[{"scopus_import":"1","editor":[{"first_name":"Franck","last_name":"Cassez","full_name":"Cassez, Franck"},{"first_name":"Jean-François","last_name":"Raskin","full_name":"Raskin, Jean-François"}],"doi":"10.1007/978-3-319-11936-6_17","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publist_id":"5045","citation":{"mla":"Komárková, Zuzana, and Jan Kretinsky. “Rabinizer 3: Safraless Translation of Ltl to Small Deterministic Automata.” <i>Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>, edited by Franck Cassez and Jean-François Raskin, vol. 8837, Springer, 2014, pp. 235–41, doi:<a href=\"https://doi.org/10.1007/978-3-319-11936-6_17\">10.1007/978-3-319-11936-6_17</a>.","apa":"Komárková, Z., &#38; Kretinsky, J. (2014). Rabinizer 3: Safraless translation of ltl to small deterministic automata. In F. Cassez &#38; J.-F. Raskin (Eds.), <i>Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i> (Vol. 8837, pp. 235–241). Sydney, Australia: Springer. <a href=\"https://doi.org/10.1007/978-3-319-11936-6_17\">https://doi.org/10.1007/978-3-319-11936-6_17</a>","ama":"Komárková Z, Kretinsky J. Rabinizer 3: Safraless translation of ltl to small deterministic automata. In: Cassez F, Raskin J-F, eds. <i>Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>. Vol 8837. Springer; 2014:235-241. doi:<a href=\"https://doi.org/10.1007/978-3-319-11936-6_17\">10.1007/978-3-319-11936-6_17</a>","chicago":"Komárková, Zuzana, and Jan Kretinsky. “Rabinizer 3: Safraless Translation of Ltl to Small Deterministic Automata.” In <i>Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>, edited by Franck Cassez and Jean-François Raskin, 8837:235–41. Springer, 2014. <a href=\"https://doi.org/10.1007/978-3-319-11936-6_17\">https://doi.org/10.1007/978-3-319-11936-6_17</a>.","short":"Z. Komárková, J. Kretinsky, in:, F. Cassez, J.-F. Raskin (Eds.), Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Springer, 2014, pp. 235–241.","ista":"Komárková Z, Kretinsky J. 2014. Rabinizer 3: Safraless translation of ltl to small deterministic automata. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). ATVA: Automated Technology for Verification and Analysis, LNCS, vol. 8837, 235–241.","ieee":"Z. Komárková and J. Kretinsky, “Rabinizer 3: Safraless translation of ltl to small deterministic automata,” in <i>Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>, Sydney, Australia, 2014, vol. 8837, pp. 235–241."},"quality_controlled":"1","volume":8837,"status":"public","page":"235 - 241","date_published":"2014-01-01T00:00:00Z","month":"01","publication":"Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)","date_updated":"2024-10-21T06:02:50Z","type":"conference","department":[{"_id":"ToHe"}],"acknowledgement":"Sponsor: P202/12/G061; GACR; Czech Science Foundation\r\n\r\n","date_created":"2018-12-11T11:55:17Z","day":"01","language":[{"iso":"eng"}],"author":[{"full_name":"Komárková, Zuzana","first_name":"Zuzana","last_name":"Komárková"},{"first_name":"Jan","last_name":"Kretinsky","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8122-2881","full_name":"Kretinsky, Jan"}],"alternative_title":["LNCS"],"project":[{"call_identifier":"FP7","grant_number":"267989","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"_id":"25F5A88A-B435-11E9-9278-68D0E5697425","name":"Moderne Concurrency Paradigms","call_identifier":"FWF","grant_number":"S11402-N23"}],"publisher":"Springer","intvolume":"      8837","ec_funded":1,"publication_status":"published","_id":"2026","title":"Rabinizer 3: Safraless translation of ltl to small deterministic automata","oa_version":"None","year":"2014","abstract":[{"text":"We present a tool for translating LTL formulae into deterministic ω-automata. It is the first tool that covers the whole LTL that does not use Safra’s determinization or any of its variants. This leads to smaller automata. There are several outputs of the tool: firstly, deterministic Rabin automata, which are the standard input for probabilistic model checking, e.g. for the probabilistic model-checker PRISM; secondly, deterministic generalized Rabin automata, which can also be used for probabilistic model checking and are sometimes by orders of magnitude smaller. We also link our tool to PRISM and show that this leads to a significant speed-up of probabilistic LTL model checking, especially with the generalized Rabin automata.","lang":"eng"}],"conference":{"start_date":"2014-11-03","location":"Sydney, Australia","name":"ATVA: Automated Technology for Verification and Analysis","end_date":"2014-11-07"}},{"article_processing_charge":"No","isi":1,"scopus_import":"1","publist_id":"5044","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","doi":"10.1209/0295-5075/108/20003","volume":108,"quality_controlled":"1","citation":{"ieee":"M. Correggi, A. Giuliani, and R. Seiringer, “Validity of spin-wave theory for the quantum Heisenberg model,” <i>EPL</i>, vol. 108, no. 2. IOP Publishing, 2014.","short":"M. Correggi, A. Giuliani, R. Seiringer, EPL 108 (2014).","ista":"Correggi M, Giuliani A, Seiringer R. 2014. Validity of spin-wave theory for the quantum Heisenberg model. EPL. 108(2), 20003.","chicago":"Correggi, Michele, Alessandro Giuliani, and Robert Seiringer. “Validity of Spin-Wave Theory for the Quantum Heisenberg Model.” <i>EPL</i>. IOP Publishing, 2014. <a href=\"https://doi.org/10.1209/0295-5075/108/20003\">https://doi.org/10.1209/0295-5075/108/20003</a>.","ama":"Correggi M, Giuliani A, Seiringer R. Validity of spin-wave theory for the quantum Heisenberg model. <i>EPL</i>. 2014;108(2). doi:<a href=\"https://doi.org/10.1209/0295-5075/108/20003\">10.1209/0295-5075/108/20003</a>","apa":"Correggi, M., Giuliani, A., &#38; Seiringer, R. (2014). Validity of spin-wave theory for the quantum Heisenberg model. <i>EPL</i>. IOP Publishing. <a href=\"https://doi.org/10.1209/0295-5075/108/20003\">https://doi.org/10.1209/0295-5075/108/20003</a>","mla":"Correggi, Michele, et al. “Validity of Spin-Wave Theory for the Quantum Heisenberg Model.” <i>EPL</i>, vol. 108, no. 2, 20003, IOP Publishing, 2014, doi:<a href=\"https://doi.org/10.1209/0295-5075/108/20003\">10.1209/0295-5075/108/20003</a>."},"publication":"EPL","date_published":"2014-10-13T00:00:00Z","month":"10","status":"public","department":[{"_id":"RoSe"}],"issue":"2","type":"journal_article","date_updated":"2025-09-29T11:55:55Z","acknowledgement":"239694; ERC; European Research Council","author":[{"last_name":"Correggi","first_name":"Michele","full_name":"Correggi, Michele"},{"last_name":"Giuliani","first_name":"Alessandro","full_name":"Giuliani, Alessandro"},{"orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","first_name":"Robert","last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"}],"language":[{"iso":"eng"}],"date_created":"2018-12-11T11:55:18Z","day":"13","external_id":{"arxiv":["1404.4717"],"isi":["000344913300003"]},"publisher":"IOP Publishing","article_number":"20003","oa":1,"intvolume":"       108","oa_version":"Submitted Version","title":"Validity of spin-wave theory for the quantum Heisenberg model","publication_status":"published","_id":"2029","main_file_link":[{"url":"http://arxiv.org/abs/1404.4717","open_access":"1"}],"abstract":[{"text":"Spin-wave theory is a key ingredient in our comprehension of quantum spin systems, and is used successfully for understanding a wide range of magnetic phenomena, including magnon condensation and stability of patterns in dipolar systems. Nevertheless, several decades of research failed to establish the validity of spin-wave theory rigorously, even for the simplest models of quantum spins. A rigorous justification of the method for the three-dimensional quantum Heisenberg ferromagnet at low temperatures is presented here. We derive sharp bounds on its free energy by combining a bosonic formulation of the model introduced by Holstein and Primakoff with probabilistic estimates and operator inequalities.","lang":"eng"}],"year":"2014","arxiv":1},{"file":[{"relation":"main_file","date_created":"2018-12-12T10:14:41Z","access_level":"open_access","file_name":"IST-2016-421-v1+1_e04057.full.pdf","checksum":"c240f915450d4ebe8f95043a2a8c7b1a","creator":"system","date_updated":"2020-07-14T12:45:26Z","file_id":"5094","content_type":"application/pdf","file_size":2239563}],"article_processing_charge":"No","isi":1,"scopus_import":"1","publist_id":"5041","doi":"10.7554/eLife.04057","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","quality_controlled":"1","citation":{"chicago":"Arai, itaru, and Peter M Jonas. “Nanodomain Coupling Explains Ca^2+ Independence of Transmitter Release Time Course at a Fast Central Synapse.” <i>ELife</i>. eLife Sciences Publications, 2014. <a href=\"https://doi.org/10.7554/eLife.04057\">https://doi.org/10.7554/eLife.04057</a>.","mla":"Arai, itaru, and Peter M. Jonas. “Nanodomain Coupling Explains Ca^2+ Independence of Transmitter Release Time Course at a Fast Central Synapse.” <i>ELife</i>, vol. 3, eLife Sciences Publications, 2014, doi:<a href=\"https://doi.org/10.7554/eLife.04057\">10.7554/eLife.04057</a>.","ama":"Arai  itaru, Jonas PM. Nanodomain coupling explains Ca^2+ independence of transmitter release time course at a fast central synapse. <i>eLife</i>. 2014;3. doi:<a href=\"https://doi.org/10.7554/eLife.04057\">10.7554/eLife.04057</a>","apa":"Arai,  itaru, &#38; Jonas, P. M. (2014). Nanodomain coupling explains Ca^2+ independence of transmitter release time course at a fast central synapse. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.04057\">https://doi.org/10.7554/eLife.04057</a>","ieee":"itaru Arai and P. M. Jonas, “Nanodomain coupling explains Ca^2+ independence of transmitter release time course at a fast central synapse,” <i>eLife</i>, vol. 3. eLife Sciences Publications, 2014.","short":"itaru Arai, P.M. Jonas, ELife 3 (2014).","ista":"Arai  itaru, Jonas PM. 2014. Nanodomain coupling explains Ca^2+ independence of transmitter release time course at a fast central synapse. eLife. 3."},"volume":3,"ddc":["570"],"month":"12","date_published":"2014-12-09T00:00:00Z","publication":"eLife","status":"public","type":"journal_article","department":[{"_id":"PeJo"}],"has_accepted_license":"1","date_updated":"2025-09-29T11:55:24Z","corr_author":"1","author":[{"full_name":"Arai, Itaru","first_name":"Itaru","last_name":"Arai","id":"32A73F6C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M"}],"day":"09","language":[{"iso":"eng"}],"date_created":"2018-12-11T11:55:19Z","file_date_updated":"2020-07-14T12:45:26Z","external_id":{"isi":["000346170300007"]},"project":[{"call_identifier":"FWF","grant_number":"P24909-B24","_id":"25C26B1E-B435-11E9-9278-68D0E5697425","name":"Mechanisms of transmitter release at GABAergic synapses"},{"name":"Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons","_id":"25C0F108-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"268548"}],"publisher":"eLife Sciences Publications","intvolume":"         3","oa":1,"ec_funded":1,"oa_version":"Submitted Version","_id":"2031","publication_status":"published","title":"Nanodomain coupling explains Ca^2+ independence of transmitter release time course at a fast central synapse","pubrep_id":"421","year":"2014","abstract":[{"text":"A puzzling property of synaptic transmission, originally established at the neuromuscular junction, is that the time course of transmitter release is independent of the extracellular Ca2+ concentration ([Ca2+]o), whereas the rate of release is highly [Ca2+]o-dependent. Here, we examine the time course of release at inhibitory basket cell-Purkinje cell synapses and show that it is independent of [Ca2+]o. Modeling of Ca2+-dependent transmitter release suggests that the invariant time course of release critically depends on tight coupling between Ca2+ channels and release sensors. Experiments with exogenous Ca2+ chelators reveal that channel-sensor coupling at basket cell-Purkinje cell synapses is very tight, with a mean distance of 10–20 nm. Thus, tight channel-sensor coupling provides a mechanistic explanation for the apparent [Ca2+]o independence of the time course of release.","lang":"eng"}]},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.4161/23723548.2014.964045","publist_id":"5040","volume":1,"quality_controlled":"1","citation":{"ista":"Inglés Prieto Á, Gschaider-Reichhart E, Schelch K, Janovjak HL, Grusch M. 2014. The optogenetic promise for oncology: Episode I. Molecular and Cellular Oncology. 1(4), e964045.","short":"Á. Inglés Prieto, E. Gschaider-Reichhart, K. Schelch, H.L. Janovjak, M. Grusch, Molecular and Cellular Oncology 1 (2014).","ieee":"Á. Inglés Prieto, E. Gschaider-Reichhart, K. Schelch, H. L. Janovjak, and M. Grusch, “The optogenetic promise for oncology: Episode I,” <i>Molecular and Cellular Oncology</i>, vol. 1, no. 4. Taylor &#38; Francis, 2014.","ama":"Inglés Prieto Á, Gschaider-Reichhart E, Schelch K, Janovjak HL, Grusch M. The optogenetic promise for oncology: Episode I. <i>Molecular and Cellular Oncology</i>. 2014;1(4). doi:<a href=\"https://doi.org/10.4161/23723548.2014.964045\">10.4161/23723548.2014.964045</a>","apa":"Inglés Prieto, Á., Gschaider-Reichhart, E., Schelch, K., Janovjak, H. L., &#38; Grusch, M. (2014). The optogenetic promise for oncology: Episode I. <i>Molecular and Cellular Oncology</i>. Taylor &#38; Francis. <a href=\"https://doi.org/10.4161/23723548.2014.964045\">https://doi.org/10.4161/23723548.2014.964045</a>","mla":"Inglés Prieto, Álvaro, et al. “The Optogenetic Promise for Oncology: Episode I.” <i>Molecular and Cellular Oncology</i>, vol. 1, no. 4, e964045, Taylor &#38; Francis, 2014, doi:<a href=\"https://doi.org/10.4161/23723548.2014.964045\">10.4161/23723548.2014.964045</a>.","chicago":"Inglés Prieto, Álvaro, Eva Gschaider-Reichhart, Karin Schelch, Harald L Janovjak, and Michael Grusch. “The Optogenetic Promise for Oncology: Episode I.” <i>Molecular and Cellular Oncology</i>. Taylor &#38; Francis, 2014. <a href=\"https://doi.org/10.4161/23723548.2014.964045\">https://doi.org/10.4161/23723548.2014.964045</a>."},"article_processing_charge":"Yes","file":[{"checksum":"44e17ad40577ab46eb602e88a8b0b8fd","creator":"kschuh","date_updated":"2020-07-14T12:45:26Z","file_id":"6464","file_size":1765933,"content_type":"application/pdf","relation":"main_file","access_level":"open_access","date_created":"2019-05-16T13:39:11Z","file_name":"2014_Taylor_Alvaro.pdf"}],"scopus_import":"1","article_type":"original","OA_place":"publisher","file_date_updated":"2020-07-14T12:45:26Z","language":[{"iso":"eng"}],"date_created":"2018-12-11T11:55:19Z","day":"31","author":[{"last_name":"Inglés Prieto","id":"2A9DB292-F248-11E8-B48F-1D18A9856A87","first_name":"Álvaro","full_name":"Inglés Prieto, Álvaro","orcid":"0000-0002-5409-8571"},{"full_name":"Gschaider-Reichhart, Eva","orcid":"0000-0002-7218-7738","id":"3FEE232A-F248-11E8-B48F-1D18A9856A87","last_name":"Gschaider-Reichhart","first_name":"Eva"},{"first_name":"Karin","last_name":"Schelch","full_name":"Schelch, Karin"},{"first_name":"Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","last_name":"Janovjak","orcid":"0000-0002-8023-9315","full_name":"Janovjak, Harald L"},{"full_name":"Grusch, Michael","first_name":"Michael","last_name":"Grusch"}],"status":"public","publication":"Molecular and Cellular Oncology","date_published":"2014-12-31T00:00:00Z","month":"12","ddc":["570"],"date_updated":"2025-05-20T07:37:40Z","department":[{"_id":"HaJa"}],"has_accepted_license":"1","type":"journal_article","issue":"4","publisher":"Taylor & Francis","article_number":"e964045","license":"https://creativecommons.org/licenses/by-nc/3.0/","publication_identifier":{"eissn":["2372-3556"]},"external_id":{"pmid":["27308360"]},"tmp":{"short":"CC BY-NC (3.0)","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 3.0 Unported (CC BY-NC 3.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/3.0/legalcode"},"abstract":[{"lang":"eng","text":"As light-based control of fundamental signaling pathways is becoming a reality, the field of optogenetics is rapidly moving beyond neuroscience. We have recently developed receptor tyrosine kinases that are activated by light and control cell proliferation, epithelial–mesenchymal transition, and angiogenic sprouting—cell behaviors central to cancer progression."}],"year":"2014","OA_type":"gold","DOAJ_listed":"1","pmid":1,"oa":1,"intvolume":"         1","title":"The optogenetic promise for oncology: Episode I","_id":"2032","publication_status":"published","oa_version":"Published Version"},{"status":"public","page":"837-845","month":"12","date_published":"2014-12-08T00:00:00Z","publication":"Advances in Neural Information Processing Systems","date_updated":"2025-06-03T11:45:29Z","issue":"January","type":"conference","department":[{"_id":"ChLa"}],"language":[{"iso":"eng"}],"date_created":"2018-12-11T11:55:20Z","day":"08","author":[{"full_name":"Hernandez Lobato, Daniel","first_name":"Daniel","last_name":"Hernandez Lobato"},{"orcid":"0000-0003-0192-9308","full_name":"Sharmanska, Viktoriia","first_name":"Viktoriia","last_name":"Sharmanska","id":"2EA6D09E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Kristian","last_name":"Kersting","full_name":"Kersting, Kristian"},{"first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph"},{"first_name":"Novi","last_name":"Quadrianto","full_name":"Quadrianto, Novi"}],"article_processing_charge":"No","scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"5038","quality_controlled":"1","citation":{"chicago":"Hernandez Lobato, Daniel, Viktoriia Sharmanska, Kristian Kersting, Christoph Lampert, and Novi Quadrianto. “Mind the Nuisance: Gaussian Process Classification Using Privileged Noise.” In <i>Advances in Neural Information Processing Systems</i>, 1:837–45. Neural Information Processing Systems Foundation, 2014.","mla":"Hernandez Lobato, Daniel, et al. “Mind the Nuisance: Gaussian Process Classification Using Privileged Noise.” <i>Advances in Neural Information Processing Systems</i>, vol. 1, no. January, Neural Information Processing Systems Foundation, 2014, pp. 837–45.","ama":"Hernandez Lobato D, Sharmanska V, Kersting K, Lampert C, Quadrianto N. Mind the nuisance: Gaussian process classification using privileged noise. In: <i>Advances in Neural Information Processing Systems</i>. Vol 1. Neural Information Processing Systems Foundation; 2014:837-845.","apa":"Hernandez Lobato, D., Sharmanska, V., Kersting, K., Lampert, C., &#38; Quadrianto, N. (2014). Mind the nuisance: Gaussian process classification using privileged noise. In <i>Advances in Neural Information Processing Systems</i> (Vol. 1, pp. 837–845). Montreal, Canada: Neural Information Processing Systems Foundation.","ieee":"D. Hernandez Lobato, V. Sharmanska, K. Kersting, C. Lampert, and N. Quadrianto, “Mind the nuisance: Gaussian process classification using privileged noise,” in <i>Advances in Neural Information Processing Systems</i>, Montreal, Canada, 2014, vol. 1, no. January, pp. 837–845.","ista":"Hernandez Lobato D, Sharmanska V, Kersting K, Lampert C, Quadrianto N. 2014. Mind the nuisance: Gaussian process classification using privileged noise. Advances in Neural Information Processing Systems. NIPS: Neural Information Processing Systems vol. 1, 837–845.","short":"D. Hernandez Lobato, V. Sharmanska, K. Kersting, C. Lampert, N. Quadrianto, in:, Advances in Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2014, pp. 837–845."},"volume":1,"intvolume":"         1","oa":1,"_id":"2033","publication_status":"published","title":"Mind the nuisance: Gaussian process classification using privileged noise","oa_version":"Submitted Version","year":"2014","abstract":[{"lang":"eng","text":"The learning with privileged information setting has recently attracted a lot of attention within the machine learning community, as it allows the integration of additional knowledge into the training process of a classifier, even when this comes in the form of a data modality that is not available at test time. Here, we show that privileged information can naturally be treated as noise in the latent function of a Gaussian process classifier (GPC). That is, in contrast to the standard GPC setting, the latent function is not just a nuisance but a feature: it becomes a natural measure of confidence about the training data by modulating the slope of the GPC probit likelihood function. Extensive experiments on public datasets show that the proposed GPC method using privileged noise, called GPC+, improves over a standard GPC without privileged knowledge, and also over the current state-of-the-art SVM-based method, SVM+. Moreover, we show that advanced neural networks and deep learning methods can be compressed as privileged information."}],"main_file_link":[{"open_access":"1","url":"https://papers.nips.cc/paper/5373-mind-the-nuisance-gaussian-process-classification-using-privileged-noise"}],"conference":{"start_date":"2014-12-08","location":"Montreal, Canada","name":"NIPS: Neural Information Processing Systems","end_date":"2014-12-13"},"publisher":"Neural Information Processing Systems Foundation"},{"author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"orcid":"0000-0002-8943-0722","full_name":"Pavlogiannis, Andreas","first_name":"Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","last_name":"Pavlogiannis"},{"first_name":"Ben","last_name":"Adlam","full_name":"Adlam, Ben"},{"last_name":"Nowak","first_name":"Martin","full_name":"Nowak, Martin"}],"date_created":"2018-12-11T11:55:22Z","language":[{"iso":"eng"}],"day":"11","file_date_updated":"2020-07-14T12:45:26Z","related_material":{"record":[{"relation":"research_data","status":"public","id":"9739"}]},"corr_author":"1","issue":"9","type":"journal_article","has_accepted_license":"1","department":[{"_id":"KrCh"}],"date_updated":"2025-09-29T11:53:46Z","date_published":"2014-09-11T00:00:00Z","ddc":["510"],"month":"09","publication":"PLoS Computational Biology","status":"public","quality_controlled":"1","citation":{"short":"K. Chatterjee, A. Pavlogiannis, B. Adlam, M. Nowak, PLoS Computational Biology 10 (2014).","ista":"Chatterjee K, Pavlogiannis A, Adlam B, Nowak M. 2014. The time scale of evolutionary innovation. PLoS Computational Biology. 10(9), 7p.","ieee":"K. Chatterjee, A. Pavlogiannis, B. Adlam, and M. Nowak, “The time scale of evolutionary innovation,” <i>PLoS Computational Biology</i>, vol. 10, no. 9. Public Library of Science, 2014.","mla":"Chatterjee, Krishnendu, et al. “The Time Scale of Evolutionary Innovation.” <i>PLoS Computational Biology</i>, vol. 10, no. 9, 7p, Public Library of Science, 2014, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1003818\">10.1371/journal.pcbi.1003818</a>.","apa":"Chatterjee, K., Pavlogiannis, A., Adlam, B., &#38; Nowak, M. (2014). The time scale of evolutionary innovation. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1003818\">https://doi.org/10.1371/journal.pcbi.1003818</a>","ama":"Chatterjee K, Pavlogiannis A, Adlam B, Nowak M. The time scale of evolutionary innovation. <i>PLoS Computational Biology</i>. 2014;10(9). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1003818\">10.1371/journal.pcbi.1003818</a>","chicago":"Chatterjee, Krishnendu, Andreas Pavlogiannis, Ben Adlam, and Martin Nowak. “The Time Scale of Evolutionary Innovation.” <i>PLoS Computational Biology</i>. Public Library of Science, 2014. <a href=\"https://doi.org/10.1371/journal.pcbi.1003818\">https://doi.org/10.1371/journal.pcbi.1003818</a>."},"volume":10,"publist_id":"5012","doi":"10.1371/journal.pcbi.1003818","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","scopus_import":"1","file":[{"content_type":"application/pdf","file_size":1399093,"file_id":"4890","date_updated":"2020-07-14T12:45:26Z","checksum":"712d4c5787ddf97809cfc962507f0738","creator":"system","file_name":"IST-2016-440-v1+1_journal.pcbi.1003818.pdf","relation":"main_file","date_created":"2018-12-12T10:11:35Z","access_level":"open_access"}],"article_processing_charge":"No","isi":1,"pubrep_id":"440","year":"2014","abstract":[{"lang":"eng","text":"A fundamental question in biology is the following: what is the time scale that is needed for evolutionary innovations? There are many results that characterize single steps in terms of the fixation time of new mutants arising in populations of certain size and structure. But here we ask a different question, which is concerned with the much longer time scale of evolutionary trajectories: how long does it take for a population exploring a fitness landscape to find target sequences that encode new biological functions? Our key variable is the length, (Formula presented.) of the genetic sequence that undergoes adaptation. In computer science there is a crucial distinction between problems that require algorithms which take polynomial or exponential time. The latter are considered to be intractable. Here we develop a theoretical approach that allows us to estimate the time of evolution as function of (Formula presented.) We show that adaptation on many fitness landscapes takes time that is exponential in (Formula presented.) even if there are broad selection gradients and many targets uniformly distributed in sequence space. These negative results lead us to search for specific mechanisms that allow evolution to work on polynomial time scales. We study a regeneration process and show that it enables evolution to work in polynomial time."}],"oa_version":"Published Version","publication_status":"published","_id":"2039","title":"The time scale of evolutionary innovation","intvolume":"        10","oa":1,"ec_funded":1,"article_number":"7p","publisher":"Public Library of Science","project":[{"grant_number":"P 23499-N23","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"call_identifier":"FWF","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory"},{"grant_number":"279307","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"external_id":{"isi":["000343011700018"]}},{"_id":"2040","publication_status":"published","title":"Coordination of progenitor specification and growth in mouse and chick spinal cord","oa_version":"Submitted Version","intvolume":"       345","oa":1,"year":"2014","abstract":[{"lang":"eng","text":"Development requires tissue growth as well as cell diversification. To address how these processes are coordinated, we analyzed the development of molecularly distinct domains of neural progenitors in the mouse and chick neural tube. We show that during development, these domains undergo changes in size that do not scale with changes in overall tissue size. Our data show that domain proportions are first established by opposing morphogen gradients and subsequently controlled by domain-specific regulation of differentiation rate but not differences in proliferation rate. Regulation of differentiation rate is key to maintaining domain proportions while accommodating both intra- and interspecies variations in size. Thus, the sequential control of progenitor specification and differentiation elaborates pattern without requiring that signaling gradients grow as tissues expand. "}],"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4228193/","open_access":"1"}],"external_id":{"isi":["000342164500032"]},"article_number":"1254927","publisher":"American Association for the Advancement of Science","date_updated":"2025-09-29T11:53:14Z","type":"journal_article","issue":"6204","department":[{"_id":"ToBo"}],"status":"public","date_published":"2014-09-26T00:00:00Z","month":"09","publication":"Science","day":"26","date_created":"2018-12-11T11:55:22Z","language":[{"iso":"eng"}],"author":[{"first_name":"Anna","last_name":"Kicheva","full_name":"Kicheva, Anna"},{"full_name":"Bollenbach, Mark Tobias","orcid":"0000-0003-4398-476X","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","last_name":"Bollenbach","first_name":"Mark Tobias"},{"full_name":"Ribeiro, Ana","first_name":"Ana","last_name":"Ribeiro"},{"full_name":"Pérez Valle, Helena","first_name":"Helena","last_name":"Pérez Valle"},{"last_name":"Lovell Badge","first_name":"Robin","full_name":"Lovell Badge, Robin"},{"first_name":"Vasso","last_name":"Episkopou","full_name":"Episkopou, Vasso"},{"first_name":"James","last_name":"Briscoe","full_name":"Briscoe, James"}],"scopus_import":"1","isi":1,"article_processing_charge":"No","quality_controlled":"1","citation":{"ista":"Kicheva A, Bollenbach MT, Ribeiro A, Pérez Valle H, Lovell Badge R, Episkopou V, Briscoe J. 2014. Coordination of progenitor specification and growth in mouse and chick spinal cord. Science. 345(6204), 1254927.","short":"A. Kicheva, M.T. Bollenbach, A. Ribeiro, H. Pérez Valle, R. Lovell Badge, V. Episkopou, J. Briscoe, Science 345 (2014).","ieee":"A. Kicheva <i>et al.</i>, “Coordination of progenitor specification and growth in mouse and chick spinal cord,” <i>Science</i>, vol. 345, no. 6204. American Association for the Advancement of Science, 2014.","mla":"Kicheva, Anna, et al. “Coordination of Progenitor Specification and Growth in Mouse and Chick Spinal Cord.” <i>Science</i>, vol. 345, no. 6204, 1254927, American Association for the Advancement of Science, 2014, doi:<a href=\"https://doi.org/10.1126/science.1254927\">10.1126/science.1254927</a>.","ama":"Kicheva A, Bollenbach MT, Ribeiro A, et al. Coordination of progenitor specification and growth in mouse and chick spinal cord. <i>Science</i>. 2014;345(6204). doi:<a href=\"https://doi.org/10.1126/science.1254927\">10.1126/science.1254927</a>","apa":"Kicheva, A., Bollenbach, M. T., Ribeiro, A., Pérez Valle, H., Lovell Badge, R., Episkopou, V., &#38; Briscoe, J. (2014). Coordination of progenitor specification and growth in mouse and chick spinal cord. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.1254927\">https://doi.org/10.1126/science.1254927</a>","chicago":"Kicheva, Anna, Mark Tobias Bollenbach, Ana Ribeiro, Helena Pérez Valle, Robin Lovell Badge, Vasso Episkopou, and James Briscoe. “Coordination of Progenitor Specification and Growth in Mouse and Chick Spinal Cord.” <i>Science</i>. American Association for the Advancement of Science, 2014. <a href=\"https://doi.org/10.1126/science.1254927\">https://doi.org/10.1126/science.1254927</a>."},"volume":345,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","doi":"10.1126/science.1254927","publist_id":"5011"},{"intvolume":"         8","oa":1,"_id":"2041","publication_status":"published","title":"Structure, function and plasticity of hippocampal dentate gyrus microcircuits","oa_version":"Published Version","year":"2014","abstract":[{"text":"The hippocampus mediates several higher brain functions, such as learning, memory, and spatial coding. The input region of the hippocampus, the dentate gyrus, plays a critical role in these processes. Several lines of evidence suggest that the dentate gyrus acts as a preprocessor of incoming information, preparing it for subsequent processing in CA3. For example, the dentate gyrus converts input from the entorhinal cortex, where cells have multiple spatial fields, into the spatially more specific place cell activity characteristic of the CA3 region. Furthermore, the dentate gyrus is involved in pattern separation, transforming relatively similar input patterns into substantially different output patterns. Finally, the dentate gyrus produces a very sparse coding scheme in which only a very small fraction of neurons are active at any one time.","lang":"eng"}],"pubrep_id":"424","external_id":{"isi":["000341953300001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publisher":"Frontiers Research Foundation","article_number":"2p","status":"public","date_published":"2014-09-10T00:00:00Z","month":"09","ddc":["570"],"publication":"Frontiers in Neural Circuits","date_updated":"2025-09-29T11:52:44Z","type":"journal_article","has_accepted_license":"1","department":[{"_id":"PeJo"}],"corr_author":"1","language":[{"iso":"eng"}],"day":"10","date_created":"2018-12-11T11:55:22Z","file_date_updated":"2020-07-14T12:45:26Z","author":[{"first_name":"Peter M","last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M"},{"full_name":"Lisman, John","last_name":"Lisman","first_name":"John"}],"isi":1,"file":[{"file_name":"IST-2016-424-v1+1_fncir-08-00107.pdf","date_created":"2018-12-12T10:17:38Z","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_size":201110,"file_id":"5294","date_updated":"2020-07-14T12:45:26Z","creator":"system","checksum":"3ca57b164045523f876407e9f13a9fb8"}],"article_processing_charge":"No","scopus_import":"1","doi":"10.3389/fncir.2014.00107","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publist_id":"5010","quality_controlled":"1","citation":{"ista":"Jonas PM, Lisman J. 2014. Structure, function and plasticity of hippocampal dentate gyrus microcircuits. Frontiers in Neural Circuits. 8, 2p.","short":"P.M. Jonas, J. Lisman, Frontiers in Neural Circuits 8 (2014).","ieee":"P. M. Jonas and J. Lisman, “Structure, function and plasticity of hippocampal dentate gyrus microcircuits,” <i>Frontiers in Neural Circuits</i>, vol. 8. Frontiers Research Foundation, 2014.","mla":"Jonas, Peter M., and John Lisman. “Structure, Function and Plasticity of Hippocampal Dentate Gyrus Microcircuits.” <i>Frontiers in Neural Circuits</i>, vol. 8, 2p, Frontiers Research Foundation, 2014, doi:<a href=\"https://doi.org/10.3389/fncir.2014.00107\">10.3389/fncir.2014.00107</a>.","apa":"Jonas, P. M., &#38; Lisman, J. (2014). Structure, function and plasticity of hippocampal dentate gyrus microcircuits. <i>Frontiers in Neural Circuits</i>. Frontiers Research Foundation. <a href=\"https://doi.org/10.3389/fncir.2014.00107\">https://doi.org/10.3389/fncir.2014.00107</a>","ama":"Jonas PM, Lisman J. Structure, function and plasticity of hippocampal dentate gyrus microcircuits. <i>Frontiers in Neural Circuits</i>. 2014;8. doi:<a href=\"https://doi.org/10.3389/fncir.2014.00107\">10.3389/fncir.2014.00107</a>","chicago":"Jonas, Peter M, and John Lisman. “Structure, Function and Plasticity of Hippocampal Dentate Gyrus Microcircuits.” <i>Frontiers in Neural Circuits</i>. Frontiers Research Foundation, 2014. <a href=\"https://doi.org/10.3389/fncir.2014.00107\">https://doi.org/10.3389/fncir.2014.00107</a>."},"volume":8},{"corr_author":"1","date_created":"2018-12-11T11:55:23Z","day":"08","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:45:26Z","author":[{"full_name":"Kupczok, Anne","last_name":"Kupczok","id":"2BB22BC2-F248-11E8-B48F-1D18A9856A87","first_name":"Anne"},{"id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","last_name":"Bollback","first_name":"Jonathan P","full_name":"Bollback, Jonathan P","orcid":"0000-0002-4624-4612"}],"status":"public","date_published":"2014-08-08T00:00:00Z","month":"08","ddc":["570"],"publication":"BMC Genomics","date_updated":"2025-09-29T11:52:17Z","type":"journal_article","issue":"1","has_accepted_license":"1","department":[{"_id":"JoBo"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","doi":"10.1186/1471-2164-15-663","publist_id":"5009","quality_controlled":"1","citation":{"chicago":"Kupczok, Anne, and Jonathan P Bollback. “Motif Depletion in Bacteriophages Infecting Hosts with CRISPR Systems.” <i>BMC Genomics</i>. BioMed Central, 2014. <a href=\"https://doi.org/10.1186/1471-2164-15-663\">https://doi.org/10.1186/1471-2164-15-663</a>.","mla":"Kupczok, Anne, and Jonathan P. Bollback. “Motif Depletion in Bacteriophages Infecting Hosts with CRISPR Systems.” <i>BMC Genomics</i>, vol. 15, no. 1, 663, BioMed Central, 2014, doi:<a href=\"https://doi.org/10.1186/1471-2164-15-663\">10.1186/1471-2164-15-663</a>.","apa":"Kupczok, A., &#38; Bollback, J. P. (2014). Motif depletion in bacteriophages infecting hosts with CRISPR systems. <i>BMC Genomics</i>. BioMed Central. <a href=\"https://doi.org/10.1186/1471-2164-15-663\">https://doi.org/10.1186/1471-2164-15-663</a>","ama":"Kupczok A, Bollback JP. Motif depletion in bacteriophages infecting hosts with CRISPR systems. <i>BMC Genomics</i>. 2014;15(1). doi:<a href=\"https://doi.org/10.1186/1471-2164-15-663\">10.1186/1471-2164-15-663</a>","ieee":"A. Kupczok and J. P. Bollback, “Motif depletion in bacteriophages infecting hosts with CRISPR systems,” <i>BMC Genomics</i>, vol. 15, no. 1. BioMed Central, 2014.","short":"A. Kupczok, J.P. Bollback, BMC Genomics 15 (2014).","ista":"Kupczok A, Bollback JP. 2014. Motif depletion in bacteriophages infecting hosts with CRISPR systems. BMC Genomics. 15(1), 663."},"volume":15,"isi":1,"file":[{"file_name":"IST-2015-396-v1+1_1471-2164-15-663.pdf","date_created":"2018-12-12T10:11:24Z","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_size":1489769,"file_id":"4878","date_updated":"2020-07-14T12:45:26Z","checksum":"3f6d2776b90a842a28359cc957d3d04b","creator":"system"}],"article_processing_charge":"No","scopus_import":"1","year":"2014","abstract":[{"lang":"eng","text":"Background: CRISPR is a microbial immune system likely to be involved in host-parasite coevolution. It functions using target sequences encoded by the bacterial genome, which interfere with invading nucleic acids using a homology-dependent system. The system also requires protospacer associated motifs (PAMs), short motifs close to the target sequence that are required for interference in CRISPR types I and II. Here, we investigate whether PAMs are depleted in phage genomes due to selection pressure to escape recognition.Results: To this end, we analyzed two data sets. Phages infecting all bacterial hosts were analyzed first, followed by a detailed analysis of phages infecting the genus Streptococcus, where PAMs are best understood. We use two different measures of motif underrepresentation that control for codon bias and the frequency of submotifs. We compare phages infecting species with a particular CRISPR type to those infecting species without that type. Since only known PAMs were investigated, the analysis is restricted to CRISPR types I-C and I-E and in Streptococcus to types I-C and II. We found evidence for PAM depletion in Streptococcus phages infecting hosts with CRISPR type I-C, in Vibrio phages infecting hosts with CRISPR type I-E and in Streptococcus thermopilus phages infecting hosts with type II-A, known as CRISPR3.Conclusions: The observed motif depletion in phages with hosts having CRISPR can be attributed to selection rather than to mutational bias, as mutational bias should affect the phages of all hosts. This observation implies that the CRISPR system has been efficient in the groups discussed here."}],"pubrep_id":"396","intvolume":"        15","oa":1,"publication_status":"published","_id":"2042","title":"Motif depletion in bacteriophages infecting hosts with CRISPR systems","oa_version":"Published Version","publisher":"BioMed Central","article_number":"663","license":"https://creativecommons.org/publicdomain/zero/1.0/","external_id":{"isi":["000341528300001"]},"tmp":{"legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","short":"CC0 (1.0)","image":"/images/cc_0.png","name":"Creative Commons Public Domain Dedication (CC0 1.0)"}},{"department":[{"_id":"HeEd"}],"type":"conference","date_updated":"2025-06-11T08:03:07Z","publication":"Proceedings of the Workshop on Algorithm Engineering and Experiments","month":"01","date_published":"2014-01-01T00:00:00Z","page":"31 - 38","status":"public","author":[{"full_name":"Bauer, Ulrich","orcid":"0000-0002-9683-0724","last_name":"Bauer","id":"2ADD483A-F248-11E8-B48F-1D18A9856A87","first_name":"Ulrich"},{"full_name":"Kerber, Michael","orcid":"0000-0002-8030-9299","last_name":"Kerber","first_name":"Michael"},{"full_name":"Reininghaus, Jan","id":"4505473A-F248-11E8-B48F-1D18A9856A87","last_name":"Reininghaus","first_name":"Jan"}],"date_created":"2018-12-11T11:55:23Z","language":[{"iso":"eng"}],"day":"01","scopus_import":"1","editor":[{"full_name":" McGeoch, Catherine","last_name":" McGeoch","first_name":"Catherine"},{"last_name":"Meyer","first_name":"Ulrich","full_name":"Meyer, Ulrich"}],"article_processing_charge":"No","citation":{"chicago":"Bauer, Ulrich, Michael Kerber, and Jan Reininghaus. “Distributed Computation of Persistent Homology.” In <i>Proceedings of the Workshop on Algorithm Engineering and Experiments</i>, edited by Catherine  McGeoch and Ulrich Meyer, 31–38. Society for Industrial and Applied Mathematics, 2014. <a href=\"https://doi.org/10.1137/1.9781611973198.4\">https://doi.org/10.1137/1.9781611973198.4</a>.","apa":"Bauer, U., Kerber, M., &#38; Reininghaus, J. (2014). Distributed computation of persistent homology. In C.  McGeoch &#38; U. Meyer (Eds.), <i>Proceedings of the Workshop on Algorithm Engineering and Experiments</i> (pp. 31–38). Portland, USA: Society for Industrial and Applied Mathematics. <a href=\"https://doi.org/10.1137/1.9781611973198.4\">https://doi.org/10.1137/1.9781611973198.4</a>","ama":"Bauer U, Kerber M, Reininghaus J. Distributed computation of persistent homology. In:  McGeoch C, Meyer U, eds. <i>Proceedings of the Workshop on Algorithm Engineering and Experiments</i>. Society for Industrial and Applied Mathematics; 2014:31-38. doi:<a href=\"https://doi.org/10.1137/1.9781611973198.4\">10.1137/1.9781611973198.4</a>","mla":"Bauer, Ulrich, et al. “Distributed Computation of Persistent Homology.” <i>Proceedings of the Workshop on Algorithm Engineering and Experiments</i>, edited by Catherine  McGeoch and Ulrich Meyer, Society for Industrial and Applied Mathematics, 2014, pp. 31–38, doi:<a href=\"https://doi.org/10.1137/1.9781611973198.4\">10.1137/1.9781611973198.4</a>.","ieee":"U. Bauer, M. Kerber, and J. Reininghaus, “Distributed computation of persistent homology,” in <i>Proceedings of the Workshop on Algorithm Engineering and Experiments</i>, Portland, USA, 2014, pp. 31–38.","short":"U. Bauer, M. Kerber, J. Reininghaus, in:, C.  McGeoch, U. Meyer (Eds.), Proceedings of the Workshop on Algorithm Engineering and Experiments, Society for Industrial and Applied Mathematics, 2014, pp. 31–38.","ista":"Bauer U, Kerber M, Reininghaus J. 2014. Distributed computation of persistent homology. Proceedings of the Workshop on Algorithm Engineering and Experiments. ALENEX: Algorithm Engineering and Experiments, 31–38."},"quality_controlled":"1","publist_id":"5008","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1137/1.9781611973198.4","oa_version":"Submitted Version","title":"Distributed computation of persistent homology","_id":"2043","publication_status":"published","ec_funded":1,"oa":1,"arxiv":1,"conference":{"location":"Portland, USA","end_date":"2014-01-05","name":"ALENEX: Algorithm Engineering and Experiments","start_date":"2014-01-05"},"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1310.0710"}],"abstract":[{"text":"Persistent homology is a popular and powerful tool for capturing topological features of data. Advances in algorithms for computing persistent homology have reduced the computation time drastically – as long as the algorithm does not exhaust the available memory. Following up on a recently presented parallel method for persistence computation on shared memory systems [1], we demonstrate that a simple adaption of the standard reduction algorithm leads to a variant for distributed systems. Our algorithmic design ensures that the data is distributed over the nodes without redundancy; this permits the computation of much larger instances than on a single machine. Moreover, we observe that the parallelism at least compensates for the overhead caused by communication between nodes, and often even speeds up the computation compared to sequential and even parallel shared memory algorithms. In our experiments, we were able to compute the persistent homology of filtrations with more than a billion (109) elements within seconds on a cluster with 32 nodes using less than 6GB of memory per node.","lang":"eng"}],"year":"2014","project":[{"grant_number":"318493","call_identifier":"FP7","name":"Topological Complex Systems","_id":"255D761E-B435-11E9-9278-68D0E5697425"}],"external_id":{"arxiv":["1310.0710"]},"publisher":"Society for Industrial and Applied Mathematics"},{"main_file_link":[{"url":"http://arxiv.org/abs/1303.0477","open_access":"1"}],"abstract":[{"lang":"eng","text":"We present a parallel algorithm for computing the persistent homology of a filtered chain complex. Our approach differs from the commonly used reduction algorithm by first computing persistence pairs within local chunks, then simplifying the unpaired columns, and finally applying standard reduction on the simplified matrix. The approach generalizes a technique by Günther et al., which uses discrete Morse Theory to compute persistence; we derive the same worst-case complexity bound in a more general context. The algorithm employs several practical optimization techniques, which are of independent interest. Our sequential implementation of the algorithm is competitive with state-of-the-art methods, and we further improve the performance through parallel computation."}],"year":"2014","arxiv":1,"oa":1,"ec_funded":1,"oa_version":"Submitted Version","title":"Clear and Compress: Computing Persistent Homology in Chunks","publication_status":"published","_id":"2044","publisher":"Springer","series_title":"Mathematics and Visualization","external_id":{"arxiv":["1303.0477"]},"project":[{"call_identifier":"FP7","grant_number":"318493","_id":"255D761E-B435-11E9-9278-68D0E5697425","name":"Topological Complex Systems"}],"corr_author":"1","author":[{"full_name":"Bauer, Ulrich","orcid":"0000-0002-9683-0724","last_name":"Bauer","id":"2ADD483A-F248-11E8-B48F-1D18A9856A87","first_name":"Ulrich"},{"last_name":"Kerber","first_name":"Michael","full_name":"Kerber, Michael","orcid":"0000-0002-8030-9299"},{"last_name":"Reininghaus","id":"4505473A-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","full_name":"Reininghaus, Jan"}],"language":[{"iso":"eng"}],"date_created":"2018-12-11T11:55:23Z","day":"19","publication":"Topological Methods in Data Analysis and Visualization III","date_published":"2014-03-19T00:00:00Z","month":"03","page":"103 - 117","status":"public","department":[{"_id":"HeEd"}],"type":"book_chapter","date_updated":"2025-06-11T07:56:57Z","publist_id":"5007","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1007/978-3-319-04099-8_7","quality_controlled":"1","citation":{"short":"U. Bauer, M. Kerber, J. Reininghaus, in:, P.-T. Bremer, I. Hotz, V. Pascucci, R. Peikert (Eds.), Topological Methods in Data Analysis and Visualization III, Springer, 2014, pp. 103–117.","ista":"Bauer U, Kerber M, Reininghaus J. 2014.Clear and Compress: Computing Persistent Homology in Chunks. In: Topological Methods in Data Analysis and Visualization III. , 103–117.","ieee":"U. Bauer, M. Kerber, and J. Reininghaus, “Clear and Compress: Computing Persistent Homology in Chunks,” in <i>Topological Methods in Data Analysis and Visualization III</i>, P.-T. Bremer, I. Hotz, V. Pascucci, and R. Peikert, Eds. Springer, 2014, pp. 103–117.","ama":"Bauer U, Kerber M, Reininghaus J. Clear and Compress: Computing Persistent Homology in Chunks. In: Bremer P-T, Hotz I, Pascucci V, Peikert R, eds. <i>Topological Methods in Data Analysis and Visualization III</i>. Mathematics and Visualization. Springer; 2014:103-117. doi:<a href=\"https://doi.org/10.1007/978-3-319-04099-8_7\">10.1007/978-3-319-04099-8_7</a>","apa":"Bauer, U., Kerber, M., &#38; Reininghaus, J. (2014). Clear and Compress: Computing Persistent Homology in Chunks. In P.-T. Bremer, I. Hotz, V. Pascucci, &#38; R. Peikert (Eds.), <i>Topological Methods in Data Analysis and Visualization III</i> (pp. 103–117). Springer. <a href=\"https://doi.org/10.1007/978-3-319-04099-8_7\">https://doi.org/10.1007/978-3-319-04099-8_7</a>","mla":"Bauer, Ulrich, et al. “Clear and Compress: Computing Persistent Homology in Chunks.” <i>Topological Methods in Data Analysis and Visualization III</i>, edited by Peer-Timo Bremer et al., Springer, 2014, pp. 103–17, doi:<a href=\"https://doi.org/10.1007/978-3-319-04099-8_7\">10.1007/978-3-319-04099-8_7</a>.","chicago":"Bauer, Ulrich, Michael Kerber, and Jan Reininghaus. “Clear and Compress: Computing Persistent Homology in Chunks.” In <i>Topological Methods in Data Analysis and Visualization III</i>, edited by Peer-Timo Bremer, Ingrid Hotz, Valerio Pascucci, and Ronald Peikert, 103–17. Mathematics and Visualization. Springer, 2014. <a href=\"https://doi.org/10.1007/978-3-319-04099-8_7\">https://doi.org/10.1007/978-3-319-04099-8_7</a>."},"article_processing_charge":"No","scopus_import":"1","editor":[{"full_name":"Bremer, Peer-Timo","first_name":"Peer-Timo","last_name":"Bremer"},{"first_name":"Ingrid","last_name":"Hotz","full_name":"Hotz, Ingrid"},{"last_name":"Pascucci","first_name":"Valerio","full_name":"Pascucci, Valerio"},{"full_name":"Peikert, Ronald","first_name":"Ronald","last_name":"Peikert"}]},{"month":"01","date_published":"2014-01-01T00:00:00Z","publication":"Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)","status":"public","page":"329 - 344","type":"conference","department":[{"_id":"KrPi"}],"date_updated":"2021-01-12T06:54:57Z","acknowledgement":"The second author was supported by EPSRC grant EP/H043454/1.","author":[{"last_name":"Dachman Soled","first_name":"Dana","full_name":"Dachman Soled, Dana"},{"full_name":"Fuchsbauer, Georg","last_name":"Fuchsbauer","id":"46B4C3EE-F248-11E8-B48F-1D18A9856A87","first_name":"Georg"},{"full_name":"Mohassel, Payman","first_name":"Payman","last_name":"Mohassel"},{"first_name":"Adam","last_name":"O’Neill","full_name":"O’Neill, Adam"}],"date_created":"2018-12-11T11:55:24Z","language":[{"iso":"eng"}],"day":"01","editor":[{"first_name":"Hugo","last_name":"Krawczyk","full_name":"Krawczyk, Hugo"}],"scopus_import":1,"publist_id":"5006","doi":"10.1007/978-3-642-54631-0_19","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","citation":{"short":"D. Dachman Soled, G. Fuchsbauer, P. Mohassel, A. O’Neill, in:, H. Krawczyk (Ed.), Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Springer, 2014, pp. 329–344.","ista":"Dachman Soled D, Fuchsbauer G, Mohassel P, O’Neill A. 2014. Enhanced chosen-ciphertext security and applications. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). PKC: Public Key Crypography, LNCS, vol. 8383, 329–344.","ieee":"D. Dachman Soled, G. Fuchsbauer, P. Mohassel, and A. O’Neill, “Enhanced chosen-ciphertext security and applications,” in <i>Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>, Buenos Aires, Argentina, 2014, vol. 8383, pp. 329–344.","mla":"Dachman Soled, Dana, et al. “Enhanced Chosen-Ciphertext Security and Applications.” <i>Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>, edited by Hugo Krawczyk, vol. 8383, Springer, 2014, pp. 329–44, doi:<a href=\"https://doi.org/10.1007/978-3-642-54631-0_19\">10.1007/978-3-642-54631-0_19</a>.","apa":"Dachman Soled, D., Fuchsbauer, G., Mohassel, P., &#38; O’Neill, A. (2014). Enhanced chosen-ciphertext security and applications. In H. Krawczyk (Ed.), <i>Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i> (Vol. 8383, pp. 329–344). Buenos Aires, Argentina: Springer. <a href=\"https://doi.org/10.1007/978-3-642-54631-0_19\">https://doi.org/10.1007/978-3-642-54631-0_19</a>","ama":"Dachman Soled D, Fuchsbauer G, Mohassel P, O’Neill A. Enhanced chosen-ciphertext security and applications. In: Krawczyk H, ed. <i>Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>. Vol 8383. Springer; 2014:329-344. doi:<a href=\"https://doi.org/10.1007/978-3-642-54631-0_19\">10.1007/978-3-642-54631-0_19</a>","chicago":"Dachman Soled, Dana, Georg Fuchsbauer, Payman Mohassel, and Adam O’Neill. “Enhanced Chosen-Ciphertext Security and Applications.” In <i>Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>, edited by Hugo Krawczyk, 8383:329–44. Springer, 2014. <a href=\"https://doi.org/10.1007/978-3-642-54631-0_19\">https://doi.org/10.1007/978-3-642-54631-0_19</a>."},"volume":8383,"intvolume":"      8383","oa":1,"ec_funded":1,"oa_version":"Submitted Version","publication_status":"published","_id":"2045","title":"Enhanced chosen-ciphertext security and applications","main_file_link":[{"url":"https://eprint.iacr.org/2012/543","open_access":"1"}],"year":"2014","abstract":[{"text":"We introduce and study a new notion of enhanced chosen-ciphertext security (ECCA) for public-key encryption. Loosely speaking, in the ECCA security experiment, the decryption oracle provided to the adversary is augmented to return not only the output of the decryption algorithm on a queried ciphertext but also of a randomness-recovery algorithm associated to the scheme. Our results mainly concern the case where the randomness-recovery algorithm is efficient. We provide constructions of ECCA-secure encryption from adaptive trapdoor functions as defined by Kiltz et al. (EUROCRYPT 2010), resulting in ECCA encryption from standard number-theoretic assumptions. We then give two applications of ECCA-secure encryption: (1) We use it as a unifying concept in showing equivalence of adaptive trapdoor functions and tag-based adaptive trapdoor functions, resolving an open question of Kiltz et al. (2) We show that ECCA-secure encryption can be used to securely realize an approach to public-key encryption with non-interactive opening (PKENO) originally suggested by Damgård and Thorbek (EUROCRYPT 2007), resulting in new and practical PKENO schemes quite different from those in prior work. Our results demonstrate that ECCA security is of both practical and theoretical interest.","lang":"eng"}],"conference":{"end_date":"2014-03-28","name":"PKC: Public Key Crypography","location":"Buenos Aires, Argentina","start_date":"2014-03-26"},"alternative_title":["LNCS"],"project":[{"name":"Provable Security for Physical Cryptography","_id":"258C570E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"259668"}],"publisher":"Springer"},{"editor":[{"full_name":"Krawczyk, Hugo","first_name":"Hugo","last_name":"Krawczyk"}],"scopus_import":1,"publist_id":"5005","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","doi":"10.1007/978-3-642-54631-0_30","citation":{"short":"M. Bellare, G. Fuchsbauer, in:, H. Krawczyk (Ed.), Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Springer, 2014, pp. 520–537.","ista":"Bellare M, Fuchsbauer G. 2014. Policy-based signatures. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). PKC: Public Key Crypography, LNCS, vol. 8383, 520–537.","ieee":"M. Bellare and G. Fuchsbauer, “Policy-based signatures,” in <i>Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>, Buenos Aires, Argentina, 2014, vol. 8383, pp. 520–537.","apa":"Bellare, M., &#38; Fuchsbauer, G. (2014). Policy-based signatures. In H. Krawczyk (Ed.), <i>Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i> (Vol. 8383, pp. 520–537). Buenos Aires, Argentina: Springer. <a href=\"https://doi.org/10.1007/978-3-642-54631-0_30\">https://doi.org/10.1007/978-3-642-54631-0_30</a>","ama":"Bellare M, Fuchsbauer G. Policy-based signatures. In: Krawczyk H, ed. <i>Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>. Vol 8383. Springer; 2014:520-537. doi:<a href=\"https://doi.org/10.1007/978-3-642-54631-0_30\">10.1007/978-3-642-54631-0_30</a>","mla":"Bellare, Mihir, and Georg Fuchsbauer. “Policy-Based Signatures.” <i>Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>, edited by Hugo Krawczyk, vol. 8383, Springer, 2014, pp. 520–37, doi:<a href=\"https://doi.org/10.1007/978-3-642-54631-0_30\">10.1007/978-3-642-54631-0_30</a>.","chicago":"Bellare, Mihir, and Georg Fuchsbauer. “Policy-Based Signatures.” In <i>Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>, edited by Hugo Krawczyk, 8383:520–37. Springer, 2014. <a href=\"https://doi.org/10.1007/978-3-642-54631-0_30\">https://doi.org/10.1007/978-3-642-54631-0_30</a>."},"quality_controlled":"1","volume":8383,"month":"01","date_published":"2014-01-01T00:00:00Z","publication":"Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)","status":"public","page":"520 - 537","type":"conference","department":[{"_id":"KrPi"}],"date_updated":"2021-01-12T06:54:57Z","acknowledgement":"Part of his work was done while at Bristol University, supported by EPSRC grant EP/H043454/1.","author":[{"first_name":"Mihir","last_name":"Bellare","full_name":"Bellare, Mihir"},{"first_name":"Georg","id":"46B4C3EE-F248-11E8-B48F-1D18A9856A87","last_name":"Fuchsbauer","full_name":"Fuchsbauer, Georg"}],"language":[{"iso":"eng"}],"day":"01","date_created":"2018-12-11T11:55:24Z","alternative_title":["LNCS"],"project":[{"call_identifier":"FP7","grant_number":"259668","name":"Provable Security for Physical Cryptography","_id":"258C570E-B435-11E9-9278-68D0E5697425"}],"publisher":"Springer","intvolume":"      8383","oa":1,"ec_funded":1,"oa_version":"Submitted Version","publication_status":"published","_id":"2046","title":"Policy-based signatures","main_file_link":[{"url":"https://eprint.iacr.org/2013/413","open_access":"1"}],"year":"2014","abstract":[{"lang":"eng","text":"We introduce policy-based signatures (PBS), where a signer can only sign messages conforming to some authority-specified policy. The main requirements are unforgeability and privacy, the latter meaning that signatures not reveal the policy. PBS offers value along two fronts: (1) On the practical side, they allow a corporation to control what messages its employees can sign under the corporate key. (2) On the theoretical side, they unify existing work, capturing other forms of signatures as special cases or allowing them to be easily built. Our work focuses on definitions of PBS, proofs that this challenging primitive is realizable for arbitrary policies, efficient constructions for specific policies, and a few representative applications."}],"conference":{"location":"Buenos Aires, Argentina","end_date":"2014-05-28","name":"PKC: Public Key Crypography","start_date":"2014-05-26"}},{"page":"170 - 184","status":"public","publication":"Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)","date_published":"2014-01-01T00:00:00Z","month":"01","date_updated":"2024-11-04T13:35:21Z","department":[{"_id":"KrPi"},{"_id":"CaUh"}],"type":"conference","acknowledgement":"This research was partially supported by BCS- 0941518 to the Department of Statistics at Carnegie Mellon University.","date_created":"2018-12-11T11:55:24Z","language":[{"iso":"eng"}],"day":"01","author":[{"full_name":"Yu, Fei","last_name":"Yu","first_name":"Fei"},{"full_name":"Rybar, Michal","id":"2B3E3DE8-F248-11E8-B48F-1D18A9856A87","last_name":"Rybar","first_name":"Michal"},{"orcid":"0000-0002-7008-0216","full_name":"Uhler, Caroline","first_name":"Caroline","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","last_name":"Uhler"},{"last_name":"Fienberg","first_name":"Stephen","full_name":"Fienberg, Stephen"}],"scopus_import":1,"editor":[{"full_name":"Domingo Ferrer, Josep","last_name":"Domingo Ferrer","first_name":"Josep"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1007/978-3-319-11257-2_14","publist_id":"5004","volume":8744,"citation":{"apa":"Yu, F., Rybar, M., Uhler, C., &#38; Fienberg, S. (2014). Differentially-private logistic regression for detecting multiple-SNP association in GWAS databases. In J. Domingo Ferrer (Ed.), <i>Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i> (Vol. 8744, pp. 170–184). Ibiza, Spain: Springer. <a href=\"https://doi.org/10.1007/978-3-319-11257-2_14\">https://doi.org/10.1007/978-3-319-11257-2_14</a>","ama":"Yu F, Rybar M, Uhler C, Fienberg S. Differentially-private logistic regression for detecting multiple-SNP association in GWAS databases. In: Domingo Ferrer J, ed. <i>Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>. Vol 8744. Springer; 2014:170-184. doi:<a href=\"https://doi.org/10.1007/978-3-319-11257-2_14\">10.1007/978-3-319-11257-2_14</a>","mla":"Yu, Fei, et al. “Differentially-Private Logistic Regression for Detecting Multiple-SNP Association in GWAS Databases.” <i>Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>, edited by Josep Domingo Ferrer, vol. 8744, Springer, 2014, pp. 170–84, doi:<a href=\"https://doi.org/10.1007/978-3-319-11257-2_14\">10.1007/978-3-319-11257-2_14</a>.","chicago":"Yu, Fei, Michal Rybar, Caroline Uhler, and Stephen Fienberg. “Differentially-Private Logistic Regression for Detecting Multiple-SNP Association in GWAS Databases.” In <i>Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>, edited by Josep Domingo Ferrer, 8744:170–84. Springer, 2014. <a href=\"https://doi.org/10.1007/978-3-319-11257-2_14\">https://doi.org/10.1007/978-3-319-11257-2_14</a>.","ista":"Yu F, Rybar M, Uhler C, Fienberg S. 2014. Differentially-private logistic regression for detecting multiple-SNP association in GWAS databases. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). PSD: Privacy in Statistical Databases, LNCS, vol. 8744, 170–184.","short":"F. Yu, M. Rybar, C. Uhler, S. Fienberg, in:, J. Domingo Ferrer (Ed.), Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Springer, 2014, pp. 170–184.","ieee":"F. Yu, M. Rybar, C. Uhler, and S. Fienberg, “Differentially-private logistic regression for detecting multiple-SNP association in GWAS databases,” in <i>Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>, Ibiza, Spain, 2014, vol. 8744, pp. 170–184."},"quality_controlled":"1","oa":1,"intvolume":"      8744","title":"Differentially-private logistic regression for detecting multiple-SNP association in GWAS databases","publication_status":"published","_id":"2047","oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Following the publication of an attack on genome-wide association studies (GWAS) data proposed by Homer et al., considerable attention has been given to developing methods for releasing GWAS data in a privacy-preserving way. Here, we develop an end-to-end differentially private method for solving regression problems with convex penalty functions and selecting the penalty parameters by cross-validation. In particular, we focus on penalized logistic regression with elastic-net regularization, a method widely used to in GWAS analyses to identify disease-causing genes. We show how a differentially private procedure for penalized logistic regression with elastic-net regularization can be applied to the analysis of GWAS data and evaluate our method’s performance."}],"year":"2014","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1407.8067"}],"conference":{"location":"Ibiza, Spain","end_date":"2014-09-19","name":"PSD: Privacy in Statistical Databases","start_date":"2014-09-17"},"arxiv":1,"alternative_title":["LNCS"],"external_id":{"arxiv":["1407.8067"]},"project":[{"name":"Genome-wide Analysis of Root Traits","_id":"25636330-B435-11E9-9278-68D0E5697425","grant_number":"11-NSF-1070"}],"publisher":"Springer"},{"corr_author":"1","author":[{"orcid":"0000-0003-4312-0179","full_name":"Kühnen, Jakob","first_name":"Jakob","id":"3A47AE32-F248-11E8-B48F-1D18A9856A87","last_name":"Kühnen"},{"full_name":"Holzner, Markus","last_name":"Holzner","first_name":"Markus"},{"first_name":"Björn","last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754","full_name":"Hof, Björn"},{"first_name":"Hendrik","last_name":"Kuhlmann","full_name":"Kuhlmann, Hendrik"}],"day":"10","date_created":"2018-12-11T11:55:25Z","language":[{"iso":"eng"}],"month":"01","date_published":"2014-01-10T00:00:00Z","publication":"Journal of Fluid Mechanics","status":"public","page":"463 - 491","type":"journal_article","department":[{"_id":"BjHo"}],"date_updated":"2025-09-29T11:51:23Z","publist_id":"5001","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","doi":"10.1017/jfm.2013.603","citation":{"apa":"Kühnen, J., Holzner, M., Hof, B., &#38; Kuhlmann, H. (2014). Experimental investigation of transitional flow in a toroidal pipe. <i>Journal of Fluid Mechanics</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/jfm.2013.603\">https://doi.org/10.1017/jfm.2013.603</a>","ama":"Kühnen J, Holzner M, Hof B, Kuhlmann H. Experimental investigation of transitional flow in a toroidal pipe. <i>Journal of Fluid Mechanics</i>. 2014;738:463-491. doi:<a href=\"https://doi.org/10.1017/jfm.2013.603\">10.1017/jfm.2013.603</a>","mla":"Kühnen, Jakob, et al. “Experimental Investigation of Transitional Flow in a Toroidal Pipe.” <i>Journal of Fluid Mechanics</i>, vol. 738, Cambridge University Press, 2014, pp. 463–91, doi:<a href=\"https://doi.org/10.1017/jfm.2013.603\">10.1017/jfm.2013.603</a>.","chicago":"Kühnen, Jakob, Markus Holzner, Björn Hof, and Hendrik Kuhlmann. “Experimental Investigation of Transitional Flow in a Toroidal Pipe.” <i>Journal of Fluid Mechanics</i>. Cambridge University Press, 2014. <a href=\"https://doi.org/10.1017/jfm.2013.603\">https://doi.org/10.1017/jfm.2013.603</a>.","ista":"Kühnen J, Holzner M, Hof B, Kuhlmann H. 2014. Experimental investigation of transitional flow in a toroidal pipe. Journal of Fluid Mechanics. 738, 463–491.","short":"J. Kühnen, M. Holzner, B. Hof, H. Kuhlmann, Journal of Fluid Mechanics 738 (2014) 463–491.","ieee":"J. Kühnen, M. Holzner, B. Hof, and H. Kuhlmann, “Experimental investigation of transitional flow in a toroidal pipe,” <i>Journal of Fluid Mechanics</i>, vol. 738. Cambridge University Press, pp. 463–491, 2014."},"quality_controlled":"1","volume":738,"article_processing_charge":"No","isi":1,"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1508.06546"}],"year":"2014","abstract":[{"text":"The flow instability and further transition to turbulence in a toroidal pipe (torus) with curvature ratio (tube-to-coiling diameter) 0.049 is investigated experimentally. The flow inside the toroidal pipe is driven by a steel sphere fitted to the inner pipe diameter. The sphere is moved with constant azimuthal velocity from outside the torus by a moving magnet. The experiment is designed to investigate curved pipe flow by optical measurement techniques. Using stereoscopic particle image velocimetry, laser Doppler velocimetry and pressure drop measurements, the flow is measured for Reynolds numbers ranging from 1000 to 15 000. Time- and space-resolved velocity fields are obtained and analysed. The steady axisymmetric basic flow is strongly influenced by centrifugal effects. On an increase of the Reynolds number we find a sequence of bifurcations. For Re=4075±2% a supercritical bifurcation to an oscillatory flow is found in which waves travel in the streamwise direction with a phase velocity slightly faster than the mean flow. The oscillatory flow is superseded by a presumably quasi-periodic flow at a further increase of the Reynolds number before turbulence sets in. The results are found to be compatible, in general, with earlier experimental and numerical investigations on transition to turbulence in helical and curved pipes. However, important aspects of the bifurcation scenario differ considerably.","lang":"eng"}],"arxiv":1,"intvolume":"       738","oa":1,"oa_version":"Submitted Version","publication_status":"published","_id":"2050","title":"Experimental investigation of transitional flow in a toroidal pipe","publisher":"Cambridge University Press","external_id":{"arxiv":["1508.06546"],"isi":["000328486400021"]}},{"publication_identifier":{"isbn":["9781510800410"]},"publisher":"Neural Information Processing Systems Foundation","_id":"2051","publication_status":"published","title":"Multilabel structured output learning with random spanning trees of max-margin Markov networks","oa_version":"Published Version","intvolume":"        27","oa":1,"conference":{"start_date":"2014-12-08","location":"Montreal, Canada","name":"NIPS: Neural Information Processing Systems","end_date":"2014-12-13"},"year":"2014","abstract":[{"lang":"eng","text":"We show that the usual score function for conditional Markov networks can be written as the expectation over the scores of their spanning trees. We also show that a small random sample of these output trees can attain a significant fraction of the margin obtained by the complete graph and we provide conditions under which we can perform tractable inference. The experimental results confirm that practical learning is scalable to realistic datasets using this approach."}],"OA_type":"gold","main_file_link":[{"url":"https://hal.archives-ouvertes.fr/hal-01065586","open_access":"1"}],"article_processing_charge":"No","citation":{"ama":"Marchand M, Hongyu S, Morvant E, Rousu J, Shawe Taylor J. Multilabel structured output learning with random spanning trees of max-margin Markov networks. In: <i>Advances in Neural Information Processing Systems</i>. Vol 27. Neural Information Processing Systems Foundation; 2014.","apa":"Marchand, M., Hongyu, S., Morvant, E., Rousu, J., &#38; Shawe Taylor, J. (2014). Multilabel structured output learning with random spanning trees of max-margin Markov networks. In <i>Advances in Neural Information Processing Systems</i> (Vol. 27). Montreal, Canada: Neural Information Processing Systems Foundation.","mla":"Marchand, Mario, et al. “Multilabel Structured Output Learning with Random Spanning Trees of Max-Margin Markov Networks.” <i>Advances in Neural Information Processing Systems</i>, vol. 27, Neural Information Processing Systems Foundation, 2014.","chicago":"Marchand, Mario, Su Hongyu, Emilie Morvant, Juho Rousu, and John Shawe Taylor. “Multilabel Structured Output Learning with Random Spanning Trees of Max-Margin Markov Networks.” In <i>Advances in Neural Information Processing Systems</i>, Vol. 27. Neural Information Processing Systems Foundation, 2014.","short":"M. Marchand, S. Hongyu, E. Morvant, J. Rousu, J. Shawe Taylor, in:, Advances in Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2014.","ista":"Marchand M, Hongyu S, Morvant E, Rousu J, Shawe Taylor J. 2014. Multilabel structured output learning with random spanning trees of max-margin Markov networks. Advances in Neural Information Processing Systems. NIPS: Neural Information Processing Systems vol. 27.","ieee":"M. Marchand, S. Hongyu, E. Morvant, J. Rousu, and J. Shawe Taylor, “Multilabel structured output learning with random spanning trees of max-margin Markov networks,” in <i>Advances in Neural Information Processing Systems</i>, Montreal, Canada, 2014, vol. 27."},"volume":27,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"4996","date_updated":"2026-06-18T18:24:19Z","type":"conference","department":[{"_id":"ChLa"}],"status":"public","month":"01","date_published":"2014-01-01T00:00:00Z","ddc":["000"],"publication":"Advances in Neural Information Processing Systems","language":[{"iso":"eng"}],"day":"01","date_created":"2018-12-11T11:55:26Z","author":[{"full_name":"Marchand, Mario","first_name":"Mario","last_name":"Marchand"},{"first_name":"Su","last_name":"Hongyu","full_name":"Hongyu, Su"},{"id":"4BAC2A72-F248-11E8-B48F-1D18A9856A87","last_name":"Morvant","first_name":"Emilie","full_name":"Morvant, Emilie","orcid":"0000-0002-8301-7240"},{"full_name":"Rousu, Juho","first_name":"Juho","last_name":"Rousu"},{"full_name":"Shawe Taylor, John","last_name":"Shawe Taylor","first_name":"John"}],"OA_place":"repository"},{"citation":{"chicago":"Aminof, Benjamin, Tomer Kotek, Sacha Rubin, Francesco Spegni, and Helmut Veith. “Parameterized Model Checking of Rendezvous Systems.” In <i>Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>, edited by Paolo Baldan and Daniele Gorla, 8704:109–24. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2014. <a href=\"https://doi.org/10.1007/978-3-662-44584-6_9\">https://doi.org/10.1007/978-3-662-44584-6_9</a>.","apa":"Aminof, B., Kotek, T., Rubin, S., Spegni, F., &#38; Veith, H. (2014). Parameterized model checking of rendezvous systems. In P. Baldan &#38; D. Gorla (Eds.), <i>Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i> (Vol. 8704, pp. 109–124). Rome, Italy: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.1007/978-3-662-44584-6_9\">https://doi.org/10.1007/978-3-662-44584-6_9</a>","ama":"Aminof B, Kotek T, Rubin S, Spegni F, Veith H. Parameterized model checking of rendezvous systems. In: Baldan P, Gorla D, eds. <i>Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>. Vol 8704. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2014:109-124. doi:<a href=\"https://doi.org/10.1007/978-3-662-44584-6_9\">10.1007/978-3-662-44584-6_9</a>","mla":"Aminof, Benjamin, et al. “Parameterized Model Checking of Rendezvous Systems.” <i>Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>, edited by Paolo Baldan and Daniele Gorla, vol. 8704, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2014, pp. 109–24, doi:<a href=\"https://doi.org/10.1007/978-3-662-44584-6_9\">10.1007/978-3-662-44584-6_9</a>.","ieee":"B. Aminof, T. Kotek, S. Rubin, F. Spegni, and H. Veith, “Parameterized model checking of rendezvous systems,” in <i>Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>, Rome, Italy, 2014, vol. 8704, pp. 109–124.","short":"B. Aminof, T. Kotek, S. Rubin, F. Spegni, H. Veith, in:, P. Baldan, D. Gorla (Eds.), Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2014, pp. 109–124.","ista":"Aminof B, Kotek T, Rubin S, Spegni F, Veith H. 2014. Parameterized model checking of rendezvous systems. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). CONCUR: Concurrency Theory, LNCS, vol. 8704, 109–124."},"quality_controlled":"1","volume":8704,"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","doi":"10.1007/978-3-662-44584-6_9","publist_id":"4994","editor":[{"first_name":"Paolo","last_name":"Baldan","full_name":"Baldan, Paolo"},{"first_name":"Daniele","last_name":"Gorla","full_name":"Gorla, Daniele"}],"scopus_import":"1","day":"01","date_created":"2018-12-11T11:55:26Z","language":[{"iso":"eng"}],"author":[{"full_name":"Aminof, Benjamin","first_name":"Benjamin","last_name":"Aminof","id":"4A55BD00-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kotek, Tomer","first_name":"Tomer","last_name":"Kotek"},{"full_name":"Rubin, Sacha","first_name":"Sacha","last_name":"Rubin"},{"full_name":"Spegni, Francesco","first_name":"Francesco","last_name":"Spegni"},{"first_name":"Helmut","last_name":"Veith","full_name":"Veith, Helmut"}],"acknowledgement":"The second, third, fourth and fifth authors were supported by the Austrian National Research Network S11403-N23 (RiSE) of the Austrian Science Fund (FWF) and by the Vienna Science and Technology Fund (WWTF) through grants PROSEED, ICT12-059, and VRG11-005.","date_updated":"2024-10-21T06:02:50Z","type":"conference","department":[{"_id":"KrCh"}],"status":"public","page":"109 - 124","date_published":"2014-09-01T00:00:00Z","month":"09","publication":"Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","alternative_title":["LNCS"],"conference":{"location":"Rome, Italy","name":"CONCUR: Concurrency Theory","end_date":"2014-09-05","start_date":"2014-09-02"},"year":"2014","abstract":[{"lang":"eng","text":"A standard technique for solving the parameterized model checking problem is to reduce it to the classic model checking problem of finitely many finite-state systems. This work considers some of the theoretical power and limitations of this technique. We focus on concurrent systems in which processes communicate via pairwise rendezvous, as well as the special cases of disjunctive guards and token passing; specifications are expressed in indexed temporal logic without the next operator; and the underlying network topologies are generated by suitable Monadic Second Order Logic formulas and graph operations. First, we settle the exact computational complexity of the parameterized model checking problem for some of our concurrent systems, and establish new decidability results for others. Second, we consider the cases that model checking the parameterized system can be reduced to model checking some fixed number of processes, the number is known as a cutoff. We provide many cases for when such cutoffs can be computed, establish lower bounds on the size of such cutoffs, and identify cases where no cutoff exists. Third, we consider cases for which the parameterized system is equivalent to a single finite-state system (more precisely a Büchi word automaton), and establish tight bounds on the sizes of such automata."}],"_id":"2052","publication_status":"published","title":"Parameterized model checking of rendezvous systems","oa_version":"None","intvolume":"      8704"},{"acknowledgement":"This work is supported by the EU 7th Framework Programme under grant agreements 295261 (MEALS) and 318490 (SENSATION), Czech Science Foundation under grant agreement P202/12/G061, the DFG Transregional Collaborative Research Centre SFB/TR 14 AVACS, and by the CAS/SAFEA International Partnership Program for Creative Research Teams.","author":[{"first_name":"Holger","last_name":"Hermanns","full_name":"Hermanns, Holger"},{"full_name":"Krčál, Jan","last_name":"Krčál","first_name":"Jan"},{"first_name":"Jan","last_name":"Kretinsky","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8122-2881","full_name":"Kretinsky, Jan"}],"language":[{"iso":"eng"}],"date_created":"2018-12-11T11:55:27Z","day":"01","date_published":"2014-09-01T00:00:00Z","month":"09","publication":"Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)","status":"public","page":"249 - 265","type":"conference","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"date_updated":"2025-06-11T07:57:15Z","publist_id":"4993","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1007/978-3-662-44584-6_18","citation":{"ieee":"H. Hermanns, J. Krčál, and J. Kretinsky, “Probabilistic bisimulation: Naturally on distributions,” in <i>Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>, Rome, Italy, 2014, vol. 8704, pp. 249–265.","short":"H. Hermanns, J. Krčál, J. Kretinsky, in:, P. Baldan, D. Gorla (Eds.), Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2014, pp. 249–265.","ista":"Hermanns H, Krčál J, Kretinsky J. 2014. Probabilistic bisimulation: Naturally on distributions. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). CONCUR: Concurrency Theory, LNCS, vol. 8704, 249–265.","chicago":"Hermanns, Holger, Jan Krčál, and Jan Kretinsky. “Probabilistic Bisimulation: Naturally on Distributions.” In <i>Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>, edited by Paolo Baldan and Daniele Gorla, 8704:249–65. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2014. <a href=\"https://doi.org/10.1007/978-3-662-44584-6_18\">https://doi.org/10.1007/978-3-662-44584-6_18</a>.","mla":"Hermanns, Holger, et al. “Probabilistic Bisimulation: Naturally on Distributions.” <i>Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>, edited by Paolo Baldan and Daniele Gorla, vol. 8704, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2014, pp. 249–65, doi:<a href=\"https://doi.org/10.1007/978-3-662-44584-6_18\">10.1007/978-3-662-44584-6_18</a>.","ama":"Hermanns H, Krčál J, Kretinsky J. Probabilistic bisimulation: Naturally on distributions. In: Baldan P, Gorla D, eds. <i>Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>. Vol 8704. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2014:249-265. doi:<a href=\"https://doi.org/10.1007/978-3-662-44584-6_18\">10.1007/978-3-662-44584-6_18</a>","apa":"Hermanns, H., Krčál, J., &#38; Kretinsky, J. (2014). Probabilistic bisimulation: Naturally on distributions. In P. Baldan &#38; D. Gorla (Eds.), <i>Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i> (Vol. 8704, pp. 249–265). Rome, Italy: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.1007/978-3-662-44584-6_18\">https://doi.org/10.1007/978-3-662-44584-6_18</a>"},"volume":8704,"article_processing_charge":"No","scopus_import":"1","editor":[{"full_name":"Baldan, Paolo","last_name":"Baldan","first_name":"Paolo"},{"first_name":"Daniele","last_name":"Gorla","full_name":"Gorla, Daniele"}],"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1404.5084"}],"year":"2014","abstract":[{"text":"In contrast to the usual understanding of probabilistic systems as stochastic processes, recently these systems have also been regarded as transformers of probabilities. In this paper, we give a natural definition of strong bisimulation for probabilistic systems corresponding to this view that treats probability distributions as first-class citizens. Our definition applies in the same way to discrete systems as well as to systems with uncountable state and action spaces. Several examples demonstrate that our definition refines the understanding of behavioural equivalences of probabilistic systems. In particular, it solves a longstanding open problem concerning the representation of memoryless continuous time by memoryfull continuous time. Finally, we give algorithms for computing this bisimulation not only for finite but also for classes of uncountably infinite systems.","lang":"eng"}],"arxiv":1,"conference":{"end_date":"2014-09-05","name":"CONCUR: Concurrency Theory","location":"Rome, Italy","start_date":"2014-09-02"},"intvolume":"      8704","oa":1,"ec_funded":1,"oa_version":"Submitted Version","_id":"2053","publication_status":"published","title":"Probabilistic bisimulation: Naturally on distributions","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","external_id":{"arxiv":["1404.5084"]},"alternative_title":["LNCS"],"project":[{"grant_number":"267989","call_identifier":"FP7","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"name":"Moderne Concurrency Paradigms","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","grant_number":"S11402-N23","call_identifier":"FWF"}]},{"volume":69,"citation":{"ieee":"A. Ganguly, T. Petrov, and H. Koeppl, “Markov chain aggregation and its applications to combinatorial reaction networks,” <i>Journal of Mathematical Biology</i>, vol. 69, no. 3. Springer, pp. 767–797, 2014.","ista":"Ganguly A, Petrov T, Koeppl H. 2014. Markov chain aggregation and its applications to combinatorial reaction networks. Journal of Mathematical Biology. 69(3), 767–797.","short":"A. Ganguly, T. Petrov, H. Koeppl, Journal of Mathematical Biology 69 (2014) 767–797.","chicago":"Ganguly, Arnab, Tatjana Petrov, and Heinz Koeppl. “Markov Chain Aggregation and Its Applications to Combinatorial Reaction Networks.” <i>Journal of Mathematical Biology</i>. Springer, 2014. <a href=\"https://doi.org/10.1007/s00285-013-0738-7\">https://doi.org/10.1007/s00285-013-0738-7</a>.","mla":"Ganguly, Arnab, et al. “Markov Chain Aggregation and Its Applications to Combinatorial Reaction Networks.” <i>Journal of Mathematical Biology</i>, vol. 69, no. 3, Springer, 2014, pp. 767–97, doi:<a href=\"https://doi.org/10.1007/s00285-013-0738-7\">10.1007/s00285-013-0738-7</a>.","ama":"Ganguly A, Petrov T, Koeppl H. Markov chain aggregation and its applications to combinatorial reaction networks. <i>Journal of Mathematical Biology</i>. 2014;69(3):767-797. doi:<a href=\"https://doi.org/10.1007/s00285-013-0738-7\">10.1007/s00285-013-0738-7</a>","apa":"Ganguly, A., Petrov, T., &#38; Koeppl, H. (2014). Markov chain aggregation and its applications to combinatorial reaction networks. <i>Journal of Mathematical Biology</i>. Springer. <a href=\"https://doi.org/10.1007/s00285-013-0738-7\">https://doi.org/10.1007/s00285-013-0738-7</a>"},"quality_controlled":"1","publist_id":"4990","doi":"10.1007/s00285-013-0738-7","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","scopus_import":"1","article_processing_charge":"No","isi":1,"author":[{"last_name":"Ganguly","first_name":"Arnab","full_name":"Ganguly, Arnab"},{"full_name":"Petrov, Tatjana","orcid":"0000-0002-9041-0905","last_name":"Petrov","id":"3D5811FC-F248-11E8-B48F-1D18A9856A87","first_name":"Tatjana"},{"last_name":"Koeppl","first_name":"Heinz","full_name":"Koeppl, Heinz"}],"language":[{"iso":"eng"}],"day":"20","date_created":"2018-12-11T11:55:28Z","acknowledgement":"T. Petrov is supported by SystemsX.ch—the Swiss Inititative for Systems Biology.","department":[{"_id":"CaGu"},{"_id":"ToHe"}],"issue":"3","type":"journal_article","date_updated":"2025-09-29T11:50:22Z","publication":"Journal of Mathematical Biology","month":"11","date_published":"2014-11-20T00:00:00Z","page":"767 - 797","status":"public","publisher":"Springer","external_id":{"arxiv":["1303.4532"],"isi":["000340588700008"]},"arxiv":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1303.4532"}],"abstract":[{"text":"We consider a continuous-time Markov chain (CTMC) whose state space is partitioned into aggregates, and each aggregate is assigned a probability measure. A sufficient condition for defining a CTMC over the aggregates is presented as a variant of weak lumpability, which also characterizes that the measure over the original process can be recovered from that of the aggregated one. We show how the applicability of de-aggregation depends on the initial distribution. The application section is devoted to illustrate how the developed theory aids in reducing CTMC models of biochemical systems particularly in connection to protein-protein interactions. We assume that the model is written by a biologist in form of site-graph-rewrite rules. Site-graph-rewrite rules compactly express that, often, only a local context of a protein (instead of a full molecular species) needs to be in a certain configuration in order to trigger a reaction event. This observation leads to suitable aggregate Markov chains with smaller state spaces, thereby providing sufficient reduction in computational complexity. This is further exemplified in two case studies: simple unbounded polymerization and early EGFR/insulin crosstalk.","lang":"eng"}],"year":"2014","oa_version":"Submitted Version","title":"Markov chain aggregation and its applications to combinatorial reaction networks","_id":"2056","publication_status":"published","oa":1,"intvolume":"        69"},{"ec_funded":1,"oa":1,"intvolume":"      8621","oa_version":"Preprint","title":"Majority vote of diverse classifiers for late fusion","_id":"2057","publication_status":"published","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1404.7796"}],"abstract":[{"text":"In the past few years, a lot of attention has been devoted to multimedia indexing by fusing multimodal informations. Two kinds of fusion schemes are generally considered: The early fusion and the late fusion. We focus on late classifier fusion, where one combines the scores of each modality at the decision level. To tackle this problem, we investigate a recent and elegant well-founded quadratic program named MinCq coming from the machine learning PAC-Bayesian theory. MinCq looks for the weighted combination, over a set of real-valued functions seen as voters, leading to the lowest misclassification rate, while maximizing the voters’ diversity. We propose an extension of MinCq tailored to multimedia indexing. Our method is based on an order-preserving pairwise loss adapted to ranking that allows us to improve Mean Averaged Precision measure while taking into account the diversity of the voters that we want to fuse. We provide evidence that this method is naturally adapted to late fusion procedures and confirm the good behavior of our approach on the challenging PASCAL VOC’07 benchmark.","lang":"eng"}],"year":"2014","arxiv":1,"conference":{"start_date":"2014-08-20","end_date":"2014-08-22","name":"IAPR: International Workshop on Structural, Syntactic, and Statistical Pattern Recognition","location":"Joensuu, Finland"},"alternative_title":["LNCS"],"external_id":{"arxiv":["1404.7796"]},"project":[{"_id":"2532554C-B435-11E9-9278-68D0E5697425","name":"Lifelong Learning of Visual Scene Understanding","call_identifier":"FP7","grant_number":"308036"}],"publisher":"Springer","publication":"Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)","date_published":"2014-01-01T00:00:00Z","month":"01","page":"153 - 162","status":"public","department":[{"_id":"ChLa"}],"type":"conference","date_updated":"2021-01-12T06:55:01Z","author":[{"last_name":"Morvant","id":"4BAC2A72-F248-11E8-B48F-1D18A9856A87","first_name":"Emilie","full_name":"Morvant, Emilie","orcid":"0000-0002-8301-7240"},{"full_name":"Habrard, Amaury","first_name":"Amaury","last_name":"Habrard"},{"first_name":"Stéphane","last_name":"Ayache","full_name":"Ayache, Stéphane"}],"date_created":"2018-12-11T11:55:28Z","day":"01","language":[{"iso":"eng"}],"scopus_import":1,"publist_id":"4989","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1007/978-3-662-44415-3_16","volume":8621,"citation":{"ieee":"E. Morvant, A. Habrard, and S. Ayache, “Majority vote of diverse classifiers for late fusion,” in <i>Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>, Joensuu, Finland, 2014, vol. 8621, pp. 153–162.","ista":"Morvant E, Habrard A, Ayache S. 2014. Majority vote of diverse classifiers for late fusion. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). IAPR: International Workshop on Structural, Syntactic, and Statistical Pattern Recognition, LNCS, vol. 8621, 153–162.","short":"E. Morvant, A. Habrard, S. Ayache, in:, Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Springer, 2014, pp. 153–162.","chicago":"Morvant, Emilie, Amaury Habrard, and Stéphane Ayache. “Majority Vote of Diverse Classifiers for Late Fusion.” In <i>Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>, 8621:153–62. Springer, 2014. <a href=\"https://doi.org/10.1007/978-3-662-44415-3_16\">https://doi.org/10.1007/978-3-662-44415-3_16</a>.","apa":"Morvant, E., Habrard, A., &#38; Ayache, S. (2014). Majority vote of diverse classifiers for late fusion. In <i>Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i> (Vol. 8621, pp. 153–162). Joensuu, Finland: Springer. <a href=\"https://doi.org/10.1007/978-3-662-44415-3_16\">https://doi.org/10.1007/978-3-662-44415-3_16</a>","ama":"Morvant E, Habrard A, Ayache S. Majority vote of diverse classifiers for late fusion. In: <i>Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>. Vol 8621. Springer; 2014:153-162. doi:<a href=\"https://doi.org/10.1007/978-3-662-44415-3_16\">10.1007/978-3-662-44415-3_16</a>","mla":"Morvant, Emilie, et al. “Majority Vote of Diverse Classifiers for Late Fusion.” <i>Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>, vol. 8621, Springer, 2014, pp. 153–62, doi:<a href=\"https://doi.org/10.1007/978-3-662-44415-3_16\">10.1007/978-3-662-44415-3_16</a>."},"quality_controlled":"1"}]