--- _id: '8195' 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. acknowledgement: "Bernhard Kragl and Thomas A. Henzinger were supported by\r\nthe Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award)." alternative_title: - LNCS article_processing_charge: No author: - first_name: Bernhard full_name: Kragl, Bernhard id: 320FC952-F248-11E8-B48F-1D18A9856A87 last_name: Kragl orcid: 0000-0001-7745-9117 - first_name: Shaz full_name: Qadeer, Shaz last_name: Qadeer - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000-0002-2985-7724 citation: 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 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. ista: Kragl B, Qadeer S, Henzinger TA. 2020. Refinement for structured concurrent programs. Computer Aided Verification. , LNCS, vol. 12224, 275–298. mla: Kragl, Bernhard, et al. “Refinement for Structured Concurrent Programs.” Computer Aided Verification, vol. 12224, Springer Nature, 2020, pp. 275–98, doi:10.1007/978-3-030-53288-8_14. short: B. Kragl, S. Qadeer, T.A. Henzinger, in:, Computer Aided Verification, Springer Nature, 2020, pp. 275–298. date_created: 2020-08-03T11:45:35Z date_published: 2020-07-14T00:00:00Z date_updated: 2023-09-07T13:18:00Z day: '14' ddc: - '000' department: - _id: ToHe doi: 10.1007/978-3-030-53288-8_14 external_id: isi: - '000695276000014' file: - access_level: open_access content_type: application/pdf creator: dernst date_created: 2020-08-06T08:14:54Z date_updated: 2020-08-06T08:14:54Z file_id: '8201' file_name: 2020_LNCS_Kragl.pdf file_size: 804237 relation: main_file success: 1 file_date_updated: 2020-08-06T08:14:54Z has_accepted_license: '1' intvolume: ' 12224' isi: 1 language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: 275-298 project: - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize publication: Computer Aided Verification publication_identifier: eisbn: - '9783030532888' eissn: - 1611-3349 isbn: - '9783030532871' issn: - 0302-9743 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '8332' relation: dissertation_contains status: public scopus_import: '1' status: public title: Refinement for structured concurrent programs tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 12224 year: '2020' ... --- _id: '8012' 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. article_processing_charge: No author: - first_name: Bernhard full_name: Kragl, Bernhard id: 320FC952-F248-11E8-B48F-1D18A9856A87 last_name: Kragl orcid: 0000-0001-7745-9117 - first_name: Constantin full_name: Enea, Constantin last_name: Enea - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000-0002-2985-7724 - first_name: Suha Orhun full_name: Mutluergil, Suha Orhun last_name: Mutluergil - first_name: Shaz full_name: Qadeer, Shaz last_name: Qadeer citation: 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' 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. 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. 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. conference: end_date: 2020-06-20 location: London, United Kingdom name: 'PLDI: Programming Language Design and Implementation' start_date: 2020-06-15 date_created: 2020-06-25T11:40:16Z date_published: 2020-06-01T00:00:00Z date_updated: 2023-09-07T13:18:00Z day: '01' department: - _id: ToHe doi: 10.1145/3385412.3385980 external_id: isi: - '000614622300016' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1145/3385412.3385980 month: '06' oa: 1 oa_version: Published Version page: 227-242 project: - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize publication: Proceedings of the 41st ACM SIGPLAN Conference on Programming Language Design and Implementation publication_identifier: isbn: - '9781450376136' publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' related_material: record: - id: '8332' relation: dissertation_contains status: public scopus_import: '1' status: public title: Inductive sequentialization of asynchronous programs type: conference user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 year: '2020' ... --- _id: '8358' abstract: - lang: eng 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" acknowledged_ssus: - _id: Bio 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. alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Paulo R full_name: Dos Santos Caldas, Paulo R id: 38FCDB4C-F248-11E8-B48F-1D18A9856A87 last_name: Dos Santos Caldas orcid: 0000-0001-6730-4461 citation: 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 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 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. 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. 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. 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. 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. date_created: 2020-09-10T09:26:49Z date_published: 2020-09-10T00:00:00Z date_updated: 2023-09-07T13:18:51Z day: '10' ddc: - '572' degree_awarded: PhD department: - _id: MaLo doi: 10.15479/AT:ISTA:8358 file: - access_level: open_access checksum: 882f93fe9c351962120e2669b84bf088 content_type: application/pdf creator: pcaldas date_created: 2020-09-10T12:11:29Z date_updated: 2020-09-10T12:11:29Z file_id: '8364' file_name: phd_thesis_pcaldas.pdf file_size: 141602462 relation: main_file success: 1 - access_level: closed checksum: 70cc9e399c4e41e6e6ac445ae55e8558 content_type: application/x-zip-compressed creator: pcaldas date_created: 2020-09-10T12:18:17Z date_updated: 2020-09-11T07:48:10Z file_id: '8365' file_name: phd_thesis_latex_pcaldas.zip file_size: 450437458 relation: source_file file_date_updated: 2020-09-11T07:48:10Z has_accepted_license: '1' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: '135' publication_identifier: isbn: - 978-3-99078-009-1 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '7572' relation: dissertation_contains status: public - id: '7197' relation: part_of_dissertation status: public status: public supervisor: - first_name: Martin full_name: Loose, Martin id: 462D4284-F248-11E8-B48F-1D18A9856A87 last_name: Loose orcid: 0000-0001-7309-9724 title: Organization and dynamics of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinkers tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2020' ... --- _id: '8703' abstract: - lang: eng 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. ' alternative_title: - LIPIcs article_number: '75' article_processing_charge: No author: - first_name: Georg F full_name: Osang, Georg F id: 464B40D6-F248-11E8-B48F-1D18A9856A87 last_name: Osang orcid: 0000-0002-8882-5116 - first_name: Mael full_name: Rouxel-Labbé, Mael last_name: Rouxel-Labbé - first_name: Monique full_name: Teillaud, Monique last_name: Teillaud citation: 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' 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. 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. 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.' 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. short: G.F. Osang, M. Rouxel-Labbé, M. Teillaud, in:, 28th Annual European Symposium on Algorithms, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020. conference: end_date: 2020-09-09 location: Virtual, Online; Pisa, Italy name: 'ESA: Annual European Symposium on Algorithms' start_date: 2020-09-07 date_created: 2020-10-25T23:01:18Z date_published: 2020-08-26T00:00:00Z date_updated: 2023-09-07T13:29:00Z day: '26' ddc: - '000' department: - _id: HeEd doi: 10.4230/LIPIcs.ESA.2020.75 ec_funded: 1 file: - access_level: open_access checksum: fe0f7c49a99ed870c671b911e10d5496 content_type: application/pdf creator: cziletti date_created: 2020-10-27T14:31:52Z date_updated: 2020-10-27T14:31:52Z file_id: '8712' file_name: 2020_LIPIcs_Osang.pdf file_size: 733291 relation: main_file success: 1 file_date_updated: 2020-10-27T14:31:52Z has_accepted_license: '1' intvolume: ' 173' language: - iso: eng license: https://creativecommons.org/licenses/by/3.0/ month: '08' oa: 1 oa_version: Published Version project: - _id: 266A2E9E-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '788183' name: Alpha Shape Theory Extended publication: 28th Annual European Symposium on Algorithms publication_identifier: isbn: - '9783959771627' issn: - '18688969' publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik quality_controlled: '1' related_material: record: - id: '9056' relation: dissertation_contains status: public scopus_import: '1' status: public title: Generalizing CGAL periodic Delaunay triangulations tmp: 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) short: CC BY (3.0) type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 173 year: '2020' ... --- _id: '7481' 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.' article_processing_charge: No author: - first_name: Phuong full_name: Bui Thi Mai, Phuong id: 3EC6EE64-F248-11E8-B48F-1D18A9856A87 last_name: Bui Thi Mai - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 citation: 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. chicago: Phuong, Mary, and Christoph Lampert. “Functional vs. Parametric Equivalence of ReLU Networks.” In 8th International Conference on Learning Representations, 2020. ieee: M. Phuong and C. Lampert, “Functional vs. parametric equivalence of ReLU networks,” in 8th International Conference on Learning Representations, Online, 2020. 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.' mla: Phuong, Mary, and Christoph Lampert. “Functional vs. Parametric Equivalence of ReLU Networks.” 8th International Conference on Learning Representations, 2020. short: M. Phuong, C. Lampert, in:, 8th International Conference on Learning Representations, 2020. conference: end_date: 2020-04-30 location: Online name: 'ICLR: International Conference on Learning Representations' start_date: 2020-04-27 date_created: 2020-02-11T09:07:37Z date_published: 2020-04-26T00:00:00Z date_updated: 2023-09-07T13:29:50Z day: '26' ddc: - '000' department: - _id: ChLa file: - access_level: open_access checksum: 8d372ea5defd8cb8fdc430111ed754a9 content_type: application/pdf creator: bphuong date_created: 2020-02-11T09:07:27Z date_updated: 2020-07-14T12:47:59Z file_id: '7482' file_name: main.pdf file_size: 405469 relation: main_file file_date_updated: 2020-07-14T12:47:59Z has_accepted_license: '1' language: - iso: eng month: '04' oa: 1 oa_version: Published Version publication: 8th International Conference on Learning Representations publication_status: published quality_controlled: '1' related_material: link: - relation: supplementary_material url: https://iclr.cc/virtual_2020/poster_Bylx-TNKvH.html record: - id: '9418' relation: dissertation_contains status: public status: public title: Functional vs. parametric equivalence of ReLU networks type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2020' ... --- _id: '9781' abstract: - lang: eng 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. 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. article_processing_charge: No article_type: original author: - first_name: Dario full_name: Feliciangeli, Dario id: 41A639AA-F248-11E8-B48F-1D18A9856A87 last_name: Feliciangeli orcid: 0000-0003-0754-8530 - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: 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 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. 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. 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. 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. short: D. Feliciangeli, R. Seiringer, SIAM Journal on Mathematical Analysis 52 (2020) 605–622. date_created: 2021-08-06T07:34:16Z date_published: 2020-02-12T00:00:00Z date_updated: 2023-09-07T13:30:11Z day: '12' ddc: - '510' department: - _id: RoSe doi: 10.1137/19m126284x ec_funded: 1 external_id: arxiv: - '1904.08647 ' isi: - '000546967700022' has_accepted_license: '1' intvolume: ' 52' isi: 1 issue: '1' keyword: - Applied Mathematics - Computational Mathematics - Analysis language: - iso: eng license: https://creativecommons.org/licenses/by-nc-nd/4.0/ main_file_link: - open_access: '1' url: https://arxiv.org/abs/1904.08647 month: '02' oa: 1 oa_version: Preprint page: 605-622 project: - _id: 25C6DC12-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '694227' name: Analysis of quantum many-body systems publication: SIAM Journal on Mathematical Analysis publication_identifier: eissn: - 1095-7154 issn: - 0036-1410 publication_status: published publisher: 'Society for Industrial & Applied Mathematics ' quality_controlled: '1' related_material: record: - id: '9733' relation: dissertation_contains status: public scopus_import: '1' status: public title: Uniqueness and nondegeneracy of minimizers of the Pekar functional on a ball tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 52 year: '2020' ... --- _id: '7489' abstract: - lang: eng 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.' article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Julian L full_name: Fischer, Julian L id: 2C12A0B0-F248-11E8-B48F-1D18A9856A87 last_name: Fischer orcid: 0000-0002-0479-558X - first_name: Sebastian full_name: Hensel, Sebastian id: 4D23B7DA-F248-11E8-B48F-1D18A9856A87 last_name: Hensel orcid: 0000-0001-7252-8072 citation: 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 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 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. 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. 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. 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. short: J.L. Fischer, S. Hensel, Archive for Rational Mechanics and Analysis 236 (2020) 967–1087. date_created: 2020-02-16T23:00:50Z date_published: 2020-05-01T00:00:00Z date_updated: 2023-09-07T13:30:45Z day: '01' ddc: - '530' - '532' department: - _id: JuFi doi: 10.1007/s00205-019-01486-2 ec_funded: 1 external_id: isi: - '000511060200001' file: - access_level: open_access checksum: f107e21b58f5930876f47144be37cf6c content_type: application/pdf creator: dernst date_created: 2020-11-20T09:14:22Z date_updated: 2020-11-20T09:14:22Z file_id: '8779' file_name: 2020_ArchRatMechAn_Fischer.pdf file_size: 1897571 relation: main_file success: 1 file_date_updated: 2020-11-20T09:14:22Z has_accepted_license: '1' intvolume: ' 236' isi: 1 language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: 967-1087 project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program - _id: B67AFEDC-15C9-11EA-A837-991A96BB2854 name: IST Austria Open Access Fund publication: Archive for Rational Mechanics and Analysis publication_identifier: eissn: - '14320673' issn: - '00039527' publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '10007' relation: dissertation_contains status: public scopus_import: '1' status: public title: Weak–strong uniqueness for the Navier–Stokes equation for two fluids with surface tension tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 236 year: '2020' ... --- _id: '10012' 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. 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. article_number: '2003.05478' article_processing_charge: No author: - first_name: Julian L full_name: Fischer, Julian L id: 2C12A0B0-F248-11E8-B48F-1D18A9856A87 last_name: Fischer orcid: 0000-0002-0479-558X - first_name: Sebastian full_name: Hensel, Sebastian id: 4D23B7DA-F248-11E8-B48F-1D18A9856A87 last_name: Hensel orcid: 0000-0001-7252-8072 - first_name: Tim full_name: Laux, Tim last_name: Laux - first_name: Thilo full_name: Simon, Thilo last_name: Simon citation: 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.' 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.' 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. .' 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.' 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.' short: J.L. Fischer, S. Hensel, T. Laux, T. Simon, ArXiv (n.d.). date_created: 2021-09-13T12:17:11Z date_published: 2020-03-11T00:00:00Z date_updated: 2023-09-07T13:30:45Z day: '11' department: - _id: JuFi ec_funded: 1 external_id: arxiv: - '2003.05478' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2003.05478 month: '03' oa: 1 oa_version: Preprint project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication: arXiv publication_status: submitted related_material: record: - id: '10007' relation: dissertation_contains status: public status: public title: 'The local structure of the energy landscape in multiphase mean curvature flow: weak-strong uniqueness and stability of evolutions' type: preprint user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2020' ... --- _id: '8755' 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. ' acknowledged_ssus: - _id: NanoFab 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). " article_number: '044055' article_processing_charge: No article_type: original author: - first_name: Matilda full_name: Peruzzo, Matilda id: 3F920B30-F248-11E8-B48F-1D18A9856A87 last_name: Peruzzo orcid: 0000-0002-3415-4628 - first_name: Andrea full_name: Trioni, Andrea id: 42F71B44-F248-11E8-B48F-1D18A9856A87 last_name: Trioni - first_name: Farid full_name: Hassani, Farid id: 2AED110C-F248-11E8-B48F-1D18A9856A87 last_name: Hassani orcid: 0000-0001-6937-5773 - first_name: Martin full_name: Zemlicka, Martin id: 2DCF8DE6-F248-11E8-B48F-1D18A9856A87 last_name: Zemlicka - first_name: Johannes M full_name: Fink, Johannes M id: 4B591CBA-F248-11E8-B48F-1D18A9856A87 last_name: Fink orcid: 0000-0001-8112-028X citation: 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 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. 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. 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). date_created: 2020-11-15T23:01:17Z date_published: 2020-10-29T00:00:00Z date_updated: 2023-09-07T13:31:22Z day: '29' ddc: - '530' department: - _id: JoFi doi: 10.1103/PhysRevApplied.14.044055 ec_funded: 1 external_id: arxiv: - '2007.01644' isi: - '000582797300003' file: - access_level: open_access checksum: 2a634abe75251ae7628cd54c8a4ce2e8 content_type: application/pdf creator: dernst date_created: 2021-03-29T11:43:20Z date_updated: 2021-03-29T11:43:20Z file_id: '9300' file_name: 2020_PhysReviewApplied_Peruzzo.pdf file_size: 2607823 relation: main_file success: 1 file_date_updated: 2021-03-29T11:43:20Z has_accepted_license: '1' intvolume: ' 14' isi: 1 issue: '4' language: - iso: eng month: '10' oa: 1 oa_version: Published Version project: - _id: 26927A52-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: F07105 name: Integrating superconducting quantum circuits - _id: 257EB838-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '732894' name: Hybrid Optomechanical Technologies - _id: 237CBA6C-32DE-11EA-91FC-C7463DDC885E call_identifier: H2020 grant_number: '862644' name: Quantum readout techniques and technologies - _id: 26336814-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '758053' name: A Fiber Optic Transceiver for Superconducting Qubits publication: Physical Review Applied publication_identifier: eissn: - '23317019' publication_status: published publisher: American Physical Society quality_controlled: '1' related_material: record: - id: '13070' relation: research_data status: public - id: '9920' relation: dissertation_contains status: public scopus_import: '1' status: public title: Surpassing the resistance quantum with a geometric superinductor type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 14 year: '2020' ... --- _id: '7573' abstract: - lang: eng 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. 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. article_processing_charge: No article_type: original author: - first_name: Peter full_name: Gladbach, Peter last_name: Gladbach - first_name: Eva full_name: Kopfer, Eva last_name: Kopfer - first_name: Jan full_name: Maas, Jan id: 4C5696CE-F248-11E8-B48F-1D18A9856A87 last_name: Maas orcid: 0000-0002-0845-1338 - first_name: Lorenzo full_name: Portinale, Lorenzo id: 30AD2CBC-F248-11E8-B48F-1D18A9856A87 last_name: Portinale citation: ama: Gladbach P, Kopfer E, Maas J, Portinale L. Homogenisation of one-dimensional discrete optimal transport. Journal de Mathematiques Pures et Appliquees. 2020;139(7):204-234. doi:10.1016/j.matpur.2020.02.008 apa: Gladbach, P., Kopfer, E., Maas, J., & Portinale, L. (2020). Homogenisation of one-dimensional discrete optimal transport. Journal de Mathematiques Pures et Appliquees. Elsevier. https://doi.org/10.1016/j.matpur.2020.02.008 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. 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. 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. short: P. Gladbach, E. Kopfer, J. Maas, L. Portinale, Journal de Mathematiques Pures et Appliquees 139 (2020) 204–234. date_created: 2020-03-08T23:00:47Z date_published: 2020-07-01T00:00:00Z date_updated: 2023-09-07T13:31:05Z day: '01' department: - _id: JaMa doi: 10.1016/j.matpur.2020.02.008 ec_funded: 1 external_id: arxiv: - '1905.05757' isi: - '000539439400008' intvolume: ' 139' isi: 1 issue: '7' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1905.05757 month: '07' oa: 1 oa_version: Preprint page: 204-234 project: - _id: 256E75B8-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '716117' name: Optimal Transport and Stochastic Dynamics - _id: 260482E2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: ' F06504' name: Taming Complexity in Partial Di erential Systems - _id: 260788DE-B435-11E9-9278-68D0E5697425 call_identifier: FWF name: Dissipation and Dispersion in Nonlinear Partial Differential Equations publication: Journal de Mathematiques Pures et Appliquees publication_identifier: issn: - '00217824' publication_status: published publisher: Elsevier quality_controlled: '1' related_material: record: - id: '10030' relation: dissertation_contains status: public scopus_import: '1' status: public title: Homogenisation of one-dimensional discrete optimal transport type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 139 year: '2020' ... --- _id: '10022' abstract: - lang: eng text: We consider finite-volume approximations of Fokker-Planck equations on bounded convex domains in R^d and study the corresponding gradient flow structures. We reprove the convergence of the discrete to continuous Fokker-Planck equation via the method of Evolutionary Γ-convergence, i.e., we pass to the limit at the level of the gradient flow structures, generalising the one-dimensional result obtained by Disser and Liero. The proof is of variational nature and relies on a Mosco convergence result for functionals in the discrete-to-continuum limit that is of independent interest. Our results apply to arbitrary regular meshes, even though the associated discrete transport distances may fail to converge to the Wasserstein distance in this generality. 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. article_number: '2008.10962' article_processing_charge: No author: - first_name: Dominik L full_name: Forkert, Dominik L id: 35C79D68-F248-11E8-B48F-1D18A9856A87 last_name: Forkert - first_name: Jan full_name: Maas, Jan id: 4C5696CE-F248-11E8-B48F-1D18A9856A87 last_name: Maas orcid: 0000-0002-0845-1338 - first_name: Lorenzo full_name: Portinale, Lorenzo id: 30AD2CBC-F248-11E8-B48F-1D18A9856A87 last_name: Portinale citation: ama: Forkert DL, Maas J, Portinale L. Evolutionary Γ-convergence of entropic gradient flow structures for Fokker-Planck equations in multiple dimensions. arXiv. 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. 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. 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. . 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. mla: Forkert, Dominik L., et al. “Evolutionary Γ-Convergence of Entropic Gradient Flow Structures for Fokker-Planck Equations in Multiple Dimensions.” ArXiv, 2008.10962. short: D.L. Forkert, J. Maas, L. Portinale, ArXiv (n.d.). date_created: 2021-09-17T10:57:27Z date_published: 2020-08-25T00:00:00Z date_updated: 2023-09-07T13:31:05Z day: '25' department: - _id: JaMa ec_funded: 1 external_id: arxiv: - '2008.10962' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2008.10962 month: '08' oa: 1 oa_version: Preprint page: '33' project: - _id: 256E75B8-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '716117' name: Optimal Transport and Stochastic Dynamics - _id: fc31cba2-9c52-11eb-aca3-ff467d239cd2 grant_number: F6504 name: Taming Complexity in Partial Differential Systems publication: arXiv publication_status: submitted related_material: record: - id: '11739' relation: later_version status: public - id: '10030' relation: dissertation_contains status: public status: public title: Evolutionary Γ-convergence of entropic gradient flow structures for Fokker-Planck equations in multiple dimensions type: preprint user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2020' ... --- _id: '8724' abstract: - lang: eng 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. " acknowledged_ssus: - _id: ScienComp 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). article_processing_charge: No author: - first_name: Nikola H full_name: Konstantinov, Nikola H id: 4B9D76E4-F248-11E8-B48F-1D18A9856A87 last_name: Konstantinov - first_name: Elias full_name: Frantar, Elias id: 09a8f98d-ec99-11ea-ae11-c063a7b7fe5f last_name: Frantar - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 citation: ama: 'Konstantinov NH, Frantar E, Alistarh D-A, Lampert C. On the sample complexity of adversarial multi-source PAC learning. In: Proceedings of the 37th International Conference on Machine Learning. Vol 119. ML Research Press; 2020:5416-5425.' apa: 'Konstantinov, N. H., Frantar, E., Alistarh, D.-A., & Lampert, C. (2020). On the sample complexity of adversarial multi-source PAC learning. In Proceedings of the 37th International Conference on Machine Learning (Vol. 119, pp. 5416–5425). Online: ML Research Press.' 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. 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. ista: 'Konstantinov NH, Frantar E, Alistarh D-A, Lampert C. 2020. On the sample complexity of adversarial multi-source PAC learning. Proceedings of the 37th International Conference on Machine Learning. ICML: International Conference on Machine Learning vol. 119, 5416–5425.' mla: Konstantinov, Nikola H., et al. “On the Sample Complexity of Adversarial Multi-Source PAC Learning.” Proceedings of the 37th International Conference on Machine Learning, vol. 119, ML Research Press, 2020, pp. 5416–25. short: N.H. Konstantinov, E. Frantar, D.-A. Alistarh, C. Lampert, in:, Proceedings of the 37th International Conference on Machine Learning, ML Research Press, 2020, pp. 5416–5425. conference: end_date: 2020-07-18 location: Online name: 'ICML: International Conference on Machine Learning' start_date: 2020-07-12 date_created: 2020-11-05T15:25:58Z date_published: 2020-07-12T00:00:00Z date_updated: 2023-09-07T13:42:08Z day: '12' ddc: - '000' department: - _id: DaAl - _id: ChLa ec_funded: 1 external_id: arxiv: - '2002.10384' file: - access_level: open_access checksum: cc755d0054bc4b2be778ea7aa7884d2f content_type: application/pdf creator: dernst date_created: 2021-02-15T09:00:01Z date_updated: 2021-02-15T09:00:01Z file_id: '9120' file_name: 2020_PMLR_Konstantinov.pdf file_size: 281286 relation: main_file success: 1 file_date_updated: 2021-02-15T09:00:01Z has_accepted_license: '1' intvolume: ' 119' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: 5416-5425 project: - _id: 268A44D6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '805223' name: Elastic Coordination for Scalable Machine Learning publication: Proceedings of the 37th International Conference on Machine Learning publication_identifier: issn: - 2640-3498 publication_status: published publisher: ML Research Press quality_controlled: '1' related_material: link: - relation: supplementary_material url: http://proceedings.mlr.press/v119/konstantinov20a/konstantinov20a-supp.pdf record: - id: '10799' relation: dissertation_contains status: public scopus_import: '1' status: public title: On the sample complexity of adversarial multi-source PAC learning type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 119 year: '2020' ... --- _id: '8644' 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. 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). article_number: '093026' article_processing_charge: No article_type: original author: - first_name: Wojciech full_name: Rzadkowski, Wojciech id: 48C55298-F248-11E8-B48F-1D18A9856A87 last_name: Rzadkowski orcid: 0000-0002-1106-4419 - first_name: N full_name: Defenu, N last_name: Defenu - first_name: S full_name: Chiacchiera, S last_name: Chiacchiera - first_name: A full_name: Trombettoni, A last_name: Trombettoni - first_name: Giacomo full_name: Bighin, Giacomo id: 4CA96FD4-F248-11E8-B48F-1D18A9856A87 last_name: Bighin orcid: 0000-0001-8823-9777 citation: 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 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. 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. 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. short: W. Rzadkowski, N. Defenu, S. Chiacchiera, A. Trombettoni, G. Bighin, New Journal of Physics 22 (2020). date_created: 2020-10-11T22:01:14Z date_published: 2020-09-01T00:00:00Z date_updated: 2023-09-07T13:44:16Z day: '01' ddc: - '530' department: - _id: MiLe doi: 10.1088/1367-2630/abae44 ec_funded: 1 external_id: isi: - '000573298000001' file: - access_level: open_access checksum: c9238fff422e7a957c3a0d559f756b3a content_type: application/pdf creator: dernst date_created: 2020-10-12T12:18:47Z date_updated: 2020-10-12T12:18:47Z file_id: '8650' file_name: 2020_NewJournalPhysics_Rzdkowski.pdf file_size: 2725143 relation: main_file success: 1 file_date_updated: 2020-10-12T12:18:47Z has_accepted_license: '1' intvolume: ' 22' isi: 1 issue: '9' language: - iso: eng month: '09' oa: 1 oa_version: Published Version project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program - _id: 05A235A0-7A3F-11EA-A408-12923DDC885E grant_number: '25681' name: Analytic and machine learning approaches to composite quantum impurities - _id: 26986C82-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: M02641 name: A path-integral approach to composite impurities publication: New Journal of Physics publication_identifier: issn: - '13672630' publication_status: published publisher: IOP Publishing quality_controlled: '1' related_material: record: - id: '10759' relation: dissertation_contains status: public scopus_import: '1' status: public title: Detecting composite orders in layered models via machine learning tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 22 year: '2020' ... --- _id: '8705' 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. 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) article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Krzysztof full_name: Mysliwy, Krzysztof id: 316457FC-F248-11E8-B48F-1D18A9856A87 last_name: Mysliwy - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: ama: Mysliwy K, Seiringer R. Microscopic derivation of the Fröhlich Hamiltonian for the Bose polaron in the mean-field limit. Annales Henri Poincare. 2020;21(12):4003-4025. doi:10.1007/s00023-020-00969-3 apa: Mysliwy, K., & Seiringer, R. (2020). Microscopic derivation of the Fröhlich Hamiltonian for the Bose polaron in the mean-field limit. Annales Henri Poincare. Springer Nature. https://doi.org/10.1007/s00023-020-00969-3 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. 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. 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. 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. short: K. Mysliwy, R. Seiringer, Annales Henri Poincare 21 (2020) 4003–4025. date_created: 2020-10-25T23:01:19Z date_published: 2020-12-01T00:00:00Z date_updated: 2023-09-07T13:43:51Z day: '01' ddc: - '530' department: - _id: RoSe doi: 10.1007/s00023-020-00969-3 ec_funded: 1 external_id: arxiv: - '2003.12371' isi: - '000578111800002' file: - access_level: open_access checksum: c12c9c1e6f08def245e42f3cb1d83827 content_type: application/pdf creator: cziletti date_created: 2020-10-27T12:49:04Z date_updated: 2020-10-27T12:49:04Z file_id: '8711' file_name: 2020_Annales_Mysliwy.pdf file_size: 469831 relation: main_file success: 1 file_date_updated: 2020-10-27T12:49:04Z has_accepted_license: '1' intvolume: ' 21' isi: 1 issue: '12' language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: 4003-4025 project: - _id: 25C6DC12-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '694227' name: Analysis of quantum many-body systems - _id: B67AFEDC-15C9-11EA-A837-991A96BB2854 name: IST Austria Open Access Fund - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication: Annales Henri Poincare publication_identifier: issn: - 1424-0637 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '11473' relation: dissertation_contains status: public scopus_import: '1' status: public title: Microscopic derivation of the Fröhlich Hamiltonian for the Bose polaron in the mean-field limit tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 21 year: '2020' ... --- _id: '10861' 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. article_processing_charge: No article_type: original author: - first_name: Dejan full_name: Nickovic, Dejan id: 41BCEE5C-F248-11E8-B48F-1D18A9856A87 last_name: Nickovic - first_name: Olivier full_name: Lebeltel, Olivier last_name: Lebeltel - first_name: Oded full_name: Maler, Oded last_name: Maler - first_name: Thomas full_name: Ferrere, Thomas id: 40960E6E-F248-11E8-B48F-1D18A9856A87 last_name: Ferrere orcid: 0000-0001-5199-3143 - first_name: Dogan full_name: Ulus, Dogan last_name: Ulus citation: 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' 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.' 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.' ista: 'Nickovic D, Lebeltel O, Maler O, Ferrere T, Ulus D. 2020. AMT 2.0: Qualitative and quantitative trace analysis with extended signal temporal logic. International Journal on Software Tools for Technology Transfer. 22(6), 741–758.' mla: 'Nickovic, Dejan, et al. “AMT 2.0: Qualitative and Quantitative Trace Analysis with Extended Signal Temporal Logic.” International Journal on Software Tools for Technology Transfer, vol. 22, no. 6, Springer Nature, 2020, pp. 741–58, doi:10.1007/s10009-020-00582-z.' short: D. Nickovic, O. Lebeltel, O. Maler, T. Ferrere, D. Ulus, International Journal on Software Tools for Technology Transfer 22 (2020) 741–758. date_created: 2022-03-18T10:10:53Z date_published: 2020-08-03T00:00:00Z date_updated: 2023-09-08T11:52:02Z day: '03' department: - _id: ToHe doi: 10.1007/s10009-020-00582-z external_id: isi: - '000555398600001' intvolume: ' 22' isi: 1 issue: '6' keyword: - Information Systems - Software language: - iso: eng month: '08' oa_version: None page: 741-758 publication: International Journal on Software Tools for Technology Transfer publication_identifier: eissn: - 1433-2787 issn: - 1433-2779 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '299' relation: earlier_version status: public scopus_import: '1' status: public title: 'AMT 2.0: Qualitative and quantitative trace analysis with extended signal temporal logic' type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 22 year: '2020' ... --- _id: '14125' abstract: - lang: eng 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." article_processing_charge: No article_type: original author: - first_name: Stefan G full_name: Stark, Stefan G last_name: Stark - first_name: Joanna full_name: Ficek, Joanna last_name: Ficek - first_name: Francesco full_name: Locatello, Francesco id: 26cfd52f-2483-11ee-8040-88983bcc06d4 last_name: Locatello orcid: 0000-0002-4850-0683 - first_name: Ximena full_name: Bonilla, Ximena last_name: Bonilla - first_name: Stéphane full_name: Chevrier, Stéphane last_name: Chevrier - first_name: Franziska full_name: Singer, Franziska last_name: Singer - first_name: Rudolf full_name: Aebersold, Rudolf last_name: Aebersold - first_name: Faisal S full_name: Al-Quaddoomi, Faisal S last_name: Al-Quaddoomi - first_name: Jonas full_name: Albinus, Jonas last_name: Albinus - first_name: Ilaria full_name: Alborelli, Ilaria last_name: Alborelli - first_name: Sonali full_name: Andani, Sonali last_name: Andani - first_name: Per-Olof full_name: Attinger, Per-Olof last_name: Attinger - first_name: Marina full_name: Bacac, Marina last_name: Bacac - first_name: Daniel full_name: Baumhoer, Daniel last_name: Baumhoer - first_name: Beatrice full_name: Beck-Schimmer, Beatrice last_name: Beck-Schimmer - first_name: Niko full_name: Beerenwinkel, Niko last_name: Beerenwinkel - first_name: Christian full_name: Beisel, Christian last_name: Beisel - first_name: Lara full_name: Bernasconi, Lara last_name: Bernasconi - first_name: Anne full_name: Bertolini, Anne last_name: Bertolini - first_name: Bernd full_name: Bodenmiller, Bernd last_name: Bodenmiller - first_name: Ximena full_name: Bonilla, Ximena last_name: Bonilla - first_name: Ruben full_name: Casanova, Ruben last_name: Casanova - first_name: Stéphane full_name: Chevrier, Stéphane last_name: Chevrier - first_name: Natalia full_name: Chicherova, Natalia last_name: Chicherova - first_name: Maya full_name: D'Costa, Maya last_name: D'Costa - first_name: Esther full_name: Danenberg, Esther last_name: Danenberg - first_name: Natalie full_name: Davidson, Natalie last_name: Davidson - first_name: Monica-Andreea Dră full_name: gan, Monica-Andreea Dră last_name: gan - first_name: Reinhard full_name: Dummer, Reinhard last_name: Dummer - first_name: Stefanie full_name: Engler, Stefanie last_name: Engler - first_name: Martin full_name: Erkens, Martin last_name: Erkens - first_name: Katja full_name: Eschbach, Katja last_name: Eschbach - first_name: Cinzia full_name: Esposito, Cinzia last_name: Esposito - first_name: André full_name: Fedier, André last_name: Fedier - first_name: Pedro full_name: Ferreira, Pedro last_name: Ferreira - first_name: Joanna full_name: Ficek, Joanna last_name: Ficek - first_name: Anja L full_name: Frei, Anja L last_name: Frei - first_name: Bruno full_name: Frey, Bruno last_name: Frey - first_name: Sandra full_name: Goetze, Sandra last_name: Goetze - first_name: Linda full_name: Grob, Linda last_name: Grob - first_name: Gabriele full_name: Gut, Gabriele last_name: Gut - first_name: Detlef full_name: Günther, Detlef last_name: Günther - first_name: Martina full_name: Haberecker, Martina last_name: Haberecker - first_name: Pirmin full_name: Haeuptle, Pirmin last_name: Haeuptle - first_name: Viola full_name: Heinzelmann-Schwarz, Viola last_name: Heinzelmann-Schwarz - first_name: Sylvia full_name: Herter, Sylvia last_name: Herter - first_name: Rene full_name: Holtackers, Rene last_name: Holtackers - first_name: Tamara full_name: Huesser, Tamara last_name: Huesser - first_name: Anja full_name: Irmisch, Anja last_name: Irmisch - first_name: Francis full_name: Jacob, Francis last_name: Jacob - first_name: Andrea full_name: Jacobs, Andrea last_name: Jacobs - first_name: Tim M full_name: Jaeger, Tim M last_name: Jaeger - first_name: Katharina full_name: Jahn, Katharina last_name: Jahn - first_name: Alva R full_name: James, Alva R last_name: James - first_name: Philip M full_name: Jermann, Philip M last_name: Jermann - first_name: André full_name: Kahles, André last_name: Kahles - first_name: Abdullah full_name: Kahraman, Abdullah last_name: Kahraman - first_name: Viktor H full_name: Koelzer, Viktor H last_name: Koelzer - first_name: Werner full_name: Kuebler, Werner last_name: Kuebler - first_name: Jack full_name: Kuipers, Jack last_name: Kuipers - first_name: Christian P full_name: Kunze, Christian P last_name: Kunze - first_name: Christian full_name: Kurzeder, Christian last_name: Kurzeder - first_name: Kjong-Van full_name: Lehmann, Kjong-Van last_name: Lehmann - first_name: Mitchell full_name: Levesque, Mitchell last_name: Levesque - first_name: Sebastian full_name: Lugert, Sebastian last_name: Lugert - first_name: Gerd full_name: Maass, Gerd last_name: Maass - first_name: Markus full_name: Manz, Markus last_name: Manz - first_name: Philipp full_name: Markolin, Philipp last_name: Markolin - first_name: Julien full_name: Mena, Julien last_name: Mena - first_name: Ulrike full_name: Menzel, Ulrike last_name: Menzel - first_name: Julian M full_name: Metzler, Julian M last_name: Metzler - first_name: Nicola full_name: Miglino, Nicola last_name: Miglino - first_name: Emanuela S full_name: Milani, Emanuela S last_name: Milani - first_name: Holger full_name: Moch, Holger last_name: Moch - first_name: Simone full_name: Muenst, Simone last_name: Muenst - first_name: Riccardo full_name: Murri, Riccardo last_name: Murri - first_name: Charlotte KY full_name: Ng, Charlotte KY last_name: Ng - first_name: Stefan full_name: Nicolet, Stefan last_name: Nicolet - first_name: Marta full_name: Nowak, Marta last_name: Nowak - first_name: Patrick GA full_name: Pedrioli, Patrick GA last_name: Pedrioli - first_name: Lucas full_name: Pelkmans, Lucas last_name: Pelkmans - first_name: Salvatore full_name: Piscuoglio, Salvatore last_name: Piscuoglio - first_name: Michael full_name: Prummer, Michael last_name: Prummer - first_name: Mathilde full_name: Ritter, Mathilde last_name: Ritter - first_name: Christian full_name: Rommel, Christian last_name: Rommel - first_name: María L full_name: Rosano-González, María L last_name: Rosano-González - first_name: Gunnar full_name: Rätsch, Gunnar last_name: Rätsch - first_name: Natascha full_name: Santacroce, Natascha last_name: Santacroce - first_name: Jacobo Sarabia del full_name: Castillo, Jacobo Sarabia del last_name: Castillo - first_name: Ramona full_name: Schlenker, Ramona last_name: Schlenker - first_name: Petra C full_name: Schwalie, Petra C last_name: Schwalie - first_name: Severin full_name: Schwan, Severin last_name: Schwan - first_name: Tobias full_name: Schär, Tobias last_name: Schär - first_name: Gabriela full_name: Senti, Gabriela last_name: Senti - first_name: Franziska full_name: Singer, Franziska last_name: Singer - first_name: Sujana full_name: Sivapatham, Sujana last_name: Sivapatham - first_name: Berend full_name: Snijder, Berend last_name: Snijder - first_name: Bettina full_name: Sobottka, Bettina last_name: Sobottka - first_name: Vipin T full_name: Sreedharan, Vipin T last_name: Sreedharan - first_name: Stefan full_name: Stark, Stefan last_name: Stark - first_name: Daniel J full_name: Stekhoven, Daniel J last_name: Stekhoven - first_name: Alexandre PA full_name: Theocharides, Alexandre PA last_name: Theocharides - first_name: Tinu M full_name: Thomas, Tinu M last_name: Thomas - first_name: Markus full_name: Tolnay, Markus last_name: Tolnay - first_name: Vinko full_name: Tosevski, Vinko last_name: Tosevski - first_name: Nora C full_name: Toussaint, Nora C last_name: Toussaint - first_name: Mustafa A full_name: Tuncel, Mustafa A last_name: Tuncel - first_name: Marina full_name: Tusup, Marina last_name: Tusup - first_name: Audrey Van full_name: Drogen, Audrey Van last_name: Drogen - first_name: Marcus full_name: Vetter, Marcus last_name: Vetter - first_name: Tatjana full_name: Vlajnic, Tatjana last_name: Vlajnic - first_name: Sandra full_name: Weber, Sandra last_name: Weber - first_name: Walter P full_name: Weber, Walter P last_name: Weber - first_name: Rebekka full_name: Wegmann, Rebekka last_name: Wegmann - first_name: Michael full_name: Weller, Michael last_name: Weller - first_name: Fabian full_name: Wendt, Fabian last_name: Wendt - first_name: Norbert full_name: Wey, Norbert last_name: Wey - first_name: Andreas full_name: Wicki, Andreas last_name: Wicki - first_name: Bernd full_name: Wollscheid, Bernd last_name: Wollscheid - first_name: Shuqing full_name: Yu, Shuqing last_name: Yu - first_name: Johanna full_name: Ziegler, Johanna last_name: Ziegler - first_name: Marc full_name: Zimmermann, Marc last_name: Zimmermann - first_name: Martin full_name: Zoche, Martin last_name: Zoche - first_name: Gregor full_name: Zuend, Gregor last_name: Zuend - first_name: Gunnar full_name: Rätsch, Gunnar last_name: Rätsch - first_name: Kjong-Van full_name: Lehmann, Kjong-Van last_name: Lehmann citation: 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' 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.' 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.' ista: 'Stark SG et al. 2020. SCIM: Universal single-cell matching with unpaired feature sets. Bioinformatics. 36(Supplement_2), i919–i927.' 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.' 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. date_created: 2023-08-21T12:28:20Z date_published: 2020-12-01T00:00:00Z date_updated: 2023-09-11T10:21:00Z day: '01' department: - _id: FrLo doi: 10.1093/bioinformatics/btaa843 extern: '1' external_id: pmid: - '33381818' intvolume: ' 36' issue: Supplement_2 keyword: - Computational Mathematics - Computational Theory and Mathematics - Computer Science Applications - Molecular Biology - Biochemistry - Statistics and Probability language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1093/bioinformatics/btaa843 month: '12' oa: 1 oa_version: Published Version page: i919-i927 pmid: 1 publication: Bioinformatics publication_identifier: eissn: - 1367-4811 publication_status: published publisher: Oxford University Press quality_controlled: '1' related_material: link: - relation: software url: https://github.com/ratschlab/scim scopus_import: '1' status: public title: 'SCIM: Universal single-cell matching with unpaired feature sets' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 36 year: '2020' ... --- _id: '14186' 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." article_processing_charge: No author: - first_name: Francesco full_name: Locatello, Francesco id: 26cfd52f-2483-11ee-8040-88983bcc06d4 last_name: Locatello orcid: 0000-0002-4850-0683 - first_name: Stefan full_name: Bauer, Stefan last_name: Bauer - first_name: Mario full_name: Lucic, Mario last_name: Lucic - first_name: Gunnar full_name: Rätsch, Gunnar last_name: Rätsch - first_name: Sylvain full_name: Gelly, Sylvain last_name: Gelly - first_name: Bernhard full_name: Schölkopf, Bernhard last_name: Schölkopf - first_name: Olivier full_name: Bachem, Olivier last_name: Bachem citation: 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. 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. ista: 'Locatello F, Bauer S, Lucic M, Rätsch G, Gelly S, Schölkopf B, Bachem O. 2020. A commentary on the unsupervised learning of disentangled representations. The 34th AAAI Conference on Artificial Intelligence. AAAI: Conference on Artificial Intelligence vol. 34, 13681–13684.' mla: Locatello, Francesco, et al. “A Commentary on the Unsupervised Learning of Disentangled Representations.” The 34th AAAI Conference on Artificial Intelligence, vol. 34, no. 9, Association for the Advancement of Artificial Intelligence, 2020, pp. 13681–84, doi:10.1609/aaai.v34i09.7120. 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. conference: end_date: 2020-02-12 location: New York, NY, United States name: 'AAAI: Conference on Artificial Intelligence' start_date: 2020-02-07 date_created: 2023-08-22T14:07:26Z date_published: 2020-07-28T00:00:00Z date_updated: 2023-09-12T07:44:48Z day: '28' department: - _id: FrLo doi: 10.1609/aaai.v34i09.7120 extern: '1' external_id: arxiv: - '2007.14184' intvolume: ' 34' issue: '9' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2007.14184 month: '07' oa: 1 oa_version: Preprint page: 13681-13684 publication: The 34th AAAI Conference on Artificial Intelligence publication_identifier: eissn: - 2374-3468 isbn: - '9781577358350' publication_status: published publisher: Association for the Advancement of Artificial Intelligence quality_controlled: '1' scopus_import: '1' status: public title: A commentary on the unsupervised learning of disentangled representations type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 34 year: '2020' ... --- _id: '14188' 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." alternative_title: - PMLR article_processing_charge: No author: - first_name: Francesco full_name: Locatello, Francesco id: 26cfd52f-2483-11ee-8040-88983bcc06d4 last_name: Locatello orcid: 0000-0002-4850-0683 - first_name: Ben full_name: Poole, Ben last_name: Poole - first_name: Gunnar full_name: Rätsch, Gunnar last_name: Rätsch - first_name: Bernhard full_name: Schölkopf, Bernhard last_name: Schölkopf - first_name: Olivier full_name: Bachem, Olivier last_name: Bachem - first_name: Michael full_name: Tschannen, Michael last_name: Tschannen citation: ama: 'Locatello F, Poole B, Rätsch G, Schölkopf B, Bachem O, Tschannen M. Weakly-supervised disentanglement without compromises. In: Proceedings of the 37th International Conference on Machine Learning. Vol 119. ; 2020:6348–6359.' apa: Locatello, F., Poole, B., Rätsch, G., Schölkopf, B., Bachem, O., & Tschannen, M. (2020). Weakly-supervised disentanglement without compromises. In Proceedings of the 37th International Conference on Machine Learning (Vol. 119, pp. 6348–6359). Virtual. chicago: Locatello, Francesco, Ben Poole, Gunnar Rätsch, Bernhard Schölkopf, Olivier Bachem, and Michael Tschannen. “Weakly-Supervised Disentanglement without Compromises.” In Proceedings of the 37th International Conference on Machine Learning, 119:6348–6359, 2020. 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. 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. 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. 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. conference: end_date: 2020-07-18 location: Virtual name: International Conference on Machine Learning start_date: 2020-07-13 date_created: 2023-08-22T14:08:14Z date_published: 2020-07-07T00:00:00Z date_updated: 2023-09-12T07:59:29Z day: '07' department: - _id: FrLo extern: '1' external_id: arxiv: - '2002.02886' intvolume: ' 119' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2002.02886 month: '07' oa: 1 oa_version: Preprint page: 6348–6359 publication: Proceedings of the 37th International Conference on Machine Learning publication_status: published quality_controlled: '1' scopus_import: '1' status: public title: Weakly-supervised disentanglement without compromises type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 119 year: '2020' ... --- _id: '14187' abstract: - lang: eng 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." alternative_title: - PMLR article_processing_charge: No author: - first_name: Geoffrey full_name: Négiar, Geoffrey last_name: Négiar - first_name: Gideon full_name: Dresdner, Gideon last_name: Dresdner - first_name: Alicia full_name: Tsai, Alicia last_name: Tsai - first_name: Laurent El full_name: Ghaoui, Laurent El last_name: Ghaoui - first_name: Francesco full_name: Locatello, Francesco id: 26cfd52f-2483-11ee-8040-88983bcc06d4 last_name: Locatello orcid: 0000-0002-4850-0683 - first_name: Robert M. full_name: Freund, Robert M. last_name: Freund - first_name: Fabian full_name: Pedregosa, Fabian last_name: Pedregosa citation: 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. 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. 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. 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. 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. conference: end_date: 2020-07-18 location: Virtual name: International Conference on Machine Learning start_date: 2020-07-13 date_created: 2023-08-22T14:07:52Z date_published: 2020-07-27T00:00:00Z date_updated: 2023-09-12T08:03:40Z day: '27' department: - _id: FrLo extern: '1' external_id: arxiv: - '2002.11860' intvolume: ' 119' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2002.11860 month: '07' oa: 1 oa_version: Preprint page: 7253-7262 publication: Proceedings of the 37th International Conference on Machine Learning publication_status: published quality_controlled: '1' status: public title: Stochastic Frank-Wolfe for constrained finite-sum minimization type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 119 year: '2020' ... --- _id: '14195' 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." article_number: '209' article_processing_charge: No article_type: original author: - first_name: Francesco full_name: Locatello, Francesco id: 26cfd52f-2483-11ee-8040-88983bcc06d4 last_name: Locatello orcid: 0000-0002-4850-0683 - first_name: Stefan full_name: Bauer, Stefan last_name: Bauer - first_name: Mario full_name: Lucic, Mario last_name: Lucic - first_name: Gunnar full_name: Rätsch, Gunnar last_name: Rätsch - first_name: Sylvain full_name: Gelly, Sylvain last_name: Gelly - first_name: Bernhard full_name: Schölkopf, Bernhard last_name: Schölkopf - first_name: Olivier full_name: Bachem, Olivier last_name: Bachem citation: 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. 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. 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. ista: Locatello F, Bauer S, Lucic M, Rätsch G, Gelly S, Schölkopf B, Bachem O. 2020. A sober look at the unsupervised learning of disentangled representations and their evaluation. Journal of Machine Learning Research. 21, 209. mla: Locatello, Francesco, et al. “A Sober Look at the Unsupervised Learning of Disentangled Representations and Their Evaluation.” Journal of Machine Learning Research, vol. 21, 209, MIT Press, 2020. short: F. Locatello, S. Bauer, M. Lucic, G. Rätsch, S. Gelly, B. Schölkopf, O. Bachem, Journal of Machine Learning Research 21 (2020). date_created: 2023-08-22T14:10:34Z date_published: 2020-09-01T00:00:00Z date_updated: 2023-09-12T09:23:56Z day: '01' ddc: - '000' department: - _id: FrLo extern: '1' external_id: arxiv: - '2010.14766' has_accepted_license: '1' intvolume: ' 21' language: - iso: eng main_file_link: - open_access: '1' url: https://jmlr.csail.mit.edu/papers/v21/19-976.html month: '09' oa: 1 oa_version: Published Version publication: Journal of Machine Learning Research publication_status: published publisher: MIT Press quality_controlled: '1' scopus_import: '1' status: public title: A sober look at the unsupervised learning of disentangled representations and their evaluation tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 21 year: '2020' ... --- _id: '7569' 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.' article_number: e1007642 article_processing_charge: No article_type: original author: - first_name: Rok full_name: Grah, Rok id: 483E70DE-F248-11E8-B48F-1D18A9856A87 last_name: Grah orcid: 0000-0003-2539-3560 - first_name: Tamar full_name: Friedlander, Tamar last_name: Friedlander citation: ama: Grah R, Friedlander T. The relation between crosstalk and gene regulation form revisited. PLOS Computational Biology. 2020;16(2). doi:10.1371/journal.pcbi.1007642 apa: Grah, R., & Friedlander, T. (2020). The relation between crosstalk and gene regulation form revisited. PLOS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1007642 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. 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. ista: Grah R, Friedlander T. 2020. The relation between crosstalk and gene regulation form revisited. PLOS Computational Biology. 16(2), e1007642. 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. short: R. Grah, T. Friedlander, PLOS Computational Biology 16 (2020). date_created: 2020-03-06T07:39:38Z date_published: 2020-02-25T00:00:00Z date_updated: 2023-09-12T11:02:24Z day: '25' ddc: - '000' - '570' department: - _id: CaGu - _id: GaTk doi: 10.1371/journal.pcbi.1007642 external_id: isi: - '000526725200019' file: - access_level: open_access checksum: 5239dd134dc6e1c71fe7b3ce2953da37 content_type: application/pdf creator: dernst date_created: 2020-03-09T15:12:21Z date_updated: 2020-07-14T12:48:00Z file_id: '7579' file_name: 2020_PlosCompBio_Grah.pdf file_size: 2209325 relation: main_file file_date_updated: 2020-07-14T12:48:00Z has_accepted_license: '1' intvolume: ' 16' isi: 1 issue: '2' language: - iso: eng month: '02' oa: 1 oa_version: Published Version publication: PLOS Computational Biology publication_identifier: issn: - 1553-7358 publication_status: published publisher: Public Library of Science quality_controlled: '1' related_material: record: - id: '9716' relation: research_data status: deleted - id: '9776' relation: research_data status: public - id: '9779' relation: used_in_publication status: public - id: '8155' relation: dissertation_contains status: public - id: '9777' relation: research_data status: public scopus_import: '1' status: public title: The relation between crosstalk and gene regulation form revisited tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 16 year: '2020' ... --- _id: '8813' 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.' article_processing_charge: No author: - first_name: Laura full_name: Santini, Laura last_name: Santini - first_name: Florian full_name: Halbritter, Florian last_name: Halbritter - first_name: Fabian full_name: Titz-Teixeira, Fabian last_name: Titz-Teixeira - first_name: Toru full_name: Suzuki, Toru last_name: Suzuki - first_name: Maki full_name: Asami, Maki last_name: Asami - first_name: Julia full_name: Ramesmayer, Julia last_name: Ramesmayer - first_name: Xiaoyan full_name: Ma, Xiaoyan last_name: Ma - first_name: Andreas full_name: Lackner, Andreas last_name: Lackner - first_name: Nick full_name: Warr, Nick last_name: Warr - first_name: Florian full_name: Pauler, Florian id: 48EA0138-F248-11E8-B48F-1D18A9856A87 last_name: Pauler orcid: 0000-0002-7462-0048 - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 - first_name: Ernest full_name: Laue, Ernest last_name: Laue - first_name: Matthias full_name: Farlik, Matthias last_name: Farlik - first_name: Christoph full_name: Bock, Christoph last_name: Bock - first_name: Andreas full_name: Beyer, Andreas last_name: Beyer - first_name: Anthony C. F. full_name: Perry, Anthony C. F. last_name: Perry - first_name: Martin full_name: Leeb, Martin last_name: Leeb citation: ama: Santini L, Halbritter F, Titz-Teixeira F, et al. Novel imprints in mouse blastocysts are predominantly DNA methylation independent. bioRxiv. doi:10.1101/2020.11.03.366948 apa: Santini, L., Halbritter, F., Titz-Teixeira, F., Suzuki, T., Asami, M., Ramesmayer, J., … Leeb, M. (n.d.). Novel imprints in mouse blastocysts are predominantly DNA methylation independent. bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2020.11.03.366948 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. ieee: L. Santini et al., “Novel imprints in mouse blastocysts are predominantly DNA methylation independent,” bioRxiv. Cold Spring Harbor Laboratory. 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. 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. 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.). date_created: 2020-11-26T07:17:19Z date_published: 2020-11-05T00:00:00Z date_updated: 2023-09-12T11:05:28Z day: '05' department: - _id: SiHi doi: 10.1101/2020.11.03.366948 external_id: pmid: - 'PPR234457 ' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1101/2020.11.03.366948 month: '11' oa: 1 oa_version: Preprint pmid: 1 publication: bioRxiv publication_status: submitted publisher: Cold Spring Harbor Laboratory status: public title: Novel imprints in mouse blastocysts are predominantly DNA methylation independent type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2020' ... --- _id: '9777' article_processing_charge: No author: - first_name: Rok full_name: Grah, Rok id: 483E70DE-F248-11E8-B48F-1D18A9856A87 last_name: Grah orcid: 0000-0003-2539-3560 - first_name: Tamar full_name: Friedlander, Tamar last_name: Friedlander citation: ama: Grah R, Friedlander T. Maximizing crosstalk. 2020. doi:10.1371/journal.pcbi.1007642.s002 apa: Grah, R., & Friedlander, T. (2020). Maximizing crosstalk. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1007642.s002 chicago: Grah, Rok, and Tamar Friedlander. “Maximizing Crosstalk.” Public Library of Science, 2020. https://doi.org/10.1371/journal.pcbi.1007642.s002. ieee: R. Grah and T. Friedlander, “Maximizing crosstalk.” Public Library of Science, 2020. ista: Grah R, Friedlander T. 2020. Maximizing crosstalk, Public Library of Science, 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. short: R. Grah, T. Friedlander, (2020). date_created: 2021-08-06T07:21:51Z date_published: 2020-02-25T00:00:00Z date_updated: 2023-09-12T11:02:25Z day: '25' department: - _id: GaTk doi: 10.1371/journal.pcbi.1007642.s002 main_file_link: - open_access: '1' url: https://doi.org/10.1371/journal.pcbi.1007642.s002 month: '02' oa: 1 oa_version: None publisher: Public Library of Science related_material: record: - id: '7569' relation: used_in_publication status: public status: public title: Maximizing crosstalk type: research_data_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2020' ... --- _id: '8332' 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." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Bernhard full_name: Kragl, Bernhard id: 320FC952-F248-11E8-B48F-1D18A9856A87 last_name: Kragl orcid: 0000-0001-7745-9117 citation: ama: 'Kragl B. Verifying concurrent programs: Refinement, synchronization, sequentialization. 2020. doi:10.15479/AT:ISTA:8332' apa: 'Kragl, B. (2020). Verifying concurrent programs: Refinement, synchronization, sequentialization. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8332' chicago: 'Kragl, Bernhard. “Verifying Concurrent Programs: Refinement, Synchronization, Sequentialization.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8332.' ieee: 'B. Kragl, “Verifying concurrent programs: Refinement, synchronization, sequentialization,” Institute of Science and Technology Austria, 2020.' ista: 'Kragl B. 2020. Verifying concurrent programs: Refinement, synchronization, sequentialization. Institute of Science and Technology Austria.' mla: 'Kragl, Bernhard. Verifying Concurrent Programs: Refinement, Synchronization, Sequentialization. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8332.' short: 'B. Kragl, Verifying Concurrent Programs: Refinement, Synchronization, Sequentialization, Institute of Science and Technology Austria, 2020.' date_created: 2020-09-04T12:24:12Z date_published: 2020-09-03T00:00:00Z date_updated: 2023-09-13T08:45:08Z day: '03' ddc: - '000' degree_awarded: PhD department: - _id: ToHe doi: 10.15479/AT:ISTA:8332 file: - access_level: open_access checksum: 26fe261550f691280bda4c454bf015c7 content_type: application/pdf creator: bkragl date_created: 2020-09-04T12:17:47Z date_updated: 2020-09-04T12:17:47Z file_id: '8333' file_name: kragl-thesis.pdf file_size: 1348815 relation: main_file - access_level: closed checksum: b9694ce092b7c55557122adba8337ebc content_type: application/zip creator: bkragl date_created: 2020-09-04T13:00:17Z date_updated: 2020-09-04T13:00:17Z file_id: '8335' file_name: kragl-thesis.zip file_size: 372312 relation: source_file file_date_updated: 2020-09-04T13:00:17Z has_accepted_license: '1' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: '120' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '133' relation: part_of_dissertation status: public - id: '8012' relation: part_of_dissertation status: public - id: '8195' relation: part_of_dissertation status: public - id: '160' relation: part_of_dissertation status: public status: public supervisor: - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000-0002-2985-7724 title: 'Verifying concurrent programs: Refinement, synchronization, sequentialization' type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2020' ... --- _id: '14326' 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" article_processing_charge: No author: - first_name: Francesco full_name: Locatello, Francesco id: 26cfd52f-2483-11ee-8040-88983bcc06d4 last_name: Locatello orcid: 0000-0002-4850-0683 - first_name: Dirk full_name: Weissenborn, Dirk last_name: Weissenborn - first_name: Thomas full_name: Unterthiner, Thomas last_name: Unterthiner - first_name: Aravindh full_name: Mahendran, Aravindh last_name: Mahendran - first_name: Georg full_name: Heigold, Georg last_name: Heigold - first_name: Jakob full_name: Uszkoreit, Jakob last_name: Uszkoreit - first_name: Alexey full_name: Dosovitskiy, Alexey last_name: Dosovitskiy - first_name: Thomas full_name: Kipf, Thomas last_name: Kipf citation: 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.' 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. 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. ista: 'Locatello F, Weissenborn D, Unterthiner T, Mahendran A, Heigold G, Uszkoreit J, Dosovitskiy A, Kipf T. 2020. Object-centric learning with slot attention. Advances in Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems vol. 33, 11525–11538.' mla: Locatello, Francesco, et al. “Object-Centric Learning with Slot Attention.” Advances in Neural Information Processing Systems, vol. 33, Curran Associates, 2020, pp. 11525–38. short: F. Locatello, D. Weissenborn, T. Unterthiner, A. Mahendran, G. Heigold, J. Uszkoreit, A. Dosovitskiy, T. Kipf, in:, Advances in Neural Information Processing Systems, Curran Associates, 2020, pp. 11525–11538. conference: end_date: 2020-12-12 location: Virtual name: 'NeurIPS: Neural Information Processing Systems' start_date: 2020-12-06 date_created: 2023-09-13T12:03:46Z date_published: 2020-01-01T00:00:00Z date_updated: 2023-09-13T12:19:19Z department: - _id: FrLo extern: '1' external_id: arxiv: - '2006.15055' intvolume: ' 33' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2006.15055 oa: 1 oa_version: Preprint page: 11525-11538 publication: Advances in Neural Information Processing Systems publication_identifier: isbn: - '9781713829546' publication_status: published publisher: Curran Associates quality_controlled: '1' status: public title: Object-centric learning with slot attention type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 33 year: '2020' ... --- _id: '71' abstract: - lang: eng text: "We consider dynamical transport metrics for probability measures on discretisations of a bounded convex domain in ℝd. These metrics are natural discrete counterparts to the Kantorovich metric \U0001D54E2, 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 \U0001D54E2, 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." article_processing_charge: No article_type: original author: - first_name: Peter full_name: Gladbach, Peter last_name: Gladbach - first_name: Eva full_name: Kopfer, Eva last_name: Kopfer - first_name: Jan full_name: Maas, Jan id: 4C5696CE-F248-11E8-B48F-1D18A9856A87 last_name: Maas orcid: 0000-0002-0845-1338 citation: 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 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. 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. ista: Gladbach P, Kopfer E, Maas J. 2020. Scaling limits of discrete optimal transport. SIAM Journal on Mathematical Analysis. 52(3), 2759–2802. mla: Gladbach, Peter, et al. “Scaling Limits of Discrete Optimal Transport.” SIAM Journal on Mathematical Analysis, vol. 52, no. 3, Society for Industrial and Applied Mathematics, 2020, pp. 2759–802, doi:10.1137/19M1243440. short: P. Gladbach, E. Kopfer, J. Maas, SIAM Journal on Mathematical Analysis 52 (2020) 2759–2802. date_created: 2018-12-11T11:44:28Z date_published: 2020-10-01T00:00:00Z date_updated: 2023-09-18T08:13:15Z day: '01' department: - _id: JaMa doi: 10.1137/19M1243440 external_id: arxiv: - '1809.01092' isi: - '000546975100017' intvolume: ' 52' isi: 1 issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1809.01092 month: '10' oa: 1 oa_version: Preprint page: 2759-2802 publication: SIAM Journal on Mathematical Analysis publication_identifier: eissn: - '10957154' issn: - '00361410' publication_status: published publisher: Society for Industrial and Applied Mathematics publist_id: '7983' quality_controlled: '1' scopus_import: '1' status: public title: Scaling limits of discrete optimal transport type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 52 year: '2020' ... --- _id: '5681' abstract: - lang: eng text: 'We introduce dynamically warping grids for adaptive liquid simulation. Our primary contributions are a strategy for dynamically deforming regular grids over the course of a simulation and a method for efficiently utilizing these deforming grids for liquid simulation. Prior work has shown that unstructured grids are very effective for adaptive fluid simulations. However, unstructured grids often lead to complicated implementations and a poor cache hit rate due to inconsistent memory access. Regular grids, on the other hand, provide a fast, fixed memory access pattern and straightforward implementation. Our method combines the advantages of both: we leverage the simplicity of regular grids while still achieving practical and controllable spatial adaptivity. We demonstrate that our method enables adaptive simulations that are fast, flexible, and robust to null-space issues. At the same time, our method is simple to implement and takes advantage of existing highly-tuned algorithms.' acknowledged_ssus: - _id: ScienComp 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. article_processing_charge: No article_type: original author: - first_name: Ibayashi full_name: Hikaru, Ibayashi last_name: Hikaru - first_name: Christopher J full_name: Wojtan, Christopher J id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87 last_name: Wojtan orcid: 0000-0001-6646-5546 - first_name: Nils full_name: Thuerey, Nils last_name: Thuerey - first_name: Takeo full_name: Igarashi, Takeo last_name: Igarashi - first_name: Ryoichi full_name: Ando, Ryoichi last_name: Ando citation: 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 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. 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. 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. short: I. Hikaru, C. Wojtan, N. Thuerey, T. Igarashi, R. Ando, IEEE Transactions on Visualization and Computer Graphics 26 (2020) 2288–2302. date_created: 2018-12-16T22:59:21Z date_published: 2020-06-01T00:00:00Z date_updated: 2023-09-18T09:30:01Z day: '01' ddc: - '006' department: - _id: ChWo doi: 10.1109/TVCG.2018.2883628 external_id: isi: - '000532295600014' pmid: - '30507534' file: - access_level: open_access checksum: 8d4c55443a0ee335bb5bb652de503042 content_type: application/pdf creator: wojtan date_created: 2020-10-08T08:34:53Z date_updated: 2020-10-08T08:34:53Z file_id: '8626' file_name: preprint.pdf file_size: 21910098 relation: main_file success: 1 file_date_updated: 2020-10-08T08:34:53Z has_accepted_license: '1' intvolume: ' 26' isi: 1 issue: '6' language: - iso: eng month: '06' oa: 1 oa_version: Submitted Version page: 2288-2302 pmid: 1 publication: IEEE Transactions on Visualization and Computer Graphics publication_identifier: eissn: - '19410506' issn: - '10772626' publication_status: published publisher: IEEE quality_controlled: '1' scopus_import: '1' status: public title: Simulating liquids on dynamically warping grids type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 26 year: '2020' ... --- _id: '8958' 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." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Xiang full_name: Li, Xiang id: 4B7E523C-F248-11E8-B48F-1D18A9856A87 last_name: Li citation: ama: Li X. Rotation of coupled cold molecules in the presence of a many-body environment. 2020. doi:10.15479/AT:ISTA:8958 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 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. ista: Li X. 2020. Rotation of coupled cold molecules in the presence of a many-body environment. Institute of Science and Technology Austria. 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. short: X. Li, Rotation of Coupled Cold Molecules in the Presence of a Many-Body Environment, Institute of Science and Technology Austria, 2020. date_created: 2020-12-21T09:44:30Z date_published: 2020-12-21T00:00:00Z date_updated: 2023-09-20T11:30:58Z day: '21' ddc: - '539' degree_awarded: PhD department: - _id: MiLe doi: 10.15479/AT:ISTA:8958 ec_funded: 1 file: - access_level: open_access checksum: 3994c54a1241451d561db1d4f43bad30 content_type: application/pdf creator: xli date_created: 2020-12-22T10:55:56Z date_updated: 2020-12-22T10:55:56Z file_id: '8967' file_name: THESIS_Xiang_Li.pdf file_size: 3622305 relation: main_file success: 1 - access_level: closed checksum: 0954ecfc5554c05615c14de803341f00 content_type: application/x-zip-compressed creator: xli date_created: 2020-12-22T10:56:03Z date_updated: 2020-12-30T07:18:03Z file_id: '8968' file_name: THESIS_Xiang_Li.zip file_size: 4018859 relation: source_file file_date_updated: 2020-12-30T07:18:03Z has_accepted_license: '1' language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: '125' project: - _id: 26031614-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P29902 name: Quantum rotations in the presence of a many-body environment - _id: 2688CF98-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '801770' name: 'Angulon: physics and applications of a new quasiparticle' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '5886' relation: part_of_dissertation status: public - id: '8587' relation: part_of_dissertation status: public - id: '1120' relation: part_of_dissertation status: public status: public supervisor: - first_name: Mikhail full_name: Lemeshko, Mikhail id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 title: Rotation of coupled cold molecules in the presence of a many-body environment type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2020' ... --- _id: '8386' abstract: - lang: eng 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." acknowledged_ssus: - _id: SSU 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. alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Ran full_name: Zhang, Ran id: 4DDBCEB0-F248-11E8-B48F-1D18A9856A87 last_name: Zhang orcid: 0000-0002-3808-281X citation: ama: Zhang R. Structure-aware computational design and its application to 3D printable volume scattering, mechanism, and multistability. 2020. doi:10.15479/AT:ISTA:8386 apa: Zhang, R. (2020). Structure-aware computational design and its application to 3D printable volume scattering, mechanism, and multistability. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8386 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. 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. ista: Zhang R. 2020. Structure-aware computational design and its application to 3D printable volume scattering, mechanism, and multistability. Institute of Science and Technology Austria. mla: Zhang, Ran. Structure-Aware Computational Design and Its Application to 3D Printable Volume Scattering, Mechanism, and Multistability. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8386. 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. date_created: 2020-09-14T01:04:53Z date_published: 2020-09-14T00:00:00Z date_updated: 2023-09-22T09:49:31Z day: '14' ddc: - '003' degree_awarded: PhD department: - _id: BeBi doi: 10.15479/AT:ISTA:8386 ec_funded: 1 file: - access_level: closed checksum: edcf578b6e1c9b0dd81ff72d319b66ba content_type: application/x-zip-compressed creator: rzhang date_created: 2020-09-14T01:02:59Z date_updated: 2020-09-14T12:18:43Z file_id: '8388' file_name: Thesis_Ran.zip file_size: 1245800191 relation: source_file - access_level: open_access checksum: 817e20c33be9247f906925517c56a40d content_type: application/pdf creator: rzhang date_created: 2020-09-15T12:51:53Z date_updated: 2020-09-15T12:51:53Z file_id: '8396' file_name: PhD_thesis_Ran Zhang_20200915.pdf file_size: 161385316 relation: main_file success: 1 file_date_updated: 2020-09-15T12:51:53Z has_accepted_license: '1' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: '148' project: - _id: 2508E324-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '642841' name: Distributed 3D Object Design - _id: 24F9549A-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '715767' name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '486' relation: part_of_dissertation status: public - id: '1002' relation: part_of_dissertation status: public status: public supervisor: - first_name: Bernd full_name: Bickel, Bernd id: 49876194-F248-11E8-B48F-1D18A9856A87 last_name: Bickel orcid: 0000-0001-6511-9385 title: Structure-aware computational design and its application to 3D printable volume scattering, mechanism, and multistability type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2020' ... --- _id: '7996' 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." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Josip full_name: Kukucka, Josip id: 3F5D8856-F248-11E8-B48F-1D18A9856A87 last_name: Kukucka citation: 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 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. ieee: J. Kukucka, “Implementation of a hole spin qubit in Ge hut wires and dispersive spin sensing,” Institute of Science and Technology Austria, 2020. ista: Kukucka J. 2020. Implementation of a hole spin qubit in Ge hut wires and dispersive spin sensing. Institute of Science and Technology Austria. 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. short: J. Kukucka, Implementation of a Hole Spin Qubit in Ge Hut Wires and Dispersive Spin Sensing, Institute of Science and Technology Austria, 2020. date_created: 2020-06-22T09:22:23Z date_published: 2020-06-22T00:00:00Z date_updated: 2023-09-26T15:50:22Z day: '22' ddc: - '530' degree_awarded: PhD department: - _id: GeKa doi: 10.15479/AT:ISTA:7996 file: - access_level: closed checksum: 467e52feb3e361ce8cf5fe8d5c254ece content_type: application/x-zip-compressed creator: dernst date_created: 2020-06-22T09:22:04Z date_updated: 2020-07-14T12:48:07Z file_id: '7997' file_name: JK_thesis_latex_source_files.zip file_size: 392794743 relation: main_file - access_level: open_access checksum: 1de716bf110dbd77d383e479232bf496 content_type: application/pdf creator: dernst date_created: 2020-06-22T09:21:29Z date_updated: 2020-07-14T12:48:07Z file_id: '7998' file_name: PhD_thesis_JK_pdfa.pdf file_size: 28453247 relation: main_file file_date_updated: 2020-07-14T12:48:07Z has_accepted_license: '1' language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: '178' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '1328' relation: part_of_dissertation status: public - id: '7541' relation: part_of_dissertation status: public - id: '77' relation: part_of_dissertation status: public - id: '23' relation: part_of_dissertation status: public - id: '840' relation: part_of_dissertation status: public status: public supervisor: - first_name: Georgios full_name: Katsaros, Georgios id: 38DB5788-F248-11E8-B48F-1D18A9856A87 last_name: Katsaros orcid: 0000-0001-8342-202X title: Implementation of a hole spin qubit in Ge hut wires and dispersive spin sensing type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2020' ... --- _id: '8272' 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. alternative_title: - LNCS article_processing_charge: No author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Joost P full_name: Katoen, Joost P id: 4524F760-F248-11E8-B48F-1D18A9856A87 last_name: Katoen - first_name: Maximilian full_name: Weininger, Maximilian last_name: Weininger - first_name: Tobias full_name: Winkler, Tobias last_name: Winkler citation: 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. 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. ista: 'Chatterjee K, Katoen JP, Weininger M, Winkler T. 2020. Stochastic games with lexicographic reachability-safety objectives. International Conference on Computer Aided Verification. CAV: Computer Aided Verification, LNCS, vol. 12225, 398–420.' mla: Chatterjee, Krishnendu, et al. “Stochastic Games with Lexicographic Reachability-Safety Objectives.” International Conference on Computer Aided Verification, vol. 12225, Springer Nature, 2020, pp. 398–420, doi:10.1007/978-3-030-53291-8_21. short: K. Chatterjee, J.P. Katoen, M. Weininger, T. Winkler, in:, International Conference on Computer Aided Verification, Springer Nature, 2020, pp. 398–420. conference: name: 'CAV: Computer Aided Verification' date_created: 2020-08-16T22:00:58Z date_published: 2020-07-14T00:00:00Z date_updated: 2023-10-03T11:36:13Z day: '14' ddc: - '000' department: - _id: KrCh doi: 10.1007/978-3-030-53291-8_21 ec_funded: 1 external_id: arxiv: - '2005.04018' isi: - '000695272500021' file: - access_level: open_access checksum: 093d4788d7d5b2ce0ffe64fbe7820043 content_type: application/pdf creator: dernst date_created: 2020-08-17T11:32:44Z date_updated: 2020-08-17T11:32:44Z file_id: '8276' file_name: 2020_LNCS_CAV_Chatterjee.pdf file_size: 625056 relation: main_file success: 1 file_date_updated: 2020-08-17T11:32:44Z has_accepted_license: '1' intvolume: ' 12225' isi: 1 language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: 398-420 project: - _id: 0599E47C-7A3F-11EA-A408-12923DDC885E call_identifier: H2020 grant_number: '863818' name: 'Formal Methods for Stochastic Models: Algorithms and Applications' - _id: 25892FC0-B435-11E9-9278-68D0E5697425 grant_number: ICT15-003 name: Efficient Algorithms for Computer Aided Verification publication: International Conference on Computer Aided Verification publication_identifier: eissn: - '16113349' isbn: - '9783030532901' issn: - '03029743' publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '12738' relation: later_version status: public scopus_import: '1' status: public title: Stochastic games with lexicographic reachability-safety objectives tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 12225 year: '2020' ... --- _id: '7572' 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. alternative_title: - Methods in Cell Biology article_processing_charge: No author: - first_name: Paulo R full_name: Dos Santos Caldas, Paulo R id: 38FCDB4C-F248-11E8-B48F-1D18A9856A87 last_name: Dos Santos Caldas orcid: 0000-0001-6730-4461 - first_name: Philipp full_name: Radler, Philipp id: 40136C2A-F248-11E8-B48F-1D18A9856A87 last_name: Radler orcid: '0000-0001-9198-2182 ' - first_name: Christoph M full_name: Sommer, Christoph M id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87 last_name: Sommer orcid: 0000-0003-1216-9105 - first_name: Martin full_name: Loose, Martin id: 462D4284-F248-11E8-B48F-1D18A9856A87 last_name: Loose orcid: 0000-0001-7309-9724 citation: 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' 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 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. 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. 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. date_created: 2020-03-08T23:00:47Z date_published: 2020-02-27T00:00:00Z date_updated: 2023-10-04T09:50:24Z day: '27' department: - _id: MaLo doi: 10.1016/bs.mcb.2020.01.006 ec_funded: 1 editor: - first_name: 'Phong ' full_name: 'Tran, Phong ' last_name: Tran external_id: isi: - '000611826500008' intvolume: ' 158' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1101/839571 month: '02' oa: 1 oa_version: Preprint page: 145-161 project: - _id: 2595697A-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '679239' name: Self-Organization of the Bacterial Cell - _id: 260D98C8-B435-11E9-9278-68D0E5697425 name: Reconstitution of Bacterial Cell Division Using Purified Components publication: Methods in Cell Biology publication_identifier: issn: - 0091679X publication_status: published publisher: Elsevier quality_controlled: '1' related_material: record: - id: '8358' relation: part_of_dissertation status: public scopus_import: '1' status: public title: Computational analysis of filament polymerization dynamics in cytoskeletal networks type: book_chapter user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 158 year: '2020' ... --- _id: '7387' 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. 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. article_processing_charge: No article_type: letter_note author: - first_name: Natalia S. full_name: Baranova, Natalia S. id: 38661662-F248-11E8-B48F-1D18A9856A87 last_name: Baranova orcid: 0000-0002-3086-9124 - first_name: Philipp full_name: Radler, Philipp id: 40136C2A-F248-11E8-B48F-1D18A9856A87 last_name: Radler orcid: '0000-0001-9198-2182 ' - first_name: Víctor M. full_name: Hernández-Rocamora, Víctor M. last_name: Hernández-Rocamora - first_name: Carlos full_name: Alfonso, Carlos last_name: Alfonso - first_name: Maria D full_name: Lopez Pelegrin, Maria D id: 319AA9CE-F248-11E8-B48F-1D18A9856A87 last_name: Lopez Pelegrin - first_name: Germán full_name: Rivas, Germán last_name: Rivas - first_name: Waldemar full_name: Vollmer, Waldemar last_name: Vollmer - first_name: Martin full_name: Loose, Martin id: 462D4284-F248-11E8-B48F-1D18A9856A87 last_name: Loose orcid: 0000-0001-7309-9724 citation: 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 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. 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. 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. 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. date_created: 2020-01-28T16:14:41Z date_published: 2020-01-20T00:00:00Z date_updated: 2023-10-06T12:22:38Z day: '20' department: - _id: MaLo doi: 10.1038/s41564-019-0657-5 ec_funded: 1 external_id: isi: - '000508584700007' pmid: - '31959972' intvolume: ' 5' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: http://europepmc.org/article/PMC/7048620 month: '01' oa: 1 oa_version: Submitted Version page: 407-417 pmid: 1 project: - _id: 2595697A-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '679239' name: Self-Organization of the Bacterial Cell - _id: 259B655A-B435-11E9-9278-68D0E5697425 grant_number: LT000824/2016 name: Reconstitution of bacterial cell wall sythesis - _id: 2596EAB6-B435-11E9-9278-68D0E5697425 grant_number: ALTF 2015-1163 name: Synthesis of bacterial cell wall publication: Nature Microbiology publication_identifier: issn: - 2058-5276 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - description: News on IST Homepage relation: press_release url: https://ist.ac.at/en/news/little-cell-big-cover-story/ record: - id: '14280' relation: dissertation_contains status: public scopus_import: '1' status: public title: Diffusion and capture permits dynamic coupling between treadmilling FtsZ filaments and cell division proteins type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 5 year: '2020' ... --- _id: '8163' abstract: - lang: eng text: Fejes Tóth [3] studied approximations of smooth surfaces in three-space by piecewise flat triangular meshes with a given number of vertices on the surface that are optimal with respect to Hausdorff distance. He proves that this Hausdorff distance decreases inversely proportional with the number of vertices of the approximating mesh if the surface is convex. He also claims that this Hausdorff distance is inversely proportional to the square of the number of vertices for a specific non-convex surface, namely a one-sheeted hyperboloid of revolution bounded by two congruent circles. We refute this claim, and show that the asymptotic behavior of the Hausdorff distance is linear, that is the same as for convex surfaces. 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." article_processing_charge: No article_type: original author: - first_name: Gert full_name: Vegter, Gert last_name: Vegter - first_name: Mathijs full_name: Wintraecken, Mathijs id: 307CFBC8-F248-11E8-B48F-1D18A9856A87 last_name: Wintraecken orcid: 0000-0002-7472-2220 citation: 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. 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. ista: Vegter G, Wintraecken M. 2020. Refutation of a claim made by Fejes Tóth on the accuracy of surface meshes. Studia Scientiarum Mathematicarum Hungarica. 57(2), 193–199. mla: Vegter, Gert, and Mathijs Wintraecken. “Refutation of a Claim Made by Fejes Tóth on the Accuracy of Surface Meshes.” Studia Scientiarum Mathematicarum Hungarica, vol. 57, no. 2, Akadémiai Kiadó, 2020, pp. 193–99, doi:10.1556/012.2020.57.2.1454. short: G. Vegter, M. Wintraecken, Studia Scientiarum Mathematicarum Hungarica 57 (2020) 193–199. date_created: 2020-07-24T07:09:18Z date_published: 2020-07-24T00:00:00Z date_updated: 2023-10-10T13:05:27Z day: '24' ddc: - '510' department: - _id: HeEd doi: 10.1556/012.2020.57.2.1454 ec_funded: 1 external_id: isi: - '000570978400005' file: - access_level: open_access content_type: application/pdf creator: mwintrae date_created: 2020-07-24T07:09:06Z date_updated: 2020-07-24T07:09:06Z file_id: '8164' file_name: 57-2-05_4214-1454Vegter-Wintraecken_OpenAccess_CC-BY-NC.pdf file_size: 1476072 relation: main_file file_date_updated: 2020-07-24T07:09:06Z has_accepted_license: '1' intvolume: ' 57' isi: 1 issue: '2' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: 193-199 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships - _id: 268116B8-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z00342 name: The Wittgenstein Prize publication: Studia Scientiarum Mathematicarum Hungarica publication_identifier: eissn: - 1588-2896 issn: - 0081-6906 publication_status: published publisher: Akadémiai Kiadó quality_controlled: '1' scopus_import: '1' status: public title: Refutation of a claim made by Fejes Tóth on the accuracy of surface meshes tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 57 year: '2020' ... --- _id: '8671' 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. ' 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. article_processing_charge: No article_type: original author: - first_name: A. full_name: Shakiba, A. last_name: Shakiba - first_name: Amir Kafshdar full_name: Goharshady, Amir Kafshdar id: 391365CE-F248-11E8-B48F-1D18A9856A87 last_name: Goharshady orcid: 0000-0003-1702-6584 - first_name: M.R. full_name: Hooshmandasl, M.R. last_name: Hooshmandasl - first_name: M. full_name: Alambardar Meybodi, M. last_name: Alambardar Meybodi citation: 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 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. 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. 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. date_created: 2020-10-18T22:01:36Z date_published: 2020-10-01T00:00:00Z date_updated: 2023-10-16T09:25:00Z day: '01' ddc: - '000' department: - _id: KrCh doi: 10.29252/ijmsi.15.2.117 external_id: arxiv: - '1805.10672' file: - access_level: open_access checksum: f299661a6d51cda6d255a76be696f48d content_type: application/pdf creator: dernst date_created: 2020-10-19T11:14:20Z date_updated: 2020-10-19T11:14:20Z file_id: '8676' file_name: 2020_ijmsi_Shakiba_accepted.pdf file_size: 261688 relation: main_file success: 1 file_date_updated: 2020-10-19T11:14:20Z has_accepted_license: '1' intvolume: ' 15' issue: '2' language: - iso: eng month: '10' oa: 1 oa_version: Submitted Version page: 117-128 project: - _id: 267066CE-B435-11E9-9278-68D0E5697425 name: Quantitative Analysis of Probablistic Systems with a focus on Crypto-currencies publication: Iranian Journal of Mathematical Sciences and Informatics publication_identifier: eissn: - 2008-9473 issn: - 1735-4463 publication_status: published publisher: Iranian Academic Center for Education, Culture and Research quality_controlled: '1' scopus_import: '1' status: public title: A note on belief structures and s-approximation spaces type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 15 year: '2020' ... --- _id: '6359' abstract: - lang: eng 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. article_number: '82' article_processing_charge: No article_type: original author: - first_name: Konstantinos full_name: Dareiotis, Konstantinos last_name: Dareiotis - first_name: Mate full_name: Gerencser, Mate id: 44ECEDF2-F248-11E8-B48F-1D18A9856A87 last_name: Gerencser citation: 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 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 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. 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. 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. 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. short: K. Dareiotis, M. Gerencser, Electronic Journal of Probability 25 (2020). date_created: 2019-04-30T07:40:17Z date_published: 2020-07-16T00:00:00Z date_updated: 2023-10-16T09:22:50Z day: '16' ddc: - '510' department: - _id: JaMa doi: 10.1214/20-EJP479 external_id: arxiv: - '1812.04583' isi: - '000550150700001' file: - access_level: open_access checksum: 8e7c42e72596f6889d786e8e8b89994f content_type: application/pdf creator: dernst date_created: 2020-09-21T13:15:02Z date_updated: 2020-09-21T13:15:02Z file_id: '8549' file_name: 2020_EJournProbab_Dareiotis.pdf file_size: 273042 relation: main_file success: 1 file_date_updated: 2020-09-21T13:15:02Z has_accepted_license: '1' intvolume: ' 25' isi: 1 language: - iso: eng month: '07' oa: 1 oa_version: Published Version publication: Electronic Journal of Probability publication_identifier: eissn: - 1083-6489 publication_status: published publisher: Institute of Mathematical Statistics quality_controlled: '1' scopus_import: '1' status: public title: On the regularisation of the noise for the Euler-Maruyama scheme with irregular drift tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 25 year: '2020' ... --- _id: '8390' 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 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. alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Amélie full_name: Royer, Amélie id: 3811D890-F248-11E8-B48F-1D18A9856A87 last_name: Royer orcid: 0000-0002-8407-0705 citation: 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. ieee: A. Royer, “Leveraging structure in Computer Vision tasks for flexible Deep Learning models,” Institute of Science and Technology Austria, 2020. ista: Royer A. 2020. Leveraging structure in Computer Vision tasks for flexible Deep Learning models. Institute of Science and Technology Austria. 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. date_created: 2020-09-14T13:42:09Z date_published: 2020-09-14T00:00:00Z date_updated: 2023-10-16T10:04:02Z day: '14' ddc: - '000' degree_awarded: PhD department: - _id: ChLa doi: 10.15479/AT:ISTA:8390 file: - access_level: open_access checksum: c914d2f88846032f3d8507734861b6ee content_type: application/pdf creator: dernst date_created: 2020-09-14T13:39:14Z date_updated: 2020-09-14T13:39:14Z file_id: '8391' file_name: 2020_Thesis_Royer.pdf file_size: 30224591 relation: main_file success: 1 - access_level: closed checksum: ae98fb35d912cff84a89035ae5794d3c content_type: application/x-zip-compressed creator: dernst date_created: 2020-09-14T13:39:17Z date_updated: 2020-09-14T13:39:17Z file_id: '8392' file_name: thesis_sources.zip file_size: 74227627 relation: main_file file_date_updated: 2020-09-14T13:39:17Z has_accepted_license: '1' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: '197' publication_identifier: isbn: - 978-3-99078-007-7 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '7936' relation: part_of_dissertation status: public - id: '7937' relation: part_of_dissertation status: public - id: '8193' relation: part_of_dissertation status: public - id: '8092' relation: part_of_dissertation status: public - id: '911' relation: part_of_dissertation status: public status: public supervisor: - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 title: Leveraging structure in Computer Vision tasks for flexible Deep Learning models tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) short: CC BY-NC-SA (4.0) type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2020' ... --- _id: '8186' abstract: - lang: eng text: "Numerous methods have been proposed for probabilistic generative modelling of\r\n3D objects. However, none of these is able to produce textured objects, which\r\nrenders them of limited use for practical tasks. In this work, we present the\r\nfirst generative model of textured 3D meshes. Training such a model would\r\ntraditionally require a large dataset of textured meshes, but unfortunately,\r\nexisting datasets of meshes lack detailed textures. We instead propose a new\r\ntraining methodology that allows learning from collections of 2D images without\r\nany 3D information. To do so, we train our model to explain a distribution of\r\nimages by modelling each image as a 3D foreground object placed in front of a\r\n2D background. Thus, it learns to generate meshes that when rendered, produce\r\nimages similar to those in its training set.\r\n A well-known problem when generating meshes with deep networks is the\r\nemergence of self-intersections, which are problematic for many use-cases. As a\r\nsecond contribution we therefore introduce a new generation process for 3D\r\nmeshes that guarantees no self-intersections arise, based on the physical\r\nintuition that faces should push one another out of the way as they move.\r\n We conduct extensive experiments on our approach, reporting quantitative and\r\nqualitative results on both synthetic data and natural images. These show our\r\nmethod successfully learns to generate plausible and diverse textured 3D\r\nsamples for five challenging object classes." article_processing_charge: No author: - first_name: Paul M full_name: Henderson, Paul M id: 13C09E74-18D9-11E9-8878-32CFE5697425 last_name: Henderson orcid: 0000-0002-5198-7445 - first_name: Vagia full_name: Tsiminaki, Vagia last_name: Tsiminaki - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 citation: ama: 'Henderson PM, Tsiminaki V, Lampert C. Leveraging 2D data to learn textured 3D mesh generation. In: Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition. IEEE; 2020:7498-7507. doi:10.1109/CVPR42600.2020.00752' apa: 'Henderson, P. M., Tsiminaki, V., & Lampert, C. (2020). Leveraging 2D data to learn textured 3D mesh generation. In Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition (pp. 7498–7507). Virtual: IEEE. https://doi.org/10.1109/CVPR42600.2020.00752' chicago: Henderson, Paul M, Vagia Tsiminaki, and Christoph Lampert. “Leveraging 2D Data to Learn Textured 3D Mesh Generation.” In Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition, 7498–7507. IEEE, 2020. https://doi.org/10.1109/CVPR42600.2020.00752. 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. 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.' mla: Henderson, Paul M., et al. “Leveraging 2D Data to Learn Textured 3D Mesh Generation.” Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition, IEEE, 2020, pp. 7498–507, doi:10.1109/CVPR42600.2020.00752. short: P.M. Henderson, V. Tsiminaki, C. Lampert, in:, Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition, IEEE, 2020, pp. 7498–7507. conference: end_date: 2020-06-19 location: Virtual name: 'CVPR: Conference on Computer Vision and Pattern Recognition' start_date: 2020-06-14 date_created: 2020-07-31T16:53:49Z date_published: 2020-07-01T00:00:00Z date_updated: 2023-10-17T07:37:11Z day: '01' ddc: - '004' department: - _id: ChLa doi: 10.1109/CVPR42600.2020.00752 external_id: arxiv: - '2004.04180' file: - access_level: open_access content_type: application/pdf creator: phenders date_created: 2020-07-31T16:57:12Z date_updated: 2020-07-31T16:57:12Z file_id: '8187' file_name: paper.pdf file_size: 10262773 relation: main_file success: 1 file_date_updated: 2020-07-31T16:57:12Z has_accepted_license: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://openaccess.thecvf.com/content_CVPR_2020/papers/Henderson_Leveraging_2D_Data_to_Learn_Textured_3D_Mesh_Generation_CVPR_2020_paper.pdf month: '07' oa: 1 oa_version: Submitted Version page: 7498-7507 publication: Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition publication_identifier: eisbn: - '9781728171685' eissn: - 2575-7075 publication_status: published publisher: IEEE quality_controlled: '1' scopus_import: '1' status: public title: Leveraging 2D data to learn textured 3D mesh generation type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2020' ... --- _id: '7416' abstract: - lang: eng text: Earlier, we demonstrated that transcript levels of METAL TOLERANCE PROTEIN2 (MTP2) and of HEAVY METAL ATPase2 (HMA2) increase strongly in roots of Arabidopsis upon prolonged zinc (Zn) deficiency and respond to shoot physiological Zn status, and not to the local Zn status in roots. This provided evidence for shoot-to-root communication in the acclimation of plants to Zn deficiency. Zn-deficient soils limit both the yield and quality of agricultural crops and can result in clinically relevant nutritional Zn deficiency in human populations. Implementing Zn deficiency during cultivation of the model plant Arabidopsis thaliana on agar-solidified media is difficult because trace element contaminations are present in almost all commercially available agars. Here, we demonstrate root morphological acclimations to Zn deficiency on agar-solidified medium following the effective removal of contaminants. These advancements allow reproducible phenotyping toward understanding fundamental plant responses to deficiencies of Zn and other essential trace elements. article_number: '1687175' article_processing_charge: No article_type: original author: - first_name: Scott A full_name: Sinclair, Scott A id: 2D99FE6A-F248-11E8-B48F-1D18A9856A87 last_name: Sinclair orcid: 0000-0002-4566-0593 - first_name: U. full_name: Krämer, U. last_name: Krämer citation: 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 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. 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. 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. 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. short: S.A. Sinclair, U. Krämer, Plant Signaling & Behavior 15 (2020). date_created: 2020-01-30T10:12:04Z date_published: 2020-01-01T00:00:00Z date_updated: 2023-10-17T09:01:48Z day: '01' department: - _id: JiFr doi: 10.1080/15592324.2019.1687175 external_id: isi: - '000494909300001' pmid: - '31696764' intvolume: ' 15' isi: 1 issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7012054 month: '01' oa: 1 oa_version: Submitted Version pmid: 1 publication: Plant Signaling & Behavior publication_identifier: issn: - 1559-2324 publication_status: published publisher: Taylor & Francis quality_controlled: '1' scopus_import: '1' status: public title: Generation of effective zinc-deficient agar-solidified media allows identification of root morphology changes in response to zinc limitation type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 15 year: '2020' ... --- _id: '9196' abstract: - lang: eng text: In order to provide a local description of a regular function in a small neighbourhood of a point x, it is sufficient by Taylor’s theorem to know the value of the function as well as all of its derivatives up to the required order at the point x itself. In other words, one could say that a regular function is locally modelled by the set of polynomials. The theory of regularity structures due to Hairer generalizes this observation and provides an abstract setup, which in the application to singular SPDE extends the set of polynomials by functionals constructed from, e.g., white noise. In this context, the notion of Taylor polynomials is lifted to the notion of so-called modelled distributions. The celebrated reconstruction theorem, which in turn was inspired by Gubinelli’s \textit {sewing lemma}, is of paramount importance for the theory. It enables one to reconstruct a modelled distribution as a true distribution on Rd which is locally approximated by this extended set of models or “monomials”. In the original work of Hairer, the error is measured by means of Hölder norms. This was then generalized to the whole scale of Besov spaces by Hairer and Labbé. It is the aim of this work to adapt the analytic part of the theory of regularity structures to the scale of Triebel–Lizorkin spaces. article_processing_charge: No article_type: original author: - first_name: Sebastian full_name: Hensel, Sebastian id: 4D23B7DA-F248-11E8-B48F-1D18A9856A87 last_name: Hensel orcid: 0000-0001-7252-8072 - first_name: Tommaso full_name: Rosati, Tommaso last_name: Rosati citation: ama: Hensel S, Rosati T. Modelled distributions of Triebel–Lizorkin type. Studia Mathematica. 2020;252(3):251-297. doi:10.4064/sm180411-11-2 apa: Hensel, S., & Rosati, T. (2020). Modelled distributions of Triebel–Lizorkin type. Studia Mathematica. Instytut Matematyczny. https://doi.org/10.4064/sm180411-11-2 chicago: Hensel, Sebastian, and Tommaso Rosati. “Modelled Distributions of Triebel–Lizorkin Type.” Studia Mathematica. Instytut Matematyczny, 2020. https://doi.org/10.4064/sm180411-11-2. ieee: S. Hensel and T. Rosati, “Modelled distributions of Triebel–Lizorkin type,” Studia Mathematica, vol. 252, no. 3. Instytut Matematyczny, pp. 251–297, 2020. ista: Hensel S, Rosati T. 2020. Modelled distributions of Triebel–Lizorkin type. Studia Mathematica. 252(3), 251–297. mla: Hensel, Sebastian, and Tommaso Rosati. “Modelled Distributions of Triebel–Lizorkin Type.” Studia Mathematica, vol. 252, no. 3, Instytut Matematyczny, 2020, pp. 251–97, doi:10.4064/sm180411-11-2. short: S. Hensel, T. Rosati, Studia Mathematica 252 (2020) 251–297. date_created: 2021-02-25T08:55:03Z date_published: 2020-03-01T00:00:00Z date_updated: 2023-10-17T09:15:53Z day: '01' department: - _id: JuFi - _id: GradSch doi: 10.4064/sm180411-11-2 external_id: arxiv: - '1709.05202' isi: - '000558100500002' intvolume: ' 252' isi: 1 issue: '3' keyword: - General Mathematics language: - iso: eng month: '03' oa_version: Preprint page: 251-297 publication: Studia Mathematica publication_identifier: eissn: - 1730-6337 issn: - 0039-3223 publication_status: published publisher: Instytut Matematyczny quality_controlled: '1' scopus_import: '1' status: public title: Modelled distributions of Triebel–Lizorkin type type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 252 year: '2020' ... --- _id: '7464' abstract: - lang: eng text: 'Retrovirus assembly is driven by the multidomain structural protein Gag. Interactions between the capsid domains (CA) of Gag result in Gag multimerization, leading to an immature virus particle that is formed by a protein lattice based on dimeric, trimeric, and hexameric protein contacts. Among retroviruses the inter- and intra-hexamer contacts differ, especially in the N-terminal sub-domain of CA (CANTD). For HIV-1 the cellular molecule inositol hexakisphosphate (IP6) interacts with and stabilizes the immature hexamer, and is required for production of infectious virus particles. We have used in vitro assembly, cryo-electron tomography and subtomogram averaging, atomistic molecular dynamics simulations and mutational analyses to study the HIV-related lentivirus equine infectious anemia virus (EIAV). In particular, we sought to understand the structural conservation of the immature lentivirus lattice and the role of IP6 in EIAV assembly. Similar to HIV-1, IP6 strongly promoted in vitro assembly of EIAV Gag proteins into virus-like particles (VLPs), which took three morphologically highly distinct forms: narrow tubes, wide tubes, and spheres. Structural characterization of these VLPs to sub-4Å resolution unexpectedly showed that all three morphologies are based on an immature lattice with preserved key structural components, highlighting the structural versatility of CA to form immature assemblies. A direct comparison between EIAV and HIV revealed that both lentiviruses maintain similar immature interfaces, which are established by both conserved and non-conserved residues. In both EIAV and HIV-1, IP6 regulates immature assembly via conserved lysine residues within the CACTD and SP. Lastly, we demonstrate that IP6 stimulates in vitro assembly of immature particles of several other retroviruses in the lentivirus genus, suggesting a conserved role for IP6 in lentiviral assembly.' acknowledged_ssus: - _id: ScienComp article_number: e1008277 article_processing_charge: No article_type: original author: - first_name: Robert A. full_name: Dick, Robert A. last_name: Dick - first_name: Chaoyi full_name: Xu, Chaoyi last_name: Xu - first_name: Dustin R. full_name: Morado, Dustin R. last_name: Morado - first_name: Vladyslav full_name: Kravchuk, Vladyslav id: 4D62F2A6-F248-11E8-B48F-1D18A9856A87 last_name: Kravchuk orcid: 0000-0001-9523-9089 - first_name: Clifton L. full_name: Ricana, Clifton L. last_name: Ricana - first_name: Terri D. full_name: Lyddon, Terri D. last_name: Lyddon - first_name: Arianna M. full_name: Broad, Arianna M. last_name: Broad - first_name: J. Ryan full_name: Feathers, J. Ryan last_name: Feathers - first_name: Marc C. full_name: Johnson, Marc C. last_name: Johnson - first_name: Volker M. full_name: Vogt, Volker M. last_name: Vogt - first_name: Juan R. full_name: Perilla, Juan R. last_name: Perilla - first_name: John A. G. full_name: Briggs, John A. G. last_name: Briggs - first_name: Florian KM full_name: Schur, Florian KM id: 48AD8942-F248-11E8-B48F-1D18A9856A87 last_name: Schur orcid: 0000-0003-4790-8078 citation: ama: Dick RA, Xu C, Morado DR, et al. Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly. PLOS Pathogens. 2020;16(1). doi:10.1371/journal.ppat.1008277 apa: Dick, R. A., Xu, C., Morado, D. R., Kravchuk, V., Ricana, C. L., Lyddon, T. D., … Schur, F. K. (2020). Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly. PLOS Pathogens. Public Library of Science. https://doi.org/10.1371/journal.ppat.1008277 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. 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. 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. 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). date_created: 2020-02-06T18:47:17Z date_published: 2020-01-27T00:00:00Z date_updated: 2023-10-17T12:29:34Z day: '27' ddc: - '570' department: - _id: FlSc doi: 10.1371/journal.ppat.1008277 external_id: isi: - '000510746400010' pmid: - '31986188' file: - access_level: open_access checksum: a297f54d1fef0efe4789ca00f37f241e content_type: application/pdf creator: dernst date_created: 2020-02-11T10:07:28Z date_updated: 2020-07-14T12:47:59Z file_id: '7484' file_name: 2020_PLOSPatho_Dick.pdf file_size: 4551246 relation: main_file file_date_updated: 2020-07-14T12:47:59Z has_accepted_license: '1' intvolume: ' 16' isi: 1 issue: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 26736D6A-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P31445 name: Structural conservation and diversity in retroviral capsid publication: PLOS Pathogens publication_identifier: issn: - 1553-7374 publication_status: published publisher: Public Library of Science quality_controlled: '1' related_material: record: - id: '9723' relation: research_data status: deleted scopus_import: '1' status: public title: Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 16 year: '2020' ... --- _id: '7212' 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. article_number: e1007494 article_processing_charge: No article_type: original author: - first_name: Josef full_name: Tkadlec, Josef id: 3F24CCC8-F248-11E8-B48F-1D18A9856A87 last_name: Tkadlec orcid: 0000-0002-1097-9684 - first_name: Andreas full_name: Pavlogiannis, Andreas id: 49704004-F248-11E8-B48F-1D18A9856A87 last_name: Pavlogiannis orcid: 0000-0002-8943-0722 - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Martin A. full_name: Nowak, Martin A. last_name: Nowak 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 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. 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. 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. mla: Tkadlec, Josef, et al. “Limits on Amplifiers of Natural Selection under Death-Birth Updating.” PLoS Computational Biology, vol. 16, e1007494, Public Library of Science, 2020, doi:10.1371/journal.pcbi.1007494. short: J. Tkadlec, A. Pavlogiannis, K. Chatterjee, M.A. Nowak, PLoS Computational Biology 16 (2020). date_created: 2019-12-23T13:45:11Z date_published: 2020-01-17T00:00:00Z date_updated: 2023-10-17T12:29:47Z day: '17' ddc: - '000' department: - _id: KrCh doi: 10.1371/journal.pcbi.1007494 ec_funded: 1 external_id: arxiv: - '1906.02785' isi: - '000510916500025' file: - access_level: open_access checksum: ce32ee2d2f53aed832f78bbd47e882df content_type: application/pdf creator: dernst date_created: 2020-02-03T07:32:42Z date_updated: 2020-07-14T12:47:53Z file_id: '7441' file_name: 2020_PlosCompBio_Tkadlec.pdf file_size: 1817531 relation: main_file file_date_updated: 2020-07-14T12:47:53Z has_accepted_license: '1' intvolume: ' 16' isi: 1 language: - iso: eng month: '01' oa: 1 oa_version: Published Version project: - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory publication: PLoS computational biology publication_identifier: eissn: - '15537358' publication_status: published publisher: Public Library of Science quality_controlled: '1' related_material: record: - id: '7196' relation: part_of_dissertation status: public scopus_import: '1' status: public title: Limits on amplifiers of natural selection under death-Birth updating tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 16 year: '2020' ... --- _id: '7196' abstract: - lang: eng text: 'In this thesis we study certain mathematical aspects of evolution. The two primary forces that drive an evolutionary process are mutation and selection. Mutation generates new variants in a population. Selection chooses among the variants depending on the reproductive rates of individuals. Evolutionary processes are intrinsically random – a new mutation that is initially present in the population at low frequency can go extinct, even if it confers a reproductive advantage. The overall rate of evolution is largely determined by two quantities: the probability that an invading advantageous mutation spreads through the population (called fixation probability) and the time until it does so (called fixation time). Both those quantities crucially depend not only on the strength of the invading mutation but also on the population structure. In this thesis, we aim to understand how the underlying population structure affects the overall rate of evolution. Specifically, we study population structures that increase the fixation probability of advantageous mutants (called amplifiers of selection). Broadly speaking, our results are of three different types: We present various strong amplifiers, we identify regimes under which only limited amplification is feasible, and we propose population structures that provide different tradeoffs between high fixation probability and short fixation time.' alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Josef full_name: Tkadlec, Josef id: 3F24CCC8-F248-11E8-B48F-1D18A9856A87 last_name: Tkadlec orcid: 0000-0002-1097-9684 citation: ama: Tkadlec J. A role of graphs in evolutionary processes. 2020. doi:10.15479/AT:ISTA:7196 apa: Tkadlec, J. (2020). A role of graphs in evolutionary processes. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7196 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. ieee: J. Tkadlec, “A role of graphs in evolutionary processes,” Institute of Science and Technology Austria, 2020. ista: Tkadlec J. 2020. A role of graphs in evolutionary processes. Institute of Science and Technology Austria. mla: Tkadlec, Josef. A Role of Graphs in Evolutionary Processes. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7196. short: J. Tkadlec, A Role of Graphs in Evolutionary Processes, Institute of Science and Technology Austria, 2020. date_created: 2019-12-20T12:26:36Z date_published: 2020-01-12T00:00:00Z date_updated: 2023-10-17T12:29:46Z day: '12' ddc: - '519' degree_awarded: PhD department: - _id: KrCh - _id: GradSch doi: 10.15479/AT:ISTA:7196 file: - access_level: closed checksum: 451f8e64b0eb26bf297644ac72bfcbe9 content_type: application/zip creator: jtkadlec date_created: 2020-01-12T11:49:49Z date_updated: 2020-07-14T12:47:52Z file_id: '7255' file_name: thesis.zip file_size: 21100497 relation: source_file - access_level: open_access checksum: d8c44cbc4f939c49a8efc9d4b8bb3985 content_type: application/pdf creator: dernst date_created: 2020-01-28T07:32:42Z date_updated: 2020-07-14T12:47:52Z file_id: '7367' file_name: 2020_Tkadlec_Thesis.pdf file_size: 11670983 relation: main_file file_date_updated: 2020-07-14T12:47:52Z has_accepted_license: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: '144' publication_identifier: eissn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '7210' relation: dissertation_contains status: public - id: '5751' relation: dissertation_contains status: public - id: '7212' relation: dissertation_contains status: public status: public supervisor: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X title: A role of graphs in evolutionary processes type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2020' ... --- _id: '9198' 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." 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. article_processing_charge: No author: - first_name: Alexander full_name: Shevchenko, Alexander last_name: Shevchenko - first_name: Marco full_name: Mondelli, Marco id: 27EB676C-8706-11E9-9510-7717E6697425 last_name: Mondelli orcid: 0000-0002-3242-7020 citation: 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.' 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. 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. 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. 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. date_created: 2021-02-25T09:36:22Z date_published: 2020-07-13T00:00:00Z date_updated: 2023-10-17T12:43:19Z day: '13' ddc: - '000' department: - _id: MaMo external_id: arxiv: - '1912.10095' file: - access_level: open_access checksum: f042c8d4316bd87c6361aa76f1fbdbbe content_type: application/pdf creator: dernst date_created: 2021-03-02T15:38:14Z date_updated: 2021-03-02T15:38:14Z file_id: '9217' file_name: 2020_PMLR_Shevchenko.pdf file_size: 5336380 relation: main_file success: 1 file_date_updated: 2021-03-02T15:38:14Z has_accepted_license: '1' intvolume: ' 119' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: 8773-8784 project: - _id: 059876FA-7A3F-11EA-A408-12923DDC885E name: Prix Lopez-Loretta 2019 - Marco Mondelli publication: Proceedings of the 37th International Conference on Machine Learning publication_status: published publisher: ML Research Press quality_controlled: '1' status: public title: Landscape connectivity and dropout stability of SGD solutions for over-parameterized neural networks type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 119 year: '2020' ... --- _id: '9157' 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. 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)." article_processing_charge: No article_type: original author: - first_name: Arseniy full_name: Akopyan, Arseniy id: 430D2C90-F248-11E8-B48F-1D18A9856A87 last_name: Akopyan orcid: 0000-0002-2548-617X - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 citation: 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 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 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. 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. ista: Akopyan A, Edelsbrunner H. 2020. The weighted mean curvature derivative of a space-filling diagram. Computational and Mathematical Biophysics. 8(1), 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. short: A. Akopyan, H. Edelsbrunner, Computational and Mathematical Biophysics 8 (2020) 51–67. date_created: 2021-02-17T15:13:01Z date_published: 2020-06-20T00:00:00Z date_updated: 2023-10-17T12:34:51Z day: '20' ddc: - '510' department: - _id: HeEd doi: 10.1515/cmb-2020-0100 ec_funded: 1 file: - access_level: open_access checksum: cea41de9937d07a3b927d71ee8b4e432 content_type: application/pdf creator: dernst date_created: 2021-02-19T13:56:24Z date_updated: 2021-02-19T13:56:24Z file_id: '9171' file_name: 2020_CompMathBiophysics_Akopyan2.pdf file_size: 562359 relation: main_file success: 1 file_date_updated: 2021-02-19T13:56:24Z has_accepted_license: '1' intvolume: ' 8' issue: '1' language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: 51-67 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 grant_number: I02979-N35 name: Persistence and stability of geometric complexes publication: Computational and Mathematical Biophysics publication_identifier: issn: - 2544-7297 publication_status: published publisher: De Gruyter quality_controlled: '1' status: public title: The weighted mean curvature derivative of a space-filling diagram tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8 year: '2020' ... --- _id: '9156' abstract: - lang: eng 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. 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)." article_processing_charge: No article_type: original author: - first_name: Arseniy full_name: Akopyan, Arseniy id: 430D2C90-F248-11E8-B48F-1D18A9856A87 last_name: Akopyan orcid: 0000-0002-2548-617X - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 citation: 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 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. 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. 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. short: A. Akopyan, H. Edelsbrunner, Computational and Mathematical Biophysics 8 (2020) 74–88. date_created: 2021-02-17T15:12:44Z date_published: 2020-07-21T00:00:00Z date_updated: 2023-10-17T12:35:10Z day: '21' ddc: - '510' department: - _id: HeEd doi: 10.1515/cmb-2020-0101 ec_funded: 1 external_id: arxiv: - '1908.06777' file: - access_level: open_access checksum: ca43a7440834eab6bbea29c59b56ef3a content_type: application/pdf creator: dernst date_created: 2021-02-19T13:33:19Z date_updated: 2021-02-19T13:33:19Z file_id: '9170' file_name: 2020_CompMathBiophysics_Akopyan.pdf file_size: 707452 relation: main_file success: 1 file_date_updated: 2021-02-19T13:33:19Z has_accepted_license: '1' intvolume: ' 8' issue: '1' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: 74-88 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 grant_number: I02979-N35 name: Persistence and stability of geometric complexes publication: Computational and Mathematical Biophysics publication_identifier: issn: - 2544-7297 publication_status: published publisher: De Gruyter quality_controlled: '1' status: public title: The weighted Gaussian curvature derivative of a space-filling diagram tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8 year: '2020' ... --- _id: '8973' 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. 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)." article_number: '138' article_processing_charge: No article_type: original author: - first_name: Frank full_name: Redig, Frank last_name: Redig - first_name: Ellen full_name: Saada, Ellen last_name: Saada - first_name: Federico full_name: Sau, Federico id: E1836206-9F16-11E9-8814-AEFDE5697425 last_name: Sau citation: 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.' 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.' ista: 'Redig F, Saada E, Sau F. 2020. Symmetric simple exclusion process in dynamic environment: Hydrodynamics. Electronic Journal of Probability. 25, 138.' 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). date_created: 2020-12-27T23:01:17Z date_published: 2020-10-21T00:00:00Z date_updated: 2023-10-17T12:51:56Z day: '21' ddc: - '510' department: - _id: JaMa doi: 10.1214/20-EJP536 ec_funded: 1 external_id: arxiv: - '1811.01366' isi: - '000591737500001' file: - access_level: open_access checksum: d75359b9814e78d57c0a481b7cde3751 content_type: application/pdf creator: dernst date_created: 2020-12-28T08:24:08Z date_updated: 2020-12-28T08:24:08Z file_id: '8976' file_name: 2020_ElectronJProbab_Redig.pdf file_size: 696653 relation: main_file success: 1 file_date_updated: 2020-12-28T08:24:08Z has_accepted_license: '1' intvolume: ' 25' isi: 1 language: - iso: eng month: '10' oa: 1 oa_version: Published Version project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Electronic Journal of Probability publication_identifier: eissn: - 1083-6489 publication_status: published publisher: ' Institute of Mathematical Statistics' quality_controlled: '1' scopus_import: '1' status: public title: 'Symmetric simple exclusion process in dynamic environment: Hydrodynamics' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 25 year: '2020' ... --- _id: '179' 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. article_processing_charge: No article_type: original author: - first_name: Timothy D full_name: Browning, Timothy D id: 35827D50-F248-11E8-B48F-1D18A9856A87 last_name: Browning orcid: 0000-0002-8314-0177 - first_name: Roger full_name: Heath Brown, Roger last_name: Heath Brown citation: 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 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 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. 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. ista: Browning TD, Heath Brown R. 2020. Density of rational points on a quadric bundle in ℙ3×ℙ3. Duke Mathematical Journal. 169(16), 3099–3165. mla: Browning, Timothy D., and Roger Heath Brown. “Density of Rational Points on a Quadric Bundle in ℙ3×ℙ3.” Duke Mathematical Journal, vol. 169, no. 16, Duke University Press, 2020, pp. 3099–165, doi:10.1215/00127094-2020-0031. short: T.D. Browning, R. Heath Brown, Duke Mathematical Journal 169 (2020) 3099–3165. date_created: 2018-12-11T11:45:02Z date_published: 2020-09-10T00:00:00Z date_updated: 2023-10-17T12:51:10Z day: '10' department: - _id: TiBr doi: 10.1215/00127094-2020-0031 external_id: arxiv: - '1805.10715' isi: - '000582676300002' intvolume: ' 169' isi: 1 issue: '16' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1805.10715 month: '09' oa: 1 oa_version: Preprint page: 3099-3165 publication: Duke Mathematical Journal publication_identifier: issn: - 0012-7094 publication_status: published publisher: Duke University Press quality_controlled: '1' status: public title: Density of rational points on a quadric bundle in ℙ3×ℙ3 type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 169 year: '2020' ... --- _id: '9814' abstract: - lang: eng text: Data and mathematica notebooks for plotting figures from Language learning with communication between learners article_processing_charge: No author: - first_name: Rasmus full_name: Ibsen-Jensen, Rasmus id: 3B699956-F248-11E8-B48F-1D18A9856A87 last_name: Ibsen-Jensen orcid: 0000-0003-4783-0389 - first_name: Josef full_name: Tkadlec, Josef id: 3F24CCC8-F248-11E8-B48F-1D18A9856A87 last_name: Tkadlec orcid: 0000-0002-1097-9684 - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Martin full_name: Nowak, Martin last_name: Nowak 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 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. 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. 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. 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. short: R. Ibsen-Jensen, J. Tkadlec, K. Chatterjee, M. Nowak, (2020). date_created: 2021-08-06T13:09:57Z date_published: 2020-10-15T00:00:00Z date_updated: 2023-10-18T06:36:00Z day: '15' department: - _id: KrCh doi: 10.6084/m9.figshare.5973013.v1 main_file_link: - open_access: '1' url: https://doi.org/10.6084/m9.figshare.5973013.v1 month: '10' oa: 1 oa_version: Published Version publisher: Royal Society related_material: record: - id: '198' relation: used_in_publication status: public status: public title: Data and mathematica notebooks for plotting figures from language learning with communication between learners from language acquisition with communication between learners type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2020' ... --- _id: '8285' abstract: - lang: eng text: We demonstrate the utility of optical cavity generated spin-squeezed states in free space atomic fountain clocks in ensembles of 390 000 87Rb atoms. Fluorescence imaging, correlated to an initial quantum nondemolition measurement, is used for population spectroscopy after the atoms are released from a confining lattice. For a free fall time of 4 milliseconds, we resolve a single-shot phase sensitivity of 814(61) microradians, which is 5.8(0.6) decibels (dB) below the quantum projection limit. We observe that this squeezing is preserved as the cloud expands to a roughly 200  μm radius and falls roughly 300  μm in free space. Ramsey spectroscopy with 240 000 atoms at a 3.6 ms Ramsey time results in a single-shot fractional frequency stability of 8.4(0.2)×10−12, 3.8(0.2) dB below the quantum projection limit. The sensitivity and stability are limited by the technical noise in the fluorescence detection protocol and the microwave system, respectively. 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). article_number: '043202' article_processing_charge: No article_type: original author: - first_name: Benjamin K. full_name: Malia, Benjamin K. last_name: Malia - first_name: Julián full_name: Martínez-Rincón, Julián last_name: Martínez-Rincón - first_name: Yunfan full_name: Wu, Yunfan last_name: Wu - first_name: Onur full_name: Hosten, Onur id: 4C02D85E-F248-11E8-B48F-1D18A9856A87 last_name: Hosten orcid: 0000-0002-2031-204X - first_name: Mark A. full_name: Kasevich, Mark A. last_name: Kasevich citation: 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 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. 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. 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). date_created: 2020-08-24T06:24:04Z date_published: 2020-07-24T00:00:00Z date_updated: 2023-10-18T08:38:35Z day: '24' department: - _id: OnHo doi: 10.1103/PhysRevLett.125.043202 external_id: arxiv: - '1912.10218' isi: - '000552227400008' pmid: - '32794788' intvolume: ' 125' isi: 1 issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1912.10218 month: '07' oa: 1 oa_version: Preprint pmid: 1 publication: Physical Review Letters publication_identifier: eissn: - 1079-7114 issn: - 0031-9007 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: Free space Ramsey spectroscopy in rubidium with noise below the quantum projection limit type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 125 year: '2020' ...