[{"_id":"6900","pmid":1,"abstract":[{"lang":"eng","text":"Across diverse biological systems—ranging from neural networks to intracellular signaling and genetic regulatory networks—the information about changes in the environment is frequently encoded in the full temporal dynamics of the network nodes. A pressing data-analysis challenge has thus been to efficiently estimate the amount of information that these dynamics convey from experimental data. Here we develop and evaluate decoding-based estimation methods to lower bound the mutual information about a finite set of inputs, encoded in single-cell high-dimensional time series data. For biological reaction networks governed by the chemical Master equation, we derive model-based information approximations and analytical upper bounds, against which we benchmark our proposed model-free decoding estimators. In contrast to the frequently-used k-nearest-neighbor estimator, decoding-based estimators robustly extract a large fraction of the available information from high-dimensional trajectories with a realistic number of data samples. We apply these estimators to previously published data on Erk and Ca2+ signaling in mammalian cells and to yeast stress-response, and find that substantial amount of information about environmental state can be encoded by non-trivial response statistics even in stationary signals. We argue that these single-cell, decoding-based information estimates, rather than the commonly-used tests for significant differences between selected population response statistics, provide a proper and unbiased measure for the performance of biological signaling networks."}],"project":[{"_id":"254E9036-B435-11E9-9278-68D0E5697425","name":"Biophysics of information processing in gene regulation","grant_number":"P28844-B27","call_identifier":"FWF"}],"publisher":"Public Library of Science","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_created":"2019-09-22T22:00:37Z","page":"e1007290","file_date_updated":"2020-07-14T12:47:44Z","related_material":{"record":[{"status":"public","id":"6473","relation":"part_of_dissertation"}]},"volume":15,"ddc":["570"],"scopus_import":"1","publication":"PLoS computational biology","article_processing_charge":"No","type":"journal_article","language":[{"iso":"eng"}],"author":[{"id":"3DEE19A4-F248-11E8-B48F-1D18A9856A87","last_name":"Cepeda Humerez","full_name":"Cepeda Humerez, Sarah A","first_name":"Sarah A"},{"first_name":"Jakob","full_name":"Ruess, Jakob","last_name":"Ruess","orcid":"0000-0003-1615-3282"},{"orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper","full_name":"Tkačik, Gašper","last_name":"Tkačik"}],"month":"09","quality_controlled":"1","publication_status":"published","citation":{"ama":"Cepeda Humerez SA, Ruess J, Tkačik G. Estimating information in time-varying signals. <i>PLoS computational biology</i>. 2019;15(9):e1007290. doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1007290\">10.1371/journal.pcbi.1007290</a>","apa":"Cepeda Humerez, S. A., Ruess, J., &#38; Tkačik, G. (2019). Estimating information in time-varying signals. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1007290\">https://doi.org/10.1371/journal.pcbi.1007290</a>","chicago":"Cepeda Humerez, Sarah A, Jakob Ruess, and Gašper Tkačik. “Estimating Information in Time-Varying Signals.” <i>PLoS Computational Biology</i>. Public Library of Science, 2019. <a href=\"https://doi.org/10.1371/journal.pcbi.1007290\">https://doi.org/10.1371/journal.pcbi.1007290</a>.","short":"S.A. Cepeda Humerez, J. Ruess, G. Tkačik, PLoS Computational Biology 15 (2019) e1007290.","mla":"Cepeda Humerez, Sarah A., et al. “Estimating Information in Time-Varying Signals.” <i>PLoS Computational Biology</i>, vol. 15, no. 9, Public Library of Science, 2019, p. e1007290, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1007290\">10.1371/journal.pcbi.1007290</a>.","ieee":"S. A. Cepeda Humerez, J. Ruess, and G. Tkačik, “Estimating information in time-varying signals,” <i>PLoS computational biology</i>, vol. 15, no. 9. Public Library of Science, p. e1007290, 2019.","ista":"Cepeda Humerez SA, Ruess J, Tkačik G. 2019. Estimating information in time-varying signals. PLoS computational biology. 15(9), e1007290."},"date_published":"2019-09-03T00:00:00Z","oa_version":"Published Version","file":[{"access_level":"open_access","relation":"main_file","checksum":"81bdce1361c9aa8395d6fa635fb6ab47","file_size":3081855,"file_name":"2019_PLoS_Cepeda-Humerez.pdf","date_updated":"2020-07-14T12:47:44Z","creator":"kschuh","date_created":"2019-10-01T10:53:45Z","file_id":"6925","content_type":"application/pdf"}],"department":[{"_id":"GaTk"}],"year":"2019","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"day":"03","doi":"10.1371/journal.pcbi.1007290","isi":1,"publication_identifier":{"eissn":["15537358"]},"issue":"9","title":"Estimating information in time-varying signals","has_accepted_license":"1","intvolume":"        15","status":"public","date_updated":"2023-09-07T12:55:21Z","external_id":{"pmid":["31479447"],"isi":["000489741800021"]},"license":"https://creativecommons.org/licenses/by/4.0/","oa":1},{"department":[{"_id":"LeSa"}],"oa_version":"Published Version","file":[{"creator":"kschuh","file_id":"6928","content_type":"application/pdf","date_created":"2019-10-02T11:13:54Z","file_name":"2019_AAAS_Qi.pdf","relation":"main_file","access_level":"open_access","checksum":"b2256c9117655bc15f621ba0babf219f","file_size":1236101,"date_updated":"2020-07-14T12:47:44Z"}],"date_published":"2019-09-18T00:00:00Z","citation":{"apa":"Qi, C., Minin, G. D., Vercellino, I., Wutz, A., &#38; Korkhov, V. M. (2019). Structural basis of sterol recognition by human hedgehog receptor PTCH1. <i>Science Advances</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/sciadv.aaw6490\">https://doi.org/10.1126/sciadv.aaw6490</a>","ama":"Qi C, Minin GD, Vercellino I, Wutz A, Korkhov VM. Structural basis of sterol recognition by human hedgehog receptor PTCH1. <i>Science Advances</i>. 2019;5(9). doi:<a href=\"https://doi.org/10.1126/sciadv.aaw6490\">10.1126/sciadv.aaw6490</a>","chicago":"Qi, Chao, Giulio Di Minin, Irene Vercellino, Anton Wutz, and Volodymyr M. Korkhov. “Structural Basis of Sterol Recognition by Human Hedgehog Receptor PTCH1.” <i>Science Advances</i>. American Association for the Advancement of Science, 2019. <a href=\"https://doi.org/10.1126/sciadv.aaw6490\">https://doi.org/10.1126/sciadv.aaw6490</a>.","ieee":"C. Qi, G. D. Minin, I. Vercellino, A. Wutz, and V. M. Korkhov, “Structural basis of sterol recognition by human hedgehog receptor PTCH1,” <i>Science Advances</i>, vol. 5, no. 9. American Association for the Advancement of Science, 2019.","short":"C. Qi, G.D. Minin, I. Vercellino, A. Wutz, V.M. Korkhov, Science Advances 5 (2019).","mla":"Qi, Chao, et al. “Structural Basis of Sterol Recognition by Human Hedgehog Receptor PTCH1.” <i>Science Advances</i>, vol. 5, no. 9, eaaw6490, American Association for the Advancement of Science, 2019, doi:<a href=\"https://doi.org/10.1126/sciadv.aaw6490\">10.1126/sciadv.aaw6490</a>.","ista":"Qi C, Minin GD, Vercellino I, Wutz A, Korkhov VM. 2019. Structural basis of sterol recognition by human hedgehog receptor PTCH1. Science Advances. 5(9), eaaw6490."},"publication_status":"published","quality_controlled":"1","oa":1,"license":"https://creativecommons.org/licenses/by-nc/4.0/","external_id":{"isi":["000491128800062"]},"date_updated":"2023-08-30T06:55:31Z","status":"public","intvolume":"         5","title":"Structural basis of sterol recognition by human hedgehog receptor PTCH1","publication_identifier":{"eissn":["23752548"]},"has_accepted_license":"1","issue":"9","isi":1,"tmp":{"short":"CC BY-NC (4.0)","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png"},"article_number":"eaaw6490","doi":"10.1126/sciadv.aaw6490","day":"18","year":"2019","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"American Association for the Advancement of Science","_id":"6919","month":"09","author":[{"full_name":"Qi, Chao","first_name":"Chao","last_name":"Qi"},{"last_name":"Minin","full_name":"Minin, Giulio Di","first_name":"Giulio Di"},{"id":"3ED6AF16-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5618-3449","full_name":"Vercellino, Irene","first_name":"Irene","last_name":"Vercellino"},{"last_name":"Wutz","first_name":"Anton","full_name":"Wutz, Anton"},{"last_name":"Korkhov","full_name":"Korkhov, Volodymyr M.","first_name":"Volodymyr M."}],"language":[{"iso":"eng"}],"type":"journal_article","article_processing_charge":"No","publication":"Science Advances","scopus_import":"1","volume":5,"ddc":["570"],"file_date_updated":"2020-07-14T12:47:44Z","date_created":"2019-09-29T22:00:45Z"},{"date_updated":"2023-08-30T06:55:02Z","intvolume":"        12","status":"public","external_id":{"isi":["000489132500002"],"pmid":["31541740"]},"year":"2019","publication_identifier":{"issn":["1674-2052","1752-9867"]},"issue":"10","title":"Ethylene and cytokinin - partners in root growth regulation","doi":"10.1016/j.molp.2019.09.003","day":"07","isi":1,"article_type":"original","date_published":"2019-10-07T00:00:00Z","department":[{"_id":"EvBe"}],"oa_version":"None","quality_controlled":"1","publication_status":"published","citation":{"apa":"Artner, C., &#38; Benková, E. (2019). Ethylene and cytokinin - partners in root growth regulation. <i>Molecular Plant</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.molp.2019.09.003\">https://doi.org/10.1016/j.molp.2019.09.003</a>","ama":"Artner C, Benková E. Ethylene and cytokinin - partners in root growth regulation. <i>Molecular Plant</i>. 2019;12(10):1312-1314. doi:<a href=\"https://doi.org/10.1016/j.molp.2019.09.003\">10.1016/j.molp.2019.09.003</a>","chicago":"Artner, Christina, and Eva Benková. “Ethylene and Cytokinin - Partners in Root Growth Regulation.” <i>Molecular Plant</i>. Cell Press, 2019. <a href=\"https://doi.org/10.1016/j.molp.2019.09.003\">https://doi.org/10.1016/j.molp.2019.09.003</a>.","short":"C. Artner, E. Benková, Molecular Plant 12 (2019) 1312–1314.","mla":"Artner, Christina, and Eva Benková. “Ethylene and Cytokinin - Partners in Root Growth Regulation.” <i>Molecular Plant</i>, vol. 12, no. 10, Cell Press, 2019, pp. 1312–14, doi:<a href=\"https://doi.org/10.1016/j.molp.2019.09.003\">10.1016/j.molp.2019.09.003</a>.","ieee":"C. Artner and E. Benková, “Ethylene and cytokinin - partners in root growth regulation,” <i>Molecular Plant</i>, vol. 12, no. 10. Cell Press, pp. 1312–1314, 2019.","ista":"Artner C, Benková E. 2019. Ethylene and cytokinin - partners in root growth regulation. Molecular Plant. 12(10), 1312–1314."},"publication":"Molecular Plant","article_processing_charge":"No","scopus_import":"1","type":"journal_article","author":[{"last_name":"Artner","first_name":"Christina","full_name":"Artner, Christina","id":"45DF286A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Benková","full_name":"Benková, Eva","first_name":"Eva","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"}],"language":[{"iso":"eng"}],"month":"10","page":"1312-1314","date_created":"2019-09-30T10:00:40Z","volume":12,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"_id":"2685A872-B435-11E9-9278-68D0E5697425","name":"Hormonal regulation of plant adaptive responses to environmental signals"}],"publisher":"Cell Press","pmid":1,"_id":"6920"},{"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","project":[{"call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","ec_funded":1,"abstract":[{"text":"Consider a distributed system with n processors out of which f can be Byzantine faulty. In the\r\napproximate agreement task, each processor i receives an input value xi and has to decide on an\r\noutput value yi such that\r\n1. the output values are in the convex hull of the non-faulty processors’ input values,\r\n2. the output values are within distance d of each other.\r\n\r\n\r\nClassically, the values are assumed to be from an m-dimensional Euclidean space, where m ≥ 1.\r\nIn this work, we study the task in a discrete setting, where input values with some structure\r\nexpressible as a graph. Namely, the input values are vertices of a finite graph G and the goal is to\r\noutput vertices that are within distance d of each other in G, but still remain in the graph-induced\r\nconvex hull of the input values. For d = 0, the task reduces to consensus and cannot be solved with\r\na deterministic algorithm in an asynchronous system even with a single crash fault. For any d ≥ 1,\r\nwe show that the task is solvable in asynchronous systems when G is chordal and n > (ω + 1)f,\r\nwhere ω is the clique number of G. In addition, we give the first Byzantine-tolerant algorithm for a\r\nvariant of lattice agreement. For synchronous systems, we show tight resilience bounds for the exact\r\nvariants of these and related tasks over a large class of combinatorial structures.","lang":"eng"}],"alternative_title":["LIPIcs"],"_id":"6931","type":"conference","author":[{"full_name":"Nowak, Thomas","first_name":"Thomas","last_name":"Nowak"},{"full_name":"Rybicki, Joel","first_name":"Joel","last_name":"Rybicki","orcid":"0000-0002-6432-6646","id":"334EFD2E-F248-11E8-B48F-1D18A9856A87"}],"conference":{"location":"Budapest, Hungary","name":"DISC: International Symposium on Distributed Computing","end_date":"2019-10-18","start_date":"2019-10-14"},"language":[{"iso":"eng"}],"publication":"33rd International Symposium on Distributed Computing","article_processing_charge":"No","scopus_import":1,"file_date_updated":"2020-07-14T12:47:44Z","ddc":["004"],"volume":146,"page":"29:1--29:17","date_created":"2019-10-08T12:41:38Z","department":[{"_id":"DaAl"}],"file":[{"date_updated":"2020-07-14T12:47:44Z","file_name":"LIPIcs-DISC-2019-29.pdf","relation":"main_file","access_level":"open_access","file_size":639378,"checksum":"2d2202f90c6ac991e50876451627c4b5","file_id":"6934","content_type":"application/pdf","date_created":"2019-10-08T12:47:19Z","creator":"jrybicki"}],"oa_version":"Published Version","date_published":"2019-01-01T00:00:00Z","publication_status":"published","citation":{"chicago":"Nowak, Thomas, and Joel Rybicki. “Byzantine Approximate Agreement on Graphs.” In <i>33rd International Symposium on Distributed Computing</i>, 146:29:1--29:17. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. <a href=\"https://doi.org/10.4230/LIPICS.DISC.2019.29\">https://doi.org/10.4230/LIPICS.DISC.2019.29</a>.","ama":"Nowak T, Rybicki J. Byzantine approximate agreement on graphs. In: <i>33rd International Symposium on Distributed Computing</i>. Vol 146. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2019:29:1--29:17. doi:<a href=\"https://doi.org/10.4230/LIPICS.DISC.2019.29\">10.4230/LIPICS.DISC.2019.29</a>","apa":"Nowak, T., &#38; Rybicki, J. (2019). Byzantine approximate agreement on graphs. In <i>33rd International Symposium on Distributed Computing</i> (Vol. 146, p. 29:1--29:17). Budapest, Hungary: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPICS.DISC.2019.29\">https://doi.org/10.4230/LIPICS.DISC.2019.29</a>","ista":"Nowak T, Rybicki J. 2019. Byzantine approximate agreement on graphs. 33rd International Symposium on Distributed Computing. DISC: International Symposium on Distributed Computing, LIPIcs, vol. 146, 29:1--29:17.","short":"T. Nowak, J. Rybicki, in:, 33rd International Symposium on Distributed Computing, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, p. 29:1--29:17.","mla":"Nowak, Thomas, and Joel Rybicki. “Byzantine Approximate Agreement on Graphs.” <i>33rd International Symposium on Distributed Computing</i>, vol. 146, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, p. 29:1--29:17, doi:<a href=\"https://doi.org/10.4230/LIPICS.DISC.2019.29\">10.4230/LIPICS.DISC.2019.29</a>.","ieee":"T. Nowak and J. Rybicki, “Byzantine approximate agreement on graphs,” in <i>33rd International Symposium on Distributed Computing</i>, Budapest, Hungary, 2019, vol. 146, p. 29:1--29:17."},"quality_controlled":"1","arxiv":1,"oa":1,"external_id":{"arxiv":["1908.02743"]},"date_updated":"2021-01-12T08:09:38Z","intvolume":"       146","status":"public","has_accepted_license":"1","publication_identifier":{"eisbn":["978-3-95977-126-9"]},"title":"Byzantine approximate agreement on graphs","doi":"10.4230/LIPICS.DISC.2019.29","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"keyword":["consensus","approximate agreement","Byzantine faults","chordal graphs","lattice agreement"],"year":"2019"},{"date_updated":"2024-03-07T14:43:38Z","status":"public","oa":1,"external_id":{"isi":["000570442000011"],"arxiv":["1903.05956"]},"year":"2019","title":"Fast approximate shortest paths in the congested clique","publication_identifier":{"isbn":["9781450362177"]},"isi":1,"day":"01","doi":"10.1145/3293611.3331633","date_published":"2019-08-01T00:00:00Z","department":[{"_id":"DaAl"}],"oa_version":"Preprint","arxiv":1,"quality_controlled":"1","citation":{"apa":"Censor-Hillel, K., Dory, M., Korhonen, J., &#38; Leitersdorf, D. (2019). Fast approximate shortest paths in the congested clique. In <i>Proceedings of the 2019 ACM Symposium on Principles of Distributed Computin</i> (pp. 74–83). Toronto, ON, Canada: ACM. <a href=\"https://doi.org/10.1145/3293611.3331633\">https://doi.org/10.1145/3293611.3331633</a>","ama":"Censor-Hillel K, Dory M, Korhonen J, Leitersdorf D. Fast approximate shortest paths in the congested clique. In: <i>Proceedings of the 2019 ACM Symposium on Principles of Distributed Computin</i>. ACM; 2019:74-83. doi:<a href=\"https://doi.org/10.1145/3293611.3331633\">10.1145/3293611.3331633</a>","chicago":"Censor-Hillel, Keren, Michal Dory, Janne Korhonen, and Dean Leitersdorf. “Fast Approximate Shortest Paths in the Congested Clique.” In <i>Proceedings of the 2019 ACM Symposium on Principles of Distributed Computin</i>, 74–83. ACM, 2019. <a href=\"https://doi.org/10.1145/3293611.3331633\">https://doi.org/10.1145/3293611.3331633</a>.","mla":"Censor-Hillel, Keren, et al. “Fast Approximate Shortest Paths in the Congested Clique.” <i>Proceedings of the 2019 ACM Symposium on Principles of Distributed Computin</i>, ACM, 2019, pp. 74–83, doi:<a href=\"https://doi.org/10.1145/3293611.3331633\">10.1145/3293611.3331633</a>.","short":"K. Censor-Hillel, M. Dory, J. Korhonen, D. Leitersdorf, in:, Proceedings of the 2019 ACM Symposium on Principles of Distributed Computin, ACM, 2019, pp. 74–83.","ieee":"K. Censor-Hillel, M. Dory, J. Korhonen, and D. Leitersdorf, “Fast approximate shortest paths in the congested clique,” in <i>Proceedings of the 2019 ACM Symposium on Principles of Distributed Computin</i>, Toronto, ON, Canada, 2019, pp. 74–83.","ista":"Censor-Hillel K, Dory M, Korhonen J, Leitersdorf D. 2019. Fast approximate shortest paths in the congested clique. Proceedings of the 2019 ACM Symposium on Principles of Distributed Computin. PODC: Symposium on Principles of Distributed Computing, 74–83."},"publication_status":"published","article_processing_charge":"No","publication":"Proceedings of the 2019 ACM Symposium on Principles of Distributed Computin","scopus_import":"1","conference":{"location":"Toronto, ON, Canada","name":"PODC: Symposium on Principles of Distributed Computing","end_date":"2019-08-02","start_date":"2019-07-29"},"author":[{"last_name":"Censor-Hillel","full_name":"Censor-Hillel, Keren","first_name":"Keren"},{"first_name":"Michal","full_name":"Dory, Michal","last_name":"Dory"},{"last_name":"Korhonen","full_name":"Korhonen, Janne","first_name":"Janne","id":"C5402D42-15BC-11E9-A202-CA2BE6697425"},{"first_name":"Dean","full_name":"Leitersdorf, Dean","last_name":"Leitersdorf"}],"language":[{"iso":"eng"}],"month":"08","type":"conference","page":"74-83","date_created":"2019-10-08T12:48:42Z","related_material":{"record":[{"status":"public","relation":"later_version","id":"7939"}]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"ACM","main_file_link":[{"url":"https://arxiv.org/abs/1903.05956","open_access":"1"}],"_id":"6933","abstract":[{"lang":"eng","text":"We design fast deterministic algorithms for distance computation in the CONGESTED CLIQUE model. Our key contributions include:\r\n\r\n - A (2+ε)-approximation for all-pairs shortest paths problem in O(log²n / ε) rounds on unweighted undirected graphs. With a small additional additive factor, this also applies for weighted graphs. This is the first sub-polynomial constant-factor approximation for APSP in this model.\r\n - A (1+ε)-approximation for multi-source shortest paths problem from O(√n) sources in O(log² n / ε) rounds on weighted undirected graphs. This is the first sub-polynomial algorithm obtaining this approximation for a set of sources of polynomial size.\r\n\r\nOur main techniques are new distance tools that are obtained via improved algorithms for sparse matrix multiplication, which we leverage to construct efficient hopsets and shortest paths. Furthermore, our techniques extend to additional distance problems for which we improve upon the state-of-the-art, including diameter approximation, and an exact single-source shortest paths algorithm for weighted undirected graphs in Õ(n^{1/6}) rounds."}]},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"ACM","project":[{"grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships"}],"main_file_link":[{"url":"https://arxiv.org/abs/1905.03012","open_access":"1"}],"ec_funded":1,"abstract":[{"text":"This paper investigates the power of preprocessing in the CONGEST model. Schmid and Suomela (ACM HotSDN 2013) introduced the SUPPORTED CONGEST model to study the application of distributed algorithms in Software-Defined Networks (SDNs). In this paper, we show that a large class of lower bounds in the CONGEST model still hold in the SUPPORTED model, highlighting the robustness of these bounds. This also raises the question how much does\r\npreprocessing help in the CONGEST model.","lang":"eng"}],"_id":"6935","conference":{"end_date":"2019-08-02","start_date":"2019-07-29","name":"PODC: Symposium on Principles of Distributed Computing","location":"Toronto, ON, Canada"},"month":"08","author":[{"full_name":"Foerster, Klaus-Tycho","first_name":"Klaus-Tycho","last_name":"Foerster"},{"last_name":"Korhonen","first_name":"Janne","full_name":"Korhonen, Janne","id":"C5402D42-15BC-11E9-A202-CA2BE6697425"},{"first_name":"Joel","full_name":"Rybicki, Joel","last_name":"Rybicki","id":"334EFD2E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6432-6646"},{"first_name":"Stefan","full_name":"Schmid, Stefan","last_name":"Schmid"}],"language":[{"iso":"eng"}],"type":"conference","article_processing_charge":"No","publication":"Proceedings of the 2019 ACM Symposium on Principles of Distributed Computing","scopus_import":"1","page":"259-261","date_created":"2019-10-08T12:57:14Z","department":[{"_id":"DaAl"}],"oa_version":"Preprint","date_published":"2019-08-01T00:00:00Z","publication_status":"published","citation":{"ama":"Foerster K-T, Korhonen J, Rybicki J, Schmid S. Does preprocessing help under congestion? In: <i>Proceedings of the 2019 ACM Symposium on Principles of Distributed Computing</i>. ACM; 2019:259-261. doi:<a href=\"https://doi.org/10.1145/3293611.3331581\">10.1145/3293611.3331581</a>","apa":"Foerster, K.-T., Korhonen, J., Rybicki, J., &#38; Schmid, S. (2019). Does preprocessing help under congestion? In <i>Proceedings of the 2019 ACM Symposium on Principles of Distributed Computing</i> (pp. 259–261). Toronto, ON, Canada: ACM. <a href=\"https://doi.org/10.1145/3293611.3331581\">https://doi.org/10.1145/3293611.3331581</a>","chicago":"Foerster, Klaus-Tycho, Janne Korhonen, Joel Rybicki, and Stefan Schmid. “Does Preprocessing Help under Congestion?” In <i>Proceedings of the 2019 ACM Symposium on Principles of Distributed Computing</i>, 259–61. ACM, 2019. <a href=\"https://doi.org/10.1145/3293611.3331581\">https://doi.org/10.1145/3293611.3331581</a>.","short":"K.-T. Foerster, J. Korhonen, J. Rybicki, S. Schmid, in:, Proceedings of the 2019 ACM Symposium on Principles of Distributed Computing, ACM, 2019, pp. 259–261.","mla":"Foerster, Klaus-Tycho, et al. “Does Preprocessing Help under Congestion?” <i>Proceedings of the 2019 ACM Symposium on Principles of Distributed Computing</i>, ACM, 2019, pp. 259–61, doi:<a href=\"https://doi.org/10.1145/3293611.3331581\">10.1145/3293611.3331581</a>.","ieee":"K.-T. Foerster, J. Korhonen, J. Rybicki, and S. Schmid, “Does preprocessing help under congestion?,” in <i>Proceedings of the 2019 ACM Symposium on Principles of Distributed Computing</i>, Toronto, ON, Canada, 2019, pp. 259–261.","ista":"Foerster K-T, Korhonen J, Rybicki J, Schmid S. 2019. Does preprocessing help under congestion? Proceedings of the 2019 ACM Symposium on Principles of Distributed Computing. PODC: Symposium on Principles of Distributed Computing, 259–261."},"arxiv":1,"quality_controlled":"1","oa":1,"external_id":{"isi":["000570442000037"],"arxiv":["1905.03012"]},"date_updated":"2023-09-08T11:37:22Z","status":"public","publication_identifier":{"isbn":["9781450362177"]},"title":"Does preprocessing help under congestion?","isi":1,"doi":"10.1145/3293611.3331581","day":"01","year":"2019"},{"publication":"Ecography","article_processing_charge":"No","scopus_import":"1","type":"journal_article","author":[{"last_name":"Ovaskainen","first_name":"Otso","full_name":"Ovaskainen, Otso"},{"id":"334EFD2E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6432-6646","full_name":"Rybicki, Joel","first_name":"Joel","last_name":"Rybicki"},{"last_name":"Abrego","full_name":"Abrego, Nerea","first_name":"Nerea"}],"language":[{"iso":"eng"}],"month":"11","page":"1877-1886","date_created":"2019-10-08T13:01:24Z","file_date_updated":"2020-07-14T12:47:45Z","ddc":["577"],"volume":42,"ec_funded":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"publisher":"Wiley","_id":"6936","abstract":[{"lang":"eng","text":"A key challenge for community ecology is to understand to what extent observational data can be used to infer the underlying community assembly processes. As different processes can lead to similar or even identical patterns, statistical analyses of non‐manipulative observational data never yield undisputable causal inference on the underlying processes. Still, most empirical studies in community ecology are based on observational data, and hence understanding under which circumstances such data can shed light on assembly processes is a central concern for community ecologists. We simulated a spatial agent‐based model that generates variation in metacommunity dynamics across multiple axes, including the four classic metacommunity paradigms as special cases. We further simulated a virtual ecologist who analysed snapshot data sampled from the simulations using eighteen output metrics derived from beta‐diversity and habitat variation indices, variation partitioning and joint species distribution modelling. Our results indicated two main axes of variation in the output metrics. The first axis of variation described whether the landscape has patchy or continuous variation, and thus was essentially independent of the properties of the species community. The second axis of variation related to the level of predictability of the metacommunity. The most predictable communities were niche‐based metacommunities inhabiting static landscapes with marked environmental heterogeneity, such as metacommunities following the species sorting paradigm or the mass effects paradigm. The most unpredictable communities were neutral‐based metacommunities inhabiting dynamics landscapes with little spatial heterogeneity, such as metacommunities following the neutral or patch sorting paradigms. The output metrics from joint species distribution modelling yielded generally the highest resolution to disentangle among the simulated scenarios. Yet, the different types of statistical approaches utilized in this study carried complementary information, and thus our results suggest that the most comprehensive evaluation of metacommunity structure can be obtained by combining them.\r\n"}],"date_updated":"2023-08-30T06:57:25Z","intvolume":"        42","status":"public","oa":1,"external_id":{"isi":["000486348700001"]},"year":"2019","publication_identifier":{"eissn":["1600-0587"],"issn":["0906-7590"]},"has_accepted_license":"1","title":"What can observational data reveal about metacommunity processes?","issue":"11","doi":"10.1111/ecog.04444","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"day":"01","isi":1,"article_type":"original","date_published":"2019-11-01T00:00:00Z","department":[{"_id":"DaAl"}],"file":[{"file_name":"ecog.04444.pdf","access_level":"open_access","relation":"main_file","checksum":"6c9fbbd5ea8ce10ae93e55ad560a7bf9","file_size":1682718,"date_updated":"2020-07-14T12:47:45Z","creator":"jrybicki","file_id":"6937","content_type":"application/pdf","date_created":"2019-10-08T13:07:44Z"}],"oa_version":"Published Version","quality_controlled":"1","citation":{"mla":"Ovaskainen, Otso, et al. “What Can Observational Data Reveal about Metacommunity Processes?” <i>Ecography</i>, vol. 42, no. 11, Wiley, 2019, pp. 1877–86, doi:<a href=\"https://doi.org/10.1111/ecog.04444\">10.1111/ecog.04444</a>.","short":"O. Ovaskainen, J. Rybicki, N. Abrego, Ecography 42 (2019) 1877–1886.","ieee":"O. Ovaskainen, J. Rybicki, and N. Abrego, “What can observational data reveal about metacommunity processes?,” <i>Ecography</i>, vol. 42, no. 11. Wiley, pp. 1877–1886, 2019.","ista":"Ovaskainen O, Rybicki J, Abrego N. 2019. What can observational data reveal about metacommunity processes? Ecography. 42(11), 1877–1886.","ama":"Ovaskainen O, Rybicki J, Abrego N. What can observational data reveal about metacommunity processes? <i>Ecography</i>. 2019;42(11):1877-1886. doi:<a href=\"https://doi.org/10.1111/ecog.04444\">10.1111/ecog.04444</a>","apa":"Ovaskainen, O., Rybicki, J., &#38; Abrego, N. (2019). What can observational data reveal about metacommunity processes? <i>Ecography</i>. Wiley. <a href=\"https://doi.org/10.1111/ecog.04444\">https://doi.org/10.1111/ecog.04444</a>","chicago":"Ovaskainen, Otso, Joel Rybicki, and Nerea Abrego. “What Can Observational Data Reveal about Metacommunity Processes?” <i>Ecography</i>. Wiley, 2019. <a href=\"https://doi.org/10.1111/ecog.04444\">https://doi.org/10.1111/ecog.04444</a>."},"publication_status":"published"},{"date_updated":"2024-08-07T07:16:52Z","intvolume":"       123","status":"public","oa":1,"external_id":{"isi":["000483587200004"],"arxiv":["1907.06253"]},"year":"2019","title":"Berezinskii-Kosterlitz-Thouless paired phase in coupled XY models","issue":"10","publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"day":"06","doi":"10.1103/physrevlett.123.100601","article_number":"100601","isi":1,"article_type":"original","date_published":"2019-09-06T00:00:00Z","department":[{"_id":"MiLe"}],"oa_version":"Preprint","quality_controlled":"1","arxiv":1,"publication_status":"published","citation":{"apa":"Bighin, G., Defenu, N., Nándori, I., Salasnich, L., &#38; Trombettoni, A. (2019). Berezinskii-Kosterlitz-Thouless paired phase in coupled XY models. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevlett.123.100601\">https://doi.org/10.1103/physrevlett.123.100601</a>","ama":"Bighin G, Defenu N, Nándori I, Salasnich L, Trombettoni A. Berezinskii-Kosterlitz-Thouless paired phase in coupled XY models. <i>Physical Review Letters</i>. 2019;123(10). doi:<a href=\"https://doi.org/10.1103/physrevlett.123.100601\">10.1103/physrevlett.123.100601</a>","chicago":"Bighin, Giacomo, Nicolò Defenu, István Nándori, Luca Salasnich, and Andrea Trombettoni. “Berezinskii-Kosterlitz-Thouless Paired Phase in Coupled XY Models.” <i>Physical Review Letters</i>. American Physical Society, 2019. <a href=\"https://doi.org/10.1103/physrevlett.123.100601\">https://doi.org/10.1103/physrevlett.123.100601</a>.","ieee":"G. Bighin, N. Defenu, I. Nándori, L. Salasnich, and A. Trombettoni, “Berezinskii-Kosterlitz-Thouless paired phase in coupled XY models,” <i>Physical Review Letters</i>, vol. 123, no. 10. American Physical Society, 2019.","mla":"Bighin, Giacomo, et al. “Berezinskii-Kosterlitz-Thouless Paired Phase in Coupled XY Models.” <i>Physical Review Letters</i>, vol. 123, no. 10, 100601, American Physical Society, 2019, doi:<a href=\"https://doi.org/10.1103/physrevlett.123.100601\">10.1103/physrevlett.123.100601</a>.","short":"G. Bighin, N. Defenu, I. Nándori, L. Salasnich, A. Trombettoni, Physical Review Letters 123 (2019).","ista":"Bighin G, Defenu N, Nándori I, Salasnich L, Trombettoni A. 2019. Berezinskii-Kosterlitz-Thouless paired phase in coupled XY models. Physical Review Letters. 123(10), 100601."},"publication":"Physical Review Letters","article_processing_charge":"No","scopus_import":"1","type":"journal_article","author":[{"last_name":"Bighin","first_name":"Giacomo","full_name":"Bighin, Giacomo","orcid":"0000-0001-8823-9777","id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Defenu","first_name":"Nicolò","full_name":"Defenu, Nicolò"},{"full_name":"Nándori, István","first_name":"István","last_name":"Nándori"},{"last_name":"Salasnich","first_name":"Luca","full_name":"Salasnich, Luca"},{"full_name":"Trombettoni, Andrea","first_name":"Andrea","last_name":"Trombettoni"}],"language":[{"iso":"eng"}],"month":"09","date_created":"2019-10-14T06:31:13Z","related_material":{"link":[{"url":"https://ist.ac.at/en/news/new-form-of-magnetism-found/","description":"News auf IST Website","relation":"press_release"}]},"volume":123,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","main_file_link":[{"url":"https://arxiv.org/abs/1907.06253","open_access":"1"}],"project":[{"_id":"26986C82-B435-11E9-9278-68D0E5697425","name":"A path-integral approach to composite impurities","grant_number":"M02641","call_identifier":"FWF"}],"publisher":"American Physical Society","acknowledgement":"We thank S. Chiacchiera, G. Delfino, N. Dupuis, T. Enss, M. Fabrizio and G. Gori for many stimulating discussions.\r\nG.B. acknowledges support from the Austrian Science Fund (FWF), under project No. M2461-N27. N.D. acknowledges\r\nsupport from Deutsche Forschungsgemeinschaft (DFG) under Germany’s Excellence Strategy EXC-2181/1 - 390900948 (the Heidelberg STRUCTURES Excellence Cluster) and from the DFG Collaborative Research Centre “SFB 1225 ISOQUANT”. Support from the CNR/MTA Italy-Hungary 2019-2021 Joint Project “Strongly interacting systems in confined geometries” is gratefully acknowledged.","_id":"6940","abstract":[{"lang":"eng","text":"We study the effect of a linear tunneling coupling between two-dimensional systems, each separately\r\nexhibiting the topological Berezinskii-Kosterlitz-Thouless (BKT) transition. In the uncoupled limit, there\r\nare two phases: one where the one-body correlation functions are algebraically decaying and the other with\r\nexponential decay. When the linear coupling is turned on, a third BKT-paired phase emerges, in which one-body correlations are exponentially decaying, while two-body correlation functions exhibit power-law\r\ndecay. We perform numerical simulations in the paradigmatic case of two coupled XY models at finite\r\ntemperature, finding evidences that for any finite value of the interlayer coupling, the BKT-paired phase is\r\npresent. We provide a picture of the phase diagram using a renormalization group approach."}]},{"status":"public","intvolume":"     11785","date_updated":"2025-06-02T08:53:47Z","external_id":{"arxiv":["1906.08178"],"isi":["000679281300007"]},"oa":1,"year":"2019","isi":1,"doi":"10.1007/978-3-030-30281-8_7","day":"04","publication_identifier":{"isbn":["9783030302801"],"eisbn":["9783030302818"],"issn":["0302-9743"]},"title":"Strategy representation by decision trees with linear classifiers","date_published":"2019-09-04T00:00:00Z","oa_version":"Preprint","department":[{"_id":"KrCh"},{"_id":"ChLa"}],"arxiv":1,"quality_controlled":"1","publication_status":"published","citation":{"ama":"Ashok P, Brázdil T, Chatterjee K, Křetínský J, Lampert C, Toman V. Strategy representation by decision trees with linear classifiers. In: <i>16th International Conference on Quantitative Evaluation of Systems</i>. Vol 11785. Springer Nature; 2019:109-128. doi:<a href=\"https://doi.org/10.1007/978-3-030-30281-8_7\">10.1007/978-3-030-30281-8_7</a>","apa":"Ashok, P., Brázdil, T., Chatterjee, K., Křetínský, J., Lampert, C., &#38; Toman, V. (2019). Strategy representation by decision trees with linear classifiers. In <i>16th International Conference on Quantitative Evaluation of Systems</i> (Vol. 11785, pp. 109–128). Glasgow, United Kingdom: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-30281-8_7\">https://doi.org/10.1007/978-3-030-30281-8_7</a>","chicago":"Ashok, Pranav, Tomáš Brázdil, Krishnendu Chatterjee, Jan Křetínský, Christoph Lampert, and Viktor Toman. “Strategy Representation by Decision Trees with Linear Classifiers.” In <i>16th International Conference on Quantitative Evaluation of Systems</i>, 11785:109–28. Springer Nature, 2019. <a href=\"https://doi.org/10.1007/978-3-030-30281-8_7\">https://doi.org/10.1007/978-3-030-30281-8_7</a>.","mla":"Ashok, Pranav, et al. “Strategy Representation by Decision Trees with Linear Classifiers.” <i>16th International Conference on Quantitative Evaluation of Systems</i>, vol. 11785, Springer Nature, 2019, pp. 109–28, doi:<a href=\"https://doi.org/10.1007/978-3-030-30281-8_7\">10.1007/978-3-030-30281-8_7</a>.","short":"P. Ashok, T. Brázdil, K. Chatterjee, J. Křetínský, C. Lampert, V. Toman, in:, 16th International Conference on Quantitative Evaluation of Systems, Springer Nature, 2019, pp. 109–128.","ieee":"P. Ashok, T. Brázdil, K. Chatterjee, J. Křetínský, C. Lampert, and V. Toman, “Strategy representation by decision trees with linear classifiers,” in <i>16th International Conference on Quantitative Evaluation of Systems</i>, Glasgow, United Kingdom, 2019, vol. 11785, pp. 109–128.","ista":"Ashok P, Brázdil T, Chatterjee K, Křetínský J, Lampert C, Toman V. 2019. Strategy representation by decision trees with linear classifiers. 16th International Conference on Quantitative Evaluation of Systems. QEST: Quantitative Evaluation of Systems, LNCS, vol. 11785, 109–128."},"scopus_import":"1","article_processing_charge":"No","publication":"16th International Conference on Quantitative Evaluation of Systems","month":"09","author":[{"first_name":"Pranav","full_name":"Ashok, Pranav","last_name":"Ashok"},{"first_name":"Tomáš","full_name":"Brázdil, Tomáš","last_name":"Brázdil"},{"last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"last_name":"Křetínský","full_name":"Křetínský, Jan","first_name":"Jan"},{"orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Lampert, Christoph","first_name":"Christoph","last_name":"Lampert"},{"id":"3AF3DA7C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9036-063X","full_name":"Toman, Viktor","first_name":"Viktor","last_name":"Toman"}],"language":[{"iso":"eng"}],"conference":{"start_date":"2019-09-10","end_date":"2019-09-12","name":"QEST: Quantitative Evaluation of Systems","location":"Glasgow, United Kingdom"},"type":"conference","date_created":"2019-10-14T06:57:49Z","page":"109-128","volume":11785,"publisher":"Springer Nature","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1906.08178"}],"project":[{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","grant_number":"S11407","call_identifier":"FWF"},{"name":"Rigorous Systems Engineering","_id":"25F2ACDE-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S11402-N23"},{"name":"Efficient Algorithms for Computer Aided Verification","_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6942","alternative_title":["LNCS"],"abstract":[{"text":"Graph games and Markov decision processes (MDPs) are standard models in reactive synthesis and verification of probabilistic systems with nondeterminism. The class of   𝜔 -regular winning conditions; e.g., safety, reachability, liveness, parity conditions; provides a robust and expressive specification formalism for properties that arise in analysis of reactive systems. The resolutions of nondeterminism in games and MDPs are represented as strategies, and we consider succinct representation of such strategies. The decision-tree data structure from machine learning retains the flavor of decisions of strategies and allows entropy-based minimization to obtain succinct trees. However, in contrast to traditional machine-learning problems where small errors are allowed, for winning strategies in graph games and MDPs no error is allowed, and the decision tree must represent the entire strategy. In this work we propose decision trees with linear classifiers for representation of strategies in graph games and MDPs. We have implemented strategy representation using this data structure and we present experimental results for problems on graph games and MDPs, which show that this new data structure presents a much more efficient strategy representation as compared to standard decision trees.","lang":"eng"}]},{"project":[{"grant_number":"742985","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"}],"publisher":"Elsevier","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ec_funded":1,"abstract":[{"lang":"eng","text":"Plants as sessile organisms are constantly under attack by herbivores, rough environmental situations, or mechanical pressure. These challenges often lead to the induction of wounds or destruction of already specified and developed tissues. Additionally, wounding makes plants vulnerable to invasion by pathogens, which is why wound signalling often triggers specific defence responses. To stay competitive or, eventually, survive under these circumstances, plants need to regenerate efficiently, which in rigid, tissue migration-incompatible plant tissues requires post-embryonic patterning and organogenesis. Now, several studies used laser-assisted single cell ablation in the Arabidopsis root tip as a minimal wounding proxy. Here, we discuss their findings and put them into context of a broader spectrum of wound signalling, pathogen responses and tissue as well as organ regeneration."}],"_id":"6943","pmid":1,"type":"journal_article","month":"12","language":[{"iso":"eng"}],"author":[{"orcid":"0000-0001-8295-2926","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","full_name":"Hörmayer, Lukas","first_name":"Lukas","last_name":"Hörmayer"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","first_name":"Jiří","last_name":"Friml"}],"scopus_import":"1","publication":"Current Opinion in Plant Biology","article_processing_charge":"No","file_date_updated":"2020-07-14T12:47:45Z","related_material":{"record":[{"relation":"dissertation_contains","id":"9992","status":"public"}]},"ddc":["580"],"volume":52,"date_created":"2019-10-14T07:00:24Z","page":"124-130","oa_version":"Published Version","file":[{"file_size":1659288,"checksum":"d6fd68a6e965f1efe3f0bf2d2070a616","relation":"main_file","access_level":"open_access","file_name":"2019_CurrentOpinionPlant_Hoermayer.pdf","date_updated":"2020-07-14T12:47:45Z","creator":"dernst","date_created":"2019-10-14T14:48:21Z","content_type":"application/pdf","file_id":"6946"}],"department":[{"_id":"JiFr"}],"article_type":"original","date_published":"2019-12-01T00:00:00Z","citation":{"chicago":"Hörmayer, Lukas, and Jiří Friml. “Targeted Cell Ablation-Based Insights into Wound Healing and Restorative Patterning.” <i>Current Opinion in Plant Biology</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.pbi.2019.08.006\">https://doi.org/10.1016/j.pbi.2019.08.006</a>.","ama":"Hörmayer L, Friml J. Targeted cell ablation-based insights into wound healing and restorative patterning. <i>Current Opinion in Plant Biology</i>. 2019;52:124-130. doi:<a href=\"https://doi.org/10.1016/j.pbi.2019.08.006\">10.1016/j.pbi.2019.08.006</a>","apa":"Hörmayer, L., &#38; Friml, J. (2019). Targeted cell ablation-based insights into wound healing and restorative patterning. <i>Current Opinion in Plant Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.pbi.2019.08.006\">https://doi.org/10.1016/j.pbi.2019.08.006</a>","ista":"Hörmayer L, Friml J. 2019. Targeted cell ablation-based insights into wound healing and restorative patterning. Current Opinion in Plant Biology. 52, 124–130.","ieee":"L. Hörmayer and J. Friml, “Targeted cell ablation-based insights into wound healing and restorative patterning,” <i>Current Opinion in Plant Biology</i>, vol. 52. Elsevier, pp. 124–130, 2019.","short":"L. Hörmayer, J. Friml, Current Opinion in Plant Biology 52 (2019) 124–130.","mla":"Hörmayer, Lukas, and Jiří Friml. “Targeted Cell Ablation-Based Insights into Wound Healing and Restorative Patterning.” <i>Current Opinion in Plant Biology</i>, vol. 52, Elsevier, 2019, pp. 124–30, doi:<a href=\"https://doi.org/10.1016/j.pbi.2019.08.006\">10.1016/j.pbi.2019.08.006</a>."},"publication_status":"published","quality_controlled":"1","external_id":{"isi":["000502890600017"],"pmid":["31585333"]},"oa":1,"intvolume":"        52","status":"public","date_updated":"2024-03-25T23:30:06Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"day":"01","doi":"10.1016/j.pbi.2019.08.006","isi":1,"has_accepted_license":"1","publication_identifier":{"issn":["1369-5266"]},"title":"Targeted cell ablation-based insights into wound healing and restorative patterning","year":"2019"},{"department":[{"_id":"MiSi"}],"file":[{"creator":"fassen","file_id":"6990","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_created":"2019-11-06T12:30:02Z","embargo_to":"open_access","file_name":"PhDthesis_FrankAssen_revised2.docx","relation":"source_file","access_level":"closed","checksum":"53a739752a500f84d0f8ec953cbbd0b6","file_size":214172667,"date_updated":"2020-11-07T23:30:03Z"},{"date_created":"2019-11-06T12:30:57Z","file_id":"6991","content_type":"application/pdf","creator":"fassen","date_updated":"2020-11-07T23:30:03Z","relation":"main_file","access_level":"open_access","checksum":"8c156b65d9347bb599623a4b09f15d15","file_size":83637532,"embargo":"2020-11-06","file_name":"PhDthesis_FrankAssen_revised2.pdf"}],"oa_version":"Published Version","date_published":"2019-10-09T00:00:00Z","citation":{"ista":"Assen FP. 2019. Lymph node mechanics: Deciphering the interplay between stroma contractility, morphology and lymphocyte trafficking. Institute of Science and Technology Austria.","mla":"Assen, Frank P. <i>Lymph Node Mechanics: Deciphering the Interplay between Stroma Contractility, Morphology and Lymphocyte Trafficking</i>. Institute of Science and Technology Austria, 2019, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6947\">10.15479/AT:ISTA:6947</a>.","short":"F.P. Assen, Lymph Node Mechanics: Deciphering the Interplay between Stroma Contractility, Morphology and Lymphocyte Trafficking, Institute of Science and Technology Austria, 2019.","ieee":"F. P. Assen, “Lymph node mechanics: Deciphering the interplay between stroma contractility, morphology and lymphocyte trafficking,” Institute of Science and Technology Austria, 2019.","chicago":"Assen, Frank P. “Lymph Node Mechanics: Deciphering the Interplay between Stroma Contractility, Morphology and Lymphocyte Trafficking.” Institute of Science and Technology Austria, 2019. <a href=\"https://doi.org/10.15479/AT:ISTA:6947\">https://doi.org/10.15479/AT:ISTA:6947</a>.","ama":"Assen FP. Lymph node mechanics: Deciphering the interplay between stroma contractility, morphology and lymphocyte trafficking. 2019. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6947\">10.15479/AT:ISTA:6947</a>","apa":"Assen, F. P. (2019). <i>Lymph node mechanics: Deciphering the interplay between stroma contractility, morphology and lymphocyte trafficking</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:6947\">https://doi.org/10.15479/AT:ISTA:6947</a>"},"publication_status":"published","supervisor":[{"full_name":"Sixt, Michael K","first_name":"Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179"}],"oa":1,"date_updated":"2023-09-13T08:50:57Z","status":"public","title":"Lymph node mechanics: Deciphering the interplay between stroma contractility, morphology and lymphocyte trafficking","publication_identifier":{"issn":["2663-337X"]},"has_accepted_license":"1","day":"9","doi":"10.15479/AT:ISTA:6947","year":"2019","degree_awarded":"PhD","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Institute of Science and Technology Austria","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"EM-Fac"}],"abstract":[{"lang":"eng","text":"Lymph nodes  are es s ential organs  of the immune  s ys tem where adaptive immune responses originate, and consist of various leukocyte populations and a stromal backbone. Fibroblastic reticular  cells (FRCs) are  the  main  stromal  cells and  form  a sponge-like extracellular matrix network,   called  conduits ,  which  they   thems elves   enwrap   and  contract.  Lymph,  containing  s oluble  antigens ,  arrive in  lymph  nodes  via afferent lymphatic  vessels that  connect  to  the  s ubcaps ular  s inus   and  conduit  network.  According  to  the  current  paradigm,  the  conduit  network   dis tributes   afferent  lymph  through   lymph  nodes   and  thus   provides   acces s   for  immune  cells to lymph-borne  antigens. An  elas tic  caps ule  s urrounds   the  organ  and  confines   the immune  cells and  FRC  network.   Lymph   nodes   are  completely  packed  with  lymphocytes   and  lymphocyte  numbers  directly  dictates  the size  of  the  organ.  Although  lymphocytes   cons tantly  enter  and  leave  the  lymph  node,  its   s ize  remains   remarkedly   s table  under  homeostatic conditions. It is only partly known  how the cellularity and s ize of the lymph node is regulated and  how  the  lymph  node  is able to swell in inflammation.  The role of the FRC network   in  lymph  node   s welling  and  trans fer  of  fluids   are  inves tigated in  this   thes is.  Furthermore,   we  s tudied  what  trafficking  routes   are  us ed  by  cancer  cells   in  lymph  nodes   to  form  distal metastases.We examined the role of a mechanical feedback in regulation of lymph  node swelling. Using parallel plate compression  and UV-las er  cutting  experiments   we  dis s ected  the  mechanical  force dynamics  of the whole lymph  node, and individually for FRCs  and the  caps ule. Physical forces   generated  by  packed  lymphocytes   directly  affect  the  tens ion  on  the  FRC  network  and  capsule,  which  increases  its  resistance  to   swelling.  This  implies  a  feedback  mechanism  between   tis s ue   pres s ure   and   ability   of   lymphocytes    to   enter   the   organ.   Following   inflammation,  the  lymph  node  swells ∼10 fold in two weeks . Yet, what  is  the role  for tens ion on  the  FRC  network   and  caps ule,  and  how  are  lymphocytes   able  to  enter  in  conditions  that resist swelling remain open ques tions . We s how that tens ion on the FRC network is  important to  limit  the  swelling  rate  of  the  organ  so  that  the  FRC  network  can  grow  in  a  coordinated  fashion. This is illustrated by interfering with FRC contractility, which leads to faster swelling rates  and a dis organized FRC network  in the inflamed lymph  node. Growth  of the FRC network  in  turn  is   expected  to  releas e  tens ion  on  thes e  s tructures   and  lowers   the  res is tance  to  swelling, thereby allowing more lymphocytes to enter the organ and drive more swelling. Halt of  swelling coincides   with  a  thickening  of  the  caps ule,  which  forms   a  thick  res is tant  band  around  the organ and lowers  tens ion on the FRC network  to form a new force equilibrium.The  FRC  and  conduit   network   are  further   believed  to  be  a  privileged  s ite  of  s oluble  information  within  the  lymph  node,  although  many  details   remain  uns olved.  We  s how  by  3D  ultra-recons truction   that  FRCs   and  antigen  pres enting  cells   cover  the  s urface  of  conduit  s ys tem for more  than 99% and we dis cus s  the implications  for s oluble information  exchangeat the conduit level.Finally, there  is an ongoing debate in the cancer field whether and how cancer cells  in lymph nodes   s eed  dis tal  metas tas es .  We  s how  that  cancer  cells   infus ed  into  the  lymph  node  can  utilize trafficking routes of immune  cells and  rapidly  migrate  to  blood  vessels. Once  in  the  blood circulation,  these cells are able to form  metastases in distal tissues."}],"alternative_title":["ISTA Thesis"],"_id":"6947","type":"dissertation","author":[{"first_name":"Frank P","full_name":"Assen, Frank P","last_name":"Assen","id":"3A8E7F24-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3470-6119"}],"month":"10","language":[{"iso":"eng"}],"article_processing_charge":"No","file_date_updated":"2020-11-07T23:30:03Z","related_material":{"record":[{"status":"public","id":"664","relation":"part_of_dissertation"},{"id":"402","relation":"part_of_dissertation","status":"public"}]},"ddc":["570"],"page":"142","date_created":"2019-10-14T16:54:52Z"},{"oa_version":"Published Version","file":[{"date_created":"2019-10-25T12:47:04Z","file_id":"6974","content_type":"application/pdf","creator":"dernst","date_updated":"2020-07-14T12:47:46Z","relation":"main_file","access_level":"open_access","checksum":"d27f983b34ea7dafdf356afbf9472fbf","file_size":528362,"file_name":"2019_PhysicsLettersB_Schmickler.pdf"}],"department":[{"_id":"MiLe"}],"date_published":"2019-11-10T00:00:00Z","article_type":"original","citation":{"ista":"Schmickler CH, Hammer H-W, Volosniev A. 2019. Universal physics of bound states of a few charged particles. Physics Letters B. 798, 135016.","short":"C.H. Schmickler, H.-W. Hammer, A. Volosniev, Physics Letters B 798 (2019).","mla":"Schmickler, C. H., et al. “Universal Physics of Bound States of a Few Charged Particles.” <i>Physics Letters B</i>, vol. 798, 135016, Elsevier, 2019, doi:<a href=\"https://doi.org/10.1016/j.physletb.2019.135016\">10.1016/j.physletb.2019.135016</a>.","ieee":"C. H. Schmickler, H.-W. Hammer, and A. Volosniev, “Universal physics of bound states of a few charged particles,” <i>Physics Letters B</i>, vol. 798. Elsevier, 2019.","chicago":"Schmickler, C.H., H.-W. Hammer, and Artem Volosniev. “Universal Physics of Bound States of a Few Charged Particles.” <i>Physics Letters B</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.physletb.2019.135016\">https://doi.org/10.1016/j.physletb.2019.135016</a>.","ama":"Schmickler CH, Hammer H-W, Volosniev A. Universal physics of bound states of a few charged particles. <i>Physics Letters B</i>. 2019;798. doi:<a href=\"https://doi.org/10.1016/j.physletb.2019.135016\">10.1016/j.physletb.2019.135016</a>","apa":"Schmickler, C. H., Hammer, H.-W., &#38; Volosniev, A. (2019). Universal physics of bound states of a few charged particles. <i>Physics Letters B</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.physletb.2019.135016\">https://doi.org/10.1016/j.physletb.2019.135016</a>"},"publication_status":"published","arxiv":1,"quality_controlled":"1","external_id":{"isi":["000494939000086"],"arxiv":["1904.00913"]},"oa":1,"status":"public","intvolume":"       798","date_updated":"2023-08-30T07:06:42Z","isi":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"doi":"10.1016/j.physletb.2019.135016","day":"10","article_number":"135016","publication_identifier":{"issn":["0370-2693"]},"has_accepted_license":"1","title":"Universal physics of bound states of a few charged particles","year":"2019","publisher":"Elsevier","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"lang":"eng","text":"We study few-body bound states of charged particles subject to attractive zero-range/short-range plus repulsive Coulomb interparticle forces. The characteristic length scales of the system at zero energy are set by the Coulomb length scale D and the Coulomb-modified effective range r eff. We study shallow bound states of charged particles with D >> r eff and show that these systems obey universal scaling laws different from neutral particles. An accurate description of these states requires both the Coulomb-modified scattering length and the effective range unless the Coulomb interaction is very weak (D -> ). Our findings are relevant for bound states whose spatial extent is significantly larger than the range of the attractive potential. These states enjoy universality – their character is independent of the shape of the short-range potential."}],"_id":"6955","author":[{"first_name":"C.H.","full_name":"Schmickler, C.H.","last_name":"Schmickler"},{"last_name":"Hammer","first_name":"H.-W.","full_name":"Hammer, H.-W."},{"orcid":"0000-0003-0393-5525","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","full_name":"Volosniev, Artem","first_name":"Artem","last_name":"Volosniev"}],"month":"11","language":[{"iso":"eng"}],"type":"journal_article","scopus_import":"1","article_processing_charge":"No","publication":"Physics Letters B","ddc":["530"],"volume":798,"file_date_updated":"2020-07-14T12:47:46Z","date_created":"2019-10-18T18:33:32Z"},{"publication_status":"published","citation":{"apa":"Paranjape, C. S. (2019). <i>Onset of turbulence in plane Poiseuille flow</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:6957\">https://doi.org/10.15479/AT:ISTA:6957</a>","ama":"Paranjape CS. Onset of turbulence in plane Poiseuille flow. 2019. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6957\">10.15479/AT:ISTA:6957</a>","chicago":"Paranjape, Chaitanya S. “Onset of Turbulence in Plane Poiseuille Flow.” Institute of Science and Technology Austria, 2019. <a href=\"https://doi.org/10.15479/AT:ISTA:6957\">https://doi.org/10.15479/AT:ISTA:6957</a>.","mla":"Paranjape, Chaitanya S. <i>Onset of Turbulence in Plane Poiseuille Flow</i>. Institute of Science and Technology Austria, 2019, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6957\">10.15479/AT:ISTA:6957</a>.","short":"C.S. Paranjape, Onset of Turbulence in Plane Poiseuille Flow, Institute of Science and Technology Austria, 2019.","ieee":"C. S. Paranjape, “Onset of turbulence in plane Poiseuille flow,” Institute of Science and Technology Austria, 2019.","ista":"Paranjape CS. 2019. Onset of turbulence in plane Poiseuille flow. Institute of Science and Technology Austria."},"department":[{"_id":"BjHo"}],"file":[{"content_type":"application/zip","file_id":"6962","date_created":"2019-10-23T09:54:43Z","creator":"cparanjape","date_updated":"2020-07-14T12:47:46Z","file_name":"Chaitanya_Paranjape_source_files_tex_figures.zip","file_size":45828099,"checksum":"7ba298ba0ce7e1d11691af6b8eaf0a0a","access_level":"closed","relation":"source_file"},{"date_created":"2019-10-23T10:37:09Z","content_type":"application/pdf","file_id":"6963","creator":"cparanjape","date_updated":"2020-07-14T12:47:46Z","file_size":19504197,"checksum":"642697618314e31ac31392da7909c2d9","access_level":"open_access","relation":"main_file","file_name":"Chaitanya_Paranjape_Thesis.pdf"}],"oa_version":"Published Version","date_published":"2019-10-24T00:00:00Z","has_accepted_license":"1","title":"Onset of turbulence in plane Poiseuille flow","publication_identifier":{"eissn":["2663-337X"]},"keyword":["Instabilities","Turbulence","Nonlinear dynamics"],"doi":"10.15479/AT:ISTA:6957","day":"24","year":"2019","degree_awarded":"PhD","oa":1,"supervisor":[{"orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof","full_name":"Hof, Björn","first_name":"Björn"}],"date_updated":"2023-09-07T12:53:25Z","status":"public","abstract":[{"lang":"eng","text":"In many shear flows like pipe flow, plane Couette flow, plane Poiseuille flow,  etc. turbulence emerges subcritically. Here, when subjected to strong enough perturbations, the flow becomes turbulent in spite of the laminar base flow being linearly stable.  The nature of this instability has puzzled the scientific community for decades. At onset, turbulence appears in localized patches and flows are spatio-temporally intermittent.  In pipe flow the localized turbulent structures are referred to as puffs and in planar flows like plane Couette and channel flow, patches arise in the form of localized oblique bands. In this thesis, we study the onset of turbulence in channel flow in direct numerical simulations from a dynamical system theory perspective, as well as by performing experiments in a large aspect ratio channel.\r\n\r\nThe aim of the experimental work is to determine the critical Reynolds number where turbulence first becomes sustained. Recently, the onset of turbulence has been described in analogy to absorbing state phase transition (i.e. directed percolation). In particular, it has been shown that the critical point can be estimated from the competition between spreading and decay processes. Here, by performing experiments, we identify the mechanisms underlying turbulence proliferation in channel flow and find the critical Reynolds number, above which turbulence becomes sustained. Above the critical point, the continuous growth at the tip of the stripes outweighs the stochastic shedding of turbulent patches at the tail and the stripes expand. For growing stripes, the probability to decay decreases while the probability of stripe splitting increases. Consequently, and unlike for the puffs in pipe flow, neither of these two processes is time-independent i.e. memoryless. Coupling between stripe expansion and creation of new stripes via splitting leads to a significantly lower critical point ($Re_c=670+/-10$) than most earlier studies suggest.  \r\n\r\nWhile the above approach sheds light on how turbulence first becomes sustained, it provides no insight into the origin of the stripes themselves. In the numerical part of the thesis we investigate how turbulent stripes form from invariant solutions of the Navier-Stokes equations. The origin of these turbulent stripes can be identified by applying concepts from the dynamical system theory. In doing so, we identify the exact coherent structures underlying stripes and their bifurcations and how they give rise to the turbulent attractor in phase space. We first report a family of localized nonlinear traveling wave solutions of the Navier-Stokes equations in channel flow. These solutions show structural similarities with turbulent stripes in experiments like obliqueness, quasi-streamwise streaks and vortices, etc. A parametric study of these traveling wave solution is performed, with parameters like Reynolds number, stripe tilt angle and domain size, including the stability of the solutions. These solutions emerge through saddle-node bifurcations and form a phase space skeleton for the turbulent stripes observed in the experiments. The lower branches of these TW solutions at different tilt angles undergo Hopf bifurcation and new solutions branches of relative periodic orbits emerge. These RPO solutions do not belong to the same family and therefore the routes to chaos for different angles are different.  \r\n\r\nIn shear flows, turbulence at onset is transient in nature.  Consequently,turbulence can not be tracked to lower Reynolds numbers, where the dynamics may simplify. Before this happens, turbulence becomes short-lived and laminarizes. In the last part of the thesis, we show that using numerical simulations we can continue turbulent stripes in channel flow past the 'relaminarization barrier' all the way to their origin. Here, turbulent stripe dynamics simplifies and the fluctuations are no longer stochastic and the stripe settles down to a relative periodic orbit. This relative periodic orbit originates from the aforementioned traveling wave solutions. Starting from the relative periodic orbit, a small increase in speed i.e. Reynolds number gives rise to chaos and the attractor dimension sharply increases in contrast to the classical transition scenario where the instabilities affect the flow globally and give rise to much more gradual route to turbulence."}],"_id":"6957","alternative_title":["ISTA Thesis"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Institute of Science and Technology Austria","ddc":["532"],"file_date_updated":"2020-07-14T12:47:46Z","page":"138","date_created":"2019-10-22T12:08:43Z","month":"10","author":[{"last_name":"Paranjape","first_name":"Chaitanya S","full_name":"Paranjape, Chaitanya S","id":"3D85B7C4-F248-11E8-B48F-1D18A9856A87"}],"language":[{"iso":"eng"}],"type":"dissertation","article_processing_charge":"No"},{"language":[{"iso":"eng"}],"author":[{"full_name":"Lenzen, Christoph","first_name":"Christoph","last_name":"Lenzen"},{"orcid":"0000-0002-6432-6646","id":"334EFD2E-F248-11E8-B48F-1D18A9856A87","last_name":"Rybicki","full_name":"Rybicki, Joel","first_name":"Joel"}],"month":"09","type":"journal_article","article_processing_charge":"Yes","publication":"Journal of the ACM","scopus_import":"1","volume":66,"ddc":["000"],"file_date_updated":"2020-07-14T12:47:46Z","date_created":"2019-10-24T17:12:48Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"ACM","project":[{"call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"ec_funded":1,"abstract":[{"text":"We give fault-tolerant algorithms for establishing synchrony in distributed systems in which each of thennodes has its own clock. Our algorithms operate in a very strong fault model: we require self-stabilisation, i.e.,the initial state of the system may be arbitrary, and there can be up to f<n/3 ongoing Byzantine faults, i.e.,nodes that deviate from the protocol in an arbitrary manner. Furthermore, we assume that the local clocks ofthe nodes may progress at different speeds (clock drift) and communication has bounded delay. In this model,we study the pulse synchronisation problem, where the task is to guarantee that eventually all correct nodesgenerate well-separated local pulse events (i.e., unlabelled logical clock ticks) in a synchronised manner.Compared to prior work, we achieveexponentialimprovements in stabilisation time and the number ofcommunicated bits, and give the first sublinear-time algorithm for the problem:•In the deterministic setting, the state-of-the-art solutions stabilise in timeΘ(f)and have each nodebroadcastΘ(flogf)bits per time unit. We exponentially reduce the number of bits broadcasted pertime unit toΘ(logf)while retaining the same stabilisation time.•In the randomised setting, the state-of-the-art solutions stabilise in timeΘ(f)and have each nodebroadcastO(1)bits per time unit. We exponentially reduce the stabilisation time to polylogfwhileeach node broadcasts polylogfbits per time unit.These results are obtained by means of a recursive approach reducing the above task ofself-stabilisingpulse synchronisation in thebounded-delaymodel tonon-self-stabilisingbinary consensus in thesynchro-nousmodel. In general, our approach introduces at most logarithmic overheads in terms of stabilisation timeand broadcasted bits over the underlying consensus routine.","lang":"eng"}],"_id":"6972","oa":1,"external_id":{"arxiv":["1705.06173"],"isi":["000496514100001"]},"date_updated":"2023-08-30T07:07:23Z","status":"public","intvolume":"        66","publication_identifier":{"issn":["0004-5411"]},"issue":"5","has_accepted_license":"1","title":"Self-stabilising Byzantine clock synchronisation is almost as easy as consensus","isi":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"day":"01","article_number":"32","doi":"10.1145/3339471","year":"2019","department":[{"_id":"DaAl"}],"file":[{"file_name":"2019_JACM_Lenzen.pdf","access_level":"open_access","relation":"main_file","checksum":"7e5d95c478e0e393f4927fcf7e48194e","file_size":2183085,"date_updated":"2020-07-14T12:47:46Z","creator":"dernst","file_id":"6975","content_type":"application/pdf","date_created":"2019-10-25T12:58:38Z"}],"oa_version":"Published Version","date_published":"2019-09-01T00:00:00Z","article_type":"original","publication_status":"published","citation":{"chicago":"Lenzen, Christoph, and Joel Rybicki. “Self-Stabilising Byzantine Clock Synchronisation Is Almost as Easy as Consensus.” <i>Journal of the ACM</i>. ACM, 2019. <a href=\"https://doi.org/10.1145/3339471\">https://doi.org/10.1145/3339471</a>.","apa":"Lenzen, C., &#38; Rybicki, J. (2019). Self-stabilising Byzantine clock synchronisation is almost as easy as consensus. <i>Journal of the ACM</i>. ACM. <a href=\"https://doi.org/10.1145/3339471\">https://doi.org/10.1145/3339471</a>","ama":"Lenzen C, Rybicki J. Self-stabilising Byzantine clock synchronisation is almost as easy as consensus. <i>Journal of the ACM</i>. 2019;66(5). doi:<a href=\"https://doi.org/10.1145/3339471\">10.1145/3339471</a>","ista":"Lenzen C, Rybicki J. 2019. Self-stabilising Byzantine clock synchronisation is almost as easy as consensus. Journal of the ACM. 66(5), 32.","ieee":"C. Lenzen and J. Rybicki, “Self-stabilising Byzantine clock synchronisation is almost as easy as consensus,” <i>Journal of the ACM</i>, vol. 66, no. 5. ACM, 2019.","short":"C. Lenzen, J. Rybicki, Journal of the ACM 66 (2019).","mla":"Lenzen, Christoph, and Joel Rybicki. “Self-Stabilising Byzantine Clock Synchronisation Is Almost as Easy as Consensus.” <i>Journal of the ACM</i>, vol. 66, no. 5, 32, ACM, 2019, doi:<a href=\"https://doi.org/10.1145/3339471\">10.1145/3339471</a>."},"arxiv":1,"quality_controlled":"1"},{"intvolume":"         4","status":"public","date_updated":"2023-08-30T07:20:03Z","external_id":{"isi":["000493510400001"],"arxiv":["1810.02211"]},"oa":1,"year":"2019","day":"01","doi":"10.1103/PhysRevFluids.4.102401","isi":1,"issue":"10","title":"Geometry of transient chaos in streamwise-localized pipe flow turbulence","article_type":"original","date_published":"2019-10-01T00:00:00Z","oa_version":"Preprint","department":[{"_id":"BjHo"}],"quality_controlled":"1","arxiv":1,"citation":{"ama":"Budanur NB, Dogra A, Hof B. Geometry of transient chaos in streamwise-localized pipe flow turbulence. <i>Physical Review Fluids</i>. 2019;4(10):102401. doi:<a href=\"https://doi.org/10.1103/PhysRevFluids.4.102401\">10.1103/PhysRevFluids.4.102401</a>","apa":"Budanur, N. B., Dogra, A., &#38; Hof, B. (2019). Geometry of transient chaos in streamwise-localized pipe flow turbulence. <i>Physical Review Fluids</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevFluids.4.102401\">https://doi.org/10.1103/PhysRevFluids.4.102401</a>","chicago":"Budanur, Nazmi B, Akshunna Dogra, and Björn Hof. “Geometry of Transient Chaos in Streamwise-Localized Pipe Flow Turbulence.” <i>Physical Review Fluids</i>. American Physical Society, 2019. <a href=\"https://doi.org/10.1103/PhysRevFluids.4.102401\">https://doi.org/10.1103/PhysRevFluids.4.102401</a>.","short":"N.B. Budanur, A. Dogra, B. Hof, Physical Review Fluids 4 (2019) 102401.","mla":"Budanur, Nazmi B., et al. “Geometry of Transient Chaos in Streamwise-Localized Pipe Flow Turbulence.” <i>Physical Review Fluids</i>, vol. 4, no. 10, American Physical Society, 2019, p. 102401, doi:<a href=\"https://doi.org/10.1103/PhysRevFluids.4.102401\">10.1103/PhysRevFluids.4.102401</a>.","ieee":"N. B. Budanur, A. Dogra, and B. Hof, “Geometry of transient chaos in streamwise-localized pipe flow turbulence,” <i>Physical Review Fluids</i>, vol. 4, no. 10. American Physical Society, p. 102401, 2019.","ista":"Budanur NB, Dogra A, Hof B. 2019. Geometry of transient chaos in streamwise-localized pipe flow turbulence. Physical Review Fluids. 4(10), 102401."},"publication_status":"published","scopus_import":"1","publication":"Physical Review Fluids","article_processing_charge":"No","type":"journal_article","author":[{"full_name":"Budanur, Nazmi B","first_name":"Nazmi B","last_name":"Budanur","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0423-5010"},{"last_name":"Dogra","first_name":"Akshunna","full_name":"Dogra, Akshunna"},{"last_name":"Hof","full_name":"Hof, Björn","first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754"}],"language":[{"iso":"eng"}],"month":"10","date_created":"2019-11-04T10:04:01Z","page":"102401","volume":4,"acknowledged_ssus":[{"_id":"ScienComp"}],"main_file_link":[{"url":"https://arxiv.org/abs/1810.02211","open_access":"1"}],"publisher":"American Physical Society","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6978","abstract":[{"text":"In  pipes  and  channels,  the  onset  of  turbulence  is  initially  dominated  by  localizedtransients,  which  lead  to  sustained  turbulence  through  their  collective  dynamics.  In  thepresent work, we study numerically the localized turbulence in pipe flow and elucidate astate space structure that gives rise to transient chaos. Starting from the basin boundaryseparating  laminar  and  turbulent  flow,  we  identify  transverse  homoclinic  orbits,  thepresence of which necessitates a homoclinic tangle and chaos. A direct consequence ofthe homoclinic tangle is the fractal nature of the laminar-turbulent boundary, which wasconjectured in various earlier studies. By mapping the transverse intersections between thestable and unstable manifold of a periodic orbit, we identify the gateways that promote anescape from turbulence.","lang":"eng"}]},{"publication_identifier":{"eissn":["1879-0445"],"issn":["0960-9822"]},"title":"Gut homeostasis: Active migration of intestinal epithelial cells in tissue renewal","issue":"20","isi":1,"doi":"10.1016/j.cub.2019.08.068","day":"21","year":"2019","external_id":{"isi":["000491286200016"],"pmid":["31639357"]},"date_updated":"2023-09-05T12:43:43Z","status":"public","intvolume":"        29","publication_status":"published","citation":{"apa":"Kopf, A., &#38; Sixt, M. K. (2019). Gut homeostasis: Active migration of intestinal epithelial cells in tissue renewal. <i>Current Biology</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cub.2019.08.068\">https://doi.org/10.1016/j.cub.2019.08.068</a>","ama":"Kopf A, Sixt MK. Gut homeostasis: Active migration of intestinal epithelial cells in tissue renewal. <i>Current Biology</i>. 2019;29(20):R1091-R1093. doi:<a href=\"https://doi.org/10.1016/j.cub.2019.08.068\">10.1016/j.cub.2019.08.068</a>","chicago":"Kopf, Aglaja, and Michael K Sixt. “Gut Homeostasis: Active Migration of Intestinal Epithelial Cells in Tissue Renewal.” <i>Current Biology</i>. Cell Press, 2019. <a href=\"https://doi.org/10.1016/j.cub.2019.08.068\">https://doi.org/10.1016/j.cub.2019.08.068</a>.","ieee":"A. Kopf and M. K. Sixt, “Gut homeostasis: Active migration of intestinal epithelial cells in tissue renewal,” <i>Current Biology</i>, vol. 29, no. 20. Cell Press, pp. R1091–R1093, 2019.","mla":"Kopf, Aglaja, and Michael K. Sixt. “Gut Homeostasis: Active Migration of Intestinal Epithelial Cells in Tissue Renewal.” <i>Current Biology</i>, vol. 29, no. 20, Cell Press, 2019, pp. R1091–93, doi:<a href=\"https://doi.org/10.1016/j.cub.2019.08.068\">10.1016/j.cub.2019.08.068</a>.","short":"A. Kopf, M.K. Sixt, Current Biology 29 (2019) R1091–R1093.","ista":"Kopf A, Sixt MK. 2019. Gut homeostasis: Active migration of intestinal epithelial cells in tissue renewal. Current Biology. 29(20), R1091–R1093."},"quality_controlled":"1","department":[{"_id":"MiSi"}],"oa_version":"None","date_published":"2019-10-21T00:00:00Z","article_type":"original","volume":29,"page":"R1091-R1093","date_created":"2019-11-04T15:18:29Z","author":[{"last_name":"Kopf","full_name":"Kopf, Aglaja","first_name":"Aglaja","id":"31DAC7B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2187-6656"},{"orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","first_name":"Michael K","full_name":"Sixt, Michael K"}],"month":"10","language":[{"iso":"eng"}],"type":"journal_article","article_processing_charge":"No","publication":"Current Biology","scopus_import":"1","pmid":1,"_id":"6979","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Cell Press"},{"article_type":"review","date_published":"2019-10-15T00:00:00Z","department":[{"_id":"CaHe"}],"file":[{"creator":"dernst","date_created":"2019-11-04T15:30:08Z","file_id":"6981","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_size":847356,"checksum":"76f7f4e79ab6d850c30017a69726fd85","file_name":"2019_Embo_Petridou.pdf","date_updated":"2020-07-14T12:47:46Z"}],"oa_version":"Published Version","quality_controlled":"1","publication_status":"published","citation":{"ista":"Petridou N, Heisenberg C-PJ. 2019. Tissue rheology in embryonic organization. The EMBO Journal. 38(20), e102497.","ieee":"N. Petridou and C.-P. J. Heisenberg, “Tissue rheology in embryonic organization,” <i>The EMBO Journal</i>, vol. 38, no. 20. EMBO, 2019.","mla":"Petridou, Nicoletta, and Carl-Philipp J. Heisenberg. “Tissue Rheology in Embryonic Organization.” <i>The EMBO Journal</i>, vol. 38, no. 20, e102497, EMBO, 2019, doi:<a href=\"https://doi.org/10.15252/embj.2019102497\">10.15252/embj.2019102497</a>.","short":"N. Petridou, C.-P.J. Heisenberg, The EMBO Journal 38 (2019).","chicago":"Petridou, Nicoletta, and Carl-Philipp J Heisenberg. “Tissue Rheology in Embryonic Organization.” <i>The EMBO Journal</i>. EMBO, 2019. <a href=\"https://doi.org/10.15252/embj.2019102497\">https://doi.org/10.15252/embj.2019102497</a>.","ama":"Petridou N, Heisenberg C-PJ. Tissue rheology in embryonic organization. <i>The EMBO Journal</i>. 2019;38(20). doi:<a href=\"https://doi.org/10.15252/embj.2019102497\">10.15252/embj.2019102497</a>","apa":"Petridou, N., &#38; Heisenberg, C.-P. J. (2019). Tissue rheology in embryonic organization. <i>The EMBO Journal</i>. EMBO. <a href=\"https://doi.org/10.15252/embj.2019102497\">https://doi.org/10.15252/embj.2019102497</a>"},"date_updated":"2023-09-05T13:04:13Z","intvolume":"        38","status":"public","oa":1,"external_id":{"pmid":["31512749"],"isi":["000485561900001"]},"year":"2019","title":"Tissue rheology in embryonic organization","issue":"20","has_accepted_license":"1","publication_identifier":{"issn":["0261-4189"],"eissn":["1460-2075"]},"day":"15","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"doi":"10.15252/embj.2019102497","article_number":"e102497","isi":1,"ec_funded":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","_id":"260F1432-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"742573"},{"_id":"2693FD8C-B435-11E9-9278-68D0E5697425","name":"Tissue material properties in embryonic development","grant_number":"V00736","call_identifier":"FWF"}],"publisher":"EMBO","pmid":1,"_id":"6980","abstract":[{"lang":"eng","text":"Tissue morphogenesis in multicellular organisms is brought about by spatiotemporal coordination of mechanical and chemical signals. Extensive work on how mechanical forces together with the well‐established morphogen signalling pathways can actively shape living tissues has revealed evolutionary conserved mechanochemical features of embryonic development. More recently, attention has been drawn to the description of tissue material properties and how they can influence certain morphogenetic processes. Interestingly, besides the role of tissue material properties in determining how much tissues deform in response to force application, there is increasing theoretical and experimental evidence, suggesting that tissue material properties can abruptly and drastically change in development. These changes resemble phase transitions, pointing at the intriguing possibility that important morphogenetic processes in development, such as symmetry breaking and self‐organization, might be mediated by tissue phase transitions. In this review, we summarize recent findings on the regulation and role of tissue material properties in the context of the developing embryo. We posit that abrupt changes of tissue rheological properties may have important implications in maintaining the balance between robustness and adaptability during embryonic development."}],"publication":"The EMBO Journal","article_processing_charge":"Yes (via OA deal)","scopus_import":"1","type":"journal_article","month":"10","author":[{"last_name":"Petridou","full_name":"Petridou, Nicoletta","first_name":"Nicoletta","id":"2A003F6C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8451-1195"},{"last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"language":[{"iso":"eng"}],"date_created":"2019-11-04T15:24:29Z","file_date_updated":"2020-07-14T12:47:46Z","ddc":["570"],"volume":38},{"title":"Recognizing weak embeddings of graphs","issue":"4","article_number":"50","doi":"10.1145/3344549","day":"01","year":"2019","oa":1,"external_id":{"arxiv":["1709.09209"]},"date_updated":"2023-09-15T12:19:31Z","intvolume":"        15","status":"public","citation":{"ama":"Akitaya H, Fulek R, Tóth C. Recognizing weak embeddings of graphs. <i>ACM Transactions on Algorithms</i>. 2019;15(4). doi:<a href=\"https://doi.org/10.1145/3344549\">10.1145/3344549</a>","apa":"Akitaya, H., Fulek, R., &#38; Tóth, C. (2019). Recognizing weak embeddings of graphs. <i>ACM Transactions on Algorithms</i>. ACM. <a href=\"https://doi.org/10.1145/3344549\">https://doi.org/10.1145/3344549</a>","chicago":"Akitaya, Hugo, Radoslav Fulek, and Csaba Tóth. “Recognizing Weak Embeddings of Graphs.” <i>ACM Transactions on Algorithms</i>. ACM, 2019. <a href=\"https://doi.org/10.1145/3344549\">https://doi.org/10.1145/3344549</a>.","short":"H. Akitaya, R. Fulek, C. Tóth, ACM Transactions on Algorithms 15 (2019).","mla":"Akitaya, Hugo, et al. “Recognizing Weak Embeddings of Graphs.” <i>ACM Transactions on Algorithms</i>, vol. 15, no. 4, 50, ACM, 2019, doi:<a href=\"https://doi.org/10.1145/3344549\">10.1145/3344549</a>.","ieee":"H. Akitaya, R. Fulek, and C. Tóth, “Recognizing weak embeddings of graphs,” <i>ACM Transactions on Algorithms</i>, vol. 15, no. 4. ACM, 2019.","ista":"Akitaya H, Fulek R, Tóth C. 2019. Recognizing weak embeddings of graphs. ACM Transactions on Algorithms. 15(4), 50."},"publication_status":"published","quality_controlled":"1","arxiv":1,"department":[{"_id":"UlWa"}],"oa_version":"Preprint","article_type":"original","date_published":"2019-10-01T00:00:00Z","related_material":{"record":[{"relation":"earlier_version","id":"309","status":"public"}]},"volume":15,"date_created":"2019-11-04T15:45:17Z","type":"journal_article","author":[{"last_name":"Akitaya","first_name":"Hugo","full_name":"Akitaya, Hugo"},{"last_name":"Fulek","full_name":"Fulek, Radoslav","first_name":"Radoslav","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8485-1774"},{"full_name":"Tóth, Csaba","first_name":"Csaba","last_name":"Tóth"}],"month":"10","language":[{"iso":"eng"}],"publication":"ACM Transactions on Algorithms","scopus_import":1,"abstract":[{"text":"We present an efficient algorithm for a problem in the interface between clustering and graph embeddings. An embedding ϕ : G → M of a graph G into a 2-manifold M maps the vertices in V(G) to distinct points and the edges in E(G) to interior-disjoint Jordan arcs between the corresponding vertices. In applications in clustering, cartography, and visualization, nearby vertices and edges are often bundled to the same point or overlapping arcs due to data compression or low resolution. This raises the computational problem of deciding whether a given map ϕ : G → M comes from an embedding. A map ϕ : G → M is a weak embedding if it can be perturbed into an embedding ψ ϵ : G → M with ‖ ϕ − ψ ϵ ‖ < ϵ for every ϵ > 0, where ‖.‖ is the unform norm.\r\nA polynomial-time algorithm for recognizing weak embeddings has recently been found by Fulek and Kynčl. It reduces the problem to solving a system of linear equations over Z2. It runs in O(n2ω)≤ O(n4.75) time, where ω ∈ [2,2.373) is the matrix multiplication exponent and n is the number of vertices and edges of G. We improve the running time to O(n log n). Our algorithm is also conceptually simpler: We perform a sequence of local operations that gradually “untangles” the image ϕ(G) into an embedding ψ(G) or reports that ϕ is not a weak embedding. It combines local constraints on the orientation of subgraphs directly, thereby eliminating the need for solving large systems of linear equations.\r\n","lang":"eng"}],"_id":"6982","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"grant_number":"M02281","call_identifier":"FWF","_id":"261FA626-B435-11E9-9278-68D0E5697425","name":"Eliminating intersections in drawings of graphs"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1709.09209"}],"publisher":"ACM"},{"scopus_import":"1","article_processing_charge":"No","publication":"Frontiers in Immunology","language":[{"iso":"eng"}],"author":[{"first_name":"Réka K","full_name":"Kelemen, Réka K","last_name":"Kelemen","orcid":"0000-0002-8489-9281","id":"48D3F8DE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Rajakaruna, H","first_name":"H","last_name":"Rajakaruna"},{"full_name":"Cockburn, IA","first_name":"IA","last_name":"Cockburn"},{"last_name":"Ganusov","first_name":"VV","full_name":"Ganusov, VV"}],"month":"09","type":"journal_article","date_created":"2019-11-04T15:50:06Z","ddc":["570"],"volume":10,"file_date_updated":"2020-07-14T12:47:46Z","publisher":"Frontiers","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6983","pmid":1,"abstract":[{"lang":"eng","text":"Malaria, a disease caused by parasites of the Plasmodium genus, begins when Plasmodium-infected mosquitoes inject malaria sporozoites while searching for blood. Sporozoites migrate from the skin via blood to the liver, infect hepatocytes, and form liver stages which in mice 48 h later escape into blood and cause clinical malaria. Vaccine-induced activated or memory CD8 T cells are capable of locating and eliminating all liver stages in 48 h, thus preventing the blood-stage disease. However, the rules of how CD8 T cells are able to locate all liver stages within a relatively short time period remains poorly understood. We recently reported formation of clusters consisting of variable numbers of activated CD8 T cells around Plasmodium yoelii (Py)-infected hepatocytes. Using a combination of experimental data and mathematical models we now provide additional insights into mechanisms of formation of these clusters. First, we show that a model in which cluster formation is driven exclusively by T-cell-extrinsic factors, such as variability in “attractiveness” of different liver stages, cannot explain distribution of cluster sizes in different experimental conditions. In contrast, the model in which cluster formation is driven by the positive feedback loop (i.e., larger clusters attract more CD8 T cells) can accurately explain the available data. Second, while both Py-specific CD8 T cells and T cells of irrelevant specificity (non-specific CD8 T cells) are attracted to the clusters, we found no evidence that non-specific CD8 T cells play a role in cluster formation. Third and finally, mathematical modeling suggested that formation of clusters occurs rapidly, within few hours after adoptive transfer of CD8 T cells, thus illustrating high efficiency of CD8 T cells in locating their targets in complex peripheral organs, such as the liver. Taken together, our analysis provides novel insights into and attempts to discriminate between alternative mechanisms driving the formation of clusters of antigen-specific CD8 T cells in the liver."}],"status":"public","intvolume":"        10","date_updated":"2023-08-30T07:18:23Z","external_id":{"pmid":["31616407"],"isi":["000487187000001"]},"oa":1,"year":"2019","isi":1,"article_number":"2153","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"day":"20","doi":"10.3389/fimmu.2019.02153","has_accepted_license":"1","publication_identifier":{"issn":["1664-3224"]},"title":"Clustering of activated CD8 T cells around Malaria-infected hepatocytes is rapid and is driven by antigen-specific cells","date_published":"2019-09-20T00:00:00Z","article_type":"original","file":[{"date_updated":"2020-07-14T12:47:46Z","relation":"main_file","access_level":"open_access","file_size":2083061,"checksum":"68d1708f7aa412544159b498ef17a6b9","file_name":"2019_FrontiersImmonology_Kelemen.pdf","date_created":"2019-11-04T15:54:00Z","file_id":"6984","content_type":"application/pdf","creator":"dernst"}],"oa_version":"Published Version","department":[{"_id":"BeVi"}],"quality_controlled":"1","publication_status":"published","citation":{"chicago":"Kelemen, Réka K, H Rajakaruna, IA Cockburn, and VV Ganusov. “Clustering of Activated CD8 T Cells around Malaria-Infected Hepatocytes Is Rapid and Is Driven by Antigen-Specific Cells.” <i>Frontiers in Immunology</i>. Frontiers, 2019. <a href=\"https://doi.org/10.3389/fimmu.2019.02153\">https://doi.org/10.3389/fimmu.2019.02153</a>.","apa":"Kelemen, R. K., Rajakaruna, H., Cockburn, I., &#38; Ganusov, V. (2019). Clustering of activated CD8 T cells around Malaria-infected hepatocytes is rapid and is driven by antigen-specific cells. <i>Frontiers in Immunology</i>. Frontiers. <a href=\"https://doi.org/10.3389/fimmu.2019.02153\">https://doi.org/10.3389/fimmu.2019.02153</a>","ama":"Kelemen RK, Rajakaruna H, Cockburn I, Ganusov V. Clustering of activated CD8 T cells around Malaria-infected hepatocytes is rapid and is driven by antigen-specific cells. <i>Frontiers in Immunology</i>. 2019;10. doi:<a href=\"https://doi.org/10.3389/fimmu.2019.02153\">10.3389/fimmu.2019.02153</a>","ista":"Kelemen RK, Rajakaruna H, Cockburn I, Ganusov V. 2019. Clustering of activated CD8 T cells around Malaria-infected hepatocytes is rapid and is driven by antigen-specific cells. Frontiers in Immunology. 10, 2153.","mla":"Kelemen, Réka K., et al. “Clustering of Activated CD8 T Cells around Malaria-Infected Hepatocytes Is Rapid and Is Driven by Antigen-Specific Cells.” <i>Frontiers in Immunology</i>, vol. 10, 2153, Frontiers, 2019, doi:<a href=\"https://doi.org/10.3389/fimmu.2019.02153\">10.3389/fimmu.2019.02153</a>.","short":"R.K. Kelemen, H. Rajakaruna, I. Cockburn, V. Ganusov, Frontiers in Immunology 10 (2019).","ieee":"R. K. Kelemen, H. Rajakaruna, I. Cockburn, and V. Ganusov, “Clustering of activated CD8 T cells around Malaria-infected hepatocytes is rapid and is driven by antigen-specific cells,” <i>Frontiers in Immunology</i>, vol. 10. Frontiers, 2019."}},{"oa":1,"conference":{"start_date":"2019-07-14","end_date":"2019-07-19","name":"IJCNN: International Joint Conference on Neural Networks","location":"Budapest, Hungary"},"month":"09","author":[{"last_name":"Hasani","first_name":"Ramin","full_name":"Hasani, Ramin"},{"first_name":"Alexander","full_name":"Amini, Alexander","last_name":"Amini"},{"last_name":"Lechner","first_name":"Mathias","full_name":"Lechner, Mathias","id":"3DC22916-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Felix","full_name":"Naser, Felix","last_name":"Naser"},{"full_name":"Grosu, Radu","first_name":"Radu","last_name":"Grosu"},{"first_name":"Daniela","full_name":"Rus, Daniela","last_name":"Rus"}],"language":[{"iso":"eng"}],"type":"conference","external_id":{"arxiv":["1809.03864"]},"publication":"Proceedings of the International Joint Conference on Neural Networks","date_updated":"2021-01-12T08:11:19Z","status":"public","scopus_import":1,"title":"Response characterization for auditing cell dynamics in long short-term memory networks","publication_identifier":{"isbn":["9781728119854"]},"doi":"10.1109/ijcnn.2019.8851954","day":"30","article_number":"8851954","year":"2019","date_created":"2019-11-04T15:59:58Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"ToHe"}],"publisher":"IEEE","oa_version":"Preprint","main_file_link":[{"url":"https://arxiv.org/abs/1809.03864","open_access":"1"}],"date_published":"2019-09-30T00:00:00Z","citation":{"chicago":"Hasani, Ramin, Alexander Amini, Mathias Lechner, Felix Naser, Radu Grosu, and Daniela Rus. “Response Characterization for Auditing Cell Dynamics in Long Short-Term Memory Networks.” In <i>Proceedings of the International Joint Conference on Neural Networks</i>. IEEE, 2019. <a href=\"https://doi.org/10.1109/ijcnn.2019.8851954\">https://doi.org/10.1109/ijcnn.2019.8851954</a>.","apa":"Hasani, R., Amini, A., Lechner, M., Naser, F., Grosu, R., &#38; Rus, D. (2019). Response characterization for auditing cell dynamics in long short-term memory networks. In <i>Proceedings of the International Joint Conference on Neural Networks</i>. Budapest, Hungary: IEEE. <a href=\"https://doi.org/10.1109/ijcnn.2019.8851954\">https://doi.org/10.1109/ijcnn.2019.8851954</a>","ama":"Hasani R, Amini A, Lechner M, Naser F, Grosu R, Rus D. Response characterization for auditing cell dynamics in long short-term memory networks. In: <i>Proceedings of the International Joint Conference on Neural Networks</i>. IEEE; 2019. doi:<a href=\"https://doi.org/10.1109/ijcnn.2019.8851954\">10.1109/ijcnn.2019.8851954</a>","ista":"Hasani R, Amini A, Lechner M, Naser F, Grosu R, Rus D. 2019. Response characterization for auditing cell dynamics in long short-term memory networks. Proceedings of the International Joint Conference on Neural Networks. IJCNN: International Joint Conference on Neural Networks, 8851954.","short":"R. Hasani, A. Amini, M. Lechner, F. Naser, R. Grosu, D. Rus, in:, Proceedings of the International Joint Conference on Neural Networks, IEEE, 2019.","mla":"Hasani, Ramin, et al. “Response Characterization for Auditing Cell Dynamics in Long Short-Term Memory Networks.” <i>Proceedings of the International Joint Conference on Neural Networks</i>, 8851954, IEEE, 2019, doi:<a href=\"https://doi.org/10.1109/ijcnn.2019.8851954\">10.1109/ijcnn.2019.8851954</a>.","ieee":"R. Hasani, A. Amini, M. Lechner, F. Naser, R. Grosu, and D. Rus, “Response characterization for auditing cell dynamics in long short-term memory networks,” in <i>Proceedings of the International Joint Conference on Neural Networks</i>, Budapest, Hungary, 2019."},"publication_status":"published","abstract":[{"lang":"eng","text":"In this paper, we introduce a novel method to interpret recurrent neural networks (RNNs), particularly long short-term memory networks (LSTMs) at the cellular level. We propose a systematic pipeline for interpreting individual hidden state dynamics within the network using response characterization methods. The ranked contribution of individual cells to the network's output is computed by analyzing a set of interpretable metrics of their decoupled step and sinusoidal responses. As a result, our method is able to uniquely identify neurons with insightful dynamics, quantify relationships between dynamical properties and test accuracy through ablation analysis, and interpret the impact of network capacity on a network's dynamical distribution. Finally, we demonstrate the generalizability and scalability of our method by evaluating a series of different benchmark sequential datasets."}],"arxiv":1,"quality_controlled":"1","_id":"6985"}]