[{"month":"01","oa_version":"Preprint","publication":"SIAM Journal on Mathematical Analysis","keyword":["Energy-Reaction-Diffusion Systems","Cross Diffusion","Global-In-Time Existence of Weak/Renormalised Solutions","Entropy Method","Onsager System","Soret/Dufour Effect"],"language":[{"iso":"eng"}],"oa":1,"publication_identifier":{"issn":["0036-1410"]},"type":"journal_article","date_published":"2022-01-04T00:00:00Z","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","main_file_link":[{"url":"https://arxiv.org/abs/2012.03792","open_access":"1"}],"intvolume":"        54","title":"Global existence analysis of energy-reaction-diffusion systems","date_created":"2021-12-16T12:08:56Z","article_processing_charge":"No","department":[{"_id":"JuFi"}],"publication_status":"published","issue":"1","author":[{"full_name":"Fischer, Julian L","orcid":"0000-0002-0479-558X","last_name":"Fischer","first_name":"Julian L","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hopf","first_name":"Katharina","full_name":"Hopf, Katharina"},{"id":"2CA2C08C-F248-11E8-B48F-1D18A9856A87","last_name":"Kniely","first_name":"Michael","full_name":"Kniely, Michael","orcid":"0000-0001-5645-4333"},{"full_name":"Mielke, Alexander","last_name":"Mielke","first_name":"Alexander"}],"scopus_import":"1","_id":"10547","article_type":"original","publisher":"Society for Industrial and Applied Mathematics","quality_controlled":"1","page":"220-267","abstract":[{"text":"We establish global-in-time existence results for thermodynamically consistent reaction-(cross-)diffusion systems coupled to an equation describing heat transfer. Our main interest is to model species-dependent diffusivities,\r\nwhile at the same time ensuring thermodynamic consistency. A key difficulty of the non-isothermal case lies in the intrinsic presence of cross-diffusion type phenomena like the Soret and the Dufour effect: due to the temperature/energy dependence of the thermodynamic equilibria, a nonvanishing temperature gradient may drive a concentration flux even in a situation with constant concentrations; likewise, a nonvanishing concentration gradient may drive a heat flux even in a case of spatially constant temperature. We use time discretisation and regularisation techniques and derive a priori estimates based on a suitable entropy and the associated entropy production. Renormalised solutions are used in cases where non-integrable diffusion fluxes or reaction terms appear.","lang":"eng"}],"day":"04","doi":"10.1137/20M1387237","arxiv":1,"external_id":{"arxiv":["2012.03792 "],"isi":["000762768000006"]},"isi":1,"citation":{"ieee":"J. L. Fischer, K. Hopf, M. Kniely, and A. Mielke, “Global existence analysis of energy-reaction-diffusion systems,” <i>SIAM Journal on Mathematical Analysis</i>, vol. 54, no. 1. Society for Industrial and Applied Mathematics, pp. 220–267, 2022.","chicago":"Fischer, Julian L, Katharina Hopf, Michael Kniely, and Alexander Mielke. “Global Existence Analysis of Energy-Reaction-Diffusion Systems.” <i>SIAM Journal on Mathematical Analysis</i>. Society for Industrial and Applied Mathematics, 2022. <a href=\"https://doi.org/10.1137/20M1387237\">https://doi.org/10.1137/20M1387237</a>.","ama":"Fischer JL, Hopf K, Kniely M, Mielke A. Global existence analysis of energy-reaction-diffusion systems. <i>SIAM Journal on Mathematical Analysis</i>. 2022;54(1):220-267. doi:<a href=\"https://doi.org/10.1137/20M1387237\">10.1137/20M1387237</a>","apa":"Fischer, J. L., Hopf, K., Kniely, M., &#38; Mielke, A. (2022). Global existence analysis of energy-reaction-diffusion systems. <i>SIAM Journal on Mathematical Analysis</i>. Society for Industrial and Applied Mathematics. <a href=\"https://doi.org/10.1137/20M1387237\">https://doi.org/10.1137/20M1387237</a>","ista":"Fischer JL, Hopf K, Kniely M, Mielke A. 2022. Global existence analysis of energy-reaction-diffusion systems. SIAM Journal on Mathematical Analysis. 54(1), 220–267.","mla":"Fischer, Julian L., et al. “Global Existence Analysis of Energy-Reaction-Diffusion Systems.” <i>SIAM Journal on Mathematical Analysis</i>, vol. 54, no. 1, Society for Industrial and Applied Mathematics, 2022, pp. 220–67, doi:<a href=\"https://doi.org/10.1137/20M1387237\">10.1137/20M1387237</a>.","short":"J.L. Fischer, K. Hopf, M. Kniely, A. Mielke, SIAM Journal on Mathematical Analysis 54 (2022) 220–267."},"year":"2022","date_updated":"2023-08-02T13:37:03Z","volume":54,"acknowledgement":"M.K. gratefully acknowledges the hospitality of WIAS Berlin, where a major part of the project was carried out. The research stay of M.K. at WIAS Berlin was funded by the Austrian Federal Ministry of Education, Science and Research through a research fellowship for graduates of a promotio sub auspiciis. The research of A.M. has been partially supported by Deutsche Forschungsgemeinschaft (DFG) through the Collaborative Research Center SFB 1114 “Scaling Cascades in Complex Systems” (Project no. 235221301), Subproject C05 “Effective models for materials and interfaces with multiple scales”. J.F. and A.M. are grateful for the hospitality of the Erwin Schrödinger Institute in Vienna, where some ideas for this work have been developed. The authors are grateful to two anonymous referees for several helpful comments, in particular for the short proof of estimate (2.7)."},{"article_type":"original","publisher":"Springer Nature","file_date_updated":"2022-01-03T11:08:31Z","page":"1815-1832","quality_controlled":"1","ec_funded":1,"title":"Sobolev-to-Lipschitz property on QCD- spaces and applications","intvolume":"       384","publication_status":"published","article_processing_charge":"Yes (via OA deal)","department":[{"_id":"JaMa"}],"date_created":"2022-01-02T23:01:35Z","author":[{"id":"ECEBF480-9E4F-11EA-B557-B0823DDC885E","full_name":"Dello Schiavo, Lorenzo","orcid":"0000-0002-9881-6870","last_name":"Dello Schiavo","first_name":"Lorenzo"},{"last_name":"Suzuki","first_name":"Kohei","full_name":"Suzuki, Kohei"}],"_id":"10588","scopus_import":"1","ddc":["510"],"volume":384,"acknowledgement":"The authors are grateful to Dr. Bang-Xian Han for helpful discussions on the Sobolev-to-Lipschitz property on metric measure spaces, and to Professor Kazuhiro Kuwae, Professor Emanuel Milman, Dr. Giorgio Stefani, and Dr. Gioacchino Antonelli for reading a preliminary version of this work and for their valuable comments and suggestions. Finally, they wish to express their gratitude to two anonymous Reviewers whose suggestions improved the presentation of this work.\r\n\r\nL.D.S. gratefully acknowledges funding of his position by the Austrian Science Fund (FWF) grant F65, and by the European Research Council (ERC, grant No. 716117, awarded to Prof. Dr. Jan Maas).\r\n\r\nK.S. gratefully acknowledges funding by: the JSPS Overseas Research Fellowships, Grant Nr. 290142; World Premier International Research Center Initiative (WPI), MEXT, Japan; JSPS Grant-in-Aid for Scientific Research on Innovative Areas “Discrete Geometric Analysis for Materials Design”, Grant Number 17H06465; and the Alexander von Humboldt Stiftung, Humboldt-Forschungsstipendium.","abstract":[{"lang":"eng","text":"We prove the Sobolev-to-Lipschitz property for metric measure spaces satisfying the quasi curvature-dimension condition recently introduced in Milman (Commun Pure Appl Math, to appear). We provide several applications to properties of the corresponding heat semigroup. In particular, under the additional assumption of infinitesimal Hilbertianity, we show the Varadhan short-time asymptotics for the heat semigroup with respect to the distance, and prove the irreducibility of the heat semigroup. These results apply in particular to large classes of (ideal) sub-Riemannian manifolds."}],"doi":"10.1007/s00208-021-02331-2","arxiv":1,"day":"01","isi":1,"external_id":{"arxiv":["2110.05137"],"isi":["000734150200001"]},"date_updated":"2023-08-02T13:39:05Z","citation":{"short":"L. Dello Schiavo, K. Suzuki, Mathematische Annalen 384 (2022) 1815–1832.","mla":"Dello Schiavo, Lorenzo, and Kohei Suzuki. “Sobolev-to-Lipschitz Property on QCD- Spaces and Applications.” <i>Mathematische Annalen</i>, vol. 384, Springer Nature, 2022, pp. 1815–32, doi:<a href=\"https://doi.org/10.1007/s00208-021-02331-2\">10.1007/s00208-021-02331-2</a>.","ista":"Dello Schiavo L, Suzuki K. 2022. Sobolev-to-Lipschitz property on QCD- spaces and applications. Mathematische Annalen. 384, 1815–1832.","ama":"Dello Schiavo L, Suzuki K. Sobolev-to-Lipschitz property on QCD- spaces and applications. <i>Mathematische Annalen</i>. 2022;384:1815-1832. doi:<a href=\"https://doi.org/10.1007/s00208-021-02331-2\">10.1007/s00208-021-02331-2</a>","apa":"Dello Schiavo, L., &#38; Suzuki, K. (2022). Sobolev-to-Lipschitz property on QCD- spaces and applications. <i>Mathematische Annalen</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00208-021-02331-2\">https://doi.org/10.1007/s00208-021-02331-2</a>","ieee":"L. Dello Schiavo and K. Suzuki, “Sobolev-to-Lipschitz property on QCD- spaces and applications,” <i>Mathematische Annalen</i>, vol. 384. Springer Nature, pp. 1815–1832, 2022.","chicago":"Dello Schiavo, Lorenzo, and Kohei Suzuki. “Sobolev-to-Lipschitz Property on QCD- Spaces and Applications.” <i>Mathematische Annalen</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/s00208-021-02331-2\">https://doi.org/10.1007/s00208-021-02331-2</a>."},"year":"2022","language":[{"iso":"eng"}],"keyword":["quasi curvature-dimension condition","sub-riemannian geometry","Sobolev-to-Lipschitz property","Varadhan short-time asymptotics"],"month":"12","oa_version":"Published Version","project":[{"call_identifier":"H2020","_id":"256E75B8-B435-11E9-9278-68D0E5697425","name":"Optimal Transport and Stochastic Dynamics","grant_number":"716117"},{"_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","grant_number":"F6504","name":"Taming Complexity in Partial Differential Systems"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"publication":"Mathematische Annalen","has_accepted_license":"1","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"date_created":"2022-01-03T11:08:31Z","checksum":"2593abbf195e38efa93b6006b1e90eb1","file_size":410090,"date_updated":"2022-01-03T11:08:31Z","file_name":"2021_MathAnn_DelloSchiavo.pdf","content_type":"application/pdf","access_level":"open_access","success":1,"relation":"main_file","file_id":"10596","creator":"alisjak"}],"oa":1,"publication_identifier":{"issn":["0025-5831"],"eissn":["1432-1807"]},"date_published":"2022-12-01T00:00:00Z","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"}},{"_id":"10023","issue":"4","author":[{"full_name":"Karatzas, Ioannis","last_name":"Karatzas","first_name":"Ioannis"},{"full_name":"Maas, Jan","orcid":"0000-0002-0845-1338","last_name":"Maas","first_name":"Jan","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Schachermayer","first_name":"Walter","full_name":"Schachermayer, Walter"}],"date_created":"2021-09-19T08:53:19Z","department":[{"_id":"JaMa"}],"article_processing_charge":"No","publication_status":"published","intvolume":"        21","title":"Trajectorial dissipation and gradient flow for the relative entropy in Markov chains","ec_funded":1,"quality_controlled":"1","page":"481-536","publisher":"International Press","article_type":"original","year":"2021","citation":{"ista":"Karatzas I, Maas J, Schachermayer W. 2021. Trajectorial dissipation and gradient flow for the relative entropy in Markov chains. Communications in Information and Systems. 21(4), 481–536.","short":"I. Karatzas, J. Maas, W. Schachermayer, Communications in Information and Systems 21 (2021) 481–536.","mla":"Karatzas, Ioannis, et al. “Trajectorial Dissipation and Gradient Flow for the Relative Entropy in Markov Chains.” <i>Communications in Information and Systems</i>, vol. 21, no. 4, International Press, 2021, pp. 481–536, doi:<a href=\"https://doi.org/10.4310/CIS.2021.v21.n4.a1\">10.4310/CIS.2021.v21.n4.a1</a>.","chicago":"Karatzas, Ioannis, Jan Maas, and Walter Schachermayer. “Trajectorial Dissipation and Gradient Flow for the Relative Entropy in Markov Chains.” <i>Communications in Information and Systems</i>. International Press, 2021. <a href=\"https://doi.org/10.4310/CIS.2021.v21.n4.a1\">https://doi.org/10.4310/CIS.2021.v21.n4.a1</a>.","ieee":"I. Karatzas, J. Maas, and W. Schachermayer, “Trajectorial dissipation and gradient flow for the relative entropy in Markov chains,” <i>Communications in Information and Systems</i>, vol. 21, no. 4. International Press, pp. 481–536, 2021.","apa":"Karatzas, I., Maas, J., &#38; Schachermayer, W. (2021). Trajectorial dissipation and gradient flow for the relative entropy in Markov chains. <i>Communications in Information and Systems</i>. International Press. <a href=\"https://doi.org/10.4310/CIS.2021.v21.n4.a1\">https://doi.org/10.4310/CIS.2021.v21.n4.a1</a>","ama":"Karatzas I, Maas J, Schachermayer W. Trajectorial dissipation and gradient flow for the relative entropy in Markov chains. <i>Communications in Information and Systems</i>. 2021;21(4):481-536. doi:<a href=\"https://doi.org/10.4310/CIS.2021.v21.n4.a1\">10.4310/CIS.2021.v21.n4.a1</a>"},"date_updated":"2021-09-20T12:51:18Z","external_id":{"arxiv":["2005.14177"]},"day":"04","doi":"10.4310/CIS.2021.v21.n4.a1","arxiv":1,"abstract":[{"lang":"eng","text":"We study the temporal dissipation of variance and relative entropy for ergodic Markov Chains in continuous time, and compute explicitly the corresponding dissipation rates. These are identified, as is well known, in the case of the variance in terms of an appropriate Hilbertian norm; and in the case of the relative entropy, in terms of a Dirichlet form which morphs into a version of the familiar Fisher information under conditions of detailed balance. Here we obtain trajectorial versions of these results, valid along almost every path of the random motion and most transparent in the backwards direction of time. Martingale arguments and time reversal play crucial roles, as in the recent work of Karatzas, Schachermayer and Tschiderer for conservative diffusions. Extensions are developed to general “convex divergences” and to countable state-spaces. The steepest descent and gradient flow properties for the variance, the relative entropy, and appropriate generalizations, are studied along with their respective geometries under conditions of detailed balance, leading to a very direct proof for the HWI inequality of Otto and Villani in the present context."}],"acknowledgement":"I.K. acknowledges support from the U.S. National Science Foundation under Grant NSF-DMS-20-04997. J.M. acknowledges support from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 716117) and from the Austrian Science Fund (FWF) through project F65. W.S. acknowledges support from the Austrian Science Fund (FWF) under grant P28861 and by the Vienna Science and Technology Fund (WWTF) through projects MA14-008 and MA16-021.","volume":21,"publication":"Communications in Information and Systems","project":[{"_id":"256E75B8-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"716117","name":"Optimal Transport and Stochastic Dynamics"},{"_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","grant_number":"F6504","name":"Taming Complexity in Partial Differential Systems"}],"oa_version":"Preprint","month":"06","keyword":["Markov Chain","relative entropy","time reversal","steepest descent","gradient flow"],"language":[{"iso":"eng"}],"type":"journal_article","date_published":"2021-06-04T00:00:00Z","publication_identifier":{"issn":["1526-7555"]},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/2005.14177","open_access":"1"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","status":"public"},{"department":[{"_id":"ToHe"}],"article_processing_charge":"No","date_created":"2021-10-07T23:30:10Z","publication_status":"published","intvolume":"     12974","alternative_title":["LNCS"],"title":"Differential monitoring","scopus_import":"1","_id":"10108","author":[{"full_name":"Mühlböck, Fabian","orcid":"0000-0003-1548-0177","last_name":"Mühlböck","first_name":"Fabian","id":"6395C5F6-89DF-11E9-9C97-6BDFE5697425"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724","last_name":"Henzinger","first_name":"Thomas A"}],"publisher":"Springer Nature","quality_controlled":"1","page":"231-243","file_date_updated":"2021-10-07T23:32:18Z","day":"06","doi":"10.1007/978-3-030-88494-9_12","abstract":[{"lang":"eng","text":"We argue that the time is ripe to investigate differential monitoring, in which the specification of a program's behavior is implicitly given by a second program implementing the same informal specification. Similar ideas have been proposed before, and are currently implemented in restricted form for testing and specialized run-time analyses, aspects of which we combine. We discuss the challenges of implementing differential monitoring as a general-purpose, black-box run-time monitoring framework, and present promising results of a preliminary implementation, showing low monitoring overheads for diverse programs."}],"citation":{"ista":"Mühlböck F, Henzinger TA. 2021. Differential monitoring. International Conference on Runtime Verification. RV: Runtime Verification, LNCS, vol. 12974, 231–243.","short":"F. Mühlböck, T.A. Henzinger, in:, International Conference on Runtime Verification, Springer Nature, Cham, 2021, pp. 231–243.","mla":"Mühlböck, Fabian, and Thomas A. Henzinger. “Differential Monitoring.” <i>International Conference on Runtime Verification</i>, vol. 12974, Springer Nature, 2021, pp. 231–43, doi:<a href=\"https://doi.org/10.1007/978-3-030-88494-9_12\">10.1007/978-3-030-88494-9_12</a>.","chicago":"Mühlböck, Fabian, and Thomas A Henzinger. “Differential Monitoring.” In <i>International Conference on Runtime Verification</i>, 12974:231–43. Cham: Springer Nature, 2021. <a href=\"https://doi.org/10.1007/978-3-030-88494-9_12\">https://doi.org/10.1007/978-3-030-88494-9_12</a>.","ieee":"F. Mühlböck and T. A. Henzinger, “Differential monitoring,” in <i>International Conference on Runtime Verification</i>, Virtual, 2021, vol. 12974, pp. 231–243.","apa":"Mühlböck, F., &#38; Henzinger, T. A. (2021). Differential monitoring. In <i>International Conference on Runtime Verification</i> (Vol. 12974, pp. 231–243). Cham: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-88494-9_12\">https://doi.org/10.1007/978-3-030-88494-9_12</a>","ama":"Mühlböck F, Henzinger TA. Differential monitoring. In: <i>International Conference on Runtime Verification</i>. Vol 12974. Cham: Springer Nature; 2021:231-243. doi:<a href=\"https://doi.org/10.1007/978-3-030-88494-9_12\">10.1007/978-3-030-88494-9_12</a>"},"year":"2021","date_updated":"2023-08-14T07:20:30Z","external_id":{"isi":["000719383800012"]},"isi":1,"volume":12974,"acknowledgement":"The authors would like to thank Borzoo Bonakdarpour, Derek Dreyer, Adrian Francalanza, Owolabi Legunsen, Mae Milano, Manuel Rigger, Cesar Sanchez, and the members of the IST Verification Seminar for their helpful comments and insights on various stages of this work, as well as the reviewers of RV’21 for their helpful suggestions on the actual paper.","ddc":["005"],"project":[{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize","grant_number":"Z211"}],"oa_version":"Preprint","month":"10","has_accepted_license":"1","publication":"International Conference on Runtime Verification","conference":{"location":"Virtual","end_date":"2021-10-14","start_date":"2021-10-11","name":"RV: Runtime Verification"},"keyword":["run-time verification","software engineering","implicit specification"],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"eisbn":["978-3-030-88494-9"],"isbn":["978-3-030-88493-2"]},"oa":1,"type":"conference","date_published":"2021-10-06T00:00:00Z","file":[{"checksum":"554c7fdb259eda703a8b6328a6dad55a","file_size":350632,"date_created":"2021-10-07T23:32:18Z","file_name":"differentialmonitoring-cameraready-openaccess.pdf","content_type":"application/pdf","date_updated":"2021-10-07T23:32:18Z","success":1,"access_level":"open_access","relation":"main_file","creator":"fmuehlbo","file_id":"10109"}],"place":"Cham","related_material":{"record":[{"id":"9946","relation":"extended_version","status":"public"}]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public"},{"title":"Differential monitoring","alternative_title":["IST Austria Technical Report"],"publication_status":"published","article_processing_charge":"No","date_created":"2021-08-20T20:00:37Z","department":[{"_id":"ToHe"}],"author":[{"id":"6395C5F6-89DF-11E9-9C97-6BDFE5697425","last_name":"Mühlböck","first_name":"Fabian","full_name":"Mühlböck, Fabian","orcid":"0000-0003-1548-0177"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger","orcid":"0000-0002-2985-7724","full_name":"Henzinger, Thomas A"}],"_id":"9946","publisher":"IST Austria","file_date_updated":"2021-09-03T12:34:28Z","page":"17","abstract":[{"lang":"eng","text":"We argue that the time is ripe to investigate differential monitoring, in which the specification of a program's behavior is implicitly given by a second program implementing the same informal specification. Similar ideas have been proposed before, and are currently implemented in restricted form for testing and specialized run-time analyses, aspects of which we combine. We discuss the challenges of implementing differential monitoring as a general-purpose, black-box run-time monitoring framework, and present promising results of a preliminary implementation, showing low monitoring overheads for diverse programs."}],"doi":"10.15479/AT:ISTA:9946","day":"01","date_updated":"2023-08-14T07:20:29Z","citation":{"ama":"Mühlböck F, Henzinger TA. <i>Differential Monitoring</i>. IST Austria; 2021. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:9946\">10.15479/AT:ISTA:9946</a>","apa":"Mühlböck, F., &#38; Henzinger, T. A. (2021). <i>Differential monitoring</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:9946\">https://doi.org/10.15479/AT:ISTA:9946</a>","chicago":"Mühlböck, Fabian, and Thomas A Henzinger. <i>Differential Monitoring</i>. IST Austria, 2021. <a href=\"https://doi.org/10.15479/AT:ISTA:9946\">https://doi.org/10.15479/AT:ISTA:9946</a>.","ieee":"F. Mühlböck and T. A. Henzinger, <i>Differential monitoring</i>. IST Austria, 2021.","mla":"Mühlböck, Fabian, and Thomas A. Henzinger. <i>Differential Monitoring</i>. IST Austria, 2021, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:9946\">10.15479/AT:ISTA:9946</a>.","short":"F. Mühlböck, T.A. Henzinger, Differential Monitoring, IST Austria, 2021.","ista":"Mühlböck F, Henzinger TA. 2021. Differential monitoring, IST Austria, 17p."},"year":"2021","ddc":["005"],"acknowledgement":"The authors would like to thank Borzoo Bonakdarpour, Derek Dreyer, Adrian Francalanza, Owolabi Legunsen, Matthew Milano, Manuel Rigger, Cesar Sanchez, and the members of the IST Verification Seminar for their helpful comments and insights on various stages of this work, as well as the reviewers of RV’21 for their helpful suggestions on the actual paper.","month":"09","oa_version":"Published Version","project":[{"grant_number":"Z211","name":"The Wittgenstein Prize","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"has_accepted_license":"1","language":[{"iso":"eng"}],"keyword":["run-time verification","software engineering","implicit specification"],"oa":1,"publication_identifier":{"issn":["2664-1690"]},"date_published":"2021-09-01T00:00:00Z","type":"technical_report","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","related_material":{"record":[{"relation":"other","id":"9281","status":"public"},{"relation":"shorter_version","id":"10108","status":"public"}]},"status":"public","file":[{"date_created":"2021-08-20T19:59:44Z","file_size":"320453","checksum":"0f9aafd59444cb6bdca6925d163ab946","date_updated":"2021-09-03T12:34:28Z","content_type":"application/pdf","file_name":"differentialmonitoring-techreport.pdf","relation":"main_file","access_level":"open_access","file_id":"9948","creator":"fmuehlbo"}]},{"publication":"Journal of Computational Neuroscience","has_accepted_license":"1","oa_version":"Published Version","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"}],"month":"02","language":[{"iso":"eng"}],"keyword":["Time series analysis","Multiple time scale analysis","Spike train data","Information theory","Bayesian decoding"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_published":"2020-02-01T00:00:00Z","type":"journal_article","publication_identifier":{"issn":["0929-5313"],"eissn":["1573-6873"]},"oa":1,"file":[{"date_created":"2020-01-28T09:31:09Z","file_size":1941355,"checksum":"036e9451d6cd0c190ad25791bf82393b","date_updated":"2020-07-14T12:47:56Z","content_type":"application/pdf","file_name":"10827_2020_740_MOESM1_ESM.pdf","relation":"supplementary_material","access_level":"open_access","file_id":"7380","creator":"rcubero"},{"access_level":"open_access","relation":"main_file","file_id":"7381","creator":"rcubero","date_created":"2020-01-28T09:31:09Z","file_size":3257880,"checksum":"4dd8b1fd4b54486f79d82ac7b2a412b2","date_updated":"2020-07-14T12:47:56Z","content_type":"application/pdf","file_name":"Cubero2020_Article_MultiscaleRelevanceAndInformat.pdf"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","_id":"7369","scopus_import":"1","author":[{"id":"850B2E12-9CD4-11E9-837F-E719E6697425","orcid":"0000-0003-0002-1867","full_name":"Cubero, Ryan J","first_name":"Ryan J","last_name":"Cubero"},{"full_name":"Marsili, Matteo","first_name":"Matteo","last_name":"Marsili"},{"first_name":"Yasser","last_name":"Roudi","full_name":"Roudi, Yasser"}],"publication_status":"published","article_processing_charge":"Yes (via OA deal)","department":[{"_id":"SaSi"}],"date_created":"2020-01-28T10:34:00Z","title":"Multiscale relevance and informative encoding in neuronal spike trains","intvolume":"        48","page":"85-102","quality_controlled":"1","ec_funded":1,"file_date_updated":"2020-07-14T12:47:56Z","publisher":"Springer Nature","article_type":"original","date_updated":"2023-08-17T14:35:22Z","citation":{"chicago":"Cubero, Ryan J, Matteo Marsili, and Yasser Roudi. “Multiscale Relevance and Informative Encoding in Neuronal Spike Trains.” <i>Journal of Computational Neuroscience</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1007/s10827-020-00740-x\">https://doi.org/10.1007/s10827-020-00740-x</a>.","ieee":"R. J. Cubero, M. Marsili, and Y. Roudi, “Multiscale relevance and informative encoding in neuronal spike trains,” <i>Journal of Computational Neuroscience</i>, vol. 48. Springer Nature, pp. 85–102, 2020.","ama":"Cubero RJ, Marsili M, Roudi Y. Multiscale relevance and informative encoding in neuronal spike trains. <i>Journal of Computational Neuroscience</i>. 2020;48:85-102. doi:<a href=\"https://doi.org/10.1007/s10827-020-00740-x\">10.1007/s10827-020-00740-x</a>","apa":"Cubero, R. J., Marsili, M., &#38; Roudi, Y. (2020). Multiscale relevance and informative encoding in neuronal spike trains. <i>Journal of Computational Neuroscience</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s10827-020-00740-x\">https://doi.org/10.1007/s10827-020-00740-x</a>","ista":"Cubero RJ, Marsili M, Roudi Y. 2020. Multiscale relevance and informative encoding in neuronal spike trains. Journal of Computational Neuroscience. 48, 85–102.","mla":"Cubero, Ryan J., et al. “Multiscale Relevance and Informative Encoding in Neuronal Spike Trains.” <i>Journal of Computational Neuroscience</i>, vol. 48, Springer Nature, 2020, pp. 85–102, doi:<a href=\"https://doi.org/10.1007/s10827-020-00740-x\">10.1007/s10827-020-00740-x</a>.","short":"R.J. Cubero, M. Marsili, Y. Roudi, Journal of Computational Neuroscience 48 (2020) 85–102."},"year":"2020","isi":1,"external_id":{"isi":["000515321800006"]},"doi":"10.1007/s10827-020-00740-x","day":"01","abstract":[{"lang":"eng","text":"Neuronal responses to complex stimuli and tasks can encompass a wide range of time scales. Understanding these responses requires measures that characterize how the information on these response patterns are represented across multiple temporal resolutions. In this paper we propose a metric – which we call multiscale relevance (MSR) – to capture the dynamical variability of the activity of single neurons across different time scales. The MSR is a non-parametric, fully featureless indicator in that it uses only the time stamps of the firing activity without resorting to any a priori covariate or invoking any specific structure in the tuning curve for neural activity. When applied to neural data from the mEC and from the ADn and PoS regions of freely-behaving rodents, we found that neurons having low MSR tend to have low mutual information and low firing sparsity across the correlates that are believed to be encoded by the region of the brain where the recordings were made. In addition, neurons with high MSR contain significant information on spatial navigation and allow to decode spatial position or head direction as efficiently as those neurons whose firing activity has high mutual information with the covariate to be decoded and significantly better than the set of neurons with high local variations in their interspike intervals. Given these results, we propose that the MSR can be used as a measure to rank and select neurons for their information content without the need to appeal to any a priori covariate."}],"volume":48,"acknowledgement":"This research was supported by the Kavli Foundation and the Centre of Excellence scheme of the Research Council of Norway (Centre for Neural Computation). RJC is currently receiving funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411.","ddc":["004","519","570"]},{"publisher":"Institute of Science and Technology Austria","file_date_updated":"2020-07-14T12:47:31Z","page":"135","title":"Estimating information flow in single cells","alternative_title":["ISTA Thesis"],"publication_status":"published","department":[{"_id":"GaTk"}],"article_processing_charge":"No","date_created":"2019-05-21T00:11:23Z","author":[{"full_name":"Cepeda Humerez, Sarah A","last_name":"Cepeda Humerez","first_name":"Sarah A","id":"3DEE19A4-F248-11E8-B48F-1D18A9856A87"}],"_id":"6473","ddc":["004"],"abstract":[{"text":"Single cells are constantly interacting with their environment and each other, more importantly, the accurate perception of environmental cues is crucial for growth, survival, and reproduction. This communication between cells and their environment can be formalized in mathematical terms and be quantified as the information flow between them, as prescribed by information theory. \r\nThe recent availability of real–time dynamical patterns of signaling molecules in single cells has allowed us to identify encoding about the identity of the environment in the time–series. However, efficient estimation of the information transmitted by these signals has been a data–analysis challenge due to the high dimensionality of the trajectories and the limited number of samples. In the first part of this thesis, we develop and evaluate decoding–based estimation methods to lower bound the mutual information and derive model–based precise information estimates for biological reaction networks governed by the chemical master equation. This is followed by applying the decoding-based methods to study the intracellular representation of extracellular changes in budding yeast, by observing the transient dynamics of nuclear translocation of 10 transcription factors in response to 3 stress conditions. Additionally, we apply these estimators to previously published data on ERK and Ca2+ signaling and yeast stress response. We argue that this single cell decoding-based measure of information provides an unbiased, quantitative and interpretable measure for the fidelity of biological signaling processes. \r\nFinally, in the last section, we deal with gene regulation which is primarily controlled by transcription factors (TFs) that bind to the DNA to activate gene expression. The possibility that non-cognate TFs activate transcription diminishes the accuracy of regulation with potentially disastrous effects for the cell. This ’crosstalk’ acts as a previously unexplored source of noise in biochemical networks and puts a strong constraint on their performance. To mitigate erroneous initiation we propose an out of equilibrium scheme that implements kinetic proofreading. We show that such architectures are favored  over their equilibrium counterparts for complex organisms despite introducing noise in gene expression. ","lang":"eng"}],"doi":"10.15479/AT:ISTA:6473","degree_awarded":"PhD","day":"23","date_updated":"2025-05-28T11:57:00Z","citation":{"ieee":"S. A. Cepeda Humerez, “Estimating information flow in single cells,” Institute of Science and Technology Austria, 2019.","chicago":"Cepeda Humerez, Sarah A. “Estimating Information Flow in Single Cells.” Institute of Science and Technology Austria, 2019. <a href=\"https://doi.org/10.15479/AT:ISTA:6473\">https://doi.org/10.15479/AT:ISTA:6473</a>.","apa":"Cepeda Humerez, S. A. (2019). <i>Estimating information flow in single cells</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:6473\">https://doi.org/10.15479/AT:ISTA:6473</a>","ama":"Cepeda Humerez SA. Estimating information flow in single cells. 2019. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6473\">10.15479/AT:ISTA:6473</a>","ista":"Cepeda Humerez SA. 2019. Estimating information flow in single cells. Institute of Science and Technology Austria.","short":"S.A. Cepeda Humerez, Estimating Information Flow in Single Cells, Institute of Science and Technology Austria, 2019.","mla":"Cepeda Humerez, Sarah A. <i>Estimating Information Flow in Single Cells</i>. Institute of Science and Technology Austria, 2019, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6473\">10.15479/AT:ISTA:6473</a>."},"year":"2019","language":[{"iso":"eng"}],"keyword":["Information estimation","Time-series","data analysis"],"month":"05","oa_version":"Published Version","has_accepted_license":"1","status":"public","related_material":{"record":[{"id":"6900","relation":"dissertation_contains","status":"public"},{"status":"public","id":"281","relation":"dissertation_contains"},{"relation":"dissertation_contains","id":"2016","status":"public"},{"status":"public","id":"1576","relation":"dissertation_contains"}]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"access_level":"closed","relation":"source_file","file_id":"6480","creator":"scepeda","date_created":"2019-05-23T11:18:16Z","file_size":23937464,"checksum":"75f9184c1346e10a5de5f9cc7338309a","date_updated":"2020-07-14T12:47:31Z","content_type":"application/zip","file_name":"Thesis_Cepeda.zip"},{"date_created":"2019-05-23T11:18:13Z","file_size":16646985,"checksum":"afdc0633ddbd71d5b13550d7fb4f4454","date_updated":"2020-07-14T12:47:31Z","file_name":"CepedaThesis.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"6481","creator":"scepeda"}],"supervisor":[{"first_name":"Gašper","last_name":"Tkačik","orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"oa":1,"publication_identifier":{"issn":["2663-337X"]},"date_published":"2019-05-23T00:00:00Z","type":"dissertation","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"}},{"scopus_import":"1","_id":"11691","publication":"Proceedings of the 31st annual ACM symposium on Theory of computing","author":[{"last_name":"Goel","first_name":"Ashish","full_name":"Goel, Ashish"},{"full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530","last_name":"Henzinger","first_name":"Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630"},{"first_name":"Serge","last_name":"Plotkin","full_name":"Plotkin, Serge"},{"first_name":"Eva","last_name":"Tardos","full_name":"Tardos, Eva"}],"date_created":"2022-07-29T07:43:00Z","article_processing_charge":"No","publication_status":"published","oa_version":"None","month":"05","title":"Scheduling data transfers in a network and the set scheduling problem","quality_controlled":"1","page":"189-197","keyword":["Scheduling","Flow time"],"language":[{"iso":"eng"}],"publisher":"Association for Computing Machinery","conference":{"start_date":"1999-05-01","name":"STOC: Symposium on Theory of Computing","end_date":"1999-05-04","location":" Atlanta, GA, United States"},"year":"1999","citation":{"ieee":"A. Goel, M. H. Henzinger, S. Plotkin, and E. Tardos, “Scheduling data transfers in a network and the set scheduling problem,” in <i>Proceedings of the 31st annual ACM symposium on Theory of computing</i>,  Atlanta, GA, United States, 1999, pp. 189–197.","chicago":"Goel, Ashish, Monika H Henzinger, Serge Plotkin, and Eva Tardos. “Scheduling Data Transfers in a Network and the Set Scheduling Problem.” In <i>Proceedings of the 31st Annual ACM Symposium on Theory of Computing</i>, 189–97. Association for Computing Machinery, 1999. <a href=\"https://doi.org/10.1145/301250.301300\">https://doi.org/10.1145/301250.301300</a>.","apa":"Goel, A., Henzinger, M. H., Plotkin, S., &#38; Tardos, E. (1999). Scheduling data transfers in a network and the set scheduling problem. In <i>Proceedings of the 31st annual ACM symposium on Theory of computing</i> (pp. 189–197).  Atlanta, GA, United States: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/301250.301300\">https://doi.org/10.1145/301250.301300</a>","ama":"Goel A, Henzinger MH, Plotkin S, Tardos E. Scheduling data transfers in a network and the set scheduling problem. In: <i>Proceedings of the 31st Annual ACM Symposium on Theory of Computing</i>. Association for Computing Machinery; 1999:189-197. doi:<a href=\"https://doi.org/10.1145/301250.301300\">10.1145/301250.301300</a>","ista":"Goel A, Henzinger MH, Plotkin S, Tardos E. 1999. Scheduling data transfers in a network and the set scheduling problem. Proceedings of the 31st annual ACM symposium on Theory of computing. STOC: Symposium on Theory of Computing, 189–197.","mla":"Goel, Ashish, et al. “Scheduling Data Transfers in a Network and the Set Scheduling Problem.” <i>Proceedings of the 31st Annual ACM Symposium on Theory of Computing</i>, Association for Computing Machinery, 1999, pp. 189–97, doi:<a href=\"https://doi.org/10.1145/301250.301300\">10.1145/301250.301300</a>.","short":"A. Goel, M.H. Henzinger, S. Plotkin, E. Tardos, in:, Proceedings of the 31st Annual ACM Symposium on Theory of Computing, Association for Computing Machinery, 1999, pp. 189–197."},"date_updated":"2023-02-09T11:47:09Z","type":"conference","date_published":"1999-05-01T00:00:00Z","day":"01","publication_identifier":{"issn":["0196-6774"]},"doi":"10.1145/301250.301300","abstract":[{"lang":"eng","text":"In this paper we consider the online ftp problem. The goal is to service a sequence of file transfer requests given bandwidth constraints of the underlying communication network. The main result of the paper is a technique that leads to algorithms that optimize several natural metrics, such as max-stretch, total flow time, max flow time, and total completion time. In particular, we show how to achieve optimum total flow time and optimum max-stretch if we increase the capacity of the underlying network by a logarithmic factor. We show that the resource augmentation is necessary by proving polynomial lower bounds on the max-stretch and total flow time for the case where online and offline algorithms are using same-capacity edges. Moreover, we also give polylogarithmic lower bounds on the resource augmentation factor necessary in order to keep the total flow time and max-stretch within a constant factor of optimum."}],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1"},{"date_published":"1994-01-01T00:00:00Z","type":"book_chapter","publication_identifier":{"isbn":[" 9789810219239"]},"publist_id":"117","main_file_link":[{"url":"https://link.springer.com/article/10.1007/s100090050007"}],"status":"public","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","publication":"Theories and Experiences for Real-Time System Development","oa_version":"None","month":"01","language":[{"iso":"eng"}],"keyword":["real-time systems","clock variables"],"date_updated":"2022-06-02T08:07:57Z","year":"1994","citation":{"ama":"Alur R, Henzinger TA. Real-time system = discrete system + clock variables. In: Rus T, Rattray C, eds. <i>Theories and Experiences for Real-Time System Development</i>. Vol 2. AMAST Series in Computing. World Scientific Publishing; 1994:1-29. doi:<a href=\"https://doi.org/10.1142/9789812831583_0001\">10.1142/9789812831583_0001</a>","apa":"Alur, R., &#38; Henzinger, T. A. (1994). Real-time system = discrete system + clock variables. In T. Rus &#38; C. Rattray (Eds.), <i>Theories and Experiences for Real-Time System Development</i> (Vol. 2, pp. 1–29). World Scientific Publishing. <a href=\"https://doi.org/10.1142/9789812831583_0001\">https://doi.org/10.1142/9789812831583_0001</a>","ieee":"R. Alur and T. A. Henzinger, “Real-time system = discrete system + clock variables,” in <i>Theories and Experiences for Real-Time System Development</i>, vol. 2, T. Rus and C. Rattray, Eds. World Scientific Publishing, 1994, pp. 1–29.","chicago":"Alur, Rajeev, and Thomas A Henzinger. “Real-Time System = Discrete System + Clock Variables.” In <i>Theories and Experiences for Real-Time System Development</i>, edited by Teodor Rus and Charles Rattray, 2:1–29. AMAST Series in Computing. World Scientific Publishing, 1994. <a href=\"https://doi.org/10.1142/9789812831583_0001\">https://doi.org/10.1142/9789812831583_0001</a>.","mla":"Alur, Rajeev, and Thomas A. Henzinger. “Real-Time System = Discrete System + Clock Variables.” <i>Theories and Experiences for Real-Time System Development</i>, edited by Teodor Rus and Charles Rattray, vol. 2, World Scientific Publishing, 1994, pp. 1–29, doi:<a href=\"https://doi.org/10.1142/9789812831583_0001\">10.1142/9789812831583_0001</a>.","short":"R. Alur, T.A. Henzinger, in:, T. Rus, C. Rattray (Eds.), Theories and Experiences for Real-Time System Development, World Scientific Publishing, 1994, pp. 1–29.","ista":"Alur R, Henzinger TA. 1994.Real-time system = discrete system + clock variables. In: Theories and Experiences for Real-Time System Development. AMAST Series in Computing, vol. 2, 1–29."},"doi":"10.1142/9789812831583_0001","day":"01","abstract":[{"text":"We introduce a temporal logic for the specification of real-time systems. Our logic, TPTL, employs a novel quantifier construct for referencing time: the &quot;freeze&quot; quantifier binds a variable to the time of the local temporal context. TPTL is both a natural language for specification and a suitable formalism for verification. We present a tableau-based decision procedure and a model-checking algorithm for TPTL. Several generalizations of TPTL are shown to be highly undecidable.","lang":"eng"}],"volume":2,"acknowledgement":"The authors thank Rance Cleaveland, Limor Fix, David Karr, Peter Kopke, Fred Schneider, and Bernhard Steffen for helpful comments.","extern":"1","_id":"4590","author":[{"first_name":"Rajeev","last_name":"Alur","full_name":"Alur, Rajeev"},{"orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","date_created":"2018-12-11T12:09:38Z","article_processing_charge":"No","alternative_title":["AMAST Series in Computing"],"title":"Real-time system = discrete system + clock variables","intvolume":"         2","page":"1 - 29","quality_controlled":"1","series_title":"AMAST Series in Computing","publisher":"World Scientific Publishing","editor":[{"full_name":"Rus, Teodor","first_name":"Teodor","last_name":"Rus"},{"full_name":"Rattray, Charles","last_name":"Rattray","first_name":"Charles"}]}]