[{"citation":{"chicago":"Foerster, Klaus-Tycho, Janne Korhonen, Joel Rybicki, and Stefan Schmid. “Does Preprocessing Help under Congestion?” In Proceedings of the 2019 ACM Symposium on Principles of Distributed Computing, 259–61. ACM, 2019. https://doi.org/10.1145/3293611.3331581.","ista":"Foerster K-T, Korhonen J, Rybicki J, Schmid S. 2019. Does preprocessing help under congestion? Proceedings of the 2019 ACM Symposium on Principles of Distributed Computing. PODC: Symposium on Principles of Distributed Computing, 259–261.","mla":"Foerster, Klaus-Tycho, et al. “Does Preprocessing Help under Congestion?” Proceedings of the 2019 ACM Symposium on Principles of Distributed Computing, ACM, 2019, pp. 259–61, doi:10.1145/3293611.3331581.","apa":"Foerster, K.-T., Korhonen, J., Rybicki, J., & Schmid, S. (2019). Does preprocessing help under congestion? In Proceedings of the 2019 ACM Symposium on Principles of Distributed Computing (pp. 259–261). Toronto, ON, Canada: ACM. https://doi.org/10.1145/3293611.3331581","ama":"Foerster K-T, Korhonen J, Rybicki J, Schmid S. Does preprocessing help under congestion? In: Proceedings of the 2019 ACM Symposium on Principles of Distributed Computing. ACM; 2019:259-261. doi:10.1145/3293611.3331581","ieee":"K.-T. Foerster, J. Korhonen, J. Rybicki, and S. Schmid, “Does preprocessing help under congestion?,” in Proceedings of the 2019 ACM Symposium on Principles of Distributed Computing, Toronto, ON, Canada, 2019, pp. 259–261.","short":"K.-T. Foerster, J. Korhonen, J. Rybicki, S. Schmid, in:, Proceedings of the 2019 ACM Symposium on Principles of Distributed Computing, ACM, 2019, pp. 259–261."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","external_id":{"arxiv":["1905.03012"],"isi":["000570442000037"]},"author":[{"last_name":"Foerster","full_name":"Foerster, Klaus-Tycho","first_name":"Klaus-Tycho"},{"first_name":"Janne","id":"C5402D42-15BC-11E9-A202-CA2BE6697425","full_name":"Korhonen, Janne","last_name":"Korhonen"},{"orcid":"0000-0002-6432-6646","full_name":"Rybicki, Joel","last_name":"Rybicki","id":"334EFD2E-F248-11E8-B48F-1D18A9856A87","first_name":"Joel"},{"last_name":"Schmid","full_name":"Schmid, Stefan","first_name":"Stefan"}],"title":"Does preprocessing help under congestion?","project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"}],"year":"2019","isi":1,"publication":"Proceedings of the 2019 ACM Symposium on Principles of Distributed Computing","day":"01","page":"259-261","date_created":"2019-10-08T12:57:14Z","doi":"10.1145/3293611.3331581","date_published":"2019-08-01T00:00:00Z","oa":1,"quality_controlled":"1","publisher":"ACM","date_updated":"2023-09-08T11:37:22Z","department":[{"_id":"DaAl"}],"_id":"6935","conference":{"name":"PODC: Symposium on Principles of Distributed Computing","start_date":"2019-07-29","end_date":"2019-08-02","location":"Toronto, ON, Canada"},"type":"conference","status":"public","publication_status":"published","publication_identifier":{"isbn":["9781450362177"]},"language":[{"iso":"eng"}],"ec_funded":1,"abstract":[{"text":"This paper investigates the power of preprocessing in the CONGEST model. Schmid and Suomela (ACM HotSDN 2013) introduced the SUPPORTED CONGEST model to study the application of distributed algorithms in Software-Defined Networks (SDNs). In this paper, we show that a large class of lower bounds in the CONGEST model still hold in the SUPPORTED model, highlighting the robustness of these bounds. This also raises the question how much does\r\npreprocessing help in the CONGEST model.","lang":"eng"}],"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1905.03012"}],"scopus_import":"1","month":"08"},{"project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["000456958800017"]},"publist_id":"7785","author":[{"first_name":"Nela","id":"42D9CABC-F248-11E8-B48F-1D18A9856A87","full_name":"Nikolic, Nela","orcid":"0000-0001-9068-6090","last_name":"Nikolic"}],"title":"Autoregulation of bacterial gene expression: lessons from the MazEF toxin–antitoxin system","citation":{"ista":"Nikolic N. 2019. Autoregulation of bacterial gene expression: lessons from the MazEF toxin–antitoxin system. Current Genetics. 65(1), 133–138.","chicago":"Nikolic, Nela. “Autoregulation of Bacterial Gene Expression: Lessons from the MazEF Toxin–Antitoxin System.” Current Genetics. Springer, 2019. https://doi.org/10.1007/s00294-018-0879-8.","apa":"Nikolic, N. (2019). Autoregulation of bacterial gene expression: lessons from the MazEF toxin–antitoxin system. Current Genetics. Springer. https://doi.org/10.1007/s00294-018-0879-8","ama":"Nikolic N. Autoregulation of bacterial gene expression: lessons from the MazEF toxin–antitoxin system. Current Genetics. 2019;65(1):133-138. doi:10.1007/s00294-018-0879-8","short":"N. Nikolic, Current Genetics 65 (2019) 133–138.","ieee":"N. Nikolic, “Autoregulation of bacterial gene expression: lessons from the MazEF toxin–antitoxin system,” Current Genetics, vol. 65, no. 1. Springer, pp. 133–138, 2019.","mla":"Nikolic, Nela. “Autoregulation of Bacterial Gene Expression: Lessons from the MazEF Toxin–Antitoxin System.” Current Genetics, vol. 65, no. 1, Springer, 2019, pp. 133–38, doi:10.1007/s00294-018-0879-8."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"quality_controlled":"1","publisher":"Springer","page":"133-138","date_created":"2018-12-11T11:44:50Z","doi":"10.1007/s00294-018-0879-8","date_published":"2019-02-01T00:00:00Z","year":"2019","isi":1,"has_accepted_license":"1","publication":"Current Genetics","day":"01","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","status":"public","_id":"138","department":[{"_id":"CaGu"}],"file_date_updated":"2020-07-14T12:44:47Z","date_updated":"2023-09-08T13:23:42Z","ddc":["570"],"scopus_import":"1","intvolume":" 65","month":"02","abstract":[{"lang":"eng","text":"Autoregulation is the direct modulation of gene expression by the product of the corresponding gene. Autoregulation of bacterial gene expression has been mostly studied at the transcriptional level, when a protein acts as the cognate transcriptional repressor. A recent study investigating dynamics of the bacterial toxin–antitoxin MazEF system has shown how autoregulation at both the transcriptional and post-transcriptional levels affects the heterogeneity of Escherichia coli populations. Toxin–antitoxin systems hold a crucial but still elusive part in bacterial response to stress. This perspective highlights how these modules can also serve as a great model system for investigating basic concepts in gene regulation. However, as the genomic background and environmental conditions substantially influence toxin activation, it is important to study (auto)regulation of toxin–antitoxin systems in well-defined setups as well as in conditions that resemble the environmental niche."}],"oa_version":"Published Version","ec_funded":1,"license":"https://creativecommons.org/licenses/by/4.0/","issue":"1","volume":65,"publication_status":"published","language":[{"iso":"eng"}],"file":[{"checksum":"6779708b0b632a1a6ed28c56f5161142","file_id":"5930","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2019_CurrentGenetics_Nikolic.pdf","date_created":"2019-02-06T07:50:58Z","creator":"dernst","file_size":776399,"date_updated":"2020-07-14T12:44:47Z"}]},{"quality_controlled":"1","publisher":"Elsevier","oa":1,"page":"257 - 311","date_published":"2019-01-05T00:00:00Z","doi":"10.1016/j.jde.2018.07.045","date_created":"2018-12-11T11:44:54Z","isi":1,"year":"2019","day":"05","publication":"Journal of Differential Equations","publist_id":"7770","author":[{"id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","first_name":"Julian L","orcid":"0000-0002-0479-558X","full_name":"Fischer, Julian L","last_name":"Fischer"},{"full_name":"Kneuss, Olivier","last_name":"Kneuss","first_name":"Olivier"}],"external_id":{"isi":["000449108500010"],"arxiv":["1408.1587"]},"article_processing_charge":"No","title":"Bi-Sobolev solutions to the prescribed Jacobian inequality in the plane with L p data and applications to nonlinear elasticity","citation":{"mla":"Fischer, Julian L., and Olivier Kneuss. “Bi-Sobolev Solutions to the Prescribed Jacobian Inequality in the Plane with L p Data and Applications to Nonlinear Elasticity.” Journal of Differential Equations, vol. 266, no. 1, Elsevier, 2019, pp. 257–311, doi:10.1016/j.jde.2018.07.045.","ama":"Fischer JL, Kneuss O. Bi-Sobolev solutions to the prescribed Jacobian inequality in the plane with L p data and applications to nonlinear elasticity. Journal of Differential Equations. 2019;266(1):257-311. doi:10.1016/j.jde.2018.07.045","apa":"Fischer, J. L., & Kneuss, O. (2019). Bi-Sobolev solutions to the prescribed Jacobian inequality in the plane with L p data and applications to nonlinear elasticity. Journal of Differential Equations. Elsevier. https://doi.org/10.1016/j.jde.2018.07.045","short":"J.L. Fischer, O. Kneuss, Journal of Differential Equations 266 (2019) 257–311.","ieee":"J. L. Fischer and O. Kneuss, “Bi-Sobolev solutions to the prescribed Jacobian inequality in the plane with L p data and applications to nonlinear elasticity,” Journal of Differential Equations, vol. 266, no. 1. Elsevier, pp. 257–311, 2019.","chicago":"Fischer, Julian L, and Olivier Kneuss. “Bi-Sobolev Solutions to the Prescribed Jacobian Inequality in the Plane with L p Data and Applications to Nonlinear Elasticity.” Journal of Differential Equations. Elsevier, 2019. https://doi.org/10.1016/j.jde.2018.07.045.","ista":"Fischer JL, Kneuss O. 2019. Bi-Sobolev solutions to the prescribed Jacobian inequality in the plane with L p data and applications to nonlinear elasticity. Journal of Differential Equations. 266(1), 257–311."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1408.1587"}],"month":"01","intvolume":" 266","abstract":[{"lang":"eng","text":"We construct planar bi-Sobolev mappings whose local volume distortion is bounded from below by a given function f∈Lp with p>1. More precisely, for any 1<q<(p+1)/2 we construct W1,q-bi-Sobolev maps with identity boundary conditions; for f∈L∞, we provide bi-Lipschitz maps. The basic building block of our construction are bi-Lipschitz maps which stretch a given compact subset of the unit square by a given factor while preserving the boundary. The construction of these stretching maps relies on a slight strengthening of the celebrated covering result of Alberti, Csörnyei, and Preiss for measurable planar sets in the case of compact sets. We apply our result to a model functional in nonlinear elasticity, the integrand of which features fast blowup as the Jacobian determinant of the deformation becomes small. For such functionals, the derivation of the equilibrium equations for minimizers requires an additional regularization of test functions, which our maps provide."}],"oa_version":"Preprint","issue":"1","volume":266,"publication_status":"published","language":[{"iso":"eng"}],"type":"journal_article","status":"public","_id":"151","department":[{"_id":"JuFi"}],"date_updated":"2023-09-08T13:25:35Z"},{"file":[{"checksum":"db027721a95d36f5de36aadcd0bdf7e6","file_id":"7239","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2020-01-07T13:35:52Z","file_name":"2019_Wiley_Amberg.pdf","date_updated":"2020-07-14T12:45:45Z","file_size":889709,"creator":"kschuh"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":149,"issue":"1","ec_funded":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"The cerebral cortex is composed of a large variety of distinct cell-types including projection neurons, interneurons and glial cells which emerge from distinct neural stem cell (NSC) lineages. The vast majority of cortical projection neurons and certain classes of glial cells are generated by radial glial progenitor cells (RGPs) in a highly orchestrated manner. Recent studies employing single cell analysis and clonal lineage tracing suggest that NSC and RGP lineage progression are regulated in a profound deterministic manner. In this review we focus on recent advances based mainly on correlative phenotypic data emerging from functional genetic studies in mice. We establish hypotheses to test in future research and outline a conceptual framework how epigenetic cues modulate the generation of cell-type diversity during cortical development. This article is protected by copyright. All rights reserved."}],"month":"04","intvolume":" 149","scopus_import":"1","ddc":["570"],"date_updated":"2023-09-11T13:40:26Z","file_date_updated":"2020-07-14T12:45:45Z","department":[{"_id":"SiHi"}],"_id":"27","status":"public","article_type":"review","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"day":"01","publication":"Journal of Neurochemistry","has_accepted_license":"1","isi":1,"year":"2019","doi":"10.1111/jnc.14601","date_published":"2019-04-01T00:00:00Z","date_created":"2018-12-11T11:44:14Z","page":"12-26","acknowledgement":" This work was supported by IST Austria institutional funds; NÖ Forschung und Bildung \r\nn[f+b] (C13-002) to SH; a program grant from the Human Frontiers Science Program (RGP0053/2014) to SH; the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement No 618444 to SH, and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 725780 LinPro)to SH.\r\n","publisher":"Wiley","quality_controlled":"1","oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"apa":"Amberg, N., Laukoter, S., & Hippenmeyer, S. (2019). Epigenetic cues modulating the generation of cell type diversity in the cerebral cortex. Journal of Neurochemistry. Wiley. https://doi.org/10.1111/jnc.14601","ama":"Amberg N, Laukoter S, Hippenmeyer S. Epigenetic cues modulating the generation of cell type diversity in the cerebral cortex. Journal of Neurochemistry. 2019;149(1):12-26. doi:10.1111/jnc.14601","ieee":"N. Amberg, S. Laukoter, and S. Hippenmeyer, “Epigenetic cues modulating the generation of cell type diversity in the cerebral cortex,” Journal of Neurochemistry, vol. 149, no. 1. Wiley, pp. 12–26, 2019.","short":"N. Amberg, S. Laukoter, S. Hippenmeyer, Journal of Neurochemistry 149 (2019) 12–26.","mla":"Amberg, Nicole, et al. “Epigenetic Cues Modulating the Generation of Cell Type Diversity in the Cerebral Cortex.” Journal of Neurochemistry, vol. 149, no. 1, Wiley, 2019, pp. 12–26, doi:10.1111/jnc.14601.","ista":"Amberg N, Laukoter S, Hippenmeyer S. 2019. Epigenetic cues modulating the generation of cell type diversity in the cerebral cortex. Journal of Neurochemistry. 149(1), 12–26.","chicago":"Amberg, Nicole, Susanne Laukoter, and Simon Hippenmeyer. “Epigenetic Cues Modulating the Generation of Cell Type Diversity in the Cerebral Cortex.” Journal of Neurochemistry. Wiley, 2019. https://doi.org/10.1111/jnc.14601."},"title":"Epigenetic cues modulating the generation of cell type diversity in the cerebral cortex","author":[{"last_name":"Amberg","full_name":"Amberg, Nicole","orcid":"0000-0002-3183-8207","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","first_name":"Nicole"},{"orcid":"0000-0002-7903-3010","full_name":"Laukoter, Susanne","last_name":"Laukoter","first_name":"Susanne","id":"2D6B7A9A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer"}],"article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["000462680200002"]},"project":[{"grant_number":"LS13-002","name":"Mapping Cell-Type Specificity of the Genomic Imprintome in the Brain","_id":"25D92700-B435-11E9-9278-68D0E5697425"},{"grant_number":"RGP0053/2014","name":"Quantitative Structure-Function Analysis of Cerebral Cortex Assembly at Clonal Level","_id":"25D7962E-B435-11E9-9278-68D0E5697425"},{"_id":"25D61E48-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Molecular Mechanisms of Cerebral Cortex Development","grant_number":"618444"},{"grant_number":"725780","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","_id":"260018B0-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}]},{"publisher":"Nature Publishing Group","quality_controlled":"1","oa":1,"has_accepted_license":"1","isi":1,"year":"2019","day":"01","publication":"Nature Cell Biology","page":"169–178","date_published":"2019-02-01T00:00:00Z","doi":"10.1038/s41556-018-0247-4","date_created":"2018-12-30T22:59:15Z","project":[{"_id":"260F1432-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","grant_number":"742573"},{"_id":"253E54C8-B435-11E9-9278-68D0E5697425","name":"Molecular mechanism of auxindriven formative divisions delineating lateral root organogenesis in plants (EMBO fellowship)","grant_number":"ALTF710-2016"}],"citation":{"ieee":"N. Petridou, S. Grigolon, G. Salbreux, E. B. Hannezo, and C.-P. J. Heisenberg, “Fluidization-mediated tissue spreading by mitotic cell rounding and non-canonical Wnt signalling,” Nature Cell Biology, vol. 21. Nature Publishing Group, pp. 169–178, 2019.","short":"N. Petridou, S. Grigolon, G. Salbreux, E.B. Hannezo, C.-P.J. Heisenberg, Nature Cell Biology 21 (2019) 169–178.","ama":"Petridou N, Grigolon S, Salbreux G, Hannezo EB, Heisenberg C-PJ. Fluidization-mediated tissue spreading by mitotic cell rounding and non-canonical Wnt signalling. Nature Cell Biology. 2019;21:169–178. doi:10.1038/s41556-018-0247-4","apa":"Petridou, N., Grigolon, S., Salbreux, G., Hannezo, E. B., & Heisenberg, C.-P. J. (2019). Fluidization-mediated tissue spreading by mitotic cell rounding and non-canonical Wnt signalling. Nature Cell Biology. Nature Publishing Group. https://doi.org/10.1038/s41556-018-0247-4","mla":"Petridou, Nicoletta, et al. “Fluidization-Mediated Tissue Spreading by Mitotic Cell Rounding and Non-Canonical Wnt Signalling.” Nature Cell Biology, vol. 21, Nature Publishing Group, 2019, pp. 169–178, doi:10.1038/s41556-018-0247-4.","ista":"Petridou N, Grigolon S, Salbreux G, Hannezo EB, Heisenberg C-PJ. 2019. Fluidization-mediated tissue spreading by mitotic cell rounding and non-canonical Wnt signalling. Nature Cell Biology. 21, 169–178.","chicago":"Petridou, Nicoletta, Silvia Grigolon, Guillaume Salbreux, Edouard B Hannezo, and Carl-Philipp J Heisenberg. “Fluidization-Mediated Tissue Spreading by Mitotic Cell Rounding and Non-Canonical Wnt Signalling.” Nature Cell Biology. Nature Publishing Group, 2019. https://doi.org/10.1038/s41556-018-0247-4."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"full_name":"Petridou, Nicoletta","orcid":"0000-0002-8451-1195","last_name":"Petridou","id":"2A003F6C-F248-11E8-B48F-1D18A9856A87","first_name":"Nicoletta"},{"full_name":"Grigolon, Silvia","last_name":"Grigolon","first_name":"Silvia"},{"last_name":"Salbreux","full_name":"Salbreux, Guillaume","first_name":"Guillaume"},{"last_name":"Hannezo","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Heisenberg","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J"}],"article_processing_charge":"No","external_id":{"pmid":["30559456"],"isi":["000457468300011"]},"title":"Fluidization-mediated tissue spreading by mitotic cell rounding and non-canonical Wnt signalling","abstract":[{"text":"Tissue morphogenesis is driven by mechanical forces that elicit changes in cell size, shape and motion. The extent by which forces deform tissues critically depends on the rheological properties of the recipient tissue. Yet, whether and how dynamic changes in tissue rheology affect tissue morphogenesis and how they are regulated within the developing organism remain unclear. Here, we show that blastoderm spreading at the onset of zebrafish morphogenesis relies on a rapid, pronounced and spatially patterned tissue fluidization. Blastoderm fluidization is temporally controlled by mitotic cell rounding-dependent cell–cell contact disassembly during the last rounds of cell cleavages. Moreover, fluidization is spatially restricted to the central blastoderm by local activation of non-canonical Wnt signalling within the blastoderm margin, increasing cell cohesion and thereby counteracting the effect of mitotic rounding on contact disassembly. Overall, our results identify a fluidity transition mediated by loss of cell cohesion as a critical regulator of embryo morphogenesis.","lang":"eng"}],"acknowledged_ssus":[{"_id":"Bio"}],"pmid":1,"oa_version":"Submitted Version","scopus_import":"1","month":"02","intvolume":" 21","publication_identifier":{"issn":["14657392"]},"publication_status":"published","file":[{"checksum":"e38523787b3bc84006f2793de99ad70f","file_id":"8685","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2020-10-21T07:18:35Z","file_name":"2018_NatureCellBio_Petridou_accepted.pdf","date_updated":"2020-10-21T07:18:35Z","file_size":71590590,"creator":"dernst"}],"language":[{"iso":"eng"}],"related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/when-a-fish-becomes-fluid/","description":"News on IST Homepage"}]},"volume":21,"ec_funded":1,"_id":"5789","article_type":"original","type":"journal_article","status":"public","date_updated":"2023-09-11T14:03:28Z","ddc":["570"],"department":[{"_id":"CaHe"},{"_id":"EdHa"}],"file_date_updated":"2020-10-21T07:18:35Z"},{"department":[{"_id":"CaGu"},{"_id":"GaTk"},{"_id":"TaHa"}],"date_updated":"2023-09-11T14:09:34Z","article_type":"original","type":"journal_article","status":"public","_id":"196","issue":"8","related_material":{"link":[{"url":"https://ist.ac.at/en/news/famous-sandpile-model-shown-to-move-like-a-traveling-sand-dune/","relation":"press_release","description":"News on IST Webpage"}]},"volume":116,"publication_status":"published","publication_identifier":{"eissn":["1091-6490"]},"language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1073/pnas.1812015116"}],"scopus_import":"1","intvolume":" 116","month":"02","abstract":[{"lang":"eng","text":"The abelian sandpile serves as a model to study self-organized criticality, a phenomenon occurring in biological, physical and social processes. The identity of the abelian group is a fractal composed of self-similar patches, and its limit is subject of extensive collaborative research. Here, we analyze the evolution of the sandpile identity under harmonic fields of different orders. We show that this evolution corresponds to periodic cycles through the abelian group characterized by the smooth transformation and apparent conservation of the patches constituting the identity. The dynamics induced by second and third order harmonics resemble smooth stretchings, respectively translations, of the identity, while the ones induced by fourth order harmonics resemble magnifications and rotations. Starting with order three, the dynamics pass through extended regions of seemingly random configurations which spontaneously reassemble into accentuated patterns. We show that the space of harmonic functions projects to the extended analogue of the sandpile group, thus providing a set of universal coordinates identifying configurations between different domains. Since the original sandpile group is a subgroup of the extended one, this directly implies that it admits a natural renormalization. Furthermore, we show that the harmonic fields can be induced by simple Markov processes, and that the corresponding stochastic dynamics show remarkable robustness over hundreds of periods. Finally, we encode information into seemingly random configurations, and decode this information with an algorithm requiring minimal prior knowledge. Our results suggest that harmonic fields might split the sandpile group into sub-sets showing different critical coefficients, and that it might be possible to extend the fractal structure of the identity beyond the boundaries of its domain. "}],"pmid":1,"oa_version":"Published Version","article_processing_charge":"No","external_id":{"arxiv":["1806.10823"],"isi":["000459074400013"],"pmid":[" 30728300"]},"author":[{"id":"29E0800A-F248-11E8-B48F-1D18A9856A87","first_name":"Moritz","full_name":"Lang, Moritz","last_name":"Lang"},{"orcid":"0000-0002-4310-178X","full_name":"Shkolnikov, Mikhail","last_name":"Shkolnikov","first_name":"Mikhail","id":"35084A62-F248-11E8-B48F-1D18A9856A87"}],"title":"Harmonic dynamics of the Abelian sandpile","citation":{"short":"M. Lang, M. Shkolnikov, Proceedings of the National Academy of Sciences 116 (2019) 2821–2830.","ieee":"M. Lang and M. Shkolnikov, “Harmonic dynamics of the Abelian sandpile,” Proceedings of the National Academy of Sciences, vol. 116, no. 8. National Academy of Sciences, pp. 2821–2830, 2019.","ama":"Lang M, Shkolnikov M. Harmonic dynamics of the Abelian sandpile. Proceedings of the National Academy of Sciences. 2019;116(8):2821-2830. doi:10.1073/pnas.1812015116","apa":"Lang, M., & Shkolnikov, M. (2019). Harmonic dynamics of the Abelian sandpile. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1812015116","mla":"Lang, Moritz, and Mikhail Shkolnikov. “Harmonic Dynamics of the Abelian Sandpile.” Proceedings of the National Academy of Sciences, vol. 116, no. 8, National Academy of Sciences, 2019, pp. 2821–30, doi:10.1073/pnas.1812015116.","ista":"Lang M, Shkolnikov M. 2019. Harmonic dynamics of the Abelian sandpile. Proceedings of the National Academy of Sciences. 116(8), 2821–2830.","chicago":"Lang, Moritz, and Mikhail Shkolnikov. “Harmonic Dynamics of the Abelian Sandpile.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2019. https://doi.org/10.1073/pnas.1812015116."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","page":"2821-2830","date_created":"2018-12-11T11:45:08Z","doi":"10.1073/pnas.1812015116","date_published":"2019-02-19T00:00:00Z","year":"2019","isi":1,"publication":"Proceedings of the National Academy of Sciences","day":"19","oa":1,"publisher":"National Academy of Sciences","quality_controlled":"1","acknowledgement":"M.L. is grateful to the members of the C Guet and G Tkacik groups for valuable comments and support. M.S. is grateful to Nikita Kalinin for inspiring communications.\r\n"},{"citation":{"mla":"Locatello, Francesco, et al. “Disentangling Factors of Variation Using Few Labels.” 8th International Conference on Learning Representations, 2019.","short":"F. Locatello, M. Tschannen, S. Bauer, G. Rätsch, B. Schölkopf, O. Bachem, in:, 8th International Conference on Learning Representations, 2019.","ieee":"F. Locatello, M. Tschannen, S. Bauer, G. Rätsch, B. Schölkopf, and O. Bachem, “Disentangling factors of variation using few labels,” in 8th International Conference on Learning Representations, Virtual, 2019.","apa":"Locatello, F., Tschannen, M., Bauer, S., Rätsch, G., Schölkopf, B., & Bachem, O. (2019). Disentangling factors of variation using few labels. In 8th International Conference on Learning Representations. Virtual.","ama":"Locatello F, Tschannen M, Bauer S, Rätsch G, Schölkopf B, Bachem O. Disentangling factors of variation using few labels. In: 8th International Conference on Learning Representations. ; 2019.","chicago":"Locatello, Francesco, Michael Tschannen, Stefan Bauer, Gunnar Rätsch, Bernhard Schölkopf, and Olivier Bachem. “Disentangling Factors of Variation Using Few Labels.” In 8th International Conference on Learning Representations, 2019.","ista":"Locatello F, Tschannen M, Bauer S, Rätsch G, Schölkopf B, Bachem O. 2019. Disentangling factors of variation using few labels. 8th International Conference on Learning Representations. ICLR: International Conference on Learning Representations."},"date_updated":"2023-09-12T07:01:34Z","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Locatello","full_name":"Locatello, Francesco","orcid":"0000-0002-4850-0683","first_name":"Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4"},{"first_name":"Michael","full_name":"Tschannen, Michael","last_name":"Tschannen"},{"last_name":"Bauer","full_name":"Bauer, Stefan","first_name":"Stefan"},{"last_name":"Rätsch","full_name":"Rätsch, Gunnar","first_name":"Gunnar"},{"full_name":"Schölkopf, Bernhard","last_name":"Schölkopf","first_name":"Bernhard"},{"first_name":"Olivier","full_name":"Bachem, Olivier","last_name":"Bachem"}],"article_processing_charge":"No","external_id":{"arxiv":["1905.01258"]},"department":[{"_id":"FrLo"}],"title":"Disentangling factors of variation using few labels","_id":"14184","type":"conference","conference":{"location":"Virtual","end_date":"2020-05-01","start_date":"2020-04-26","name":"ICLR: International Conference on Learning Representations"},"status":"public","year":"2019","publication_status":"published","day":"20","publication":"8th International Conference on Learning Representations","language":[{"iso":"eng"}],"date_published":"2019-12-20T00:00:00Z","date_created":"2023-08-22T14:06:37Z","abstract":[{"text":"Learning disentangled representations is considered a cornerstone problem in\r\nrepresentation learning. Recently, Locatello et al. (2019) demonstrated that\r\nunsupervised disentanglement learning without inductive biases is theoretically\r\nimpossible and that existing inductive biases and unsupervised methods do not\r\nallow to consistently learn disentangled representations. However, in many\r\npractical settings, one might have access to a limited amount of supervision,\r\nfor example through manual labeling of (some) factors of variation in a few\r\ntraining examples. In this paper, we investigate the impact of such supervision\r\non state-of-the-art disentanglement methods and perform a large scale study,\r\ntraining over 52000 models under well-defined and reproducible experimental\r\nconditions. We observe that a small number of labeled examples (0.01--0.5\\% of\r\nthe data set), with potentially imprecise and incomplete labels, is sufficient\r\nto perform model selection on state-of-the-art unsupervised models. Further, we\r\ninvestigate the benefit of incorporating supervision into the training process.\r\nOverall, we empirically validate that with little and imprecise supervision it\r\nis possible to reliably learn disentangled representations.","lang":"eng"}],"oa_version":"Preprint","quality_controlled":"1","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1905.01258","open_access":"1"}],"oa":1,"month":"12"},{"volume":115,"publication_status":"published","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1905.06642","open_access":"1"}],"alternative_title":["PMLR"],"scopus_import":"1","intvolume":" 115","month":"05","abstract":[{"lang":"eng","text":"We consider the problem of recovering a common latent source with independent\r\ncomponents from multiple views. This applies to settings in which a variable is\r\nmeasured with multiple experimental modalities, and where the goal is to\r\nsynthesize the disparate measurements into a single unified representation. We\r\nconsider the case that the observed views are a nonlinear mixing of\r\ncomponent-wise corruptions of the sources. When the views are considered\r\nseparately, this reduces to nonlinear Independent Component Analysis (ICA) for\r\nwhich it is provably impossible to undo the mixing. We present novel\r\nidentifiability proofs that this is possible when the multiple views are\r\nconsidered jointly, showing that the mixing can theoretically be undone using\r\nfunction approximators such as deep neural networks. In contrast to known\r\nidentifiability results for nonlinear ICA, we prove that independent latent\r\nsources with arbitrary mixing can be recovered as long as multiple,\r\nsufficiently different noisy views are available."}],"oa_version":"Preprint","department":[{"_id":"FrLo"}],"date_updated":"2023-09-12T08:07:38Z","extern":"1","conference":{"start_date":"2019-07-22","end_date":"2019-07-25","location":"Tel Aviv, Israel","name":"UAI: Uncertainty in Artificial Intelligence"},"type":"conference","status":"public","_id":"14189","page":"217-227","date_created":"2023-08-22T14:08:35Z","date_published":"2019-05-16T00:00:00Z","year":"2019","publication":"Proceedings of the 35th Conference on Uncertainty in Artificial Intelligence","day":"16","oa":1,"publisher":"ML Research Press","quality_controlled":"1","external_id":{"arxiv":["1905.06642"]},"article_processing_charge":"No","author":[{"first_name":"Luigi","last_name":"Gresele","full_name":"Gresele, Luigi"},{"first_name":"Paul K.","full_name":"Rubenstein, Paul K.","last_name":"Rubenstein"},{"full_name":"Mehrjou, Arash","last_name":"Mehrjou","first_name":"Arash"},{"full_name":"Locatello, Francesco","orcid":"0000-0002-4850-0683","last_name":"Locatello","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","first_name":"Francesco"},{"full_name":"Schölkopf, Bernhard","last_name":"Schölkopf","first_name":"Bernhard"}],"title":"The incomplete Rosetta Stone problem: Identifiability results for multi-view nonlinear ICA","citation":{"mla":"Gresele, Luigi, et al. “The Incomplete Rosetta Stone Problem: Identifiability Results for Multi-View Nonlinear ICA.” Proceedings of the 35th Conference on Uncertainty in Artificial Intelligence, vol. 115, ML Research Press, 2019, pp. 217–27.","ama":"Gresele L, Rubenstein PK, Mehrjou A, Locatello F, Schölkopf B. The incomplete Rosetta Stone problem: Identifiability results for multi-view nonlinear ICA. In: Proceedings of the 35th Conference on Uncertainty in Artificial Intelligence. Vol 115. ML Research Press; 2019:217-227.","apa":"Gresele, L., Rubenstein, P. K., Mehrjou, A., Locatello, F., & Schölkopf, B. (2019). The incomplete Rosetta Stone problem: Identifiability results for multi-view nonlinear ICA. In Proceedings of the 35th Conference on Uncertainty in Artificial Intelligence (Vol. 115, pp. 217–227). Tel Aviv, Israel: ML Research Press.","short":"L. Gresele, P.K. Rubenstein, A. Mehrjou, F. Locatello, B. Schölkopf, in:, Proceedings of the 35th Conference on Uncertainty in Artificial Intelligence, ML Research Press, 2019, pp. 217–227.","ieee":"L. Gresele, P. K. Rubenstein, A. Mehrjou, F. Locatello, and B. Schölkopf, “The incomplete Rosetta Stone problem: Identifiability results for multi-view nonlinear ICA,” in Proceedings of the 35th Conference on Uncertainty in Artificial Intelligence, Tel Aviv, Israel, 2019, vol. 115, pp. 217–227.","chicago":"Gresele, Luigi, Paul K. Rubenstein, Arash Mehrjou, Francesco Locatello, and Bernhard Schölkopf. “The Incomplete Rosetta Stone Problem: Identifiability Results for Multi-View Nonlinear ICA.” In Proceedings of the 35th Conference on Uncertainty in Artificial Intelligence, 115:217–27. ML Research Press, 2019.","ista":"Gresele L, Rubenstein PK, Mehrjou A, Locatello F, Schölkopf B. 2019. The incomplete Rosetta Stone problem: Identifiability results for multi-view nonlinear ICA. Proceedings of the 35th Conference on Uncertainty in Artificial Intelligence. UAI: Uncertainty in Artificial Intelligence, PMLR, vol. 115, 217–227."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"_id":"14197","conference":{"name":"NeurIPS: Neural Information Processing Systems","end_date":"2019-12-14","location":"Vancouver, Canada","start_date":"2019-12-08"},"type":"conference","status":"public","date_updated":"2023-09-12T09:37:22Z","extern":"1","department":[{"_id":"FrLo"}],"abstract":[{"text":"Recently there has been a significant interest in learning disentangled\r\nrepresentations, as they promise increased interpretability, generalization to\r\nunseen scenarios and faster learning on downstream tasks. In this paper, we\r\ninvestigate the usefulness of different notions of disentanglement for\r\nimproving the fairness of downstream prediction tasks based on representations.\r\nWe consider the setting where the goal is to predict a target variable based on\r\nthe learned representation of high-dimensional observations (such as images)\r\nthat depend on both the target variable and an \\emph{unobserved} sensitive\r\nvariable. We show that in this setting both the optimal and empirical\r\npredictions can be unfair, even if the target variable and the sensitive\r\nvariable are independent. Analyzing the representations of more than\r\n\\num{12600} trained state-of-the-art disentangled models, we observe that\r\nseveral disentanglement scores are consistently correlated with increased\r\nfairness, suggesting that disentanglement may be a useful property to encourage\r\nfairness when sensitive variables are not observed.","lang":"eng"}],"oa_version":"Preprint","main_file_link":[{"url":"https://arxiv.org/abs/1905.13662","open_access":"1"}],"scopus_import":"1","intvolume":" 32","month":"12","publication_status":"published","publication_identifier":{"isbn":["9781713807933"]},"language":[{"iso":"eng"}],"volume":32,"citation":{"ista":"Locatello F, Abbati G, Rainforth T, Bauer S, Schölkopf B, Bachem O. 2019. On the fairness of disentangled representations. Advances in Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems vol. 32, 14611–14624.","chicago":"Locatello, Francesco, Gabriele Abbati, Tom Rainforth, Stefan Bauer, Bernhard Schölkopf, and Olivier Bachem. “On the Fairness of Disentangled Representations.” In Advances in Neural Information Processing Systems, 32:14611–14624, 2019.","short":"F. Locatello, G. Abbati, T. Rainforth, S. Bauer, B. Schölkopf, O. Bachem, in:, Advances in Neural Information Processing Systems, 2019, pp. 14611–14624.","ieee":"F. Locatello, G. Abbati, T. Rainforth, S. Bauer, B. Schölkopf, and O. Bachem, “On the fairness of disentangled representations,” in Advances in Neural Information Processing Systems, Vancouver, Canada, 2019, vol. 32, pp. 14611–14624.","apa":"Locatello, F., Abbati, G., Rainforth, T., Bauer, S., Schölkopf, B., & Bachem, O. (2019). On the fairness of disentangled representations. In Advances in Neural Information Processing Systems (Vol. 32, pp. 14611–14624). Vancouver, Canada.","ama":"Locatello F, Abbati G, Rainforth T, Bauer S, Schölkopf B, Bachem O. On the fairness of disentangled representations. In: Advances in Neural Information Processing Systems. Vol 32. ; 2019:14611–14624.","mla":"Locatello, Francesco, et al. “On the Fairness of Disentangled Representations.” Advances in Neural Information Processing Systems, vol. 32, 2019, pp. 14611–14624."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["1905.13662"]},"article_processing_charge":"No","author":[{"first_name":"Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","orcid":"0000-0002-4850-0683","full_name":"Locatello, Francesco","last_name":"Locatello"},{"last_name":"Abbati","full_name":"Abbati, Gabriele","first_name":"Gabriele"},{"first_name":"Tom","last_name":"Rainforth","full_name":"Rainforth, Tom"},{"first_name":"Stefan","last_name":"Bauer","full_name":"Bauer, Stefan"},{"first_name":"Bernhard","full_name":"Schölkopf, Bernhard","last_name":"Schölkopf"},{"full_name":"Bachem, Olivier","last_name":"Bachem","first_name":"Olivier"}],"title":"On the fairness of disentangled representations","oa":1,"quality_controlled":"1","year":"2019","publication":"Advances in Neural Information Processing Systems","day":"08","page":"14611–14624","date_created":"2023-08-22T14:12:28Z","date_published":"2019-12-08T00:00:00Z"},{"volume":32,"publication_status":"published","publication_identifier":{"isbn":["9781713807933"]},"language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1901.10348"}],"scopus_import":"1","intvolume":" 32","month":"12","abstract":[{"lang":"eng","text":"A broad class of convex optimization problems can be formulated as a semidefinite program (SDP), minimization of a convex function over the positive-semidefinite cone subject to some affine constraints. The majority of classical SDP solvers are designed for the deterministic setting where problem data is readily available. In this setting, generalized conditional gradient methods (aka Frank-Wolfe-type methods) provide scalable solutions by leveraging the so-called linear minimization oracle instead of the projection onto the semidefinite cone. Most problems in machine learning and modern engineering applications, however, contain some degree of stochasticity. In this work, we propose the first conditional-gradient-type method for solving stochastic optimization problems under affine constraints. Our method guarantees O(k−1/3) convergence rate in expectation on the objective residual and O(k−5/12) on the feasibility gap."}],"oa_version":"Preprint","department":[{"_id":"FrLo"}],"date_updated":"2023-09-12T08:48:45Z","extern":"1","conference":{"name":"NeurIPS: Neural Information Processing Systems","start_date":"2019-12-08","end_date":"2019-12-14","location":"Vancouver, Canada"},"type":"conference","status":"public","_id":"14191","page":"14291–14301","date_created":"2023-08-22T14:09:35Z","date_published":"2019-12-29T00:00:00Z","year":"2019","publication":"Advances in Neural Information Processing Systems","day":"29","oa":1,"quality_controlled":"1","external_id":{"arxiv":["1901.10348"]},"article_processing_charge":"No","author":[{"first_name":"Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","last_name":"Locatello","full_name":"Locatello, Francesco","orcid":"0000-0002-4850-0683"},{"last_name":"Yurtsever","full_name":"Yurtsever, Alp","first_name":"Alp"},{"last_name":"Fercoq","full_name":"Fercoq, Olivier","first_name":"Olivier"},{"last_name":"Cevher","full_name":"Cevher, Volkan","first_name":"Volkan"}],"title":"Stochastic Frank-Wolfe for composite convex minimization","citation":{"chicago":"Locatello, Francesco, Alp Yurtsever, Olivier Fercoq, and Volkan Cevher. “Stochastic Frank-Wolfe for Composite Convex Minimization.” In Advances in Neural Information Processing Systems, 32:14291–14301, 2019.","ista":"Locatello F, Yurtsever A, Fercoq O, Cevher V. 2019. Stochastic Frank-Wolfe for composite convex minimization. Advances in Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems vol. 32, 14291–14301.","mla":"Locatello, Francesco, et al. “Stochastic Frank-Wolfe for Composite Convex Minimization.” Advances in Neural Information Processing Systems, vol. 32, 2019, pp. 14291–14301.","ama":"Locatello F, Yurtsever A, Fercoq O, Cevher V. Stochastic Frank-Wolfe for composite convex minimization. In: Advances in Neural Information Processing Systems. Vol 32. ; 2019:14291–14301.","apa":"Locatello, F., Yurtsever, A., Fercoq, O., & Cevher, V. (2019). Stochastic Frank-Wolfe for composite convex minimization. In Advances in Neural Information Processing Systems (Vol. 32, pp. 14291–14301). Vancouver, Canada.","short":"F. Locatello, A. Yurtsever, O. Fercoq, V. Cevher, in:, Advances in Neural Information Processing Systems, 2019, pp. 14291–14301.","ieee":"F. Locatello, A. Yurtsever, O. Fercoq, and V. Cevher, “Stochastic Frank-Wolfe for composite convex minimization,” in Advances in Neural Information Processing Systems, Vancouver, Canada, 2019, vol. 32, pp. 14291–14301."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","citation":{"chicago":"Steenkiste, Sjoerd van, Francesco Locatello, Jürgen Schmidhuber, and Olivier Bachem. “Are Disentangled Representations Helpful for Abstract Visual Reasoning?” In Advances in Neural Information Processing Systems, Vol. 32, 2019.","ista":"Steenkiste S van, Locatello F, Schmidhuber J, Bachem O. 2019. Are disentangled representations helpful for abstract visual reasoning? Advances in Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems vol. 32.","mla":"Steenkiste, Sjoerd van, et al. “Are Disentangled Representations Helpful for Abstract Visual Reasoning?” Advances in Neural Information Processing Systems, vol. 32, 2019.","ama":"Steenkiste S van, Locatello F, Schmidhuber J, Bachem O. Are disentangled representations helpful for abstract visual reasoning? In: Advances in Neural Information Processing Systems. Vol 32. ; 2019.","apa":"Steenkiste, S. van, Locatello, F., Schmidhuber, J., & Bachem, O. (2019). Are disentangled representations helpful for abstract visual reasoning? In Advances in Neural Information Processing Systems (Vol. 32). Vancouver, Canada.","ieee":"S. van Steenkiste, F. Locatello, J. Schmidhuber, and O. Bachem, “Are disentangled representations helpful for abstract visual reasoning?,” in Advances in Neural Information Processing Systems, Vancouver, Canada, 2019, vol. 32.","short":"S. van Steenkiste, F. Locatello, J. Schmidhuber, O. Bachem, in:, Advances in Neural Information Processing Systems, 2019."},"date_updated":"2023-09-12T09:02:43Z","title":"Are disentangled representations helpful for abstract visual reasoning?","department":[{"_id":"FrLo"}],"article_processing_charge":"No","external_id":{"arxiv":["1905.12506"]},"author":[{"full_name":"Steenkiste, Sjoerd van","last_name":"Steenkiste","first_name":"Sjoerd van"},{"id":"26cfd52f-2483-11ee-8040-88983bcc06d4","first_name":"Francesco","last_name":"Locatello","orcid":"0000-0002-4850-0683","full_name":"Locatello, Francesco"},{"first_name":"Jürgen","full_name":"Schmidhuber, Jürgen","last_name":"Schmidhuber"},{"first_name":"Olivier","full_name":"Bachem, Olivier","last_name":"Bachem"}],"_id":"14193","status":"public","conference":{"name":"NeurIPS: Neural Information Processing Systems","start_date":"2019-12-08","end_date":"2019-12-14","location":"Vancouver, Canada"},"type":"conference","publication":"Advances in Neural Information Processing Systems","language":[{"iso":"eng"}],"day":"29","year":"2019","publication_status":"published","publication_identifier":{"isbn":["9781713807933"]},"date_created":"2023-08-22T14:09:53Z","volume":32,"date_published":"2019-05-29T00:00:00Z","oa_version":"Preprint","abstract":[{"text":"A disentangled representation encodes information about the salient factors\r\nof variation in the data independently. Although it is often argued that this\r\nrepresentational format is useful in learning to solve many real-world\r\ndown-stream tasks, there is little empirical evidence that supports this claim.\r\nIn this paper, we conduct a large-scale study that investigates whether\r\ndisentangled representations are more suitable for abstract reasoning tasks.\r\nUsing two new tasks similar to Raven's Progressive Matrices, we evaluate the\r\nusefulness of the representations learned by 360 state-of-the-art unsupervised\r\ndisentanglement models. Based on these representations, we train 3600 abstract\r\nreasoning models and observe that disentangled representations do in fact lead\r\nto better down-stream performance. In particular, they enable quicker learning\r\nusing fewer samples.","lang":"eng"}],"intvolume":" 32","month":"05","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.1905.12506"}],"quality_controlled":"1"},{"title":"Challenging common assumptions in the unsupervised learning of disentangled representations","article_processing_charge":"No","external_id":{"arxiv":["1811.12359"]},"author":[{"id":"26cfd52f-2483-11ee-8040-88983bcc06d4","first_name":"Francesco","last_name":"Locatello","full_name":"Locatello, Francesco","orcid":"0000-0002-4850-0683"},{"last_name":"Bauer","full_name":"Bauer, Stefan","first_name":"Stefan"},{"first_name":"Mario","full_name":"Lucic, Mario","last_name":"Lucic"},{"first_name":"Gunnar","full_name":"Rätsch, Gunnar","last_name":"Rätsch"},{"full_name":"Gelly, Sylvain","last_name":"Gelly","first_name":"Sylvain"},{"last_name":"Schölkopf","full_name":"Schölkopf, Bernhard","first_name":"Bernhard"},{"first_name":"Olivier","full_name":"Bachem, Olivier","last_name":"Bachem"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Locatello, Francesco, Stefan Bauer, Mario Lucic, Gunnar Rätsch, Sylvain Gelly, Bernhard Schölkopf, and Olivier Bachem. “Challenging Common Assumptions in the Unsupervised Learning of Disentangled Representations.” In Proceedings of the 36th International Conference on Machine Learning, 97:4114–24. ML Research Press, 2019.","ista":"Locatello F, Bauer S, Lucic M, Rätsch G, Gelly S, Schölkopf B, Bachem O. 2019. Challenging common assumptions in the unsupervised learning of disentangled representations. Proceedings of the 36th International Conference on Machine Learning. International Conference on Machine Learning vol. 97, 4114–4124.","mla":"Locatello, Francesco, et al. “Challenging Common Assumptions in the Unsupervised Learning of Disentangled Representations.” Proceedings of the 36th International Conference on Machine Learning, vol. 97, ML Research Press, 2019, pp. 4114–24.","apa":"Locatello, F., Bauer, S., Lucic, M., Rätsch, G., Gelly, S., Schölkopf, B., & Bachem, O. (2019). Challenging common assumptions in the unsupervised learning of disentangled representations. In Proceedings of the 36th International Conference on Machine Learning (Vol. 97, pp. 4114–4124). Long Beach, CA, United States: ML Research Press.","ama":"Locatello F, Bauer S, Lucic M, et al. Challenging common assumptions in the unsupervised learning of disentangled representations. In: Proceedings of the 36th International Conference on Machine Learning. Vol 97. ML Research Press; 2019:4114-4124.","short":"F. Locatello, S. Bauer, M. Lucic, G. Rätsch, S. Gelly, B. Schölkopf, O. Bachem, in:, Proceedings of the 36th International Conference on Machine Learning, ML Research Press, 2019, pp. 4114–4124.","ieee":"F. Locatello et al., “Challenging common assumptions in the unsupervised learning of disentangled representations,” in Proceedings of the 36th International Conference on Machine Learning, Long Beach, CA, United States, 2019, vol. 97, pp. 4114–4124."},"oa":1,"publisher":"ML Research Press","quality_controlled":"1","date_created":"2023-08-22T14:13:08Z","date_published":"2019-06-09T00:00:00Z","page":"4114-4124","publication":"Proceedings of the 36th International Conference on Machine Learning","day":"09","year":"2019","status":"public","conference":{"start_date":"2019-06-10","end_date":"2019-06-15","location":"Long Beach, CA, United States","name":"International Conference on Machine Learning"},"type":"conference","_id":"14200","department":[{"_id":"FrLo"}],"extern":"1","date_updated":"2023-09-13T07:45:30Z","intvolume":" 97","month":"06","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1811.12359"}],"scopus_import":"1","oa_version":"Preprint","abstract":[{"lang":"eng","text":"The key idea behind the unsupervised learning of disentangled representations\r\nis that real-world data is generated by a few explanatory factors of variation\r\nwhich can be recovered by unsupervised learning algorithms. In this paper, we\r\nprovide a sober look at recent progress in the field and challenge some common\r\nassumptions. We first theoretically show that the unsupervised learning of\r\ndisentangled representations is fundamentally impossible without inductive\r\nbiases on both the models and the data. Then, we train more than 12000 models\r\ncovering most prominent methods and evaluation metrics in a reproducible\r\nlarge-scale experimental study on seven different data sets. We observe that\r\nwhile the different methods successfully enforce properties ``encouraged'' by\r\nthe corresponding losses, well-disentangled models seemingly cannot be\r\nidentified without supervision. Furthermore, increased disentanglement does not\r\nseem to lead to a decreased sample complexity of learning for downstream tasks.\r\nOur results suggest that future work on disentanglement learning should be\r\nexplicit about the role of inductive biases and (implicit) supervision,\r\ninvestigate concrete benefits of enforcing disentanglement of the learned\r\nrepresentations, and consider a reproducible experimental setup covering\r\nseveral data sets."}],"volume":97,"language":[{"iso":"eng"}],"publication_status":"published"},{"title":"Limiting shapes of confined lipid vesicles","article_processing_charge":"No","external_id":{"isi":["000457329700003"],"pmid":["30629082"]},"author":[{"last_name":"Kavcic","orcid":"0000-0001-6041-254X","full_name":"Kavcic, Bor","first_name":"Bor","id":"350F91D2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Sakashita, A.","last_name":"Sakashita","first_name":"A."},{"first_name":"H.","full_name":"Noguchi, H.","last_name":"Noguchi"},{"first_name":"P.","full_name":"Ziherl, P.","last_name":"Ziherl"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Kavcic, Bor, A. Sakashita, H. Noguchi, and P. Ziherl. “Limiting Shapes of Confined Lipid Vesicles.” Soft Matter. Royal Society of Chemistry, 2019. https://doi.org/10.1039/c8sm01956h.","ista":"Kavcic B, Sakashita A, Noguchi H, Ziherl P. 2019. Limiting shapes of confined lipid vesicles. Soft Matter. 15(4), 602–614.","mla":"Kavcic, Bor, et al. “Limiting Shapes of Confined Lipid Vesicles.” Soft Matter, vol. 15, no. 4, Royal Society of Chemistry, 2019, pp. 602–14, doi:10.1039/c8sm01956h.","ama":"Kavcic B, Sakashita A, Noguchi H, Ziherl P. Limiting shapes of confined lipid vesicles. Soft Matter. 2019;15(4):602-614. doi:10.1039/c8sm01956h","apa":"Kavcic, B., Sakashita, A., Noguchi, H., & Ziherl, P. (2019). Limiting shapes of confined lipid vesicles. Soft Matter. Royal Society of Chemistry. https://doi.org/10.1039/c8sm01956h","ieee":"B. Kavcic, A. Sakashita, H. Noguchi, and P. Ziherl, “Limiting shapes of confined lipid vesicles,” Soft Matter, vol. 15, no. 4. Royal Society of Chemistry, pp. 602–614, 2019.","short":"B. Kavcic, A. Sakashita, H. Noguchi, P. Ziherl, Soft Matter 15 (2019) 602–614."},"oa":1,"quality_controlled":"1","publisher":"Royal Society of Chemistry","date_created":"2019-01-11T07:37:47Z","doi":"10.1039/c8sm01956h","date_published":"2019-01-10T00:00:00Z","page":"602-614","publication":"Soft Matter","day":"10","year":"2019","isi":1,"has_accepted_license":"1","status":"public","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported (CC BY-NC-ND 3.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/3.0/legalcode","short":"CC BY-NC-ND (3.0)"},"article_type":"original","type":"journal_article","_id":"5817","file_date_updated":"2020-10-09T11:00:05Z","department":[{"_id":"GaTk"}],"ddc":["530"],"date_updated":"2023-09-13T08:47:16Z","intvolume":" 15","month":"01","scopus_import":"1","oa_version":"Submitted Version","pmid":1,"abstract":[{"text":"We theoretically study the shapes of lipid vesicles confined to a spherical cavity, elaborating a framework based on the so-called limiting shapes constructed from geometrically simple structural elements such as double-membrane walls and edges. Partly inspired by numerical results, the proposed non-compartmentalized and compartmentalized limiting shapes are arranged in the bilayer-couple phase diagram which is then compared to its free-vesicle counterpart. We also compute the area-difference-elasticity phase diagram of the limiting shapes and we use it to interpret shape transitions experimentally observed in vesicles confined within another vesicle. The limiting-shape framework may be generalized to theoretically investigate the structure of certain cell organelles such as the mitochondrion.","lang":"eng"}],"license":"https://creativecommons.org/licenses/by-nc-nd/3.0/","volume":15,"issue":"4","language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"614c337d6424ccd3d48d1b1f9513510d","file_id":"8641","success":1,"creator":"bkavcic","date_updated":"2020-10-09T11:00:05Z","file_size":5370762,"date_created":"2020-10-09T11:00:05Z","file_name":"lmt_sftmtr_V8.pdf"}],"publication_status":"published","publication_identifier":{"eissn":["1744-6848"],"issn":["1744-683X"]}},{"date_updated":"2023-09-13T09:12:35Z","ddc":["510"],"department":[{"_id":"JaMa"}],"file_date_updated":"2020-07-14T12:47:55Z","_id":"73","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","publication_identifier":{"issn":["09442669"]},"publication_status":"published","file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"5895","checksum":"ba05ac2d69de4c58d2cd338b63512798","creator":"dernst","date_updated":"2020-07-14T12:47:55Z","file_size":645565,"date_created":"2019-01-28T15:37:11Z","file_name":"2018_Calculus_Erbar.pdf"}],"language":[{"iso":"eng"}],"issue":"1","volume":58,"ec_funded":1,"abstract":[{"lang":"eng","text":"We consider the space of probability measures on a discrete set X, endowed with a dynamical optimal transport metric. Given two probability measures supported in a subset Y⊆X, it is natural to ask whether they can be connected by a constant speed geodesic with support in Y at all times. Our main result answers this question affirmatively, under a suitable geometric condition on Y introduced in this paper. The proof relies on an extension result for subsolutions to discrete Hamilton-Jacobi equations, which is of independent interest."}],"oa_version":"Published Version","scopus_import":"1","month":"02","intvolume":" 58","citation":{"mla":"Erbar, Matthias, et al. “On the Geometry of Geodesics in Discrete Optimal Transport.” Calculus of Variations and Partial Differential Equations, vol. 58, no. 1, 19, Springer, 2019, doi:10.1007/s00526-018-1456-1.","ama":"Erbar M, Maas J, Wirth M. On the geometry of geodesics in discrete optimal transport. Calculus of Variations and Partial Differential Equations. 2019;58(1). doi:10.1007/s00526-018-1456-1","apa":"Erbar, M., Maas, J., & Wirth, M. (2019). On the geometry of geodesics in discrete optimal transport. Calculus of Variations and Partial Differential Equations. Springer. https://doi.org/10.1007/s00526-018-1456-1","short":"M. Erbar, J. Maas, M. Wirth, Calculus of Variations and Partial Differential Equations 58 (2019).","ieee":"M. Erbar, J. Maas, and M. Wirth, “On the geometry of geodesics in discrete optimal transport,” Calculus of Variations and Partial Differential Equations, vol. 58, no. 1. Springer, 2019.","chicago":"Erbar, Matthias, Jan Maas, and Melchior Wirth. “On the Geometry of Geodesics in Discrete Optimal Transport.” Calculus of Variations and Partial Differential Equations. Springer, 2019. https://doi.org/10.1007/s00526-018-1456-1.","ista":"Erbar M, Maas J, Wirth M. 2019. On the geometry of geodesics in discrete optimal transport. Calculus of Variations and Partial Differential Equations. 58(1), 19."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"first_name":"Matthias","last_name":"Erbar","full_name":"Erbar, Matthias"},{"orcid":"0000-0002-0845-1338","full_name":"Maas, Jan","last_name":"Maas","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","first_name":"Jan"},{"full_name":"Wirth, Melchior","last_name":"Wirth","first_name":"Melchior"}],"external_id":{"arxiv":["1805.06040"],"isi":["000452849400001"]},"article_processing_charge":"Yes (via OA deal)","title":"On the geometry of geodesics in discrete optimal transport","article_number":"19","project":[{"call_identifier":"H2020","_id":"256E75B8-B435-11E9-9278-68D0E5697425","grant_number":"716117","name":"Optimal Transport and Stochastic Dynamics"},{"grant_number":" F06504","name":"Taming Complexity in Partial Di erential Systems","call_identifier":"FWF","_id":"260482E2-B435-11E9-9278-68D0E5697425"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"isi":1,"has_accepted_license":"1","year":"2019","day":"01","publication":"Calculus of Variations and Partial Differential Equations","date_published":"2019-02-01T00:00:00Z","doi":"10.1007/s00526-018-1456-1","date_created":"2018-12-11T11:44:29Z","quality_controlled":"1","publisher":"Springer","oa":1},{"title":"On the transfer of inductive bias from simulation to the real world: a new disentanglement dataset","department":[{"_id":"FrLo"}],"author":[{"full_name":"Gondal, Muhammad Waleed","last_name":"Gondal","first_name":"Muhammad Waleed"},{"last_name":"Wüthrich","full_name":"Wüthrich, Manuel","first_name":"Manuel"},{"full_name":"Miladinović, Đorđe","last_name":"Miladinović","first_name":"Đorđe"},{"orcid":"0000-0002-4850-0683","full_name":"Locatello, Francesco","last_name":"Locatello","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","first_name":"Francesco"},{"first_name":"Martin","last_name":"Breidt","full_name":"Breidt, Martin"},{"first_name":"Valentin","full_name":"Volchkov, Valentin","last_name":"Volchkov"},{"first_name":"Joel","full_name":"Akpo, Joel","last_name":"Akpo"},{"first_name":"Olivier","last_name":"Bachem","full_name":"Bachem, Olivier"},{"last_name":"Schölkopf","full_name":"Schölkopf, Bernhard","first_name":"Bernhard"},{"last_name":"Bauer","full_name":"Bauer, Stefan","first_name":"Stefan"}],"article_processing_charge":"No","external_id":{"arxiv":["1906.03292"]},"extern":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_updated":"2023-09-13T09:46:38Z","citation":{"ieee":"M. W. Gondal et al., “On the transfer of inductive bias from simulation to the real world: a new disentanglement dataset,” in Advances in Neural Information Processing Systems, Vancouver, Canada, 2019, vol. 32.","short":"M.W. Gondal, M. Wüthrich, Đ. Miladinović, F. Locatello, M. Breidt, V. Volchkov, J. Akpo, O. Bachem, B. Schölkopf, S. Bauer, in:, Advances in Neural Information Processing Systems, 2019.","apa":"Gondal, M. W., Wüthrich, M., Miladinović, Đ., Locatello, F., Breidt, M., Volchkov, V., … Bauer, S. (2019). On the transfer of inductive bias from simulation to the real world: a new disentanglement dataset. In Advances in Neural Information Processing Systems (Vol. 32). Vancouver, Canada.","ama":"Gondal MW, Wüthrich M, Miladinović Đ, et al. On the transfer of inductive bias from simulation to the real world: a new disentanglement dataset. In: Advances in Neural Information Processing Systems. Vol 32. ; 2019.","mla":"Gondal, Muhammad Waleed, et al. “On the Transfer of Inductive Bias from Simulation to the Real World: A New Disentanglement Dataset.” Advances in Neural Information Processing Systems, vol. 32, 2019.","ista":"Gondal MW, Wüthrich M, Miladinović Đ, Locatello F, Breidt M, Volchkov V, Akpo J, Bachem O, Schölkopf B, Bauer S. 2019. On the transfer of inductive bias from simulation to the real world: a new disentanglement dataset. Advances in Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems vol. 32.","chicago":"Gondal, Muhammad Waleed, Manuel Wüthrich, Đorđe Miladinović, Francesco Locatello, Martin Breidt, Valentin Volchkov, Joel Akpo, Olivier Bachem, Bernhard Schölkopf, and Stefan Bauer. “On the Transfer of Inductive Bias from Simulation to the Real World: A New Disentanglement Dataset.” In Advances in Neural Information Processing Systems, Vol. 32, 2019."},"status":"public","type":"conference","conference":{"name":"NeurIPS: Neural Information Processing Systems","end_date":"2019-12-14","location":"Vancouver, Canada","start_date":"2019-12-08"},"_id":"14190","volume":32,"date_published":"2019-06-07T00:00:00Z","date_created":"2023-08-22T14:09:13Z","day":"07","publication":"Advances in Neural Information Processing Systems","language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9781713807933"]},"publication_status":"published","year":"2019","month":"06","intvolume":" 32","quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1906.03292","open_access":"1"}],"oa":1,"oa_version":"Preprint","abstract":[{"lang":"eng","text":"Learning meaningful and compact representations with disentangled semantic\r\naspects is considered to be of key importance in representation learning. Since\r\nreal-world data is notoriously costly to collect, many recent state-of-the-art\r\ndisentanglement models have heavily relied on synthetic toy data-sets. In this\r\npaper, we propose a novel data-set which consists of over one million images of\r\nphysical 3D objects with seven factors of variation, such as object color,\r\nshape, size and position. In order to be able to control all the factors of\r\nvariation precisely, we built an experimental platform where the objects are\r\nbeing moved by a robotic arm. In addition, we provide two more datasets which\r\nconsist of simulations of the experimental setup. These datasets provide for\r\nthe first time the possibility to systematically investigate how well different\r\ndisentanglement methods perform on real data in comparison to simulation, and\r\nhow simulated data can be leveraged to build better representations of the real\r\nworld. We provide a first experimental study of these questions and our results\r\nindicate that learned models transfer poorly, but that model and hyperparameter\r\nselection is an effective means of transferring information to the real world."}]},{"publisher":"ACM","quality_controlled":"1","oa":1,"date_published":"2019-10-01T00:00:00Z","doi":"10.1145/3344549","date_created":"2019-11-04T15:45:17Z","day":"01","publication":"ACM Transactions on Algorithms","year":"2019","project":[{"name":"Eliminating intersections in drawings of graphs","grant_number":"M02281","_id":"261FA626-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"article_number":"50","title":"Recognizing weak embeddings of graphs","author":[{"first_name":"Hugo","last_name":"Akitaya","full_name":"Akitaya, Hugo"},{"last_name":"Fulek","full_name":"Fulek, Radoslav","orcid":"0000-0001-8485-1774","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","first_name":"Radoslav"},{"first_name":"Csaba","last_name":"Tóth","full_name":"Tóth, Csaba"}],"external_id":{"arxiv":["1709.09209"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Akitaya H, Fulek R, Tóth C. Recognizing weak embeddings of graphs. ACM Transactions on Algorithms. 2019;15(4). doi:10.1145/3344549","apa":"Akitaya, H., Fulek, R., & Tóth, C. (2019). Recognizing weak embeddings of graphs. ACM Transactions on Algorithms. ACM. https://doi.org/10.1145/3344549","ieee":"H. Akitaya, R. Fulek, and C. Tóth, “Recognizing weak embeddings of graphs,” ACM Transactions on Algorithms, vol. 15, no. 4. ACM, 2019.","short":"H. Akitaya, R. Fulek, C. Tóth, ACM Transactions on Algorithms 15 (2019).","mla":"Akitaya, Hugo, et al. “Recognizing Weak Embeddings of Graphs.” ACM Transactions on Algorithms, vol. 15, no. 4, 50, ACM, 2019, doi:10.1145/3344549.","ista":"Akitaya H, Fulek R, Tóth C. 2019. Recognizing weak embeddings of graphs. ACM Transactions on Algorithms. 15(4), 50.","chicago":"Akitaya, Hugo, Radoslav Fulek, and Csaba Tóth. “Recognizing Weak Embeddings of Graphs.” ACM Transactions on Algorithms. ACM, 2019. https://doi.org/10.1145/3344549."},"month":"10","intvolume":" 15","scopus_import":1,"main_file_link":[{"url":"https://arxiv.org/abs/1709.09209","open_access":"1"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"We present an efficient algorithm for a problem in the interface between clustering and graph embeddings. An embedding ϕ : G → M of a graph G into a 2-manifold M maps the vertices in V(G) to distinct points and the edges in E(G) to interior-disjoint Jordan arcs between the corresponding vertices. In applications in clustering, cartography, and visualization, nearby vertices and edges are often bundled to the same point or overlapping arcs due to data compression or low resolution. This raises the computational problem of deciding whether a given map ϕ : G → M comes from an embedding. A map ϕ : G → M is a weak embedding if it can be perturbed into an embedding ψ ϵ : G → M with ‖ ϕ − ψ ϵ ‖ < ϵ for every ϵ > 0, where ‖.‖ is the unform norm.\r\nA polynomial-time algorithm for recognizing weak embeddings has recently been found by Fulek and Kynčl. It reduces the problem to solving a system of linear equations over Z2. It runs in O(n2ω)≤ O(n4.75) time, where ω ∈ [2,2.373) is the matrix multiplication exponent and n is the number of vertices and edges of G. We improve the running time to O(n log n). Our algorithm is also conceptually simpler: We perform a sequence of local operations that gradually “untangles” the image ϕ(G) into an embedding ψ(G) or reports that ϕ is not a weak embedding. It combines local constraints on the orientation of subgraphs directly, thereby eliminating the need for solving large systems of linear equations.\r\n"}],"issue":"4","volume":15,"related_material":{"record":[{"relation":"earlier_version","id":"309","status":"public"}]},"language":[{"iso":"eng"}],"publication_status":"published","status":"public","article_type":"original","type":"journal_article","_id":"6982","department":[{"_id":"UlWa"}],"date_updated":"2023-09-15T12:19:31Z"},{"month":"09","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Hybrid automata combine finite automata and dynamical systems, and model the interaction of digital with physical systems. Formal analysis that can guarantee the safety of all behaviors or rigorously witness failures, while unsolvable in general, has been tackled algorithmically using, e.g., abstraction, bounded model-checking, assisted theorem proving.\r\nNevertheless, very few methods have addressed the time-unbounded reachability analysis of hybrid automata and, for current sound and automatic tools, scalability remains critical. We develop methods for the polyhedral abstraction of hybrid automata, which construct coarse overapproximations and tightens them incrementally, in a CEGAR fashion. We use template polyhedra, i.e., polyhedra whose facets are normal to a given set of directions.\r\nWhile, previously, directions were given by the user, we introduce (1) the first method\r\nfor computing template directions from spurious counterexamples, so as to generalize and\r\neliminate them. The method applies naturally to convex hybrid automata, i.e., hybrid\r\nautomata with (possibly non-linear) convex constraints on derivatives only, while for linear\r\nODE requires further abstraction. Specifically, we introduce (2) the conic abstractions,\r\nwhich, partitioning the state space into appropriate (possibly non-uniform) cones, divide\r\ncurvy trajectories into relatively straight sections, suitable for polyhedral abstractions.\r\nFinally, we introduce (3) space-time interpolation, which, combining interval arithmetic\r\nand template refinement, computes appropriate (possibly non-uniform) time partitioning\r\nand template directions along spurious trajectories, so as to eliminate them.\r\nWe obtain sound and automatic methods for the reachability analysis over dense\r\nand unbounded time of convex hybrid automata and hybrid automata with linear ODE.\r\nWe build prototype tools and compare—favorably—our methods against the respective\r\nstate-of-the-art tools, on several benchmarks."}],"related_material":{"record":[{"id":"631","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"647"},{"relation":"part_of_dissertation","id":"140","status":"public"}]},"file":[{"date_updated":"2020-07-14T12:47:43Z","file_size":4100685,"creator":"mgiacobbe","date_created":"2019-09-27T14:15:05Z","file_name":"giacobbe_thesis.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"773beaf4a85dc2acc2c12b578fbe1965","file_id":"6916"},{"date_updated":"2020-07-14T12:47:43Z","file_size":7959732,"creator":"mgiacobbe","date_created":"2019-09-27T14:22:04Z","file_name":"giacobbe_thesis_src.tar.gz","content_type":"application/gzip","access_level":"closed","relation":"source_file","checksum":"97f1c3da71feefd27e6e625d32b4c75b","file_id":"6917"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2663-337X"]},"degree_awarded":"PhD","publication_status":"published","status":"public","type":"dissertation","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"6894","file_date_updated":"2020-07-14T12:47:43Z","department":[{"_id":"ToHe"}],"ddc":["000"],"supervisor":[{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"}],"date_updated":"2023-09-19T09:30:43Z","publisher":"Institute of Science and Technology Austria","oa":1,"date_published":"2019-09-30T00:00:00Z","doi":"10.15479/AT:ISTA:6894","date_created":"2019-09-22T14:08:44Z","page":"132","day":"30","has_accepted_license":"1","year":"2019","title":"Automatic time-unbounded reachability analysis of hybrid systems","author":[{"first_name":"Mirco","id":"3444EA5E-F248-11E8-B48F-1D18A9856A87","last_name":"Giacobbe","orcid":"0000-0001-8180-0904","full_name":"Giacobbe, Mirco"}],"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"apa":"Giacobbe, M. (2019). Automatic time-unbounded reachability analysis of hybrid systems. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6894","ama":"Giacobbe M. Automatic time-unbounded reachability analysis of hybrid systems. 2019. doi:10.15479/AT:ISTA:6894","short":"M. Giacobbe, Automatic Time-Unbounded Reachability Analysis of Hybrid Systems, Institute of Science and Technology Austria, 2019.","ieee":"M. Giacobbe, “Automatic time-unbounded reachability analysis of hybrid systems,” Institute of Science and Technology Austria, 2019.","mla":"Giacobbe, Mirco. Automatic Time-Unbounded Reachability Analysis of Hybrid Systems. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6894.","ista":"Giacobbe M. 2019. Automatic time-unbounded reachability analysis of hybrid systems. Institute of Science and Technology Austria.","chicago":"Giacobbe, Mirco. “Automatic Time-Unbounded Reachability Analysis of Hybrid Systems.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6894."}},{"abstract":[{"lang":"eng","text":"The spread of adaptive alleles is fundamental to evolution, and in theory, this process is well‐understood. However, only rarely can we follow this process—whether it originates from the spread of a new mutation, or by introgression from another population. In this issue of Molecular Ecology, Hanemaaijer et al. (2018) report on a 25‐year long study of the mosquitoes Anopheles gambiae (Figure 1) and Anopheles coluzzi in Mali, based on genotypes at 15 single‐nucleotide polymorphism (SNP). The species are usually reproductively isolated from each other, but in 2002 and 2006, bursts of hybridization were observed, when F1 hybrids became abundant. Alleles backcrossed from A. gambiae into A. coluzzi, but after the first event, these declined over the following years. In contrast, after 2006, an insecticide resistance allele that had established in A. gambiae spread into A. coluzzi, and rose to high frequency there, over 6 years (~75 generations). Whole genome sequences of 74 individuals showed that A. gambiae SNP from across the genome had become common in the A. coluzzi population, but that most of these were clustered in 34 genes around the resistance locus. A new set of SNP from 25 of these genes were assayed over time; over the 4 years since near‐fixation of the resistance allele; some remained common, whereas others declined. What do these patterns tell us about this introgression event?"}],"oa_version":"Published Version","oa":1,"main_file_link":[{"url":"https://doi.org/10.5061/dryad.2kb6fh4","open_access":"1"}],"publisher":"Dryad","month":"01","year":"2019","day":"09","date_created":"2021-08-06T12:03:50Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"40"}]},"date_published":"2019-01-09T00:00:00Z","doi":"10.5061/dryad.2kb6fh4","_id":"9805","type":"research_data_reference","status":"public","date_updated":"2023-09-19T10:06:07Z","citation":{"chicago":"Barton, Nicholas H. “Data from: The Consequences of an Introgression Event.” Dryad, 2019. https://doi.org/10.5061/dryad.2kb6fh4.","ista":"Barton NH. 2019. Data from: The consequences of an introgression event, Dryad, 10.5061/dryad.2kb6fh4.","mla":"Barton, Nicholas H. Data from: The Consequences of an Introgression Event. Dryad, 2019, doi:10.5061/dryad.2kb6fh4.","short":"N.H. Barton, (2019).","ieee":"N. H. Barton, “Data from: The consequences of an introgression event.” Dryad, 2019.","apa":"Barton, N. H. (2019). Data from: The consequences of an introgression event. Dryad. https://doi.org/10.5061/dryad.2kb6fh4","ama":"Barton NH. Data from: The consequences of an introgression event. 2019. doi:10.5061/dryad.2kb6fh4"},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","article_processing_charge":"No","author":[{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"}],"department":[{"_id":"NiBa"}],"title":"Data from: The consequences of an introgression event"},{"acknowledgement":"This work was supported by INSERM, CNRS, UDS, Ligue Régionale contre le Cancer, Hôpital de Strasbourg, Association pour la Recherche sur le Cancer (ARC) and Agence Nationale de la Recherche (ANR) grants. P.B.C. was funded by the ANR and by the ARSEP (Fondation pour l'Aide à la Recherche sur la Sclérose en Plaques), and G.T. by governmental and ARC fellowships. This work was also supported by grants from the Ataxia UK (2491) and the NC3R (NC/L000199/1) awarded to M.F. The Institut de Génétique et de Biologie Moléculaire et Cellulaire was also supported by a French state fund through the ANR labex. D.E.S. was funded by Marie Curie Grant CIG 334077/IRTIM. We thank B. Altenhein, K. Brückner, M. Crozatier, L. Waltzer, M. Logan, E. Kurant, R. Reuter, E. Kurucz, J.L Dimarcq, J. Hoffmann, C. Goodman, the DHSB, and the BDSC for reagents and flies. We also thank all of the laboratory members for comments on the manuscript; C. Diebold, C. Delaporte, M. Pezze, the fly, and imaging and antibody facilities for technical assistance; and D. Dembele for help with statistics. In addition, we thank Alison Brewer for help with Luciferase assays.","oa":1,"publisher":"Society for Neuroscience","quality_controlled":"1","publication":"Journal of Neuroscience","day":"09","year":"2019","has_accepted_license":"1","isi":1,"date_created":"2018-12-11T11:44:07Z","date_published":"2019-01-09T00:00:00Z","doi":"10.1523/JNEUROSCI.1059-18.2018","page":"238-255","project":[{"_id":"2536F660-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"334077","name":"Investigating the role of transporters in invasive migration through junctions"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Trébuchet, Guillaume, et al. “The Repo Homeodomain Transcription Factor Suppresses Hematopoiesis in Drosophila and Preserves the Glial Fate.” Journal of Neuroscience, vol. 39, no. 2, Society for Neuroscience, 2019, pp. 238–55, doi:10.1523/JNEUROSCI.1059-18.2018.","apa":"Trébuchet, G., Cattenoz, P. B., Zsámboki, J., Mazaud, D., Siekhaus, D. E., Fanto, M., & Giangrande, A. (2019). The Repo homeodomain transcription factor suppresses hematopoiesis in Drosophila and preserves the glial fate. Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.1059-18.2018","ama":"Trébuchet G, Cattenoz PB, Zsámboki J, et al. The Repo homeodomain transcription factor suppresses hematopoiesis in Drosophila and preserves the glial fate. Journal of Neuroscience. 2019;39(2):238-255. doi:10.1523/JNEUROSCI.1059-18.2018","short":"G. Trébuchet, P.B. Cattenoz, J. Zsámboki, D. Mazaud, D.E. Siekhaus, M. Fanto, A. Giangrande, Journal of Neuroscience 39 (2019) 238–255.","ieee":"G. Trébuchet et al., “The Repo homeodomain transcription factor suppresses hematopoiesis in Drosophila and preserves the glial fate,” Journal of Neuroscience, vol. 39, no. 2. Society for Neuroscience, pp. 238–255, 2019.","chicago":"Trébuchet, Guillaume, Pierre B Cattenoz, János Zsámboki, David Mazaud, Daria E Siekhaus, Manolis Fanto, and Angela Giangrande. “The Repo Homeodomain Transcription Factor Suppresses Hematopoiesis in Drosophila and Preserves the Glial Fate.” Journal of Neuroscience. Society for Neuroscience, 2019. https://doi.org/10.1523/JNEUROSCI.1059-18.2018.","ista":"Trébuchet G, Cattenoz PB, Zsámboki J, Mazaud D, Siekhaus DE, Fanto M, Giangrande A. 2019. The Repo homeodomain transcription factor suppresses hematopoiesis in Drosophila and preserves the glial fate. Journal of Neuroscience. 39(2), 238–255."},"title":"The Repo homeodomain transcription factor suppresses hematopoiesis in Drosophila and preserves the glial fate","external_id":{"isi":["000455189900006"],"pmid":["30504274"]},"article_processing_charge":"No","publist_id":"8048","author":[{"first_name":"Guillaume","last_name":"Trébuchet","full_name":"Trébuchet, Guillaume"},{"full_name":"Cattenoz, Pierre B","last_name":"Cattenoz","first_name":"Pierre B"},{"first_name":"János","last_name":"Zsámboki","full_name":"Zsámboki, János"},{"first_name":"David","full_name":"Mazaud, David","last_name":"Mazaud"},{"last_name":"Siekhaus","full_name":"Siekhaus, Daria E","orcid":"0000-0001-8323-8353","first_name":"Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Fanto","full_name":"Fanto, Manolis","first_name":"Manolis"},{"first_name":"Angela","last_name":"Giangrande","full_name":"Giangrande, Angela"}],"pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Despite their different origins, Drosophila glia and hemocytes are related cell populations that provide an immune function. Drosophila hemocytes patrol the body cavity and act as macrophages outside the nervous system whereas glia originate from the neuroepithelium and provide the scavenger population of the nervous system. Drosophila glia are hence the functional orthologs of vertebrate microglia, even though the latter are cells of immune origin that subsequently move into the brain during development. Interestingly, the Drosophila immune cells within (glia) and outside the nervous system (hemocytes) require the same transcription factor Glide/Gcm for their development. This raises the issue of how do glia specifically differentiate in the nervous system and hemocytes in the procephalic mesoderm. The Repo homeodomain transcription factor and pan-glial direct target of Glide/Gcm is known to ensure glial terminal differentiation. Here we show that Repo also takes center stage in the process that discriminates between glia and hemocytes. First, Repo expression is repressed in the hemocyte anlagen by mesoderm-specific factors. Second, Repo ectopic activation in the procephalic mesoderm is sufficient to repress the expression of hemocyte-specific genes. Third, the lack of Repo triggers the expression of hemocyte markers in glia. Thus, a complex network of tissue-specific cues biases the potential of Glide/Gcm. These data allow us to revise the concept of fate determinants and help us understand the bases of cell specification. Both sexes were analyzed.SIGNIFICANCE STATEMENTDistinct cell types often require the same pioneer transcription factor, raising the issue of how does one factor trigger different fates. In Drosophila, glia and hemocytes provide a scavenger activity within and outside the nervous system, respectively. While they both require the Glide/Gcm transcription factor, glia originate from the ectoderm, hemocytes from the mesoderm. Here we show that tissue-specific factors inhibit the gliogenic potential of Glide/Gcm in the mesoderm by repressing the expression of the homeodomain protein Repo, a major glial-specific target of Glide/Gcm. Repo expression in turn inhibits the expression of hemocyte-specific genes in the nervous system. These cell-specific networks secure the establishment of the glial fate only in the nervous system and allow cell diversification."}],"intvolume":" 39","month":"01","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"date_created":"2020-10-02T09:33:28Z","file_name":"2019_JournNeuroscience_Trebuchet.pdf","creator":"dernst","date_updated":"2020-10-02T09:33:28Z","file_size":9455414,"checksum":"8f6925eb4cd1e8747d8ea25929c68de6","file_id":"8596","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"publication_status":"published","ec_funded":1,"issue":"2","volume":39,"_id":"8","status":"public","type":"journal_article","article_type":"original","ddc":["570"],"date_updated":"2023-09-19T10:10:55Z","department":[{"_id":"DaSi"}],"file_date_updated":"2020-10-02T09:33:28Z"},{"citation":{"mla":"Ganev, Iordan V. “The Wonderful Compactification for Quantum Groups.” Journal of the London Mathematical Society, vol. 99, no. 3, Wiley, 2019, pp. 778–806, doi:10.1112/jlms.12193.","ama":"Ganev IV. The wonderful compactification for quantum groups. Journal of the London Mathematical Society. 2019;99(3):778-806. doi:10.1112/jlms.12193","apa":"Ganev, I. V. (2019). The wonderful compactification for quantum groups. Journal of the London Mathematical Society. Wiley. https://doi.org/10.1112/jlms.12193","ieee":"I. V. Ganev, “The wonderful compactification for quantum groups,” Journal of the London Mathematical Society, vol. 99, no. 3. Wiley, pp. 778–806, 2019.","short":"I.V. Ganev, Journal of the London Mathematical Society 99 (2019) 778–806.","chicago":"Ganev, Iordan V. “The Wonderful Compactification for Quantum Groups.” Journal of the London Mathematical Society. Wiley, 2019. https://doi.org/10.1112/jlms.12193.","ista":"Ganev IV. 2019. The wonderful compactification for quantum groups. Journal of the London Mathematical Society. 99(3), 778–806."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"id":"447491B8-F248-11E8-B48F-1D18A9856A87","first_name":"Iordan V","full_name":"Ganev, Iordan V","last_name":"Ganev"}],"publist_id":"8052","external_id":{"isi":["000470025900008"]},"article_processing_charge":"Yes (via OA deal)","title":"The wonderful compactification for quantum groups","quality_controlled":"1","publisher":"Wiley","oa":1,"has_accepted_license":"1","isi":1,"year":"2019","day":"01","publication":"Journal of the London Mathematical Society","page":"778-806","date_published":"2019-06-01T00:00:00Z","doi":"10.1112/jlms.12193","date_created":"2018-12-11T11:44:06Z","_id":"5","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","date_updated":"2023-09-19T10:13:08Z","ddc":["510"],"department":[{"_id":"TaHa"}],"file_date_updated":"2020-07-14T12:46:35Z","abstract":[{"text":"In this paper, we introduce a quantum version of the wonderful compactification of a group as a certain noncommutative projective scheme. Our approach stems from the fact that the wonderful compactification encodes the asymptotics of matrix coefficients, and from its realization as a GIT quotient of the Vinberg semigroup. In order to define the wonderful compactification for a quantum group, we adopt a generalized formalism of Proj categories in the spirit of Artin and Zhang. Key to our construction is a quantum version of the Vinberg semigroup, which we define as a q-deformation of a certain Rees algebra, compatible with a standard Poisson structure. Furthermore, we discuss quantum analogues of the stratification of the wonderful compactification by orbits for a certain group action, and provide explicit computations in the case of SL2.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","month":"06","intvolume":" 99","publication_status":"published","file":[{"checksum":"1be56239b2cd740a0e9a084f773c22f6","file_id":"7238","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2020-01-07T13:31:53Z","file_name":"2019_Wiley_Ganev.pdf","creator":"kschuh","date_updated":"2020-07-14T12:46:35Z","file_size":431754}],"language":[{"iso":"eng"}],"volume":99,"issue":"3"}]