[{"department":[{"_id":"JuFi"},{"_id":"GradSch"}],"publisher":"Instytut Matematyczny","publication_status":"published","year":"2020","volume":252,"date_updated":"2023-10-17T09:15:53Z","date_created":"2021-02-25T08:55:03Z","author":[{"full_name":"Hensel, Sebastian","first_name":"Sebastian","last_name":"Hensel","id":"4D23B7DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7252-8072"},{"first_name":"Tommaso","last_name":"Rosati","full_name":"Rosati, Tommaso"}],"isi":1,"quality_controlled":"1","external_id":{"arxiv":["1709.05202"],"isi":["000558100500002"]},"language":[{"iso":"eng"}],"doi":"10.4064/sm180411-11-2","publication_identifier":{"eissn":["1730-6337"],"issn":["0039-3223"]},"month":"03","intvolume":" 252","title":"Modelled distributions of Triebel–Lizorkin type","status":"public","_id":"9196","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","type":"journal_article","issue":"3","abstract":[{"text":"In order to provide a local description of a regular function in a small neighbourhood of a point x, it is sufficient by Taylor’s theorem to know the value of the function as well as all of its derivatives up to the required order at the point x itself. In other words, one could say that a regular function is locally modelled by the set of polynomials. The theory of regularity structures due to Hairer generalizes this observation and provides an abstract setup, which in the application to singular SPDE extends the set of polynomials by functionals constructed from, e.g., white noise. In this context, the notion of Taylor polynomials is lifted to the notion of so-called modelled distributions. The celebrated reconstruction theorem, which in turn was inspired by Gubinelli’s \\textit {sewing lemma}, is of paramount importance for the theory. It enables one to reconstruct a modelled distribution as a true distribution on Rd which is locally approximated by this extended set of models or “monomials”. In the original work of Hairer, the error is measured by means of Hölder norms. This was then generalized to the whole scale of Besov spaces by Hairer and Labbé. It is the aim of this work to adapt the analytic part of the theory of regularity structures to the scale of Triebel–Lizorkin spaces.","lang":"eng"}],"page":"251-297","article_type":"original","citation":{"ista":"Hensel S, Rosati T. 2020. Modelled distributions of Triebel–Lizorkin type. Studia Mathematica. 252(3), 251–297.","apa":"Hensel, S., & Rosati, T. (2020). Modelled distributions of Triebel–Lizorkin type. Studia Mathematica. Instytut Matematyczny. https://doi.org/10.4064/sm180411-11-2","ieee":"S. Hensel and T. Rosati, “Modelled distributions of Triebel–Lizorkin type,” Studia Mathematica, vol. 252, no. 3. Instytut Matematyczny, pp. 251–297, 2020.","ama":"Hensel S, Rosati T. Modelled distributions of Triebel–Lizorkin type. Studia Mathematica. 2020;252(3):251-297. doi:10.4064/sm180411-11-2","chicago":"Hensel, Sebastian, and Tommaso Rosati. “Modelled Distributions of Triebel–Lizorkin Type.” Studia Mathematica. Instytut Matematyczny, 2020. https://doi.org/10.4064/sm180411-11-2.","mla":"Hensel, Sebastian, and Tommaso Rosati. “Modelled Distributions of Triebel–Lizorkin Type.” Studia Mathematica, vol. 252, no. 3, Instytut Matematyczny, 2020, pp. 251–97, doi:10.4064/sm180411-11-2.","short":"S. Hensel, T. Rosati, Studia Mathematica 252 (2020) 251–297."},"publication":"Studia Mathematica","date_published":"2020-03-01T00:00:00Z","keyword":["General Mathematics"],"scopus_import":"1","article_processing_charge":"No","day":"01"},{"issue":"1","abstract":[{"text":"Retrovirus assembly is driven by the multidomain structural protein Gag. Interactions between the capsid domains (CA) of Gag result in Gag multimerization, leading to an immature virus particle that is formed by a protein lattice based on dimeric, trimeric, and hexameric protein contacts. Among retroviruses the inter- and intra-hexamer contacts differ, especially in the N-terminal sub-domain of CA (CANTD). For HIV-1 the cellular molecule inositol hexakisphosphate (IP6) interacts with and stabilizes the immature hexamer, and is required for production of infectious virus particles. We have used in vitro assembly, cryo-electron tomography and subtomogram averaging, atomistic molecular dynamics simulations and mutational analyses to study the HIV-related lentivirus equine infectious anemia virus (EIAV). In particular, we sought to understand the structural conservation of the immature lentivirus lattice and the role of IP6 in EIAV assembly. Similar to HIV-1, IP6 strongly promoted in vitro assembly of EIAV Gag proteins into virus-like particles (VLPs), which took three morphologically highly distinct forms: narrow tubes, wide tubes, and spheres. Structural characterization of these VLPs to sub-4Å resolution unexpectedly showed that all three morphologies are based on an immature lattice with preserved key structural components, highlighting the structural versatility of CA to form immature assemblies. A direct comparison between EIAV and HIV revealed that both lentiviruses maintain similar immature interfaces, which are established by both conserved and non-conserved residues. In both EIAV and HIV-1, IP6 regulates immature assembly via conserved lysine residues within the CACTD and SP. Lastly, we demonstrate that IP6 stimulates in vitro assembly of immature particles of several other retroviruses in the lentivirus genus, suggesting a conserved role for IP6 in lentiviral assembly.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","file":[{"creator":"dernst","file_size":4551246,"content_type":"application/pdf","access_level":"open_access","file_name":"2020_PLOSPatho_Dick.pdf","checksum":"a297f54d1fef0efe4789ca00f37f241e","date_created":"2020-02-11T10:07:28Z","date_updated":"2020-07-14T12:47:59Z","file_id":"7484","relation":"main_file"}],"_id":"7464","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 16","title":"Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly","ddc":["570"],"status":"public","has_accepted_license":"1","article_processing_charge":"No","day":"27","scopus_import":"1","date_published":"2020-01-27T00:00:00Z","citation":{"ama":"Dick RA, Xu C, Morado DR, et al. Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly. PLOS Pathogens. 2020;16(1). doi:10.1371/journal.ppat.1008277","ieee":"R. A. Dick et al., “Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly,” PLOS Pathogens, vol. 16, no. 1. Public Library of Science, 2020.","apa":"Dick, R. A., Xu, C., Morado, D. R., Kravchuk, V., Ricana, C. L., Lyddon, T. D., … Schur, F. K. (2020). Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly. PLOS Pathogens. Public Library of Science. https://doi.org/10.1371/journal.ppat.1008277","ista":"Dick RA, Xu C, Morado DR, Kravchuk V, Ricana CL, Lyddon TD, Broad AM, Feathers JR, Johnson MC, Vogt VM, Perilla JR, Briggs JAG, Schur FK. 2020. Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly. PLOS Pathogens. 16(1), e1008277.","short":"R.A. Dick, C. Xu, D.R. Morado, V. Kravchuk, C.L. Ricana, T.D. Lyddon, A.M. Broad, J.R. Feathers, M.C. Johnson, V.M. Vogt, J.R. Perilla, J.A.G. Briggs, F.K. Schur, PLOS Pathogens 16 (2020).","mla":"Dick, Robert A., et al. “Structures of Immature EIAV Gag Lattices Reveal a Conserved Role for IP6 in Lentivirus Assembly.” PLOS Pathogens, vol. 16, no. 1, e1008277, Public Library of Science, 2020, doi:10.1371/journal.ppat.1008277.","chicago":"Dick, Robert A., Chaoyi Xu, Dustin R. Morado, Vladyslav Kravchuk, Clifton L. Ricana, Terri D. Lyddon, Arianna M. Broad, et al. “Structures of Immature EIAV Gag Lattices Reveal a Conserved Role for IP6 in Lentivirus Assembly.” PLOS Pathogens. Public Library of Science, 2020. https://doi.org/10.1371/journal.ppat.1008277."},"publication":"PLOS Pathogens","article_type":"original","file_date_updated":"2020-07-14T12:47:59Z","license":"https://creativecommons.org/licenses/by/4.0/","article_number":"e1008277","related_material":{"record":[{"status":"deleted","relation":"research_data","id":"9723"}]},"author":[{"first_name":"Robert A.","last_name":"Dick","full_name":"Dick, Robert A."},{"first_name":"Chaoyi","last_name":"Xu","full_name":"Xu, Chaoyi"},{"full_name":"Morado, Dustin R.","last_name":"Morado","first_name":"Dustin R."},{"full_name":"Kravchuk, Vladyslav","last_name":"Kravchuk","first_name":"Vladyslav","orcid":"0000-0001-9523-9089","id":"4D62F2A6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Ricana, Clifton L.","last_name":"Ricana","first_name":"Clifton L."},{"last_name":"Lyddon","first_name":"Terri D.","full_name":"Lyddon, Terri D."},{"last_name":"Broad","first_name":"Arianna M.","full_name":"Broad, Arianna M."},{"first_name":"J. Ryan","last_name":"Feathers","full_name":"Feathers, J. Ryan"},{"full_name":"Johnson, Marc C.","first_name":"Marc C.","last_name":"Johnson"},{"last_name":"Vogt","first_name":"Volker M.","full_name":"Vogt, Volker M."},{"last_name":"Perilla","first_name":"Juan R.","full_name":"Perilla, Juan R."},{"first_name":"John A. G.","last_name":"Briggs","full_name":"Briggs, John A. G."},{"orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur","first_name":"Florian KM","full_name":"Schur, Florian KM"}],"volume":16,"date_created":"2020-02-06T18:47:17Z","date_updated":"2023-10-17T12:29:34Z","pmid":1,"year":"2020","department":[{"_id":"FlSc"}],"publisher":"Public Library of Science","publication_status":"published","publication_identifier":{"issn":["1553-7374"]},"month":"01","doi":"10.1371/journal.ppat.1008277","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["31986188"],"isi":["000510746400010"]},"oa":1,"project":[{"name":"Structural conservation and diversity in retroviral capsid","call_identifier":"FWF","grant_number":"P31445","_id":"26736D6A-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1},{"doi":"10.1371/journal.pcbi.1007494","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["1906.02785"],"isi":["000510916500025"]},"project":[{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"},{"grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Game Theory"}],"isi":1,"quality_controlled":"1","publication_identifier":{"eissn":["15537358"]},"month":"01","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"7196"}]},"author":[{"full_name":"Tkadlec, Josef","first_name":"Josef","last_name":"Tkadlec","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1097-9684"},{"first_name":"Andreas","last_name":"Pavlogiannis","id":"49704004-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8943-0722","full_name":"Pavlogiannis, Andreas"},{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Nowak, Martin A.","first_name":"Martin A.","last_name":"Nowak"}],"volume":16,"date_created":"2019-12-23T13:45:11Z","date_updated":"2023-10-17T12:29:47Z","year":"2020","publisher":"Public Library of Science","department":[{"_id":"KrCh"}],"publication_status":"published","ec_funded":1,"file_date_updated":"2020-07-14T12:47:53Z","article_number":"e1007494","date_published":"2020-01-17T00:00:00Z","citation":{"chicago":"Tkadlec, Josef, Andreas Pavlogiannis, Krishnendu Chatterjee, and Martin A. Nowak. “Limits on Amplifiers of Natural Selection under Death-Birth Updating.” PLoS Computational Biology. Public Library of Science, 2020. https://doi.org/10.1371/journal.pcbi.1007494.","short":"J. Tkadlec, A. Pavlogiannis, K. Chatterjee, M.A. Nowak, PLoS Computational Biology 16 (2020).","mla":"Tkadlec, Josef, et al. “Limits on Amplifiers of Natural Selection under Death-Birth Updating.” PLoS Computational Biology, vol. 16, e1007494, Public Library of Science, 2020, doi:10.1371/journal.pcbi.1007494.","ieee":"J. Tkadlec, A. Pavlogiannis, K. Chatterjee, and M. A. Nowak, “Limits on amplifiers of natural selection under death-Birth updating,” PLoS computational biology, vol. 16. Public Library of Science, 2020.","apa":"Tkadlec, J., Pavlogiannis, A., Chatterjee, K., & Nowak, M. A. (2020). Limits on amplifiers of natural selection under death-Birth updating. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1007494","ista":"Tkadlec J, Pavlogiannis A, Chatterjee K, Nowak MA. 2020. Limits on amplifiers of natural selection under death-Birth updating. PLoS computational biology. 16, e1007494.","ama":"Tkadlec J, Pavlogiannis A, Chatterjee K, Nowak MA. Limits on amplifiers of natural selection under death-Birth updating. PLoS computational biology. 2020;16. doi:10.1371/journal.pcbi.1007494"},"publication":"PLoS computational biology","article_type":"original","article_processing_charge":"No","has_accepted_license":"1","day":"17","scopus_import":"1","file":[{"content_type":"application/pdf","file_size":1817531,"creator":"dernst","access_level":"open_access","file_name":"2020_PlosCompBio_Tkadlec.pdf","checksum":"ce32ee2d2f53aed832f78bbd47e882df","date_updated":"2020-07-14T12:47:53Z","date_created":"2020-02-03T07:32:42Z","relation":"main_file","file_id":"7441"}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7212","intvolume":" 16","ddc":["000"],"status":"public","title":"Limits on amplifiers of natural selection under death-Birth updating","abstract":[{"lang":"eng","text":"The fixation probability of a single mutant invading a population of residents is among the most widely-studied quantities in evolutionary dynamics. Amplifiers of natural selection are population structures that increase the fixation probability of advantageous mutants, compared to well-mixed populations. Extensive studies have shown that many amplifiers exist for the Birth-death Moran process, some of them substantially increasing the fixation probability or even guaranteeing fixation in the limit of large population size. On the other hand, no amplifiers are known for the death-Birth Moran process, and computer-assisted exhaustive searches have failed to discover amplification. In this work we resolve this disparity, by showing that any amplification under death-Birth updating is necessarily bounded and transient. Our boundedness result states that even if a population structure does amplify selection, the resulting fixation probability is close to that of the well-mixed population. Our transience result states that for any population structure there exists a threshold r⋆ such that the population structure ceases to amplify selection if the mutant fitness advantage r is larger than r⋆. Finally, we also extend the above results to δ-death-Birth updating, which is a combination of Birth-death and death-Birth updating. On the positive side, we identify population structures that maintain amplification for a wide range of values r and δ. These results demonstrate that amplification of natural selection depends on the specific mechanisms of the evolutionary process."}],"type":"journal_article"},{"ddc":["519"],"status":"public","title":"A role of graphs in evolutionary processes","_id":"7196","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","file":[{"relation":"source_file","file_id":"7255","checksum":"451f8e64b0eb26bf297644ac72bfcbe9","date_updated":"2020-07-14T12:47:52Z","date_created":"2020-01-12T11:49:49Z","access_level":"closed","file_name":"thesis.zip","content_type":"application/zip","file_size":21100497,"creator":"jtkadlec"},{"access_level":"open_access","file_name":"2020_Tkadlec_Thesis.pdf","file_size":11670983,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"7367","checksum":"d8c44cbc4f939c49a8efc9d4b8bb3985","date_updated":"2020-07-14T12:47:52Z","date_created":"2020-01-28T07:32:42Z"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"text":"In this thesis we study certain mathematical aspects of evolution. The two primary forces that drive an evolutionary process are mutation and selection. Mutation generates new variants in a population. Selection chooses among the variants depending on the reproductive rates of individuals. Evolutionary processes are intrinsically random – a new mutation that is initially present in the population at low frequency can go extinct, even if it confers a reproductive advantage. The overall rate of evolution is largely determined by two quantities: the probability that an invading advantageous mutation spreads through the population (called fixation probability) and the time until it does so (called fixation time). Both those quantities crucially depend not only on the strength of the invading mutation but also on the population structure. In this thesis, we aim to understand how the underlying population structure affects the overall rate of evolution. Specifically, we study population structures that increase the fixation probability of advantageous mutants (called amplifiers of selection). Broadly speaking, our results are of three different types: We present various strong amplifiers, we identify regimes under which only limited amplification is feasible, and we propose population structures that provide different tradeoffs between high fixation probability and short fixation time.","lang":"eng"}],"page":"144","citation":{"chicago":"Tkadlec, Josef. “A Role of Graphs in Evolutionary Processes.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7196.","mla":"Tkadlec, Josef. A Role of Graphs in Evolutionary Processes. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7196.","short":"J. Tkadlec, A Role of Graphs in Evolutionary Processes, Institute of Science and Technology Austria, 2020.","ista":"Tkadlec J. 2020. A role of graphs in evolutionary processes. Institute of Science and Technology Austria.","apa":"Tkadlec, J. (2020). A role of graphs in evolutionary processes. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7196","ieee":"J. Tkadlec, “A role of graphs in evolutionary processes,” Institute of Science and Technology Austria, 2020.","ama":"Tkadlec J. A role of graphs in evolutionary processes. 2020. doi:10.15479/AT:ISTA:7196"},"date_published":"2020-01-12T00:00:00Z","has_accepted_license":"1","article_processing_charge":"No","day":"12","department":[{"_id":"KrCh"},{"_id":"GradSch"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","year":"2020","date_created":"2019-12-20T12:26:36Z","date_updated":"2023-10-17T12:29:46Z","related_material":{"record":[{"id":"7210","status":"public","relation":"dissertation_contains"},{"status":"public","relation":"dissertation_contains","id":"5751"},{"relation":"dissertation_contains","status":"public","id":"7212"}]},"author":[{"last_name":"Tkadlec","first_name":"Josef","orcid":"0000-0002-1097-9684","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","full_name":"Tkadlec, Josef"}],"file_date_updated":"2020-07-14T12:47:52Z","oa":1,"language":[{"iso":"eng"}],"supervisor":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"}],"degree_awarded":"PhD","doi":"10.15479/AT:ISTA:7196","publication_identifier":{"eissn":["2663-337X"]},"month":"01"},{"external_id":{"arxiv":["1912.10095"]},"oa":1,"quality_controlled":"1","project":[{"_id":"059876FA-7A3F-11EA-A408-12923DDC885E","name":"Prix Lopez-Loretta 2019 - Marco Mondelli"}],"language":[{"iso":"eng"}],"month":"07","acknowledgement":"M. Mondelli was partially supported by the 2019 LopezLoreta Prize. The authors thank Phan-Minh Nguyen for helpful discussions and the IST Distributed Algorithms and Systems Lab for providing computational resources.","year":"2020","publication_status":"published","publisher":"ML Research Press","department":[{"_id":"MaMo"}],"author":[{"last_name":"Shevchenko","first_name":"Alexander","full_name":"Shevchenko, Alexander"},{"full_name":"Mondelli, Marco","last_name":"Mondelli","first_name":"Marco","orcid":"0000-0002-3242-7020","id":"27EB676C-8706-11E9-9510-7717E6697425"}],"date_updated":"2023-10-17T12:43:19Z","date_created":"2021-02-25T09:36:22Z","volume":119,"file_date_updated":"2021-03-02T15:38:14Z","publication":"Proceedings of the 37th International Conference on Machine Learning","citation":{"ama":"Shevchenko A, Mondelli M. Landscape connectivity and dropout stability of SGD solutions for over-parameterized neural networks. In: Proceedings of the 37th International Conference on Machine Learning. Vol 119. ML Research Press; 2020:8773-8784.","ista":"Shevchenko A, Mondelli M. 2020. Landscape connectivity and dropout stability of SGD solutions for over-parameterized neural networks. Proceedings of the 37th International Conference on Machine Learning. vol. 119, 8773–8784.","apa":"Shevchenko, A., & Mondelli, M. (2020). Landscape connectivity and dropout stability of SGD solutions for over-parameterized neural networks. In Proceedings of the 37th International Conference on Machine Learning (Vol. 119, pp. 8773–8784). ML Research Press.","ieee":"A. Shevchenko and M. Mondelli, “Landscape connectivity and dropout stability of SGD solutions for over-parameterized neural networks,” in Proceedings of the 37th International Conference on Machine Learning, 2020, vol. 119, pp. 8773–8784.","mla":"Shevchenko, Alexander, and Marco Mondelli. “Landscape Connectivity and Dropout Stability of SGD Solutions for Over-Parameterized Neural Networks.” Proceedings of the 37th International Conference on Machine Learning, vol. 119, ML Research Press, 2020, pp. 8773–84.","short":"A. Shevchenko, M. Mondelli, in:, Proceedings of the 37th International Conference on Machine Learning, ML Research Press, 2020, pp. 8773–8784.","chicago":"Shevchenko, Alexander, and Marco Mondelli. “Landscape Connectivity and Dropout Stability of SGD Solutions for Over-Parameterized Neural Networks.” In Proceedings of the 37th International Conference on Machine Learning, 119:8773–84. ML Research Press, 2020."},"page":"8773-8784","date_published":"2020-07-13T00:00:00Z","day":"13","article_processing_charge":"No","has_accepted_license":"1","_id":"9198","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","ddc":["000"],"title":"Landscape connectivity and dropout stability of SGD solutions for over-parameterized neural networks","intvolume":" 119","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":5336380,"creator":"dernst","access_level":"open_access","file_name":"2020_PMLR_Shevchenko.pdf","checksum":"f042c8d4316bd87c6361aa76f1fbdbbe","success":1,"date_updated":"2021-03-02T15:38:14Z","date_created":"2021-03-02T15:38:14Z","relation":"main_file","file_id":"9217"}],"type":"conference","abstract":[{"text":"The optimization of multilayer neural networks typically leads to a solution\r\nwith zero training error, yet the landscape can exhibit spurious local minima\r\nand the minima can be disconnected. In this paper, we shed light on this\r\nphenomenon: we show that the combination of stochastic gradient descent (SGD)\r\nand over-parameterization makes the landscape of multilayer neural networks\r\napproximately connected and thus more favorable to optimization. More\r\nspecifically, we prove that SGD solutions are connected via a piecewise linear\r\npath, and the increase in loss along this path vanishes as the number of\r\nneurons grows large. This result is a consequence of the fact that the\r\nparameters found by SGD are increasingly dropout stable as the network becomes\r\nwider. We show that, if we remove part of the neurons (and suitably rescale the\r\nremaining ones), the change in loss is independent of the total number of\r\nneurons, and it depends only on how many neurons are left. Our results exhibit\r\na mild dependence on the input dimension: they are dimension-free for two-layer\r\nnetworks and depend linearly on the dimension for multilayer networks. We\r\nvalidate our theoretical findings with numerical experiments for different\r\narchitectures and classification tasks.","lang":"eng"}]},{"publication_identifier":{"issn":["2544-7297"]},"month":"06","project":[{"call_identifier":"H2020","name":"Alpha Shape Theory Extended","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","grant_number":"788183"},{"grant_number":"I02979-N35","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","name":"Persistence and stability of geometric complexes","call_identifier":"FWF"}],"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1515/cmb-2020-0100","ec_funded":1,"file_date_updated":"2021-02-19T13:56:24Z","department":[{"_id":"HeEd"}],"publisher":"De Gruyter","publication_status":"published","acknowledgement":"The authors of this paper thank Roland Roth for suggesting the analysis of the weighted\r\ncurvature derivatives for the purpose of improving molecular dynamics simulations and for his continued encouragement. They also thank Patrice Koehl for the implementation of the formulas and for his encouragement and advise along the road. Finally, they thank two anonymous reviewers for their constructive criticism.\r\nThis project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 78818 Alpha). It is also partially supported by the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, through grant no. I02979-N35 of the Austrian Science Fund (FWF).","year":"2020","volume":8,"date_updated":"2023-10-17T12:34:51Z","date_created":"2021-02-17T15:13:01Z","author":[{"orcid":"0000-0002-2548-617X","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","last_name":"Akopyan","first_name":"Arseniy","full_name":"Akopyan, Arseniy"},{"full_name":"Edelsbrunner, Herbert","first_name":"Herbert","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833"}],"article_processing_charge":"No","has_accepted_license":"1","day":"20","page":"51-67","article_type":"original","citation":{"ama":"Akopyan A, Edelsbrunner H. The weighted mean curvature derivative of a space-filling diagram. Computational and Mathematical Biophysics. 2020;8(1):51-67. doi:10.1515/cmb-2020-0100","ieee":"A. Akopyan and H. Edelsbrunner, “The weighted mean curvature derivative of a space-filling diagram,” Computational and Mathematical Biophysics, vol. 8, no. 1. De Gruyter, pp. 51–67, 2020.","apa":"Akopyan, A., & Edelsbrunner, H. (2020). The weighted mean curvature derivative of a space-filling diagram. Computational and Mathematical Biophysics. De Gruyter. https://doi.org/10.1515/cmb-2020-0100","ista":"Akopyan A, Edelsbrunner H. 2020. The weighted mean curvature derivative of a space-filling diagram. Computational and Mathematical Biophysics. 8(1), 51–67.","short":"A. Akopyan, H. Edelsbrunner, Computational and Mathematical Biophysics 8 (2020) 51–67.","mla":"Akopyan, Arseniy, and Herbert Edelsbrunner. “The Weighted Mean Curvature Derivative of a Space-Filling Diagram.” Computational and Mathematical Biophysics, vol. 8, no. 1, De Gruyter, 2020, pp. 51–67, doi:10.1515/cmb-2020-0100.","chicago":"Akopyan, Arseniy, and Herbert Edelsbrunner. “The Weighted Mean Curvature Derivative of a Space-Filling Diagram.” Computational and Mathematical Biophysics. De Gruyter, 2020. https://doi.org/10.1515/cmb-2020-0100."},"publication":"Computational and Mathematical Biophysics","date_published":"2020-06-20T00:00:00Z","type":"journal_article","issue":"1","abstract":[{"lang":"eng","text":"Representing an atom by a solid sphere in 3-dimensional Euclidean space, we get the space-filling diagram of a molecule by taking the union. Molecular dynamics simulates its motion subject to bonds and other forces, including the solvation free energy. The morphometric approach [12, 17] writes the latter as a linear combination of weighted versions of the volume, area, mean curvature, and Gaussian curvature of the space-filling diagram. We give a formula for the derivative of the weighted mean curvature. Together with the derivatives of the weighted volume in [7], the weighted area in [3], and the weighted Gaussian curvature [1], this yields the derivative of the morphometric expression of the solvation free energy."}],"intvolume":" 8","title":"The weighted mean curvature derivative of a space-filling diagram","status":"public","ddc":["510"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"9157","file":[{"file_name":"2020_CompMathBiophysics_Akopyan2.pdf","access_level":"open_access","creator":"dernst","file_size":562359,"content_type":"application/pdf","file_id":"9171","relation":"main_file","date_updated":"2021-02-19T13:56:24Z","date_created":"2021-02-19T13:56:24Z","success":1,"checksum":"cea41de9937d07a3b927d71ee8b4e432"}],"oa_version":"Published Version"},{"issue":"1","abstract":[{"text":"The morphometric approach [11, 14] writes the solvation free energy as a linear combination of weighted versions of the volume, area, mean curvature, and Gaussian curvature of the space-filling diagram. We give a formula for the derivative of the weighted Gaussian curvature. Together with the derivatives of the weighted volume in [7], the weighted area in [4], and the weighted mean curvature in [1], this yields the derivative of the morphometric expression of solvation free energy.","lang":"eng"}],"type":"journal_article","file":[{"date_created":"2021-02-19T13:33:19Z","date_updated":"2021-02-19T13:33:19Z","success":1,"checksum":"ca43a7440834eab6bbea29c59b56ef3a","file_id":"9170","relation":"main_file","creator":"dernst","file_size":707452,"content_type":"application/pdf","file_name":"2020_CompMathBiophysics_Akopyan.pdf","access_level":"open_access"}],"oa_version":"Published Version","intvolume":" 8","ddc":["510"],"status":"public","title":"The weighted Gaussian curvature derivative of a space-filling diagram","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"9156","has_accepted_license":"1","article_processing_charge":"No","day":"21","date_published":"2020-07-21T00:00:00Z","page":"74-88","article_type":"original","citation":{"ista":"Akopyan A, Edelsbrunner H. 2020. The weighted Gaussian curvature derivative of a space-filling diagram. Computational and Mathematical Biophysics. 8(1), 74–88.","ieee":"A. Akopyan and H. Edelsbrunner, “The weighted Gaussian curvature derivative of a space-filling diagram,” Computational and Mathematical Biophysics, vol. 8, no. 1. De Gruyter, pp. 74–88, 2020.","apa":"Akopyan, A., & Edelsbrunner, H. (2020). The weighted Gaussian curvature derivative of a space-filling diagram. Computational and Mathematical Biophysics. De Gruyter. https://doi.org/10.1515/cmb-2020-0101","ama":"Akopyan A, Edelsbrunner H. The weighted Gaussian curvature derivative of a space-filling diagram. Computational and Mathematical Biophysics. 2020;8(1):74-88. doi:10.1515/cmb-2020-0101","chicago":"Akopyan, Arseniy, and Herbert Edelsbrunner. “The Weighted Gaussian Curvature Derivative of a Space-Filling Diagram.” Computational and Mathematical Biophysics. De Gruyter, 2020. https://doi.org/10.1515/cmb-2020-0101.","mla":"Akopyan, Arseniy, and Herbert Edelsbrunner. “The Weighted Gaussian Curvature Derivative of a Space-Filling Diagram.” Computational and Mathematical Biophysics, vol. 8, no. 1, De Gruyter, 2020, pp. 74–88, doi:10.1515/cmb-2020-0101.","short":"A. Akopyan, H. Edelsbrunner, Computational and Mathematical Biophysics 8 (2020) 74–88."},"publication":"Computational and Mathematical Biophysics","ec_funded":1,"file_date_updated":"2021-02-19T13:33:19Z","volume":8,"date_created":"2021-02-17T15:12:44Z","date_updated":"2023-10-17T12:35:10Z","author":[{"full_name":"Akopyan, Arseniy","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2548-617X","first_name":"Arseniy","last_name":"Akopyan"},{"full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner","first_name":"Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"}],"publisher":"De Gruyter","department":[{"_id":"HeEd"}],"publication_status":"published","year":"2020","acknowledgement":"The authors of this paper thank Roland Roth for suggesting the analysis of theweighted\r\ncurvature derivatives for the purpose of improving molecular dynamics simulations. They also thank Patrice Koehl for the implementation of the formulas and for his encouragement and advise along the road. Finally, they thank two anonymous reviewers for their constructive criticism.\r\nThis project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 78818 Alpha). It is also partially supported by the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, through grant no. I02979-N35 of the Austrian Science Fund (FWF).","publication_identifier":{"issn":["2544-7297"]},"month":"07","language":[{"iso":"eng"}],"doi":"10.1515/cmb-2020-0101","project":[{"_id":"266A2E9E-B435-11E9-9278-68D0E5697425","grant_number":"788183","name":"Alpha Shape Theory Extended","call_identifier":"H2020"},{"_id":"2561EBF4-B435-11E9-9278-68D0E5697425","grant_number":"I02979-N35","call_identifier":"FWF","name":"Persistence and stability of geometric complexes"}],"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"arxiv":["1908.06777"]}},{"publication_status":"published","department":[{"_id":"JaMa"}],"publisher":" Institute of Mathematical Statistics","acknowledgement":"We warmly thank S.R.S. Varadhan for many enlightening discussions at an early stage of this work. We are indebted to Francesca Collet for fruitful discussions and constant support all throughout this work. We thank Simone Floreani\r\nand Alberto Chiarini for helpful conversations on the final part of this paper as well as both referees for their careful reading and for raising relevant issues on some weak points contained in a previous version of this manuscript; we believe this helped us to improve it.\r\nPart of this work was done during the authors’ stay at the Institut Henri Poincaré (UMS 5208 CNRS-Sorbonne Université) – Centre Emile Borel during the trimester Stochastic Dynamics Out of Equilibrium. The authors thank this institution for hospitality and support (through LabEx CARMIN, ANR-10-LABX-59-01). F.S. thanks laboratoire\r\nMAP5 of Université de Paris, and E.S. thanks Delft University, for financial support and hospitality. F.S. acknowledges NWO for financial support via the TOP1 grant 613.001.552 as well as funding from the European Union’s Horizon 2020 research and innovation programme under the Marie-Skłodowska-Curie grant agreement No. 754411. This research has been conducted within the FP2M federation (CNRS FR 2036).","year":"2020","date_created":"2020-12-27T23:01:17Z","date_updated":"2023-10-17T12:51:56Z","volume":25,"author":[{"first_name":"Frank","last_name":"Redig","full_name":"Redig, Frank"},{"full_name":"Saada, Ellen","last_name":"Saada","first_name":"Ellen"},{"full_name":"Sau, Federico","first_name":"Federico","last_name":"Sau","id":"E1836206-9F16-11E9-8814-AEFDE5697425"}],"article_number":"138","file_date_updated":"2020-12-28T08:24:08Z","ec_funded":1,"quality_controlled":"1","isi":1,"project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"external_id":{"isi":["000591737500001"],"arxiv":["1811.01366"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1214/20-EJP536","month":"10","publication_identifier":{"eissn":["1083-6489"]},"title":"Symmetric simple exclusion process in dynamic environment: Hydrodynamics","ddc":["510"],"status":"public","intvolume":" 25","_id":"8973","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2020_ElectronJProbab_Redig.pdf","creator":"dernst","content_type":"application/pdf","file_size":696653,"file_id":"8976","relation":"main_file","success":1,"checksum":"d75359b9814e78d57c0a481b7cde3751","date_updated":"2020-12-28T08:24:08Z","date_created":"2020-12-28T08:24:08Z"}],"type":"journal_article","abstract":[{"lang":"eng","text":"We consider the symmetric simple exclusion process in Zd with quenched bounded dynamic random conductances and prove its hydrodynamic limit in path space. The main tool is the connection, due to the self-duality of the process, between the invariance principle for single particles starting from all points and the macroscopic behavior of the density field. While the hydrodynamic limit at fixed macroscopic times is obtained via a generalization to the time-inhomogeneous context of the strategy introduced in [41], in order to prove tightness for the sequence of empirical density fields we develop a new criterion based on the notion of uniform conditional stochastic continuity, following [50]. In conclusion, we show that uniform elliptic dynamic conductances provide an example of environments in which the so-called arbitrary starting point invariance principle may be derived from the invariance principle of a single particle starting from the origin. Therefore, our hydrodynamics result applies to the examples of quenched environments considered in, e.g., [1], [3], [6] in combination with the hypothesis of uniform ellipticity."}],"article_type":"original","publication":"Electronic Journal of Probability","citation":{"mla":"Redig, Frank, et al. “Symmetric Simple Exclusion Process in Dynamic Environment: Hydrodynamics.” Electronic Journal of Probability, vol. 25, 138, Institute of Mathematical Statistics, 2020, doi:10.1214/20-EJP536.","short":"F. Redig, E. Saada, F. Sau, Electronic Journal of Probability 25 (2020).","chicago":"Redig, Frank, Ellen Saada, and Federico Sau. “Symmetric Simple Exclusion Process in Dynamic Environment: Hydrodynamics.” Electronic Journal of Probability. Institute of Mathematical Statistics, 2020. https://doi.org/10.1214/20-EJP536.","ama":"Redig F, Saada E, Sau F. Symmetric simple exclusion process in dynamic environment: Hydrodynamics. Electronic Journal of Probability. 2020;25. doi:10.1214/20-EJP536","ista":"Redig F, Saada E, Sau F. 2020. Symmetric simple exclusion process in dynamic environment: Hydrodynamics. Electronic Journal of Probability. 25, 138.","apa":"Redig, F., Saada, E., & Sau, F. (2020). Symmetric simple exclusion process in dynamic environment: Hydrodynamics. Electronic Journal of Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/20-EJP536","ieee":"F. Redig, E. Saada, and F. Sau, “Symmetric simple exclusion process in dynamic environment: Hydrodynamics,” Electronic Journal of Probability, vol. 25. Institute of Mathematical Statistics, 2020."},"date_published":"2020-10-21T00:00:00Z","scopus_import":"1","day":"21","article_processing_charge":"No","has_accepted_license":"1"},{"oa":1,"external_id":{"arxiv":["1805.10715"],"isi":["000582676300002"]},"main_file_link":[{"url":"https://arxiv.org/abs/1805.10715","open_access":"1"}],"isi":1,"quality_controlled":"1","doi":"10.1215/00127094-2020-0031","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0012-7094"]},"month":"09","year":"2020","department":[{"_id":"TiBr"}],"publisher":"Duke University Press","publication_status":"published","author":[{"id":"35827D50-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8314-0177","first_name":"Timothy D","last_name":"Browning","full_name":"Browning, Timothy D"},{"full_name":"Heath Brown, Roger","last_name":"Heath Brown","first_name":"Roger"}],"volume":169,"date_created":"2018-12-11T11:45:02Z","date_updated":"2023-10-17T12:51:10Z","citation":{"ama":"Browning TD, Heath Brown R. Density of rational points on a quadric bundle in ℙ3×ℙ3. Duke Mathematical Journal. 2020;169(16):3099-3165. doi:10.1215/00127094-2020-0031","apa":"Browning, T. D., & Heath Brown, R. (2020). Density of rational points on a quadric bundle in ℙ3×ℙ3. Duke Mathematical Journal. Duke University Press. https://doi.org/10.1215/00127094-2020-0031","ieee":"T. D. Browning and R. Heath Brown, “Density of rational points on a quadric bundle in ℙ3×ℙ3,” Duke Mathematical Journal, vol. 169, no. 16. Duke University Press, pp. 3099–3165, 2020.","ista":"Browning TD, Heath Brown R. 2020. Density of rational points on a quadric bundle in ℙ3×ℙ3. Duke Mathematical Journal. 169(16), 3099–3165.","short":"T.D. Browning, R. Heath Brown, Duke Mathematical Journal 169 (2020) 3099–3165.","mla":"Browning, Timothy D., and Roger Heath Brown. “Density of Rational Points on a Quadric Bundle in ℙ3×ℙ3.” Duke Mathematical Journal, vol. 169, no. 16, Duke University Press, 2020, pp. 3099–165, doi:10.1215/00127094-2020-0031.","chicago":"Browning, Timothy D, and Roger Heath Brown. “Density of Rational Points on a Quadric Bundle in ℙ3×ℙ3.” Duke Mathematical Journal. Duke University Press, 2020. https://doi.org/10.1215/00127094-2020-0031."},"publication":"Duke Mathematical Journal","page":"3099-3165","article_type":"original","date_published":"2020-09-10T00:00:00Z","article_processing_charge":"No","day":"10","_id":"179","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 169","title":"Density of rational points on a quadric bundle in ℙ3×ℙ3","status":"public","oa_version":"Preprint","type":"journal_article","issue":"16","abstract":[{"lang":"eng","text":"An asymptotic formula is established for the number of rational points of bounded anticanonical height which lie on a certain Zariski dense subset of the biprojective hypersurface x1y21+⋯+x4y24=0 in ℙ3×ℙ3. This confirms the modified Manin conjecture for this variety, in which the removal of a thin set of rational points is allowed."}]},{"article_processing_charge":"No","day":"15","month":"10","main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.5973013.v1","open_access":"1"}],"citation":{"short":"R. Ibsen-Jensen, J. Tkadlec, K. Chatterjee, M. Nowak, (2020).","mla":"Ibsen-Jensen, Rasmus, et al. Data and Mathematica Notebooks for Plotting Figures from Language Learning with Communication between Learners from Language Acquisition with Communication between Learners. Royal Society, 2020, doi:10.6084/m9.figshare.5973013.v1.","chicago":"Ibsen-Jensen, Rasmus, Josef Tkadlec, Krishnendu Chatterjee, and Martin Nowak. “Data and Mathematica Notebooks for Plotting Figures from Language Learning with Communication between Learners from Language Acquisition with Communication between Learners.” Royal Society, 2020. https://doi.org/10.6084/m9.figshare.5973013.v1.","ama":"Ibsen-Jensen R, Tkadlec J, Chatterjee K, Nowak M. Data and mathematica notebooks for plotting figures from language learning with communication between learners from language acquisition with communication between learners. 2020. doi:10.6084/m9.figshare.5973013.v1","ieee":"R. Ibsen-Jensen, J. Tkadlec, K. Chatterjee, and M. Nowak, “Data and mathematica notebooks for plotting figures from language learning with communication between learners from language acquisition with communication between learners.” Royal Society, 2020.","apa":"Ibsen-Jensen, R., Tkadlec, J., Chatterjee, K., & Nowak, M. (2020). Data and mathematica notebooks for plotting figures from language learning with communication between learners from language acquisition with communication between learners. Royal Society. https://doi.org/10.6084/m9.figshare.5973013.v1","ista":"Ibsen-Jensen R, Tkadlec J, Chatterjee K, Nowak M. 2020. Data and mathematica notebooks for plotting figures from language learning with communication between learners from language acquisition with communication between learners, Royal Society, 10.6084/m9.figshare.5973013.v1."},"oa":1,"date_published":"2020-10-15T00:00:00Z","doi":"10.6084/m9.figshare.5973013.v1","type":"research_data_reference","abstract":[{"text":"Data and mathematica notebooks for plotting figures from Language learning with communication between learners","lang":"eng"}],"_id":"9814","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","year":"2020","department":[{"_id":"KrCh"}],"publisher":"Royal Society","status":"public","title":"Data and mathematica notebooks for plotting figures from language learning with communication between learners from language acquisition with communication between learners","related_material":{"record":[{"id":"198","status":"public","relation":"used_in_publication"}]},"author":[{"full_name":"Ibsen-Jensen, Rasmus","id":"3B699956-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4783-0389","first_name":"Rasmus","last_name":"Ibsen-Jensen"},{"id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1097-9684","first_name":"Josef","last_name":"Tkadlec","full_name":"Tkadlec, Josef"},{"first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"full_name":"Nowak, Martin","last_name":"Nowak","first_name":"Martin"}],"oa_version":"Published Version","date_created":"2021-08-06T13:09:57Z","date_updated":"2023-10-18T06:36:00Z"}]