"status":"public","id":"6179","relation":"dissertation_contains"}]},"volume":48,"issue":"2","project":[{"call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","name":"Random matrices, universality and disordered quantum systems","grant_number":"338804"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Alt, Johannes, László Erdös, Torben H Krüger, and Dominik J Schröder. “Correlated Random Matrices: Band Rigidity and Edge Universality.” Annals of Probability. Institute of Mathematical Statistics, 2020. https://doi.org/10.1214/19-AOP1379.","ista":"Alt J, Erdös L, Krüger TH, Schröder DJ. 2020. Correlated random matrices: Band rigidity and edge universality. Annals of Probability. 48(2), 963–1001.","mla":"Alt, Johannes, et al. “Correlated Random Matrices: Band Rigidity and Edge Universality.” Annals of Probability, vol. 48, no. 2, Institute of Mathematical Statistics, 2020, pp. 963–1001, doi:10.1214/19-AOP1379.","apa":"Alt, J., Erdös, L., Krüger, T. H., & Schröder, D. J. (2020). Correlated random matrices: Band rigidity and edge universality. Annals of Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/19-AOP1379","ama":"Alt J, Erdös L, Krüger TH, Schröder DJ. Correlated random matrices: Band rigidity and edge universality. Annals of Probability. 2020;48(2):963-1001. doi:10.1214/19-AOP1379","short":"J. Alt, L. Erdös, T.H. Krüger, D.J. Schröder, Annals of Probability 48 (2020) 963–1001.","ieee":"J. Alt, L. Erdös, T. H. Krüger, and D. J. Schröder, “Correlated random matrices: Band rigidity and edge universality,” Annals of Probability, vol. 48, no. 2. Institute of Mathematical Statistics, pp. 963–1001, 2020."},"title":"Correlated random matrices: Band rigidity and edge universality","article_processing_charge":"No","external_id":{"isi":["000528269100013"],"arxiv":["1804.07744"]},"author":[{"full_name":"Alt, Johannes","last_name":"Alt","first_name":"Johannes","id":"36D3D8B6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Erdös, László","orcid":"0000-0001-5366-9603","last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László"},{"orcid":"0000-0002-4821-3297","full_name":"Krüger, Torben H","last_name":"Krüger","id":"3020C786-F248-11E8-B48F-1D18A9856A87","first_name":"Torben H"},{"id":"408ED176-F248-11E8-B48F-1D18A9856A87","first_name":"Dominik J","last_name":"Schröder","full_name":"Schröder, Dominik J","orcid":"0000-0002-2904-1856"}],"oa":1,"publisher":"Institute of Mathematical Statistics","quality_controlled":"1","publication":"Annals of Probability","day":"01","year":"2020","isi":1,"date_created":"2019-03-28T09:20:08Z","date_published":"2020-03-01T00:00:00Z","doi":"10.1214/19-AOP1379","page":"963-1001"},{"ddc":["580"],"date_updated":"2024-02-28T12:41:52Z","department":[{"_id":"EvBe"}],"file_date_updated":"2024-02-28T12:39:56Z","_id":"15037","keyword":["Plant Science","Molecular Biology"],"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","language":[{"iso":"eng"}],"file":[{"file_name":"2020_MolecularPlant_MoulinierAnzola.pdf","date_created":"2024-02-28T12:39:56Z","file_size":3089212,"date_updated":"2024-02-28T12:39:56Z","creator":"dernst","success":1,"checksum":"c538a5008f7827f62d17d40a3bfabe65","file_id":"15038","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"publication_status":"published","publication_identifier":{"issn":["1674-2052"]},"volume":13,"issue":"5","pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Protein abundance and localization at the plasma membrane (PM) shapes plant development and mediates adaptation to changing environmental conditions. It is regulated by ubiquitination, a post-translational modification crucial for the proper sorting of endocytosed PM proteins to the vacuole for subsequent degradation. To understand the significance and the variety of roles played by this reversible modification, the function of ubiquitin receptors, which translate the ubiquitin signature into a cellular response, needs to be elucidated. In this study, we show that TOL (TOM1-like) proteins function in plants as multivalent ubiquitin receptors, governing ubiquitinated cargo delivery to the vacuole via the conserved Endosomal Sorting Complex Required for Transport (ESCRT) pathway. TOL2 and TOL6 interact with components of the ESCRT machinery and bind to K63-linked ubiquitin via two tandemly arranged conserved ubiquitin-binding domains. Mutation of these domains results not only in a loss of ubiquitin binding but also altered localization, abolishing TOL6 ubiquitin receptor activity. Function and localization of TOL6 is itself regulated by ubiquitination, whereby TOL6 ubiquitination potentially modulates degradation of PM-localized cargoes, assisting in the fine-tuning of the delicate interplay between protein recycling and downregulation. Taken together, our findings demonstrate the function and regulation of a ubiquitin receptor that mediates vacuolar degradation of PM proteins in higher plants."}],"intvolume":" 13","month":"05","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Moulinier-Anzola, Jeanette, Maximilian Schwihla, Lucinda De-Araújo, Christina Artner, Lisa Jörg, Nataliia Konstantinova, Christian Luschnig, and Barbara Korbei. “TOLs Function as Ubiquitin Receptors in the Early Steps of the ESCRT Pathway in Higher Plants.” Molecular Plant. Elsevier, 2020. https://doi.org/10.1016/j.molp.2020.02.012.","ista":"Moulinier-Anzola J, Schwihla M, De-Araújo L, Artner C, Jörg L, Konstantinova N, Luschnig C, Korbei B. 2020. TOLs function as ubiquitin receptors in the early steps of the ESCRT pathway in higher plants. Molecular Plant. 13(5), 717–731.","mla":"Moulinier-Anzola, Jeanette, et al. “TOLs Function as Ubiquitin Receptors in the Early Steps of the ESCRT Pathway in Higher Plants.” Molecular Plant, vol. 13, no. 5, Elsevier, 2020, pp. 717–31, doi:10.1016/j.molp.2020.02.012.","short":"J. Moulinier-Anzola, M. Schwihla, L. De-Araújo, C. Artner, L. Jörg, N. Konstantinova, C. Luschnig, B. Korbei, Molecular Plant 13 (2020) 717–731.","ieee":"J. Moulinier-Anzola et al., “TOLs function as ubiquitin receptors in the early steps of the ESCRT pathway in higher plants,” Molecular Plant, vol. 13, no. 5. Elsevier, pp. 717–731, 2020.","ama":"Moulinier-Anzola J, Schwihla M, De-Araújo L, et al. TOLs function as ubiquitin receptors in the early steps of the ESCRT pathway in higher plants. Molecular Plant. 2020;13(5):717-731. doi:10.1016/j.molp.2020.02.012","apa":"Moulinier-Anzola, J., Schwihla, M., De-Araújo, L., Artner, C., Jörg, L., Konstantinova, N., … Korbei, B. (2020). TOLs function as ubiquitin receptors in the early steps of the ESCRT pathway in higher plants. Molecular Plant. Elsevier. https://doi.org/10.1016/j.molp.2020.02.012"},"title":"TOLs function as ubiquitin receptors in the early steps of the ESCRT pathway in higher plants","external_id":{"pmid":["32087370"]},"article_processing_charge":"No","author":[{"last_name":"Moulinier-Anzola","full_name":"Moulinier-Anzola, Jeanette","first_name":"Jeanette"},{"first_name":"Maximilian","full_name":"Schwihla, Maximilian","last_name":"Schwihla"},{"first_name":"Lucinda","full_name":"De-Araújo, Lucinda","last_name":"De-Araújo"},{"full_name":"Artner, Christina","last_name":"Artner","first_name":"Christina","id":"45DF286A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Lisa","last_name":"Jörg","full_name":"Jörg, Lisa"},{"last_name":"Konstantinova","full_name":"Konstantinova, Nataliia","first_name":"Nataliia"},{"first_name":"Christian","last_name":"Luschnig","full_name":"Luschnig, Christian"},{"first_name":"Barbara","last_name":"Korbei","full_name":"Korbei, Barbara"}],"publication":"Molecular Plant","day":"04","year":"2020","has_accepted_license":"1","date_created":"2024-02-28T08:55:56Z","date_published":"2020-05-04T00:00:00Z","doi":"10.1016/j.molp.2020.02.012","page":"717-731","oa":1,"publisher":"Elsevier","quality_controlled":"1"},{"author":[{"first_name":"Higor Vinícius Dias","last_name":"Rosa","full_name":"Rosa, Higor Vinícius Dias"},{"last_name":"Leonardo","full_name":"Leonardo, Diego Antonio","first_name":"Diego Antonio"},{"last_name":"Brognara","full_name":"Brognara, Gabriel","first_name":"Gabriel","id":"D96FFDA0-A884-11E9-9968-DC26E6697425"},{"last_name":"Brandão-Neto","full_name":"Brandão-Neto, José","first_name":"José"},{"first_name":"Humberto","last_name":"D'Muniz Pereira","full_name":"D'Muniz Pereira, Humberto"},{"full_name":"Araújo, Ana Paula Ulian","last_name":"Araújo","first_name":"Ana Paula Ulian"},{"first_name":"Richard Charles","full_name":"Garratt, Richard Charles","last_name":"Garratt"}],"external_id":{"pmid":["32910969"]},"article_processing_charge":"No","title":"Molecular recognition at septin interfaces: The switches hold the key","citation":{"chicago":"Rosa, Higor Vinícius Dias, Diego Antonio Leonardo, Gabriel Brognara, José Brandão-Neto, Humberto D’Muniz Pereira, Ana Paula Ulian Araújo, and Richard Charles Garratt. “Molecular Recognition at Septin Interfaces: The Switches Hold the Key.” Journal of Molecular Biology. Elsevier, 2020. https://doi.org/10.1016/j.jmb.2020.09.001.","ista":"Rosa HVD, Leonardo DA, Brognara G, Brandão-Neto J, D’Muniz Pereira H, Araújo APU, Garratt RC. 2020. Molecular recognition at septin interfaces: The switches hold the key. Journal of Molecular Biology. 432(21), 5784–5801.","mla":"Rosa, Higor Vinícius Dias, et al. “Molecular Recognition at Septin Interfaces: The Switches Hold the Key.” Journal of Molecular Biology, vol. 432, no. 21, Elsevier, 2020, pp. 5784–801, doi:10.1016/j.jmb.2020.09.001.","short":"H.V.D. Rosa, D.A. Leonardo, G. Brognara, J. Brandão-Neto, H. D’Muniz Pereira, A.P.U. Araújo, R.C. Garratt, Journal of Molecular Biology 432 (2020) 5784–5801.","ieee":"H. V. D. Rosa et al., “Molecular recognition at septin interfaces: The switches hold the key,” Journal of Molecular Biology, vol. 432, no. 21. Elsevier, pp. 5784–5801, 2020.","ama":"Rosa HVD, Leonardo DA, Brognara G, et al. Molecular recognition at septin interfaces: The switches hold the key. Journal of Molecular Biology. 2020;432(21):5784-5801. doi:10.1016/j.jmb.2020.09.001","apa":"Rosa, H. V. D., Leonardo, D. A., Brognara, G., Brandão-Neto, J., D’Muniz Pereira, H., Araújo, A. P. U., & Garratt, R. C. (2020). Molecular recognition at septin interfaces: The switches hold the key. Journal of Molecular Biology. Elsevier. https://doi.org/10.1016/j.jmb.2020.09.001"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"5784-5801","doi":"10.1016/j.jmb.2020.09.001","date_published":"2020-10-02T00:00:00Z","date_created":"2024-02-28T08:50:34Z","year":"2020","day":"02","publication":"Journal of Molecular Biology","publisher":"Elsevier","quality_controlled":"1","oa":1,"department":[{"_id":"MaLo"}],"date_updated":"2024-02-28T12:37:54Z","article_type":"original","type":"journal_article","status":"public","keyword":["Molecular Biology","Structural Biology"],"_id":"15036","volume":432,"issue":"21","publication_identifier":{"issn":["0022-2836"]},"publication_status":"published","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.jmb.2020.09.001"}],"month":"10","intvolume":" 432","abstract":[{"text":"The assembly of a septin filament requires that homologous monomers must distinguish between one another in establishing appropriate interfaces with their neighbors. To understand this phenomenon at the molecular level, we present the first four crystal structures of heterodimeric septin complexes. We describe in detail the two distinct types of G-interface present within the octameric particles, which must polymerize to form filaments. These are formed between SEPT2 and SEPT6 and between SEPT7 and SEPT3, and their description permits an understanding of the structural basis for the selectivity necessary for correct filament assembly. By replacing SEPT6 by SEPT8 or SEPT11, it is possible to rationalize Kinoshita's postulate, which predicts the exchangeability of septins from within a subgroup. Switches I and II, which in classical small GTPases provide a mechanism for nucleotide-dependent conformational change, have been repurposed in septins to play a fundamental role in molecular recognition. Specifically, it is switch I which holds the key to discriminating between the two different G-interfaces. Moreover, residues which are characteristic for a given subgroup play subtle, but pivotal, roles in guaranteeing that the correct interfaces are formed.","lang":"eng"}],"pmid":1,"oa_version":"Published Version"},{"ddc":["000"],"date_updated":"2024-02-28T12:57:31Z","department":[{"_id":"ChWo"}],"file_date_updated":"2020-11-23T09:03:19Z","_id":"8384","status":"public","type":"journal_article","article_type":"original","file":[{"file_name":"2020_soapfilm_submitted.pdf","date_created":"2020-11-23T09:03:19Z","creator":"dernst","file_size":14935529,"date_updated":"2020-11-23T09:03:19Z","success":1,"checksum":"813831ca91319d794d9748c276b24578","file_id":"8795","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["07300301"],"eissn":["15577368"]},"publication_status":"published","volume":39,"issue":"4","ec_funded":1,"oa_version":"Submitted Version","acknowledged_ssus":[{"_id":"ScienComp"}],"abstract":[{"lang":"eng","text":"Previous research on animations of soap bubbles, films, and foams largely focuses on the motion and geometric shape of the bubble surface. These works neglect the evolution of the bubble’s thickness, which is normally responsible for visual phenomena like surface vortices, Newton’s interference patterns, capillary waves, and deformation-dependent rupturing of films in a foam. In this paper, we model these natural phenomena by introducing the film thickness as a reduced degree of freedom in the Navier-Stokes equations and deriving their equations of motion. We discretize the equations on a nonmanifold triangle mesh surface and couple it to an existing bubble solver. In doing so, we also introduce an incompressible fluid solver for 2.5D films and a novel advection algorithm for convecting fields across non-manifold surface junctions. Our simulations enhance state-of-the-art bubble solvers with additional effects caused by convection, rippling, draining, and evaporation of the thin film."}],"month":"07","intvolume":" 39","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1145/3386569.3392405","open_access":"1"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Ishida, Sadashige, Peter Synak, Fumiya Narita, Toshiya Hachisuka, and Chris Wojtan. “A Model for Soap Film Dynamics with Evolving Thickness.” ACM Transactions on Graphics. Association for Computing Machinery, 2020. https://doi.org/10.1145/3386569.3392405.","ista":"Ishida S, Synak P, Narita F, Hachisuka T, Wojtan C. 2020. A model for soap film dynamics with evolving thickness. ACM Transactions on Graphics. 39(4), 31.","mla":"Ishida, Sadashige, et al. “A Model for Soap Film Dynamics with Evolving Thickness.” ACM Transactions on Graphics, vol. 39, no. 4, 31, Association for Computing Machinery, 2020, doi:10.1145/3386569.3392405.","ama":"Ishida S, Synak P, Narita F, Hachisuka T, Wojtan C. A model for soap film dynamics with evolving thickness. ACM Transactions on Graphics. 2020;39(4). doi:10.1145/3386569.3392405","apa":"Ishida, S., Synak, P., Narita, F., Hachisuka, T., & Wojtan, C. (2020). A model for soap film dynamics with evolving thickness. ACM Transactions on Graphics. Association for Computing Machinery. https://doi.org/10.1145/3386569.3392405","ieee":"S. Ishida, P. Synak, F. Narita, T. Hachisuka, and C. Wojtan, “A model for soap film dynamics with evolving thickness,” ACM Transactions on Graphics, vol. 39, no. 4. Association for Computing Machinery, 2020.","short":"S. Ishida, P. Synak, F. Narita, T. Hachisuka, C. Wojtan, ACM Transactions on Graphics 39 (2020)."},"title":"A model for soap film dynamics with evolving thickness","author":[{"first_name":"Sadashige","id":"6F7C4B96-A8E9-11E9-A7CA-09ECE5697425","full_name":"Ishida, Sadashige","last_name":"Ishida"},{"last_name":"Synak","full_name":"Synak, Peter","id":"331776E2-F248-11E8-B48F-1D18A9856A87","first_name":"Peter"},{"first_name":"Fumiya","full_name":"Narita, Fumiya","last_name":"Narita"},{"last_name":"Hachisuka","full_name":"Hachisuka, Toshiya","first_name":"Toshiya"},{"first_name":"Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","last_name":"Wojtan","full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546"}],"external_id":{"isi":["000583700300004"]},"article_processing_charge":"No","article_number":"31","project":[{"_id":"2533E772-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","grant_number":"638176"}],"day":"08","publication":"ACM Transactions on Graphics","isi":1,"has_accepted_license":"1","year":"2020","doi":"10.1145/3386569.3392405","date_published":"2020-07-08T00:00:00Z","date_created":"2020-09-13T22:01:18Z","acknowledgement":"We wish to thank the anonymous reviewers and the members of the Visual Computing Group at IST Austria for their valuable feedback, especially Camille Schreck for her help in rendering. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing. We would like to thank the authors of [Belcour and Barla 2017] for providing their implementation, the authors of [Atkins and Elliott 2010] and [Seychelles et al. 2008] for allowing us to use their results, and Rok Grah for helpful discussions. Finally, we thank Ryoichi Ando for many discussions from the beginning of the project that resulted in important contents of the paper including our formulation, numerical scheme, and initial implementation. This project has received funding from the\r\nEuropean Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 638176.","publisher":"Association for Computing Machinery","quality_controlled":"1","oa":1},{"project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"short":"A. Czumaj, P. Davies, M. Parter, in:, Proceedings of the 32nd ACM Symposium on Parallelism in Algorithms and Architectures (SPAA 2020), Association for Computing Machinery, 2020, pp. 175–185.","ieee":"A. Czumaj, P. Davies, and M. Parter, “Graph sparsification for derandomizing massively parallel computation with low space,” in Proceedings of the 32nd ACM Symposium on Parallelism in Algorithms and Architectures (SPAA 2020), Virtual Event, United States, 2020, no. 7, pp. 175–185.","ama":"Czumaj A, Davies P, Parter M. Graph sparsification for derandomizing massively parallel computation with low space. In: Proceedings of the 32nd ACM Symposium on Parallelism in Algorithms and Architectures (SPAA 2020). Association for Computing Machinery; 2020:175-185. doi:10.1145/3350755.3400282","apa":"Czumaj, A., Davies, P., & Parter, M. (2020). Graph sparsification for derandomizing massively parallel computation with low space. In Proceedings of the 32nd ACM Symposium on Parallelism in Algorithms and Architectures (SPAA 2020) (pp. 175–185). Virtual Event, United States: Association for Computing Machinery. https://doi.org/10.1145/3350755.3400282","mla":"Czumaj, Artur, et al. “Graph Sparsification for Derandomizing Massively Parallel Computation with Low Space.” Proceedings of the 32nd ACM Symposium on Parallelism in Algorithms and Architectures (SPAA 2020), no. 7, Association for Computing Machinery, 2020, pp. 175–85, doi:10.1145/3350755.3400282.","ista":"Czumaj A, Davies P, Parter M. 2020. Graph sparsification for derandomizing massively parallel computation with low space. Proceedings of the 32nd ACM Symposium on Parallelism in Algorithms and Architectures (SPAA 2020). SPAA: Symposium on Parallelism in Algorithms and Architectures, 175–185.","chicago":"Czumaj, Artur, Peter Davies, and Merav Parter. “Graph Sparsification for Derandomizing Massively Parallel Computation with Low Space.” In Proceedings of the 32nd ACM Symposium on Parallelism in Algorithms and Architectures (SPAA 2020), 175–85. Association for Computing Machinery, 2020. https://doi.org/10.1145/3350755.3400282."},"title":"Graph sparsification for derandomizing massively parallel computation with low space","author":[{"first_name":"Artur","last_name":"Czumaj","full_name":"Czumaj, Artur","orcid":"0000-0002-5646-9524"},{"id":"11396234-BB50-11E9-B24C-90FCE5697425","first_name":"Peter","orcid":"0000-0002-5646-9524","full_name":"Davies, Peter","last_name":"Davies"},{"last_name":"Parter","full_name":"Parter, Merav","first_name":"Merav"}],"external_id":{"isi":["000744436200015"],"arxiv":["1912.05390"]},"article_processing_charge":"No","publisher":"Association for Computing Machinery","quality_controlled":"1","oa":1,"day":"01","publication":"Proceedings of the 32nd ACM Symposium on Parallelism in Algorithms and Architectures (SPAA 2020)","isi":1,"year":"2020","date_published":"2020-07-01T00:00:00Z","doi":"10.1145/3350755.3400282","date_created":"2020-05-06T08:53:34Z","page":"175-185","_id":"7802","status":"public","type":"conference","conference":{"end_date":"2020-07-17","location":"Virtual Event, United States","start_date":"2020-07-15","name":"SPAA: Symposium on Parallelism in Algorithms and Architectures"},"date_updated":"2024-02-28T12:53:09Z","department":[{"_id":"DaAl"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"The Massively Parallel Computation (MPC) model is an emerging model which distills core aspects of distributed and parallel computation. It has been developed as a tool to solve (typically graph) problems in systems where the input is distributed over many machines with limited space.\r\n\t\r\nRecent work has focused on the regime in which machines have sublinear (in $n$, the number of nodes in the input graph) space, with randomized algorithms presented for fundamental graph problems of Maximal Matching and Maximal Independent Set. However, there have been no prior corresponding deterministic algorithms.\r\n\t\r\n\tA major challenge underlying the sublinear space setting is that the local space of each machine might be too small to store all the edges incident to a single node. This poses a considerable obstacle compared to the classical models in which each node is assumed to know and have easy access to its incident edges. To overcome this barrier we introduce a new graph sparsification technique that deterministically computes a low-degree subgraph with additional desired properties. The degree of the nodes in this subgraph is small in the sense that the edges of each node can be now stored on a single machine. This low-degree subgraph also has the property that solving the problem on this subgraph provides \\emph{significant} global progress, i.e., progress towards solving the problem for the original input graph.\r\n\t\r\nUsing this framework to derandomize the well-known randomized algorithm of Luby [SICOMP'86], we obtain $O(\\log \\Delta+\\log\\log n)$-round deterministic MPC algorithms for solving the fundamental problems of Maximal Matching and Maximal Independent Set with $O(n^{\\epsilon})$ space on each machine for any constant $\\epsilon > 0$. Based on the recent work of Ghaffari et al. [FOCS'18], this additive $O(\\log\\log n)$ factor is conditionally essential. These algorithms can also be shown to run in $O(\\log \\Delta)$ rounds in the closely related model of CONGESTED CLIQUE, improving upon the state-of-the-art bound of $O(\\log^2 \\Delta)$ rounds by Censor-Hillel et al. [DISC'17]."}],"month":"07","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1912.05390","open_access":"1"}],"language":[{"iso":"eng"}],"publication_status":"published","related_material":{"record":[{"status":"public","id":"9541","relation":"later_version"}]},"issue":"7","ec_funded":1},{"date_created":"2020-04-05T22:00:49Z","doi":"10.1145/3332466.3374542","date_published":"2020-02-19T00:00:00Z","page":"276-291","publication":"Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming","day":"19","year":"2020","isi":1,"oa":1,"publisher":"Association for Computing Machinery","quality_controlled":"1","acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union Horizon 2020 research and innovation program, grant agreement No 805223, ERC Starting Grant ScaleML. We acknowledge the support of the Natural Sciences and\r\nEngineering Research Council of Canada (NSERC). ","title":"Non-blocking interpolation search trees with doubly-logarithmic running time","article_processing_charge":"No","external_id":{"isi":["000564476500020"]},"author":[{"first_name":"Trevor A","id":"3569F0A0-F248-11E8-B48F-1D18A9856A87","full_name":"Brown, Trevor A","last_name":"Brown"},{"first_name":"Aleksandar","last_name":"Prokopec","full_name":"Prokopec, Aleksandar"},{"first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"T.A. Brown, A. Prokopec, D.-A. Alistarh, in:, Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, Association for Computing Machinery, 2020, pp. 276–291.","ieee":"T. A. Brown, A. Prokopec, and D.-A. Alistarh, “Non-blocking interpolation search trees with doubly-logarithmic running time,” in Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, San Diego, CA, United States, 2020, pp. 276–291.","apa":"Brown, T. A., Prokopec, A., & Alistarh, D.-A. (2020). Non-blocking interpolation search trees with doubly-logarithmic running time. In Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming (pp. 276–291). San Diego, CA, United States: Association for Computing Machinery. https://doi.org/10.1145/3332466.3374542","ama":"Brown TA, Prokopec A, Alistarh D-A. Non-blocking interpolation search trees with doubly-logarithmic running time. In: Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming. Association for Computing Machinery; 2020:276-291. doi:10.1145/3332466.3374542","mla":"Brown, Trevor A., et al. “Non-Blocking Interpolation Search Trees with Doubly-Logarithmic Running Time.” Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, Association for Computing Machinery, 2020, pp. 276–91, doi:10.1145/3332466.3374542.","ista":"Brown TA, Prokopec A, Alistarh D-A. 2020. Non-blocking interpolation search trees with doubly-logarithmic running time. Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming. PPOPP: Principles and Practice of Parallel Programming, 276–291.","chicago":"Brown, Trevor A, Aleksandar Prokopec, and Dan-Adrian Alistarh. “Non-Blocking Interpolation Search Trees with Doubly-Logarithmic Running Time.” In Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, 276–91. Association for Computing Machinery, 2020. https://doi.org/10.1145/3332466.3374542."},"project":[{"name":"Elastic Coordination for Scalable Machine Learning","grant_number":"805223","call_identifier":"H2020","_id":"268A44D6-B435-11E9-9278-68D0E5697425"}],"ec_funded":1,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"isbn":["9781450368186"]},"month":"02","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1145/3332466.3374542"}],"scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"Balanced search trees typically use key comparisons to guide their operations, and achieve logarithmic running time. By relying on numerical properties of the keys, interpolation search achieves lower search complexity and better performance. Although interpolation-based data structures were investigated in the past, their non-blocking concurrent variants have received very little attention so far.\r\nIn this paper, we propose the first non-blocking implementation of the classic interpolation search tree (IST) data structure. For arbitrary key distributions, the data structure ensures worst-case O(log n + p) amortized time for search, insertion and deletion traversals. When the input key distributions are smooth, lookups run in expected O(log log n + p) time, and insertion and deletion run in expected amortized O(log log n + p) time, where p is a bound on the number of threads. To improve the scalability of concurrent insertion and deletion, we propose a novel parallel rebuilding technique, which should be of independent interest.\r\nWe evaluate whether the theoretical improvements translate to practice by implementing the concurrent interpolation search tree, and benchmarking it on uniform and nonuniform key distributions, for dataset sizes in the millions to billions of keys. Relative to the state-of-the-art concurrent data structures, the concurrent interpolation search tree achieves performance improvements of up to 15% under high update rates, and of up to 50% under moderate update rates. Further, ISTs exhibit up to 2X less cache-misses, and consume 1.2 -- 2.6X less memory compared to the next best alternative on typical dataset sizes. We find that the results are surprisingly robust to distributional skew, which suggests that our data structure can be a promising alternative to classic concurrent search structures.","lang":"eng"}],"department":[{"_id":"DaAl"}],"date_updated":"2024-02-28T12:55:14Z","status":"public","conference":{"location":"San Diego, CA, United States","end_date":"2020-02-26","start_date":"2020-02-22","name":"PPOPP: Principles and Practice of Parallel Programming"},"type":"conference","_id":"7636"},{"quality_controlled":"1","publisher":"Association for Computing Machinery","scopus_import":"1","month":"07","abstract":[{"lang":"eng","text":"There has been a significant amount of research on hardware and software support for efficient concurrent data structures; yet, the question of how to build correct, simple, and scalable data structures has not yet been definitively settled. In this paper, we revisit this question from a minimalist perspective, and ask: what is the smallest amount of synchronization required for correct and efficient concurrent search data structures, and how could this minimal synchronization support be provided in hardware?\r\n\r\nTo address these questions, we introduce memory tagging, a simple hardware mechanism which enables the programmer to \"tag\" a dynamic set of memory locations, at cache-line granularity, and later validate whether the memory has been concurrently modified, with the possibility of updating one of the underlying locations atomically if validation succeeds. We provide several examples showing that this mechanism can enable fast and arguably simple concurrent data structure designs, such as lists, binary search trees, balanced search trees, range queries, and Software Transactional Memory (STM) implementations. We provide an implementation of memory tags in the Graphite multi-core simulator, showing that the mechanism can be implemented entirely at the level of L1 cache, and that it can enable non-trivial speedups versus existing implementations of the above data structures."}],"oa_version":"None","page":"37-49","issue":"7","doi":"10.1145/3350755.3400213","date_published":"2020-07-06T00:00:00Z","date_created":"2020-08-02T22:00:58Z","publication_identifier":{"isbn":["9781450369350"]},"isi":1,"publication_status":"published","year":"2020","day":"06","language":[{"iso":"eng"}],"publication":"Annual ACM Symposium on Parallelism in Algorithms and Architectures","type":"conference","conference":{"end_date":"2020-07-17","location":"Virtual Event, United States","start_date":"2020-07-15","name":"SPAA: Symposium on Parallelism in Algorithms and Architectures"},"status":"public","_id":"8191","author":[{"last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Brown","full_name":"Brown, Trevor A","id":"3569F0A0-F248-11E8-B48F-1D18A9856A87","first_name":"Trevor A"},{"last_name":"Singhal","full_name":"Singhal, Nandini","first_name":"Nandini"}],"article_processing_charge":"No","external_id":{"isi":["000744436200004"]},"department":[{"_id":"DaAl"}],"title":"Memory tagging: Minimalist synchronization for scalable concurrent data structures","citation":{"mla":"Alistarh, Dan-Adrian, et al. “Memory Tagging: Minimalist Synchronization for Scalable Concurrent Data Structures.” Annual ACM Symposium on Parallelism in Algorithms and Architectures, no. 7, Association for Computing Machinery, 2020, pp. 37–49, doi:10.1145/3350755.3400213.","short":"D.-A. Alistarh, T.A. Brown, N. Singhal, in:, Annual ACM Symposium on Parallelism in Algorithms and Architectures, Association for Computing Machinery, 2020, pp. 37–49.","ieee":"D.-A. Alistarh, T. A. Brown, and N. Singhal, “Memory tagging: Minimalist synchronization for scalable concurrent data structures,” in Annual ACM Symposium on Parallelism in Algorithms and Architectures, Virtual Event, United States, 2020, no. 7, pp. 37–49.","ama":"Alistarh D-A, Brown TA, Singhal N. Memory tagging: Minimalist synchronization for scalable concurrent data structures. In: Annual ACM Symposium on Parallelism in Algorithms and Architectures. Association for Computing Machinery; 2020:37-49. doi:10.1145/3350755.3400213","apa":"Alistarh, D.-A., Brown, T. A., & Singhal, N. (2020). Memory tagging: Minimalist synchronization for scalable concurrent data structures. In Annual ACM Symposium on Parallelism in Algorithms and Architectures (pp. 37–49). Virtual Event, United States: Association for Computing Machinery. https://doi.org/10.1145/3350755.3400213","chicago":"Alistarh, Dan-Adrian, Trevor A Brown, and Nandini Singhal. “Memory Tagging: Minimalist Synchronization for Scalable Concurrent Data Structures.” In Annual ACM Symposium on Parallelism in Algorithms and Architectures, 37–49. Association for Computing Machinery, 2020. https://doi.org/10.1145/3350755.3400213.","ista":"Alistarh D-A, Brown TA, Singhal N. 2020. Memory tagging: Minimalist synchronization for scalable concurrent data structures. Annual ACM Symposium on Parallelism in Algorithms and Architectures. SPAA: Symposium on Parallelism in Algorithms and Architectures, 37–49."},"date_updated":"2024-02-28T12:56:32Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"status":"public","conference":{"name":"PPOPP: Principles and Practice of Parallel Programming","start_date":"2020-02-22","location":"San Diego, CA, United States","end_date":"2020-02-26"},"type":"conference","_id":"7635","title":"Testing concurrency on the JVM with Lincheck","department":[{"_id":"DaAl"}],"article_processing_charge":"No","author":[{"first_name":"Nikita","id":"2F4DB10C-F248-11E8-B48F-1D18A9856A87","last_name":"Koval","full_name":"Koval, Nikita"},{"first_name":"Mariia","id":"26217AE4-77FF-11EA-8101-AD24D49E41F4","last_name":"Sokolova","full_name":"Sokolova, Mariia"},{"full_name":"Fedorov, Alexander","last_name":"Fedorov","first_name":"Alexander"},{"orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh","first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Dmitry","last_name":"Tsitelov","full_name":"Tsitelov, Dmitry"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Koval N, Sokolova M, Fedorov A, Alistarh D-A, Tsitelov D. 2020. Testing concurrency on the JVM with Lincheck. Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, PPOPP. PPOPP: Principles and Practice of Parallel Programming, 423–424.","chicago":"Koval, Nikita, Mariia Sokolova, Alexander Fedorov, Dan-Adrian Alistarh, and Dmitry Tsitelov. “Testing Concurrency on the JVM with Lincheck.” In Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, PPOPP, 423–24. Association for Computing Machinery, 2020. https://doi.org/10.1145/3332466.3374503.","short":"N. Koval, M. Sokolova, A. Fedorov, D.-A. Alistarh, D. Tsitelov, in:, Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, PPOPP, Association for Computing Machinery, 2020, pp. 423–424.","ieee":"N. Koval, M. Sokolova, A. Fedorov, D.-A. Alistarh, and D. Tsitelov, “Testing concurrency on the JVM with Lincheck,” in Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, PPOPP, San Diego, CA, United States, 2020, pp. 423–424.","apa":"Koval, N., Sokolova, M., Fedorov, A., Alistarh, D.-A., & Tsitelov, D. (2020). Testing concurrency on the JVM with Lincheck. In Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, PPOPP (pp. 423–424). San Diego, CA, United States: Association for Computing Machinery. https://doi.org/10.1145/3332466.3374503","ama":"Koval N, Sokolova M, Fedorov A, Alistarh D-A, Tsitelov D. Testing concurrency on the JVM with Lincheck. In: Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, PPOPP. Association for Computing Machinery; 2020:423-424. doi:10.1145/3332466.3374503","mla":"Koval, Nikita, et al. “Testing Concurrency on the JVM with Lincheck.” Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, PPOPP, Association for Computing Machinery, 2020, pp. 423–24, doi:10.1145/3332466.3374503."},"date_updated":"2024-02-28T12:53:46Z","month":"02","scopus_import":"1","quality_controlled":"1","publisher":"Association for Computing Machinery","oa_version":"None","abstract":[{"text":"Concurrent programming can be notoriously complex and error-prone. Programming bugs can arise from a variety of sources, such as operation re-reordering, or incomplete understanding of the memory model. A variety of formal and model checking methods have been developed to address this fundamental difficulty. While technically interesting, existing academic methods are still hard to apply to the large codebases typical of industrial deployments, which limits their practical impact.","lang":"eng"}],"date_created":"2020-04-05T22:00:48Z","date_published":"2020-02-19T00:00:00Z","doi":"10.1145/3332466.3374503","page":"423-424","language":[{"iso":"eng"}],"publication":"Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, PPOPP","day":"19","year":"2020","publication_status":"published","publication_identifier":{"isbn":["9781450368186"]}},{"oa_version":"None","abstract":[{"text":"We introduce extension-based proofs, a class of impossibility proofs that includes valency arguments. They are modelled as an interaction between a prover and a protocol. Using proofs based on combinatorial topology, it has been shown that it is impossible to deterministically solve k-set agreement among n > k ≥ 2 processes in a wait-free manner. However, it was unknown whether proofs based on simpler techniques were possible. We explain why this impossibility result cannot be obtained by an extension-based proof and, hence, extension-based proofs are limited in power.","lang":"eng"}],"month":"07","publisher":"Association for Computing Machinery","scopus_import":"1","quality_controlled":"1","language":[{"iso":"eng"}],"publication":"Proceedings of the 39th Symposium on Principles of Distributed Computing","day":"31","publication_status":"published","year":"2020","publication_identifier":{"isbn":["9781450375825"]},"date_created":"2020-09-13T22:01:18Z","doi":"10.1145/3382734.3405743","date_published":"2020-07-31T00:00:00Z","page":"54-56","_id":"8383","status":"public","conference":{"end_date":"2020-08-07","location":"Virtual, Italy","start_date":"2020-08-03","name":"PODC: Principles of Distributed Computing"},"type":"conference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-02-28T12:54:19Z","citation":{"mla":"Alistarh, Dan-Adrian, et al. “Brief Announcement: Why Extension-Based Proofs Fail.” Proceedings of the 39th Symposium on Principles of Distributed Computing, Association for Computing Machinery, 2020, pp. 54–56, doi:10.1145/3382734.3405743.","short":"D.-A. Alistarh, J. Aspnes, F. Ellen, R. Gelashvili, L. Zhu, in:, Proceedings of the 39th Symposium on Principles of Distributed Computing, Association for Computing Machinery, 2020, pp. 54–56.","ieee":"D.-A. Alistarh, J. Aspnes, F. Ellen, R. Gelashvili, and L. Zhu, “Brief Announcement: Why Extension-Based Proofs Fail,” in Proceedings of the 39th Symposium on Principles of Distributed Computing, Virtual, Italy, 2020, pp. 54–56.","apa":"Alistarh, D.-A., Aspnes, J., Ellen, F., Gelashvili, R., & Zhu, L. (2020). Brief Announcement: Why Extension-Based Proofs Fail. In Proceedings of the 39th Symposium on Principles of Distributed Computing (pp. 54–56). Virtual, Italy: Association for Computing Machinery. https://doi.org/10.1145/3382734.3405743","ama":"Alistarh D-A, Aspnes J, Ellen F, Gelashvili R, Zhu L. Brief Announcement: Why Extension-Based Proofs Fail. In: Proceedings of the 39th Symposium on Principles of Distributed Computing. Association for Computing Machinery; 2020:54-56. doi:10.1145/3382734.3405743","chicago":"Alistarh, Dan-Adrian, James Aspnes, Faith Ellen, Rati Gelashvili, and Leqi Zhu. “Brief Announcement: Why Extension-Based Proofs Fail.” In Proceedings of the 39th Symposium on Principles of Distributed Computing, 54–56. Association for Computing Machinery, 2020. https://doi.org/10.1145/3382734.3405743.","ista":"Alistarh D-A, Aspnes J, Ellen F, Gelashvili R, Zhu L. 2020. Brief Announcement: Why Extension-Based Proofs Fail. Proceedings of the 39th Symposium on Principles of Distributed Computing. PODC: Principles of Distributed Computing, 54–56."},"department":[{"_id":"DaAl"}],"title":"Brief Announcement: Why Extension-Based Proofs Fail","article_processing_charge":"No","author":[{"full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian"},{"last_name":"Aspnes","full_name":"Aspnes, James","first_name":"James"},{"first_name":"Faith","full_name":"Ellen, Faith","last_name":"Ellen"},{"last_name":"Gelashvili","full_name":"Gelashvili, Rati","first_name":"Rati"},{"last_name":"Zhu","full_name":"Zhu, Leqi","first_name":"Leqi"}]},{"abstract":[{"lang":"eng","text":"We present a method for animating yarn-level cloth effects using a thin-shell solver. We accomplish this through numerical homogenization: we first use a large number of yarn-level simulations to build a model of the potential energy density of the cloth, and then use this energy density function to compute forces in a thin shell simulator. We model several yarn-based materials, including both woven and knitted fabrics. Our model faithfully reproduces expected effects like the stiffness of woven fabrics, and the highly deformable nature and anisotropy of knitted fabrics. Our approach does not require any real-world experiments nor measurements; because the method is based entirely on simulations, it can generate entirely new material models quickly, without the need for testing apparatuses or human intervention. We provide data-driven models of several woven and knitted fabrics, which can be used for efficient simulation with an off-the-shelf cloth solver."}],"acknowledged_ssus":[{"_id":"ScienComp"}],"oa_version":"Submitted Version","main_file_link":[{"url":"https://doi.org/10.1145/3386569.3392412","open_access":"1"}],"scopus_import":"1","intvolume":" 39","month":"07","publication_status":"published","publication_identifier":{"eissn":["15577368"],"issn":["07300301"]},"language":[{"iso":"eng"}],"file":[{"date_created":"2020-11-23T09:01:22Z","file_name":"2020_hylc_submitted.pdf","date_updated":"2020-11-23T09:01:22Z","file_size":38922662,"creator":"dernst","checksum":"cf4c1d361c3196c4bd424520a5588205","file_id":"8794","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"ec_funded":1,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"12358"}]},"issue":"4","volume":39,"_id":"8385","article_type":"original","type":"journal_article","status":"public","date_updated":"2024-02-28T12:57:47Z","ddc":["000"],"department":[{"_id":"ChWo"}],"file_date_updated":"2020-11-23T09:01:22Z","acknowledgement":"We wish to thank the anonymous reviewers and the members of the Visual Computing Group at IST Austria for their valuable feedback. We also thank the creators of the Berkeley Garment Library [de Joya et al. 2012] for providing garment meshes, [Krishnamurthy and Levoy 1996] and [Turk and Levoy 1994] for the armadillo and bunny meshes, the creators of libWetCloth [Fei et al. 2018] for their implementation of discrete elastic rod forces, and Tomáš Skřivan for\r\ninspiring discussions and help with Mathematica code generation. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 638176. Rahul Narain is supported by a Pankaj Gupta Young Faculty Fellowship and a gift from Adobe Inc.","oa":1,"quality_controlled":"1","publisher":"Association for Computing Machinery","year":"2020","has_accepted_license":"1","isi":1,"publication":"ACM Transactions on Graphics","day":"08","date_created":"2020-09-13T22:01:18Z","doi":"10.1145/3386569.3392412","date_published":"2020-07-08T00:00:00Z","article_number":"48","project":[{"name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","grant_number":"638176","_id":"2533E772-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"citation":{"apa":"Sperl, G., Narain, R., & Wojtan, C. (2020). Homogenized yarn-level cloth. ACM Transactions on Graphics. Association for Computing Machinery. https://doi.org/10.1145/3386569.3392412","ama":"Sperl G, Narain R, Wojtan C. Homogenized yarn-level cloth. ACM Transactions on Graphics. 2020;39(4). doi:10.1145/3386569.3392412","short":"G. Sperl, R. Narain, C. Wojtan, ACM Transactions on Graphics 39 (2020).","ieee":"G. Sperl, R. Narain, and C. Wojtan, “Homogenized yarn-level cloth,” ACM Transactions on Graphics, vol. 39, no. 4. Association for Computing Machinery, 2020.","mla":"Sperl, Georg, et al. “Homogenized Yarn-Level Cloth.” ACM Transactions on Graphics, vol. 39, no. 4, 48, Association for Computing Machinery, 2020, doi:10.1145/3386569.3392412.","ista":"Sperl G, Narain R, Wojtan C. 2020. Homogenized yarn-level cloth. ACM Transactions on Graphics. 39(4), 48.","chicago":"Sperl, Georg, Rahul Narain, and Chris Wojtan. “Homogenized Yarn-Level Cloth.” ACM Transactions on Graphics. Association for Computing Machinery, 2020. https://doi.org/10.1145/3386569.3392412."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","external_id":{"isi":["000583700300021"]},"author":[{"last_name":"Sperl","full_name":"Sperl, Georg","first_name":"Georg","id":"4DD40360-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Narain, Rahul","last_name":"Narain","first_name":"Rahul"},{"last_name":"Wojtan","full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher J"}],"title":"Homogenized yarn-level cloth"},{"external_id":{"isi":["000537900300001"],"arxiv":["2002.07294"]},"article_processing_charge":"No","author":[{"full_name":"Pȩkalski, J.","last_name":"Pȩkalski","first_name":"J."},{"last_name":"Rzadkowski","full_name":"Rzadkowski, Wojciech","orcid":"0000-0002-1106-4419","first_name":"Wojciech","id":"48C55298-F248-11E8-B48F-1D18A9856A87"},{"first_name":"A. Z.","full_name":"Panagiotopoulos, A. Z.","last_name":"Panagiotopoulos"}],"title":"Shear-induced ordering in systems with competing interactions: A machine learning study","citation":{"ista":"Pȩkalski J, Rzadkowski W, Panagiotopoulos AZ. 2020. Shear-induced ordering in systems with competing interactions: A machine learning study. The Journal of chemical physics. 152(20), 204905.","chicago":"Pȩkalski, J., Wojciech Rzadkowski, and A. Z. Panagiotopoulos. “Shear-Induced Ordering in Systems with Competing Interactions: A Machine Learning Study.” The Journal of Chemical Physics. AIP Publishing, 2020. https://doi.org/10.1063/5.0005194.","apa":"Pȩkalski, J., Rzadkowski, W., & Panagiotopoulos, A. Z. (2020). Shear-induced ordering in systems with competing interactions: A machine learning study. The Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/5.0005194","ama":"Pȩkalski J, Rzadkowski W, Panagiotopoulos AZ. Shear-induced ordering in systems with competing interactions: A machine learning study. The Journal of chemical physics. 2020;152(20). doi:10.1063/5.0005194","ieee":"J. Pȩkalski, W. Rzadkowski, and A. Z. Panagiotopoulos, “Shear-induced ordering in systems with competing interactions: A machine learning study,” The Journal of chemical physics, vol. 152, no. 20. AIP Publishing, 2020.","short":"J. Pȩkalski, W. Rzadkowski, A.Z. Panagiotopoulos, The Journal of Chemical Physics 152 (2020).","mla":"Pȩkalski, J., et al. “Shear-Induced Ordering in Systems with Competing Interactions: A Machine Learning Study.” The Journal of Chemical Physics, vol. 152, no. 20, 204905, AIP Publishing, 2020, doi:10.1063/5.0005194."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program"}],"article_number":"204905","date_created":"2020-06-14T22:00:49Z","date_published":"2020-05-29T00:00:00Z","doi":"10.1063/5.0005194","year":"2020","isi":1,"publication":"The Journal of chemical physics","day":"29","oa":1,"publisher":"AIP Publishing","quality_controlled":"1","department":[{"_id":"MiLe"}],"date_updated":"2024-02-28T13:00:28Z","article_type":"original","type":"journal_article","status":"public","_id":"7956","ec_funded":1,"related_material":{"record":[{"id":"10759","status":"public","relation":"dissertation_contains"}]},"issue":"20","volume":152,"publication_status":"published","publication_identifier":{"eissn":["10897690"]},"language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1063/5.0005194"}],"scopus_import":"1","intvolume":" 152","month":"05","abstract":[{"text":"When short-range attractions are combined with long-range repulsions in colloidal particle systems, complex microphases can emerge. Here, we study a system of isotropic particles, which can form lamellar structures or a disordered fluid phase when temperature is varied. We show that, at equilibrium, the lamellar structure crystallizes, while out of equilibrium, the system forms a variety of structures at different shear rates and temperatures above melting. The shear-induced ordering is analyzed by means of principal component analysis and artificial neural networks, which are applied to data of reduced dimensionality. Our results reveal the possibility of inducing ordering by shear, potentially providing a feasible route to the fabrication of ordered lamellar structures from isotropic particles.","lang":"eng"}],"oa_version":"Published Version"},{"conference":{"name":"PODC: Principles of Distributed Computing","location":"Virtual, Italy","end_date":"2020-08-07","start_date":"2020-08-03"},"type":"conference","status":"public","_id":"8382","article_processing_charge":"No","author":[{"first_name":"Mirza Ahad","id":"3EDE6DE4-AA5A-11E9-986D-341CE6697425","last_name":"Baig","full_name":"Baig, Mirza Ahad"},{"first_name":"Danny","full_name":"Hendler, Danny","last_name":"Hendler"},{"full_name":"Milani, Alessia","last_name":"Milani","first_name":"Alessia"},{"first_name":"Corentin","full_name":"Travers, Corentin","last_name":"Travers"}],"title":"Long-lived snapshots with polylogarithmic amortized step complexity","citation":{"short":"M.A. Baig, D. Hendler, A. Milani, C. Travers, in:, Proceedings of the 39th Symposium on Principles of Distributed Computing, Association for Computing Machinery, 2020, pp. 31–40.","ieee":"M. A. Baig, D. Hendler, A. Milani, and C. Travers, “Long-lived snapshots with polylogarithmic amortized step complexity,” in Proceedings of the 39th Symposium on Principles of Distributed Computing, Virtual, Italy, 2020, pp. 31–40.","ama":"Baig MA, Hendler D, Milani A, Travers C. Long-lived snapshots with polylogarithmic amortized step complexity. In: Proceedings of the 39th Symposium on Principles of Distributed Computing. Association for Computing Machinery; 2020:31-40. doi:10.1145/3382734.3406005","apa":"Baig, M. A., Hendler, D., Milani, A., & Travers, C. (2020). Long-lived snapshots with polylogarithmic amortized step complexity. In Proceedings of the 39th Symposium on Principles of Distributed Computing (pp. 31–40). Virtual, Italy: Association for Computing Machinery. https://doi.org/10.1145/3382734.3406005","mla":"Baig, Mirza Ahad, et al. “Long-Lived Snapshots with Polylogarithmic Amortized Step Complexity.” Proceedings of the 39th Symposium on Principles of Distributed Computing, Association for Computing Machinery, 2020, pp. 31–40, doi:10.1145/3382734.3406005.","ista":"Baig MA, Hendler D, Milani A, Travers C. 2020. Long-lived snapshots with polylogarithmic amortized step complexity. Proceedings of the 39th Symposium on Principles of Distributed Computing. PODC: Principles of Distributed Computing, 31–40.","chicago":"Baig, Mirza Ahad, Danny Hendler, Alessia Milani, and Corentin Travers. “Long-Lived Snapshots with Polylogarithmic Amortized Step Complexity.” In Proceedings of the 39th Symposium on Principles of Distributed Computing, 31–40. Association for Computing Machinery, 2020. https://doi.org/10.1145/3382734.3406005."},"date_updated":"2024-02-28T12:54:30Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"url":"https://hal.archives-ouvertes.fr/hal-02860087/document","open_access":"1"}],"oa":1,"quality_controlled":"1","publisher":"Association for Computing Machinery","scopus_import":"1","month":"07","abstract":[{"text":"We present the first deterministic wait-free long-lived snapshot algorithm, using only read and write operations, that guarantees polylogarithmic amortized step complexity in all executions. This is the first non-blocking snapshot algorithm, using reads and writes only, that has sub-linear amortized step complexity in executions of arbitrary length. The key to our construction is a novel implementation of a 2-component max array object which may be of independent interest.","lang":"eng"}],"oa_version":"Preprint","page":"31-40","date_created":"2020-09-13T22:01:17Z","date_published":"2020-07-31T00:00:00Z","doi":"10.1145/3382734.3406005","publication_status":"published","year":"2020","publication_identifier":{"isbn":["9781450375825"]},"language":[{"iso":"eng"}],"publication":"Proceedings of the 39th Symposium on Principles of Distributed Computing","day":"31"},{"volume":101,"issue":"2","language":[{"iso":"eng"}],"publication_identifier":{"issn":["24699950"],"eissn":["24699969"]},"publication_status":"published","month":"01","intvolume":" 101","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1907.02077","open_access":"1"}],"oa_version":"Preprint","abstract":[{"text":"In the superconducting regime of FeTe(1−x)Sex, there exist two types of vortices which are distinguished by the presence or absence of zero-energy states in their core. To understand their origin, we examine the interplay of Zeeman coupling and superconducting pairings in three-dimensional metals with band inversion. Weak Zeeman fields are found to suppress intraorbital spin-singlet pairing, known to localize the states at the ends of the vortices on the surface. On the other hand, an orbital-triplet pairing is shown to be stable against Zeeman interactions, but leads to delocalized zero-energy Majorana modes which extend through the vortex. In contrast, the finite-energy vortex modes remain localized at the vortex ends even when the pairing is of orbital-triplet form. Phenomenologically, this manifests as an observed disappearance of zero-bias peaks within the cores of topological vortices upon an increase of the applied magnetic field. The presence of magnetic impurities in FeTe(1−x)Sex, which are attracted to the vortices, would lead to such Zeeman-induced delocalization of Majorana modes in a fraction of vortices that capture a large enough number of magnetic impurities. Our results provide an explanation for the dichotomy between topological and nontopological vortices recently observed in FeTe(1−x)Sex.","lang":"eng"}],"department":[{"_id":"MiLe"}],"date_updated":"2024-02-28T13:11:13Z","status":"public","article_type":"original","type":"journal_article","_id":"7428","doi":"10.1103/PhysRevB.101.020504","date_published":"2020-01-13T00:00:00Z","date_created":"2020-02-02T23:01:01Z","day":"13","publication":"Physical Review B","isi":1,"year":"2020","publisher":"American Physical Society","quality_controlled":"1","oa":1,"title":"Effect of Zeeman coupling on the Majorana vortex modes in iron-based topological superconductors","author":[{"first_name":"Areg","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","last_name":"Ghazaryan","orcid":"0000-0001-9666-3543","full_name":"Ghazaryan, Areg"},{"last_name":"Lopes","full_name":"Lopes, P. L.S.","first_name":"P. L.S."},{"last_name":"Hosur","full_name":"Hosur, Pavan","first_name":"Pavan"},{"first_name":"Matthew J.","full_name":"Gilbert, Matthew J.","last_name":"Gilbert"},{"full_name":"Ghaemi, Pouyan","last_name":"Ghaemi","first_name":"Pouyan"}],"article_processing_charge":"No","external_id":{"arxiv":["1907.02077"],"isi":["000506843500001"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Ghazaryan, Areg, P. L.S. Lopes, Pavan Hosur, Matthew J. Gilbert, and Pouyan Ghaemi. “Effect of Zeeman Coupling on the Majorana Vortex Modes in Iron-Based Topological Superconductors.” Physical Review B. American Physical Society, 2020. https://doi.org/10.1103/PhysRevB.101.020504.","ista":"Ghazaryan A, Lopes PLS, Hosur P, Gilbert MJ, Ghaemi P. 2020. Effect of Zeeman coupling on the Majorana vortex modes in iron-based topological superconductors. Physical Review B. 101(2), 020504.","mla":"Ghazaryan, Areg, et al. “Effect of Zeeman Coupling on the Majorana Vortex Modes in Iron-Based Topological Superconductors.” Physical Review B, vol. 101, no. 2, 020504, American Physical Society, 2020, doi:10.1103/PhysRevB.101.020504.","ama":"Ghazaryan A, Lopes PLS, Hosur P, Gilbert MJ, Ghaemi P. Effect of Zeeman coupling on the Majorana vortex modes in iron-based topological superconductors. Physical Review B. 2020;101(2). doi:10.1103/PhysRevB.101.020504","apa":"Ghazaryan, A., Lopes, P. L. S., Hosur, P., Gilbert, M. J., & Ghaemi, P. (2020). Effect of Zeeman coupling on the Majorana vortex modes in iron-based topological superconductors. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.101.020504","ieee":"A. Ghazaryan, P. L. S. Lopes, P. Hosur, M. J. Gilbert, and P. Ghaemi, “Effect of Zeeman coupling on the Majorana vortex modes in iron-based topological superconductors,” Physical Review B, vol. 101, no. 2. American Physical Society, 2020.","short":"A. Ghazaryan, P.L.S. Lopes, P. Hosur, M.J. Gilbert, P. Ghaemi, Physical Review B 101 (2020)."},"article_number":"020504"},{"issue":"1","volume":102,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["24699926"],"eissn":["24699934"]},"publication_status":"published","month":"07","intvolume":" 102","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1912.08334"}],"oa_version":"Preprint","abstract":[{"text":"We demonstrate that releasing atoms into free space from an optical lattice does not deteriorate cavity-generated spin squeezing for metrological purposes. In this work, an ensemble of 500000 spin-squeezed atoms in a high-finesse optical cavity with near-uniform atom-cavity coupling is prepared, released into free space, recaptured in the cavity, and probed. Up to ∼10 dB of metrologically relevant squeezing is retrieved for 700μs free-fall times, and decaying levels of squeezing are realized for up to 3 ms free-fall times. The degradation of squeezing results from loss of atom-cavity coupling homogeneity between the initial squeezed state generation and final collective state readout. A theoretical model is developed to quantify this degradation and this model is experimentally validated.","lang":"eng"}],"department":[{"_id":"OnHo"}],"date_updated":"2024-02-28T13:11:28Z","status":"public","article_type":"original","type":"journal_article","_id":"8319","date_published":"2020-07-30T00:00:00Z","doi":"10.1103/PhysRevA.102.012224","date_created":"2020-08-30T22:01:10Z","day":"30","publication":"Physical Review A","isi":1,"year":"2020","quality_controlled":"1","publisher":"American Physical Society","oa":1,"acknowledgement":"We thank N. Engelsen for comments on the manuscript. This work was supported by the Office of Naval Research, Vannevar Bush Faculty Fellowship, Department of Energy, and Defense Threat Reduction Agency. R.K. was partly supported by the AQT/INQNET program at Caltech.","title":"Retrieval of cavity-generated atomic spin squeezing after free-space release","author":[{"last_name":"Wu","full_name":"Wu, Yunfan","first_name":"Yunfan"},{"first_name":"Rajiv","full_name":"Krishnakumar, Rajiv","last_name":"Krishnakumar"},{"first_name":"Julián","full_name":"Martínez-Rincón, Julián","last_name":"Martínez-Rincón"},{"first_name":"Benjamin K.","full_name":"Malia, Benjamin K.","last_name":"Malia"},{"first_name":"Onur","id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2031-204X","full_name":"Hosten, Onur","last_name":"Hosten"},{"last_name":"Kasevich","full_name":"Kasevich, Mark A.","first_name":"Mark A."}],"external_id":{"arxiv":["1912.08334"],"isi":["000555104200011"]},"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"Y. Wu, R. Krishnakumar, J. Martínez-Rincón, B.K. Malia, O. Hosten, M.A. Kasevich, Physical Review A 102 (2020).","ieee":"Y. Wu, R. Krishnakumar, J. Martínez-Rincón, B. K. Malia, O. Hosten, and M. A. Kasevich, “Retrieval of cavity-generated atomic spin squeezing after free-space release,” Physical Review A, vol. 102, no. 1. American Physical Society, 2020.","apa":"Wu, Y., Krishnakumar, R., Martínez-Rincón, J., Malia, B. K., Hosten, O., & Kasevich, M. A. (2020). Retrieval of cavity-generated atomic spin squeezing after free-space release. Physical Review A. American Physical Society. https://doi.org/10.1103/PhysRevA.102.012224","ama":"Wu Y, Krishnakumar R, Martínez-Rincón J, Malia BK, Hosten O, Kasevich MA. Retrieval of cavity-generated atomic spin squeezing after free-space release. Physical Review A. 2020;102(1). doi:10.1103/PhysRevA.102.012224","mla":"Wu, Yunfan, et al. “Retrieval of Cavity-Generated Atomic Spin Squeezing after Free-Space Release.” Physical Review A, vol. 102, no. 1, 012224, American Physical Society, 2020, doi:10.1103/PhysRevA.102.012224.","ista":"Wu Y, Krishnakumar R, Martínez-Rincón J, Malia BK, Hosten O, Kasevich MA. 2020. Retrieval of cavity-generated atomic spin squeezing after free-space release. Physical Review A. 102(1), 012224.","chicago":"Wu, Yunfan, Rajiv Krishnakumar, Julián Martínez-Rincón, Benjamin K. Malia, Onur Hosten, and Mark A. Kasevich. “Retrieval of Cavity-Generated Atomic Spin Squeezing after Free-Space Release.” Physical Review A. American Physical Society, 2020. https://doi.org/10.1103/PhysRevA.102.012224."},"article_number":"012224"},{"department":[{"_id":"ChWo"},{"_id":"BeBi"}],"date_updated":"2024-02-28T13:58:11Z","status":"public","conference":{"end_date":"2020-10-09","location":"Online Symposium","start_date":"2020-10-06","name":"SCA: Symposium on Computer Animation"},"article_type":"original","type":"journal_article","_id":"8766","ec_funded":1,"issue":"8","volume":39,"language":[{"iso":"eng"}],"publication_status":"published","intvolume":" 39","month":"12","scopus_import":"1","oa_version":"None","abstract":[{"text":"The “procedural” approach to animating ocean waves is the dominant algorithm for animating larger bodies of water in\r\ninteractive applications as well as in off-line productions — it provides high visual quality with a low computational demand. In this paper, we widen the applicability of procedural water wave animation with an extension that guarantees the satisfaction of boundary conditions imposed by terrain while still approximating physical wave behavior. In combination with a particle system that models wave breaking, foam, and spray, this allows us to naturally model waves interacting with beaches and rocks. Our system is able to animate waves at large scales at interactive frame rates on a commodity PC.","lang":"eng"}],"title":"Making procedural water waves boundary-aware","article_processing_charge":"No","external_id":{"isi":["000591780400005"]},"author":[{"last_name":"Jeschke","full_name":"Jeschke, Stefan","id":"44D6411A-F248-11E8-B48F-1D18A9856A87","first_name":"Stefan"},{"first_name":"Christian","id":"400429CC-F248-11E8-B48F-1D18A9856A87","full_name":"Hafner, Christian","last_name":"Hafner"},{"first_name":"Nuttapong","full_name":"Chentanez, Nuttapong","last_name":"Chentanez"},{"last_name":"Macklin","full_name":"Macklin, Miles","first_name":"Miles"},{"full_name":"Müller-Fischer, Matthias","last_name":"Müller-Fischer","first_name":"Matthias"},{"first_name":"Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546","last_name":"Wojtan"}],"user_id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Jeschke, Stefan, et al. “Making Procedural Water Waves Boundary-Aware.” Computer Graphics Forum, vol. 39, no. 8, Wiley, 2020, pp. 47–54, doi:10.1111/cgf.14100.","ama":"Jeschke S, Hafner C, Chentanez N, Macklin M, Müller-Fischer M, Wojtan C. Making procedural water waves boundary-aware. Computer Graphics forum. 2020;39(8):47-54. doi:10.1111/cgf.14100","apa":"Jeschke, S., Hafner, C., Chentanez, N., Macklin, M., Müller-Fischer, M., & Wojtan, C. (2020). Making procedural water waves boundary-aware. Computer Graphics Forum. Online Symposium: Wiley. https://doi.org/10.1111/cgf.14100","short":"S. Jeschke, C. Hafner, N. Chentanez, M. Macklin, M. Müller-Fischer, C. Wojtan, Computer Graphics Forum 39 (2020) 47–54.","ieee":"S. Jeschke, C. Hafner, N. Chentanez, M. Macklin, M. Müller-Fischer, and C. Wojtan, “Making procedural water waves boundary-aware,” Computer Graphics forum, vol. 39, no. 8. Wiley, pp. 47–54, 2020.","chicago":"Jeschke, Stefan, Christian Hafner, Nuttapong Chentanez, Miles Macklin, Matthias Müller-Fischer, and Chris Wojtan. “Making Procedural Water Waves Boundary-Aware.” Computer Graphics Forum. Wiley, 2020. https://doi.org/10.1111/cgf.14100.","ista":"Jeschke S, Hafner C, Chentanez N, Macklin M, Müller-Fischer M, Wojtan C. 2020. Making procedural water waves boundary-aware. Computer Graphics forum. 39(8), 47–54."},"project":[{"grant_number":"638176","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","call_identifier":"H2020","_id":"2533E772-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","_id":"24F9549A-B435-11E9-9278-68D0E5697425","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","grant_number":"715767"}],"date_created":"2020-11-17T10:47:48Z","date_published":"2020-12-01T00:00:00Z","doi":"10.1111/cgf.14100","page":"47-54","publication":"Computer Graphics forum","day":"01","year":"2020","isi":1,"quality_controlled":"1","publisher":"Wiley"},{"volume":34,"issue":"06","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["2374-3468"]},"intvolume":" 34","month":"04","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2002.12086","open_access":"1"}],"oa_version":"Preprint","abstract":[{"text":"Markov decision processes (MDPs) are the defacto framework for sequential decision making in the presence of stochastic uncertainty. A classical optimization criterion for MDPs is to maximize the expected discounted-sum payoff, which ignores low probability catastrophic events with highly negative impact on the system. On the other hand, risk-averse policies require the probability of undesirable events to be below a given threshold, but they do not account for optimization of the expected payoff. We consider MDPs with discounted-sum payoff with failure states which represent catastrophic outcomes. The objective of risk-constrained planning is to maximize the expected discounted-sum payoff among risk-averse policies that ensure the probability to encounter a failure state is below a desired threshold. Our main contribution is an efficient risk-constrained planning algorithm that combines UCT-like search with a predictor learned through interaction with the MDP (in the style of AlphaZero) and with a risk-constrained action selection via linear programming. We demonstrate the effectiveness of our approach with experiments on classical MDPs from the literature, including benchmarks with an order of 106 states.","lang":"eng"}],"department":[{"_id":"KrCh"}],"date_updated":"2024-03-04T08:30:16Z","keyword":["General Medicine"],"status":"public","conference":{"end_date":"2020-02-12","location":"New York, NY, United States","start_date":"2020-02-07","name":"AAAI: Conference on Artificial Intelligence"},"article_type":"original","type":"journal_article","_id":"15055","date_created":"2024-03-04T08:07:22Z","date_published":"2020-04-03T00:00:00Z","doi":"10.1609/aaai.v34i06.6531","page":"9794-9801","publication":"Proceedings of the 34th AAAI Conference on Artificial Intelligence","day":"03","year":"2020","oa":1,"quality_controlled":"1","publisher":"Association for the Advancement of Artificial Intelligence","acknowledgement":"Krishnendu Chatterjee is supported by the Austrian Science Fund (FWF) NFN Grant No. S11407-N23 (RiSE/SHiNE), and COST Action GAMENET. Tomas Brazdil is supported by the Grant Agency of Masaryk University grant no. MUNI/G/0739/2017 and by the Czech Science Foundation grant No. 18-11193S. Petr Novotny and Jirı Vahala are supported by the Czech Science Foundation grant No. GJ19-15134Y.","title":"Reinforcement learning of risk-constrained policies in Markov decision processes","external_id":{"arxiv":["2002.12086"]},"article_processing_charge":"No","author":[{"first_name":"Tomáš","full_name":"Brázdil, Tomáš","last_name":"Brázdil"},{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Petr","full_name":"Novotný, Petr","last_name":"Novotný"},{"last_name":"Vahala","full_name":"Vahala, Jiří","first_name":"Jiří"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Brázdil, Tomáš, Krishnendu Chatterjee, Petr Novotný, and Jiří Vahala. “Reinforcement Learning of Risk-Constrained Policies in Markov Decision Processes.” Proceedings of the 34th AAAI Conference on Artificial Intelligence. Association for the Advancement of Artificial Intelligence, 2020. https://doi.org/10.1609/aaai.v34i06.6531.","ista":"Brázdil T, Chatterjee K, Novotný P, Vahala J. 2020. Reinforcement learning of risk-constrained policies in Markov decision processes. Proceedings of the 34th AAAI Conference on Artificial Intelligence. 34(06), 9794–9801.","mla":"Brázdil, Tomáš, et al. “Reinforcement Learning of Risk-Constrained Policies in Markov Decision Processes.” Proceedings of the 34th AAAI Conference on Artificial Intelligence, vol. 34, no. 06, Association for the Advancement of Artificial Intelligence, 2020, pp. 9794–801, doi:10.1609/aaai.v34i06.6531.","ama":"Brázdil T, Chatterjee K, Novotný P, Vahala J. Reinforcement learning of risk-constrained policies in Markov decision processes. Proceedings of the 34th AAAI Conference on Artificial Intelligence. 2020;34(06):9794-9801. doi:10.1609/aaai.v34i06.6531","apa":"Brázdil, T., Chatterjee, K., Novotný, P., & Vahala, J. (2020). Reinforcement learning of risk-constrained policies in Markov decision processes. Proceedings of the 34th AAAI Conference on Artificial Intelligence. New York, NY, United States: Association for the Advancement of Artificial Intelligence. https://doi.org/10.1609/aaai.v34i06.6531","short":"T. Brázdil, K. Chatterjee, P. Novotný, J. Vahala, Proceedings of the 34th AAAI Conference on Artificial Intelligence 34 (2020) 9794–9801.","ieee":"T. Brázdil, K. Chatterjee, P. Novotný, and J. Vahala, “Reinforcement learning of risk-constrained policies in Markov decision processes,” Proceedings of the 34th AAAI Conference on Artificial Intelligence, vol. 34, no. 06. Association for the Advancement of Artificial Intelligence, pp. 9794–9801, 2020."},"project":[{"name":"Game Theory","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}]}]