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Auzinger, W. Heidrich, and B. Bickel, “Computational design of nanostructural color for additive manufacturing,” ACM Transactions on Graphics, vol. 37, no. 4. ACM, 2018.","apa":"Auzinger, T., Heidrich, W., & Bickel, B. (2018). Computational design of nanostructural color for additive manufacturing. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/3197517.3201376","mla":"Auzinger, Thomas, et al. “Computational Design of Nanostructural Color for Additive Manufacturing.” ACM Transactions on Graphics, vol. 37, no. 4, 159, ACM, 2018, doi:10.1145/3197517.3201376.","ama":"Auzinger T, Heidrich W, Bickel B. Computational design of nanostructural color for additive manufacturing. ACM Transactions on Graphics. 2018;37(4). doi:10.1145/3197517.3201376","chicago":"Auzinger, Thomas, Wolfgang Heidrich, and Bernd Bickel. “Computational Design of Nanostructural Color for Additive Manufacturing.” ACM Transactions on Graphics. ACM, 2018. https://doi.org/10.1145/3197517.3201376.","ista":"Auzinger T, Heidrich W, Bickel B. 2018. Computational design of nanostructural color for additive manufacturing. ACM Transactions on Graphics. 37(4), 159.","short":"T. Auzinger, W. Heidrich, B. Bickel, ACM Transactions on Graphics 37 (2018)."},"publisher":"ACM","ddc":["000","535","680"],"date_published":"2018-08-01T00:00:00Z","isi":1,"intvolume":" 37","publication_status":"published","publication":"ACM Transactions on Graphics","has_accepted_license":"1","ec_funded":1,"doi":"10.1145/3197517.3201376","article_processing_charge":"No","related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/color-effects-from-transparent-3d-printed-nanostructures/","description":"News on IST Homepage"}]},"language":[{"iso":"eng"}],"author":[{"first_name":"Thomas","full_name":"Auzinger, Thomas","id":"4718F954-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1546-3265","last_name":"Auzinger"},{"first_name":"Wolfgang","last_name":"Heidrich","full_name":"Heidrich, Wolfgang"},{"full_name":"Bickel, Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385","last_name":"Bickel","first_name":"Bernd"}],"date_created":"2018-12-11T11:45:43Z","quality_controlled":"1","volume":37,"date_updated":"2025-04-14T07:28:57Z","acknowledgement":"This work was in part supported by King Abdullah University of Science and Technology Baseline Funding.","article_number":"159","_id":"304","alternative_title":["ACM Transactions on Graphics"],"issue":"4","month":"08","type":"journal_article","file_date_updated":"2020-07-14T12:45:59Z","project":[{"_id":"24F9549A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","grant_number":"715767"}],"abstract":[{"text":"Additive manufacturing has recently seen drastic improvements in resolution, making it now possible to fabricate features at scales of hundreds or even dozens of nanometers, which previously required very expensive lithographic methods.\r\nAs a result, additive manufacturing now seems poised for optical applications, including those relevant to computer graphics, such as material design, as well as display and imaging applications.\r\n \r\nIn this work, we explore the use of additive manufacturing for generating structural colors, where the structures are designed using a fabrication-aware optimization process.\r\nThis requires a combination of full-wave simulation, a feasible parameterization of the design space, and a tailored optimization procedure.\r\nMany of these components should be re-usable for the design of other optical structures at this scale.\r\n \r\nWe show initial results of material samples fabricated based on our designs.\r\nWhile these suffer from the prototype character of state-of-the-art fabrication hardware, we believe they clearly demonstrate the potential of additive nanofabrication for structural colors and other graphics applications.","lang":"eng"}],"day":"01","year":"2018","status":"public","pubrep_id":"1028","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000448185000120"]},"title":"Computational design of nanostructural color for additive manufacturing","scopus_import":"1"},{"department":[{"_id":"CaGu"},{"_id":"GaTk"}],"oa_version":"None","publisher":"Springer","citation":{"apa":"Misun, P., Birchler, A., Lang, M., Hierlemann, A., & Frey, O. (2018). Fabrication and operation of microfluidic hanging drop networks. Methods in Molecular Biology. Springer. https://doi.org/10.1007/978-1-4939-7792-5_15","mla":"Misun, Patrick, et al. “Fabrication and Operation of Microfluidic Hanging Drop Networks.” Methods in Molecular Biology, vol. 1771, Springer, 2018, pp. 183–202, doi:10.1007/978-1-4939-7792-5_15.","ieee":"P. Misun, A. Birchler, M. Lang, A. Hierlemann, and O. Frey, “Fabrication and operation of microfluidic hanging drop networks,” Methods in Molecular Biology, vol. 1771. Springer, pp. 183–202, 2018.","ista":"Misun P, Birchler A, Lang M, Hierlemann A, Frey O. 2018. Fabrication and operation of microfluidic hanging drop networks. Methods in Molecular Biology. 1771, 183–202.","short":"P. Misun, A. Birchler, M. Lang, A. Hierlemann, O. Frey, Methods in Molecular Biology 1771 (2018) 183–202.","chicago":"Misun, Patrick, Axel Birchler, Moritz Lang, Andreas Hierlemann, and Olivier Frey. “Fabrication and Operation of Microfluidic Hanging Drop Networks.” Methods in Molecular Biology. Springer, 2018. https://doi.org/10.1007/978-1-4939-7792-5_15.","ama":"Misun P, Birchler A, Lang M, Hierlemann A, Frey O. Fabrication and operation of microfluidic hanging drop networks. Methods in Molecular Biology. 2018;1771:183-202. doi:10.1007/978-1-4939-7792-5_15"},"date_published":"2018-01-01T00:00:00Z","intvolume":" 1771","publication_status":"published","doi":"10.1007/978-1-4939-7792-5_15","publication":"Methods in Molecular Biology","ec_funded":1,"publist_id":"7574","language":[{"iso":"eng"}],"author":[{"first_name":"Patrick","full_name":"Misun, Patrick","last_name":"Misun"},{"first_name":"Axel","full_name":"Birchler, Axel","last_name":"Birchler"},{"first_name":"Moritz","full_name":"Lang, Moritz","id":"29E0800A-F248-11E8-B48F-1D18A9856A87","last_name":"Lang"},{"first_name":"Andreas","last_name":"Hierlemann","full_name":"Hierlemann, Andreas"},{"first_name":"Olivier","last_name":"Frey","full_name":"Frey, Olivier"}],"date_created":"2018-12-11T11:45:43Z","quality_controlled":"1","date_updated":"2021-01-12T07:40:42Z","volume":1771,"acknowledgement":"This work was financially supported by FP7 of the EU through the project “Body on a chip,” ICT-FET-296257, and the ERC Advanced Grant “NeuroCMOS” (contract 267351), as well as by an individual Ambizione Grant 142440 from the Swiss National Science Foundation for Olivier Frey. The research leading to these results also received funding from the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no. [291734]. We would like to thank Alexander Stettler, ETH Zurich for his expertise and support in the cleanroom, and we acknowledge the Single Cell Unit of D-BSSE, ETH Zurich for assistance in microscopy issues. M.L. is grateful to the members of the Guet and Tkačik groups, IST Austria, for valuable comments and support.","_id":"305","month":"01","alternative_title":["MIMB"],"type":"journal_article","page":"183 - 202","abstract":[{"lang":"eng","text":"The hanging-drop network (HDN) is a technology platform based on a completely open microfluidic network at the bottom of an inverted, surface-patterned substrate. The platform is predominantly used for the formation, culturing, and interaction of self-assembled spherical microtissues (spheroids) under precisely controlled flow conditions. Here, we describe design, fabrication, and operation of microfluidic hanging-drop networks."}],"project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"year":"2018","day":"01","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Fabrication and operation of microfluidic hanging drop networks","scopus_import":1},{"status":"public","day":"01","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2018","scopus_import":1,"title":"An introduction to the maximum entropy approach and its application to inference problems in biology","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"abstract":[{"text":"A cornerstone of statistical inference, the maximum entropy framework is being increasingly applied to construct descriptive and predictive models of biological systems, especially complex biological networks, from large experimental data sets. Both its broad applicability and the success it obtained in different contexts hinge upon its conceptual simplicity and mathematical soundness. Here we try to concisely review the basic elements of the maximum entropy principle, starting from the notion of ‘entropy’, and describe its usefulness for the analysis of biological systems. As examples, we focus specifically on the problem of reconstructing gene interaction networks from expression data and on recent work attempting to expand our system-level understanding of bacterial metabolism. Finally, we highlight some extensions and potential limitations of the maximum entropy approach, and point to more recent developments that are likely to play a key role in the upcoming challenges of extracting structures and information from increasingly rich, high-throughput biological data.","lang":"eng"}],"file_date_updated":"2020-07-14T12:45:59Z","_id":"306","article_number":"e00596","type":"journal_article","issue":"4","month":"04","quality_controlled":"1","volume":4,"date_updated":"2024-10-09T20:58:19Z","language":[{"iso":"eng"}],"author":[{"full_name":"De Martino, Andrea","last_name":"De Martino","first_name":"Andrea"},{"last_name":"De Martino","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5214-4706","full_name":"De Martino, Daniele","first_name":"Daniele"}],"date_created":"2018-12-11T11:45:44Z","publication_status":"published","intvolume":" 4","publication":"Heliyon","has_accepted_license":"1","ec_funded":1,"doi":"10.1016/j.heliyon.2018.e00596","corr_author":"1","citation":{"chicago":"De Martino, Andrea, and Daniele De Martino. “An Introduction to the Maximum Entropy Approach and Its Application to Inference Problems in Biology.” Heliyon. Elsevier, 2018. https://doi.org/10.1016/j.heliyon.2018.e00596.","ista":"De Martino A, De Martino D. 2018. An introduction to the maximum entropy approach and its application to inference problems in biology. Heliyon. 4(4), e00596.","short":"A. De Martino, D. De Martino, Heliyon 4 (2018).","ama":"De Martino A, De Martino D. An introduction to the maximum entropy approach and its application to inference problems in biology. Heliyon. 2018;4(4). doi:10.1016/j.heliyon.2018.e00596","mla":"De Martino, Andrea, and Daniele De Martino. “An Introduction to the Maximum Entropy Approach and Its Application to Inference Problems in Biology.” Heliyon, vol. 4, no. 4, e00596, Elsevier, 2018, doi:10.1016/j.heliyon.2018.e00596.","apa":"De Martino, A., & De Martino, D. (2018). An introduction to the maximum entropy approach and its application to inference problems in biology. Heliyon. Elsevier. https://doi.org/10.1016/j.heliyon.2018.e00596","ieee":"A. De Martino and D. De Martino, “An introduction to the maximum entropy approach and its application to inference problems in biology,” Heliyon, vol. 4, no. 4. Elsevier, 2018."},"publisher":"Elsevier","date_published":"2018-04-01T00:00:00Z","ddc":["530"],"department":[{"_id":"GaTk"}],"file":[{"relation":"main_file","content_type":"application/pdf","file_id":"5929","creator":"dernst","date_created":"2019-02-06T07:36:24Z","checksum":"67010cf5e3b3e0637c659371714a715a","file_name":"2018_Heliyon_DeMartino.pdf","access_level":"open_access","file_size":994490,"date_updated":"2020-07-14T12:45:59Z"}],"oa_version":"Published Version","oa":1},{"corr_author":"1","citation":{"ieee":"A. Ratheesh et al., “Drosophila TNF modulates tissue tension in the embryo to facilitate macrophage invasive migration,” Developmental Cell, vol. 45, no. 3. Elsevier, pp. 331–346, 2018.","mla":"Ratheesh, Aparna, et al. “Drosophila TNF Modulates Tissue Tension in the Embryo to Facilitate Macrophage Invasive Migration.” Developmental Cell, vol. 45, no. 3, Elsevier, 2018, pp. 331–46, doi:10.1016/j.devcel.2018.04.002.","apa":"Ratheesh, A., Bicher, J., Smutny, M., Veselá, J., Papusheva, E., Krens, G., … Siekhaus, D. E. (2018). Drosophila TNF modulates tissue tension in the embryo to facilitate macrophage invasive migration. Developmental Cell. Elsevier. https://doi.org/10.1016/j.devcel.2018.04.002","ama":"Ratheesh A, Bicher J, Smutny M, et al. Drosophila TNF modulates tissue tension in the embryo to facilitate macrophage invasive migration. Developmental Cell. 2018;45(3):331-346. doi:10.1016/j.devcel.2018.04.002","chicago":"Ratheesh, Aparna, Julia Bicher, Michael Smutny, Jana Veselá, Ekaterina Papusheva, Gabriel Krens, Walter Kaufmann, Attila György, Alessandra M Casano, and Daria E Siekhaus. “Drosophila TNF Modulates Tissue Tension in the Embryo to Facilitate Macrophage Invasive Migration.” Developmental Cell. Elsevier, 2018. https://doi.org/10.1016/j.devcel.2018.04.002.","ista":"Ratheesh A, Bicher J, Smutny M, Veselá J, Papusheva E, Krens G, Kaufmann W, György A, Casano AM, Siekhaus DE. 2018. Drosophila TNF modulates tissue tension in the embryo to facilitate macrophage invasive migration. Developmental Cell. 45(3), 331–346.","short":"A. Ratheesh, J. Bicher, M. Smutny, J. Veselá, E. Papusheva, G. Krens, W. Kaufmann, A. György, A.M. Casano, D.E. Siekhaus, Developmental Cell 45 (2018) 331–346."},"publisher":"Elsevier","ddc":["570"],"date_published":"2018-05-07T00:00:00Z","main_file_link":[{"url":"https://doi.org/10.1016/j.devcel.2018.04.002","open_access":"1"}],"department":[{"_id":"DaSi"},{"_id":"CaHe"},{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"MiSi"}],"oa_version":"Published Version","oa":1,"language":[{"iso":"eng"}],"author":[{"first_name":"Aparna","full_name":"Ratheesh, Aparna","last_name":"Ratheesh","id":"2F064CFE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7190-0776"},{"id":"3CCBB46E-F248-11E8-B48F-1D18A9856A87","last_name":"Biebl","full_name":"Biebl, Julia","first_name":"Julia"},{"first_name":"Michael","last_name":"Smutny","full_name":"Smutny, Michael"},{"full_name":"Veselá, Jana","id":"433253EE-F248-11E8-B48F-1D18A9856A87","last_name":"Veselá","first_name":"Jana"},{"id":"41DB591E-F248-11E8-B48F-1D18A9856A87","last_name":"Papusheva","full_name":"Papusheva, Ekaterina","first_name":"Ekaterina"},{"first_name":"Gabriel","orcid":"0000-0003-4761-5996","id":"2B819732-F248-11E8-B48F-1D18A9856A87","last_name":"Krens","full_name":"Krens, Gabriel"},{"first_name":"Walter","full_name":"Kaufmann, Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9735-5315","last_name":"Kaufmann"},{"first_name":"Attila","full_name":"György, Attila","orcid":"0000-0002-1819-198X","id":"3BCEDBE0-F248-11E8-B48F-1D18A9856A87","last_name":"György"},{"id":"3DBA3F4E-F248-11E8-B48F-1D18A9856A87","last_name":"Casano","orcid":"0000-0002-6009-6804","full_name":"Casano, Alessandra M","first_name":"Alessandra M"},{"id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","last_name":"Siekhaus","orcid":"0000-0001-8323-8353","full_name":"Siekhaus, Daria E","first_name":"Daria E"}],"pmid":1,"related_material":{"link":[{"url":"https://ist.ac.at/en/news/cells-change-tension-to-make-tissue-barriers-easier-to-get-through/","description":"News on IST Homepage","relation":"press_release"}]},"date_created":"2018-12-11T11:45:44Z","publication_status":"published","article_type":"original","intvolume":" 45","isi":1,"publication":"Developmental Cell","ec_funded":1,"doi":"10.1016/j.devcel.2018.04.002","acknowledged_ssus":[{"_id":"SSU"}],"article_processing_charge":"No","_id":"308","type":"journal_article","issue":"3","month":"05","quality_controlled":"1","volume":45,"date_updated":"2026-06-18T18:37:46Z","status":"public","day":"07","year":"2018","scopus_import":"1","title":"Drosophila TNF modulates tissue tension in the embryo to facilitate macrophage invasive migration","external_id":{"isi":["000432461400009"],"pmid":["29738712"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"_id":"253B6E48-B435-11E9-9278-68D0E5697425","name":"The role of Drosophila TNF alpha in immune cell invasion","grant_number":"P29638","call_identifier":"FWF"},{"grant_number":"334077","name":"Investigating the role of transporters in invasive migration through junctions","call_identifier":"FP7","_id":"2536F660-B435-11E9-9278-68D0E5697425"}],"abstract":[{"lang":"eng","text":"Migrating cells penetrate tissue barriers during development, inflammatory responses, and tumor metastasis. We study if migration in vivo in such three-dimensionally confined environments requires changes in the mechanical properties of the surrounding cells using embryonic Drosophila melanogaster hemocytes, also called macrophages, as a model. We find that macrophage invasion into the germband through transient separation of the apposing ectoderm and mesoderm requires cell deformations and reductions in apical tension in the ectoderm. Interestingly, the genetic pathway governing these mechanical shifts acts downstream of the only known tumor necrosis factor superfamily member in Drosophila, Eiger, and its receptor, Grindelwald. Eiger-Grindelwald signaling reduces levels of active Myosin in the germband ectodermal cortex through the localization of a Crumbs complex component, Patj (Pals-1-associated tight junction protein). We therefore elucidate a distinct molecular pathway that controls tissue tension and demonstrate the importance of such regulation for invasive migration in vivo."}],"page":"331 - 346"},{"oa":1,"department":[{"_id":"JaMa"}],"file":[{"access_level":"open_access","date_updated":"2020-07-14T12:44:39Z","file_size":671125,"content_type":"application/pdf","relation":"main_file","date_created":"2018-12-12T10:17:13Z","checksum":"47686d58ec21c164540f1a980ff2163f","creator":"system","file_id":"5266","file_name":"IST-2016-712-v1+1_s10959-016-0724-2.pdf"}],"oa_version":"Published Version","date_published":"2018-06-01T00:00:00Z","ddc":["519"],"corr_author":"1","citation":{"ieee":"F. Flandoli, F. Russo, and G. A. Zanco, “Infinite-dimensional calculus under weak spatial regularity of the processes,” Journal of Theoretical Probability, vol. 31, no. 2. Springer, pp. 789–826, 2018.","apa":"Flandoli, F., Russo, F., & Zanco, G. A. (2018). Infinite-dimensional calculus under weak spatial regularity of the processes. Journal of Theoretical Probability. Springer. https://doi.org/10.1007/s10959-016-0724-2","mla":"Flandoli, Franco, et al. “Infinite-Dimensional Calculus under Weak Spatial Regularity of the Processes.” Journal of Theoretical Probability, vol. 31, no. 2, Springer, 2018, pp. 789–826, doi:10.1007/s10959-016-0724-2.","ama":"Flandoli F, Russo F, Zanco GA. Infinite-dimensional calculus under weak spatial regularity of the processes. Journal of Theoretical Probability. 2018;31(2):789-826. doi:10.1007/s10959-016-0724-2","chicago":"Flandoli, Franco, Francesco Russo, and Giovanni A Zanco. “Infinite-Dimensional Calculus under Weak Spatial Regularity of the Processes.” Journal of Theoretical Probability. Springer, 2018. https://doi.org/10.1007/s10959-016-0724-2.","short":"F. Flandoli, F. Russo, G.A. Zanco, Journal of Theoretical Probability 31 (2018) 789–826.","ista":"Flandoli F, Russo F, Zanco GA. 2018. Infinite-dimensional calculus under weak spatial regularity of the processes. Journal of Theoretical Probability. 31(2), 789–826."},"publisher":"Springer","has_accepted_license":"1","publication":"Journal of Theoretical Probability","article_processing_charge":"Yes (via OA deal)","doi":"10.1007/s10959-016-0724-2","publication_status":"published","intvolume":" 31","isi":1,"date_created":"2018-12-11T11:50:45Z","author":[{"full_name":"Flandoli, Franco","last_name":"Flandoli","first_name":"Franco"},{"last_name":"Russo","full_name":"Russo, Francesco","first_name":"Francesco"},{"first_name":"Giovanni A","full_name":"Zanco, Giovanni A","id":"47491882-F248-11E8-B48F-1D18A9856A87","last_name":"Zanco"}],"language":[{"iso":"eng"}],"publist_id":"6119","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). The second named author benefited partially from the support of the “FMJH Program Gaspard Monge in Optimization and Operations Research” (Project 2014-1607H). He is also grateful for the invitation to the Department of Mathematics of the University of Pisa. The third named author is grateful for the invitation to ENSTA.","date_updated":"2025-09-22T09:36:02Z","volume":31,"quality_controlled":"1","type":"journal_article","issue":"2","month":"06","_id":"1215","project":[{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"abstract":[{"text":"Two generalizations of Itô formula to infinite-dimensional spaces are given.\r\nThe first one, in Hilbert spaces, extends the classical one by taking advantage of\r\ncancellations when they occur in examples and it is applied to the case of a group\r\ngenerator. The second one, based on the previous one and a limit procedure, is an Itô\r\nformula in a special class of Banach spaces having a product structure with the noise\r\nin a Hilbert component; again the key point is the extension due to a cancellation. This\r\nextension to Banach spaces and in particular the specific cancellation are motivated\r\nby path-dependent Itô calculus.","lang":"eng"}],"page":"789-826","file_date_updated":"2020-07-14T12:44:39Z","scopus_import":"1","pubrep_id":"712","title":"Infinite-dimensional calculus under weak spatial regularity of the processes","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","external_id":{"isi":["000432743300007"]},"status":"public","day":"01","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2018"},{"abstract":[{"text":"Dataset for manuscript 'Social network plasticity decreases disease transmission in a eusocial insect'\r\nCompared to previous versions: - raw image files added\r\n - correction of URLs within README.txt file\r\n","lang":"eng"}],"doi":"10.5281/ZENODO.1322669","article_processing_charge":"No","date_created":"2023-05-23T13:24:51Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Social network plasticity decreases disease transmission in a eusocial insect","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"23","year":"2018","related_material":{"record":[{"relation":"used_in_publication","id":"7","status":"public"}]},"status":"public","author":[{"first_name":"Nathalie","last_name":"Stroeymeyt","full_name":"Stroeymeyt, Nathalie"},{"full_name":"Grasse, Anna V","last_name":"Grasse","id":"406F989C-F248-11E8-B48F-1D18A9856A87","first_name":"Anna V"},{"first_name":"Alessandro","full_name":"Crespi, Alessandro","last_name":"Crespi"},{"full_name":"Mersch, Danielle","last_name":"Mersch","first_name":"Danielle"},{"full_name":"Cremer, Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","last_name":"Cremer","orcid":"0000-0002-2193-3868","first_name":"Sylvia"},{"last_name":"Keller","full_name":"Keller, Laurent","first_name":"Laurent"}],"date_updated":"2026-06-18T19:15:22Z","oa":1,"department":[{"_id":"SyCr"}],"oa_version":"Published Version","month":"10","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.1480665"}],"type":"research_data_reference","date_published":"2018-10-23T00:00:00Z","ddc":["570"],"citation":{"ama":"Stroeymeyt N, Grasse AV, Crespi A, Mersch D, Cremer S, Keller L. 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Zenodo, 2018, doi:10.5281/ZENODO.1322669.","apa":"Stroeymeyt, N., Grasse, A. V., Crespi, A., Mersch, D., Cremer, S., & Keller, L. (2018). Social network plasticity decreases disease transmission in a eusocial insect. Zenodo. https://doi.org/10.5281/ZENODO.1322669"},"publisher":"Zenodo","_id":"13055"},{"doi":"10.5281/ZENODO.2025846","article_processing_charge":"No","abstract":[{"lang":"eng","text":"This dataset contains a GitHub repository containing all the data, analysis, Nextflow workflows and Jupyter notebooks to replicate the manuscript titled \"Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method\".\r\nIt also contains the Multiple Sequence Alignments (MSAs) generated and well as the main figures and tables from the manuscript.\r\nThe repository is also available at GitHub (https://github.com/cbcrg/dpa-analysis) release `v1.2`.\r\nFor details on how to use the regressive alignment algorithm, see the T-Coffee software suite (https://github.com/cbcrg/tcoffee)."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method","date_created":"2023-05-23T16:08:20Z","related_material":{"record":[{"relation":"used_in_publication","id":"7181","status":"public"}]},"year":"2018","day":"07","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"author":[{"first_name":"Edgar","last_name":"Garriga","full_name":"Garriga, Edgar"},{"full_name":"di Tommaso, Paolo","last_name":"di Tommaso","first_name":"Paolo"},{"first_name":"Cedrik","full_name":"Magis, Cedrik","last_name":"Magis"},{"last_name":"Erb","full_name":"Erb, Ionas","first_name":"Ionas"},{"first_name":"Leila","full_name":"Mansouri, Leila","last_name":"Mansouri"},{"full_name":"Baltzis, Athanasios","last_name":"Baltzis","first_name":"Athanasios"},{"first_name":"Hafid","full_name":"Laayouni, Hafid","last_name":"Laayouni"},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694","last_name":"Kondrashov","full_name":"Kondrashov, Fyodor","first_name":"Fyodor"},{"full_name":"Floden, Evan","last_name":"Floden","first_name":"Evan"},{"first_name":"Cedric","full_name":"Notredame, Cedric","last_name":"Notredame"}],"status":"public","oa":1,"date_updated":"2025-07-10T11:54:19Z","department":[{"_id":"FyKo"}],"oa_version":"Published Version","month":"12","type":"research_data_reference","ddc":["570"],"date_published":"2018-12-07T00:00:00Z","main_file_link":[{"url":"https://doi.org/10.5281/zenodo.3271452","open_access":"1"}],"publisher":"Zenodo","citation":{"ama":"Garriga E, di Tommaso P, Magis C, et al. Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method. 2018. doi:10.5281/ZENODO.2025846","ista":"Garriga E, di Tommaso P, Magis C, Erb I, Mansouri L, Baltzis A, Laayouni H, Kondrashov F, Floden E, Notredame C. 2018. Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method, Zenodo, 10.5281/ZENODO.2025846.","chicago":"Garriga, Edgar, Paolo di Tommaso, Cedrik Magis, Ionas Erb, Leila Mansouri, Athanasios Baltzis, Hafid Laayouni, Fyodor Kondrashov, Evan Floden, and Cedric Notredame. “Fast and Accurate Large Multiple Sequence Alignments with a Root-to-Leaf Regressive Method.” Zenodo, 2018. https://doi.org/10.5281/ZENODO.2025846.","short":"E. Garriga, P. di Tommaso, C. Magis, I. Erb, L. Mansouri, A. Baltzis, H. Laayouni, F. Kondrashov, E. Floden, C. Notredame, (2018).","ieee":"E. Garriga et al., “Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method.” Zenodo, 2018.","mla":"Garriga, Edgar, et al. Fast and Accurate Large Multiple Sequence Alignments with a Root-to-Leaf Regressive Method. Zenodo, 2018, doi:10.5281/ZENODO.2025846.","apa":"Garriga, E., di Tommaso, P., Magis, C., Erb, I., Mansouri, L., Baltzis, A., … Notredame, C. (2018). Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method. Zenodo. https://doi.org/10.5281/ZENODO.2025846"},"_id":"13059"},{"issue":"3","month":"08","type":"journal_article","_id":"132","date_updated":"2023-09-11T12:52:41Z","volume":46,"acknowledgement":"E.H. is funded by a Junior Research Fellowship from Trinity College, Cam-bridge, a Sir Henry Wellcome Fellowship from the Wellcome Trust, and theBettencourt-Schueller Young Researcher Prize for support.","quality_controlled":"1","external_id":{"isi":["000441327300012"]},"title":"Defining lineage potential and fate behavior of precursors during pancreas development","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","scopus_import":"1","day":"06","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2018","status":"public","file_date_updated":"2020-07-14T12:44:43Z","page":"360 - 375","abstract":[{"lang":"eng","text":"Pancreas development involves a coordinated process in which an early phase of cell segregation is followed by a longer phase of lineage restriction, expansion, and tissue remodeling. By combining clonal tracing and whole-mount reconstruction with proliferation kinetics and single-cell transcriptional profiling, we define the functional basis of pancreas morphogenesis. We show that the large-scale organization of mouse pancreas can be traced to the activity of self-renewing precursors positioned at the termini of growing ducts, which act collectively to drive serial rounds of stochastic ductal bifurcation balanced by termination. During this phase of branching morphogenesis, multipotent precursors become progressively fate-restricted, giving rise to self-renewing acinar-committed precursors that are conveyed with growing ducts, as well as ductal progenitors that expand the trailing ducts and give rise to delaminating endocrine cells. These findings define quantitatively how the functional behavior and lineage progression of precursor pools determine the large-scale patterning of pancreatic sub-compartments."}],"ddc":["570"],"date_published":"2018-08-06T00:00:00Z","citation":{"ista":"Sznurkowska M, Hannezo EB, Azzarelli R, Rulands S, Nestorowa S, Hindley C, Nichols J, Göttgens B, Huch M, Philpott A, Simons B. 2018. Defining lineage potential and fate behavior of precursors during pancreas development. Developmental Cell. 46(3), 360–375.","chicago":"Sznurkowska, Magdalena, Edouard B Hannezo, Roberta Azzarelli, Steffen Rulands, Sonia Nestorowa, Christopher Hindley, Jennifer Nichols, et al. “Defining Lineage Potential and Fate Behavior of Precursors during Pancreas Development.” Developmental Cell. Cell Press, 2018. https://doi.org/10.1016/j.devcel.2018.06.028.","short":"M. Sznurkowska, E.B. Hannezo, R. Azzarelli, S. Rulands, S. Nestorowa, C. Hindley, J. Nichols, B. Göttgens, M. Huch, A. Philpott, B. Simons, Developmental Cell 46 (2018) 360–375.","ama":"Sznurkowska M, Hannezo EB, Azzarelli R, et al. Defining lineage potential and fate behavior of precursors during pancreas development. Developmental Cell. 2018;46(3):360-375. doi:10.1016/j.devcel.2018.06.028","mla":"Sznurkowska, Magdalena, et al. “Defining Lineage Potential and Fate Behavior of Precursors during Pancreas Development.” Developmental Cell, vol. 46, no. 3, Cell Press, 2018, pp. 360–75, doi:10.1016/j.devcel.2018.06.028.","apa":"Sznurkowska, M., Hannezo, E. B., Azzarelli, R., Rulands, S., Nestorowa, S., Hindley, C., … Simons, B. (2018). Defining lineage potential and fate behavior of precursors during pancreas development. Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2018.06.028","ieee":"M. Sznurkowska et al., “Defining lineage potential and fate behavior of precursors during pancreas development,” Developmental Cell, vol. 46, no. 3. Cell Press, pp. 360–375, 2018."},"publisher":"Cell Press","oa":1,"file":[{"file_size":8948384,"date_updated":"2020-07-14T12:44:43Z","access_level":"open_access","file_name":"2018_DevelopmentalCell_Sznurkowska.pdf","file_id":"5694","date_created":"2018-12-17T10:49:49Z","creator":"dernst","checksum":"78d2062b9e3c3b90fe71545aeb6d2f65","relation":"main_file","content_type":"application/pdf"}],"oa_version":"Published Version","department":[{"_id":"EdHa"}],"date_created":"2018-12-11T11:44:48Z","language":[{"iso":"eng"}],"author":[{"full_name":"Sznurkowska, Magdalena","last_name":"Sznurkowska","first_name":"Magdalena"},{"full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","orcid":"0000-0001-6005-1561","first_name":"Edouard B"},{"last_name":"Azzarelli","full_name":"Azzarelli, Roberta","first_name":"Roberta"},{"last_name":"Rulands","full_name":"Rulands, Steffen","first_name":"Steffen"},{"first_name":"Sonia","full_name":"Nestorowa, Sonia","last_name":"Nestorowa"},{"first_name":"Christopher","last_name":"Hindley","full_name":"Hindley, Christopher"},{"full_name":"Nichols, Jennifer","last_name":"Nichols","first_name":"Jennifer"},{"first_name":"Berthold","full_name":"Göttgens, Berthold","last_name":"Göttgens"},{"full_name":"Huch, Meritxell","last_name":"Huch","first_name":"Meritxell"},{"last_name":"Philpott","full_name":"Philpott, Anna","first_name":"Anna"},{"first_name":"Benjamin","last_name":"Simons","full_name":"Simons, Benjamin"}],"publist_id":"7791","has_accepted_license":"1","publication":"Developmental Cell","doi":"10.1016/j.devcel.2018.06.028","article_processing_charge":"No","isi":1,"intvolume":" 46","publication_status":"published","article_type":"original"},{"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","citation":{"mla":"Kragl, Bernhard, et al. Synchronizing the Asynchronous. Vol. 118, 21, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, doi:10.4230/LIPIcs.CONCUR.2018.21.","apa":"Kragl, B., Qadeer, S., & Henzinger, T. A. (2018). Synchronizing the asynchronous (Vol. 118). Presented at the CONCUR: International Conference on Concurrency Theory, Beijing, China: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.CONCUR.2018.21","ieee":"B. Kragl, S. Qadeer, and T. A. Henzinger, “Synchronizing the asynchronous,” presented at the CONCUR: International Conference on Concurrency Theory, Beijing, China, 2018, vol. 118.","short":"B. Kragl, S. Qadeer, T.A. Henzinger, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018.","ista":"Kragl B, Qadeer S, Henzinger TA. 2018. Synchronizing the asynchronous. CONCUR: International Conference on Concurrency Theory, LIPIcs, vol. 118, 21.","chicago":"Kragl, Bernhard, Shaz Qadeer, and Thomas A Henzinger. “Synchronizing the Asynchronous,” Vol. 118. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPIcs.CONCUR.2018.21.","ama":"Kragl B, Qadeer S, Henzinger TA. Synchronizing the asynchronous. In: Vol 118. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018. doi:10.4230/LIPIcs.CONCUR.2018.21"},"date_published":"2018-08-13T00:00:00Z","ddc":["000"],"OA_type":"gold","publication_identifier":{"issn":["1868-8969"]},"file":[{"relation":"main_file","content_type":"application/pdf","file_id":"5368","date_created":"2018-12-12T10:18:46Z","checksum":"c90895f4c5fafc18ddc54d1c8848077e","creator":"system","file_name":"IST-2018-853-v2+2_concur2018.pdf","access_level":"open_access","file_size":745438,"date_updated":"2020-07-14T12:44:44Z"}],"oa_version":"Published Version","department":[{"_id":"ToHe"}],"conference":{"location":"Beijing, China","end_date":"2018-09-07","start_date":"2018-09-04","name":"CONCUR: International Conference on Concurrency Theory"},"oa":1,"publist_id":"7790","language":[{"iso":"eng"}],"author":[{"full_name":"Kragl, Bernhard","last_name":"Kragl","orcid":"0000-0001-7745-9117","id":"320FC952-F248-11E8-B48F-1D18A9856A87","first_name":"Bernhard"},{"first_name":"Shaz","full_name":"Qadeer, Shaz","last_name":"Qadeer"},{"first_name":"Thomas A","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"id":"6426","relation":"earlier_version","status":"public"},{"status":"public","id":"8332","relation":"dissertation_contains"}]},"date_created":"2018-12-11T11:44:48Z","publication_status":"published","intvolume":" 118","doi":"10.4230/LIPIcs.CONCUR.2018.21","article_processing_charge":"No","has_accepted_license":"1","_id":"133","article_number":"21","type":"conference","month":"08","alternative_title":["LIPIcs"],"extern":"1","quality_controlled":"1","OA_place":"publisher","date_updated":"2026-04-08T07:23:52Z","volume":118,"status":"public","year":"2018","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"13","scopus_import":"1","title":"Synchronizing the asynchronous","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pubrep_id":"1039","abstract":[{"lang":"eng","text":"Synchronous programs are easy to specify because the side effects of an operation are finished by the time the invocation of the operation returns to the caller. Asynchronous programs, on the other hand, are difficult to specify because there are side effects due to pending computation scheduled as a result of the invocation of an operation. They are also difficult to verify because of the large number of possible interleavings of concurrent computation threads. We present synchronization, a new proof rule that simplifies the verification of asynchronous programs by introducing the fiction, for proof purposes, that asynchronous operations complete synchronously. Synchronization summarizes an asynchronous computation as immediate atomic effect. Modular verification is enabled via pending asynchronous calls in atomic summaries, and a complementary proof rule that eliminates pending asynchronous calls when components and their specifications are composed. We evaluate synchronization in the context of a multi-layer refinement verification methodology on a collection of benchmark programs."}],"project":[{"name":"Rigorous Systems Engineering","grant_number":"S11402-N23","call_identifier":"FWF","_id":"25F2ACDE-B435-11E9-9278-68D0E5697425"},{"name":"Moderne Concurrency Paradigms","grant_number":"S11402-N23","call_identifier":"FWF","_id":"25F5A88A-B435-11E9-9278-68D0E5697425"}],"file_date_updated":"2020-07-14T12:44:44Z"},{"related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/new-water-simulation-captures-small-details-even-in-large-scenes/","description":"News on IST Homepage"}]},"publist_id":"7789","language":[{"iso":"eng"}],"author":[{"id":"44D6411A-F248-11E8-B48F-1D18A9856A87","last_name":"Jeschke","full_name":"Jeschke, Stefan","first_name":"Stefan"},{"full_name":"Skrivan, Tomas","id":"486A5A46-F248-11E8-B48F-1D18A9856A87","last_name":"Skrivan","first_name":"Tomas"},{"last_name":"Mueller Fischer","full_name":"Mueller Fischer, Matthias","first_name":"Matthias"},{"last_name":"Chentanez","full_name":"Chentanez, Nuttapong","first_name":"Nuttapong"},{"first_name":"Miles","full_name":"Macklin, Miles","last_name":"Macklin"},{"id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6646-5546","last_name":"Wojtan","full_name":"Wojtan, Christopher J","first_name":"Christopher J"}],"date_created":"2018-12-11T11:44:48Z","intvolume":" 37","isi":1,"publication_status":"published","article_processing_charge":"No","doi":"10.1145/3197517.3201336","acknowledged_ssus":[{"_id":"ScienComp"}],"publication":"ACM Transactions on Graphics","ec_funded":1,"has_accepted_license":"1","publisher":"ACM","citation":{"mla":"Jeschke, Stefan, et al. “Water Surface Wavelets.” ACM Transactions on Graphics, vol. 37, no. 4, 94, ACM, 2018, doi:10.1145/3197517.3201336.","apa":"Jeschke, S., Skrivan, T., Mueller Fischer, M., Chentanez, N., Macklin, M., & Wojtan, C. (2018). Water surface wavelets. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/3197517.3201336","ieee":"S. Jeschke, T. Skrivan, M. Mueller Fischer, N. Chentanez, M. Macklin, and C. Wojtan, “Water surface wavelets,” ACM Transactions on Graphics, vol. 37, no. 4. ACM, 2018.","ista":"Jeschke S, Skrivan T, Mueller Fischer M, Chentanez N, Macklin M, Wojtan C. 2018. Water surface wavelets. ACM Transactions on Graphics. 37(4), 94.","short":"S. Jeschke, T. Skrivan, M. Mueller Fischer, N. Chentanez, M. Macklin, C. Wojtan, ACM Transactions on Graphics 37 (2018).","chicago":"Jeschke, Stefan, Tomas Skrivan, Matthias Mueller Fischer, Nuttapong Chentanez, Miles Macklin, and Chris Wojtan. “Water Surface Wavelets.” ACM Transactions on Graphics. ACM, 2018. https://doi.org/10.1145/3197517.3201336.","ama":"Jeschke S, Skrivan T, Mueller Fischer M, Chentanez N, Macklin M, Wojtan C. Water surface wavelets. ACM Transactions on Graphics. 2018;37(4). doi:10.1145/3197517.3201336"},"date_published":"2018-07-30T00:00:00Z","ddc":["000"],"oa_version":"Published Version","file":[{"file_size":22185016,"date_updated":"2020-07-14T12:44:45Z","access_level":"open_access","file_name":"2018_ACM_Jeschke.pdf","file_id":"5744","date_created":"2018-12-18T09:59:23Z","creator":"dernst","checksum":"db75ebabe2ec432bf41389e614d6ef62","relation":"main_file","content_type":"application/pdf"}],"department":[{"_id":"ChWo"}],"oa":1,"year":"2018","day":"30","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png"},"status":"public","title":"Water surface wavelets","external_id":{"isi":["000448185000055"]},"user_id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","file_date_updated":"2020-07-14T12:44:45Z","abstract":[{"lang":"eng","text":"The current state of the art in real-time two-dimensional water wave simulation requires developers to choose between efficient Fourier-based methods, which lack interactions with moving obstacles, and finite-difference or finite element methods, which handle environmental interactions but are significantly more expensive. This paper attempts to bridge this long-standing gap between complexity and performance, by proposing a new wave simulation method that can faithfully simulate wave interactions with moving obstacles in real time while simultaneously preserving minute details and accommodating very large simulation domains.\r\n\r\nPrevious methods for simulating 2D water waves directly compute the change in height of the water surface, a strategy which imposes limitations based on the CFL condition (fast moving waves require small time steps) and Nyquist's limit (small wave details require closely-spaced simulation variables). This paper proposes a novel wavelet transformation that discretizes the liquid motion in terms of amplitude-like functions that vary over space, frequency, and direction, effectively generalizing Fourier-based methods to handle local interactions. Because these new variables change much more slowly over space than the original water height function, our change of variables drastically reduces the limitations of the CFL condition and Nyquist limit, allowing us to simulate highly detailed water waves at very large visual resolutions. Our discretization is amenable to fast summation and easy to parallelize. We also present basic extensions like pre-computed wave paths and two-way solid fluid coupling. Finally, we argue that our discretization provides a convenient set of variables for artistic manipulation, which we illustrate with a novel wave-painting interface."}],"project":[{"name":"Big Splash: Efficient Simulation of Natural Phenomena at Extremely Large Scales","grant_number":"638176","call_identifier":"H2020","_id":"2533E772-B435-11E9-9278-68D0E5697425"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385"}],"article_number":"94","_id":"134","month":"07","alternative_title":["SIGGRAPH"],"issue":"4","type":"journal_article","quality_controlled":"1","date_updated":"2024-10-22T09:58:20Z","volume":37},{"project":[{"_id":"2533E772-B435-11E9-9278-68D0E5697425","grant_number":"638176","name":"Big Splash: Efficient Simulation of Natural Phenomena at Extremely Large Scales","call_identifier":"H2020"}],"abstract":[{"lang":"eng","text":"The Fluid Implicit Particle method (FLIP) reduces numerical dissipation by combining particles with grids. To improve performance, the subsequent narrow band FLIP method (NB‐FLIP) uses a FLIP‐based fluid simulation only near the liquid surface and a traditional grid‐based fluid simulation away from the surface. This spatially‐limited FLIP simulation significantly reduces the number of particles and alleviates a computational bottleneck. In this paper, we extend the NB‐FLIP idea even further, by allowing a simulation to transition between a FLIP‐like fluid simulation and a grid‐based simulation in arbitrary locations, not just near the surface. This approach leads to even more savings in memory and computation, because we can concentrate the particles only in areas where they are needed. More importantly, this new method allows us to seamlessly transition to smooth implicit surface geometry wherever the particle‐based simulation is unnecessary. Consequently, our method leads to a practical algorithm for avoiding the noisy surface artifacts associated with particle‐based liquid simulations, while simultaneously maintaining the benefits of a FLIP simulation in regions of dynamic motion."}],"file_date_updated":"2020-10-08T08:38:23Z","page":"169 - 177","scopus_import":"1","external_id":{"isi":["000434085600016"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Extended narrow band FLIP for liquid simulations","status":"public","day":"22","year":"2018","date_updated":"2024-10-22T09:58:20Z","volume":37,"quality_controlled":"1","type":"journal_article","alternative_title":["Eurographics"],"issue":"2","month":"05","_id":"135","ec_funded":1,"publication":"Computer Graphics Forum","has_accepted_license":"1","doi":"10.1111/cgf.13351","article_processing_charge":"No","publication_status":"published","article_type":"original","isi":1,"intvolume":" 37","date_created":"2018-12-11T11:44:49Z","author":[{"last_name":"Sato","full_name":"Sato, Takahiro","first_name":"Takahiro"},{"id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","last_name":"Wojtan","orcid":"0000-0001-6646-5546","full_name":"Wojtan, Christopher J","first_name":"Christopher J"},{"full_name":"Thuerey, Nils","last_name":"Thuerey","first_name":"Nils"},{"first_name":"Takeo","full_name":"Igarashi, Takeo","last_name":"Igarashi"},{"first_name":"Ryoichi","last_name":"Ando","full_name":"Ando, Ryoichi"}],"language":[{"iso":"eng"}],"oa":1,"publication_identifier":{"issn":["0167-7055"]},"oa_version":"Submitted Version","file":[{"file_name":"exnbflip.pdf","content_type":"application/pdf","relation":"main_file","checksum":"8edb90da8a72395eb5d970580e0925b6","success":1,"date_created":"2020-10-08T08:38:23Z","creator":"wojtan","file_id":"8627","access_level":"open_access","date_updated":"2020-10-08T08:38:23Z","file_size":54309947}],"department":[{"_id":"ChWo"}],"ddc":["006"],"date_published":"2018-05-22T00:00:00Z","citation":{"apa":"Sato, T., Wojtan, C., Thuerey, N., Igarashi, T., & Ando, R. (2018). Extended narrow band FLIP for liquid simulations. Computer Graphics Forum. Wiley. https://doi.org/10.1111/cgf.13351","mla":"Sato, Takahiro, et al. “Extended Narrow Band FLIP for Liquid Simulations.” Computer Graphics Forum, vol. 37, no. 2, Wiley, 2018, pp. 169–77, doi:10.1111/cgf.13351.","ieee":"T. Sato, C. Wojtan, N. Thuerey, T. Igarashi, and R. Ando, “Extended narrow band FLIP for liquid simulations,” Computer Graphics Forum, vol. 37, no. 2. Wiley, pp. 169–177, 2018.","ista":"Sato T, Wojtan C, Thuerey N, Igarashi T, Ando R. 2018. Extended narrow band FLIP for liquid simulations. Computer Graphics Forum. 37(2), 169–177.","short":"T. Sato, C. Wojtan, N. Thuerey, T. Igarashi, R. Ando, Computer Graphics Forum 37 (2018) 169–177.","chicago":"Sato, Takahiro, Chris Wojtan, Nils Thuerey, Takeo Igarashi, and Ryoichi Ando. “Extended Narrow Band FLIP for Liquid Simulations.” Computer Graphics Forum. Wiley, 2018. https://doi.org/10.1111/cgf.13351.","ama":"Sato T, Wojtan C, Thuerey N, Igarashi T, Ando R. Extended narrow band FLIP for liquid simulations. Computer Graphics Forum. 2018;37(2):169-177. doi:10.1111/cgf.13351"},"publisher":"Wiley"},{"oa":1,"oa_version":"Submitted Version","department":[{"_id":"BjHo"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1808.02088"}],"date_published":"2018-08-13T00:00:00Z","publisher":"American Physical Society","citation":{"ista":"Suri B, Tithof J, Grigoriev R, Schatz M. 2018. Unstable equilibria and invariant manifolds in quasi-two-dimensional Kolmogorov-like flow. Physical Review E. 98(2).","short":"B. Suri, J. Tithof, R. Grigoriev, M. Schatz, Physical Review E 98 (2018).","chicago":"Suri, Balachandra, Jeffrey Tithof, Roman Grigoriev, and Michael Schatz. “Unstable Equilibria and Invariant Manifolds in Quasi-Two-Dimensional Kolmogorov-like Flow.” Physical Review E. American Physical Society, 2018. https://doi.org/10.1103/PhysRevE.98.023105.","ama":"Suri B, Tithof J, Grigoriev R, Schatz M. Unstable equilibria and invariant manifolds in quasi-two-dimensional Kolmogorov-like flow. Physical Review E. 2018;98(2). doi:10.1103/PhysRevE.98.023105","mla":"Suri, Balachandra, et al. “Unstable Equilibria and Invariant Manifolds in Quasi-Two-Dimensional Kolmogorov-like Flow.” Physical Review E, vol. 98, no. 2, American Physical Society, 2018, doi:10.1103/PhysRevE.98.023105.","apa":"Suri, B., Tithof, J., Grigoriev, R., & Schatz, M. (2018). Unstable equilibria and invariant manifolds in quasi-two-dimensional Kolmogorov-like flow. Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.98.023105","ieee":"B. Suri, J. Tithof, R. Grigoriev, and M. Schatz, “Unstable equilibria and invariant manifolds in quasi-two-dimensional Kolmogorov-like flow,” Physical Review E, vol. 98, no. 2. American Physical Society, 2018."},"article_processing_charge":"No","doi":"10.1103/PhysRevE.98.023105","publication":"Physical Review E","isi":1,"intvolume":" 98","publication_status":"published","date_created":"2018-12-11T11:44:49Z","author":[{"first_name":"Balachandra","full_name":"Suri, Balachandra","id":"47A5E706-F248-11E8-B48F-1D18A9856A87","last_name":"Suri"},{"last_name":"Tithof","full_name":"Tithof, Jeffrey","first_name":"Jeffrey"},{"last_name":"Grigoriev","full_name":"Grigoriev, Roman","first_name":"Roman"},{"full_name":"Schatz, Michael","last_name":"Schatz","first_name":"Michael"}],"language":[{"iso":"eng"}],"volume":98,"date_updated":"2023-10-10T13:29:10Z","quality_controlled":"1","month":"08","issue":"2","type":"journal_article","_id":"136","abstract":[{"text":"Recent studies suggest that unstable, nonchaotic solutions of the Navier-Stokes equation may provide deep insights into fluid turbulence. In this article, we present a combined experimental and numerical study exploring the dynamical role of unstable equilibrium solutions and their invariant manifolds in a weakly turbulent, electromagnetically driven, shallow fluid layer. Identifying instants when turbulent evolution slows down, we compute 31 unstable equilibria of a realistic two-dimensional model of the flow. We establish the dynamical relevance of these unstable equilibria by showing that they are closely visited by the turbulent flow. We also establish the dynamical relevance of unstable manifolds by verifying that they are shadowed by turbulent trajectories departing from the neighborhoods of unstable equilibria over large distances in state space.","lang":"eng"}],"arxiv":1,"title":"Unstable equilibria and invariant manifolds in quasi-two-dimensional Kolmogorov-like flow","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"isi":["000441466800010"],"arxiv":["1808.02088"]},"scopus_import":"1","year":"2018","day":"13","status":"public"},{"pmid":1,"author":[{"last_name":"Zhang","full_name":"Zhang, William","first_name":"William"},{"first_name":"Michel","last_name":"Herde","full_name":"Herde, Michel"},{"last_name":"Mitchell","full_name":"Mitchell, Joshua","first_name":"Joshua"},{"first_name":"Jason","last_name":"Whitfield","full_name":"Whitfield, Jason"},{"first_name":"Andreas","last_name":"Wulff","full_name":"Wulff, Andreas"},{"first_name":"Vanessa","full_name":"Vongsouthi, Vanessa","last_name":"Vongsouthi"},{"full_name":"Sanchez Romero, Inmaculada","last_name":"Sanchez Romero","id":"3D9C5D30-F248-11E8-B48F-1D18A9856A87","first_name":"Inmaculada"},{"full_name":"Gulakova, Polina","last_name":"Gulakova","first_name":"Polina"},{"last_name":"Minge","full_name":"Minge, Daniel","first_name":"Daniel"},{"full_name":"Breithausen, Björn","last_name":"Breithausen","first_name":"Björn"},{"full_name":"Schoch, Susanne","last_name":"Schoch","first_name":"Susanne"},{"first_name":"Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8023-9315","last_name":"Janovjak","full_name":"Janovjak, Harald L"},{"first_name":"Colin","full_name":"Jackson, Colin","last_name":"Jackson"},{"first_name":"Christian","last_name":"Henneberger","full_name":"Henneberger, Christian"}],"language":[{"iso":"eng"}],"publist_id":"7786","date_created":"2018-12-11T11:44:49Z","intvolume":" 14","isi":1,"publication_status":"published","article_type":"original","publication":"Nature Chemical Biology","doi":"10.1038/s41589-018-0108-2","article_processing_charge":"No","citation":{"apa":"Zhang, W., Herde, M., Mitchell, J., Whitfield, J., Wulff, A., Vongsouthi, V., … Henneberger, C. (2018). Monitoring hippocampal glycine with the computationally designed optical sensor GlyFS. Nature Chemical Biology. Nature Publishing Group. https://doi.org/10.1038/s41589-018-0108-2","mla":"Zhang, William, et al. “Monitoring Hippocampal Glycine with the Computationally Designed Optical Sensor GlyFS.” Nature Chemical Biology, vol. 14, no. 9, Nature Publishing Group, 2018, pp. 861–69, doi:10.1038/s41589-018-0108-2.","ieee":"W. Zhang et al., “Monitoring hippocampal glycine with the computationally designed optical sensor GlyFS,” Nature Chemical Biology, vol. 14, no. 9. Nature Publishing Group, pp. 861–869, 2018.","ista":"Zhang W, Herde M, Mitchell J, Whitfield J, Wulff A, Vongsouthi V, Sanchez-Romero I, Gulakova P, Minge D, Breithausen B, Schoch S, Janovjak HL, Jackson C, Henneberger C. 2018. Monitoring hippocampal glycine with the computationally designed optical sensor GlyFS. Nature Chemical Biology. 14(9), 861–869.","chicago":"Zhang, William, Michel Herde, Joshua Mitchell, Jason Whitfield, Andreas Wulff, Vanessa Vongsouthi, Inmaculada Sanchez-Romero, et al. “Monitoring Hippocampal Glycine with the Computationally Designed Optical Sensor GlyFS.” Nature Chemical Biology. Nature Publishing Group, 2018. https://doi.org/10.1038/s41589-018-0108-2.","short":"W. Zhang, M. Herde, J. Mitchell, J. Whitfield, A. Wulff, V. Vongsouthi, I. Sanchez-Romero, P. Gulakova, D. Minge, B. Breithausen, S. Schoch, H.L. Janovjak, C. Jackson, C. Henneberger, Nature Chemical Biology 14 (2018) 861–869.","ama":"Zhang W, Herde M, Mitchell J, et al. Monitoring hippocampal glycine with the computationally designed optical sensor GlyFS. Nature Chemical Biology. 2018;14(9):861-869. doi:10.1038/s41589-018-0108-2"},"publisher":"Nature Publishing Group","date_published":"2018-07-30T00:00:00Z","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/30061718","open_access":"1"}],"department":[{"_id":"HaJa"}],"oa_version":"Submitted Version","oa":1,"day":"30","year":"2018","status":"public","external_id":{"isi":["000442174500013"],"pmid":["30061718 "]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Monitoring hippocampal glycine with the computationally designed optical sensor GlyFS","scopus_import":"1","page":"861 - 869","project":[{"name":"In situ real-time imaging of neurotransmitter signaling using designer optical sensors","grant_number":"RGY0084/2012","_id":"255BFFFA-B435-11E9-9278-68D0E5697425"}],"abstract":[{"text":"Fluorescent sensors are an essential part of the experimental toolbox of the life sciences, where they are used ubiquitously to visualize intra- and extracellular signaling. In the brain, optical neurotransmitter sensors can shed light on temporal and spatial aspects of signal transmission by directly observing, for instance, neurotransmitter release and spread. Here we report the development and application of the first optical sensor for the amino acid glycine, which is both an inhibitory neurotransmitter and a co-agonist of the N-methyl-d-aspartate receptors (NMDARs) involved in synaptic plasticity. Computational design of a glycine-specific binding protein allowed us to produce the optical glycine FRET sensor (GlyFS), which can be used with single and two-photon excitation fluorescence microscopy. We took advantage of this newly developed sensor to test predictions about the uneven spatial distribution of glycine in extracellular space and to demonstrate that extracellular glycine levels are controlled by plasticity-inducing stimuli.","lang":"eng"}],"_id":"137","issue":"9","month":"07","type":"journal_article","quality_controlled":"1","volume":14,"date_updated":"2025-04-15T06:43:11Z"},{"oa":1,"oa_version":"Published Version","file":[{"file_id":"5739","checksum":"7d55ae22598a1c70759cd671600cff53","creator":"dernst","date_created":"2018-12-18T09:42:11Z","relation":"main_file","content_type":"application/pdf","file_name":"2018_PeerJ_Fraisse.pdf","file_size":1480792,"date_updated":"2020-07-14T12:44:48Z","access_level":"open_access"}],"department":[{"_id":"BeVi"},{"_id":"NiBa"}],"date_published":"2018-07-30T00:00:00Z","ddc":["576"],"publisher":"PeerJ","citation":{"ieee":"C. Fraisse et al., “The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: The effects of sequencing techniques and sampling strategies,” PeerJ, vol. 2018, no. 7. PeerJ, 2018.","mla":"Fraisse, Christelle, et al. “The Divergence History of European Blue Mussel Species Reconstructed from Approximate Bayesian Computation: The Effects of Sequencing Techniques and Sampling Strategies.” PeerJ, vol. 2018, no. 7, 30083438, PeerJ, 2018, doi:10.7717/peerj.5198.","apa":"Fraisse, C., Roux, C., Gagnaire, P., Romiguier, J., Faivre, N., Welch, J., & Bierne, N. (2018). The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: The effects of sequencing techniques and sampling strategies. PeerJ. PeerJ. https://doi.org/10.7717/peerj.5198","ama":"Fraisse C, Roux C, Gagnaire P, et al. The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: The effects of sequencing techniques and sampling strategies. PeerJ. 2018;2018(7). doi:10.7717/peerj.5198","chicago":"Fraisse, Christelle, Camille Roux, Pierre Gagnaire, Jonathan Romiguier, Nicolas Faivre, John Welch, and Nicolas Bierne. “The Divergence History of European Blue Mussel Species Reconstructed from Approximate Bayesian Computation: The Effects of Sequencing Techniques and Sampling Strategies.” PeerJ. PeerJ, 2018. https://doi.org/10.7717/peerj.5198.","ista":"Fraisse C, Roux C, Gagnaire P, Romiguier J, Faivre N, Welch J, Bierne N. 2018. The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: The effects of sequencing techniques and sampling strategies. PeerJ. 2018(7), 30083438.","short":"C. Fraisse, C. Roux, P. Gagnaire, J. Romiguier, N. Faivre, J. Welch, N. Bierne, PeerJ 2018 (2018)."},"article_processing_charge":"No","doi":"10.7717/peerj.5198","publication":"PeerJ","has_accepted_license":"1","publication_status":"published","isi":1,"intvolume":" 2018","date_created":"2018-12-11T11:44:50Z","publist_id":"7784","author":[{"first_name":"Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","last_name":"Fraisse","orcid":"0000-0001-8441-5075","full_name":"Fraisse, Christelle"},{"full_name":"Roux, Camille","last_name":"Roux","first_name":"Camille"},{"last_name":"Gagnaire","full_name":"Gagnaire, Pierre","first_name":"Pierre"},{"first_name":"Jonathan","full_name":"Romiguier, Jonathan","last_name":"Romiguier"},{"first_name":"Nicolas","full_name":"Faivre, Nicolas","last_name":"Faivre"},{"first_name":"John","full_name":"Welch, John","last_name":"Welch"},{"first_name":"Nicolas","full_name":"Bierne, Nicolas","last_name":"Bierne"}],"language":[{"iso":"eng"}],"volume":2018,"date_updated":"2023-10-17T12:25:28Z","quality_controlled":"1","type":"journal_article","month":"07","issue":"7","_id":"139","article_number":"30083438","abstract":[{"lang":"eng","text":"Genome-scale diversity data are increasingly available in a variety of biological systems, and can be used to reconstruct the past evolutionary history of species divergence. However, extracting the full demographic information from these data is not trivial, and requires inferential methods that account for the diversity of coalescent histories throughout the genome. Here, we evaluate the potential and limitations of one such approach. We reexamine a well-known system of mussel sister species, using the joint site frequency spectrum (jSFS) of synonymousmutations computed either fromexome capture or RNA-seq, in an Approximate Bayesian Computation (ABC) framework. We first assess the best sampling strategy (number of: individuals, loci, and bins in the jSFS), and show that model selection is robust to variation in the number of individuals and loci. In contrast, different binning choices when summarizing the jSFS, strongly affect the results: including classes of low and high frequency shared polymorphisms can more effectively reveal recent migration events. We then take advantage of the flexibility of ABC to compare more realistic models of speciation, including variation in migration rates through time (i.e., periodic connectivity) and across genes (i.e., genome-wide heterogeneity in migration rates). We show that these models were consistently selected as the most probable, suggesting that mussels have experienced a complex history of gene flow during divergence and that the species boundary is semi-permeable. Our work provides a comprehensive evaluation of ABC demographic inference in mussels based on the coding jSFS, and supplies guidelines for employing different sequencing techniques and sampling strategies. We emphasize, perhaps surprisingly, that inferences are less limited by the volume of data, than by the way in which they are analyzed."}],"file_date_updated":"2020-07-14T12:44:48Z","scopus_import":"1","external_id":{"isi":["000440484800002"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: The effects of sequencing techniques and sampling strategies","status":"public","year":"2018","day":"30","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"}},{"acknowledgement":"European Research Council (ERC): 742985 to Jiri Friml; M.A. was supported by the Austrian Science Fund (FWF) (M2379-B28); AJ was supported by the Austria Science Fund (FWF): I03630 to Jiri Friml.","volume":19,"date_updated":"2025-04-14T07:45:00Z","quality_controlled":"1","type":"journal_article","issue":"11","month":"11","_id":"14","project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"},{"_id":"26538374-B435-11E9-9278-68D0E5697425","grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants","call_identifier":"FWF"}],"abstract":[{"lang":"eng","text":"The intercellular transport of auxin is driven by PIN-formed (PIN) auxin efflux carriers. PINs are localized at the plasma membrane (PM) and on constitutively recycling endomembrane vesicles. Therefore, PINs can mediate auxin transport either by direct translocation across the PM or by pumping auxin into secretory vesicles (SVs), leading to its secretory release upon fusion with the PM. Which of these two mechanisms dominates is a matter of debate. Here, we addressed the issue with a mathematical modeling approach. We demonstrate that the efficiency of secretory transport depends on SV size, half-life of PINs on the PM, pH, exocytosis frequency and PIN density. 3D structured illumination microscopy (SIM) was used to determine PIN density on the PM. Combining this data with published values of the other parameters, we show that the transport activity of PINs in SVs would have to be at least 1000× greater than on the PM in order to produce a comparable macroscopic auxin transport. If both transport mechanisms operated simultaneously and PINs were equally active on SVs and PM, the contribution of secretion to the total auxin flux would be negligible. In conclusion, while secretory vesicle-mediated transport of auxin is an intriguing and theoretically possible model, it is unlikely to be a major mechanism of auxin transport inplanta."}],"file_date_updated":"2020-07-14T12:44:50Z","scopus_import":"1","title":"Relative contribution of PIN-containing secretory vesicles and plasma membrane PINs to the directed auxin transport: Theoretical estimation","external_id":{"isi":["000451528500282"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","day":"12","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2018","oa":1,"publication_identifier":{"eissn":["1422-0067"]},"file":[{"creator":"dernst","checksum":"e4b59c2599b0ca26ebf5b8434bcde94a","date_created":"2018-12-17T16:04:11Z","file_id":"5719","content_type":"application/pdf","relation":"main_file","file_name":"2018_IJMS_Hille.pdf","date_updated":"2020-07-14T12:44:50Z","file_size":2200593,"access_level":"open_access"}],"department":[{"_id":"DaSi"},{"_id":"JiFr"}],"oa_version":"Published Version","ddc":["580"],"date_published":"2018-11-12T00:00:00Z","citation":{"chicago":"Hille, Sander, Maria Akhmanova, Matous Glanc, Alexander J Johnson, and Jiří Friml. “Relative Contribution of PIN-Containing Secretory Vesicles and Plasma Membrane PINs to the Directed Auxin Transport: Theoretical Estimation.” International Journal of Molecular Sciences. MDPI, 2018. https://doi.org/10.3390/ijms19113566.","ista":"Hille S, Akhmanova M, Glanc M, Johnson AJ, Friml J. 2018. Relative contribution of PIN-containing secretory vesicles and plasma membrane PINs to the directed auxin transport: Theoretical estimation. International Journal of Molecular Sciences. 19(11).","short":"S. Hille, M. Akhmanova, M. Glanc, A.J. Johnson, J. Friml, International Journal of Molecular Sciences 19 (2018).","ama":"Hille S, Akhmanova M, Glanc M, Johnson AJ, Friml J. Relative contribution of PIN-containing secretory vesicles and plasma membrane PINs to the directed auxin transport: Theoretical estimation. International Journal of Molecular Sciences. 2018;19(11). doi:10.3390/ijms19113566","apa":"Hille, S., Akhmanova, M., Glanc, M., Johnson, A. J., & Friml, J. (2018). Relative contribution of PIN-containing secretory vesicles and plasma membrane PINs to the directed auxin transport: Theoretical estimation. International Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms19113566","mla":"Hille, Sander, et al. “Relative Contribution of PIN-Containing Secretory Vesicles and Plasma Membrane PINs to the Directed Auxin Transport: Theoretical Estimation.” International Journal of Molecular Sciences, vol. 19, no. 11, MDPI, 2018, doi:10.3390/ijms19113566.","ieee":"S. Hille, M. Akhmanova, M. Glanc, A. J. Johnson, and J. Friml, “Relative contribution of PIN-containing secretory vesicles and plasma membrane PINs to the directed auxin transport: Theoretical estimation,” International Journal of Molecular Sciences, vol. 19, no. 11. MDPI, 2018."},"publisher":"MDPI","has_accepted_license":"1","ec_funded":1,"publication":"International Journal of Molecular Sciences","article_processing_charge":"No","doi":"10.3390/ijms19113566","publication_status":"published","article_type":"original","isi":1,"intvolume":" 19","date_created":"2018-12-11T11:44:09Z","language":[{"iso":"eng"}],"author":[{"full_name":"Hille, Sander","last_name":"Hille","first_name":"Sander"},{"full_name":"Akhmanova, Maria","id":"3425EC26-F248-11E8-B48F-1D18A9856A87","last_name":"Akhmanova","orcid":"0000-0003-1522-3162","first_name":"Maria"},{"first_name":"Matous","full_name":"Glanc, Matous","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","last_name":"Glanc","orcid":"0000-0003-0619-7783"},{"first_name":"Alexander J","full_name":"Johnson, Alexander J","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","last_name":"Johnson","orcid":"0000-0002-2739-8843"},{"last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","first_name":"Jirí"}],"publist_id":"8042"},{"status":"public","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"18","year":"2018","scopus_import":"1","pubrep_id":"1010","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","external_id":{"isi":["000491481600025"]},"title":"Space-time interpolants","project":[{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"_id":"25F5A88A-B435-11E9-9278-68D0E5697425","name":"Moderne Concurrency Paradigms","grant_number":"S11402-N23","call_identifier":"FWF"}],"abstract":[{"text":"Reachability analysis is difficult for hybrid automata with affine differential equations, because the reach set needs to be approximated. Promising abstraction techniques usually employ interval methods or template polyhedra. Interval methods account for dense time and guarantee soundness, and there are interval-based tools that overapproximate affine flowpipes. But interval methods impose bounded and rigid shapes, which make refinement expensive and fixpoint detection difficult. Template polyhedra, on the other hand, can be adapted flexibly and can be unbounded, but sound template refinement for unbounded reachability analysis has been implemented only for systems with piecewise constant dynamics. We capitalize on the advantages of both techniques, combining interval arithmetic and template polyhedra, using the former to abstract time and the latter to abstract space. During a CEGAR loop, whenever a spurious error trajectory is found, we compute additional space constraints and split time intervals, and use these space-time interpolants to eliminate the counterexample. Space-time interpolation offers a lazy, flexible framework for increasing precision while guaranteeing soundness, both for error avoidance and fixpoint detection. To the best of out knowledge, this is the first abstraction refinement scheme for the reachability analysis over unbounded and dense time of affine hybrid systems, which is both sound and automatic. We demonstrate the effectiveness of our algorithm with several benchmark examples, which cannot be handled by other tools.","lang":"eng"}],"file_date_updated":"2020-07-14T12:44:50Z","page":"468 - 486","_id":"140","type":"conference","alternative_title":["LNCS"],"month":"07","quality_controlled":"1","volume":10981,"date_updated":"2026-04-16T09:55:04Z","author":[{"last_name":"Frehse","full_name":"Frehse, Goran","first_name":"Goran"},{"id":"3444EA5E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8180-0904","last_name":"Giacobbe","full_name":"Giacobbe, Mirco","first_name":"Mirco"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","last_name":"Henzinger","full_name":"Henzinger, Thomas A"}],"language":[{"iso":"eng"}],"publist_id":"7783","related_material":{"record":[{"status":"public","id":"6894","relation":"dissertation_contains"}]},"date_created":"2018-12-11T11:44:50Z","publication_status":"published","intvolume":" 10981","isi":1,"has_accepted_license":"1","doi":"10.1007/978-3-319-96145-3_25","article_processing_charge":"No","citation":{"ieee":"G. Frehse, M. Giacobbe, and T. A. Henzinger, “Space-time interpolants,” presented at the CAV: Computer Aided Verification, Oxford, United Kingdom, 2018, vol. 10981, pp. 468–486.","apa":"Frehse, G., Giacobbe, M., & Henzinger, T. A. (2018). Space-time interpolants (Vol. 10981, pp. 468–486). Presented at the CAV: Computer Aided Verification, Oxford, United Kingdom: Springer. https://doi.org/10.1007/978-3-319-96145-3_25","mla":"Frehse, Goran, et al. Space-Time Interpolants. Vol. 10981, Springer, 2018, pp. 468–86, doi:10.1007/978-3-319-96145-3_25.","ama":"Frehse G, Giacobbe M, Henzinger TA. Space-time interpolants. In: Vol 10981. Springer; 2018:468-486. doi:10.1007/978-3-319-96145-3_25","ista":"Frehse G, Giacobbe M, Henzinger TA. 2018. Space-time interpolants. CAV: Computer Aided Verification, LNCS, vol. 10981, 468–486.","short":"G. Frehse, M. Giacobbe, T.A. Henzinger, in:, Springer, 2018, pp. 468–486.","chicago":"Frehse, Goran, Mirco Giacobbe, and Thomas A Henzinger. “Space-Time Interpolants,” 10981:468–86. Springer, 2018. https://doi.org/10.1007/978-3-319-96145-3_25."},"publisher":"Springer","ddc":["005"],"date_published":"2018-07-18T00:00:00Z","publication_identifier":{"issn":["0302-9743"]},"conference":{"location":"Oxford, United Kingdom","start_date":"2018-07-14","end_date":"2018-07-17","name":"CAV: Computer Aided Verification"},"department":[{"_id":"ToHe"}],"file":[{"date_updated":"2020-07-14T12:44:50Z","file_size":563710,"access_level":"open_access","file_name":"IST-2018-1010-v1+1_space-time_interpolants.pdf","checksum":"6dca832f575d6b3f0ea9dff56f579142","creator":"system","date_created":"2018-12-12T10:17:53Z","file_id":"5310","content_type":"application/pdf","relation":"main_file"}],"oa_version":"Published Version","oa":1},{"quality_controlled":"1","acknowledgement":"Acknowledgements. K. C. and M. H. are partially supported by the Vienna Science and Technology Fund (WWTF) grant ICT15-003. K. C. is partially supported by the Austrian Science Fund (FWF): S11407-N23 (RiSE/SHiNE), and an ERC Start Grant (279307: Graph Games). V. T. is partially supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Sk lodowska-Curie Grant Agreement No. 665385.","date_updated":"2026-04-08T07:00:31Z","volume":10982,"_id":"141","type":"conference","month":"07","alternative_title":["LNCS"],"abstract":[{"text":"Given a model and a specification, the fundamental model-checking problem asks for algorithmic verification of whether the model satisfies the specification. We consider graphs and Markov decision processes (MDPs), which are fundamental models for reactive systems. One of the very basic specifications that arise in verification of reactive systems is the strong fairness (aka Streett) objective. Given different types of requests and corresponding grants, the objective requires that for each type, if the request event happens infinitely often, then the corresponding grant event must also happen infinitely often. All ω -regular objectives can be expressed as Streett objectives and hence they are canonical in verification. To handle the state-space explosion, symbolic algorithms are required that operate on a succinct implicit representation of the system rather than explicitly accessing the system. While explicit algorithms for graphs and MDPs with Streett objectives have been widely studied, there has been no improvement of the basic symbolic algorithms. The worst-case numbers of symbolic steps required for the basic symbolic algorithms are as follows: quadratic for graphs and cubic for MDPs. In this work we present the first sub-quadratic symbolic algorithm for graphs with Streett objectives, and our algorithm is sub-quadratic even for MDPs. Based on our algorithmic insights we present an implementation of the new symbolic approach and show that it improves the existing approach on several academic benchmark examples.","lang":"eng"}],"project":[{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","call_identifier":"FWF"},{"call_identifier":"H2020","grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"file_date_updated":"2020-07-14T12:44:53Z","page":"178-197","status":"public","year":"2018","day":"18","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"scopus_import":"1","external_id":{"isi":["000491469700013"]},"title":"Symbolic algorithms for graphs and Markov decision processes with fairness objectives","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"file_name":"2018_LNCS_Chatterjee.pdf","relation":"main_file","content_type":"application/pdf","file_id":"5737","creator":"dernst","date_created":"2018-12-18T08:52:38Z","checksum":"1a6ffa4febe8bb8ac28be3adb3eafebc","access_level":"open_access","file_size":675606,"date_updated":"2020-07-14T12:44:53Z"}],"department":[{"_id":"KrCh"}],"conference":{"location":"Oxford, United Kingdom","name":"CAV: Computer Aided Verification","end_date":"2018-07-17","start_date":"2018-07-14"},"oa":1,"publisher":"Springer","citation":{"ama":"Chatterjee K, Henzinger M, Loitzenbauer V, Oraee S, Toman V. Symbolic algorithms for graphs and Markov decision processes with fairness objectives. In: Vol 10982. Springer; 2018:178-197. doi:10.1007/978-3-319-96142-2_13","chicago":"Chatterjee, Krishnendu, Monika Henzinger, Veronika Loitzenbauer, Simin Oraee, and Viktor Toman. “Symbolic Algorithms for Graphs and Markov Decision Processes with Fairness Objectives,” 10982:178–97. Springer, 2018. https://doi.org/10.1007/978-3-319-96142-2_13.","ista":"Chatterjee K, Henzinger M, Loitzenbauer V, Oraee S, Toman V. 2018. Symbolic algorithms for graphs and Markov decision processes with fairness objectives. CAV: Computer Aided Verification, LNCS, vol. 10982, 178–197.","short":"K. Chatterjee, M. Henzinger, V. Loitzenbauer, S. Oraee, V. Toman, in:, Springer, 2018, pp. 178–197.","ieee":"K. Chatterjee, M. Henzinger, V. Loitzenbauer, S. Oraee, and V. Toman, “Symbolic algorithms for graphs and Markov decision processes with fairness objectives,” presented at the CAV: Computer Aided Verification, Oxford, United Kingdom, 2018, vol. 10982, pp. 178–197.","mla":"Chatterjee, Krishnendu, et al. Symbolic Algorithms for Graphs and Markov Decision Processes with Fairness Objectives. Vol. 10982, Springer, 2018, pp. 178–97, doi:10.1007/978-3-319-96142-2_13.","apa":"Chatterjee, K., Henzinger, M., Loitzenbauer, V., Oraee, S., & Toman, V. (2018). Symbolic algorithms for graphs and Markov decision processes with fairness objectives (Vol. 10982, pp. 178–197). Presented at the CAV: Computer Aided Verification, Oxford, United Kingdom: Springer. https://doi.org/10.1007/978-3-319-96142-2_13"},"ddc":["000"],"date_published":"2018-07-18T00:00:00Z","publication_status":"published","intvolume":" 10982","isi":1,"doi":"10.1007/978-3-319-96142-2_13","article_processing_charge":"No","has_accepted_license":"1","ec_funded":1,"publist_id":"7782","author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"},{"full_name":"Henzinger, Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","last_name":"Henzinger","orcid":"0000-0002-5008-6530","first_name":"Monika H"},{"first_name":"Veronika","full_name":"Loitzenbauer, Veronika","last_name":"Loitzenbauer"},{"last_name":"Oraee","full_name":"Oraee, Simin","first_name":"Simin"},{"full_name":"Toman, Viktor","last_name":"Toman","id":"3AF3DA7C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9036-063X","first_name":"Viktor"}],"language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"dissertation_contains","id":"10199","status":"public"}]},"date_created":"2018-12-11T11:44:51Z"},{"day":"06","year":"2018","language":[{"iso":"eng"}],"status":"public","author":[{"full_name":"Fortuin, Vincent","last_name":"Fortuin","first_name":"Vincent"},{"last_name":"Hüser","full_name":"Hüser, Matthias","first_name":"Matthias"},{"orcid":"0000-0002-4850-0683","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","last_name":"Locatello","full_name":"Locatello, Francesco","first_name":"Francesco"},{"full_name":"Strathmann, Heiko","last_name":"Strathmann","first_name":"Heiko"},{"last_name":"Rätsch","full_name":"Rätsch, Gunnar","first_name":"Gunnar"}],"date_created":"2023-08-22T14:12:48Z","arxiv":1,"title":"SOM-VAE: Interpretable discrete representation learning on time series","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["1806.02199"]},"publication_status":"published","publication":"International Conference on Learning Representations","abstract":[{"lang":"eng","text":"High-dimensional time series are common in many domains. Since human\r\ncognition is not optimized to work well in high-dimensional spaces, these areas\r\ncould benefit from interpretable low-dimensional representations. However, most\r\nrepresentation learning algorithms for time series data are difficult to\r\ninterpret. This is due to non-intuitive mappings from data features to salient\r\nproperties of the representation and non-smoothness over time. To address this\r\nproblem, we propose a new representation learning framework building on ideas\r\nfrom interpretable discrete dimensionality reduction and deep generative\r\nmodeling. This framework allows us to learn discrete representations of time\r\nseries, which give rise to smooth and interpretable embeddings with superior\r\nclustering performance. We introduce a new way to overcome the\r\nnon-differentiability in discrete representation learning and present a\r\ngradient-based version of the traditional self-organizing map algorithm that is\r\nmore performant than the original. Furthermore, to allow for a probabilistic\r\ninterpretation of our method, we integrate a Markov model in the representation\r\nspace. This model uncovers the temporal transition structure, improves\r\nclustering performance even further and provides additional explanatory\r\ninsights as well as a natural representation of uncertainty. We evaluate our\r\nmodel in terms of clustering performance and interpretability on static\r\n(Fashion-)MNIST data, a time series of linearly interpolated (Fashion-)MNIST\r\nimages, a chaotic Lorenz attractor system with two macro states, as well as on\r\na challenging real world medical time series application on the eICU data set.\r\nOur learned representations compare favorably with competitor methods and\r\nfacilitate downstream tasks on the real world data."}],"article_processing_charge":"No","citation":{"ama":"Fortuin V, Hüser M, Locatello F, Strathmann H, Rätsch G. SOM-VAE: Interpretable discrete representation learning on time series. In: International Conference on Learning Representations. ; 2018.","short":"V. Fortuin, M. Hüser, F. Locatello, H. Strathmann, G. Rätsch, in:, International Conference on Learning Representations, 2018.","ista":"Fortuin V, Hüser M, Locatello F, Strathmann H, Rätsch G. 2018. SOM-VAE: Interpretable discrete representation learning on time series. International Conference on Learning Representations. ICLR: International Conference on Learning Representations.","chicago":"Fortuin, Vincent, Matthias Hüser, Francesco Locatello, Heiko Strathmann, and Gunnar Rätsch. “SOM-VAE: Interpretable Discrete Representation Learning on Time Series.” In International Conference on Learning Representations, 2018.","ieee":"V. Fortuin, M. Hüser, F. Locatello, H. Strathmann, and G. Rätsch, “SOM-VAE: Interpretable discrete representation learning on time series,” in International Conference on Learning Representations, New Orleans, LA, United States, 2018.","mla":"Fortuin, Vincent, et al. “SOM-VAE: Interpretable Discrete Representation Learning on Time Series.” International Conference on Learning Representations, 2018.","apa":"Fortuin, V., Hüser, M., Locatello, F., Strathmann, H., & Rätsch, G. (2018). SOM-VAE: Interpretable discrete representation learning on time series. In International Conference on Learning Representations. New Orleans, LA, United States."},"_id":"14198","extern":"1","month":"06","type":"conference","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1806.02199"}],"date_published":"2018-06-06T00:00:00Z","conference":{"start_date":"2019-05-06","end_date":"2019-05-09","name":"ICLR: International Conference on Learning Representations","location":"New Orleans, LA, United States"},"oa_version":"Preprint","department":[{"_id":"FrLo"}],"quality_controlled":"1","date_updated":"2023-09-13T06:35:12Z","oa":1},{"_id":"142","type":"conference","month":"07","alternative_title":["LNCS"],"quality_controlled":"1","acknowledgement":"Austrian Science Fund FWF: S11402-N23, S11405-N23, Z211-N32","date_updated":"2025-04-15T06:25:58Z","volume":10981,"status":"public","year":"2018","day":"18","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"scopus_import":"1","title":"Reachable set over-approximation for nonlinear systems using piecewise barrier tubes","external_id":{"isi":["000491481600024"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"text":"We address the problem of analyzing the reachable set of a polynomial nonlinear continuous system by over-approximating the flowpipe of its dynamics. The common approach to tackle this problem is to perform a numerical integration over a given time horizon based on Taylor expansion and interval arithmetic. However, this method results to be very conservative when there is a large difference in speed between trajectories as time progresses. In this paper, we propose to use combinations of barrier functions, which we call piecewise barrier tube (PBT), to over-approximate flowpipe. The basic idea of PBT is that for each segment of a flowpipe, a coarse box which is big enough to contain the segment is constructed using sampled simulation and then in the box we compute by linear programming a set of barrier functions (called barrier tube or BT for short) which work together to form a tube surrounding the flowpipe. The benefit of using PBT is that (1) BT is independent of time and hence can avoid being stretched and deformed by time; and (2) a small number of BTs can form a tight over-approximation for the flowpipe, which means that the computation required to decide whether the BTs intersect the unsafe set can be reduced significantly. We implemented a prototype called PBTS in C++. Experiments on some benchmark systems show that our approach is effective.","lang":"eng"}],"project":[{"call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"grant_number":"Z211","name":"Formal methods for the design and analysis of complex systems","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"file_date_updated":"2020-07-14T12:44:53Z","page":"449 - 467","publisher":"Springer","citation":{"ama":"Kong H, Bartocci E, Henzinger TA. Reachable set over-approximation for nonlinear systems using piecewise barrier tubes. In: Vol 10981. Springer; 2018:449-467. doi:10.1007/978-3-319-96145-3_24","ista":"Kong H, Bartocci E, Henzinger TA. 2018. Reachable set over-approximation for nonlinear systems using piecewise barrier tubes. CAV: Computer Aided Verification, LNCS, vol. 10981, 449–467.","chicago":"Kong, Hui, Ezio Bartocci, and Thomas A Henzinger. “Reachable Set Over-Approximation for Nonlinear Systems Using Piecewise Barrier Tubes,” 10981:449–67. Springer, 2018. https://doi.org/10.1007/978-3-319-96145-3_24.","short":"H. Kong, E. Bartocci, T.A. Henzinger, in:, Springer, 2018, pp. 449–467.","ieee":"H. Kong, E. Bartocci, and T. A. Henzinger, “Reachable set over-approximation for nonlinear systems using piecewise barrier tubes,” presented at the CAV: Computer Aided Verification, Oxford, United Kingdom, 2018, vol. 10981, pp. 449–467.","mla":"Kong, Hui, et al. Reachable Set Over-Approximation for Nonlinear Systems Using Piecewise Barrier Tubes. Vol. 10981, Springer, 2018, pp. 449–67, doi:10.1007/978-3-319-96145-3_24.","apa":"Kong, H., Bartocci, E., & Henzinger, T. A. (2018). Reachable set over-approximation for nonlinear systems using piecewise barrier tubes (Vol. 10981, pp. 449–467). Presented at the CAV: Computer Aided Verification, Oxford, United Kingdom: Springer. https://doi.org/10.1007/978-3-319-96145-3_24"},"ddc":["000"],"date_published":"2018-07-18T00:00:00Z","department":[{"_id":"ToHe"}],"file":[{"file_name":"2018_LNCS_Kong.pdf","checksum":"fd95e8026deacef3dc752a733bb9355f","date_created":"2018-12-17T15:57:06Z","creator":"dernst","file_id":"5718","content_type":"application/pdf","relation":"main_file","date_updated":"2020-07-14T12:44:53Z","file_size":5591566,"access_level":"open_access"}],"oa_version":"Published Version","conference":{"name":"CAV: Computer Aided Verification","start_date":"2018-07-14","end_date":"2018-07-17","location":"Oxford, United Kingdom"},"oa":1,"publist_id":"7781","author":[{"first_name":"Hui","last_name":"Kong","id":"3BDE25AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3066-6941","full_name":"Kong, Hui"},{"first_name":"Ezio","last_name":"Bartocci","full_name":"Bartocci, Ezio"},{"first_name":"Thomas A","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","last_name":"Henzinger"}],"language":[{"iso":"eng"}],"date_created":"2018-12-11T11:44:51Z","publication_status":"published","isi":1,"intvolume":" 10981","doi":"10.1007/978-3-319-96145-3_24","article_processing_charge":"No","has_accepted_license":"1"},{"publication":"Proceedings of the 21st International Conference on Artificial Intelligence and Statistics","article_processing_charge":"No","publication_status":"published","intvolume":" 84","date_created":"2023-08-22T14:15:20Z","language":[{"iso":"eng"}],"author":[{"first_name":"Francesco","full_name":"Locatello, Francesco","last_name":"Locatello","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","orcid":"0000-0002-4850-0683"},{"first_name":"Rajiv","last_name":"Khanna","full_name":"Khanna, Rajiv"},{"first_name":"Joydeep","full_name":"Ghosh, Joydeep","last_name":"Ghosh"},{"first_name":"Gunnar","last_name":"Rätsch","full_name":"Rätsch, Gunnar"}],"oa":1,"conference":{"location":"Playa Blanca, Lanzarote","end_date":"2018-04-11","start_date":"2018-04-09","name":"AISTATS: Conference on Artificial Intelligence and Statistics"},"oa_version":"Preprint","department":[{"_id":"FrLo"}],"main_file_link":[{"url":"https://arxiv.org/abs/1708.01733","open_access":"1"}],"date_published":"2018-04-15T00:00:00Z","citation":{"chicago":"Locatello, Francesco, Rajiv Khanna, Joydeep Ghosh, and Gunnar Rätsch. “Boosting Variational Inference: An Optimization Perspective.” In Proceedings of the 21st International Conference on Artificial Intelligence and Statistics, 84:464–72. ML Research Press, 2018.","short":"F. Locatello, R. Khanna, J. Ghosh, G. Rätsch, in:, Proceedings of the 21st International Conference on Artificial Intelligence and Statistics, ML Research Press, 2018, pp. 464–472.","ista":"Locatello F, Khanna R, Ghosh J, Rätsch G. 2018. Boosting variational inference: An optimization perspective. Proceedings of the 21st International Conference on Artificial Intelligence and Statistics. AISTATS: Conference on Artificial Intelligence and Statistics, PMLR, vol. 84, 464–472.","ama":"Locatello F, Khanna R, Ghosh J, Rätsch G. Boosting variational inference: An optimization perspective. In: Proceedings of the 21st International Conference on Artificial Intelligence and Statistics. Vol 84. ML Research Press; 2018:464-472.","apa":"Locatello, F., Khanna, R., Ghosh, J., & Rätsch, G. (2018). Boosting variational inference: An optimization perspective. In Proceedings of the 21st International Conference on Artificial Intelligence and Statistics (Vol. 84, pp. 464–472). Playa Blanca, Lanzarote: ML Research Press.","mla":"Locatello, Francesco, et al. “Boosting Variational Inference: An Optimization Perspective.” Proceedings of the 21st International Conference on Artificial Intelligence and Statistics, vol. 84, ML Research Press, 2018, pp. 464–72.","ieee":"F. Locatello, R. Khanna, J. Ghosh, and G. Rätsch, “Boosting variational inference: An optimization perspective,” in Proceedings of the 21st International Conference on Artificial Intelligence and Statistics, Playa Blanca, Lanzarote, 2018, vol. 84, pp. 464–472."},"publisher":"ML Research Press","abstract":[{"lang":"eng","text":"Variational inference is a popular technique to approximate a possibly\r\nintractable Bayesian posterior with a more tractable one. Recently, boosting\r\nvariational inference has been proposed as a new paradigm to approximate the\r\nposterior by a mixture of densities by greedily adding components to the\r\nmixture. However, as is the case with many other variational inference\r\nalgorithms, its theoretical properties have not been studied. In the present\r\nwork, we study the convergence properties of this approach from a modern\r\noptimization viewpoint by establishing connections to the classic Frank-Wolfe\r\nalgorithm. Our analyses yields novel theoretical insights regarding the\r\nsufficient conditions for convergence, explicit rates, and algorithmic\r\nsimplifications. Since a lot of focus in previous works for variational\r\ninference has been on tractability, our work is especially important as a much\r\nneeded attempt to bridge the gap between probabilistic models and their\r\ncorresponding theoretical properties."}],"page":"464-472","scopus_import":"1","arxiv":1,"title":"Boosting variational inference: An optimization perspective","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["1708.01733"]},"status":"public","day":"15","year":"2018","date_updated":"2024-10-14T12:29:27Z","volume":84,"quality_controlled":"1","type":"conference","extern":"1","alternative_title":["PMLR"],"month":"04","_id":"14201"}]