[{"publication_identifier":{"eissn":["1432-0541"],"issn":["0178-4617"]},"isi":1,"project":[{"grant_number":"101019564","_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62","name":"The design and evaluation of modern fully dynamic data structures","call_identifier":"H2020"},{"_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe","name":"Fast Algorithms for a Reactive Network Layer","grant_number":"P33775 "}],"year":"2023","month":"12","department":[{"_id":"MoHe"}],"article_type":"original","publisher":"Springer Nature","oa_version":"Preprint","type":"journal_article","external_id":{"arxiv":["2010.16316"],"isi":["001041254900002"]},"publication_status":"published","_id":"14043","status":"public","author":[{"orcid":"0000-0002-5008-6530","last_name":"Henzinger","full_name":"Henzinger, Monika H","first_name":"Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630"},{"first_name":"Billy","full_name":"Jin, Billy","last_name":"Jin"},{"first_name":"Richard","last_name":"Peng","full_name":"Peng, Richard"},{"full_name":"Williamson, David P.","last_name":"Williamson","first_name":"David P."}],"date_updated":"2024-01-30T12:33:10Z","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2010.16316"}],"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."}],"scopus_import":"1","page":"2680-3716","title":"A combinatorial cut-toggling algorithm for solving Laplacian linear systems","oa":1,"date_created":"2023-08-13T22:01:13Z","citation":{"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>","ista":"Henzinger MH, Jin B, Peng R, Williamson DP. 2023. A combinatorial cut-toggling algorithm for solving Laplacian linear systems. Algorithmica. 85, 2680–3716.","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.","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>.","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>","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>."},"arxiv":1,"quality_controlled":"1","doi":"10.1007/s00453-023-01154-8","article_processing_charge":"No","ec_funded":1,"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.","day":"01","publication":"Algorithmica","volume":85,"intvolume":"        85","date_published":"2023-12-01T00:00:00Z"},{"citation":{"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.","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.","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.","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>","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>.","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>","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>."},"date_created":"2023-08-15T10:20:40Z","oa":1,"title":"The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation","page":"230","date_published":"2023-08-15T00:00:00Z","has_accepted_license":"1","degree_awarded":"PhD","day":"15","ec_funded":1,"article_processing_charge":"No","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file_date_updated":"2023-08-18T10:47:55Z","doi":"10.15479/at:ista:14058","_id":"14058","alternative_title":["ISTA Thesis"],"publication_status":"published","type":"dissertation","oa_version":"Published Version","file":[{"date_updated":"2023-08-17T06:55:24Z","access_level":"closed","content_type":"application/zip","date_created":"2023-08-16T18:15:17Z","checksum":"4e44e169f2724ee8c9324cd60bcc2b71","file_size":10891454,"file_name":"Thesis_latex_forpdfa.zip","relation":"source_file","file_id":"14075","creator":"gpuixeus"},{"content_type":"application/pdf","access_level":"open_access","date_updated":"2023-08-18T10:47:55Z","checksum":"e10b04cd8f3fecc0d9ef6e6868b6e1e8","success":1,"file_size":19856686,"date_created":"2023-08-18T10:47:55Z","file_name":"PhDThesis_PuixeuG.pdf","creator":"gpuixeus","file_id":"14079","relation":"main_file"}],"ddc":["576"],"supervisor":[{"first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz","last_name":"Vicoso","orcid":"0000-0002-4579-8306"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","full_name":"Barton, Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240"}],"publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"NiBa"},{"_id":"BeVi"}],"year":"2023","month":"08","project":[{"grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"_id":"9B9DFC9E-BA93-11EA-9121-9846C619BF3A","name":"Sexual conflict: resolution, constraints and biomedical implications","grant_number":"25817"}],"publication_identifier":{"isbn":["978-3-99078-035-0"],"issn":["2663-337X"]},"abstract":[{"lang":"eng","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."}],"related_material":{"record":[{"status":"public","relation":"research_data","id":"9803"},{"id":"12933","relation":"research_data","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"6831"},{"id":"14077","relation":"part_of_dissertation","status":"public"}]},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","language":[{"iso":"eng"}],"date_updated":"2023-12-13T12:15:36Z","author":[{"first_name":"Gemma","id":"33AB266C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8330-1754","last_name":"Puixeu Sala","full_name":"Puixeu Sala, Gemma"}],"status":"public","license":"https://creativecommons.org/licenses/by/4.0/"},{"page":"168-190","title":"Monitoring hyperproperties with prefix transducers","oa":1,"quality_controlled":"1","conference":{"location":"Thessaloniki, Greek","end_date":"2023-10-07","start_date":"2023-10-04","name":"RV: Conference on Runtime Verification"},"date_created":"2023-08-16T20:46:08Z","citation":{"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>","short":"M. Chalupa, T.A. Henzinger, in:, 23nd International Conference on Runtime Verification, Springer Nature, 2023, pp. 168–190.","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.","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.","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>","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>.","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>."},"file_date_updated":"2023-10-16T07:15:11Z","doi":"10.1007/978-3-031-44267-4_9","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_processing_charge":"Yes (in subscription journal)","ec_funded":1,"day":"01","publication":"23nd International Conference on Runtime Verification","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.","volume":14245,"date_published":"2023-10-01T00:00:00Z","intvolume":"     14245","has_accepted_license":"1","project":[{"name":"Vigilant Algorithmic Monitoring of Software","call_identifier":"H2020","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","grant_number":"101020093"}],"month":"10","year":"2023","publication_identifier":{"isbn":["978-3-031-44266-7"],"eisbn":["978-3-031-44267-4"]},"department":[{"_id":"ToHe"}],"publisher":"Springer Nature","publication_status":"published","alternative_title":["LNCS"],"_id":"14076","type":"conference","oa_version":"Published Version","ddc":["000"],"file":[{"file_name":"2023_LNCS_RV_Chalupa.pdf","relation":"main_file","file_id":"14430","creator":"dernst","date_updated":"2023-10-16T07:15:11Z","access_level":"open_access","content_type":"application/pdf","date_created":"2023-10-16T07:15:11Z","file_size":867256,"checksum":"ee33bd6f1a26f4dae7a8192584869fd8","success":1}],"status":"public","author":[{"first_name":"Marek","id":"87e34708-d6c6-11ec-9f5b-9391e7be2463","full_name":"Chalupa, Marek","last_name":"Chalupa"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","full_name":"Henzinger, Thomas A","last_name":"Henzinger","orcid":"0000-0002-2985-7724"}],"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-02-28T12:33:08Z","related_material":{"record":[{"id":"15035","status":"public","relation":"research_data"}]},"abstract":[{"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.","lang":"eng"}]},{"keyword":["Genetics (clinical)","Genetics","Molecular Biology"],"related_material":{"record":[{"relation":"research_data","status":"public","id":"12933"},{"id":"14058","relation":"dissertation_contains","status":"public"}]},"abstract":[{"lang":"eng","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."}],"scopus_import":"1","date_updated":"2023-12-13T12:15:37Z","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","author":[{"first_name":"Gemma","id":"33AB266C-F248-11E8-B48F-1D18A9856A87","last_name":"Puixeu Sala","full_name":"Puixeu Sala, Gemma","orcid":"0000-0001-8330-1754"},{"first_name":"Ariana","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","full_name":"Macon, Ariana","last_name":"Macon"},{"orcid":"0000-0002-4579-8306","last_name":"Vicoso","full_name":"Vicoso, Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz"}],"oa_version":"Published Version","type":"journal_article","file":[{"date_updated":"2023-11-07T09:00:19Z","access_level":"open_access","content_type":"application/pdf","date_created":"2023-11-07T09:00:19Z","checksum":"c62e29fc7c5efbf8356f4c60cab4a2d1","file_size":845642,"success":1,"file_name":"2023_G3_Puixeu.pdf","relation":"main_file","file_id":"14498","creator":"dernst"}],"ddc":["570"],"publication_status":"published","external_id":{"isi":["001002997200001"]},"issue":"8","_id":"14077","publisher":"Oxford University Press","department":[{"_id":"BeVi"},{"_id":"NiBa"},{"_id":"GradSch"}],"article_type":"original","publication_identifier":{"issn":["2160-1836"]},"isi":1,"project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385"},{"grant_number":"25817","name":"Sexual conflict: resolution, constraints and biomedical implications","_id":"9B9DFC9E-BA93-11EA-9121-9846C619BF3A"}],"month":"08","year":"2023","intvolume":"        13","has_accepted_license":"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).","publication":"G3: Genes, Genomes, Genetics","day":"01","volume":13,"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ec_funded":1,"article_processing_charge":"Yes","doi":"10.1093/g3journal/jkad121","file_date_updated":"2023-11-07T09:00:19Z","acknowledged_ssus":[{"_id":"ScienComp"}],"date_created":"2023-08-18T06:52:14Z","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>","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).","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.","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>","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>.","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>."},"quality_controlled":"1","oa":1,"title":"Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster"},{"author":[{"first_name":"Tsuyoshi","full_name":"Hirashima, Tsuyoshi","last_name":"Hirashima"},{"last_name":"Hino","full_name":"Hino, Naoya","first_name":"Naoya","id":"5299a9ce-7679-11eb-a7bc-d1e62b936307"},{"first_name":"Kazuhiro","full_name":"Aoki, Kazuhiro","last_name":"Aoki"},{"first_name":"Michiyuki","full_name":"Matsuda, Michiyuki","last_name":"Matsuda"}],"status":"public","scopus_import":"1","abstract":[{"lang":"eng","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."}],"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-01-30T12:52:42Z","article_type":"review","department":[{"_id":"CaHe"}],"month":"10","year":"2023","isi":1,"publication_identifier":{"eissn":["1879-0410"],"issn":["0955-0674"]},"issue":"10","_id":"14080","publication_status":"published","external_id":{"pmid":["37574635"],"isi":["001054692200001"]},"oa_version":"Published Version","type":"journal_article","ddc":["570"],"file":[{"file_name":"2023_CurrentOpinionCellBio_Hirashima.pdf","creator":"dernst","file_id":"14909","relation":"main_file","content_type":"application/pdf","access_level":"open_access","date_updated":"2024-01-30T12:52:12Z","file_size":1173762,"success":1,"checksum":"25923f8ae71344e8974530dd23c71bdc","date_created":"2024-01-30T12:52:12Z"}],"publisher":"Elsevier","article_processing_charge":"Yes (in subscription journal)","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file_date_updated":"2024-01-30T12:52:12Z","doi":"10.1016/j.ceb.2023.102217","date_published":"2023-10-01T00:00:00Z","has_accepted_license":"1","intvolume":"        84","pmid":1,"volume":84,"day":"01","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.","publication":"Current Opinion in Cell Biology","title":"Stretching the limits of extracellular signal-related kinase (ERK) signaling — Cell mechanosensing to ERK activation","quality_controlled":"1","citation":{"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>","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>.","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>.","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>","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.","short":"T. Hirashima, N. Hino, K. Aoki, M. Matsuda, Current Opinion in Cell Biology 84 (2023).","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."},"date_created":"2023-08-20T22:01:12Z","article_number":"102217","oa":1},{"type":"journal_article","ddc":["570"],"file":[{"relation":"main_file","creator":"dernst","file_id":"14092","file_name":"2023_JourCellScience_Higashi.pdf","date_created":"2023-08-21T07:37:54Z","embargo_to":"open_access","checksum":"a399389b7e3d072f1788b63e612a10b3","file_size":18665315,"date_updated":"2023-08-21T07:37:54Z","content_type":"application/pdf","embargo":"2024-08-10","access_level":"closed"}],"oa_version":"None","issue":"15","_id":"14082","external_id":{"isi":["001070149000001"]},"publication_status":"published","publisher":"The Company of Biologists","department":[{"_id":"CaHe"},{"_id":"EvBe"}],"article_type":"original","isi":1,"publication_identifier":{"issn":["0021-9533"],"eissn":["1477-9137"]},"month":"08","year":"2023","project":[{"grant_number":"742573","_id":"260F1432-B435-11E9-9278-68D0E5697425","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","call_identifier":"H2020"}],"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."}],"scopus_import":"1","date_updated":"2023-12-13T12:11:18Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"author":[{"full_name":"Higashi, Tomohito","last_name":"Higashi","first_name":"Tomohito"},{"first_name":"Rachel E.","full_name":"Stephenson, Rachel E.","last_name":"Stephenson"},{"id":"3436488C-F248-11E8-B48F-1D18A9856A87","first_name":"Cornelia","full_name":"Schwayer, Cornelia","last_name":"Schwayer","orcid":"0000-0001-5130-2226"},{"last_name":"Huljev","full_name":"Huljev, Karla","id":"44C6F6A6-F248-11E8-B48F-1D18A9856A87","first_name":"Karla"},{"first_name":"Atsuko Y.","full_name":"Higashi, Atsuko Y.","last_name":"Higashi"},{"first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566"},{"full_name":"Chiba, Hideki","last_name":"Chiba","first_name":"Hideki"},{"last_name":"Miller","full_name":"Miller, Ann L.","first_name":"Ann L."}],"status":"public","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"}],"citation":{"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>.","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>","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>.","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>","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).","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.","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."},"date_created":"2023-08-20T22:01:13Z","quality_controlled":"1","article_number":"jcs260668","title":"ZnUMBA - a live imaging method to detect local barrier breaches","intvolume":"       136","has_accepted_license":"1","date_published":"2023-08-01T00:00:00Z","volume":136,"publication":"Journal of Cell Science","day":"01","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.]. ","article_processing_charge":"No","ec_funded":1,"doi":"10.1242/jcs.260668","file_date_updated":"2023-08-21T07:37:54Z"},{"status":"public","author":[{"last_name":"Resch","full_name":"Resch, Nicolas","first_name":"Nicolas"},{"first_name":"Chen","last_name":"Yuan","full_name":"Yuan, Chen"},{"first_name":"Yihan","id":"2ce5da42-b2ea-11eb-bba5-9f264e9d002c","full_name":"Zhang, Yihan","last_name":"Zhang","orcid":"0000-0002-6465-6258"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"date_updated":"2023-08-21T07:26:01Z","scopus_import":"1","abstract":[{"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.","lang":"eng"}],"month":"07","year":"2023","publication_identifier":{"issn":["1868-8969"],"isbn":["9783959772785"]},"department":[{"_id":"MaMo"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","external_id":{"arxiv":["2210.07754"]},"publication_status":"published","alternative_title":["LIPIcs"],"_id":"14083","file":[{"file_id":"14091","creator":"dernst","relation":"main_file","file_name":"2023_LIPIcsICALP_Resch.pdf","file_size":1141497,"success":1,"checksum":"a449143fec3fbebb092cb8ef3b53c226","date_created":"2023-08-21T07:23:18Z","access_level":"open_access","content_type":"application/pdf","date_updated":"2023-08-21T07:23:18Z"}],"type":"conference","oa_version":"Published Version","ddc":["000"],"file_date_updated":"2023-08-21T07:23:18Z","doi":"10.4230/LIPIcs.ICALP.2023.99","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_processing_charge":"Yes","day":"01","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","volume":261,"date_published":"2023-07-01T00:00:00Z","intvolume":"       261","has_accepted_license":"1","title":"Zero-rate thresholds and new capacity bounds for list-decoding and list-recovery","oa":1,"article_number":"99","quality_controlled":"1","arxiv":1,"conference":{"start_date":"2023-07-10","name":"ICALP: International Colloquium on Automata, Languages, and Programming","location":"Paderborn, Germany","end_date":"2023-07-14"},"citation":{"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>.","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>.","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>","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.","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.","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>"},"date_created":"2023-08-20T22:01:13Z"},{"article_processing_charge":"Yes","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file_date_updated":"2023-08-21T06:45:16Z","doi":"10.4230/LIPIcs.ICALP.2023.72","date_published":"2023-07-01T00:00:00Z","intvolume":"       261","has_accepted_license":"1","volume":261,"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.","day":"01","title":"Parameter estimation for Gibbs distributions","conference":{"start_date":"2023-07-10","name":"ICALP: International Colloquium on Automata, Languages, and Programming","location":"Paderborn, Germany","end_date":"2023-07-14"},"arxiv":1,"quality_controlled":"1","date_created":"2023-08-20T22:01:14Z","citation":{"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.","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.","short":"D.G. Harris, V. Kolmogorov, in:, 50th International Colloquium on Automata, Languages, and Programming, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023.","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>","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>.","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>."},"article_number":"72","oa":1,"author":[{"full_name":"Harris, David G.","last_name":"Harris","first_name":"David G."},{"first_name":"Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","last_name":"Kolmogorov","full_name":"Kolmogorov, Vladimir"}],"status":"public","scopus_import":"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"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"date_updated":"2023-08-21T06:49:11Z","department":[{"_id":"VlKo"}],"year":"2023","month":"07","publication_identifier":{"issn":["1868-8969"],"isbn":["9783959772785"]},"_id":"14084","publication_status":"published","external_id":{"arxiv":["2007.10824"]},"alternative_title":["LIPIcs"],"oa_version":"Published Version","type":"conference","ddc":["000","510"],"file":[{"checksum":"6dee0684245bb1c524b9c955db1e933d","success":1,"file_size":917791,"date_created":"2023-08-21T06:45:16Z","access_level":"open_access","content_type":"application/pdf","date_updated":"2023-08-21T06:45:16Z","file_id":"14088","creator":"dernst","relation":"main_file","file_name":"2023_LIPIcsICALP_Harris.pdf"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik"},{"status":"public","author":[{"last_name":"Goranci","full_name":"Goranci, Gramoz","first_name":"Gramoz"},{"orcid":"0000-0002-5008-6530","last_name":"Henzinger","full_name":"Henzinger, Monika H","first_name":"Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630"}],"scopus_import":"1","abstract":[{"lang":"eng","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."}],"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-08-21T07:00:49Z","department":[{"_id":"MoHe"}],"project":[{"_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62","name":"The design and evaluation of modern fully dynamic data structures","call_identifier":"H2020","grant_number":"101019564"},{"name":"Static and Dynamic Hierarchical Graph Decompositions","_id":"bda196b2-d553-11ed-ba76-8e8ee6c21103","grant_number":"I05982"},{"grant_number":"P33775 ","_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe","name":"Fast Algorithms for a Reactive Network Layer"}],"year":"2023","month":"07","publication_identifier":{"issn":["1868-8969"],"isbn":["9783959772785"]},"alternative_title":["LIPIcs"],"publication_status":"published","external_id":{"unknown":["2211.09606"]},"_id":"14085","type":"conference","ddc":["000"],"oa_version":"Published Version","file":[{"relation":"main_file","creator":"dernst","file_id":"14089","file_name":"2023_LIPIcsICALP_Goranci.pdf","date_created":"2023-08-21T06:59:05Z","success":1,"checksum":"074177e815a1656de5d4071c7a3dffa6","file_size":875910,"date_updated":"2023-08-21T06:59:05Z","content_type":"application/pdf","access_level":"open_access"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ec_funded":1,"article_processing_charge":"Yes","file_date_updated":"2023-08-21T06:59:05Z","doi":"10.4230/LIPIcs.ICALP.2023.69","date_published":"2023-07-01T00:00:00Z","has_accepted_license":"1","intvolume":"       261","publication":"50th International Colloquium on Automata, Languages, and Programming","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.","day":"01","volume":261,"title":"Efficient data structures for incremental exact and approximate maximum flow","quality_controlled":"1","conference":{"location":"Paderborn, Germany","end_date":"2023-07-14","start_date":"2023-07-10","name":"ICALP: International Colloquium on Automata, Languages, and Programming"},"citation":{"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>.","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>","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>.","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>","short":"G. Goranci, M.H. Henzinger, in:, 50th International Colloquium on Automata, Languages, and Programming, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023.","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.","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."},"date_created":"2023-08-20T22:01:14Z","oa":1,"article_number":"69"},{"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_processing_charge":"Yes","ec_funded":1,"file_date_updated":"2023-08-21T07:04:36Z","doi":"10.4230/LIPIcs.ICALP.2023.74","date_published":"2023-07-01T00:00:00Z","intvolume":"       261","has_accepted_license":"1","publication":"50th International Colloquium on Automata, Languages, and Programming","day":"01","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.","volume":261,"title":"Faster submodular maximization for several classes of matroids","quality_controlled":"1","arxiv":1,"conference":{"name":"ICALP: International Colloquium on Automata, Languages, and Programming","start_date":"2023-07-10","end_date":"2023-07-14","location":"Paderborn, Germany"},"date_created":"2023-08-20T22:01:14Z","citation":{"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>.","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>.","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>","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.","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.","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.","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>"},"oa":1,"article_number":"74","status":"public","author":[{"first_name":"Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","last_name":"Henzinger","full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530"},{"first_name":"Paul","last_name":"Liu","full_name":"Liu, Paul"},{"first_name":"Jan","last_name":"Vondrák","full_name":"Vondrák, Jan"},{"last_name":"Zheng","full_name":"Zheng, Da Wei","first_name":"Da Wei"}],"scopus_import":"1","abstract":[{"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.","lang":"eng"}],"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-08-21T07:05:47Z","department":[{"_id":"MoHe"}],"project":[{"name":"The design and evaluation of modern fully dynamic data structures","call_identifier":"H2020","_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62","grant_number":"101019564"},{"grant_number":"I05982","name":"Static and Dynamic Hierarchical Graph Decompositions","_id":"bda196b2-d553-11ed-ba76-8e8ee6c21103"},{"name":"Fast Algorithms for a Reactive Network Layer","_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe","grant_number":"P33775 "}],"month":"07","year":"2023","publication_identifier":{"isbn":["9783959772785"],"issn":["18688969"]},"external_id":{"arxiv":["2305.00122"]},"publication_status":"published","alternative_title":["LIPIcs"],"_id":"14086","ddc":["000"],"file":[{"date_updated":"2023-08-21T07:04:36Z","content_type":"application/pdf","access_level":"open_access","date_created":"2023-08-21T07:04:36Z","checksum":"a5eef225014e003efbfbe4830fdd23cb","success":1,"file_size":930943,"file_name":"2023_LIPIcsICALP_HenzingerM.pdf","relation":"main_file","creator":"dernst","file_id":"14090"}],"oa_version":"Published Version","type":"conference","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik"},{"article_processing_charge":"No","doi":"10.1109/wacv56688.2023.00278","date_published":"2023-02-06T00:00:00Z","publication":"2023 IEEE/CVF Winter Conference on Applications of Computer Vision","day":"06","title":"TeST: Test-time Self-Training under distribution shift","arxiv":1,"quality_controlled":"1","conference":{"end_date":"2023-01-07","location":"Waikoloa, HI, United States","name":"WACV: Winter Conference on Applications of Computer Vision","start_date":"2023-01-02"},"date_created":"2023-08-21T12:11:38Z","citation":{"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>.","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>","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>.","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.","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.","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>"},"oa":1,"status":"public","author":[{"full_name":"Sinha, Samarth","last_name":"Sinha","first_name":"Samarth"},{"full_name":"Gehler, Peter","last_name":"Gehler","first_name":"Peter"},{"first_name":"Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","orcid":"0000-0002-4850-0683","full_name":"Locatello, Francesco","last_name":"Locatello"},{"first_name":"Bernt","full_name":"Schiele, Bernt","last_name":"Schiele"}],"scopus_import":"1","extern":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2209.11459"}],"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. "}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"date_updated":"2023-09-06T10:26:56Z","department":[{"_id":"FrLo"}],"month":"02","year":"2023","publication_identifier":{"isbn":["9781665493475"],"eissn":["2642-9381"]},"external_id":{"arxiv":["2209.11459"]},"publication_status":"published","_id":"14105","type":"conference","oa_version":"Preprint","publisher":"Institute of Electrical and Electronics Engineers"},{"doi":"10.1007/s11040-023-09460-x","file_date_updated":"2023-08-23T10:59:15Z","article_processing_charge":"Yes (via OA deal)","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"volume":26,"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.","publication":"Mathematical Physics, Analysis and Geometry","day":"26","intvolume":"        26","has_accepted_license":"1","date_published":"2023-07-26T00:00:00Z","title":"On the global minimum of the energy–momentum relation for the polaron","article_number":"17","oa":1,"date_created":"2023-08-22T14:09:47Z","citation":{"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>","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>.","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>","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.","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.","short":"J. Lampart, D.J. Mitrouskas, K. Mysliwy, Mathematical Physics, Analysis and Geometry 26 (2023)."},"arxiv":1,"quality_controlled":"1","author":[{"first_name":"Jonas","last_name":"Lampart","full_name":"Lampart, Jonas"},{"last_name":"Mitrouskas","full_name":"Mitrouskas, David Johannes","first_name":"David Johannes","id":"cbddacee-2b11-11eb-a02e-a2e14d04e52d"},{"full_name":"Mysliwy, Krzysztof","last_name":"Mysliwy","id":"316457FC-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof"}],"status":"public","date_updated":"2023-12-13T12:16:19Z","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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"}],"keyword":["Geometry and Topology","Mathematical Physics"],"scopus_import":"1","isi":1,"publication_identifier":{"eissn":["1572-9656"],"issn":["1385-0172"]},"year":"2023","month":"07","department":[{"_id":"RoSe"}],"article_type":"original","publisher":"Springer Nature","ddc":["510"],"file":[{"content_type":"application/pdf","access_level":"open_access","date_updated":"2023-08-23T10:59:15Z","file_size":317026,"checksum":"f0941cc66cb3ed06a12ca4b7e356cfd6","success":1,"date_created":"2023-08-23T10:59:15Z","file_name":"2023_MathPhysics_Lampart.pdf","creator":"dernst","file_id":"14225","relation":"main_file"}],"oa_version":"Published Version","type":"journal_article","issue":"3","_id":"14192","external_id":{"isi":["001032992600001"],"arxiv":["2206.14708"]},"publication_status":"published"},{"_id":"14207","publication_status":"submitted","arxiv":1,"external_id":{"arxiv":["2306.00600"]},"citation":{"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>","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>.","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>.","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>","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.).","ista":"Löwe S, Lippe P, Locatello F, Welling M. Rotating features for object discovery. arXiv, 2306.00600."},"date_created":"2023-08-22T14:18:00Z","oa_version":"Preprint","type":"preprint","article_number":"2306.00600","oa":1,"title":"Rotating features for object discovery","department":[{"_id":"FrLo"}],"month":"06","year":"2023","date_published":"2023-06-01T00:00:00Z","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"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2306.00600"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"date_updated":"2024-02-12T09:53:44Z","day":"01","publication":"arXiv","author":[{"full_name":"Löwe, Sindy","last_name":"Löwe","first_name":"Sindy"},{"first_name":"Phillip","full_name":"Lippe, Phillip","last_name":"Lippe"},{"id":"26cfd52f-2483-11ee-8040-88983bcc06d4","first_name":"Francesco","last_name":"Locatello","full_name":"Locatello, Francesco","orcid":"0000-0002-4850-0683"},{"first_name":"Max","full_name":"Welling, Max","last_name":"Welling"}],"article_processing_charge":"No","status":"public","doi":"10.48550/arXiv.2306.00600"},{"abstract":[{"lang":"eng","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."}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2305.19377"}],"extern":"1","date_updated":"2023-09-13T08:46:46Z","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Zhenyu","full_name":"Zhu, Zhenyu","last_name":"Zhu"},{"last_name":"Liu","full_name":"Liu, Fanghui","first_name":"Fanghui"},{"first_name":"Grigorios G","last_name":"Chrysos","full_name":"Chrysos, Grigorios G"},{"orcid":"0000-0002-4850-0683","full_name":"Locatello, Francesco","last_name":"Locatello","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","first_name":"Francesco"},{"first_name":"Volkan","full_name":"Cevher, Volkan","last_name":"Cevher"}],"status":"public","type":"conference","oa_version":"Preprint","_id":"14208","external_id":{"arxiv":["2305.19377"]},"publication_status":"published","alternative_title":["PMLR"],"publisher":"ML Research Press","department":[{"_id":"FrLo"}],"year":"2023","month":"05","intvolume":"       202","date_published":"2023-05-30T00:00:00Z","volume":202,"publication":"Proceedings of the 40th International Conference on Machine Learning","day":"30","article_processing_charge":"No","citation":{"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.","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.","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.","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.","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."},"date_created":"2023-08-22T14:18:18Z","conference":{"end_date":"2023-07-29","location":"Honolulu, Hawaii, United States","start_date":"2023-07-23","name":"International Conference on Machine Learning"},"arxiv":1,"quality_controlled":"1","oa":1,"title":"Benign overfitting in deep neural networks under lazy training","page":"43105-43128"},{"title":"A data augmentation perspective on diffusion models and retrieval","department":[{"_id":"FrLo"}],"month":"04","year":"2023","_id":"14209","external_id":{"arxiv":["2304.10253"]},"publication_status":"submitted","arxiv":1,"date_created":"2023-08-22T14:18:43Z","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>","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.","short":"M.F. Burg, F. Wenzel, D. Zietlow, M. Horn, O. Makansi, F. Locatello, C. Russell, ArXiv (n.d.).","ieee":"M. F. Burg <i>et al.</i>, “A data augmentation perspective on diffusion models and retrieval,” <i>arXiv</i>. .","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>.","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>","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>."},"type":"preprint","oa_version":"Preprint","article_number":"2304.10253","oa":1,"article_processing_charge":"No","author":[{"first_name":"Max F.","last_name":"Burg","full_name":"Burg, Max F."},{"last_name":"Wenzel","full_name":"Wenzel, Florian","first_name":"Florian"},{"full_name":"Zietlow, Dominik","last_name":"Zietlow","first_name":"Dominik"},{"first_name":"Max","last_name":"Horn","full_name":"Horn, Max"},{"first_name":"Osama","full_name":"Makansi, Osama","last_name":"Makansi"},{"orcid":"0000-0002-4850-0683","last_name":"Locatello","full_name":"Locatello, Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","first_name":"Francesco"},{"first_name":"Chris","last_name":"Russell","full_name":"Russell, Chris"}],"status":"public","doi":"10.48550/arXiv.2304.10253","date_published":"2023-04-20T00:00:00Z","extern":"1","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":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2304.10253"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"date_updated":"2023-09-13T08:51:56Z","day":"20","publication":"arXiv"},{"doi":"10.48550/arXiv.2304.07939","status":"public","article_processing_charge":"No","author":[{"last_name":"Fumero","full_name":"Fumero, Marco","first_name":"Marco"},{"first_name":"Florian","last_name":"Wenzel","full_name":"Wenzel, Florian"},{"first_name":"Luca","last_name":"Zancato","full_name":"Zancato, Luca"},{"first_name":"Alessandro","last_name":"Achille","full_name":"Achille, Alessandro"},{"last_name":"Rodolà","full_name":"Rodolà, Emanuele","first_name":"Emanuele"},{"first_name":"Stefano","full_name":"Soatto, Stefano","last_name":"Soatto"},{"last_name":"Schölkopf","full_name":"Schölkopf, Bernhard","first_name":"Bernhard"},{"id":"26cfd52f-2483-11ee-8040-88983bcc06d4","first_name":"Francesco","last_name":"Locatello","full_name":"Locatello, Francesco","orcid":"0000-0002-4850-0683"}],"publication":"arXiv","day":"17","date_updated":"2024-02-12T09:55:48Z","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2304.07939"}],"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_published":"2023-04-17T00:00:00Z","month":"04","year":"2023","department":[{"_id":"FrLo"}],"title":"Leveraging sparse and shared feature activations for disentangled representation learning","oa":1,"article_number":"2304.07939","oa_version":"Preprint","type":"preprint","date_created":"2023-08-22T14:19:03Z","citation":{"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>","ieee":"M. Fumero <i>et al.</i>, “Leveraging sparse and shared feature activations for disentangled representation learning,” <i>arXiv</i>. .","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.","short":"M. Fumero, F. Wenzel, L. Zancato, A. Achille, E. Rodolà, S. Soatto, B. Schölkopf, F. Locatello, ArXiv (n.d.).","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>","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>."},"publication_status":"submitted","external_id":{"arxiv":["2304.07939"]},"arxiv":1,"_id":"14210"},{"year":"2023","month":"04","title":"Causal discovery with score matching on additive models with arbitrary noise","department":[{"_id":"FrLo"}],"oa":1,"conference":{"end_date":"2023-04-14","location":"Tübingen, Germany","start_date":"2023-04-11","name":"CLeaR: Conference on Causal Learning and Reasoning"},"_id":"14211","publication_status":"published","quality_controlled":"1","arxiv":1,"external_id":{"arxiv":["2304.03265"]},"date_created":"2023-08-22T14:19:21Z","citation":{"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.","short":"F. Montagna, N. Noceti, L. Rosasco, K. Zhang, F. Locatello, in:, 2nd Conference on Causal Learning and Reasoning, 2023.","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.","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.","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.","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."},"type":"conference","oa_version":"Preprint","article_processing_charge":"No","author":[{"first_name":"Francesco","last_name":"Montagna","full_name":"Montagna, Francesco"},{"full_name":"Noceti, Nicoletta","last_name":"Noceti","first_name":"Nicoletta"},{"full_name":"Rosasco, Lorenzo","last_name":"Rosasco","first_name":"Lorenzo"},{"first_name":"Kun","last_name":"Zhang","full_name":"Zhang, Kun"},{"last_name":"Locatello","full_name":"Locatello, Francesco","orcid":"0000-0002-4850-0683","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","first_name":"Francesco"}],"status":"public","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-09-13T09:00:31Z","day":"01","publication":"2nd Conference on Causal Learning and Reasoning","extern":"1","date_published":"2023-04-01T00:00:00Z","scopus_import":"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."}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2304.03265"}]},{"status":"public","article_processing_charge":"No","author":[{"last_name":"Montagna","full_name":"Montagna, Francesco","first_name":"Francesco"},{"first_name":"Nicoletta","last_name":"Noceti","full_name":"Noceti, Nicoletta"},{"full_name":"Rosasco, Lorenzo","last_name":"Rosasco","first_name":"Lorenzo"},{"first_name":"Kun","full_name":"Zhang, Kun","last_name":"Zhang"},{"full_name":"Locatello, Francesco","last_name":"Locatello","orcid":"0000-0002-4850-0683","first_name":"Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4"}],"main_file_link":[{"url":"https://arxiv.org/abs/2304.03382","open_access":"1"}],"abstract":[{"text":"This paper demonstrates how to discover the whole causal graph from the second derivative of the log-likelihood in observational non-linear additive Gaussian noise models. Leveraging scalable machine learning approaches to approximate the score function ∇logp(X), we extend the work of Rolland et al. (2022) that only recovers the topological order from the score and requires an expensive pruning step removing spurious edges among those admitted by the ordering. Our analysis leads to DAS (acronym for Discovery At Scale), a practical algorithm that reduces the complexity of the pruning by a factor proportional to the graph size. In practice, DAS achieves competitive accuracy with current state-of-the-art while being over an order of magnitude faster. Overall, our approach enables principled and scalable causal discovery, significantly lowering the compute bar.","lang":"eng"}],"extern":"1","scopus_import":"1","date_published":"2023-04-01T00:00:00Z","day":"01","publication":"2nd Conference on Causal Learning and Reasoning","date_updated":"2023-09-13T09:03:24Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"department":[{"_id":"FrLo"}],"title":"Scalable causal discovery with score matching","month":"04","year":"2023","type":"conference","oa_version":"Preprint","date_created":"2023-08-22T14:19:40Z","citation":{"ama":"Montagna F, Noceti N, Rosasco L, Zhang K, Locatello F. Scalable causal discovery with score matching. In: <i>2nd Conference on Causal Learning and Reasoning</i>. ; 2023.","short":"F. Montagna, N. Noceti, L. Rosasco, K. Zhang, F. Locatello, in:, 2nd Conference on Causal Learning and Reasoning, 2023.","ieee":"F. Montagna, N. Noceti, L. Rosasco, K. Zhang, and F. Locatello, “Scalable causal discovery with score matching,” in <i>2nd Conference on Causal Learning and Reasoning</i>, Tübingen, Germany, 2023.","ista":"Montagna F, Noceti N, Rosasco L, Zhang K, Locatello F. 2023. Scalable causal discovery with score matching. 2nd Conference on Causal Learning and Reasoning. CLeaR: Conference on Causal Learning and Reasoning.","apa":"Montagna, F., Noceti, N., Rosasco, L., Zhang, K., &#38; Locatello, F. (2023). Scalable causal discovery with score matching. In <i>2nd Conference on Causal Learning and Reasoning</i>. Tübingen, Germany.","chicago":"Montagna, Francesco, Nicoletta Noceti, Lorenzo Rosasco, Kun Zhang, and Francesco Locatello. “Scalable Causal Discovery with Score Matching.” In <i>2nd Conference on Causal Learning and Reasoning</i>, 2023.","mla":"Montagna, Francesco, et al. “Scalable Causal Discovery with Score Matching.” <i>2nd Conference on Causal Learning and Reasoning</i>, 2023."},"arxiv":1,"external_id":{"arxiv":["2304.03382"]},"publication_status":"published","quality_controlled":"1","_id":"14212","conference":{"end_date":"2023-04-14","location":"Tübingen, Germany","name":"CLeaR: Conference on Causal Learning and Reasoning","start_date":"2023-04-11"},"oa":1},{"month":"04","year":"2023","department":[{"_id":"FrLo"}],"title":"Causal triplet: An open challenge for intervention-centric causal representation learning","oa":1,"type":"conference","oa_version":"Preprint","citation":{"ista":"Liu Y, Alahi A, Russell C, Horn M, Zietlow D, Schölkopf B, Locatello F. 2023. Causal triplet: An open challenge for intervention-centric causal representation learning. 2nd Conference on Causal Learning and Reasoning. CLeaR: Conference on Causal Learning and Reasoning.","ieee":"Y. Liu <i>et al.</i>, “Causal triplet: An open challenge for intervention-centric causal representation learning,” in <i>2nd Conference on Causal Learning and Reasoning</i>, Tübingen, Germany, 2023.","short":"Y. Liu, A. Alahi, C. Russell, M. Horn, D. Zietlow, B. Schölkopf, F. Locatello, in:, 2nd Conference on Causal Learning and Reasoning, 2023.","ama":"Liu Y, Alahi A, Russell C, et al. Causal triplet: An open challenge for intervention-centric causal representation learning. In: <i>2nd Conference on Causal Learning and Reasoning</i>. ; 2023.","chicago":"Liu, Yuejiang, Alexandre Alahi, Chris Russell, Max Horn, Dominik Zietlow, Bernhard Schölkopf, and Francesco Locatello. “Causal Triplet: An Open Challenge for Intervention-Centric Causal Representation Learning.” In <i>2nd Conference on Causal Learning and Reasoning</i>, 2023.","apa":"Liu, Y., Alahi, A., Russell, C., Horn, M., Zietlow, D., Schölkopf, B., &#38; Locatello, F. (2023). Causal triplet: An open challenge for intervention-centric causal representation learning. In <i>2nd Conference on Causal Learning and Reasoning</i>. Tübingen, Germany.","mla":"Liu, Yuejiang, et al. “Causal Triplet: An Open Challenge for Intervention-Centric Causal Representation Learning.” <i>2nd Conference on Causal Learning and Reasoning</i>, 2023."},"date_created":"2023-08-22T14:20:18Z","quality_controlled":"1","publication_status":"published","external_id":{"arxiv":["2301.05169"]},"arxiv":1,"_id":"14214","conference":{"end_date":"2023-04-14","location":"Tübingen, Germany","start_date":"2023-04-11","name":"CLeaR: Conference on Causal Learning and Reasoning"},"status":"public","article_processing_charge":"No","author":[{"first_name":"Yuejiang","full_name":"Liu, Yuejiang","last_name":"Liu"},{"last_name":"Alahi","full_name":"Alahi, Alexandre","first_name":"Alexandre"},{"full_name":"Russell, Chris","last_name":"Russell","first_name":"Chris"},{"full_name":"Horn, Max","last_name":"Horn","first_name":"Max"},{"full_name":"Zietlow, Dominik","last_name":"Zietlow","first_name":"Dominik"},{"full_name":"Schölkopf, Bernhard","last_name":"Schölkopf","first_name":"Bernhard"},{"full_name":"Locatello, Francesco","last_name":"Locatello","orcid":"0000-0002-4850-0683","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","first_name":"Francesco"}],"day":"12","publication":"2nd Conference on Causal Learning and Reasoning","date_updated":"2023-09-13T09:23:08Z","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2301.05169"}],"abstract":[{"text":"Recent years have seen a surge of interest in learning high-level causal representations from low-level image pairs under interventions. Yet, existing efforts are largely limited to simple synthetic settings that are far away from real-world problems. In this paper, we present Causal Triplet, a causal representation learning benchmark featuring not only visually more complex scenes, but also two crucial desiderata commonly overlooked in previous works: (i) an actionable counterfactual setting, where only certain object-level variables allow for counterfactual observations whereas others do not; (ii) an interventional downstream task with an emphasis on out-of-distribution robustness from the independent causal mechanisms principle. Through extensive experiments, we find that models built with the knowledge of disentangled or object-centric representations significantly outperform their distributed counterparts. However, recent causal representation learning methods still struggle to identify such latent structures, indicating substantial challenges and opportunities for future work.","lang":"eng"}],"date_published":"2023-04-12T00:00:00Z","extern":"1"},{"article_processing_charge":"No","author":[{"first_name":"Luca","last_name":"Moschella","full_name":"Moschella, Luca"},{"first_name":"Valentino","full_name":"Maiorca, Valentino","last_name":"Maiorca"},{"last_name":"Fumero","full_name":"Fumero, Marco","first_name":"Marco"},{"full_name":"Norelli, Antonio","last_name":"Norelli","first_name":"Antonio"},{"last_name":"Locatello","full_name":"Locatello, Francesco","orcid":"0000-0002-4850-0683","first_name":"Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4"},{"first_name":"Emanuele","full_name":"Rodolà, Emanuele","last_name":"Rodolà"}],"status":"public","date_published":"2023-05-01T00:00:00Z","extern":"1","abstract":[{"text":"Neural networks embed the geometric structure of a data manifold lying in a high-dimensional space into latent representations. Ideally, the distribution of the data points in the latent space should depend only on the task, the data, the loss, and other architecture-specific constraints. However, factors such as the random weights initialization, training hyperparameters, or other sources of randomness in the training phase may induce incoherent latent spaces that hinder any form of reuse. Nevertheless, we empirically observe that, under the same data and modeling choices, the angles between the encodings within distinct latent spaces do not change. In this work, we propose the latent similarity between each sample and a fixed set of anchors as an alternative data representation, demonstrating that it can enforce the desired invariances without any additional training. We show how neural architectures can leverage these relative representations to guarantee, in practice, invariance to latent isometries and rescalings, effectively enabling latent space communication: from zero-shot model stitching to latent space comparison between diverse settings. We extensively validate the generalization capability of our approach on different datasets, spanning various modalities (images, text, graphs), tasks (e.g., classification, reconstruction) and architectures (e.g., CNNs, GCNs, transformers).","lang":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/2209.15430","open_access":"1"}],"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-09-13T09:44:26Z","day":"01","publication":"The 11th International Conference on Learning Representations","title":"Relative representations enable zero-shot latent space communication","department":[{"_id":"FrLo"}],"month":"05","year":"2023","_id":"14217","conference":{"location":"Kigali, Rwanda","end_date":"2023-05-05","start_date":"2023-05-01","name":"International Conference on Machine Learning Representations"},"external_id":{"arxiv":["2209.15430"]},"publication_status":"published","quality_controlled":"1","arxiv":1,"date_created":"2023-08-22T14:22:20Z","citation":{"short":"L. Moschella, V. Maiorca, M. Fumero, A. Norelli, F. Locatello, E. Rodolà, in:, The 11th International Conference on Learning Representations, 2023.","ista":"Moschella L, Maiorca V, Fumero M, Norelli A, Locatello F, Rodolà E. 2023. Relative representations enable zero-shot latent space communication. The 11th International Conference on Learning Representations. International Conference on Machine Learning Representations.","ieee":"L. Moschella, V. Maiorca, M. Fumero, A. Norelli, F. Locatello, and E. Rodolà, “Relative representations enable zero-shot latent space communication,” in <i>The 11th International Conference on Learning Representations</i>, Kigali, Rwanda, 2023.","ama":"Moschella L, Maiorca V, Fumero M, Norelli A, Locatello F, Rodolà E. Relative representations enable zero-shot latent space communication. In: <i>The 11th International Conference on Learning Representations</i>. ; 2023.","mla":"Moschella, Luca, et al. “Relative Representations Enable Zero-Shot Latent Space Communication.” <i>The 11th International Conference on Learning Representations</i>, 2023.","chicago":"Moschella, Luca, Valentino Maiorca, Marco Fumero, Antonio Norelli, Francesco Locatello, and Emanuele Rodolà. “Relative Representations Enable Zero-Shot Latent Space Communication.” In <i>The 11th International Conference on Learning Representations</i>, 2023.","apa":"Moschella, L., Maiorca, V., Fumero, M., Norelli, A., Locatello, F., &#38; Rodolà, E. (2023). Relative representations enable zero-shot latent space communication. In <i>The 11th International Conference on Learning Representations</i>. Kigali, Rwanda."},"oa_version":"Preprint","type":"conference","oa":1}]