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Henzinger were supported by\r\nthe Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award).","external_id":{"isi":["000695276000014"]},"article_processing_charge":"No","author":[{"orcid":"0000-0001-7745-9117","full_name":"Kragl, Bernhard","last_name":"Kragl","first_name":"Bernhard","id":"320FC952-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Qadeer","full_name":"Qadeer, Shaz","first_name":"Shaz"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724"}],"title":"Refinement for structured concurrent programs","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.","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.","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","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","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","name":"The Wittgenstein Prize"}],"related_material":{"record":[{"status":"public","id":"8332","relation":"dissertation_contains"}]},"volume":12224,"publication_status":"published","publication_identifier":{"eisbn":["9783030532888"],"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["9783030532871"]},"language":[{"iso":"eng"}],"file":[{"date_created":"2020-08-06T08:14:54Z","file_name":"2020_LNCS_Kragl.pdf","date_updated":"2020-08-06T08:14:54Z","file_size":804237,"creator":"dernst","file_id":"8201","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"scopus_import":"1","alternative_title":["LNCS"],"intvolume":" 12224","month":"07","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."}],"oa_version":"Published Version","file_date_updated":"2020-08-06T08:14:54Z","department":[{"_id":"ToHe"}],"date_updated":"2023-09-07T13:18:00Z","ddc":["000"],"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","status":"public","_id":"8195"},{"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"8332"}]},"publication_identifier":{"isbn":["9781450376136"]},"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1145/3385412.3385980","open_access":"1"}],"month":"06","abstract":[{"lang":"eng","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."}],"oa_version":"Published Version","department":[{"_id":"ToHe"}],"date_updated":"2023-09-07T13:18:00Z","type":"conference","conference":{"name":"PLDI: Programming Language Design and Implementation","end_date":"2020-06-20","location":"London, United Kingdom","start_date":"2020-06-15"},"status":"public","_id":"8012","page":"227-242","doi":"10.1145/3385412.3385980","date_published":"2020-06-01T00:00:00Z","date_created":"2020-06-25T11:40:16Z","isi":1,"year":"2020","day":"01","publication":"Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation","quality_controlled":"1","publisher":"Association for Computing Machinery","oa":1,"author":[{"id":"320FC952-F248-11E8-B48F-1D18A9856A87","first_name":"Bernhard","full_name":"Kragl, Bernhard","orcid":"0000-0001-7745-9117","last_name":"Kragl"},{"last_name":"Enea","full_name":"Enea, Constantin","first_name":"Constantin"},{"last_name":"Henzinger","orcid":"0000-0002-2985-7724","full_name":"Henzinger, Thomas A","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Mutluergil","full_name":"Mutluergil, Suha Orhun","first_name":"Suha Orhun"},{"full_name":"Qadeer, Shaz","last_name":"Qadeer","first_name":"Shaz"}],"article_processing_charge":"No","external_id":{"isi":["000614622300016"]},"title":"Inductive sequentialization of asynchronous programs","citation":{"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.","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.","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","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"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"grant_number":"Z211","name":"The Wittgenstein Prize","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}]},{"day":"10","has_accepted_license":"1","year":"2020","date_published":"2020-09-10T00:00:00Z","doi":"10.15479/AT:ISTA:8358","date_created":"2020-09-10T09:26:49Z","page":"135","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.","publisher":"Institute of Science and Technology Austria","oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","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."},"title":"Organization and dynamics of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinkers","author":[{"id":"38FCDB4C-F248-11E8-B48F-1D18A9856A87","first_name":"Paulo R","full_name":"Dos Santos Caldas, Paulo R","orcid":"0000-0001-6730-4461","last_name":"Dos Santos Caldas"}],"article_processing_charge":"No","file":[{"creator":"pcaldas","file_size":141602462,"date_updated":"2020-09-10T12:11:29Z","file_name":"phd_thesis_pcaldas.pdf","date_created":"2020-09-10T12:11:29Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"8364","checksum":"882f93fe9c351962120e2669b84bf088"},{"date_created":"2020-09-10T12:18:17Z","file_name":"phd_thesis_latex_pcaldas.zip","date_updated":"2020-09-11T07:48:10Z","file_size":450437458,"creator":"pcaldas","checksum":"70cc9e399c4e41e6e6ac445ae55e8558","file_id":"8365","content_type":"application/x-zip-compressed","access_level":"closed","relation":"source_file"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-009-1"]},"degree_awarded":"PhD","publication_status":"published","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"7572"},{"id":"7197","status":"public","relation":"part_of_dissertation"}]},"oa_version":"Published Version","acknowledged_ssus":[{"_id":"Bio"}],"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"}],"month":"09","alternative_title":["ISTA Thesis"],"ddc":["572"],"supervisor":[{"first_name":"Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","last_name":"Loose","orcid":"0000-0001-7309-9724","full_name":"Loose, Martin"}],"date_updated":"2023-09-07T13:18:51Z","department":[{"_id":"MaLo"}],"file_date_updated":"2020-09-11T07:48:10Z","_id":"8358","status":"public","type":"dissertation","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":"8703","status":"public","type":"conference","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)"},"conference":{"name":"ESA: Annual European Symposium on Algorithms","start_date":"2020-09-07","location":"Virtual, Online; Pisa, Italy","end_date":"2020-09-09"},"ddc":["000"],"date_updated":"2023-09-07T13:29:00Z","file_date_updated":"2020-10-27T14:31:52Z","department":[{"_id":"HeEd"}],"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"}],"month":"08","intvolume":" 173","scopus_import":"1","alternative_title":["LIPIcs"],"file":[{"date_created":"2020-10-27T14:31:52Z","file_name":"2020_LIPIcs_Osang.pdf","creator":"cziletti","date_updated":"2020-10-27T14:31:52Z","file_size":733291,"checksum":"fe0f7c49a99ed870c671b911e10d5496","file_id":"8712","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["18688969"],"isbn":["9783959771627"]},"publication_status":"published","volume":173,"related_material":{"record":[{"relation":"dissertation_contains","id":"9056","status":"public"}]},"license":"https://creativecommons.org/licenses/by/3.0/","ec_funded":1,"article_number":"75","project":[{"_id":"266A2E9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"788183","name":"Alpha Shape Theory Extended"}],"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.","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","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","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.","short":"G.F. Osang, M. Rouxel-Labbé, M. Teillaud, in:, 28th Annual European Symposium on Algorithms, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020.","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","author":[{"full_name":"Osang, Georg F","orcid":"0000-0002-8882-5116","last_name":"Osang","first_name":"Georg F","id":"464B40D6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Rouxel-Labbé, Mael","last_name":"Rouxel-Labbé","first_name":"Mael"},{"first_name":"Monique","last_name":"Teillaud","full_name":"Teillaud, Monique"}],"article_processing_charge":"No","quality_controlled":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","oa":1,"day":"26","publication":"28th Annual European Symposium on Algorithms","has_accepted_license":"1","year":"2020","doi":"10.4230/LIPIcs.ESA.2020.75","date_published":"2020-08-26T00:00:00Z","date_created":"2020-10-25T23:01:18Z"},{"abstract":[{"lang":"eng","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."}],"oa_version":"Published Version","oa":1,"quality_controlled":"1","month":"04","publication_status":"published","year":"2020","has_accepted_license":"1","language":[{"iso":"eng"}],"publication":"8th International Conference on Learning Representations","file":[{"file_name":"main.pdf","date_created":"2020-02-11T09:07:27Z","creator":"bphuong","file_size":405469,"date_updated":"2020-07-14T12:47:59Z","checksum":"8d372ea5defd8cb8fdc430111ed754a9","file_id":"7482","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"day":"26","date_created":"2020-02-11T09:07:37Z","date_published":"2020-04-26T00:00:00Z","related_material":{"link":[{"url":"https://iclr.cc/virtual_2020/poster_Bylx-TNKvH.html","relation":"supplementary_material"}],"record":[{"relation":"dissertation_contains","id":"9418","status":"public"}]},"_id":"7481","conference":{"start_date":"2020-04-27","location":"Online","end_date":"2020-04-30","name":"ICLR: International Conference on Learning Representations"},"type":"conference","status":"public","date_updated":"2023-09-07T13:29:50Z","citation":{"mla":"Phuong, Mary, and Christoph Lampert. “Functional vs. Parametric Equivalence of ReLU Networks.” 8th International Conference on Learning Representations, 2020.","ama":"Phuong M, Lampert C. Functional vs. parametric equivalence of ReLU networks. In: 8th International Conference on Learning Representations. ; 2020.","apa":"Phuong, M., & Lampert, C. (2020). Functional vs. parametric equivalence of ReLU networks. In 8th International Conference on Learning Representations. Online.","ieee":"M. Phuong and C. Lampert, “Functional vs. parametric equivalence of ReLU networks,” in 8th International Conference on Learning Representations, Online, 2020.","short":"M. Phuong, C. Lampert, in:, 8th International Conference on Learning Representations, 2020.","chicago":"Phuong, Mary, and Christoph Lampert. “Functional vs. Parametric Equivalence of ReLU Networks.” In 8th International Conference on Learning Representations, 2020.","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."},"ddc":["000"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","author":[{"full_name":"Bui Thi Mai, Phuong","last_name":"Bui Thi Mai","first_name":"Phuong","id":"3EC6EE64-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph"}],"file_date_updated":"2020-07-14T12:47:59Z","title":"Functional vs. parametric equivalence of ReLU networks","department":[{"_id":"ChLa"}]},{"month":"02","intvolume":" 52","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1904.08647","open_access":"1"}],"oa_version":"Preprint","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"}],"related_material":{"record":[{"status":"public","id":"9733","relation":"dissertation_contains"}]},"issue":"1","volume":52,"ec_funded":1,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0036-1410"],"eissn":["1095-7154"]},"publication_status":"published","status":"public","keyword":["Applied Mathematics","Computational Mathematics","Analysis"],"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"},"_id":"9781","department":[{"_id":"RoSe"}],"ddc":["510"],"date_updated":"2023-09-07T13:30:11Z","quality_controlled":"1","publisher":"Society for Industrial & Applied Mathematics ","oa":1,"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.","date_published":"2020-02-12T00:00:00Z","doi":"10.1137/19m126284x","date_created":"2021-08-06T07:34:16Z","page":"605-622","day":"12","publication":"SIAM Journal on Mathematical Analysis","isi":1,"has_accepted_license":"1","year":"2020","project":[{"_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"694227","name":"Analysis of quantum many-body systems"}],"title":"Uniqueness and nondegeneracy of minimizers of the Pekar functional on a ball","author":[{"last_name":"Feliciangeli","orcid":"0000-0003-0754-8530","full_name":"Feliciangeli, Dario","first_name":"Dario","id":"41A639AA-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert"}],"external_id":{"arxiv":["1904.08647 "],"isi":["000546967700022"]},"article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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","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","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."}},{"file":[{"checksum":"f107e21b58f5930876f47144be37cf6c","file_id":"8779","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2020-11-20T09:14:22Z","file_name":"2020_ArchRatMechAn_Fischer.pdf","date_updated":"2020-11-20T09:14:22Z","file_size":1897571,"creator":"dernst"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["14320673"],"issn":["00039527"]},"publication_status":"published","volume":236,"related_material":{"record":[{"relation":"dissertation_contains","id":"10007","status":"public"}]},"ec_funded":1,"oa_version":"Published Version","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"}],"month":"05","intvolume":" 236","scopus_import":"1","ddc":["530","532"],"date_updated":"2023-09-07T13:30:45Z","file_date_updated":"2020-11-20T09:14:22Z","department":[{"_id":"JuFi"}],"_id":"7489","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":"01","publication":"Archive for Rational Mechanics and Analysis","has_accepted_license":"1","isi":1,"year":"2020","date_published":"2020-05-01T00:00:00Z","doi":"10.1007/s00205-019-01486-2","date_created":"2020-02-16T23:00:50Z","page":"967-1087","quality_controlled":"1","publisher":"Springer Nature","oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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.","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","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.","short":"J.L. Fischer, S. Hensel, Archive for Rational Mechanics and Analysis 236 (2020) 967–1087.","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."},"title":"Weak–strong uniqueness for the Navier–Stokes equation for two fluids with surface tension","author":[{"full_name":"Fischer, Julian L","orcid":"0000-0002-0479-558X","last_name":"Fischer","first_name":"Julian L","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Sebastian","id":"4D23B7DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7252-8072","full_name":"Hensel, Sebastian","last_name":"Hensel"}],"article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["000511060200001"]},"project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}]},{"title":"The local structure of the energy landscape in multiphase mean curvature flow: weak-strong uniqueness and stability of evolutions","department":[{"_id":"JuFi"}],"external_id":{"arxiv":["2003.05478"]},"article_processing_charge":"No","author":[{"id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","first_name":"Julian L","last_name":"Fischer","full_name":"Fischer, Julian L","orcid":"0000-0002-0479-558X"},{"full_name":"Hensel, Sebastian","orcid":"0000-0001-7252-8072","last_name":"Hensel","id":"4D23B7DA-F248-11E8-B48F-1D18A9856A87","first_name":"Sebastian"},{"first_name":"Tim","full_name":"Laux, Tim","last_name":"Laux"},{"full_name":"Simon, Thilo","last_name":"Simon","first_name":"Thilo"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_updated":"2023-09-07T13:30:45Z","citation":{"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.","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.","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.).","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.","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."},"status":"public","project":[{"grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"type":"preprint","article_number":"2003.05478","_id":"10012","date_created":"2021-09-13T12:17:11Z","ec_funded":1,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"10007"}]},"date_published":"2020-03-11T00:00:00Z","language":[{"iso":"eng"}],"publication":"arXiv","day":"11","publication_status":"submitted","year":"2020","month":"03","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2003.05478"}],"oa":1,"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.","oa_version":"Preprint","abstract":[{"lang":"eng","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."}]},{"project":[{"_id":"26927A52-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"F07105","name":"Integrating superconducting quantum circuits"},{"call_identifier":"H2020","_id":"257EB838-B435-11E9-9278-68D0E5697425","name":"Hybrid Optomechanical Technologies","grant_number":"732894"},{"call_identifier":"H2020","_id":"237CBA6C-32DE-11EA-91FC-C7463DDC885E","name":"Quantum readout techniques and technologies","grant_number":"862644"},{"call_identifier":"H2020","_id":"26336814-B435-11E9-9278-68D0E5697425","grant_number":"758053","name":"A Fiber Optic Transceiver for Superconducting Qubits"}],"article_number":"044055","title":"Surpassing the resistance quantum with a geometric superinductor","author":[{"last_name":"Peruzzo","full_name":"Peruzzo, Matilda","orcid":"0000-0002-3415-4628","id":"3F920B30-F248-11E8-B48F-1D18A9856A87","first_name":"Matilda"},{"last_name":"Trioni","full_name":"Trioni, Andrea","id":"42F71B44-F248-11E8-B48F-1D18A9856A87","first_name":"Andrea"},{"first_name":"Farid","id":"2AED110C-F248-11E8-B48F-1D18A9856A87","last_name":"Hassani","orcid":"0000-0001-6937-5773","full_name":"Hassani, Farid"},{"last_name":"Zemlicka","full_name":"Zemlicka, Martin","first_name":"Martin","id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87"},{"id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M","last_name":"Fink","orcid":"0000-0001-8112-028X","full_name":"Fink, Johannes M"}],"article_processing_charge":"No","external_id":{"arxiv":["2007.01644"],"isi":["000582797300003"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","ista":"Peruzzo M, Trioni A, Hassani F, Zemlicka M, Fink JM. 2020. Surpassing the resistance quantum with a geometric superinductor. Physical Review Applied. 14(4), 044055.","mla":"Peruzzo, Matilda, et al. “Surpassing the Resistance Quantum with a Geometric Superinductor.” Physical Review Applied, vol. 14, no. 4, 044055, American Physical Society, 2020, doi:10.1103/PhysRevApplied.14.044055.","short":"M. Peruzzo, A. Trioni, F. Hassani, M. Zemlicka, J.M. Fink, Physical Review Applied 14 (2020).","ieee":"M. Peruzzo, A. Trioni, F. Hassani, M. Zemlicka, and J. M. Fink, “Surpassing the resistance quantum with a geometric superinductor,” Physical Review Applied, vol. 14, no. 4. American Physical Society, 2020.","ama":"Peruzzo M, Trioni A, Hassani F, Zemlicka M, Fink JM. Surpassing the resistance quantum with a geometric superinductor. Physical Review Applied. 2020;14(4). doi:10.1103/PhysRevApplied.14.044055","apa":"Peruzzo, M., Trioni, A., Hassani, F., Zemlicka, M., & Fink, J. M. (2020). Surpassing the resistance quantum with a geometric superinductor. Physical Review Applied. American Physical Society. https://doi.org/10.1103/PhysRevApplied.14.044055"},"publisher":"American Physical Society","quality_controlled":"1","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). ","date_published":"2020-10-29T00:00:00Z","doi":"10.1103/PhysRevApplied.14.044055","date_created":"2020-11-15T23:01:17Z","day":"29","publication":"Physical Review Applied","isi":1,"has_accepted_license":"1","year":"2020","status":"public","type":"journal_article","article_type":"original","_id":"8755","department":[{"_id":"JoFi"}],"file_date_updated":"2021-03-29T11:43:20Z","ddc":["530"],"date_updated":"2023-09-07T13:31:22Z","month":"10","intvolume":" 14","scopus_import":"1","oa_version":"Published Version","acknowledged_ssus":[{"_id":"NanoFab"}],"abstract":[{"lang":"eng","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. "}],"volume":14,"issue":"4","related_material":{"record":[{"id":"13070","status":"public","relation":"research_data"},{"status":"public","id":"9920","relation":"dissertation_contains"}]},"ec_funded":1,"file":[{"date_created":"2021-03-29T11:43:20Z","file_name":"2020_PhysReviewApplied_Peruzzo.pdf","date_updated":"2021-03-29T11:43:20Z","file_size":2607823,"creator":"dernst","file_id":"9300","checksum":"2a634abe75251ae7628cd54c8a4ce2e8","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["23317019"]},"publication_status":"published"},{"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":[{"id":"10030","status":"public","relation":"dissertation_contains"}]},"ec_funded":1,"_id":"7573","status":"public","article_type":"original","type":"journal_article","date_updated":"2023-09-07T13:31:05Z","department":[{"_id":"JaMa"}],"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.","publisher":"Elsevier","quality_controlled":"1","oa":1,"day":"01","publication":"Journal de Mathematiques Pures et Appliquees","isi":1,"year":"2020","date_published":"2020-07-01T00:00:00Z","doi":"10.1016/j.matpur.2020.02.008","date_created":"2020-03-08T23:00:47Z","page":"204-234","project":[{"grant_number":"716117","name":"Optimal Transport and Stochastic Dynamics","call_identifier":"H2020","_id":"256E75B8-B435-11E9-9278-68D0E5697425"},{"grant_number":" F06504","name":"Taming Complexity in Partial Di erential Systems","_id":"260482E2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"FWF","_id":"260788DE-B435-11E9-9278-68D0E5697425","name":"Dissipation and Dispersion in Nonlinear Partial Differential Equations"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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.","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","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","short":"P. Gladbach, E. Kopfer, J. Maas, L. Portinale, Journal de Mathematiques Pures et Appliquees 139 (2020) 204–234.","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."},"title":"Homogenisation of one-dimensional discrete optimal transport","author":[{"first_name":"Peter","last_name":"Gladbach","full_name":"Gladbach, Peter"},{"first_name":"Eva","full_name":"Kopfer, Eva","last_name":"Kopfer"},{"id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","last_name":"Maas","orcid":"0000-0002-0845-1338","full_name":"Maas, Jan"},{"last_name":"Portinale","full_name":"Portinale, Lorenzo","id":"30AD2CBC-F248-11E8-B48F-1D18A9856A87","first_name":"Lorenzo"}],"external_id":{"isi":["000539439400008"],"arxiv":["1905.05757"]},"article_processing_charge":"No"},{"type":"preprint","project":[{"call_identifier":"H2020","_id":"256E75B8-B435-11E9-9278-68D0E5697425","grant_number":"716117","name":"Optimal Transport and Stochastic Dynamics"},{"grant_number":"F6504","name":"Taming Complexity in Partial Differential Systems","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2"}],"status":"public","_id":"10022","article_number":"2008.10962","author":[{"full_name":"Forkert, Dominik L","last_name":"Forkert","first_name":"Dominik L","id":"35C79D68-F248-11E8-B48F-1D18A9856A87"},{"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","first_name":"Lorenzo","id":"30AD2CBC-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","external_id":{"arxiv":["2008.10962"]},"title":"Evolutionary Γ-convergence of entropic gradient flow structures for Fokker-Planck equations in multiple dimensions","department":[{"_id":"JaMa"}],"date_updated":"2023-09-07T13:31:05Z","citation":{"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.).","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.","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."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/2008.10962","open_access":"1"}],"month":"08","abstract":[{"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.","lang":"eng"}],"oa_version":"Preprint","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.","page":"33","date_published":"2020-08-25T00:00:00Z","related_material":{"record":[{"status":"public","id":"11739","relation":"later_version"},{"relation":"dissertation_contains","status":"public","id":"10030"}]},"date_created":"2021-09-17T10:57:27Z","ec_funded":1,"year":"2020","publication_status":"submitted","day":"25","publication":"arXiv","language":[{"iso":"eng"}]},{"ec_funded":1,"volume":119,"related_material":{"link":[{"url":"http://proceedings.mlr.press/v119/konstantinov20a/konstantinov20a-supp.pdf","relation":"supplementary_material"}],"record":[{"relation":"dissertation_contains","id":"10799","status":"public"}]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"9120","checksum":"cc755d0054bc4b2be778ea7aa7884d2f","success":1,"date_updated":"2021-02-15T09:00:01Z","file_size":281286,"creator":"dernst","date_created":"2021-02-15T09:00:01Z","file_name":"2020_PMLR_Konstantinov.pdf"}],"publication_status":"published","publication_identifier":{"issn":["2640-3498"]},"intvolume":" 119","month":"07","scopus_import":"1","oa_version":"Published Version","acknowledged_ssus":[{"_id":"ScienComp"}],"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"}],"file_date_updated":"2021-02-15T09:00:01Z","department":[{"_id":"DaAl"},{"_id":"ChLa"}],"ddc":["000"],"date_updated":"2023-09-07T13:42:08Z","status":"public","conference":{"name":"ICML: International Conference on Machine Learning","start_date":"2020-07-12","end_date":"2020-07-18","location":"Online"},"type":"conference","_id":"8724","date_created":"2020-11-05T15:25:58Z","date_published":"2020-07-12T00:00:00Z","page":"5416-5425","publication":"Proceedings of the 37th International Conference on Machine Learning","day":"12","year":"2020","has_accepted_license":"1","oa":1,"publisher":"ML Research Press","quality_controlled":"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).","title":"On the sample complexity of adversarial multi-source PAC learning","article_processing_charge":"No","external_id":{"arxiv":["2002.10384"]},"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"},{"last_name":"Alistarh","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","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.","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.","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.","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."},"project":[{"call_identifier":"H2020","_id":"268A44D6-B435-11E9-9278-68D0E5697425","grant_number":"805223","name":"Elastic Coordination for Scalable Machine Learning"}]},{"doi":"10.1088/1367-2630/abae44","date_published":"2020-09-01T00:00:00Z","date_created":"2020-10-11T22:01:14Z","day":"01","publication":"New Journal of Physics","has_accepted_license":"1","isi":1,"year":"2020","publisher":"IOP Publishing","quality_controlled":"1","oa":1,"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).","title":"Detecting composite orders in layered models via machine learning","author":[{"first_name":"Wojciech","id":"48C55298-F248-11E8-B48F-1D18A9856A87","last_name":"Rzadkowski","full_name":"Rzadkowski, Wojciech","orcid":"0000-0002-1106-4419"},{"full_name":"Defenu, N","last_name":"Defenu","first_name":"N"},{"full_name":"Chiacchiera, S","last_name":"Chiacchiera","first_name":"S"},{"last_name":"Trombettoni","full_name":"Trombettoni, A","first_name":"A"},{"id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87","first_name":"Giacomo","last_name":"Bighin","full_name":"Bighin, Giacomo","orcid":"0000-0001-8823-9777"}],"article_processing_charge":"No","external_id":{"isi":["000573298000001"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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).","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","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","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."},"project":[{"name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"grant_number":"25681","name":"Analytic and machine learning approaches to composite quantum impurities","_id":"05A235A0-7A3F-11EA-A408-12923DDC885E"},{"_id":"26986C82-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"M02641","name":"A path-integral approach to composite impurities"}],"article_number":"093026","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"10759"}]},"volume":22,"issue":"9","ec_funded":1,"file":[{"date_created":"2020-10-12T12:18:47Z","file_name":"2020_NewJournalPhysics_Rzdkowski.pdf","creator":"dernst","date_updated":"2020-10-12T12:18:47Z","file_size":2725143,"file_id":"8650","checksum":"c9238fff422e7a957c3a0d559f756b3a","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["13672630"]},"publication_status":"published","month":"09","intvolume":" 22","scopus_import":"1","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."}],"file_date_updated":"2020-10-12T12:18:47Z","department":[{"_id":"MiLe"}],"ddc":["530"],"date_updated":"2023-09-07T13:44:16Z","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":"8644"},{"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","_id":"8705","file_date_updated":"2020-10-27T12:49:04Z","department":[{"_id":"RoSe"}],"date_updated":"2023-09-07T13:43:51Z","ddc":["530"],"scopus_import":"1","intvolume":" 21","month":"12","abstract":[{"lang":"eng","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."}],"oa_version":"Published Version","ec_funded":1,"volume":21,"related_material":{"record":[{"status":"public","id":"11473","relation":"dissertation_contains"}]},"issue":"12","publication_status":"published","publication_identifier":{"issn":["1424-0637"]},"language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"c12c9c1e6f08def245e42f3cb1d83827","file_id":"8711","creator":"cziletti","file_size":469831,"date_updated":"2020-10-27T12:49:04Z","file_name":"2020_Annales_Mysliwy.pdf","date_created":"2020-10-27T12:49:04Z"}],"project":[{"grant_number":"694227","name":"Analysis of quantum many-body systems","call_identifier":"H2020","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385"}],"article_processing_charge":"Yes (via OA deal)","external_id":{"arxiv":["2003.12371"],"isi":["000578111800002"]},"author":[{"first_name":"Krzysztof","id":"316457FC-F248-11E8-B48F-1D18A9856A87","full_name":"Mysliwy, Krzysztof","last_name":"Mysliwy"},{"orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","last_name":"Seiringer","first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"}],"title":"Microscopic derivation of the Fröhlich Hamiltonian for the Bose polaron in the mean-field limit","citation":{"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","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","short":"K. Mysliwy, R. Seiringer, Annales Henri Poincare 21 (2020) 4003–4025.","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.","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.","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"quality_controlled":"1","publisher":"Springer Nature","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"},{"intvolume":" 22","month":"08","scopus_import":"1","oa_version":"None","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."}],"volume":22,"issue":"6","related_material":{"record":[{"status":"public","id":"299","relation":"earlier_version"}]},"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1433-2787"],"issn":["1433-2779"]},"keyword":["Information Systems","Software"],"status":"public","type":"journal_article","article_type":"original","_id":"10861","department":[{"_id":"ToHe"}],"date_updated":"2023-09-08T11:52:02Z","publisher":"Springer Nature","quality_controlled":"1","date_created":"2022-03-18T10:10:53Z","date_published":"2020-08-03T00:00:00Z","doi":"10.1007/s10009-020-00582-z","page":"741-758","publication":"International Journal on Software Tools for Technology Transfer","day":"03","year":"2020","isi":1,"title":"AMT 2.0: Qualitative and quantitative trace analysis with extended signal temporal logic","article_processing_charge":"No","external_id":{"isi":["000555398600001"]},"author":[{"first_name":"Dejan","id":"41BCEE5C-F248-11E8-B48F-1D18A9856A87","full_name":"Nickovic, Dejan","last_name":"Nickovic"},{"first_name":"Olivier","last_name":"Lebeltel","full_name":"Lebeltel, Olivier"},{"first_name":"Oded","full_name":"Maler, Oded","last_name":"Maler"},{"first_name":"Thomas","id":"40960E6E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5199-3143","full_name":"Ferrere, Thomas","last_name":"Ferrere"},{"full_name":"Ulus, Dogan","last_name":"Ulus","first_name":"Dogan"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","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.","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","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","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.","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."}},{"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1367-4811"]},"publication_status":"published","related_material":{"link":[{"url":"https://github.com/ratschlab/scim","relation":"software"}]},"issue":"Supplement_2","volume":36,"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"}],"month":"12","intvolume":" 36","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1093/bioinformatics/btaa843"}],"extern":"1","date_updated":"2023-09-11T10:21:00Z","department":[{"_id":"FrLo"}],"_id":"14125","status":"public","keyword":["Computational Mathematics","Computational Theory and Mathematics","Computer Science Applications","Molecular Biology","Biochemistry","Statistics and Probability"],"article_type":"original","type":"journal_article","day":"01","publication":"Bioinformatics","year":"2020","doi":"10.1093/bioinformatics/btaa843","date_published":"2020-12-01T00:00:00Z","date_created":"2023-08-21T12:28:20Z","page":"i919-i927","publisher":"Oxford University Press","quality_controlled":"1","oa":1,"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.","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","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","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."},"title":"SCIM: Universal single-cell matching with unpaired feature sets","author":[{"first_name":"Stefan G","last_name":"Stark","full_name":"Stark, Stefan G"},{"full_name":"Ficek, Joanna","last_name":"Ficek","first_name":"Joanna"},{"first_name":"Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","last_name":"Locatello","full_name":"Locatello, Francesco","orcid":"0000-0002-4850-0683"},{"first_name":"Ximena","last_name":"Bonilla","full_name":"Bonilla, Ximena"},{"first_name":"Stéphane","full_name":"Chevrier, Stéphane","last_name":"Chevrier"},{"first_name":"Franziska","last_name":"Singer","full_name":"Singer, Franziska"},{"first_name":"Rudolf","full_name":"Aebersold, Rudolf","last_name":"Aebersold"},{"first_name":"Faisal S","full_name":"Al-Quaddoomi, Faisal S","last_name":"Al-Quaddoomi"},{"full_name":"Albinus, Jonas","last_name":"Albinus","first_name":"Jonas"},{"full_name":"Alborelli, 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Marc","first_name":"Marc"},{"full_name":"Zoche, Martin","last_name":"Zoche","first_name":"Martin"},{"first_name":"Gregor","last_name":"Zuend","full_name":"Zuend, Gregor"},{"full_name":"Rätsch, Gunnar","last_name":"Rätsch","first_name":"Gunnar"},{"first_name":"Kjong-Van","full_name":"Lehmann, Kjong-Van","last_name":"Lehmann"}],"external_id":{"pmid":["33381818"]},"article_processing_charge":"No"},{"date_updated":"2023-09-12T07:44:48Z","extern":"1","department":[{"_id":"FrLo"}],"_id":"14186","type":"conference","conference":{"location":"New York, NY, United States","end_date":"2020-02-12","start_date":"2020-02-07","name":"AAAI: Conference on Artificial Intelligence"},"status":"public","publication_identifier":{"isbn":["9781577358350"],"eissn":["2374-3468"]},"publication_status":"published","language":[{"iso":"eng"}],"issue":"9","volume":34,"abstract":[{"lang":"eng","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."}],"oa_version":"Preprint","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/2007.14184","open_access":"1"}],"month":"07","intvolume":" 34","citation":{"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.","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.","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","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","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Locatello, Francesco","orcid":"0000-0002-4850-0683","last_name":"Locatello","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","first_name":"Francesco"},{"full_name":"Bauer, Stefan","last_name":"Bauer","first_name":"Stefan"},{"first_name":"Mario","last_name":"Lucic","full_name":"Lucic, Mario"},{"first_name":"Gunnar","last_name":"Rätsch","full_name":"Rätsch, Gunnar"},{"first_name":"Sylvain","full_name":"Gelly, Sylvain","last_name":"Gelly"},{"first_name":"Bernhard","last_name":"Schölkopf","full_name":"Schölkopf, Bernhard"},{"full_name":"Bachem, Olivier","last_name":"Bachem","first_name":"Olivier"}],"article_processing_charge":"No","external_id":{"arxiv":["2007.14184"]},"title":"A commentary on the unsupervised learning of disentangled representations","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","publisher":"Association for the Advancement of Artificial Intelligence","quality_controlled":"1","oa":1},{"title":"Weakly-supervised disentanglement without compromises","author":[{"first_name":"Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","full_name":"Locatello, Francesco","orcid":"0000-0002-4850-0683","last_name":"Locatello"},{"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","last_name":"Bachem","full_name":"Bachem, Olivier"},{"first_name":"Michael","full_name":"Tschannen, Michael","last_name":"Tschannen"}],"external_id":{"arxiv":["2002.02886"]},"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","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.","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.","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.","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.","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."},"date_published":"2020-07-07T00:00:00Z","date_created":"2023-08-22T14:08:14Z","page":"6348–6359","day":"07","publication":"Proceedings of the 37th International Conference on Machine Learning","year":"2020","quality_controlled":"1","oa":1,"department":[{"_id":"FrLo"}],"extern":"1","date_updated":"2023-09-12T07:59:29Z","status":"public","type":"conference","conference":{"name":"International Conference on Machine Learning","end_date":"2020-07-18","location":"Virtual","start_date":"2020-07-13"},"_id":"14188","volume":119,"language":[{"iso":"eng"}],"publication_status":"published","month":"07","intvolume":" 119","alternative_title":["PMLR"],"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2002.02886"}],"oa_version":"Preprint","abstract":[{"lang":"eng","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."}]},{"type":"conference","conference":{"name":"International Conference on Machine Learning","location":"Virtual","end_date":"2020-07-18","start_date":"2020-07-13"},"status":"public","_id":"14187","author":[{"last_name":"Négiar","full_name":"Négiar, Geoffrey","first_name":"Geoffrey"},{"first_name":"Gideon","full_name":"Dresdner, Gideon","last_name":"Dresdner"},{"first_name":"Alicia","last_name":"Tsai","full_name":"Tsai, Alicia"},{"first_name":"Laurent El","last_name":"Ghaoui","full_name":"Ghaoui, Laurent El"},{"id":"26cfd52f-2483-11ee-8040-88983bcc06d4","first_name":"Francesco","last_name":"Locatello","full_name":"Locatello, Francesco","orcid":"0000-0002-4850-0683"},{"last_name":"Freund","full_name":"Freund, Robert M.","first_name":"Robert M."},{"last_name":"Pedregosa","full_name":"Pedregosa, Fabian","first_name":"Fabian"}],"external_id":{"arxiv":["2002.11860"]},"article_processing_charge":"No","title":"Stochastic Frank-Wolfe for constrained finite-sum minimization","department":[{"_id":"FrLo"}],"date_updated":"2023-09-12T08:03:40Z","citation":{"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.","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.","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.","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.","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.","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."},"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","alternative_title":["PMLR"],"quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/2002.11860","open_access":"1"}],"oa":1,"month":"07","intvolume":" 119","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","page":"7253-7262","date_published":"2020-07-27T00:00:00Z","volume":119,"date_created":"2023-08-22T14:07:52Z","publication_status":"published","year":"2020","day":"27","publication":"Proceedings of the 37th International Conference on Machine Learning","language":[{"iso":"eng"}]},{"article_processing_charge":"No","external_id":{"arxiv":["2010.14766"]},"author":[{"id":"26cfd52f-2483-11ee-8040-88983bcc06d4","first_name":"Francesco","last_name":"Locatello","orcid":"0000-0002-4850-0683","full_name":"Locatello, Francesco"},{"first_name":"Stefan","full_name":"Bauer, Stefan","last_name":"Bauer"},{"full_name":"Lucic, Mario","last_name":"Lucic","first_name":"Mario"},{"first_name":"Gunnar","last_name":"Rätsch","full_name":"Rätsch, Gunnar"},{"full_name":"Gelly, Sylvain","last_name":"Gelly","first_name":"Sylvain"},{"first_name":"Bernhard","full_name":"Schölkopf, Bernhard","last_name":"Schölkopf"},{"full_name":"Bachem, Olivier","last_name":"Bachem","first_name":"Olivier"}],"title":"A sober look at the unsupervised learning of disentangled representations and their evaluation","citation":{"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.","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.","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.","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).","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"209","date_created":"2023-08-22T14:10:34Z","date_published":"2020-09-01T00:00:00Z","year":"2020","has_accepted_license":"1","publication":"Journal of Machine Learning Research","day":"01","oa":1,"quality_controlled":"1","publisher":"MIT Press","department":[{"_id":"FrLo"}],"date_updated":"2023-09-12T09:23:56Z","ddc":["000"],"extern":"1","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","_id":"14195","volume":21,"publication_status":"published","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://jmlr.csail.mit.edu/papers/v21/19-976.html"}],"scopus_import":"1","intvolume":" 21","month":"09","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."}],"oa_version":"Published Version"},{"department":[{"_id":"CaGu"},{"_id":"GaTk"}],"file_date_updated":"2020-07-14T12:48:00Z","date_updated":"2023-09-12T11:02:24Z","ddc":["000","570"],"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","_id":"7569","issue":"2","related_material":{"record":[{"relation":"research_data","id":"9716","status":"deleted"},{"relation":"research_data","status":"public","id":"9776"},{"relation":"used_in_publication","id":"9779","status":"public"},{"relation":"dissertation_contains","status":"public","id":"8155"},{"relation":"research_data","status":"public","id":"9777"}]},"volume":16,"publication_status":"published","publication_identifier":{"issn":["1553-7358"]},"language":[{"iso":"eng"}],"file":[{"file_name":"2020_PlosCompBio_Grah.pdf","date_created":"2020-03-09T15:12:21Z","file_size":2209325,"date_updated":"2020-07-14T12:48:00Z","creator":"dernst","checksum":"5239dd134dc6e1c71fe7b3ce2953da37","file_id":"7579","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"scopus_import":"1","intvolume":" 16","month":"02","abstract":[{"lang":"eng","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."}],"oa_version":"Published Version","article_processing_charge":"No","external_id":{"isi":["000526725200019"]},"author":[{"full_name":"Grah, Rok","orcid":"0000-0003-2539-3560","last_name":"Grah","id":"483E70DE-F248-11E8-B48F-1D18A9856A87","first_name":"Rok"},{"first_name":"Tamar","last_name":"Friedlander","full_name":"Friedlander, Tamar"}],"title":"The relation between crosstalk and gene regulation form revisited","citation":{"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.","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).","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","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","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.","ista":"Grah R, Friedlander T. 2020. The relation between crosstalk and gene regulation form revisited. PLOS Computational Biology. 16(2), e1007642."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_number":"e1007642","date_created":"2020-03-06T07:39:38Z","doi":"10.1371/journal.pcbi.1007642","date_published":"2020-02-25T00:00:00Z","year":"2020","has_accepted_license":"1","isi":1,"publication":"PLOS Computational Biology","day":"25","oa":1,"publisher":"Public Library of Science","quality_controlled":"1"},{"date_published":"2020-11-05T00:00:00Z","doi":"10.1101/2020.11.03.366948","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."}],"pmid":1,"oa_version":"Preprint","author":[{"last_name":"Santini","full_name":"Santini, Laura","first_name":"Laura"},{"first_name":"Florian","full_name":"Halbritter, Florian","last_name":"Halbritter"},{"last_name":"Titz-Teixeira","full_name":"Titz-Teixeira, Fabian","first_name":"Fabian"},{"first_name":"Toru","last_name":"Suzuki","full_name":"Suzuki, Toru"},{"last_name":"Asami","full_name":"Asami, Maki","first_name":"Maki"},{"first_name":"Julia","last_name":"Ramesmayer","full_name":"Ramesmayer, Julia"},{"last_name":"Ma","full_name":"Ma, Xiaoyan","first_name":"Xiaoyan"},{"full_name":"Lackner, Andreas","last_name":"Lackner","first_name":"Andreas"},{"first_name":"Nick","full_name":"Warr, Nick","last_name":"Warr"},{"id":"48EA0138-F248-11E8-B48F-1D18A9856A87","first_name":"Florian","full_name":"Pauler, Florian","orcid":"0000-0002-7462-0048","last_name":"Pauler"},{"last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Laue, Ernest","last_name":"Laue","first_name":"Ernest"},{"last_name":"Farlik","full_name":"Farlik, Matthias","first_name":"Matthias"},{"full_name":"Bock, Christoph","last_name":"Bock","first_name":"Christoph"},{"full_name":"Beyer, Andreas","last_name":"Beyer","first_name":"Andreas"},{"last_name":"Perry","full_name":"Perry, Anthony C. F.","first_name":"Anthony C. F."},{"first_name":"Martin","full_name":"Leeb, Martin","last_name":"Leeb"}],"article_processing_charge":"No","external_id":{"pmid":["PPR234457 "]},"title":"Novel imprints in mouse blastocysts are predominantly DNA methylation independent","department":[{"_id":"SiHi"}],"citation":{"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.","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","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","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","citation":{"ieee":"R. Grah and T. Friedlander, “Maximizing crosstalk.” Public Library of Science, 2020.","short":"R. Grah, T. Friedlander, (2020).","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","mla":"Grah, Rok, and Tamar Friedlander. Maximizing Crosstalk. Public Library of Science, 2020, doi:10.1371/journal.pcbi.1007642.s002.","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."},"date_updated":"2023-09-12T11:02:25Z","title":"Maximizing crosstalk","department":[{"_id":"GaTk"}],"article_processing_charge":"No","author":[{"first_name":"Rok","id":"483E70DE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2539-3560","full_name":"Grah, Rok","last_name":"Grah"},{"full_name":"Friedlander, Tamar","last_name":"Friedlander","first_name":"Tamar"}],"_id":"9777","status":"public","type":"research_data_reference","day":"25","year":"2020","date_created":"2021-08-06T07:21:51Z","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","oa_version":"None","month":"02","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1371/journal.pcbi.1007642.s002"}],"publisher":"Public Library of Science"},{"author":[{"full_name":"Kragl, Bernhard","orcid":"0000-0001-7745-9117","last_name":"Kragl","first_name":"Bernhard","id":"320FC952-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","title":"Verifying concurrent programs: Refinement, synchronization, sequentialization","citation":{"mla":"Kragl, Bernhard. Verifying Concurrent Programs: Refinement, Synchronization, Sequentialization. Institute of Science and Technology Austria, 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","ama":"Kragl B. Verifying concurrent programs: Refinement, synchronization, sequentialization. 2020. doi:10.15479/AT:ISTA:8332","ieee":"B. Kragl, “Verifying concurrent programs: Refinement, synchronization, sequentialization,” Institute of Science and Technology Austria, 2020.","short":"B. Kragl, Verifying Concurrent Programs: Refinement, Synchronization, Sequentialization, Institute of Science and Technology Austria, 2020.","chicago":"Kragl, Bernhard. “Verifying Concurrent Programs: Refinement, Synchronization, Sequentialization.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8332.","ista":"Kragl B. 2020. Verifying concurrent programs: Refinement, synchronization, sequentialization. Institute of Science and Technology Austria."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","page":"120","date_published":"2020-09-03T00:00:00Z","doi":"10.15479/AT:ISTA:8332","date_created":"2020-09-04T12:24:12Z","has_accepted_license":"1","year":"2020","day":"03","publisher":"Institute of Science and Technology Austria","oa":1,"file_date_updated":"2020-09-04T13:00:17Z","department":[{"_id":"ToHe"}],"supervisor":[{"orcid":"0000-0002-2985-7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-09-13T08:45:08Z","ddc":["000"],"type":"dissertation","status":"public","_id":"8332","related_material":{"record":[{"relation":"part_of_dissertation","id":"133","status":"public"},{"status":"public","id":"8012","relation":"part_of_dissertation"},{"status":"public","id":"8195","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"160","status":"public"}]},"publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","publication_status":"published","file":[{"checksum":"26fe261550f691280bda4c454bf015c7","file_id":"8333","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2020-09-04T12:17:47Z","file_name":"kragl-thesis.pdf","date_updated":"2020-09-04T12:17:47Z","file_size":1348815,"creator":"bkragl"},{"date_updated":"2020-09-04T13:00:17Z","file_size":372312,"creator":"bkragl","date_created":"2020-09-04T13:00:17Z","file_name":"kragl-thesis.zip","content_type":"application/zip","access_level":"closed","relation":"source_file","checksum":"b9694ce092b7c55557122adba8337ebc","file_id":"8335"}],"language":[{"iso":"eng"}],"alternative_title":["ISTA Thesis"],"month":"09","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."}],"oa_version":"Published Version"},{"status":"public","type":"conference","conference":{"name":"NeurIPS: Neural Information Processing Systems","location":"Virtual","end_date":"2020-12-12","start_date":"2020-12-06"},"_id":"14326","title":"Object-centric learning with slot attention","department":[{"_id":"FrLo"}],"author":[{"id":"26cfd52f-2483-11ee-8040-88983bcc06d4","first_name":"Francesco","last_name":"Locatello","full_name":"Locatello, Francesco","orcid":"0000-0002-4850-0683"},{"first_name":"Dirk","last_name":"Weissenborn","full_name":"Weissenborn, Dirk"},{"full_name":"Unterthiner, Thomas","last_name":"Unterthiner","first_name":"Thomas"},{"first_name":"Aravindh","last_name":"Mahendran","full_name":"Mahendran, Aravindh"},{"full_name":"Heigold, Georg","last_name":"Heigold","first_name":"Georg"},{"first_name":"Jakob","last_name":"Uszkoreit","full_name":"Uszkoreit, Jakob"},{"last_name":"Dosovitskiy","full_name":"Dosovitskiy, Alexey","first_name":"Alexey"},{"first_name":"Thomas","full_name":"Kipf, Thomas","last_name":"Kipf"}],"article_processing_charge":"No","external_id":{"arxiv":["2006.15055"]},"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-09-13T12:19:19Z","citation":{"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.","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.","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.","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.","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.","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.","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."},"intvolume":" 33","publisher":"Curran Associates","quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2006.15055"}],"oa_version":"Preprint","abstract":[{"lang":"eng","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"}],"date_published":"2020-01-01T00:00:00Z","volume":33,"date_created":"2023-09-13T12:03:46Z","page":"11525-11538","publication":"Advances in Neural Information Processing Systems","language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9781713829546"]},"publication_status":"published","year":"2020"},{"publist_id":"7983","author":[{"last_name":"Gladbach","full_name":"Gladbach, Peter","first_name":"Peter"},{"full_name":"Kopfer, Eva","last_name":"Kopfer","first_name":"Eva"},{"last_name":"Maas","orcid":"0000-0002-0845-1338","full_name":"Maas, Jan","first_name":"Jan","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","external_id":{"isi":["000546975100017"],"arxiv":["1809.01092"]},"title":"Scaling limits of discrete optimal transport","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.","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","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.","short":"P. Gladbach, E. Kopfer, J. Maas, SIAM Journal on Mathematical Analysis 52 (2020) 2759–2802."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","page":"2759-2802","doi":"10.1137/19M1243440","date_published":"2020-10-01T00:00:00Z","date_created":"2018-12-11T11:44:28Z","isi":1,"year":"2020","day":"01","publication":"SIAM Journal on Mathematical Analysis","quality_controlled":"1","publisher":"Society for Industrial and Applied Mathematics","oa":1,"department":[{"_id":"JaMa"}],"date_updated":"2023-09-18T08:13:15Z","article_type":"original","type":"journal_article","status":"public","_id":"71","issue":"3","volume":52,"publication_identifier":{"eissn":["10957154"],"issn":["00361410"]},"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1809.01092","open_access":"1"}],"month":"10","intvolume":" 52","abstract":[{"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.","lang":"eng"}],"oa_version":"Preprint"},{"volume":26,"issue":"6","publication_status":"published","publication_identifier":{"eissn":["19410506"],"issn":["10772626"]},"language":[{"iso":"eng"}],"file":[{"file_name":"preprint.pdf","date_created":"2020-10-08T08:34:53Z","file_size":21910098,"date_updated":"2020-10-08T08:34:53Z","creator":"wojtan","success":1,"checksum":"8d4c55443a0ee335bb5bb652de503042","file_id":"8626","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"scopus_import":"1","intvolume":" 26","month":"06","abstract":[{"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.","lang":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"pmid":1,"oa_version":"Submitted Version","file_date_updated":"2020-10-08T08:34:53Z","department":[{"_id":"ChWo"}],"date_updated":"2023-09-18T09:30:01Z","ddc":["006"],"type":"journal_article","article_type":"original","status":"public","_id":"5681","page":"2288-2302","date_created":"2018-12-16T22:59:21Z","doi":"10.1109/TVCG.2018.2883628","date_published":"2020-06-01T00:00:00Z","year":"2020","isi":1,"has_accepted_license":"1","publication":"IEEE Transactions on Visualization and Computer Graphics","day":"01","oa":1,"publisher":"IEEE","quality_controlled":"1","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.","external_id":{"isi":["000532295600014"],"pmid":["30507534"]},"article_processing_charge":"No","author":[{"full_name":"Hikaru, Ibayashi","last_name":"Hikaru","first_name":"Ibayashi"},{"first_name":"Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546","last_name":"Wojtan"},{"first_name":"Nils","last_name":"Thuerey","full_name":"Thuerey, Nils"},{"full_name":"Igarashi, Takeo","last_name":"Igarashi","first_name":"Takeo"},{"full_name":"Ando, Ryoichi","last_name":"Ando","first_name":"Ryoichi"}],"title":"Simulating liquids on dynamically warping grids","citation":{"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.","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.","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.","short":"I. Hikaru, C. Wojtan, N. Thuerey, T. Igarashi, R. Ando, IEEE Transactions on Visualization and Computer Graphics 26 (2020) 2288–2302.","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","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"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"file_id":"8967","checksum":"3994c54a1241451d561db1d4f43bad30","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2020-12-22T10:55:56Z","file_name":"THESIS_Xiang_Li.pdf","creator":"xli","date_updated":"2020-12-22T10:55:56Z","file_size":3622305},{"date_updated":"2020-12-30T07:18:03Z","file_size":4018859,"creator":"xli","date_created":"2020-12-22T10:56:03Z","file_name":"THESIS_Xiang_Li.zip","content_type":"application/x-zip-compressed","access_level":"closed","relation":"source_file","checksum":"0954ecfc5554c05615c14de803341f00","file_id":"8968"}],"ec_funded":1,"related_material":{"record":[{"status":"public","id":"5886","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"8587","status":"public"},{"relation":"part_of_dissertation","id":"1120","status":"public"}]},"abstract":[{"lang":"eng","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."}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"12","date_updated":"2023-09-20T11:30:58Z","supervisor":[{"first_name":"Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail","last_name":"Lemeshko"}],"ddc":["539"],"department":[{"_id":"MiLe"}],"file_date_updated":"2020-12-30T07:18:03Z","_id":"8958","type":"dissertation","status":"public","year":"2020","has_accepted_license":"1","day":"21","page":"125","date_created":"2020-12-21T09:44:30Z","doi":"10.15479/AT:ISTA:8958","date_published":"2020-12-21T00:00:00Z","oa":1,"publisher":"Institute of Science and Technology Austria","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","author":[{"first_name":"Xiang","id":"4B7E523C-F248-11E8-B48F-1D18A9856A87","full_name":"Li, Xiang","last_name":"Li"}],"title":"Rotation of coupled cold molecules in the presence of a many-body environment","project":[{"name":"Quantum rotations in the presence of a many-body environment","grant_number":"P29902","call_identifier":"FWF","_id":"26031614-B435-11E9-9278-68D0E5697425"},{"_id":"2688CF98-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"801770","name":"Angulon: physics and applications of a new quasiparticle"}]},{"article_processing_charge":"No","author":[{"id":"4DDBCEB0-F248-11E8-B48F-1D18A9856A87","first_name":"Ran","full_name":"Zhang, Ran","orcid":"0000-0002-3808-281X","last_name":"Zhang"}],"title":"Structure-aware computational design and its application to 3D printable volume scattering, mechanism, and multistability","citation":{"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.","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","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","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.","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.","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"call_identifier":"H2020","_id":"2508E324-B435-11E9-9278-68D0E5697425","name":"Distributed 3D Object Design","grant_number":"642841"},{"_id":"24F9549A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"715767","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling"}],"page":"148","date_created":"2020-09-14T01:04:53Z","date_published":"2020-09-14T00:00:00Z","doi":"10.15479/AT:ISTA:8386","year":"2020","has_accepted_license":"1","day":"14","oa":1,"publisher":"Institute of Science and Technology Austria","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.","file_date_updated":"2020-09-15T12:51:53Z","department":[{"_id":"BeBi"}],"date_updated":"2023-09-22T09:49:31Z","supervisor":[{"orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd","last_name":"Bickel","first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87"}],"ddc":["003"],"type":"dissertation","status":"public","_id":"8386","ec_funded":1,"related_material":{"record":[{"status":"public","id":"486","relation":"part_of_dissertation"},{"status":"public","id":"1002","relation":"part_of_dissertation"}]},"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"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":"8388","checksum":"edcf578b6e1c9b0dd81ff72d319b66ba","content_type":"application/x-zip-compressed","relation":"source_file","access_level":"closed"},{"date_updated":"2020-09-15T12:51:53Z","file_size":161385316,"creator":"rzhang","date_created":"2020-09-15T12:51:53Z","file_name":"PhD_thesis_Ran Zhang_20200915.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"817e20c33be9247f906925517c56a40d","file_id":"8396","success":1}],"alternative_title":["ISTA Thesis"],"month":"09","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"}],"acknowledged_ssus":[{"_id":"SSU"}],"oa_version":"Published Version"},{"supervisor":[{"first_name":"Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","full_name":"Katsaros, Georgios","orcid":"0000-0001-8342-202X","last_name":"Katsaros"}],"date_updated":"2023-09-26T15:50:22Z","ddc":["530"],"file_date_updated":"2020-07-14T12:48:07Z","department":[{"_id":"GeKa"}],"_id":"7996","type":"dissertation","status":"public","publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","file":[{"file_id":"7997","checksum":"467e52feb3e361ce8cf5fe8d5c254ece","relation":"main_file","access_level":"closed","content_type":"application/x-zip-compressed","file_name":"JK_thesis_latex_source_files.zip","date_created":"2020-06-22T09:22:04Z","creator":"dernst","file_size":392794743,"date_updated":"2020-07-14T12:48:07Z"},{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"1de716bf110dbd77d383e479232bf496","file_id":"7998","date_updated":"2020-07-14T12:48:07Z","file_size":28453247,"creator":"dernst","date_created":"2020-06-22T09:21:29Z","file_name":"PhD_thesis_JK_pdfa.pdf"}],"language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"1328","status":"public"},{"status":"public","id":"7541","relation":"part_of_dissertation"},{"id":"77","status":"public","relation":"part_of_dissertation"},{"status":"public","id":"23","relation":"part_of_dissertation"},{"status":"public","id":"840","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","citation":{"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.","ama":"Kukucka J. Implementation of a hole spin qubit in Ge hut wires and dispersive spin sensing. 2020. doi:10.15479/AT:ISTA:7996","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","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.","ista":"Kukucka J. 2020. Implementation of a hole spin qubit in Ge hut wires and dispersive spin sensing. Institute of Science and Technology Austria.","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"first_name":"Josip","id":"3F5D8856-F248-11E8-B48F-1D18A9856A87","last_name":"Kukucka","full_name":"Kukucka, Josip"}],"article_processing_charge":"No","title":"Implementation of a hole spin qubit in Ge hut wires and dispersive spin sensing","has_accepted_license":"1","year":"2020","day":"22","page":"178","doi":"10.15479/AT:ISTA:7996","date_published":"2020-06-22T00:00:00Z","date_created":"2020-06-22T09:22:23Z","publisher":"Institute of Science and Technology Austria","oa":1},{"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."}],"oa_version":"Published Version","alternative_title":["LNCS"],"scopus_import":"1","intvolume":" 12225","month":"07","publication_status":"published","publication_identifier":{"isbn":["9783030532901"],"eissn":["16113349"],"issn":["03029743"]},"language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"093d4788d7d5b2ce0ffe64fbe7820043","file_id":"8276","creator":"dernst","file_size":625056,"date_updated":"2020-08-17T11:32:44Z","file_name":"2020_LNCS_CAV_Chatterjee.pdf","date_created":"2020-08-17T11:32:44Z"}],"ec_funded":1,"related_material":{"record":[{"status":"public","id":"12738","relation":"later_version"}]},"volume":12225,"_id":"8272","conference":{"name":"CAV: Computer Aided Verification"},"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","status":"public","date_updated":"2023-10-03T11:36:13Z","ddc":["000"],"file_date_updated":"2020-08-17T11:32:44Z","department":[{"_id":"KrCh"}],"oa":1,"publisher":"Springer Nature","quality_controlled":"1","year":"2020","isi":1,"has_accepted_license":"1","publication":"International Conference on Computer Aided Verification","day":"14","page":"398-420","date_created":"2020-08-16T22:00:58Z","doi":"10.1007/978-3-030-53291-8_21","date_published":"2020-07-14T00:00:00Z","project":[{"call_identifier":"H2020","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818"},{"grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification","_id":"25892FC0-B435-11E9-9278-68D0E5697425"}],"citation":{"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.","short":"K. Chatterjee, J.P. Katoen, M. Weininger, T. Winkler, in:, International Conference on Computer Aided Verification, Springer Nature, 2020, pp. 398–420.","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.","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","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","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","external_id":{"arxiv":["2005.04018"],"isi":["000695272500021"]},"author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"},{"first_name":"Joost P","id":"4524F760-F248-11E8-B48F-1D18A9856A87","last_name":"Katoen","full_name":"Katoen, Joost P"},{"last_name":"Weininger","full_name":"Weininger, Maximilian","first_name":"Maximilian"},{"full_name":"Winkler, Tobias","last_name":"Winkler","first_name":"Tobias"}],"title":"Stochastic games with lexicographic reachability-safety objectives"},{"date_created":"2020-03-08T23:00:47Z","doi":"10.1016/bs.mcb.2020.01.006","date_published":"2020-02-27T00:00:00Z","page":"145-161","publication":"Methods in Cell Biology","day":"27","year":"2020","isi":1,"oa":1,"publisher":"Elsevier","quality_controlled":"1","editor":[{"last_name":"Tran","full_name":"Tran, Phong ","first_name":"Phong "}],"title":"Computational analysis of filament polymerization dynamics in cytoskeletal networks","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"},{"first_name":"Philipp","id":"40136C2A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9198-2182 ","full_name":"Radler, Philipp","last_name":"Radler"},{"last_name":"Sommer","full_name":"Sommer, Christoph M","orcid":"0000-0003-1216-9105","first_name":"Christoph M","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Loose","full_name":"Loose, Martin","orcid":"0000-0001-7309-9724","first_name":"Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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.","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.","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.","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"},"project":[{"name":"Self-Organization of the Bacterial Cell","grant_number":"679239","call_identifier":"H2020","_id":"2595697A-B435-11E9-9278-68D0E5697425"},{"_id":"260D98C8-B435-11E9-9278-68D0E5697425","name":"Reconstitution of Bacterial Cell Division Using Purified Components"}],"ec_funded":1,"related_material":{"record":[{"status":"public","id":"8358","relation":"part_of_dissertation"}]},"volume":158,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0091679X"]},"intvolume":" 158","month":"02","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/839571"}],"alternative_title":["Methods in Cell Biology"],"scopus_import":"1","oa_version":"Preprint","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."}],"department":[{"_id":"MaLo"}],"date_updated":"2023-10-04T09:50:24Z","status":"public","type":"book_chapter","_id":"7572"},{"volume":5,"related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/little-cell-big-cover-story/"}],"record":[{"status":"public","id":"14280","relation":"dissertation_contains"}]},"ec_funded":1,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2058-5276"]},"publication_status":"published","month":"01","intvolume":" 5","scopus_import":"1","main_file_link":[{"open_access":"1","url":"http://europepmc.org/article/PMC/7048620"}],"pmid":1,"oa_version":"Submitted Version","abstract":[{"lang":"eng","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."}],"department":[{"_id":"MaLo"}],"date_updated":"2023-10-06T12:22:38Z","status":"public","type":"journal_article","article_type":"letter_note","_id":"7387","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","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.","title":"Diffusion and capture permits dynamic coupling between treadmilling FtsZ filaments and cell division proteins","author":[{"first_name":"Natalia S.","id":"38661662-F248-11E8-B48F-1D18A9856A87","full_name":"Baranova, Natalia S.","orcid":"0000-0002-3086-9124","last_name":"Baranova"},{"id":"40136C2A-F248-11E8-B48F-1D18A9856A87","first_name":"Philipp","full_name":"Radler, Philipp","orcid":"0000-0001-9198-2182 ","last_name":"Radler"},{"last_name":"Hernández-Rocamora","full_name":"Hernández-Rocamora, Víctor M.","first_name":"Víctor M."},{"first_name":"Carlos","full_name":"Alfonso, Carlos","last_name":"Alfonso"},{"full_name":"Lopez Pelegrin, Maria D","last_name":"Lopez Pelegrin","id":"319AA9CE-F248-11E8-B48F-1D18A9856A87","first_name":"Maria D"},{"full_name":"Rivas, Germán","last_name":"Rivas","first_name":"Germán"},{"full_name":"Vollmer, Waldemar","last_name":"Vollmer","first_name":"Waldemar"},{"full_name":"Loose, Martin","orcid":"0000-0001-7309-9724","last_name":"Loose","first_name":"Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","external_id":{"pmid":["31959972"],"isi":["000508584700007"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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.","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.","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.","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"},"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"},{"name":"Synthesis of bacterial cell wall","grant_number":"ALTF 2015-1163","_id":"2596EAB6-B435-11E9-9278-68D0E5697425"}]},{"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,"publisher":"Akadémiai Kiadó","quality_controlled":"1","publication":"Studia Scientiarum Mathematicarum Hungarica","day":"24","year":"2020","has_accepted_license":"1","isi":1,"date_created":"2020-07-24T07:09:18Z","doi":"10.1556/012.2020.57.2.1454","date_published":"2020-07-24T00:00:00Z","page":"193-199","project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"268116B8-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z00342","name":"The Wittgenstein Prize"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","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","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","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."},"title":"Refutation of a claim made by Fejes Tóth on the accuracy of surface meshes","article_processing_charge":"No","external_id":{"isi":["000570978400005"]},"author":[{"first_name":"Gert","last_name":"Vegter","full_name":"Vegter, Gert"},{"last_name":"Wintraecken","full_name":"Wintraecken, Mathijs","orcid":"0000-0002-7472-2220","id":"307CFBC8-F248-11E8-B48F-1D18A9856A87","first_name":"Mathijs"}],"oa_version":"Published Version","abstract":[{"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.","lang":"eng"}],"intvolume":" 57","month":"07","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"file_name":"57-2-05_4214-1454Vegter-Wintraecken_OpenAccess_CC-BY-NC.pdf","date_created":"2020-07-24T07:09:06Z","file_size":1476072,"date_updated":"2020-07-24T07:09:06Z","creator":"mwintrae","file_id":"8164","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"publication_status":"published","publication_identifier":{"issn":["0081-6906"],"eissn":["1588-2896"]},"ec_funded":1,"volume":57,"issue":"2","_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","ddc":["510"],"date_updated":"2023-10-10T13:05:27Z","department":[{"_id":"HeEd"}],"file_date_updated":"2020-07-24T07:09:06Z"},{"project":[{"name":"Quantitative Analysis of Probablistic Systems with a focus on Crypto-currencies","_id":"267066CE-B435-11E9-9278-68D0E5697425"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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.","short":"A. Shakiba, A.K. Goharshady, M.R. Hooshmandasl, M. Alambardar Meybodi, Iranian Journal of Mathematical Sciences and Informatics 15 (2020) 117–128.","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.","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","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"},"title":"A note on belief structures and s-approximation spaces","author":[{"full_name":"Shakiba, A.","last_name":"Shakiba","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"},{"first_name":"M.R.","last_name":"Hooshmandasl","full_name":"Hooshmandasl, M.R."},{"last_name":"Alambardar Meybodi","full_name":"Alambardar Meybodi, M.","first_name":"M."}],"external_id":{"arxiv":["1805.10672"]},"article_processing_charge":"No","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.","quality_controlled":"1","publisher":"Iranian Academic Center for Education, Culture and Research","oa":1,"day":"01","publication":"Iranian Journal of Mathematical Sciences and Informatics","has_accepted_license":"1","year":"2020","date_published":"2020-10-01T00:00:00Z","doi":"10.29252/ijmsi.15.2.117","date_created":"2020-10-18T22:01:36Z","page":"117-128","_id":"8671","status":"public","type":"journal_article","article_type":"original","ddc":["000"],"date_updated":"2023-10-16T09:25:00Z","file_date_updated":"2020-10-19T11:14:20Z","department":[{"_id":"KrCh"}],"oa_version":"Submitted Version","abstract":[{"lang":"eng","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. "}],"month":"10","intvolume":" 15","scopus_import":"1","file":[{"date_created":"2020-10-19T11:14:20Z","file_name":"2020_ijmsi_Shakiba_accepted.pdf","date_updated":"2020-10-19T11:14:20Z","file_size":261688,"creator":"dernst","checksum":"f299661a6d51cda6d255a76be696f48d","file_id":"8676","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2008-9473"],"issn":["1735-4463"]},"publication_status":"published","volume":15,"issue":"2"},{"article_number":"82","citation":{"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","short":"K. Dareiotis, M. Gerencser, Electronic Journal of Probability 25 (2020).","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.","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","external_id":{"arxiv":["1812.04583"],"isi":["000550150700001"]},"author":[{"full_name":"Dareiotis, Konstantinos","last_name":"Dareiotis","first_name":"Konstantinos"},{"full_name":"Gerencser, Mate","last_name":"Gerencser","id":"44ECEDF2-F248-11E8-B48F-1D18A9856A87","first_name":"Mate"}],"title":"On the regularisation of the noise for the Euler-Maruyama scheme with irregular drift","oa":1,"quality_controlled":"1","publisher":"Institute of Mathematical Statistics","year":"2020","has_accepted_license":"1","isi":1,"publication":"Electronic Journal of Probability","day":"16","date_created":"2019-04-30T07:40:17Z","doi":"10.1214/20-EJP479","date_published":"2020-07-16T00:00:00Z","_id":"6359","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","date_updated":"2023-10-16T09:22:50Z","ddc":["510"],"file_date_updated":"2020-09-21T13:15:02Z","department":[{"_id":"JaMa"}],"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","scopus_import":"1","intvolume":" 25","month":"07","publication_status":"published","publication_identifier":{"eissn":["1083-6489"]},"language":[{"iso":"eng"}],"file":[{"checksum":"8e7c42e72596f6889d786e8e8b89994f","file_id":"8549","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2020-09-21T13:15:02Z","file_name":"2020_EJournProbab_Dareiotis.pdf","creator":"dernst","date_updated":"2020-09-21T13:15:02Z","file_size":273042}],"volume":25},{"file_date_updated":"2020-09-14T13:39:17Z","department":[{"_id":"ChLa"}],"date_updated":"2023-10-16T10:04:02Z","supervisor":[{"first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert","full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887"}],"ddc":["000"],"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)"},"type":"dissertation","status":"public","_id":"8390","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","related_material":{"record":[{"status":"public","id":"7936","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"7937","status":"public"},{"relation":"part_of_dissertation","id":"8193","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"8092"},{"id":"911","status":"public","relation":"part_of_dissertation"}]},"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-007-7"]},"language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"c914d2f88846032f3d8507734861b6ee","file_id":"8391","success":1,"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"},{"file_size":74227627,"date_updated":"2020-09-14T13:39:17Z","creator":"dernst","file_name":"thesis_sources.zip","date_created":"2020-09-14T13:39:17Z","content_type":"application/x-zip-compressed","relation":"main_file","access_level":"closed","checksum":"ae98fb35d912cff84a89035ae5794d3c","file_id":"8392"}],"alternative_title":["ISTA Thesis"],"month":"09","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"}],"oa_version":"Published Version","article_processing_charge":"No","author":[{"id":"3811D890-F248-11E8-B48F-1D18A9856A87","first_name":"Amélie","last_name":"Royer","orcid":"0000-0002-8407-0705","full_name":"Royer, Amélie"}],"title":"Leveraging structure in Computer Vision tasks for flexible Deep Learning models","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.","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.","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","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","page":"197","date_created":"2020-09-14T13:42:09Z","doi":"10.15479/AT:ISTA:8390","date_published":"2020-09-14T00:00:00Z","year":"2020","has_accepted_license":"1","day":"14","oa":1,"publisher":"Institute of Science and Technology Austria","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."},{"_id":"8186","conference":{"start_date":"2020-06-14","end_date":"2020-06-19","location":"Virtual","name":"CVPR: Conference on Computer Vision and Pattern Recognition"},"type":"conference","status":"public","date_updated":"2023-10-17T07:37:11Z","ddc":["004"],"department":[{"_id":"ChLa"}],"file_date_updated":"2020-07-31T16:57:12Z","abstract":[{"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.","lang":"eng"}],"oa_version":"Submitted Version","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"}],"scopus_import":"1","month":"07","publication_status":"published","publication_identifier":{"eissn":["2575-7075"],"eisbn":["9781728171685"]},"language":[{"iso":"eng"}],"file":[{"creator":"phenders","file_size":10262773,"date_updated":"2020-07-31T16:57:12Z","file_name":"paper.pdf","date_created":"2020-07-31T16:57:12Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"8187"}],"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.","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","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.","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["2004.04180"]},"article_processing_charge":"No","author":[{"orcid":"0000-0002-5198-7445","full_name":"Henderson, Paul M","last_name":"Henderson","id":"13C09E74-18D9-11E9-8878-32CFE5697425","first_name":"Paul M"},{"first_name":"Vagia","full_name":"Tsiminaki, Vagia","last_name":"Tsiminaki"},{"last_name":"Lampert","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph","first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"}],"title":"Leveraging 2D data to learn textured 3D mesh generation","oa":1,"publisher":"IEEE","quality_controlled":"1","year":"2020","has_accepted_license":"1","publication":"Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition","day":"01","page":"7498-7507","date_created":"2020-07-31T16:53:49Z","doi":"10.1109/CVPR42600.2020.00752","date_published":"2020-07-01T00:00:00Z"},{"isi":1,"year":"2020","day":"01","publication":"Plant Signaling & Behavior","date_published":"2020-01-01T00:00:00Z","doi":"10.1080/15592324.2019.1687175","date_created":"2020-01-30T10:12:04Z","publisher":"Taylor & Francis","quality_controlled":"1","oa":1,"citation":{"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.","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","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","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"orcid":"0000-0002-4566-0593","full_name":"Sinclair, Scott A","last_name":"Sinclair","first_name":"Scott A","id":"2D99FE6A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"U.","full_name":"Krämer, U.","last_name":"Krämer"}],"external_id":{"isi":["000494909300001"],"pmid":["31696764"]},"article_processing_charge":"No","title":"Generation of effective zinc-deficient agar-solidified media allows identification of root morphology changes in response to zinc limitation","article_number":"1687175","publication_identifier":{"issn":["1559-2324"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":15,"issue":"1","abstract":[{"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.","lang":"eng"}],"pmid":1,"oa_version":"Submitted Version","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7012054"}],"month":"01","intvolume":" 15","date_updated":"2023-10-17T09:01:48Z","department":[{"_id":"JiFr"}],"_id":"7416","article_type":"original","type":"journal_article","status":"public"},{"type":"journal_article","article_type":"original","keyword":["General Mathematics"],"status":"public","_id":"9196","department":[{"_id":"JuFi"},{"_id":"GradSch"}],"date_updated":"2023-10-17T09:15:53Z","scopus_import":"1","intvolume":" 252","month":"03","abstract":[{"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.","lang":"eng"}],"oa_version":"Preprint","issue":"3","volume":252,"publication_status":"published","publication_identifier":{"eissn":["1730-6337"],"issn":["0039-3223"]},"language":[{"iso":"eng"}],"article_processing_charge":"No","external_id":{"arxiv":["1709.05202"],"isi":["000558100500002"]},"author":[{"id":"4D23B7DA-F248-11E8-B48F-1D18A9856A87","first_name":"Sebastian","full_name":"Hensel, Sebastian","orcid":"0000-0001-7252-8072","last_name":"Hensel"},{"first_name":"Tommaso","last_name":"Rosati","full_name":"Rosati, Tommaso"}],"title":"Modelled distributions of Triebel–Lizorkin type","citation":{"ista":"Hensel S, Rosati T. 2020. Modelled distributions of Triebel–Lizorkin type. Studia Mathematica. 252(3), 251–297.","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.","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","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Instytut Matematyczny","quality_controlled":"1","page":"251-297","date_created":"2021-02-25T08:55:03Z","date_published":"2020-03-01T00:00:00Z","doi":"10.4064/sm180411-11-2","year":"2020","isi":1,"publication":"Studia Mathematica","day":"01"},{"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":"7464","department":[{"_id":"FlSc"}],"file_date_updated":"2020-07-14T12:47:59Z","date_updated":"2023-10-17T12:29:34Z","ddc":["570"],"scopus_import":"1","intvolume":" 16","month":"01","abstract":[{"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.","lang":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"oa_version":"Published Version","pmid":1,"issue":"1","volume":16,"related_material":{"record":[{"id":"9723","status":"deleted","relation":"research_data"}]},"publication_status":"published","publication_identifier":{"issn":["1553-7374"]},"language":[{"iso":"eng"}],"file":[{"creator":"dernst","date_updated":"2020-07-14T12:47:59Z","file_size":4551246,"date_created":"2020-02-11T10:07:28Z","file_name":"2020_PLOSPatho_Dick.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"a297f54d1fef0efe4789ca00f37f241e","file_id":"7484"}],"project":[{"_id":"26736D6A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P31445","name":"Structural conservation and diversity in retroviral capsid"}],"article_number":"e1008277","article_processing_charge":"No","external_id":{"isi":["000510746400010"],"pmid":["31986188"]},"author":[{"first_name":"Robert A.","full_name":"Dick, Robert A.","last_name":"Dick"},{"first_name":"Chaoyi","last_name":"Xu","full_name":"Xu, Chaoyi"},{"first_name":"Dustin R.","last_name":"Morado","full_name":"Morado, Dustin R."},{"first_name":"Vladyslav","id":"4D62F2A6-F248-11E8-B48F-1D18A9856A87","last_name":"Kravchuk","full_name":"Kravchuk, Vladyslav","orcid":"0000-0001-9523-9089"},{"first_name":"Clifton L.","full_name":"Ricana, Clifton L.","last_name":"Ricana"},{"first_name":"Terri D.","last_name":"Lyddon","full_name":"Lyddon, Terri D."},{"first_name":"Arianna M.","last_name":"Broad","full_name":"Broad, Arianna M."},{"last_name":"Feathers","full_name":"Feathers, J. Ryan","first_name":"J. Ryan"},{"full_name":"Johnson, Marc C.","last_name":"Johnson","first_name":"Marc C."},{"first_name":"Volker M.","last_name":"Vogt","full_name":"Vogt, Volker M."},{"first_name":"Juan R.","full_name":"Perilla, Juan R.","last_name":"Perilla"},{"first_name":"John A. G.","last_name":"Briggs","full_name":"Briggs, John A. G."},{"orcid":"0000-0003-4790-8078","full_name":"Schur, Florian KM","last_name":"Schur","first_name":"Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87"}],"title":"Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly","citation":{"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.","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.","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.","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)."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"quality_controlled":"1","publisher":"Public Library of Science","date_created":"2020-02-06T18:47:17Z","date_published":"2020-01-27T00:00:00Z","doi":"10.1371/journal.ppat.1008277","year":"2020","has_accepted_license":"1","isi":1,"publication":"PLOS Pathogens","day":"27"},{"abstract":[{"lang":"eng","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."}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 16","month":"01","publication_status":"published","publication_identifier":{"eissn":["15537358"]},"language":[{"iso":"eng"}],"file":[{"date_created":"2020-02-03T07:32:42Z","file_name":"2020_PlosCompBio_Tkadlec.pdf","creator":"dernst","date_updated":"2020-07-14T12:47:53Z","file_size":1817531,"file_id":"7441","checksum":"ce32ee2d2f53aed832f78bbd47e882df","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"ec_funded":1,"related_material":{"record":[{"relation":"part_of_dissertation","id":"7196","status":"public"}]},"volume":16,"_id":"7212","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","date_updated":"2023-10-17T12:29:47Z","ddc":["000"],"file_date_updated":"2020-07-14T12:47:53Z","department":[{"_id":"KrCh"}],"oa":1,"quality_controlled":"1","publisher":"Public Library of Science","year":"2020","has_accepted_license":"1","isi":1,"publication":"PLoS computational biology","day":"17","date_created":"2019-12-23T13:45:11Z","date_published":"2020-01-17T00:00:00Z","doi":"10.1371/journal.pcbi.1007494","article_number":"e1007494","project":[{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23"},{"call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","name":"Game Theory"}],"citation":{"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","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.","short":"J. Tkadlec, A. Pavlogiannis, K. Chatterjee, M.A. Nowak, PLoS Computational Biology 16 (2020).","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.","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"isi":["000510916500025"],"arxiv":["1906.02785"]},"article_processing_charge":"No","author":[{"first_name":"Josef","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","full_name":"Tkadlec, Josef","orcid":"0000-0002-1097-9684","last_name":"Tkadlec"},{"id":"49704004-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas","last_name":"Pavlogiannis","orcid":"0000-0002-8943-0722","full_name":"Pavlogiannis, Andreas"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"full_name":"Nowak, Martin A.","last_name":"Nowak","first_name":"Martin A."}],"title":"Limits on amplifiers of natural selection under death-Birth updating"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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","short":"J. Tkadlec, A Role of Graphs in Evolutionary Processes, Institute of Science and Technology Austria, 2020.","ieee":"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.","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."},"title":"A role of graphs in evolutionary processes","author":[{"last_name":"Tkadlec","full_name":"Tkadlec, Josef","orcid":"0000-0002-1097-9684","first_name":"Josef","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","day":"12","has_accepted_license":"1","year":"2020","date_published":"2020-01-12T00:00:00Z","doi":"10.15479/AT:ISTA:7196","date_created":"2019-12-20T12:26:36Z","page":"144","publisher":"Institute of Science and Technology Austria","oa":1,"ddc":["519"],"supervisor":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"}],"date_updated":"2023-10-17T12:29:46Z","file_date_updated":"2020-07-14T12:47:52Z","department":[{"_id":"KrCh"},{"_id":"GradSch"}],"_id":"7196","status":"public","type":"dissertation","file":[{"content_type":"application/zip","access_level":"closed","relation":"source_file","file_id":"7255","checksum":"451f8e64b0eb26bf297644ac72bfcbe9","date_updated":"2020-07-14T12:47:52Z","file_size":21100497,"creator":"jtkadlec","date_created":"2020-01-12T11:49:49Z","file_name":"thesis.zip"},{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"d8c44cbc4f939c49a8efc9d4b8bb3985","file_id":"7367","creator":"dernst","date_updated":"2020-07-14T12:47:52Z","file_size":11670983,"date_created":"2020-01-28T07:32:42Z","file_name":"2020_Tkadlec_Thesis.pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2663-337X"]},"degree_awarded":"PhD","publication_status":"published","related_material":{"record":[{"id":"7210","status":"public","relation":"dissertation_contains"},{"relation":"dissertation_contains","id":"5751","status":"public"},{"relation":"dissertation_contains","id":"7212","status":"public"}]},"oa_version":"Published Version","abstract":[{"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.","lang":"eng"}],"month":"01","alternative_title":["ISTA Thesis"]},{"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.","oa":1,"quality_controlled":"1","publisher":"ML Research Press","publication":"Proceedings of the 37th International Conference on Machine Learning","day":"13","year":"2020","has_accepted_license":"1","date_created":"2021-02-25T09:36:22Z","date_published":"2020-07-13T00:00:00Z","page":"8773-8784","project":[{"name":"Prix Lopez-Loretta 2019 - Marco Mondelli","_id":"059876FA-7A3F-11EA-A408-12923DDC885E"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","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.","short":"A. Shevchenko, M. Mondelli, in:, Proceedings of the 37th International Conference on Machine Learning, ML Research Press, 2020, pp. 8773–8784.","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.","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."},"title":"Landscape connectivity and dropout stability of SGD solutions for over-parameterized neural networks","external_id":{"arxiv":["1912.10095"]},"article_processing_charge":"No","author":[{"first_name":"Alexander","full_name":"Shevchenko, Alexander","last_name":"Shevchenko"},{"id":"27EB676C-8706-11E9-9510-7717E6697425","first_name":"Marco","full_name":"Mondelli, Marco","orcid":"0000-0002-3242-7020","last_name":"Mondelli"}],"oa_version":"Published Version","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."}],"intvolume":" 119","month":"07","language":[{"iso":"eng"}],"file":[{"success":1,"file_id":"9217","checksum":"f042c8d4316bd87c6361aa76f1fbdbbe","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2020_PMLR_Shevchenko.pdf","date_created":"2021-03-02T15:38:14Z","creator":"dernst","file_size":5336380,"date_updated":"2021-03-02T15:38:14Z"}],"publication_status":"published","volume":119,"_id":"9198","status":"public","type":"conference","ddc":["000"],"date_updated":"2023-10-17T12:43:19Z","file_date_updated":"2021-03-02T15:38:14Z","department":[{"_id":"MaMo"}]},{"oa":1,"publisher":"De Gruyter","quality_controlled":"1","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).","page":"51-67","date_created":"2021-02-17T15:13:01Z","doi":"10.1515/cmb-2020-0100","date_published":"2020-06-20T00:00:00Z","year":"2020","has_accepted_license":"1","publication":"Computational and Mathematical Biophysics","day":"20","project":[{"call_identifier":"H2020","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","name":"Alpha Shape Theory Extended","grant_number":"788183"},{"name":"Persistence and stability of geometric complexes","grant_number":"I02979-N35","call_identifier":"FWF","_id":"2561EBF4-B435-11E9-9278-68D0E5697425"}],"article_processing_charge":"No","author":[{"full_name":"Akopyan, Arseniy","orcid":"0000-0002-2548-617X","last_name":"Akopyan","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","first_name":"Arseniy"},{"full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert"}],"title":"The weighted mean curvature derivative of a space-filling diagram","citation":{"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.","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","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.","short":"A. Akopyan, H. Edelsbrunner, Computational and Mathematical Biophysics 8 (2020) 51–67.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 8","month":"06","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","ec_funded":1,"issue":"1","volume":8,"publication_status":"published","publication_identifier":{"issn":["2544-7297"]},"language":[{"iso":"eng"}],"file":[{"checksum":"cea41de9937d07a3b927d71ee8b4e432","file_id":"9171","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2021-02-19T13:56:24Z","file_name":"2020_CompMathBiophysics_Akopyan2.pdf","creator":"dernst","date_updated":"2021-02-19T13:56:24Z","file_size":562359}],"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","_id":"9157","department":[{"_id":"HeEd"}],"file_date_updated":"2021-02-19T13:56:24Z","date_updated":"2023-10-17T12:34:51Z","ddc":["510"]},{"ddc":["510"],"date_updated":"2023-10-17T12:35:10Z","file_date_updated":"2021-02-19T13:33:19Z","department":[{"_id":"HeEd"}],"_id":"9156","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)"},"file":[{"checksum":"ca43a7440834eab6bbea29c59b56ef3a","file_id":"9170","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_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"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2544-7297"]},"publication_status":"published","issue":"1","volume":8,"ec_funded":1,"oa_version":"Published Version","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"}],"month":"07","intvolume":" 8","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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."},"title":"The weighted Gaussian curvature derivative of a space-filling diagram","author":[{"first_name":"Arseniy","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","last_name":"Akopyan","full_name":"Akopyan, Arseniy","orcid":"0000-0002-2548-617X"},{"orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert"}],"article_processing_charge":"No","external_id":{"arxiv":["1908.06777"]},"project":[{"_id":"266A2E9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"788183","name":"Alpha Shape Theory Extended"},{"_id":"2561EBF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Persistence and stability of geometric complexes","grant_number":"I02979-N35"}],"day":"21","publication":"Computational and Mathematical Biophysics","has_accepted_license":"1","year":"2020","doi":"10.1515/cmb-2020-0101","date_published":"2020-07-21T00:00:00Z","date_created":"2021-02-17T15:12:44Z","page":"74-88","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).","quality_controlled":"1","publisher":"De Gruyter","oa":1},{"volume":25,"ec_funded":1,"publication_identifier":{"eissn":["1083-6489"]},"publication_status":"published","file":[{"date_created":"2020-12-28T08:24:08Z","file_name":"2020_ElectronJProbab_Redig.pdf","creator":"dernst","date_updated":"2020-12-28T08:24:08Z","file_size":696653,"file_id":"8976","checksum":"d75359b9814e78d57c0a481b7cde3751","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"10","intvolume":" 25","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."}],"oa_version":"Published Version","department":[{"_id":"JaMa"}],"file_date_updated":"2020-12-28T08:24:08Z","date_updated":"2023-10-17T12:51:56Z","ddc":["510"],"article_type":"original","type":"journal_article","status":"public","_id":"8973","doi":"10.1214/20-EJP536","date_published":"2020-10-21T00:00:00Z","date_created":"2020-12-27T23:01:17Z","has_accepted_license":"1","isi":1,"year":"2020","day":"21","publication":"Electronic Journal of Probability","quality_controlled":"1","publisher":" Institute of Mathematical Statistics","oa":1,"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).","author":[{"first_name":"Frank","last_name":"Redig","full_name":"Redig, Frank"},{"full_name":"Saada, Ellen","last_name":"Saada","first_name":"Ellen"},{"id":"E1836206-9F16-11E9-8814-AEFDE5697425","first_name":"Federico","full_name":"Sau, Federico","last_name":"Sau"}],"external_id":{"isi":["000591737500001"],"arxiv":["1811.01366"]},"article_processing_charge":"No","title":"Symmetric simple exclusion process in dynamic environment: Hydrodynamics","citation":{"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.","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.","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","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","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.","ista":"Redig F, Saada E, Sau F. 2020. Symmetric simple exclusion process in dynamic environment: Hydrodynamics. Electronic Journal of Probability. 25, 138."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"}],"article_number":"138"},{"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0012-7094"]},"publication_status":"published","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."}],"month":"09","intvolume":" 169","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1805.10715"}],"date_updated":"2023-10-17T12:51:10Z","department":[{"_id":"TiBr"}],"_id":"179","status":"public","article_type":"original","type":"journal_article","day":"10","publication":"Duke Mathematical Journal","isi":1,"year":"2020","doi":"10.1215/00127094-2020-0031","date_published":"2020-09-10T00:00:00Z","date_created":"2018-12-11T11:45:02Z","page":"3099-3165","publisher":"Duke University Press","quality_controlled":"1","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","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","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.","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."},"title":"Density of rational points on a quadric bundle in ℙ3×ℙ3","author":[{"orcid":"0000-0002-8314-0177","full_name":"Browning, Timothy D","last_name":"Browning","first_name":"Timothy D","id":"35827D50-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Roger","full_name":"Heath Brown, Roger","last_name":"Heath Brown"}],"article_processing_charge":"No","external_id":{"arxiv":["1805.10715"],"isi":["000582676300002"]}},{"citation":{"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","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","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.","short":"R. Ibsen-Jensen, J. Tkadlec, K. Chatterjee, M. Nowak, (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.","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."},"date_updated":"2023-10-18T06:36:00Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","author":[{"id":"3B699956-F248-11E8-B48F-1D18A9856A87","first_name":"Rasmus","orcid":"0000-0003-4783-0389","full_name":"Ibsen-Jensen, Rasmus","last_name":"Ibsen-Jensen"},{"last_name":"Tkadlec","orcid":"0000-0002-1097-9684","full_name":"Tkadlec, Josef","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","first_name":"Josef"},{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"},{"full_name":"Nowak, Martin","last_name":"Nowak","first_name":"Martin"}],"article_processing_charge":"No","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","_id":"9814","type":"research_data_reference","status":"public","year":"2020","day":"15","doi":"10.6084/m9.figshare.5973013.v1","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"198"}]},"date_published":"2020-10-15T00:00:00Z","date_created":"2021-08-06T13:09:57Z","abstract":[{"text":"Data and mathematica notebooks for plotting figures from Language learning with communication between learners","lang":"eng"}],"oa_version":"Published Version","publisher":"Royal Society","main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.5973013.v1","open_access":"1"}],"oa":1,"month":"10"},{"volume":125,"issue":"4","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"intvolume":" 125","month":"07","main_file_link":[{"url":"https://arxiv.org/abs/1912.10218","open_access":"1"}],"scopus_import":"1","oa_version":"Preprint","pmid":1,"abstract":[{"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.","lang":"eng"}],"department":[{"_id":"OnHo"}],"date_updated":"2023-10-18T08:38:35Z","status":"public","article_type":"original","type":"journal_article","_id":"8285","date_created":"2020-08-24T06:24:04Z","date_published":"2020-07-24T00:00:00Z","doi":"10.1103/PhysRevLett.125.043202","publication":"Physical Review Letters","day":"24","year":"2020","isi":1,"oa":1,"quality_controlled":"1","publisher":"American Physical Society","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).","title":"Free space Ramsey spectroscopy in rubidium with noise below the quantum projection limit","external_id":{"pmid":["32794788"],"isi":["000552227400008"],"arxiv":["1912.10218"]},"article_processing_charge":"No","author":[{"full_name":"Malia, Benjamin K.","last_name":"Malia","first_name":"Benjamin K."},{"first_name":"Julián","full_name":"Martínez-Rincón, Julián","last_name":"Martínez-Rincón"},{"first_name":"Yunfan","last_name":"Wu","full_name":"Wu, Yunfan"},{"first_name":"Onur","id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2031-204X","full_name":"Hosten, Onur","last_name":"Hosten"},{"first_name":"Mark A.","full_name":"Kasevich, Mark A.","last_name":"Kasevich"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","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.","short":"B.K. Malia, J. Martínez-Rincón, Y. Wu, O. Hosten, M.A. Kasevich, Physical Review Letters 125 (2020).","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.","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","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"},"article_number":"043202"}]