[{"external_id":{"pmid":["37542157"],"isi":["001042544100001"]},"isi":1,"year":"2023","acknowledgement":"We thank Marton Gulyas (ELTE Eötvös University) for development of videomicroscopy experiment manager and image analysis software. Authors are grateful to Gabor Forgacs (University of Missouri) for critical reading of earlier versions of this manuscript as well as to Zsuzsa Akos and Andras Czirok (ELTE Eötvös University) for fruitful discussions. This work was supported by EU FP7, ERC COLLMOT Project No 227878 to TV, the National Research Development and Innovation Fund of Hungary, K119359 and also Project No 2018-1.2.1-NKP-2018-00005 to LN. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 955576. MV was supported by the Ja´nos Bolyai Fellowship of the Hungarian Academy of Sciences.\r\nOpen access funding provided by Eötvös Loránd University.","date_published":"2023-08-04T00:00:00Z","pmid":1,"status":"public","publication":"Communications Biology","type":"journal_article","date_updated":"2023-12-13T12:07:33Z","_id":"14041","publisher":"Springer Nature","doi":"10.1038/s42003-023-05181-7","article_processing_charge":"Yes","quality_controlled":"1","ddc":["570"],"article_number":"817","file":[{"file_id":"14045","creator":"dernst","date_updated":"2023-08-14T07:17:36Z","date_created":"2023-08-14T07:17:36Z","file_size":10181997,"checksum":"1f9324f736bdbb76426b07736651c4cd","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_name":"2023_CommBiology_Mehes.pdf"}],"department":[{"_id":"CaHe"},{"_id":"Bio"}],"month":"08","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Méhes E, Mones E, Varga M, Zsigmond Á, Biri-Kovács B, Nyitray L, Barone V, Krens G, Heisenberg C-PJ, Vicsek T. 2023. 3D cell segregation geometry and dynamics are governed by tissue surface tension regulation. Communications Biology. 6, 817.","chicago":"Méhes, Elod, Enys Mones, Máté Varga, Áron Zsigmond, Beáta Biri-Kovács, László Nyitray, Vanessa Barone, Gabriel Krens, Carl-Philipp J Heisenberg, and Tamás Vicsek. “3D Cell Segregation Geometry and Dynamics Are Governed by Tissue Surface Tension Regulation.” <i>Communications Biology</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s42003-023-05181-7\">https://doi.org/10.1038/s42003-023-05181-7</a>.","apa":"Méhes, E., Mones, E., Varga, M., Zsigmond, Á., Biri-Kovács, B., Nyitray, L., … Vicsek, T. (2023). 3D cell segregation geometry and dynamics are governed by tissue surface tension regulation. <i>Communications Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s42003-023-05181-7\">https://doi.org/10.1038/s42003-023-05181-7</a>","mla":"Méhes, Elod, et al. “3D Cell Segregation Geometry and Dynamics Are Governed by Tissue Surface Tension Regulation.” <i>Communications Biology</i>, vol. 6, 817, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s42003-023-05181-7\">10.1038/s42003-023-05181-7</a>.","ama":"Méhes E, Mones E, Varga M, et al. 3D cell segregation geometry and dynamics are governed by tissue surface tension regulation. <i>Communications Biology</i>. 2023;6. doi:<a href=\"https://doi.org/10.1038/s42003-023-05181-7\">10.1038/s42003-023-05181-7</a>","ieee":"E. Méhes <i>et al.</i>, “3D cell segregation geometry and dynamics are governed by tissue surface tension regulation,” <i>Communications Biology</i>, vol. 6. Springer Nature, 2023.","short":"E. Méhes, E. Mones, M. Varga, Á. Zsigmond, B. Biri-Kovács, L. Nyitray, V. Barone, G. Krens, C.-P.J. Heisenberg, T. Vicsek, Communications Biology 6 (2023)."},"language":[{"iso":"eng"}],"oa":1,"article_type":"original","date_created":"2023-08-13T22:01:13Z","volume":6,"title":"3D cell segregation geometry and dynamics are governed by tissue surface tension regulation","oa_version":"Published Version","author":[{"first_name":"Elod","full_name":"Méhes, Elod","last_name":"Méhes"},{"first_name":"Enys","full_name":"Mones, Enys","last_name":"Mones"},{"first_name":"Máté","last_name":"Varga","full_name":"Varga, Máté"},{"last_name":"Zsigmond","full_name":"Zsigmond, Áron","first_name":"Áron"},{"last_name":"Biri-Kovács","full_name":"Biri-Kovács, Beáta","first_name":"Beáta"},{"first_name":"László","last_name":"Nyitray","full_name":"Nyitray, László"},{"last_name":"Barone","full_name":"Barone, Vanessa","id":"419EECCC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2676-3367","first_name":"Vanessa"},{"first_name":"Gabriel","orcid":"0000-0003-4761-5996","last_name":"Krens","id":"2B819732-F248-11E8-B48F-1D18A9856A87","full_name":"Krens, Gabriel"},{"orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg"},{"full_name":"Vicsek, Tamás","last_name":"Vicsek","first_name":"Tamás"}],"scopus_import":"1","day":"04","publication_identifier":{"eissn":["2399-3642"]},"publication_status":"published","file_date_updated":"2023-08-14T07:17:36Z","intvolume":"         6","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"abstract":[{"text":"Tissue morphogenesis and patterning during development involve the segregation of cell types. Segregation is driven by differential tissue surface tensions generated by cell types through controlling cell-cell contact formation by regulating adhesion and actomyosin contractility-based cellular cortical tensions. We use vertebrate tissue cell types and zebrafish germ layer progenitors as in vitro models of 3-dimensional heterotypic segregation and developed a quantitative analysis of their dynamics based on 3D time-lapse microscopy. We show that general inhibition of actomyosin contractility by the Rho kinase inhibitor Y27632 delays segregation. Cell type-specific inhibition of non-muscle myosin2 activity by overexpression of myosin assembly inhibitor S100A4 reduces tissue surface tension, manifested in decreased compaction during aggregation and inverted geometry observed during segregation. The same is observed when we express a constitutively active Rho kinase isoform to ubiquitously keep actomyosin contractility high at cell-cell and cell-medium interfaces and thus overriding the interface-specific regulation of cortical tensions. Tissue surface tension regulation can become an effective tool in tissue engineering.","lang":"eng"}],"has_accepted_license":"1"},{"volume":25,"article_type":"original","date_created":"2023-08-13T22:01:13Z","author":[{"first_name":"Miroslav","last_name":"Bulíček","full_name":"Bulíček, Miroslav"},{"full_name":"Málek, Josef","last_name":"Málek","first_name":"Josef"},{"id":"dbabca31-66eb-11eb-963a-fb9c22c880b4","full_name":"Maringová, Erika","last_name":"Maringová","first_name":"Erika"}],"day":"01","scopus_import":"1","oa_version":"Published Version","title":"On unsteady internal flows of incompressible fluids characterized by implicit constitutive equations in the bulk and on the boundary","publication_identifier":{"issn":["1422-6928"],"eissn":["1422-6952"]},"publication_status":"published","file_date_updated":"2023-08-14T07:24:17Z","has_accepted_license":"1","intvolume":"        25","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"abstract":[{"text":"Long-time and large-data existence of weak solutions for initial- and boundary-value problems concerning three-dimensional flows of incompressible fluids is nowadays available not only for Navier–Stokes fluids but also for various fluid models where the relation between the Cauchy stress tensor and the symmetric part of the velocity gradient is nonlinear. The majority of such studies however concerns models where such a dependence is explicit (the stress is a function of the velocity gradient), which makes the class of studied models unduly restrictive. The same concerns boundary conditions, or more precisely the slipping mechanisms on the boundary, where the no-slip is still the most preferred condition considered in the literature. Our main objective is to develop a robust mathematical theory for unsteady internal flows of implicitly constituted incompressible fluids with implicit relations between the tangential projections of the velocity and the normal traction on the boundary. The theory covers numerous rheological models used in chemistry, biorheology, polymer and food industry as well as in geomechanics. It also includes, as special cases, nonlinear slip as well as stick–slip boundary conditions. Unlike earlier studies, the conditions characterizing admissible classes of constitutive equations are expressed by means of tools of elementary calculus. In addition, a fully constructive proof (approximation scheme) is incorporated. Finally, we focus on the question of uniqueness of such weak solutions.","lang":"eng"}],"department":[{"_id":"JuFi"}],"file":[{"access_level":"open_access","content_type":"application/pdf","success":1,"file_name":"2023_JourMathFluidMech_Bulicek.pdf","checksum":"c549cd8f0dd02ed60477a05ca045f481","relation":"main_file","creator":"dernst","date_updated":"2023-08-14T07:24:17Z","file_size":845748,"date_created":"2023-08-14T07:24:17Z","file_id":"14046"}],"article_number":"72","arxiv":1,"month":"08","issue":"3","citation":{"ieee":"M. Bulíček, J. Málek, and E. Maringová, “On unsteady internal flows of incompressible fluids characterized by implicit constitutive equations in the bulk and on the boundary,” <i>Journal of Mathematical Fluid Mechanics</i>, vol. 25, no. 3. Springer Nature, 2023.","short":"M. Bulíček, J. Málek, E. Maringová, Journal of Mathematical Fluid Mechanics 25 (2023).","ama":"Bulíček M, Málek J, Maringová E. On unsteady internal flows of incompressible fluids characterized by implicit constitutive equations in the bulk and on the boundary. <i>Journal of Mathematical Fluid Mechanics</i>. 2023;25(3). doi:<a href=\"https://doi.org/10.1007/s00021-023-00803-w\">10.1007/s00021-023-00803-w</a>","apa":"Bulíček, M., Málek, J., &#38; Maringová, E. (2023). On unsteady internal flows of incompressible fluids characterized by implicit constitutive equations in the bulk and on the boundary. <i>Journal of Mathematical Fluid Mechanics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00021-023-00803-w\">https://doi.org/10.1007/s00021-023-00803-w</a>","mla":"Bulíček, Miroslav, et al. “On Unsteady Internal Flows of Incompressible Fluids Characterized by Implicit Constitutive Equations in the Bulk and on the Boundary.” <i>Journal of Mathematical Fluid Mechanics</i>, vol. 25, no. 3, 72, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1007/s00021-023-00803-w\">10.1007/s00021-023-00803-w</a>.","ista":"Bulíček M, Málek J, Maringová E. 2023. On unsteady internal flows of incompressible fluids characterized by implicit constitutive equations in the bulk and on the boundary. Journal of Mathematical Fluid Mechanics. 25(3), 72.","chicago":"Bulíček, Miroslav, Josef Málek, and Erika Maringová. “On Unsteady Internal Flows of Incompressible Fluids Characterized by Implicit Constitutive Equations in the Bulk and on the Boundary.” <i>Journal of Mathematical Fluid Mechanics</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s00021-023-00803-w\">https://doi.org/10.1007/s00021-023-00803-w</a>."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"language":[{"iso":"eng"}],"date_updated":"2023-12-13T12:08:08Z","_id":"14042","type":"journal_article","doi":"10.1007/s00021-023-00803-w","article_processing_charge":"Yes (via OA deal)","publisher":"Springer Nature","quality_controlled":"1","ddc":["510"],"isi":1,"year":"2023","external_id":{"arxiv":["2301.12834"],"isi":["001040354900001"]},"acknowledgement":"M. Bulíček and J. Málek acknowledge the support of the project No. 20-11027X financed by the Czech Science foundation (GAČR). M. Bulíček and J. Málek are members of the Nečas Center for Mathematical Modelling.\r\nOpen access publishing supported by the National Technical Library in Prague.","date_published":"2023-08-01T00:00:00Z","status":"public","publication":"Journal of Mathematical Fluid Mechanics"},{"month":"12","arxiv":1,"department":[{"_id":"MoHe"}],"oa":1,"language":[{"iso":"eng"}],"citation":{"ista":"Henzinger MH, Jin B, Peng R, Williamson DP. 2023. A combinatorial cut-toggling algorithm for solving Laplacian linear systems. Algorithmica. 85, 2680–3716.","chicago":"Henzinger, Monika H, Billy Jin, Richard Peng, and David P. Williamson. “A Combinatorial Cut-Toggling Algorithm for Solving Laplacian Linear Systems.” <i>Algorithmica</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s00453-023-01154-8\">https://doi.org/10.1007/s00453-023-01154-8</a>.","apa":"Henzinger, M. H., Jin, B., Peng, R., &#38; Williamson, D. P. (2023). A combinatorial cut-toggling algorithm for solving Laplacian linear systems. <i>Algorithmica</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00453-023-01154-8\">https://doi.org/10.1007/s00453-023-01154-8</a>","mla":"Henzinger, Monika H., et al. “A Combinatorial Cut-Toggling Algorithm for Solving Laplacian Linear Systems.” <i>Algorithmica</i>, vol. 85, Springer Nature, 2023, pp. 2680–3716, doi:<a href=\"https://doi.org/10.1007/s00453-023-01154-8\">10.1007/s00453-023-01154-8</a>.","ama":"Henzinger MH, Jin B, Peng R, Williamson DP. A combinatorial cut-toggling algorithm for solving Laplacian linear systems. <i>Algorithmica</i>. 2023;85:2680-3716. doi:<a href=\"https://doi.org/10.1007/s00453-023-01154-8\">10.1007/s00453-023-01154-8</a>","ieee":"M. H. Henzinger, B. Jin, R. Peng, and D. P. Williamson, “A combinatorial cut-toggling algorithm for solving Laplacian linear systems,” <i>Algorithmica</i>, vol. 85. Springer Nature, pp. 2680–3716, 2023.","short":"M.H. Henzinger, B. Jin, R. Peng, D.P. Williamson, Algorithmica 85 (2023) 2680–3716."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","scopus_import":"1","author":[{"last_name":"Henzinger","full_name":"Henzinger, Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","first_name":"Monika H","orcid":"0000-0002-5008-6530"},{"first_name":"Billy","last_name":"Jin","full_name":"Jin, Billy"},{"full_name":"Peng, Richard","last_name":"Peng","first_name":"Richard"},{"first_name":"David P.","full_name":"Williamson, David P.","last_name":"Williamson"}],"title":"A combinatorial cut-toggling algorithm for solving Laplacian linear systems","oa_version":"Preprint","volume":85,"date_created":"2023-08-13T22:01:13Z","article_type":"original","abstract":[{"lang":"eng","text":"Over the last two decades, a significant line of work in theoretical algorithms has made progress in solving linear systems of the form Lx=b, where L is the Laplacian matrix of a weighted graph with weights w(i,j)>0 on the edges. The solution x of the linear system can be interpreted as the potentials of an electrical flow in which the resistance on edge (i, j) is 1/w(i, j). Kelner et al. (in: Proceedings of the 45th Annual ACM Symposium on the Theory of Computing, pp 911–920, 2013. https://doi.org/10.1145/2488608.2488724) give a combinatorial, near-linear time algorithm that maintains the Kirchoff Current Law, and gradually enforces the Kirchoff Potential Law by updating flows around cycles (cycle toggling). In this paper, we consider a dual version of the algorithm that maintains the Kirchoff Potential Law, and gradually enforces the Kirchoff Current Law by cut toggling: each iteration updates all potentials on one side of a fundamental cut of a spanning tree by the same amount. We prove that this dual algorithm also runs in a near-linear number of iterations. We show, however, that if we abstract cut toggling as a natural data structure problem, this problem can be reduced to the online vector–matrix-vector problem, which has been conjectured to be difficult for dynamic algorithms (Henzinger et al., in: Proceedings of the 47th Annual ACM Symposium on the Theory of Computing, pp 21–30, 2015. https://doi.org/10.1145/2746539.2746609). The conjecture implies that the data structure does not have an O(n1−ϵ) time algorithm for any ϵ>0, and thus a straightforward implementation of the cut-toggling algorithm requires essentially linear time per iteration. To circumvent the lower bound, we batch update steps, and perform them simultaneously instead of sequentially. An appropriate choice of batching leads to an O˜(m1.5) time cut-toggling algorithm for solving Laplacian systems. Furthermore, we show that if we sparsify the graph and call our algorithm recursively on the Laplacian system implied by batching and sparsifying, we can reduce the running time to O(m1+ϵ) for any ϵ>0. Thus, the dual cut-toggling algorithm can achieve (almost) the same running time as its primal cycle-toggling counterpart."}],"intvolume":"        85","publication_identifier":{"issn":["0178-4617"],"eissn":["1432-0541"]},"publication_status":"published","year":"2023","isi":1,"external_id":{"arxiv":["2010.16316"],"isi":["001041254900002"]},"status":"public","publication":"Algorithmica","project":[{"name":"The design and evaluation of modern fully dynamic data structures","grant_number":"101019564","call_identifier":"H2020","_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62"},{"_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe","grant_number":"P33775 ","name":"Fast Algorithms for a Reactive Network Layer"}],"ec_funded":1,"date_published":"2023-12-01T00:00:00Z","acknowledgement":"Monika Henzinger was supported by funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme Grant agreement No. 101019564 “The Design of Modern Fully Dynamic Data Structures (MoDynStruct)” and from the Austrian Science Fund (FWF) project “Fast Algorithms for a Reactive Network Layer (ReactNet)”, P 33775-N, with additional funding from the netidee SCIENCE Stiftung, 2020–2024. Billy Jin was Supported in part by NSERC fellowship PGSD3-532673-2019 and NSF grant CCF-2007009. Richard Peng was supported in part by an NSERC Discovery Grant and NSF grant CCF-1846218. David P. Williamson was supported in part by NSF grant CCF-2007009.","article_processing_charge":"No","doi":"10.1007/s00453-023-01154-8","publisher":"Springer Nature","_id":"14043","date_updated":"2024-01-30T12:33:10Z","type":"journal_article","page":"2680-3716","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2010.16316"}],"quality_controlled":"1"},{"ddc":["576"],"page":"230","publisher":"Institute of Science and Technology Austria","doi":"10.15479/at:ista:14058","article_processing_charge":"No","alternative_title":["ISTA Thesis"],"type":"dissertation","date_updated":"2023-12-13T12:15:36Z","_id":"14058","project":[{"grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"name":"Sexual conflict: resolution, constraints and biomedical implications","grant_number":"25817","_id":"9B9DFC9E-BA93-11EA-9121-9846C619BF3A"}],"status":"public","degree_awarded":"PhD","date_published":"2023-08-15T00:00:00Z","ec_funded":1,"related_material":{"record":[{"status":"public","relation":"research_data","id":"9803"},{"id":"12933","status":"public","relation":"research_data"},{"id":"6831","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"14077"}]},"year":"2023","abstract":[{"text":"Females and males across species are subject to divergent selective pressures arising\r\nfrom di↵erent reproductive interests and ecological niches. This often translates into a\r\nintricate array of sex-specific natural and sexual selection on traits that have a shared\r\ngenetic basis between both sexes, causing a genetic sexual conflict. The resolution of\r\nthis conflict mostly relies on the evolution of sex-specific expression of the shared genes,\r\nleading to phenotypic sexual dimorphism. Such sex-specific gene expression is thought\r\nto evolve via modifications of the genetic networks ultimately linked to sex-determining\r\ntranscription factors. Although much empirical and theoretical evidence supports this\r\nstandard picture of the molecular basis of sexual conflict resolution, there still are a\r\nfew open questions regarding the complex array of selective forces driving phenotypic\r\ndi↵erentiation between the sexes, as well as the molecular mechanisms underlying sexspecific adaptation. I address some of these open questions in my PhD thesis.\r\nFirst, how do patterns of phenotypic sexual dimorphism vary within populations,\r\nas a response to the temporal and spatial changes in sex-specific selective forces? To\r\ntackle this question, I analyze the patterns of sex-specific phenotypic variation along\r\nthree life stages and across populations spanning the whole geographical range of Rumex\r\nhastatulus, a wind-pollinated angiosperm, in the first Chapter of the thesis.\r\nSecond, how do gene expression patterns lead to phenotypic dimorphism, and what\r\nare the molecular mechanisms underlying the observed transcriptomic variation? I\r\naddress this question by examining the sex- and tissue-specific expression variation in\r\nnewly-generated datasets of sex-specific expression in heads and gonads of Drosophila\r\nmelanogaster. I additionally used two complementary approaches for the study of the\r\ngenetic basis of sex di↵erences in gene expression in the second and third Chapters of\r\nthe thesis.\r\nThird, how does intersex correlation, thought to be one of the main aspects constraining the ability for the two sexes to decouple, interact with the evolution of sexual\r\ndimorphism? I develop models of sex-specific stabilizing selection, mutation and drift\r\nto formalize common intuition regarding the patterns of covariation between intersex\r\ncorrelation and sexual dimorphism in the fourth Chapter of the thesis.\r\nAlltogether, the work described in this PhD thesis provides useful insights into the\r\nlinks between genetic, transcriptomic and phenotypic layers of sex-specific variation,\r\nand contributes to our general understanding of the dynamics of sexual dimorphism\r\nevolution.","lang":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"has_accepted_license":"1","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-035-0"]},"publication_status":"published","file_date_updated":"2023-08-18T10:47:55Z","title":"The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation","oa_version":"Published Version","author":[{"id":"33AB266C-F248-11E8-B48F-1D18A9856A87","full_name":"Puixeu Sala, Gemma","last_name":"Puixeu Sala","orcid":"0000-0001-8330-1754","first_name":"Gemma"}],"day":"15","date_created":"2023-08-15T10:20:40Z","language":[{"iso":"eng"}],"oa":1,"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"ama":"Puixeu Sala G. The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:14058\">10.15479/at:ista:14058</a>","short":"G. Puixeu Sala, The Molecular Basis of Sexual Dimorphism: Experimental and Theoretical Characterization of Phenotypic, Transcriptomic and Genetic Patterns of Sex-Specific Adaptation, Institute of Science and Technology Austria, 2023.","ieee":"G. Puixeu Sala, “The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation,” Institute of Science and Technology Austria, 2023.","ista":"Puixeu Sala G. 2023. The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation. Institute of Science and Technology Austria.","chicago":"Puixeu Sala, Gemma. “The Molecular Basis of Sexual Dimorphism: Experimental and Theoretical Characterization of Phenotypic, Transcriptomic and Genetic Patterns of Sex-Specific Adaptation.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:14058\">https://doi.org/10.15479/at:ista:14058</a>.","mla":"Puixeu Sala, Gemma. <i>The Molecular Basis of Sexual Dimorphism: Experimental and Theoretical Characterization of Phenotypic, Transcriptomic and Genetic Patterns of Sex-Specific Adaptation</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:14058\">10.15479/at:ista:14058</a>.","apa":"Puixeu Sala, G. (2023). <i>The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14058\">https://doi.org/10.15479/at:ista:14058</a>"},"month":"08","supervisor":[{"last_name":"Vicoso","full_name":"Vicoso, Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","orcid":"0000-0002-4579-8306"},{"orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"file":[{"checksum":"4e44e169f2724ee8c9324cd60bcc2b71","relation":"source_file","access_level":"closed","content_type":"application/zip","file_name":"Thesis_latex_forpdfa.zip","file_id":"14075","creator":"gpuixeus","date_updated":"2023-08-17T06:55:24Z","file_size":10891454,"date_created":"2023-08-16T18:15:17Z"},{"relation":"main_file","checksum":"e10b04cd8f3fecc0d9ef6e6868b6e1e8","success":1,"file_name":"PhDThesis_PuixeuG.pdf","access_level":"open_access","content_type":"application/pdf","file_id":"14079","date_created":"2023-08-18T10:47:55Z","file_size":19856686,"date_updated":"2023-08-18T10:47:55Z","creator":"gpuixeus"}],"department":[{"_id":"GradSch"},{"_id":"NiBa"},{"_id":"BeVi"}]},{"file":[{"file_id":"14430","date_created":"2023-10-16T07:15:11Z","file_size":867256,"date_updated":"2023-10-16T07:15:11Z","creator":"dernst","relation":"main_file","checksum":"ee33bd6f1a26f4dae7a8192584869fd8","file_name":"2023_LNCS_RV_Chalupa.pdf","success":1,"content_type":"application/pdf","access_level":"open_access"}],"department":[{"_id":"ToHe"}],"month":"10","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Chalupa M, Henzinger TA. 2023. Monitoring hyperproperties with prefix transducers. 23nd International Conference on Runtime Verification. RV: Conference on Runtime Verification, LNCS, vol. 14245, 168–190.","chicago":"Chalupa, Marek, and Thomas A Henzinger. “Monitoring Hyperproperties with Prefix Transducers.” In <i>23nd International Conference on Runtime Verification</i>, 14245:168–90. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/978-3-031-44267-4_9\">https://doi.org/10.1007/978-3-031-44267-4_9</a>.","apa":"Chalupa, M., &#38; Henzinger, T. A. (2023). Monitoring hyperproperties with prefix transducers. In <i>23nd International Conference on Runtime Verification</i> (Vol. 14245, pp. 168–190). Thessaloniki, Greek: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-44267-4_9\">https://doi.org/10.1007/978-3-031-44267-4_9</a>","mla":"Chalupa, Marek, and Thomas A. Henzinger. “Monitoring Hyperproperties with Prefix Transducers.” <i>23nd International Conference on Runtime Verification</i>, vol. 14245, Springer Nature, 2023, pp. 168–90, doi:<a href=\"https://doi.org/10.1007/978-3-031-44267-4_9\">10.1007/978-3-031-44267-4_9</a>.","ama":"Chalupa M, Henzinger TA. Monitoring hyperproperties with prefix transducers. In: <i>23nd International Conference on Runtime Verification</i>. Vol 14245. Springer Nature; 2023:168-190. doi:<a href=\"https://doi.org/10.1007/978-3-031-44267-4_9\">10.1007/978-3-031-44267-4_9</a>","ieee":"M. Chalupa and T. A. Henzinger, “Monitoring hyperproperties with prefix transducers,” in <i>23nd International Conference on Runtime Verification</i>, Thessaloniki, Greek, 2023, vol. 14245, pp. 168–190.","short":"M. Chalupa, T.A. Henzinger, in:, 23nd International Conference on Runtime Verification, Springer Nature, 2023, pp. 168–190."},"language":[{"iso":"eng"}],"oa":1,"date_created":"2023-08-16T20:46:08Z","volume":14245,"oa_version":"Published Version","title":"Monitoring hyperproperties with prefix transducers","author":[{"last_name":"Chalupa","id":"87e34708-d6c6-11ec-9f5b-9391e7be2463","full_name":"Chalupa, Marek","first_name":"Marek"},{"first_name":"Thomas A","orcid":"0000-0002-2985-7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","last_name":"Henzinger"}],"day":"01","publication_status":"published","publication_identifier":{"isbn":["978-3-031-44266-7"],"eisbn":["978-3-031-44267-4"]},"file_date_updated":"2023-10-16T07:15:11Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"abstract":[{"lang":"eng","text":"Hyperproperties are properties that relate multiple execution traces. Previous work on monitoring hyperproperties focused on synchronous hyperproperties, usually specified in HyperLTL. When monitoring synchronous hyperproperties, all traces are assumed to proceed at the same speed. We introduce (multi-trace) prefix transducers and show how to use them for monitoring synchronous as well as, for the first time, asynchronous hyperproperties. Prefix transducers map multiple input traces into one or more output traces by incrementally matching prefixes of the input traces against expressions similar to regular expressions. The prefixes of different traces which are consumed by a single matching step of the monitor may have different lengths. The deterministic and executable nature of prefix transducers makes them more suitable as an intermediate formalism for runtime verification than logical specifications, which tend to be highly non-deterministic, especially in the case of asynchronous hyperproperties. We report on a set of experiments about monitoring asynchronous version of observational determinism."}],"intvolume":"     14245","has_accepted_license":"1","related_material":{"record":[{"relation":"research_data","status":"public","id":"15035"}]},"year":"2023","date_published":"2023-10-01T00:00:00Z","acknowledgement":"This work was supported in part by the ERC-2020-AdG 101020093. The authors would like to thank Ana Oliveira da Costa for commenting on a draft of the paper.","conference":{"location":"Thessaloniki, Greek","end_date":"2023-10-07","start_date":"2023-10-04","name":"RV: Conference on Runtime Verification"},"ec_funded":1,"project":[{"name":"Vigilant Algorithmic Monitoring of Software","grant_number":"101020093","call_identifier":"H2020","_id":"62781420-2b32-11ec-9570-8d9b63373d4d"}],"publication":"23nd International Conference on Runtime Verification","status":"public","type":"conference","date_updated":"2024-02-28T12:33:08Z","_id":"14076","publisher":"Springer Nature","doi":"10.1007/978-3-031-44267-4_9","article_processing_charge":"Yes (in subscription journal)","alternative_title":["LNCS"],"quality_controlled":"1","ddc":["000"],"page":"168-190"},{"month":"08","department":[{"_id":"BeVi"},{"_id":"NiBa"},{"_id":"GradSch"}],"file":[{"checksum":"c62e29fc7c5efbf8356f4c60cab4a2d1","relation":"main_file","content_type":"application/pdf","access_level":"open_access","file_name":"2023_G3_Puixeu.pdf","success":1,"file_id":"14498","creator":"dernst","date_updated":"2023-11-07T09:00:19Z","file_size":845642,"date_created":"2023-11-07T09:00:19Z"}],"oa":1,"language":[{"iso":"eng"}],"citation":{"ama":"Puixeu Sala G, Macon A, Vicoso B. Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster. <i>G3: Genes, Genomes, Genetics</i>. 2023;13(8). doi:<a href=\"https://doi.org/10.1093/g3journal/jkad121\">10.1093/g3journal/jkad121</a>","ieee":"G. Puixeu Sala, A. Macon, and B. Vicoso, “Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster,” <i>G3: Genes, Genomes, Genetics</i>, vol. 13, no. 8. Oxford University Press, 2023.","short":"G. Puixeu Sala, A. Macon, B. Vicoso, G3: Genes, Genomes, Genetics 13 (2023).","ista":"Puixeu Sala G, Macon A, Vicoso B. 2023. Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster. G3: Genes, Genomes, Genetics. 13(8).","chicago":"Puixeu Sala, Gemma, Ariana Macon, and Beatriz Vicoso. “Sex-Specific Estimation of Cis and Trans Regulation of Gene Expression in Heads and Gonads of Drosophila Melanogaster.” <i>G3: Genes, Genomes, Genetics</i>. Oxford University Press, 2023. <a href=\"https://doi.org/10.1093/g3journal/jkad121\">https://doi.org/10.1093/g3journal/jkad121</a>.","apa":"Puixeu Sala, G., Macon, A., &#38; Vicoso, B. (2023). Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster. <i>G3: Genes, Genomes, Genetics</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/g3journal/jkad121\">https://doi.org/10.1093/g3journal/jkad121</a>","mla":"Puixeu Sala, Gemma, et al. “Sex-Specific Estimation of Cis and Trans Regulation of Gene Expression in Heads and Gonads of Drosophila Melanogaster.” <i>G3: Genes, Genomes, Genetics</i>, vol. 13, no. 8, Oxford University Press, 2023, doi:<a href=\"https://doi.org/10.1093/g3journal/jkad121\">10.1093/g3journal/jkad121</a>."},"issue":"8","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","scopus_import":"1","author":[{"orcid":"0000-0001-8330-1754","first_name":"Gemma","last_name":"Puixeu Sala","id":"33AB266C-F248-11E8-B48F-1D18A9856A87","full_name":"Puixeu Sala, Gemma"},{"full_name":"Macon, Ariana","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","last_name":"Macon","first_name":"Ariana"},{"first_name":"Beatriz","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso"}],"title":"Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster","oa_version":"Published Version","volume":13,"date_created":"2023-08-18T06:52:14Z","article_type":"original","has_accepted_license":"1","acknowledged_ssus":[{"_id":"ScienComp"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"abstract":[{"text":"The regulatory architecture of gene expression is known to differ substantially between sexes in Drosophila, but most studies performed\r\nso far used whole-body data and only single crosses, which may have limited their scope to detect patterns that are robust across tissues\r\nand biological replicates. Here, we use allele-specific gene expression of parental and reciprocal hybrid crosses between 6 Drosophila\r\nmelanogaster inbred lines to quantify cis- and trans-regulatory variation in heads and gonads of both sexes separately across 3 replicate\r\ncrosses. Our results suggest that female and male heads, as well as ovaries, have a similar regulatory architecture. On the other hand,\r\ntestes display more and substantially different cis-regulatory effects, suggesting that sex differences in the regulatory architecture that\r\nhave been previously observed may largely derive from testis-specific effects. We also examine the difference in cis-regulatory variation\r\nof genes across different levels of sex bias in gonads and heads. Consistent with the idea that intersex correlations constrain expression\r\nand can lead to sexual antagonism, we find more cis variation in unbiased and moderately biased genes in heads. In ovaries, reduced cis\r\nvariation is observed for male-biased genes, suggesting that cis variants acting on these genes in males do not lead to changes in ovary\r\nexpression. Finally, we examine the dominance patterns of gene expression and find that sex- and tissue-specific patterns of inheritance\r\nas well as trans-regulatory variation are highly variable across biological crosses, although these were performed in highly controlled\r\nexperimental conditions. This highlights the importance of using various genetic backgrounds to infer generalizable patterns.","lang":"eng"}],"intvolume":"        13","file_date_updated":"2023-11-07T09:00:19Z","publication_status":"published","publication_identifier":{"issn":["2160-1836"]},"year":"2023","isi":1,"related_material":{"record":[{"relation":"research_data","status":"public","id":"12933"},{"id":"14058","relation":"dissertation_contains","status":"public"}]},"external_id":{"isi":["001002997200001"]},"keyword":["Genetics (clinical)","Genetics","Molecular Biology"],"publication":"G3: Genes, Genomes, Genetics","status":"public","project":[{"call_identifier":"H2020","grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"name":"Sexual conflict: resolution, constraints and biomedical implications","grant_number":"25817","_id":"9B9DFC9E-BA93-11EA-9121-9846C619BF3A"}],"ec_funded":1,"date_published":"2023-08-01T00:00:00Z","acknowledgement":"We thank members of the Vicoso Group for comments on the manuscript, the Scientific Computing Unit at ISTA for technical support, and 2 anonymous reviewers for useful feedback. GP is the recipient of a DOC Fellowship of the Austrian Academy of Sciences at the Institute of Science and Technology Austria (DOC 25817) and received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant (agreement no. 665385).","article_processing_charge":"Yes","doi":"10.1093/g3journal/jkad121","publisher":"Oxford University Press","_id":"14077","date_updated":"2023-12-13T12:15:37Z","type":"journal_article","ddc":["570"],"quality_controlled":"1"},{"status":"public","publication":"Current Opinion in Cell Biology","pmid":1,"acknowledgement":"TH was supported by JSPS KAKENHI Grant (no. 21H05290) and the Ministry of Education under the Research Centres of Excellence programme through the Mechanobiology Institute at National University of Singapore and by Department of Physiology at National University of Singapore. NH was supported by JSPS KAKENHI Grant (no. 20K22653). KA was supported by JSPS KAKENHI Grants (no. 19H05798 and no. 22H02625). MM was supported by JSPS KAKENHI Grants (no. 19H00993 and no. 20H05898) and JST Moonshot R&D Grant JPMJPS2022. We appreciate Virgile Viasnoff and the lab members for their valuable comments on the manuscript. We apologize to authors whose work could not be highlighted due to space limitations.","date_published":"2023-10-01T00:00:00Z","isi":1,"year":"2023","external_id":{"pmid":["37574635"],"isi":["001054692200001"]},"ddc":["570"],"quality_controlled":"1","doi":"10.1016/j.ceb.2023.102217","article_processing_charge":"Yes (in subscription journal)","publisher":"Elsevier","date_updated":"2024-01-30T12:52:42Z","_id":"14080","type":"journal_article","oa":1,"language":[{"iso":"eng"}],"issue":"10","citation":{"ama":"Hirashima T, Hino N, Aoki K, Matsuda M. Stretching the limits of extracellular signal-related kinase (ERK) signaling — Cell mechanosensing to ERK activation. <i>Current Opinion in Cell Biology</i>. 2023;84(10). doi:<a href=\"https://doi.org/10.1016/j.ceb.2023.102217\">10.1016/j.ceb.2023.102217</a>","short":"T. Hirashima, N. Hino, K. Aoki, M. Matsuda, Current Opinion in Cell Biology 84 (2023).","ieee":"T. Hirashima, N. Hino, K. Aoki, and M. Matsuda, “Stretching the limits of extracellular signal-related kinase (ERK) signaling — Cell mechanosensing to ERK activation,” <i>Current Opinion in Cell Biology</i>, vol. 84, no. 10. Elsevier, 2023.","chicago":"Hirashima, Tsuyoshi, Naoya Hino, Kazuhiro Aoki, and Michiyuki Matsuda. “Stretching the Limits of Extracellular Signal-Related Kinase (ERK) Signaling — Cell Mechanosensing to ERK Activation.” <i>Current Opinion in Cell Biology</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.ceb.2023.102217\">https://doi.org/10.1016/j.ceb.2023.102217</a>.","ista":"Hirashima T, Hino N, Aoki K, Matsuda M. 2023. Stretching the limits of extracellular signal-related kinase (ERK) signaling — Cell mechanosensing to ERK activation. Current Opinion in Cell Biology. 84(10), 102217.","mla":"Hirashima, Tsuyoshi, et al. “Stretching the Limits of Extracellular Signal-Related Kinase (ERK) Signaling — Cell Mechanosensing to ERK Activation.” <i>Current Opinion in Cell Biology</i>, vol. 84, no. 10, 102217, Elsevier, 2023, doi:<a href=\"https://doi.org/10.1016/j.ceb.2023.102217\">10.1016/j.ceb.2023.102217</a>.","apa":"Hirashima, T., Hino, N., Aoki, K., &#38; Matsuda, M. (2023). Stretching the limits of extracellular signal-related kinase (ERK) signaling — Cell mechanosensing to ERK activation. <i>Current Opinion in Cell Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ceb.2023.102217\">https://doi.org/10.1016/j.ceb.2023.102217</a>"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"10","department":[{"_id":"CaHe"}],"file":[{"file_id":"14909","file_size":1173762,"date_created":"2024-01-30T12:52:12Z","creator":"dernst","date_updated":"2024-01-30T12:52:12Z","relation":"main_file","checksum":"25923f8ae71344e8974530dd23c71bdc","file_name":"2023_CurrentOpinionCellBio_Hirashima.pdf","success":1,"content_type":"application/pdf","access_level":"open_access"}],"article_number":"102217","has_accepted_license":"1","intvolume":"        84","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"abstract":[{"text":"Extracellular signal-regulated kinase (ERK) has been recognized as a critical regulator in various physiological and pathological processes. Extensive research has elucidated the signaling mechanisms governing ERK activation via biochemical regulations with upstream molecules, particularly receptor tyrosine kinases (RTKs). However, recent advances have highlighted the role of mechanical forces in activating the RTK–ERK signaling pathways, thereby opening new avenues of research into mechanochemical interplay in multicellular tissues. Here, we review the force-induced ERK activation in cells and propose possible mechanosensing mechanisms underlying the mechanoresponsive ERK activation. We conclude that mechanical forces are not merely passive factors shaping cells and tissues but also active regulators of cellular signaling pathways controlling collective cell behaviors.","lang":"eng"}],"publication_identifier":{"eissn":["1879-0410"],"issn":["0955-0674"]},"publication_status":"published","file_date_updated":"2024-01-30T12:52:12Z","author":[{"first_name":"Tsuyoshi","last_name":"Hirashima","full_name":"Hirashima, Tsuyoshi"},{"last_name":"Hino","full_name":"Hino, Naoya","id":"5299a9ce-7679-11eb-a7bc-d1e62b936307","first_name":"Naoya"},{"first_name":"Kazuhiro","last_name":"Aoki","full_name":"Aoki, Kazuhiro"},{"first_name":"Michiyuki","last_name":"Matsuda","full_name":"Matsuda, Michiyuki"}],"day":"01","scopus_import":"1","title":"Stretching the limits of extracellular signal-related kinase (ERK) signaling — Cell mechanosensing to ERK activation","oa_version":"Published Version","volume":84,"article_type":"review","date_created":"2023-08-20T22:01:12Z"},{"ddc":["570"],"quality_controlled":"1","publisher":"The Company of Biologists","article_processing_charge":"No","doi":"10.1242/jcs.260668","type":"journal_article","_id":"14082","date_updated":"2023-12-13T12:11:18Z","publication":"Journal of Cell Science","status":"public","project":[{"name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","grant_number":"742573","call_identifier":"H2020","_id":"260F1432-B435-11E9-9278-68D0E5697425"}],"acknowledgement":"The authors thank their respective lab members for feedback and helpful discussions. We thank the bioimaging and zebrafish facilities of IST Austria for their support.\r\nThis work was supported by the National Institutes of Health [R01GM112794 to A.L.M.], by Grants-in-Aid for Scientific Research from the Japan Society for the Promotion of Science [21K06156 to T.H.], by the Grant Program for Biomedical Engineering Research from the Nakatani Foundation for Advancement of Measuring Technologies in Biomedical Engineering [to T.H.] and by funding from the European Research Council [advanced grant 742573 to C.-P.H.]. ","date_published":"2023-08-01T00:00:00Z","ec_funded":1,"external_id":{"isi":["001070149000001"]},"isi":1,"year":"2023","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"}],"intvolume":"       136","abstract":[{"lang":"eng","text":"Epithelial barrier function is commonly analyzed using transepithelial electrical resistance, which measures ion flux across a monolayer, or by adding traceable macromolecules and monitoring their passage across the monolayer. Although these methods measure changes in global barrier function, they lack the sensitivity needed to detect local or transient barrier breaches, and they do not reveal the location of barrier leaks. Therefore, we previously developed a method that we named the zinc-based ultrasensitive microscopic barrier assay (ZnUMBA), which overcomes these limitations, allowing for detection of local tight junction leaks with high spatiotemporal resolution. Here, we present expanded applications for ZnUMBA. ZnUMBA can be used in Xenopus embryos to measure the dynamics of barrier restoration and actin accumulation following laser injury. ZnUMBA can also be effectively utilized in developing zebrafish embryos as well as cultured monolayers of Madin–Darby canine kidney (MDCK) II epithelial cells. ZnUMBA is a powerful and flexible method that, with minimal optimization, can be applied to multiple systems to measure dynamic changes in barrier function with spatiotemporal precision."}],"has_accepted_license":"1","file_date_updated":"2023-08-21T07:37:54Z","publication_identifier":{"eissn":["1477-9137"],"issn":["0021-9533"]},"publication_status":"published","oa_version":"None","title":"ZnUMBA - a live imaging method to detect local barrier breaches","scopus_import":"1","day":"01","author":[{"full_name":"Higashi, Tomohito","last_name":"Higashi","first_name":"Tomohito"},{"last_name":"Stephenson","full_name":"Stephenson, Rachel E.","first_name":"Rachel E."},{"first_name":"Cornelia","orcid":"0000-0001-5130-2226","last_name":"Schwayer","full_name":"Schwayer, Cornelia","id":"3436488C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Huljev","full_name":"Huljev, Karla","id":"44C6F6A6-F248-11E8-B48F-1D18A9856A87","first_name":"Karla"},{"first_name":"Atsuko Y.","last_name":"Higashi","full_name":"Higashi, Atsuko Y."},{"first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg"},{"last_name":"Chiba","full_name":"Chiba, Hideki","first_name":"Hideki"},{"first_name":"Ann L.","full_name":"Miller, Ann L.","last_name":"Miller"}],"date_created":"2023-08-20T22:01:13Z","article_type":"original","volume":136,"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Higashi, T., Stephenson, R. E., Schwayer, C., Huljev, K., Higashi, A. Y., Heisenberg, C.-P. J., … Miller, A. L. (2023). ZnUMBA - a live imaging method to detect local barrier breaches. <i>Journal of Cell Science</i>. The Company of Biologists. <a href=\"https://doi.org/10.1242/jcs.260668\">https://doi.org/10.1242/jcs.260668</a>","mla":"Higashi, Tomohito, et al. “ZnUMBA - a Live Imaging Method to Detect Local Barrier Breaches.” <i>Journal of Cell Science</i>, vol. 136, no. 15, jcs260668, The Company of Biologists, 2023, doi:<a href=\"https://doi.org/10.1242/jcs.260668\">10.1242/jcs.260668</a>.","ista":"Higashi T, Stephenson RE, Schwayer C, Huljev K, Higashi AY, Heisenberg C-PJ, Chiba H, Miller AL. 2023. ZnUMBA - a live imaging method to detect local barrier breaches. Journal of Cell Science. 136(15), jcs260668.","chicago":"Higashi, Tomohito, Rachel E. Stephenson, Cornelia Schwayer, Karla Huljev, Atsuko Y. Higashi, Carl-Philipp J Heisenberg, Hideki Chiba, and Ann L. Miller. “ZnUMBA - a Live Imaging Method to Detect Local Barrier Breaches.” <i>Journal of Cell Science</i>. The Company of Biologists, 2023. <a href=\"https://doi.org/10.1242/jcs.260668\">https://doi.org/10.1242/jcs.260668</a>.","ieee":"T. Higashi <i>et al.</i>, “ZnUMBA - a live imaging method to detect local barrier breaches,” <i>Journal of Cell Science</i>, vol. 136, no. 15. The Company of Biologists, 2023.","short":"T. Higashi, R.E. Stephenson, C. Schwayer, K. Huljev, A.Y. Higashi, C.-P.J. Heisenberg, H. Chiba, A.L. Miller, Journal of Cell Science 136 (2023).","ama":"Higashi T, Stephenson RE, Schwayer C, et al. ZnUMBA - a live imaging method to detect local barrier breaches. <i>Journal of Cell Science</i>. 2023;136(15). doi:<a href=\"https://doi.org/10.1242/jcs.260668\">10.1242/jcs.260668</a>"},"issue":"15","month":"08","article_number":"jcs260668","file":[{"date_updated":"2023-08-21T07:37:54Z","creator":"dernst","embargo":"2024-08-10","date_created":"2023-08-21T07:37:54Z","file_size":18665315,"embargo_to":"open_access","file_id":"14092","content_type":"application/pdf","access_level":"closed","file_name":"2023_JourCellScience_Higashi.pdf","checksum":"a399389b7e3d072f1788b63e612a10b3","relation":"main_file"}],"department":[{"_id":"CaHe"},{"_id":"EvBe"}]},{"conference":{"name":"ICALP: International Colloquium on Automata, Languages, and Programming","start_date":"2023-07-10","end_date":"2023-07-14","location":"Paderborn, Germany"},"date_published":"2023-07-01T00:00:00Z","acknowledgement":"Nicolas Resch: Research supported in part by ERC H2020 grant No.74079 (ALGSTRONGCRYPTO). Chen Yuan: Research supported in part by the National Key Research and Development Projects under Grant 2022YFA1004900 and Grant 2021YFE0109900, the National Natural Science Foundation of China under Grant 12101403 and Grant 12031011.\r\nAcknowledgements YZ is grateful to Shashank Vatedka, Diyuan Wu and Fengxing Zhu for inspiring discussions.","publication":"50th International Colloquium on Automata, Languages, and Programming","status":"public","external_id":{"arxiv":["2210.07754"]},"year":"2023","quality_controlled":"1","ddc":["000"],"type":"conference","date_updated":"2023-08-21T07:26:01Z","_id":"14083","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","doi":"10.4230/LIPIcs.ICALP.2023.99","alternative_title":["LIPIcs"],"article_processing_charge":"Yes","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Resch N, Yuan C, Zhang Y. Zero-rate thresholds and new capacity bounds for list-decoding and list-recovery. In: <i>50th International Colloquium on Automata, Languages, and Programming</i>. Vol 261. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2023. doi:<a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2023.99\">10.4230/LIPIcs.ICALP.2023.99</a>","ieee":"N. Resch, C. Yuan, and Y. Zhang, “Zero-rate thresholds and new capacity bounds for list-decoding and list-recovery,” in <i>50th International Colloquium on Automata, Languages, and Programming</i>, Paderborn, Germany, 2023, vol. 261.","short":"N. Resch, C. Yuan, Y. Zhang, in:, 50th International Colloquium on Automata, Languages, and Programming, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023.","chicago":"Resch, Nicolas, Chen Yuan, and Yihan Zhang. “Zero-Rate Thresholds and New Capacity Bounds for List-Decoding and List-Recovery.” In <i>50th International Colloquium on Automata, Languages, and Programming</i>, Vol. 261. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023. <a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2023.99\">https://doi.org/10.4230/LIPIcs.ICALP.2023.99</a>.","ista":"Resch N, Yuan C, Zhang Y. 2023. Zero-rate thresholds and new capacity bounds for list-decoding and list-recovery. 50th International Colloquium on Automata, Languages, and Programming. ICALP: International Colloquium on Automata, Languages, and Programming, LIPIcs, vol. 261, 99.","apa":"Resch, N., Yuan, C., &#38; Zhang, Y. (2023). Zero-rate thresholds and new capacity bounds for list-decoding and list-recovery. In <i>50th International Colloquium on Automata, Languages, and Programming</i> (Vol. 261). Paderborn, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2023.99\">https://doi.org/10.4230/LIPIcs.ICALP.2023.99</a>","mla":"Resch, Nicolas, et al. “Zero-Rate Thresholds and New Capacity Bounds for List-Decoding and List-Recovery.” <i>50th International Colloquium on Automata, Languages, and Programming</i>, vol. 261, 99, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, doi:<a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2023.99\">10.4230/LIPIcs.ICALP.2023.99</a>."},"language":[{"iso":"eng"}],"oa":1,"article_number":"99","file":[{"file_id":"14091","date_created":"2023-08-21T07:23:18Z","file_size":1141497,"creator":"dernst","date_updated":"2023-08-21T07:23:18Z","relation":"main_file","checksum":"a449143fec3fbebb092cb8ef3b53c226","success":1,"file_name":"2023_LIPIcsICALP_Resch.pdf","access_level":"open_access","content_type":"application/pdf"}],"department":[{"_id":"MaMo"}],"month":"07","arxiv":1,"publication_identifier":{"isbn":["9783959772785"],"issn":["1868-8969"]},"publication_status":"published","file_date_updated":"2023-08-21T07:23:18Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"abstract":[{"lang":"eng","text":"In this work we consider the list-decodability and list-recoverability of arbitrary q-ary codes, for all integer values of q ≥ 2. A code is called (p,L)_q-list-decodable if every radius pn Hamming ball contains less than L codewords; (p,𝓁,L)_q-list-recoverability is a generalization where we place radius pn Hamming balls on every point of a combinatorial rectangle with side length 𝓁 and again stipulate that there be less than L codewords.\r\nOur main contribution is to precisely calculate the maximum value of p for which there exist infinite families of positive rate (p,𝓁,L)_q-list-recoverable codes, the quantity we call the zero-rate threshold. Denoting this value by p_*, we in fact show that codes correcting a p_*+ε fraction of errors must have size O_ε(1), i.e., independent of n. Such a result is typically referred to as a \"Plotkin bound.\" To complement this, a standard random code with expurgation construction shows that there exist positive rate codes correcting a p_*-ε fraction of errors. We also follow a classical proof template (typically attributed to Elias and Bassalygo) to derive from the zero-rate threshold other tradeoffs between rate and decoding radius for list-decoding and list-recovery.\r\nTechnically, proving the Plotkin bound boils down to demonstrating the Schur convexity of a certain function defined on the q-simplex as well as the convexity of a univariate function derived from it. We remark that an earlier argument claimed similar results for q-ary list-decoding; however, we point out that this earlier proof is flawed."}],"intvolume":"       261","has_accepted_license":"1","date_created":"2023-08-20T22:01:13Z","volume":261,"title":"Zero-rate thresholds and new capacity bounds for list-decoding and list-recovery","oa_version":"Published Version","author":[{"first_name":"Nicolas","last_name":"Resch","full_name":"Resch, Nicolas"},{"first_name":"Chen","full_name":"Yuan, Chen","last_name":"Yuan"},{"orcid":"0000-0002-6465-6258","first_name":"Yihan","id":"2ce5da42-b2ea-11eb-bba5-9f264e9d002c","full_name":"Zhang, Yihan","last_name":"Zhang"}],"scopus_import":"1","day":"01"},{"has_accepted_license":"1","abstract":[{"text":"A central problem in computational statistics is to convert a procedure for sampling combinatorial objects into a procedure for counting those objects, and vice versa. We will consider sampling problems which come from Gibbs distributions, which are families of probability distributions over a discrete space Ω with probability mass function of the form μ^Ω_β(ω) ∝ e^{β H(ω)} for β in an interval [β_min, β_max] and H(ω) ∈ {0} ∪ [1, n].\r\nThe partition function is the normalization factor Z(β) = ∑_{ω ∈ Ω} e^{β H(ω)}, and the log partition ratio is defined as q = (log Z(β_max))/Z(β_min)\r\nWe develop a number of algorithms to estimate the counts c_x using roughly Õ(q/ε²) samples for general Gibbs distributions and Õ(n²/ε²) samples for integer-valued distributions (ignoring some second-order terms and parameters), We show this is optimal up to logarithmic factors. We illustrate with improved algorithms for counting connected subgraphs and perfect matchings in a graph.","lang":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"intvolume":"       261","publication_status":"published","publication_identifier":{"issn":["1868-8969"],"isbn":["9783959772785"]},"file_date_updated":"2023-08-21T06:45:16Z","author":[{"first_name":"David G.","full_name":"Harris, David G.","last_name":"Harris"},{"first_name":"Vladimir","last_name":"Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","full_name":"Kolmogorov, Vladimir"}],"scopus_import":"1","day":"01","title":"Parameter estimation for Gibbs distributions","oa_version":"Published Version","volume":261,"date_created":"2023-08-20T22:01:14Z","oa":1,"language":[{"iso":"eng"}],"citation":{"chicago":"Harris, David G., and Vladimir Kolmogorov. “Parameter Estimation for Gibbs Distributions.” In <i>50th International Colloquium on Automata, Languages, and Programming</i>, Vol. 261. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023. <a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2023.72\">https://doi.org/10.4230/LIPIcs.ICALP.2023.72</a>.","ista":"Harris DG, Kolmogorov V. 2023. Parameter estimation for Gibbs distributions. 50th International Colloquium on Automata, Languages, and Programming. ICALP: International Colloquium on Automata, Languages, and Programming, LIPIcs, vol. 261, 72.","apa":"Harris, D. G., &#38; Kolmogorov, V. (2023). Parameter estimation for Gibbs distributions. In <i>50th International Colloquium on Automata, Languages, and Programming</i> (Vol. 261). Paderborn, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2023.72\">https://doi.org/10.4230/LIPIcs.ICALP.2023.72</a>","mla":"Harris, David G., and Vladimir Kolmogorov. “Parameter Estimation for Gibbs Distributions.” <i>50th International Colloquium on Automata, Languages, and Programming</i>, vol. 261, 72, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, doi:<a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2023.72\">10.4230/LIPIcs.ICALP.2023.72</a>.","ama":"Harris DG, Kolmogorov V. Parameter estimation for Gibbs distributions. In: <i>50th International Colloquium on Automata, Languages, and Programming</i>. Vol 261. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2023. doi:<a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2023.72\">10.4230/LIPIcs.ICALP.2023.72</a>","ieee":"D. G. Harris and V. Kolmogorov, “Parameter estimation for Gibbs distributions,” in <i>50th International Colloquium on Automata, Languages, and Programming</i>, Paderborn, Germany, 2023, vol. 261.","short":"D.G. Harris, V. Kolmogorov, in:, 50th International Colloquium on Automata, Languages, and Programming, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","arxiv":1,"month":"07","department":[{"_id":"VlKo"}],"article_number":"72","file":[{"file_id":"14088","date_created":"2023-08-21T06:45:16Z","file_size":917791,"creator":"dernst","date_updated":"2023-08-21T06:45:16Z","relation":"main_file","checksum":"6dee0684245bb1c524b9c955db1e933d","success":1,"file_name":"2023_LIPIcsICALP_Harris.pdf","access_level":"open_access","content_type":"application/pdf"}],"ddc":["000","510"],"quality_controlled":"1","doi":"10.4230/LIPIcs.ICALP.2023.72","article_processing_charge":"Yes","alternative_title":["LIPIcs"],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","date_updated":"2023-08-21T06:49:11Z","_id":"14084","type":"conference","status":"public","publication":"50th International Colloquium on Automata, Languages, and Programming","acknowledgement":"We thank Heng Guo for helpful explanations of algorithms for sampling connected subgraphs and matchings, Maksym Serbyn for bringing to our attention the Wang-Landau algorithm and its use in physics.","conference":{"start_date":"2023-07-10","end_date":"2023-07-14","name":"ICALP: International Colloquium on Automata, Languages, and Programming","location":"Paderborn, Germany"},"date_published":"2023-07-01T00:00:00Z","year":"2023","external_id":{"arxiv":["2007.10824"]}},{"type":"conference","date_updated":"2023-08-21T07:00:49Z","_id":"14085","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","doi":"10.4230/LIPIcs.ICALP.2023.69","article_processing_charge":"Yes","alternative_title":["LIPIcs"],"quality_controlled":"1","ddc":["000"],"external_id":{"unknown":["2211.09606"]},"year":"2023","acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant agreement No.\r\n101019564 “The Design of Modern Fully Dynamic Data Structures (MoDynStruct)” and from the\r\nAustrian Science Fund (FWF) project “Static and Dynamic Hierarchical Graph Decompositions”,\r\nI 5982-N, and project “Fast Algorithms for a Reactive Network Layer (ReactNet)”, P 33775-N, with additional funding from the netidee SCIENCE Stiftung, 2020–2024.\r\nThis work was done in part while Gramoz Goranci was at Institute for Theoretical Studies, ETH Zurich, Switzerland. There, he was supported by Dr. Max Rössler, the Walter Haefner Foundation and the ETH Zürich Foundation. We also thank Richard Peng, Thatchaphol Saranurak, Sebastian Forster and Sushant Sachdeva for helpful discussions, and the anonymous reviewers for their insightful comments.","conference":{"location":"Paderborn, Germany","end_date":"2023-07-14","start_date":"2023-07-10","name":"ICALP: International Colloquium on Automata, Languages, and Programming"},"date_published":"2023-07-01T00:00:00Z","ec_funded":1,"project":[{"call_identifier":"H2020","grant_number":"101019564","name":"The design and evaluation of modern fully dynamic data structures","_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62"},{"grant_number":"I05982","name":"Static and Dynamic Hierarchical Graph Decompositions","_id":"bda196b2-d553-11ed-ba76-8e8ee6c21103"},{"_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe","grant_number":"P33775 ","name":"Fast Algorithms for a Reactive Network Layer"}],"status":"public","publication":"50th International Colloquium on Automata, Languages, and Programming","date_created":"2023-08-20T22:01:14Z","volume":261,"title":"Efficient data structures for incremental exact and approximate maximum flow","oa_version":"Published Version","author":[{"full_name":"Goranci, Gramoz","last_name":"Goranci","first_name":"Gramoz"},{"last_name":"Henzinger","full_name":"Henzinger, Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","first_name":"Monika H","orcid":"0000-0002-5008-6530"}],"day":"01","scopus_import":"1","publication_status":"published","publication_identifier":{"isbn":["9783959772785"],"issn":["1868-8969"]},"file_date_updated":"2023-08-21T06:59:05Z","abstract":[{"text":"We show an (1+ϵ)-approximation algorithm for maintaining maximum s-t flow under m edge insertions in m1/2+o(1)ϵ−1/2 amortized update time for directed, unweighted graphs. This constitutes the first sublinear dynamic maximum flow algorithm in general sparse graphs with arbitrarily good approximation guarantee.","lang":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"intvolume":"       261","has_accepted_license":"1","article_number":"69","file":[{"file_id":"14089","creator":"dernst","date_updated":"2023-08-21T06:59:05Z","date_created":"2023-08-21T06:59:05Z","file_size":875910,"checksum":"074177e815a1656de5d4071c7a3dffa6","relation":"main_file","content_type":"application/pdf","access_level":"open_access","file_name":"2023_LIPIcsICALP_Goranci.pdf","success":1}],"department":[{"_id":"MoHe"}],"month":"07","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Goranci, G., &#38; Henzinger, M. H. (2023). Efficient data structures for incremental exact and approximate maximum flow. In <i>50th International Colloquium on Automata, Languages, and Programming</i> (Vol. 261). Paderborn, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2023.69\">https://doi.org/10.4230/LIPIcs.ICALP.2023.69</a>","mla":"Goranci, Gramoz, and Monika H. Henzinger. “Efficient Data Structures for Incremental Exact and Approximate Maximum Flow.” <i>50th International Colloquium on Automata, Languages, and Programming</i>, vol. 261, 69, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, doi:<a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2023.69\">10.4230/LIPIcs.ICALP.2023.69</a>.","chicago":"Goranci, Gramoz, and Monika H Henzinger. “Efficient Data Structures for Incremental Exact and Approximate Maximum Flow.” In <i>50th International Colloquium on Automata, Languages, and Programming</i>, Vol. 261. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023. <a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2023.69\">https://doi.org/10.4230/LIPIcs.ICALP.2023.69</a>.","ista":"Goranci G, Henzinger MH. 2023. Efficient data structures for incremental exact and approximate maximum flow. 50th International Colloquium on Automata, Languages, and Programming. ICALP: International Colloquium on Automata, Languages, and Programming, LIPIcs, vol. 261, 69.","ieee":"G. Goranci and M. H. Henzinger, “Efficient data structures for incremental exact and approximate maximum flow,” in <i>50th International Colloquium on Automata, Languages, and Programming</i>, Paderborn, Germany, 2023, vol. 261.","short":"G. Goranci, M.H. Henzinger, in:, 50th International Colloquium on Automata, Languages, and Programming, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023.","ama":"Goranci G, Henzinger MH. Efficient data structures for incremental exact and approximate maximum flow. In: <i>50th International Colloquium on Automata, Languages, and Programming</i>. Vol 261. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2023. doi:<a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2023.69\">10.4230/LIPIcs.ICALP.2023.69</a>"},"language":[{"iso":"eng"}],"oa":1},{"quality_controlled":"1","ddc":["000"],"_id":"14086","date_updated":"2023-08-21T07:05:47Z","type":"conference","article_processing_charge":"Yes","alternative_title":["LIPIcs"],"doi":"10.4230/LIPIcs.ICALP.2023.74","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","ec_funded":1,"conference":{"end_date":"2023-07-14","start_date":"2023-07-10","name":"ICALP: International Colloquium on Automata, Languages, and Programming","location":"Paderborn, Germany"},"date_published":"2023-07-01T00:00:00Z","acknowledgement":" Monika Henzinger: This project has received funding from the European Research Council\r\n(ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant\r\nagreement No. 101019564 “The Design of Modern Fully Dynamic Data Structures (MoDynStruct)” and from the Austrian Science Fund (FWF) project “Static and Dynamic Hierarchical Graph Decompositions”, I 5982-N, and project “Fast Algorithms for a Reactive Network Layer (ReactNet)”, P 33775-N, with additional funding from the netidee SCIENCE Stiftung, 2020–2024. Jan Vondrák: Supported by NSF Award 2127781.","publication":"50th International Colloquium on Automata, Languages, and Programming","status":"public","project":[{"_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62","call_identifier":"H2020","name":"The design and evaluation of modern fully dynamic data structures","grant_number":"101019564"},{"grant_number":"I05982","name":"Static and Dynamic Hierarchical Graph Decompositions","_id":"bda196b2-d553-11ed-ba76-8e8ee6c21103"},{"_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe","grant_number":"P33775 ","name":"Fast Algorithms for a Reactive Network Layer"}],"year":"2023","external_id":{"arxiv":["2305.00122"]},"file_date_updated":"2023-08-21T07:04:36Z","publication_status":"published","publication_identifier":{"isbn":["9783959772785"],"issn":["18688969"]},"has_accepted_license":"1","abstract":[{"lang":"eng","text":"The maximization of submodular functions have found widespread application in areas such as machine learning, combinatorial optimization, and economics, where practitioners often wish to enforce various constraints; the matroid constraint has been investigated extensively due to its algorithmic properties and expressive power. Though tight approximation algorithms for general matroid constraints exist in theory, the running times of such algorithms typically scale quadratically, and are not practical for truly large scale settings. Recent progress has focused on fast algorithms for important classes of matroids given in explicit form. Currently, nearly-linear time algorithms only exist for graphic and partition matroids [Alina Ene and Huy L. Nguyen, 2019]. In this work, we develop algorithms for monotone submodular maximization constrained by graphic, transversal matroids, or laminar matroids in time near-linear in the size of their representation. Our algorithms achieve an optimal approximation of 1-1/e-ε and both generalize and accelerate the results of Ene and Nguyen [Alina Ene and Huy L. Nguyen, 2019]. In fact, the running time of our algorithm cannot be improved within the fast continuous greedy framework of Badanidiyuru and Vondrák [Ashwinkumar Badanidiyuru and Jan Vondrák, 2014].\r\nTo achieve near-linear running time, we make use of dynamic data structures that maintain bases with approximate maximum cardinality and weight under certain element updates. These data structures need to support a weight decrease operation and a novel Freeze operation that allows the algorithm to freeze elements (i.e. force to be contained) in its basis regardless of future data structure operations. For the laminar matroid, we present a new dynamic data structure using the top tree interface of Alstrup, Holm, de Lichtenberg, and Thorup [Stephen Alstrup et al., 2005] that maintains the maximum weight basis under insertions and deletions of elements in O(log n) time. This data structure needs to support certain subtree query and path update operations that are performed every insertion and deletion that are non-trivial to handle in conjunction. For the transversal matroid the Freeze operation corresponds to requiring the data structure to keep a certain set S of vertices matched, a property that we call S-stability. While there is a large body of work on dynamic matching algorithms, none are S-stable and maintain an approximate maximum weight matching under vertex updates. We give the first such algorithm for bipartite graphs with total running time linear (up to log factors) in the number of edges."}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"intvolume":"       261","volume":261,"date_created":"2023-08-20T22:01:14Z","scopus_import":"1","day":"01","author":[{"orcid":"0000-0002-5008-6530","first_name":"Monika H","full_name":"Henzinger, Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","last_name":"Henzinger"},{"full_name":"Liu, Paul","last_name":"Liu","first_name":"Paul"},{"full_name":"Vondrák, Jan","last_name":"Vondrák","first_name":"Jan"},{"full_name":"Zheng, Da Wei","last_name":"Zheng","first_name":"Da Wei"}],"title":"Faster submodular maximization for several classes of matroids","oa_version":"Published Version","citation":{"ama":"Henzinger MH, Liu P, Vondrák J, Zheng DW. Faster submodular maximization for several classes of matroids. In: <i>50th International Colloquium on Automata, Languages, and Programming</i>. Vol 261. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2023. doi:<a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2023.74\">10.4230/LIPIcs.ICALP.2023.74</a>","ieee":"M. H. Henzinger, P. Liu, J. Vondrák, and D. W. Zheng, “Faster submodular maximization for several classes of matroids,” in <i>50th International Colloquium on Automata, Languages, and Programming</i>, Paderborn, Germany, 2023, vol. 261.","short":"M.H. Henzinger, P. Liu, J. Vondrák, D.W. Zheng, in:, 50th International Colloquium on Automata, Languages, and Programming, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023.","chicago":"Henzinger, Monika H, Paul Liu, Jan Vondrák, and Da Wei Zheng. “Faster Submodular Maximization for Several Classes of Matroids.” In <i>50th International Colloquium on Automata, Languages, and Programming</i>, Vol. 261. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023. <a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2023.74\">https://doi.org/10.4230/LIPIcs.ICALP.2023.74</a>.","ista":"Henzinger MH, Liu P, Vondrák J, Zheng DW. 2023. Faster submodular maximization for several classes of matroids. 50th International Colloquium on Automata, Languages, and Programming. ICALP: International Colloquium on Automata, Languages, and Programming, LIPIcs, vol. 261, 74.","apa":"Henzinger, M. H., Liu, P., Vondrák, J., &#38; Zheng, D. W. (2023). Faster submodular maximization for several classes of matroids. In <i>50th International Colloquium on Automata, Languages, and Programming</i> (Vol. 261). Paderborn, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2023.74\">https://doi.org/10.4230/LIPIcs.ICALP.2023.74</a>","mla":"Henzinger, Monika H., et al. “Faster Submodular Maximization for Several Classes of Matroids.” <i>50th International Colloquium on Automata, Languages, and Programming</i>, vol. 261, 74, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, doi:<a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2023.74\">10.4230/LIPIcs.ICALP.2023.74</a>."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"language":[{"iso":"eng"}],"department":[{"_id":"MoHe"}],"article_number":"74","file":[{"date_updated":"2023-08-21T07:04:36Z","creator":"dernst","date_created":"2023-08-21T07:04:36Z","file_size":930943,"file_id":"14090","content_type":"application/pdf","access_level":"open_access","file_name":"2023_LIPIcsICALP_HenzingerM.pdf","success":1,"checksum":"a5eef225014e003efbfbe4830fdd23cb","relation":"main_file"}],"month":"07","arxiv":1},{"department":[{"_id":"GradSch"}],"file":[{"creator":"dernst","date_updated":"2024-01-30T12:48:24Z","file_size":7660662,"date_created":"2024-01-30T12:48:24Z","file_id":"14908","content_type":"application/pdf","access_level":"open_access","file_name":"2023_SoftMatter_Ronning.pdf","success":1,"checksum":"b936747170d0b708172b518078c4081a","relation":"main_file"}],"month":"09","arxiv":1,"citation":{"chicago":"Rønning, Jonas, Julian B Renaud, Amin Doostmohammadi, and Luiza Angheluta. “Spontaneous Flows and Dynamics of Full-Integer Topological Defects in Polar Active Matter.” <i>Soft Matter</i>. Royal Society of Chemistry, 2023. <a href=\"https://doi.org/10.1039/d3sm00316g\">https://doi.org/10.1039/d3sm00316g</a>.","ista":"Rønning J, Renaud JB, Doostmohammadi A, Angheluta L. 2023. Spontaneous flows and dynamics of full-integer topological defects in polar active matter. Soft Matter. 39, 7513–7527.","mla":"Rønning, Jonas, et al. “Spontaneous Flows and Dynamics of Full-Integer Topological Defects in Polar Active Matter.” <i>Soft Matter</i>, vol. 39, Royal Society of Chemistry, 2023, pp. 7513–27, doi:<a href=\"https://doi.org/10.1039/d3sm00316g\">10.1039/d3sm00316g</a>.","apa":"Rønning, J., Renaud, J. B., Doostmohammadi, A., &#38; Angheluta, L. (2023). Spontaneous flows and dynamics of full-integer topological defects in polar active matter. <i>Soft Matter</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/d3sm00316g\">https://doi.org/10.1039/d3sm00316g</a>","ama":"Rønning J, Renaud JB, Doostmohammadi A, Angheluta L. Spontaneous flows and dynamics of full-integer topological defects in polar active matter. <i>Soft Matter</i>. 2023;39:7513-7527. doi:<a href=\"https://doi.org/10.1039/d3sm00316g\">10.1039/d3sm00316g</a>","short":"J. Rønning, J.B. Renaud, A. Doostmohammadi, L. Angheluta, Soft Matter 39 (2023) 7513–7527.","ieee":"J. Rønning, J. B. Renaud, A. Doostmohammadi, and L. Angheluta, “Spontaneous flows and dynamics of full-integer topological defects in polar active matter,” <i>Soft Matter</i>, vol. 39. Royal Society of Chemistry, pp. 7513–7527, 2023."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"language":[{"iso":"eng"}],"volume":39,"date_created":"2023-08-20T22:01:15Z","article_type":"original","scopus_import":"1","day":"01","author":[{"last_name":"Rønning","full_name":"Rønning, Jonas","first_name":"Jonas"},{"first_name":"Julian B","last_name":"Renaud","id":"7af6767d-14eb-11ed-b536-a32449ae867c","full_name":"Renaud, Julian B"},{"full_name":"Doostmohammadi, Amin","last_name":"Doostmohammadi","first_name":"Amin"},{"first_name":"Luiza","full_name":"Angheluta, Luiza","last_name":"Angheluta"}],"oa_version":"Published Version","title":"Spontaneous flows and dynamics of full-integer topological defects in polar active matter","file_date_updated":"2024-01-30T12:48:24Z","publication_status":"published","publication_identifier":{"eissn":["1744-6848"],"issn":["1744-683X"]},"has_accepted_license":"1","abstract":[{"text":"Polar active matter of self-propelled particles sustain spontaneous flows through the full-integer topological defects. We study theoretically the incompressible flow profiles around ±1 defects induced by polar and dipolar active forces. We show that dipolar forces induce vortical flows around the +1 defect, while the flow around the −1 defect has an 8-fold rotational symmetry. The vortical flow changes its chirality near the +1 defect core in the absence of the friction with a substrate. We show analytically that the flow induced by polar active forces is vortical near the +1 defect and is 4-fold symmetric near the −1 defect, while it becomes uniform in the far-field. For a pair of oppositely charged defects, this polar flow contributes to a mutual interaction force that depends only on the orientation of the defect pair relative to the background polarization, and that enhances defect pair annihilation. This is in contradiction with the effect of dipolar active forces which decay inversely proportional with the defect separation distance. As such, our analyses reveals a long-ranged mechanism for the pairwise interaction between topological defects in polar active matter.","lang":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"intvolume":"        39","year":"2023","isi":1,"external_id":{"arxiv":["2303.07063"],"isi":["001035766100001"]},"acknowledgement":"J. Rø and L. A. acknowledge support from the Research Council of Norway through the Center of Excellence funding scheme, Project No. 262644 (PoreLab). A. D. acknowledges funding from the Novo Nordisk Foundation (grant No. NNF18SA0035142 and NERD grant No. NNF21OC0068687), Villum Fonden Grant no. 29476, and the European Union via the ERC-Starting Grant PhysCoMeT. Views and opinions expressed are however those of the authors only and do not necessarily reflect those of the European Union or the European Research Council. Neither the European Union nor the granting authority can be held responsible for them.","date_published":"2023-09-01T00:00:00Z","publication":"Soft Matter","status":"public","_id":"14087","date_updated":"2024-01-30T12:49:24Z","type":"journal_article","article_processing_charge":"Yes (in subscription journal)","doi":"10.1039/d3sm00316g","publisher":"Royal Society of Chemistry","quality_controlled":"1","page":"7513-7527","ddc":["540"]},{"doi":"10.1109/wacv56688.2023.00278","article_processing_charge":"No","publisher":"Institute of Electrical and Electronics Engineers","date_updated":"2023-09-06T10:26:56Z","_id":"14105","type":"conference","main_file_link":[{"url":"https://arxiv.org/abs/2209.11459","open_access":"1"}],"quality_controlled":"1","year":"2023","external_id":{"arxiv":["2209.11459"]},"extern":"1","publication":"2023 IEEE/CVF Winter Conference on Applications of Computer Vision","status":"public","conference":{"location":"Waikoloa, HI, United States","start_date":"2023-01-02","end_date":"2023-01-07","name":"WACV: Winter Conference on Applications of Computer Vision"},"date_published":"2023-02-06T00:00:00Z","author":[{"full_name":"Sinha, Samarth","last_name":"Sinha","first_name":"Samarth"},{"first_name":"Peter","full_name":"Gehler, Peter","last_name":"Gehler"},{"last_name":"Locatello","full_name":"Locatello, Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","orcid":"0000-0002-4850-0683","first_name":"Francesco"},{"full_name":"Schiele, Bernt","last_name":"Schiele","first_name":"Bernt"}],"day":"06","scopus_import":"1","oa_version":"Preprint","title":"TeST: Test-time Self-Training under distribution shift","date_created":"2023-08-21T12:11:38Z","abstract":[{"lang":"eng","text":"Despite their recent success, deep neural networks continue to perform poorly when they encounter distribution shifts at test time. Many recently proposed approaches try to counter this by aligning the model to the new distribution prior to inference. With no labels available this requires unsupervised objectives to adapt the model on the observed test data. In this paper, we propose Test-Time SelfTraining (TeST): a technique that takes as input a model trained on some source data and a novel data distribution at test time, and learns invariant and robust representations using a student-teacher framework. We find that models adapted using TeST significantly improve over baseline testtime adaptation algorithms. TeST achieves competitive performance to modern domain adaptation algorithms [4, 43], while having access to 5-10x less data at time of adaption. We thoroughly evaluate a variety of baselines on two tasks:\r\nobject detection and image segmentation and find that models adapted with TeST. We find that TeST sets the new stateof-the art for test-time domain adaptation algorithms. "}],"publication_identifier":{"isbn":["9781665493475"],"eissn":["2642-9381"]},"publication_status":"published","arxiv":1,"month":"02","department":[{"_id":"FrLo"}],"oa":1,"language":[{"iso":"eng"}],"citation":{"mla":"Sinha, Samarth, et al. “TeST: Test-Time Self-Training under Distribution Shift.” <i>2023 IEEE/CVF Winter Conference on Applications of Computer Vision</i>, Institute of Electrical and Electronics Engineers, 2023, doi:<a href=\"https://doi.org/10.1109/wacv56688.2023.00278\">10.1109/wacv56688.2023.00278</a>.","apa":"Sinha, S., Gehler, P., Locatello, F., &#38; Schiele, B. (2023). TeST: Test-time Self-Training under distribution shift. In <i>2023 IEEE/CVF Winter Conference on Applications of Computer Vision</i>. Waikoloa, HI, United States: Institute of Electrical and Electronics Engineers. <a href=\"https://doi.org/10.1109/wacv56688.2023.00278\">https://doi.org/10.1109/wacv56688.2023.00278</a>","chicago":"Sinha, Samarth, Peter Gehler, Francesco Locatello, and Bernt Schiele. “TeST: Test-Time Self-Training under Distribution Shift.” In <i>2023 IEEE/CVF Winter Conference on Applications of Computer Vision</i>. Institute of Electrical and Electronics Engineers, 2023. <a href=\"https://doi.org/10.1109/wacv56688.2023.00278\">https://doi.org/10.1109/wacv56688.2023.00278</a>.","ista":"Sinha S, Gehler P, Locatello F, Schiele B. 2023. TeST: Test-time Self-Training under distribution shift. 2023 IEEE/CVF Winter Conference on Applications of Computer Vision. WACV: Winter Conference on Applications of Computer Vision.","short":"S. Sinha, P. Gehler, F. Locatello, B. Schiele, in:, 2023 IEEE/CVF Winter Conference on Applications of Computer Vision, Institute of Electrical and Electronics Engineers, 2023.","ieee":"S. Sinha, P. Gehler, F. Locatello, and B. Schiele, “TeST: Test-time Self-Training under distribution shift,” in <i>2023 IEEE/CVF Winter Conference on Applications of Computer Vision</i>, Waikoloa, HI, United States, 2023.","ama":"Sinha S, Gehler P, Locatello F, Schiele B. TeST: Test-time Self-Training under distribution shift. In: <i>2023 IEEE/CVF Winter Conference on Applications of Computer Vision</i>. Institute of Electrical and Electronics Engineers; 2023. doi:<a href=\"https://doi.org/10.1109/wacv56688.2023.00278\">10.1109/wacv56688.2023.00278</a>"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"article_processing_charge":"Yes (via OA deal)","doi":"10.1007/s11040-023-09460-x","publisher":"Springer Nature","_id":"14192","date_updated":"2023-12-13T12:16:19Z","type":"journal_article","ddc":["510"],"quality_controlled":"1","year":"2023","isi":1,"external_id":{"isi":["001032992600001"],"arxiv":["2206.14708"]},"keyword":["Geometry and Topology","Mathematical Physics"],"status":"public","publication":"Mathematical Physics, Analysis and Geometry","acknowledgement":"D.M. and K.M. thank Robert Seiringer for helpful discussions. Open access funding provided by Institute of Science and Technology (IST Austria). Financial support from the Agence Nationale de la Recherche (ANR) through the projects ANR-17-CE40-0016, ANR-17-CE40-0007-01, ANR-17-EURE-0002 (J.L.) and from the European Union’s Horizon 2020 research and innovation programme under the Maria Skłodowska-Curie grant agreement No. 665386 (K.M.) is gratefully acknowledged.","date_published":"2023-07-26T00:00:00Z","scopus_import":"1","day":"26","author":[{"first_name":"Jonas","last_name":"Lampart","full_name":"Lampart, Jonas"},{"first_name":"David Johannes","id":"cbddacee-2b11-11eb-a02e-a2e14d04e52d","full_name":"Mitrouskas, David Johannes","last_name":"Mitrouskas"},{"last_name":"Mysliwy","full_name":"Mysliwy, Krzysztof","id":"316457FC-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof"}],"oa_version":"Published Version","title":"On the global minimum of the energy–momentum relation for the polaron","volume":26,"date_created":"2023-08-22T14:09:47Z","article_type":"original","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"intvolume":"        26","abstract":[{"text":"For the Fröhlich model of the large polaron, we prove that the ground state energy as a function of the total momentum has a unique global minimum at momentum zero. This implies the non-existence of a ground state of the translation invariant Fröhlich Hamiltonian and thus excludes the possibility of a localization transition at finite coupling.","lang":"eng"}],"file_date_updated":"2023-08-23T10:59:15Z","publication_status":"published","publication_identifier":{"issn":["1385-0172"],"eissn":["1572-9656"]},"month":"07","arxiv":1,"department":[{"_id":"RoSe"}],"file":[{"file_id":"14225","creator":"dernst","date_updated":"2023-08-23T10:59:15Z","file_size":317026,"date_created":"2023-08-23T10:59:15Z","checksum":"f0941cc66cb3ed06a12ca4b7e356cfd6","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_name":"2023_MathPhysics_Lampart.pdf"}],"article_number":"17","oa":1,"language":[{"iso":"eng"}],"citation":{"ama":"Lampart J, Mitrouskas DJ, Mysliwy K. On the global minimum of the energy–momentum relation for the polaron. <i>Mathematical Physics, Analysis and Geometry</i>. 2023;26(3). doi:<a href=\"https://doi.org/10.1007/s11040-023-09460-x\">10.1007/s11040-023-09460-x</a>","short":"J. Lampart, D.J. Mitrouskas, K. Mysliwy, Mathematical Physics, Analysis and Geometry 26 (2023).","ieee":"J. Lampart, D. J. Mitrouskas, and K. Mysliwy, “On the global minimum of the energy–momentum relation for the polaron,” <i>Mathematical Physics, Analysis and Geometry</i>, vol. 26, no. 3. Springer Nature, 2023.","chicago":"Lampart, Jonas, David Johannes Mitrouskas, and Krzysztof Mysliwy. “On the Global Minimum of the Energy–Momentum Relation for the Polaron.” <i>Mathematical Physics, Analysis and Geometry</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s11040-023-09460-x\">https://doi.org/10.1007/s11040-023-09460-x</a>.","ista":"Lampart J, Mitrouskas DJ, Mysliwy K. 2023. On the global minimum of the energy–momentum relation for the polaron. Mathematical Physics, Analysis and Geometry. 26(3), 17.","mla":"Lampart, Jonas, et al. “On the Global Minimum of the Energy–Momentum Relation for the Polaron.” <i>Mathematical Physics, Analysis and Geometry</i>, vol. 26, no. 3, 17, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1007/s11040-023-09460-x\">10.1007/s11040-023-09460-x</a>.","apa":"Lampart, J., Mitrouskas, D. J., &#38; Mysliwy, K. (2023). On the global minimum of the energy–momentum relation for the polaron. <i>Mathematical Physics, Analysis and Geometry</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s11040-023-09460-x\">https://doi.org/10.1007/s11040-023-09460-x</a>"},"issue":"3","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"publication_status":"submitted","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2306.00600"}],"abstract":[{"text":"The binding problem in human cognition, concerning how the brain represents and connects objects within a fixed network of neural connections, remains a subject of intense debate. Most machine learning efforts addressing this issue in an unsupervised setting have focused on slot-based methods, which may be limiting due to their discrete nature and difficulty to express uncertainty. Recently, the Complex AutoEncoder was proposed as an alternative that learns continuous and distributed object-centric representations. However, it is only applicable to simple toy data. In this paper, we present Rotating Features, a generalization of complex-valued features to higher dimensions, and a new evaluation procedure for extracting objects from distributed representations. Additionally, we show the applicability of our approach to pre-trained features. Together, these advancements enable us to scale distributed object-centric representations from simple toy to real-world data. We believe this work advances a new paradigm for addressing the binding problem in machine learning and has the potential to inspire further innovation in the field.","lang":"eng"}],"date_created":"2023-08-22T14:18:00Z","type":"preprint","_id":"14207","date_updated":"2024-02-12T09:53:44Z","oa_version":"Preprint","title":"Rotating features for object discovery","day":"01","article_processing_charge":"No","author":[{"first_name":"Sindy","last_name":"Löwe","full_name":"Löwe, Sindy"},{"last_name":"Lippe","full_name":"Lippe, Phillip","first_name":"Phillip"},{"last_name":"Locatello","full_name":"Locatello, Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","orcid":"0000-0002-4850-0683","first_name":"Francesco"},{"first_name":"Max","last_name":"Welling","full_name":"Welling, Max"}],"doi":"10.48550/arXiv.2306.00600","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2023-06-01T00:00:00Z","citation":{"ieee":"S. Löwe, P. Lippe, F. Locatello, and M. Welling, “Rotating features for object discovery,” <i>arXiv</i>. .","short":"S. Löwe, P. Lippe, F. Locatello, M. Welling, ArXiv (n.d.).","ama":"Löwe S, Lippe P, Locatello F, Welling M. Rotating features for object discovery. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2306.00600\">10.48550/arXiv.2306.00600</a>","apa":"Löwe, S., Lippe, P., Locatello, F., &#38; Welling, M. (n.d.). Rotating features for object discovery. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2306.00600\">https://doi.org/10.48550/arXiv.2306.00600</a>","mla":"Löwe, Sindy, et al. “Rotating Features for Object Discovery.” <i>ArXiv</i>, 2306.00600, doi:<a href=\"https://doi.org/10.48550/arXiv.2306.00600\">10.48550/arXiv.2306.00600</a>.","ista":"Löwe S, Lippe P, Locatello F, Welling M. Rotating features for object discovery. arXiv, 2306.00600.","chicago":"Löwe, Sindy, Phillip Lippe, Francesco Locatello, and Max Welling. “Rotating Features for Object Discovery.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2306.00600\">https://doi.org/10.48550/arXiv.2306.00600</a>."},"publication":"arXiv","language":[{"iso":"eng"}],"status":"public","oa":1,"article_number":"2306.00600","department":[{"_id":"FrLo"}],"month":"06","arxiv":1,"external_id":{"arxiv":["2306.00600"]},"year":"2023"},{"extern":"1","status":"public","publication":"Proceedings of the 40th International Conference on Machine Learning","conference":{"location":"Honolulu, Hawaii, United States","name":"International Conference on Machine Learning","end_date":"2023-07-29","start_date":"2023-07-23"},"date_published":"2023-05-30T00:00:00Z","year":"2023","external_id":{"arxiv":["2305.19377"]},"page":"43105-43128","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2305.19377"}],"quality_controlled":"1","alternative_title":["PMLR"],"article_processing_charge":"No","publisher":"ML Research Press","_id":"14208","date_updated":"2023-09-13T08:46:46Z","type":"conference","oa":1,"language":[{"iso":"eng"}],"citation":{"ista":"Zhu Z, Liu F, Chrysos GG, Locatello F, Cevher V. 2023. Benign overfitting in deep neural networks under lazy training. Proceedings of the 40th International Conference on Machine Learning. International Conference on Machine Learning, PMLR, vol. 202, 43105–43128.","chicago":"Zhu, Zhenyu, Fanghui Liu, Grigorios G Chrysos, Francesco Locatello, and Volkan Cevher. “Benign Overfitting in Deep Neural Networks under Lazy Training.” In <i>Proceedings of the 40th International Conference on Machine Learning</i>, 202:43105–28. ML Research Press, 2023.","mla":"Zhu, Zhenyu, et al. “Benign Overfitting in Deep Neural Networks under Lazy Training.” <i>Proceedings of the 40th International Conference on Machine Learning</i>, vol. 202, ML Research Press, 2023, pp. 43105–28.","apa":"Zhu, Z., Liu, F., Chrysos, G. G., Locatello, F., &#38; Cevher, V. (2023). Benign overfitting in deep neural networks under lazy training. In <i>Proceedings of the 40th International Conference on Machine Learning</i> (Vol. 202, pp. 43105–43128). Honolulu, Hawaii, United States: ML Research Press.","ama":"Zhu Z, Liu F, Chrysos GG, Locatello F, Cevher V. Benign overfitting in deep neural networks under lazy training. In: <i>Proceedings of the 40th International Conference on Machine Learning</i>. Vol 202. ML Research Press; 2023:43105-43128.","short":"Z. Zhu, F. Liu, G.G. Chrysos, F. Locatello, V. Cevher, in:, Proceedings of the 40th International Conference on Machine Learning, ML Research Press, 2023, pp. 43105–43128.","ieee":"Z. Zhu, F. Liu, G. G. Chrysos, F. Locatello, and V. Cevher, “Benign overfitting in deep neural networks under lazy training,” in <i>Proceedings of the 40th International Conference on Machine Learning</i>, Honolulu, Hawaii, United States, 2023, vol. 202, pp. 43105–43128."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"05","arxiv":1,"department":[{"_id":"FrLo"}],"intvolume":"       202","abstract":[{"text":"This paper focuses on over-parameterized deep neural networks (DNNs) with ReLU activation functions and proves that when the data distribution is well-separated, DNNs can achieve Bayes-optimal test error for classification while obtaining (nearly) zero-training error under the lazy training regime. For this purpose, we unify three interrelated concepts of overparameterization, benign overfitting, and the Lipschitz constant of DNNs. Our results indicate that interpolating with smoother functions leads to better generalization. Furthermore, we investigate the special case where interpolating smooth ground-truth functions is performed by DNNs under the Neural Tangent Kernel (NTK) regime for generalization. Our result demonstrates that the generalization error converges to a constant order that only depends on label noise and initialization noise, which theoretically verifies benign overfitting. Our analysis provides a tight lower bound on the normalized margin under non-smooth activation functions, as well as the minimum eigenvalue of NTK under high-dimensional settings, which has its own interest in learning theory.","lang":"eng"}],"publication_status":"published","day":"30","author":[{"first_name":"Zhenyu","last_name":"Zhu","full_name":"Zhu, Zhenyu"},{"last_name":"Liu","full_name":"Liu, Fanghui","first_name":"Fanghui"},{"last_name":"Chrysos","full_name":"Chrysos, Grigorios G","first_name":"Grigorios G"},{"first_name":"Francesco","orcid":"0000-0002-4850-0683","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","full_name":"Locatello, Francesco","last_name":"Locatello"},{"first_name":"Volkan","full_name":"Cevher, Volkan","last_name":"Cevher"}],"oa_version":"Preprint","title":"Benign overfitting in deep neural networks under lazy training","volume":202,"date_created":"2023-08-22T14:18:18Z"},{"article_processing_charge":"No","day":"20","doi":"10.48550/arXiv.2304.10253","author":[{"last_name":"Burg","full_name":"Burg, Max F.","first_name":"Max F."},{"first_name":"Florian","full_name":"Wenzel, Florian","last_name":"Wenzel"},{"last_name":"Zietlow","full_name":"Zietlow, Dominik","first_name":"Dominik"},{"first_name":"Max","full_name":"Horn, Max","last_name":"Horn"},{"full_name":"Makansi, Osama","last_name":"Makansi","first_name":"Osama"},{"id":"26cfd52f-2483-11ee-8040-88983bcc06d4","full_name":"Locatello, Francesco","last_name":"Locatello","orcid":"0000-0002-4850-0683","first_name":"Francesco"},{"first_name":"Chris","full_name":"Russell, Chris","last_name":"Russell"}],"oa_version":"Preprint","title":"A data augmentation perspective on diffusion models and retrieval","_id":"14209","date_updated":"2023-09-13T08:51:56Z","date_created":"2023-08-22T14:18:43Z","type":"preprint","abstract":[{"lang":"eng","text":"Diffusion models excel at generating photorealistic images from text-queries. Naturally, many approaches have been proposed to use these generative abilities to augment training datasets for downstream tasks, such as classification. However, diffusion models are themselves trained on large noisily supervised, but nonetheless, annotated datasets. It is an open question whether the generalization capabilities of diffusion models beyond using the additional data of the pre-training process for augmentation lead to improved downstream performance. We perform a systematic evaluation of existing methods to generate images from diffusion models and study new extensions to assess their benefit for data augmentation. While we find that personalizing diffusion models towards the target data outperforms simpler prompting strategies, we also show that using the training data of the diffusion model alone, via a simple nearest neighbor retrieval procedure, leads to even stronger downstream performance. Overall, our study probes the limitations of diffusion models for data augmentation but also highlights its potential in generating new training data to improve performance on simple downstream vision tasks."}],"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2304.10253","open_access":"1"}],"publication_status":"submitted","year":"2023","arxiv":1,"month":"04","external_id":{"arxiv":["2304.10253"]},"department":[{"_id":"FrLo"}],"article_number":"2304.10253","oa":1,"language":[{"iso":"eng"}],"status":"public","extern":"1","publication":"arXiv","citation":{"ama":"Burg MF, Wenzel F, Zietlow D, et al. A data augmentation perspective on diffusion models and retrieval. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2304.10253\">10.48550/arXiv.2304.10253</a>","ieee":"M. F. Burg <i>et al.</i>, “A data augmentation perspective on diffusion models and retrieval,” <i>arXiv</i>. .","short":"M.F. Burg, F. Wenzel, D. Zietlow, M. Horn, O. Makansi, F. Locatello, C. Russell, ArXiv (n.d.).","chicago":"Burg, Max F., Florian Wenzel, Dominik Zietlow, Max Horn, Osama Makansi, Francesco Locatello, and Chris Russell. “A Data Augmentation Perspective on Diffusion Models and Retrieval.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2304.10253\">https://doi.org/10.48550/arXiv.2304.10253</a>.","ista":"Burg MF, Wenzel F, Zietlow D, Horn M, Makansi O, Locatello F, Russell C. A data augmentation perspective on diffusion models and retrieval. arXiv, 2304.10253.","apa":"Burg, M. F., Wenzel, F., Zietlow, D., Horn, M., Makansi, O., Locatello, F., &#38; Russell, C. (n.d.). A data augmentation perspective on diffusion models and retrieval. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2304.10253\">https://doi.org/10.48550/arXiv.2304.10253</a>","mla":"Burg, Max F., et al. “A Data Augmentation Perspective on Diffusion Models and Retrieval.” <i>ArXiv</i>, 2304.10253, doi:<a href=\"https://doi.org/10.48550/arXiv.2304.10253\">10.48550/arXiv.2304.10253</a>."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2023-04-20T00:00:00Z"},{"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2304.07939"}],"publication_status":"submitted","abstract":[{"text":"Recovering the latent factors of variation of high dimensional data has so far focused on simple synthetic settings. Mostly building on unsupervised and weakly-supervised objectives, prior work missed out on the positive implications for representation learning on real world data. In this work, we propose to leverage knowledge extracted from a diversified set of supervised tasks to learn a common disentangled representation. Assuming each supervised task only depends on an unknown subset of the factors of variation, we disentangle the feature space of a supervised multi-task model, with features activating sparsely across different tasks and information being shared as appropriate. Importantly, we never directly observe the factors of variations but establish that access to multiple tasks is sufficient for identifiability under sufficiency and minimality assumptions. We validate our approach on six real world distribution shift benchmarks, and different data modalities (images, text), demonstrating how disentangled representations can be transferred to real settings.","lang":"eng"}],"date_updated":"2024-02-12T09:55:48Z","_id":"14210","type":"preprint","date_created":"2023-08-22T14:19:03Z","doi":"10.48550/arXiv.2304.07939","author":[{"last_name":"Fumero","full_name":"Fumero, Marco","first_name":"Marco"},{"full_name":"Wenzel, Florian","last_name":"Wenzel","first_name":"Florian"},{"first_name":"Luca","full_name":"Zancato, Luca","last_name":"Zancato"},{"first_name":"Alessandro","full_name":"Achille, Alessandro","last_name":"Achille"},{"last_name":"Rodolà","full_name":"Rodolà, Emanuele","first_name":"Emanuele"},{"first_name":"Stefano","full_name":"Soatto, Stefano","last_name":"Soatto"},{"first_name":"Bernhard","last_name":"Schölkopf","full_name":"Schölkopf, Bernhard"},{"orcid":"0000-0002-4850-0683","first_name":"Francesco","last_name":"Locatello","full_name":"Locatello, Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4"}],"article_processing_charge":"No","day":"17","oa_version":"Preprint","title":"Leveraging sparse and shared feature activations for disentangled representation learning","citation":{"mla":"Fumero, Marco, et al. “Leveraging Sparse and Shared Feature Activations for Disentangled Representation Learning.” <i>ArXiv</i>, 2304.07939, doi:<a href=\"https://doi.org/10.48550/arXiv.2304.07939\">10.48550/arXiv.2304.07939</a>.","apa":"Fumero, M., Wenzel, F., Zancato, L., Achille, A., Rodolà, E., Soatto, S., … Locatello, F. (n.d.). Leveraging sparse and shared feature activations for disentangled representation learning. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2304.07939\">https://doi.org/10.48550/arXiv.2304.07939</a>","ista":"Fumero M, Wenzel F, Zancato L, Achille A, Rodolà E, Soatto S, Schölkopf B, Locatello F. Leveraging sparse and shared feature activations for disentangled representation learning. arXiv, 2304.07939.","chicago":"Fumero, Marco, Florian Wenzel, Luca Zancato, Alessandro Achille, Emanuele Rodolà, Stefano Soatto, Bernhard Schölkopf, and Francesco Locatello. “Leveraging Sparse and Shared Feature Activations for Disentangled Representation Learning.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2304.07939\">https://doi.org/10.48550/arXiv.2304.07939</a>.","short":"M. Fumero, F. Wenzel, L. Zancato, A. Achille, E. Rodolà, S. Soatto, B. Schölkopf, F. Locatello, ArXiv (n.d.).","ieee":"M. Fumero <i>et al.</i>, “Leveraging sparse and shared feature activations for disentangled representation learning,” <i>arXiv</i>. .","ama":"Fumero M, Wenzel F, Zancato L, et al. Leveraging sparse and shared feature activations for disentangled representation learning. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2304.07939\">10.48550/arXiv.2304.07939</a>"},"date_published":"2023-04-17T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"publication":"arXiv","language":[{"iso":"eng"}],"status":"public","department":[{"_id":"FrLo"}],"article_number":"2304.07939","year":"2023","external_id":{"arxiv":["2304.07939"]},"month":"04","arxiv":1},{"date_published":"2023-04-01T00:00:00Z","conference":{"start_date":"2023-04-11","end_date":"2023-04-14","name":"CLeaR: Conference on Causal Learning and Reasoning","location":"Tübingen, Germany"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"F. Montagna, N. Noceti, L. Rosasco, K. Zhang, and F. Locatello, “Causal discovery with score matching on additive models with arbitrary noise,” in <i>2nd Conference on Causal Learning and Reasoning</i>, Tübingen, Germany, 2023.","short":"F. Montagna, N. Noceti, L. Rosasco, K. Zhang, F. Locatello, in:, 2nd Conference on Causal Learning and Reasoning, 2023.","ama":"Montagna F, Noceti N, Rosasco L, Zhang K, Locatello F. Causal discovery with score matching on additive models with arbitrary noise. In: <i>2nd Conference on Causal Learning and Reasoning</i>. ; 2023.","apa":"Montagna, F., Noceti, N., Rosasco, L., Zhang, K., &#38; Locatello, F. (2023). Causal discovery with score matching on additive models with arbitrary noise. In <i>2nd Conference on Causal Learning and Reasoning</i>. Tübingen, Germany.","mla":"Montagna, Francesco, et al. “Causal Discovery with Score Matching on Additive Models with Arbitrary Noise.” <i>2nd Conference on Causal Learning and Reasoning</i>, 2023.","chicago":"Montagna, Francesco, Nicoletta Noceti, Lorenzo Rosasco, Kun Zhang, and Francesco Locatello. “Causal Discovery with Score Matching on Additive Models with Arbitrary Noise.” In <i>2nd Conference on Causal Learning and Reasoning</i>, 2023.","ista":"Montagna F, Noceti N, Rosasco L, Zhang K, Locatello F. 2023. Causal discovery with score matching on additive models with arbitrary noise. 2nd Conference on Causal Learning and Reasoning. CLeaR: Conference on Causal Learning and Reasoning."},"publication":"2nd Conference on Causal Learning and Reasoning","status":"public","language":[{"iso":"eng"}],"extern":"1","oa":1,"department":[{"_id":"FrLo"}],"external_id":{"arxiv":["2304.03265"]},"month":"04","arxiv":1,"year":"2023","publication_status":"published","quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/2304.03265","open_access":"1"}],"abstract":[{"lang":"eng","text":"Causal discovery methods are intrinsically constrained by the set of assumptions needed to ensure structure identifiability. Moreover additional restrictions are often imposed in order to simplify the inference task: this is the case for the Gaussian noise assumption on additive non-linear models, which is common to many causal discovery approaches. In this paper we show the shortcomings of inference under this hypothesis, analyzing the risk of edge inversion under violation of Gaussianity of the noise terms. Then, we propose a novel method for inferring the topological ordering of the variables in the causal graph, from data generated according to an additive non-linear model with a generic noise distribution. This leads to NoGAM (Not only Gaussian Additive noise Models), a causal discovery algorithm with a minimal set of assumptions and state of the art performance, experimentally benchmarked on synthetic data."}],"type":"conference","date_created":"2023-08-22T14:19:21Z","date_updated":"2023-09-13T09:00:31Z","_id":"14211","oa_version":"Preprint","title":"Causal discovery with score matching on additive models with arbitrary noise","author":[{"first_name":"Francesco","full_name":"Montagna, Francesco","last_name":"Montagna"},{"first_name":"Nicoletta","last_name":"Noceti","full_name":"Noceti, Nicoletta"},{"first_name":"Lorenzo","last_name":"Rosasco","full_name":"Rosasco, Lorenzo"},{"first_name":"Kun","last_name":"Zhang","full_name":"Zhang, Kun"},{"full_name":"Locatello, Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","last_name":"Locatello","orcid":"0000-0002-4850-0683","first_name":"Francesco"}],"day":"01","scopus_import":"1","article_processing_charge":"No"}]