[{"file_date_updated":"2020-07-14T12:44:37Z","doi":"10.1007/s00145-016-9247-3","has_accepted_license":"1","publist_id":"6166","publication_status":"published","type":"journal_article","isi":1,"oa_version":"Submitted Version","project":[{"grant_number":"682815","call_identifier":"H2020","name":"Teaching Old Crypto New Tricks","_id":"258AA5B2-B435-11E9-9278-68D0E5697425"},{"name":"Provable Security for Physical Cryptography","_id":"258C570E-B435-11E9-9278-68D0E5697425","grant_number":"259668","call_identifier":"FP7"}],"ddc":["000"],"abstract":[{"lang":"eng","text":"We construct efficient authentication protocols and message authentication codes (MACs) whose security can be reduced to the learning parity with noise (LPN) problem. Despite a large body of work—starting with the (Formula presented.) protocol of Hopper and Blum in 2001—until now it was not even known how to construct an efficient authentication protocol from LPN which is secure against man-in-the-middle attacks. A MAC implies such a (two-round) protocol."}],"oa":1,"article_type":"original","date_published":"2017-10-01T00:00:00Z","date_updated":"2025-04-14T07:22:06Z","title":"Efficient authentication from hard learning problems","file":[{"checksum":"c647520d115b772a1682fc06fa273eb1","relation":"main_file","access_level":"open_access","file_size":516959,"creator":"dernst","date_created":"2020-05-14T16:30:17Z","date_updated":"2020-07-14T12:44:37Z","file_name":"2017_JournalCrypto_Kiltz.pdf","content_type":"application/pdf","file_id":"7843"}],"month":"10","day":"01","volume":30,"author":[{"last_name":"Kiltz","full_name":"Kiltz, Eike","first_name":"Eike"},{"id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","last_name":"Pietrzak","orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z","first_name":"Krzysztof Z"},{"last_name":"Venturi","first_name":"Daniele","full_name":"Venturi, Daniele"},{"last_name":"Cash","full_name":"Cash, David","first_name":"David"},{"last_name":"Jain","full_name":"Jain, Abhishek","first_name":"Abhishek"}],"page":"1238 - 1275","_id":"1187","related_material":{"record":[{"id":"3238","relation":"earlier_version","status":"public"}]},"date_created":"2018-12-11T11:50:37Z","department":[{"_id":"KrPi"}],"scopus_import":"1","ec_funded":1,"external_id":{"isi":["000410788600007"]},"publication":"Journal of Cryptology","status":"public","quality_controlled":"1","citation":{"mla":"Kiltz, Eike, et al. “Efficient Authentication from Hard Learning Problems.” <i>Journal of Cryptology</i>, vol. 30, no. 4, Springer, 2017, pp. 1238–75, doi:<a href=\"https://doi.org/10.1007/s00145-016-9247-3\">10.1007/s00145-016-9247-3</a>.","ieee":"E. Kiltz, K. Z. Pietrzak, D. Venturi, D. Cash, and A. Jain, “Efficient authentication from hard learning problems,” <i>Journal of Cryptology</i>, vol. 30, no. 4. Springer, pp. 1238–1275, 2017.","ama":"Kiltz E, Pietrzak KZ, Venturi D, Cash D, Jain A. Efficient authentication from hard learning problems. <i>Journal of Cryptology</i>. 2017;30(4):1238-1275. doi:<a href=\"https://doi.org/10.1007/s00145-016-9247-3\">10.1007/s00145-016-9247-3</a>","ista":"Kiltz E, Pietrzak KZ, Venturi D, Cash D, Jain A. 2017. Efficient authentication from hard learning problems. Journal of Cryptology. 30(4), 1238–1275.","chicago":"Kiltz, Eike, Krzysztof Z Pietrzak, Daniele Venturi, David Cash, and Abhishek Jain. “Efficient Authentication from Hard Learning Problems.” <i>Journal of Cryptology</i>. Springer, 2017. <a href=\"https://doi.org/10.1007/s00145-016-9247-3\">https://doi.org/10.1007/s00145-016-9247-3</a>.","apa":"Kiltz, E., Pietrzak, K. Z., Venturi, D., Cash, D., &#38; Jain, A. (2017). Efficient authentication from hard learning problems. <i>Journal of Cryptology</i>. Springer. <a href=\"https://doi.org/10.1007/s00145-016-9247-3\">https://doi.org/10.1007/s00145-016-9247-3</a>","short":"E. Kiltz, K.Z. Pietrzak, D. Venturi, D. Cash, A. Jain, Journal of Cryptology 30 (2017) 1238–1275."},"issue":"4","publisher":"Springer","year":"2017","language":[{"iso":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":"        30","article_processing_charge":"No"},{"project":[{"grant_number":"618091","call_identifier":"FP7","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation"},{"grant_number":"250152","call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation"}],"arxiv":1,"publication_status":"published","publist_id":"6160","doi":"10.1007/s11538-016-0244-3","type":"journal_article","main_file_link":[{"url":"https://arxiv.org/abs/1607.00944","open_access":"1"}],"isi":1,"oa_version":"Preprint","date_updated":"2025-09-22T09:44:54Z","date_published":"2017-03-01T00:00:00Z","title":"Existence of traveling waves for the generalized F–KPP equation","month":"03","oa":1,"abstract":[{"lang":"eng","text":"Variation in genotypes may be responsible for differences in dispersal rates, directional biases, and growth rates of individuals. These traits may favor certain genotypes and enhance their spatiotemporal spreading into areas occupied by the less advantageous genotypes. We study how these factors influence the speed of spreading in the case of two competing genotypes under the assumption that spatial variation of the total population is small compared to the spatial variation of the frequencies of the genotypes in the population. In that case, the dynamics of the frequency of one of the genotypes is approximately described by a generalized Fisher–Kolmogorov–Petrovskii–Piskunov (F–KPP) equation. This generalized F–KPP equation with (nonlinear) frequency-dependent diffusion and advection terms admits traveling wave solutions that characterize the invasion of the dominant genotype. Our existence results generalize the classical theory for traveling waves for the F–KPP with constant coefficients. Moreover, in the particular case of the quadratic (monostable) nonlinear growth–decay rate in the generalized F–KPP we study in detail the influence of the variance in diffusion and mean displacement rates of the two genotypes on the minimal wave propagation speed."}],"volume":79,"_id":"1191","page":"525-559","author":[{"first_name":"Richard","full_name":"Kollár, Richard","last_name":"Kollár"},{"id":"461468AE-F248-11E8-B48F-1D18A9856A87","last_name":"Novak","orcid":"0000-0002-2519-824X","full_name":"Novak, Sebastian","first_name":"Sebastian"}],"date_created":"2018-12-11T11:50:38Z","day":"01","issue":"3","year":"2017","publisher":"Springer","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","acknowledgement":"We thank Nick Barton, Katarína Bod’ová, and Sr\r\n-\r\ndan Sarikas for constructive feed-\r\nback and support. Furthermore, we would like to express our deep gratitude to the anonymous referees (one\r\nof whom, Jimmy Garnier, agreed to reveal his identity) and the editor Max Souza, for very helpful and\r\ndetailed comments and suggestions that significantly helped us to improve the manuscript. This project has\r\nreceived funding from the European Union’s Seventh Framework Programme for research, technological\r\ndevelopment and demonstration under Grant Agreement 618091 Speed of Adaptation in Population Genet-\r\nics and Evolutionary Computation (SAGE) and the European Research Council (ERC) Grant No. 250152\r\n(SN), from the Scientific Grant Agency of the Slovak Republic under the Grant 1/0459/13 and by the Slovak\r\nResearch and Development Agency under the Contract No. APVV-14-0378 (RK). RK would also like to\r\nthank IST Austria for its hospitality during the work on this project.","language":[{"iso":"eng"}],"article_processing_charge":"No","intvolume":"        79","scopus_import":"1","department":[{"_id":"NiBa"}],"ec_funded":1,"external_id":{"isi":["000395156200005"],"arxiv":["1607.00944"]},"quality_controlled":"1","citation":{"ieee":"R. Kollár and S. Novak, “Existence of traveling waves for the generalized F–KPP equation,” <i>Bulletin of Mathematical Biology</i>, vol. 79, no. 3. Springer, pp. 525–559, 2017.","mla":"Kollár, Richard, and Sebastian Novak. “Existence of Traveling Waves for the Generalized F–KPP Equation.” <i>Bulletin of Mathematical Biology</i>, vol. 79, no. 3, Springer, 2017, pp. 525–59, doi:<a href=\"https://doi.org/10.1007/s11538-016-0244-3\">10.1007/s11538-016-0244-3</a>.","ama":"Kollár R, Novak S. Existence of traveling waves for the generalized F–KPP equation. <i>Bulletin of Mathematical Biology</i>. 2017;79(3):525-559. doi:<a href=\"https://doi.org/10.1007/s11538-016-0244-3\">10.1007/s11538-016-0244-3</a>","chicago":"Kollár, Richard, and Sebastian Novak. “Existence of Traveling Waves for the Generalized F–KPP Equation.” <i>Bulletin of Mathematical Biology</i>. Springer, 2017. <a href=\"https://doi.org/10.1007/s11538-016-0244-3\">https://doi.org/10.1007/s11538-016-0244-3</a>.","ista":"Kollár R, Novak S. 2017. Existence of traveling waves for the generalized F–KPP equation. Bulletin of Mathematical Biology. 79(3), 525–559.","short":"R. Kollár, S. Novak, Bulletin of Mathematical Biology 79 (2017) 525–559.","apa":"Kollár, R., &#38; Novak, S. (2017). Existence of traveling waves for the generalized F–KPP equation. <i>Bulletin of Mathematical Biology</i>. Springer. <a href=\"https://doi.org/10.1007/s11538-016-0244-3\">https://doi.org/10.1007/s11538-016-0244-3</a>"},"publication":"Bulletin of Mathematical Biology","status":"public"},{"_id":"1192","author":[{"last_name":"Kazda","id":"3B32BAA8-F248-11E8-B48F-1D18A9856A87","full_name":"Kazda, Alexandr","first_name":"Alexandr"},{"last_name":"Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","full_name":"Kolmogorov, Vladimir","first_name":"Vladimir"},{"last_name":"Rolinek","id":"3CB3BC06-F248-11E8-B48F-1D18A9856A87","full_name":"Rolinek, Michal","first_name":"Michal"}],"page":"307 - 326","date_created":"2018-12-11T11:50:38Z","related_material":{"record":[{"status":"public","relation":"later_version","id":"6032"}]},"day":"01","year":"2017","publisher":"SIAM","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"article_processing_charge":"No","department":[{"_id":"VlKo"}],"ec_funded":1,"external_id":{"arxiv":["1602.03124"],"isi":["000426965800020"]},"quality_controlled":"1","citation":{"ama":"Kazda A, Kolmogorov V, Rolinek M. Even delta-matroids and the complexity of planar Boolean CSPs. In: SIAM; 2017:307-326. doi:<a href=\"https://doi.org/10.1137/1.9781611974782.20\">10.1137/1.9781611974782.20</a>","mla":"Kazda, Alexandr, et al. <i>Even Delta-Matroids and the Complexity of Planar Boolean CSPs</i>. SIAM, 2017, pp. 307–26, doi:<a href=\"https://doi.org/10.1137/1.9781611974782.20\">10.1137/1.9781611974782.20</a>.","ieee":"A. Kazda, V. Kolmogorov, and M. Rolinek, “Even delta-matroids and the complexity of planar Boolean CSPs,” presented at the SODA: Symposium on Discrete Algorithms, Barcelona, Spain, 2017, pp. 307–326.","apa":"Kazda, A., Kolmogorov, V., &#38; Rolinek, M. (2017). Even delta-matroids and the complexity of planar Boolean CSPs (pp. 307–326). Presented at the SODA: Symposium on Discrete Algorithms, Barcelona, Spain: SIAM. <a href=\"https://doi.org/10.1137/1.9781611974782.20\">https://doi.org/10.1137/1.9781611974782.20</a>","short":"A. Kazda, V. Kolmogorov, M. Rolinek, in:, SIAM, 2017, pp. 307–326.","ista":"Kazda A, Kolmogorov V, Rolinek M. 2017. Even delta-matroids and the complexity of planar Boolean CSPs. SODA: Symposium on Discrete Algorithms, 307–326.","chicago":"Kazda, Alexandr, Vladimir Kolmogorov, and Michal Rolinek. “Even Delta-Matroids and the Complexity of Planar Boolean CSPs,” 307–26. SIAM, 2017. <a href=\"https://doi.org/10.1137/1.9781611974782.20\">https://doi.org/10.1137/1.9781611974782.20</a>."},"status":"public","conference":{"start_date":"2017-01-16","name":"SODA: Symposium on Discrete Algorithms","end_date":"2017-01019","location":"Barcelona, Spain"},"project":[{"call_identifier":"FP7","grant_number":"616160","name":"Discrete Optimization in Computer Vision: Theory and Practice","_id":"25FBA906-B435-11E9-9278-68D0E5697425"}],"arxiv":1,"doi":"10.1137/1.9781611974782.20","publication_status":"published","publist_id":"6159","main_file_link":[{"url":"https://arxiv.org/abs/1602.03124","open_access":"1"}],"type":"conference","isi":1,"oa_version":"Submitted Version","date_updated":"2025-06-04T08:46:59Z","publication_identifier":{"isbn":["978-161197478-2"]},"date_published":"2017-01-01T00:00:00Z","title":"Even delta-matroids and the complexity of planar Boolean CSPs","month":"01","oa":1,"abstract":[{"text":"The main result of this paper is a generalization of the classical blossom algorithm for finding perfect matchings. Our algorithm can efficiently solve Boolean CSPs where each variable appears in exactly two constraints (we call it edge CSP) and all constraints are even Δ-matroid relations (represented by lists of tuples). As a consequence of this, we settle the complexity classification of planar Boolean CSPs started by Dvorak and Kupec. Knowing that edge CSP is tractable for even Δ-matroid constraints allows us to extend the tractability result to a larger class of Δ-matroids that includes many classes that were known to be tractable before, namely co-independent, compact, local and binary.","lang":"eng"}]},{"issue":"1","year":"2017","publisher":"ACM","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","intvolume":"        52","department":[{"_id":"KrCh"}],"scopus_import":"1","ec_funded":1,"external_id":{"arxiv":["1611.01063"],"isi":["000408311200013"]},"status":"public","citation":{"mla":"Chatterjee, Krishnendu, et al. <i>Stochastic Invariants for Probabilistic Termination</i>. Vol. 52, no. 1, ACM, 2017, pp. 145–60, doi:<a href=\"https://doi.org/10.1145/3009837.3009873\">10.1145/3009837.3009873</a>.","ieee":"K. Chatterjee, P. Novotný, and D. Zikelic, “Stochastic invariants for probabilistic termination,” presented at the POPL: Principles of Programming Languages, Paris, France, 2017, vol. 52, no. 1, pp. 145–160.","ama":"Chatterjee K, Novotný P, Zikelic D. Stochastic invariants for probabilistic termination. In: Vol 52. ACM; 2017:145-160. doi:<a href=\"https://doi.org/10.1145/3009837.3009873\">10.1145/3009837.3009873</a>","ista":"Chatterjee K, Novotný P, Zikelic D. 2017. Stochastic invariants for probabilistic termination. POPL: Principles of Programming Languages, ACM SIGPLAN Notices, vol. 52, 145–160.","chicago":"Chatterjee, Krishnendu, Petr Novotný, and Djordje Zikelic. “Stochastic Invariants for Probabilistic Termination,” 52:145–60. ACM, 2017. <a href=\"https://doi.org/10.1145/3009837.3009873\">https://doi.org/10.1145/3009837.3009873</a>.","short":"K. Chatterjee, P. Novotný, D. Zikelic, in:, ACM, 2017, pp. 145–160.","apa":"Chatterjee, K., Novotný, P., &#38; Zikelic, D. (2017). Stochastic invariants for probabilistic termination (Vol. 52, pp. 145–160). Presented at the POPL: Principles of Programming Languages, Paris, France: ACM. <a href=\"https://doi.org/10.1145/3009837.3009873\">https://doi.org/10.1145/3009837.3009873</a>"},"quality_controlled":"1","volume":52,"author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu"},{"last_name":"Novotny","id":"3CC3B868-F248-11E8-B48F-1D18A9856A87","full_name":"Novotny, Petr","first_name":"Petr"},{"last_name":"Zikelic","first_name":"Djordje","full_name":"Zikelic, Djordje"}],"page":"145 - 160","_id":"1194","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"14539"}]},"date_created":"2018-12-11T11:50:39Z","day":"01","date_published":"2017-01-01T00:00:00Z","date_updated":"2026-04-07T13:27:56Z","publication_identifier":{"issn":["0730-8566"]},"title":"Stochastic invariants for probabilistic termination","month":"01","abstract":[{"text":"Termination is one of the basic liveness properties, and we study the termination problem for probabilistic programs with real-valued variables. Previous works focused on the qualitative problem that asks whether an input program terminates with probability~1 (almost-sure termination). A powerful approach for this qualitative problem is the notion of ranking supermartingales with respect to a given set of invariants. The quantitative problem (probabilistic termination) asks for bounds on the termination probability. A fundamental and conceptual drawback of the existing approaches to address probabilistic termination is that even though the supermartingales consider the probabilistic behavior of the programs, the invariants are obtained completely ignoring the probabilistic aspect. In this work we address the probabilistic termination problem for linear-arithmetic probabilistic programs with nondeterminism. We define the notion of {\\em stochastic invariants}, which are constraints along with a probability bound that the constraints hold. We introduce a concept of {\\em repulsing supermartingales}. First, we show that repulsing supermartingales can be used to obtain bounds on the probability of the stochastic invariants. Second, we show the effectiveness of repulsing supermartingales in the following three ways: (1)~With a combination of ranking and repulsing supermartingales we can compute lower bounds on the probability of termination; (2)~repulsing supermartingales provide witnesses for refutation of almost-sure termination; and (3)~with a combination of ranking and repulsing supermartingales we can establish persistence properties of probabilistic programs. We also present results on related computational problems and an experimental evaluation of our approach on academic examples. ","lang":"eng"}],"oa":1,"conference":{"name":"POPL: Principles of Programming Languages","start_date":"2017-01-15","end_date":"2017-01-21","location":"Paris, France"},"alternative_title":["ACM SIGPLAN Notices"],"project":[{"grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"grant_number":"S11402-N23","call_identifier":"FWF","name":"Moderne Concurrency Paradigms","_id":"25F5A88A-B435-11E9-9278-68D0E5697425"},{"grant_number":"279307","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734"}],"arxiv":1,"publist_id":"6157","doi":"10.1145/3009837.3009873","publication_status":"published","isi":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1611.01063"}],"type":"conference","oa_version":"Submitted Version"},{"day":"01","date_created":"2018-12-11T11:50:39Z","author":[{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","orcid":"0000−0002−2985−7724","first_name":"Thomas A","full_name":"Henzinger, Thomas A"},{"first_name":"Jan","full_name":"Otop, Jan","last_name":"Otop","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87"}],"page":"166 - 190","_id":"1196","volume":23,"status":"public","publication":"Nonlinear Analysis: Hybrid Systems","citation":{"ieee":"T. A. Henzinger and J. Otop, “Model measuring for discrete and hybrid systems,” <i>Nonlinear Analysis: Hybrid Systems</i>, vol. 23. Elsevier, pp. 166–190, 2017.","mla":"Henzinger, Thomas A., and Jan Otop. “Model Measuring for Discrete and Hybrid Systems.” <i>Nonlinear Analysis: Hybrid Systems</i>, vol. 23, Elsevier, 2017, pp. 166–90, doi:<a href=\"https://doi.org/10.1016/j.nahs.2016.09.001\">10.1016/j.nahs.2016.09.001</a>.","ama":"Henzinger TA, Otop J. Model measuring for discrete and hybrid systems. <i>Nonlinear Analysis: Hybrid Systems</i>. 2017;23:166-190. doi:<a href=\"https://doi.org/10.1016/j.nahs.2016.09.001\">10.1016/j.nahs.2016.09.001</a>","chicago":"Henzinger, Thomas A, and Jan Otop. “Model Measuring for Discrete and Hybrid Systems.” <i>Nonlinear Analysis: Hybrid Systems</i>. Elsevier, 2017. <a href=\"https://doi.org/10.1016/j.nahs.2016.09.001\">https://doi.org/10.1016/j.nahs.2016.09.001</a>.","ista":"Henzinger TA, Otop J. 2017. Model measuring for discrete and hybrid systems. Nonlinear Analysis: Hybrid Systems. 23, 166–190.","apa":"Henzinger, T. A., &#38; Otop, J. (2017). Model measuring for discrete and hybrid systems. <i>Nonlinear Analysis: Hybrid Systems</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.nahs.2016.09.001\">https://doi.org/10.1016/j.nahs.2016.09.001</a>","short":"T.A. Henzinger, J. Otop, Nonlinear Analysis: Hybrid Systems 23 (2017) 166–190."},"quality_controlled":"1","external_id":{"isi":["000390637000011"]},"ec_funded":1,"department":[{"_id":"ToHe"}],"scopus_import":"1","intvolume":"        23","article_processing_charge":"No","acknowledgement":"This research was supported in part by the European Research Council (ERC) under grant 267989 (QUAREM), by the Austrian Science Fund1 (FWF) under grants S11402-N23 (RiSE) and Z211-N23 (Wittgenstein Award), and by the National Science Centre (NCN), Poland under grant 2014/15/D/ST6/04543.\r\nA Technical Report of this article is available via: https://repository.ist.ac.at/171/","language":[{"iso":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","year":"2017","publisher":"Elsevier","oa_version":"None","type":"journal_article","isi":1,"publist_id":"6154","publication_status":"published","doi":"10.1016/j.nahs.2016.09.001","project":[{"name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","call_identifier":"FP7"},{"name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF"},{"name":"Formal methods for the design and analysis of complex systems","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","call_identifier":"FWF"}],"abstract":[{"text":"We define the . model-measuring problem: given a model . M and specification . ϕ, what is the maximal distance . ρ such that all models . M' within distance . ρ from . M satisfy (or violate) . ϕ. The model-measuring problem presupposes a distance function on models. We concentrate on . automatic distance functions, which are defined by weighted automata. The model-measuring problem subsumes several generalizations of the classical model-checking problem, in particular, quantitative model-checking problems that measure the degree of satisfaction of a specification; robustness problems that measure how much a model can be perturbed without violating the specification; and parameter synthesis for hybrid systems. We show that for automatic distance functions, and (a) . ω-regular linear-time, (b) . ω-regular branching-time, and (c) hybrid specifications, the model-measuring problem can be solved.We use automata-theoretic model-checking methods for model measuring, replacing the emptiness question for word, tree, and hybrid automata by the . optimal-value question for the weighted versions of these automata. For automata over words and trees, we consider weighted automata that accumulate weights by maximizing, summing, discounting, and limit averaging. For hybrid automata, we consider monotonic (parametric) hybrid automata, a hybrid counterpart of (discrete) weighted automata.We give several examples of using the model-measuring problem to compute various notions of robustness and quantitative satisfaction for temporal specifications. Further, we propose the modeling framework for model measuring to ease the specification and reduce the likelihood of errors in modeling.Finally, we present a variant of the model-measuring problem, called the . model-repair problem. The model-repair problem applies to models that do not satisfy the specification; it can be used to derive restrictions, under which the model satisfies the specification, i.e., to repair the model.","lang":"eng"}],"month":"02","title":"Model measuring for discrete and hybrid systems","date_published":"2017-02-01T00:00:00Z","date_updated":"2025-04-15T06:25:59Z"},{"issue":"3","publisher":"Springer","year":"2017","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). ","language":[{"iso":"eng"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","intvolume":"       107","article_processing_charge":"Yes (via OA deal)","department":[{"_id":"RoSe"}],"scopus_import":"1","external_id":{"isi":["000394280200007"]},"status":"public","publication":"Letters in Mathematical Physics","quality_controlled":"1","citation":{"ista":"Moser T, Seiringer R. 2017. Triviality of a model of particles with point interactions in the thermodynamic limit. Letters in Mathematical Physics. 107(3), 533–552.","chicago":"Moser, Thomas, and Robert Seiringer. “Triviality of a Model of Particles with Point Interactions in the Thermodynamic Limit.” <i>Letters in Mathematical Physics</i>. Springer, 2017. <a href=\"https://doi.org/10.1007/s11005-016-0915-x\">https://doi.org/10.1007/s11005-016-0915-x</a>.","apa":"Moser, T., &#38; Seiringer, R. (2017). Triviality of a model of particles with point interactions in the thermodynamic limit. <i>Letters in Mathematical Physics</i>. Springer. <a href=\"https://doi.org/10.1007/s11005-016-0915-x\">https://doi.org/10.1007/s11005-016-0915-x</a>","short":"T. Moser, R. Seiringer, Letters in Mathematical Physics 107 (2017) 533–552.","mla":"Moser, Thomas, and Robert Seiringer. “Triviality of a Model of Particles with Point Interactions in the Thermodynamic Limit.” <i>Letters in Mathematical Physics</i>, vol. 107, no. 3, Springer, 2017, pp. 533–52, doi:<a href=\"https://doi.org/10.1007/s11005-016-0915-x\">10.1007/s11005-016-0915-x</a>.","ieee":"T. Moser and R. Seiringer, “Triviality of a model of particles with point interactions in the thermodynamic limit,” <i>Letters in Mathematical Physics</i>, vol. 107, no. 3. Springer, pp. 533–552, 2017.","ama":"Moser T, Seiringer R. Triviality of a model of particles with point interactions in the thermodynamic limit. <i>Letters in Mathematical Physics</i>. 2017;107(3):533-552. doi:<a href=\"https://doi.org/10.1007/s11005-016-0915-x\">10.1007/s11005-016-0915-x</a>"},"volume":107,"author":[{"id":"2B5FC9A4-F248-11E8-B48F-1D18A9856A87","last_name":"Moser","full_name":"Moser, Thomas","first_name":"Thomas"},{"first_name":"Robert","full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","last_name":"Seiringer"}],"page":" 533 - 552","_id":"1198","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"52"}]},"date_created":"2018-12-11T11:50:40Z","day":"01","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_published":"2017-03-01T00:00:00Z","pubrep_id":"723","date_updated":"2026-04-16T10:06:46Z","publication_identifier":{"issn":["0377-9017"]},"title":"Triviality of a model of particles with point interactions in the thermodynamic limit","file":[{"date_created":"2018-12-12T10:17:40Z","creator":"system","content_type":"application/pdf","file_name":"IST-2016-723-v1+1_s11005-016-0915-x.pdf","date_updated":"2020-07-14T12:44:38Z","file_id":"5296","relation":"main_file","access_level":"open_access","file_size":587207,"checksum":"c0c835def162c1bc52f978fad26e3c2f"}],"month":"03","abstract":[{"text":"We consider a model of fermions interacting via point interactions, defined via a certain weighted Dirichlet form. While for two particles the interaction corresponds to infinite scattering length, the presence of further particles effectively decreases the interaction strength. We show that the model becomes trivial in the thermodynamic limit, in the sense that the free energy density at any given particle density and temperature agrees with the corresponding expression for non-interacting particles.","lang":"eng"}],"oa":1,"project":[{"call_identifier":"FWF","grant_number":"P27533_N27","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","_id":"25C878CE-B435-11E9-9278-68D0E5697425"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"ddc":["510","539"],"publication_status":"published","file_date_updated":"2020-07-14T12:44:38Z","doi":"10.1007/s11005-016-0915-x","publist_id":"6152","has_accepted_license":"1","isi":1,"type":"journal_article","oa_version":"Published Version"},{"project":[{"name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"250152"}],"oa_version":"Submitted Version","isi":1,"type":"journal_article","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5176114/","open_access":"1"}],"publication_status":"published","doi":"10.1038/hdy.2016.109","publist_id":"6151","month":"01","title":"How does epistasis influence the response to selection?","date_published":"2017-01-01T00:00:00Z","date_updated":"2025-04-15T07:11:02Z","abstract":[{"text":"Much of quantitative genetics is based on the ‘infinitesimal model’, under which selection has a negligible effect on the genetic variance. This is typically justified by assuming a very large number of loci with additive effects. However, it applies even when genes interact, provided that the number of loci is large enough that selection on each of them is weak relative to random drift. In the long term, directional selection will change allele frequencies, but even then, the effects of epistasis on the ultimate change in trait mean due to selection may be modest. Stabilising selection can maintain many traits close to their optima, even when the underlying alleles are weakly selected. However, the number of traits that can be optimised is apparently limited to ~4Ne by the ‘drift load’, and this is hard to reconcile with the apparent complexity of many organisms. Just as for the mutation load, this limit can be evaded by a particular form of negative epistasis. A more robust limit is set by the variance in reproductive success. This suggests that selection accumulates information most efficiently in the infinitesimal regime, when selection on individual alleles is weak, and comparable with random drift. A review of evidence on selection strength suggests that although most variance in fitness may be because of alleles with large Nes, substantial amounts of adaptation may be because of alleles in the infinitesimal regime, in which epistasis has modest effects.","lang":"eng"}],"oa":1,"related_material":{"record":[{"id":"9710","relation":"research_data","status":"public"}]},"date_created":"2018-12-11T11:50:40Z","page":"96 - 109","author":[{"orcid":"0000-0002-8548-5240","first_name":"Nicholas H","full_name":"Barton, Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"_id":"1199","volume":118,"day":"01","article_processing_charge":"No","intvolume":"       118","language":[{"iso":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Nature Publishing Group","year":"2017","publication":"Heredity","status":"public","quality_controlled":"1","citation":{"ista":"Barton NH. 2017. How does epistasis influence the response to selection? Heredity. 118, 96–109.","chicago":"Barton, Nicholas H. “How Does Epistasis Influence the Response to Selection?” <i>Heredity</i>. Nature Publishing Group, 2017. <a href=\"https://doi.org/10.1038/hdy.2016.109\">https://doi.org/10.1038/hdy.2016.109</a>.","apa":"Barton, N. H. (2017). How does epistasis influence the response to selection? <i>Heredity</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/hdy.2016.109\">https://doi.org/10.1038/hdy.2016.109</a>","short":"N.H. Barton, Heredity 118 (2017) 96–109.","mla":"Barton, Nicholas H. “How Does Epistasis Influence the Response to Selection?” <i>Heredity</i>, vol. 118, Nature Publishing Group, 2017, pp. 96–109, doi:<a href=\"https://doi.org/10.1038/hdy.2016.109\">10.1038/hdy.2016.109</a>.","ieee":"N. H. Barton, “How does epistasis influence the response to selection?,” <i>Heredity</i>, vol. 118. Nature Publishing Group, pp. 96–109, 2017.","ama":"Barton NH. How does epistasis influence the response to selection? <i>Heredity</i>. 2017;118:96-109. doi:<a href=\"https://doi.org/10.1038/hdy.2016.109\">10.1038/hdy.2016.109</a>"},"external_id":{"isi":["000392229100011"]},"ec_funded":1,"department":[{"_id":"NiBa"}],"scopus_import":"1"},{"date_created":"2018-12-11T11:50:43Z","page":"947 - 990","author":[{"id":"442E6A6C-F248-11E8-B48F-1D18A9856A87","last_name":"Bao","orcid":"0000-0003-3036-1475","full_name":"Bao, Zhigang","first_name":"Zhigang"},{"orcid":"0000-0001-5366-9603","full_name":"Erdös, László","first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","last_name":"Erdös"},{"full_name":"Schnelli, Kevin","first_name":"Kevin","orcid":"0000-0003-0954-3231","id":"434AD0AE-F248-11E8-B48F-1D18A9856A87","last_name":"Schnelli"}],"_id":"1207","volume":349,"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"day":"01","article_processing_charge":"Yes (via OA deal)","intvolume":"       349","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2017","publisher":"Springer","issue":"3","publication":"Communications in Mathematical Physics","status":"public","quality_controlled":"1","citation":{"ista":"Bao Z, Erdös L, Schnelli K. 2017. Local law of addition of random matrices on optimal scale. Communications in Mathematical Physics. 349(3), 947–990.","chicago":"Bao, Zhigang, László Erdös, and Kevin Schnelli. “Local Law of Addition of Random Matrices on Optimal Scale.” <i>Communications in Mathematical Physics</i>. Springer, 2017. <a href=\"https://doi.org/10.1007/s00220-016-2805-6\">https://doi.org/10.1007/s00220-016-2805-6</a>.","apa":"Bao, Z., Erdös, L., &#38; Schnelli, K. (2017). Local law of addition of random matrices on optimal scale. <i>Communications in Mathematical Physics</i>. Springer. <a href=\"https://doi.org/10.1007/s00220-016-2805-6\">https://doi.org/10.1007/s00220-016-2805-6</a>","short":"Z. Bao, L. Erdös, K. Schnelli, Communications in Mathematical Physics 349 (2017) 947–990.","mla":"Bao, Zhigang, et al. “Local Law of Addition of Random Matrices on Optimal Scale.” <i>Communications in Mathematical Physics</i>, vol. 349, no. 3, Springer, 2017, pp. 947–90, doi:<a href=\"https://doi.org/10.1007/s00220-016-2805-6\">10.1007/s00220-016-2805-6</a>.","ieee":"Z. Bao, L. Erdös, and K. Schnelli, “Local law of addition of random matrices on optimal scale,” <i>Communications in Mathematical Physics</i>, vol. 349, no. 3. Springer, pp. 947–990, 2017.","ama":"Bao Z, Erdös L, Schnelli K. Local law of addition of random matrices on optimal scale. <i>Communications in Mathematical Physics</i>. 2017;349(3):947-990. doi:<a href=\"https://doi.org/10.1007/s00220-016-2805-6\">10.1007/s00220-016-2805-6</a>"},"external_id":{"isi":["000393696700005"]},"ec_funded":1,"department":[{"_id":"LaEr"}],"scopus_import":"1","ddc":["530"],"project":[{"grant_number":"338804","call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","name":"Random matrices, universality and disordered quantum systems"}],"oa_version":"Published Version","type":"journal_article","isi":1,"publication_status":"published","file_date_updated":"2020-07-14T12:44:39Z","doi":"10.1007/s00220-016-2805-6","has_accepted_license":"1","publist_id":"6141","file":[{"relation":"main_file","file_size":1033743,"access_level":"open_access","checksum":"ddff79154c3daf27237de5383b1264a9","creator":"system","date_created":"2018-12-12T10:14:47Z","file_id":"5102","content_type":"application/pdf","date_updated":"2020-07-14T12:44:39Z","file_name":"IST-2016-722-v1+1_s00220-016-2805-6.pdf"}],"month":"02","title":"Local law of addition of random matrices on optimal scale","date_published":"2017-02-01T00:00:00Z","pubrep_id":"722","date_updated":"2025-07-10T11:50:22Z","publication_identifier":{"issn":["0010-3616"]},"abstract":[{"lang":"eng","text":"The eigenvalue distribution of the sum of two large Hermitian matrices, when one of them is conjugated by a Haar distributed unitary matrix, is asymptotically given by the free convolution of their spectral distributions. We prove that this convergence also holds locally in the bulk of the spectrum, down to the optimal scales larger than the eigenvalue spacing. The corresponding eigenvectors are fully delocalized. Similar results hold for the sum of two real symmetric matrices, when one is conjugated by Haar orthogonal matrix."}],"oa":1},{"date_published":"2017-09-01T00:00:00Z","publication_identifier":{"issn":["1369-7412"]},"date_updated":"2025-06-04T09:41:22Z","title":"Maximum likelihood estimation for linear Gaussian covariance models","month":"09","abstract":[{"lang":"eng","text":"We study parameter estimation in linear Gaussian covariance models, which are p-dimensional Gaussian models with linear constraints on the covariance matrix. Maximum likelihood estimation for this class of models leads to a non-convex optimization problem which typically has many local maxima. Using recent results on the asymptotic distribution of extreme eigenvalues of the Wishart distribution, we provide sufficient conditions for any hill climbing method to converge to the global maximum. Although we are primarily interested in the case in which n≫p, the proofs of our results utilize large sample asymptotic theory under the scheme n/p→γ&gt;1. Remarkably, our numerical simulations indicate that our results remain valid for p as small as 2. An important consequence of this analysis is that, for sample sizes n≃14p, maximum likelihood estimation for linear Gaussian covariance models behaves as if it were a convex optimization problem. © 2016 The Royal Statistical Society and Blackwell Publishing Ltd."}],"oa":1,"project":[{"call_identifier":"FWF","grant_number":"Y 903-N35","_id":"2530CA10-B435-11E9-9278-68D0E5697425","name":"Gaussian Graphical Models: Theory and Applications"}],"arxiv":1,"publist_id":"6142","doi":"10.1111/rssb.12217","publication_status":"published","type":"journal_article","main_file_link":[{"url":"https://arxiv.org/abs/1408.5604","open_access":"1"}],"isi":1,"oa_version":"Submitted Version","issue":"4","publisher":"Wiley-Blackwell","year":"2017","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"        79","article_processing_charge":"No","department":[{"_id":"CaUh"}],"scopus_import":"1","external_id":{"isi":["000411712300012"],"arxiv":["1408.5604"]},"publication":"Journal of the Royal Statistical Society. Series B: Statistical Methodology","status":"public","quality_controlled":"1","citation":{"ieee":"P. Zwiernik, C. Uhler, and D. Richards, “Maximum likelihood estimation for linear Gaussian covariance models,” <i>Journal of the Royal Statistical Society. Series B: Statistical Methodology</i>, vol. 79, no. 4. Wiley-Blackwell, pp. 1269–1292, 2017.","mla":"Zwiernik, Piotr, et al. “Maximum Likelihood Estimation for Linear Gaussian Covariance Models.” <i>Journal of the Royal Statistical Society. Series B: Statistical Methodology</i>, vol. 79, no. 4, Wiley-Blackwell, 2017, pp. 1269–92, doi:<a href=\"https://doi.org/10.1111/rssb.12217\">10.1111/rssb.12217</a>.","ama":"Zwiernik P, Uhler C, Richards D. Maximum likelihood estimation for linear Gaussian covariance models. <i>Journal of the Royal Statistical Society Series B: Statistical Methodology</i>. 2017;79(4):1269-1292. doi:<a href=\"https://doi.org/10.1111/rssb.12217\">10.1111/rssb.12217</a>","ista":"Zwiernik P, Uhler C, Richards D. 2017. Maximum likelihood estimation for linear Gaussian covariance models. Journal of the Royal Statistical Society. Series B: Statistical Methodology. 79(4), 1269–1292.","chicago":"Zwiernik, Piotr, Caroline Uhler, and Donald Richards. “Maximum Likelihood Estimation for Linear Gaussian Covariance Models.” <i>Journal of the Royal Statistical Society. Series B: Statistical Methodology</i>. Wiley-Blackwell, 2017. <a href=\"https://doi.org/10.1111/rssb.12217\">https://doi.org/10.1111/rssb.12217</a>.","short":"P. Zwiernik, C. Uhler, D. Richards, Journal of the Royal Statistical Society. Series B: Statistical Methodology 79 (2017) 1269–1292.","apa":"Zwiernik, P., Uhler, C., &#38; Richards, D. (2017). Maximum likelihood estimation for linear Gaussian covariance models. <i>Journal of the Royal Statistical Society. Series B: Statistical Methodology</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/rssb.12217\">https://doi.org/10.1111/rssb.12217</a>"},"volume":79,"page":"1269 - 1292","author":[{"first_name":"Piotr","full_name":"Zwiernik, Piotr","last_name":"Zwiernik"},{"last_name":"Uhler","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","full_name":"Uhler, Caroline","first_name":"Caroline","orcid":"0000-0002-7008-0216"},{"full_name":"Richards, Donald","first_name":"Donald","last_name":"Richards"}],"_id":"1208","date_created":"2018-12-11T11:50:43Z","day":"01","corr_author":"1"},{"page":"636-655","author":[{"orcid":"0000-0003-0423-5010","first_name":"Nazmi B","full_name":"Budanur, Nazmi B","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","last_name":"Budanur"},{"last_name":"Cvitanović","first_name":"Predrag","full_name":"Cvitanović, Predrag"}],"_id":"1211","date_created":"2018-12-11T11:50:44Z","volume":167,"day":"01","acknowledgement":"This work was supported by the family of late G. Robinson, Jr. and NSF Grant DMS-1211827. ","language":[{"iso":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","intvolume":"       167","article_processing_charge":"No","issue":"3-4","publisher":"Springer","year":"2017","external_id":{"isi":["000400233600014"]},"status":"public","publication":"Journal of Statistical Physics","quality_controlled":"1","citation":{"ieee":"N. B. Budanur and P. Cvitanović, “Unstable manifolds of relative periodic orbits in the symmetry reduced state space of the Kuramoto–Sivashinsky system,” <i>Journal of Statistical Physics</i>, vol. 167, no. 3–4. Springer, pp. 636–655, 2017.","mla":"Budanur, Nazmi B., and Predrag Cvitanović. “Unstable Manifolds of Relative Periodic Orbits in the Symmetry Reduced State Space of the Kuramoto–Sivashinsky System.” <i>Journal of Statistical Physics</i>, vol. 167, no. 3–4, Springer, 2017, pp. 636–55, doi:<a href=\"https://doi.org/10.1007/s10955-016-1672-z\">10.1007/s10955-016-1672-z</a>.","ama":"Budanur NB, Cvitanović P. Unstable manifolds of relative periodic orbits in the symmetry reduced state space of the Kuramoto–Sivashinsky system. <i>Journal of Statistical Physics</i>. 2017;167(3-4):636-655. doi:<a href=\"https://doi.org/10.1007/s10955-016-1672-z\">10.1007/s10955-016-1672-z</a>","chicago":"Budanur, Nazmi B, and Predrag Cvitanović. “Unstable Manifolds of Relative Periodic Orbits in the Symmetry Reduced State Space of the Kuramoto–Sivashinsky System.” <i>Journal of Statistical Physics</i>. Springer, 2017. <a href=\"https://doi.org/10.1007/s10955-016-1672-z\">https://doi.org/10.1007/s10955-016-1672-z</a>.","ista":"Budanur NB, Cvitanović P. 2017. Unstable manifolds of relative periodic orbits in the symmetry reduced state space of the Kuramoto–Sivashinsky system. Journal of Statistical Physics. 167(3–4), 636–655.","apa":"Budanur, N. B., &#38; Cvitanović, P. (2017). Unstable manifolds of relative periodic orbits in the symmetry reduced state space of the Kuramoto–Sivashinsky system. <i>Journal of Statistical Physics</i>. Springer. <a href=\"https://doi.org/10.1007/s10955-016-1672-z\">https://doi.org/10.1007/s10955-016-1672-z</a>","short":"N.B. Budanur, P. Cvitanović, Journal of Statistical Physics 167 (2017) 636–655."},"department":[{"_id":"BjHo"}],"scopus_import":"1","ddc":["530"],"type":"journal_article","isi":1,"oa_version":"Submitted Version","has_accepted_license":"1","file_date_updated":"2020-07-14T12:44:39Z","publist_id":"6136","doi":"10.1007/s10955-016-1672-z","publication_status":"published","file":[{"date_updated":"2020-07-14T12:44:39Z","content_type":"application/pdf","file_name":"IST-2017-782-v1+1_BudCvi15.pdf","file_id":"5319","date_created":"2018-12-12T10:18:01Z","creator":"system","file_size":2820207,"access_level":"open_access","relation":"main_file","checksum":"3e971d09eb167761aa0888ed415b0056"}],"month":"05","date_published":"2017-05-01T00:00:00Z","pubrep_id":"782","date_updated":"2025-09-22T09:36:50Z","title":"Unstable manifolds of relative periodic orbits in the symmetry reduced state space of the Kuramoto–Sivashinsky system","abstract":[{"text":"Systems such as fluid flows in channels and pipes or the complex Ginzburg–Landau system, defined over periodic domains, exhibit both continuous symmetries, translational and rotational, as well as discrete symmetries under spatial reflections or complex conjugation. The simplest, and very common symmetry of this type is the equivariance of the defining equations under the orthogonal group O(2). We formulate a novel symmetry reduction scheme for such systems by combining the method of slices with invariant polynomial methods, and show how it works by applying it to the Kuramoto–Sivashinsky system in one spatial dimension. As an example, we track a relative periodic orbit through a sequence of bifurcations to the onset of chaos. Within the symmetry-reduced state space we are able to compute and visualize the unstable manifolds of relative periodic orbits, their torus bifurcations, a transition to chaos via torus breakdown, and heteroclinic connections between various relative periodic orbits. It would be very hard to carry through such analysis in the full state space, without a symmetry reduction such as the one we present here.","lang":"eng"}],"oa":1},{"oa_version":"None","type":"book_chapter","isi":1,"publist_id":"6134","doi":"10.1016/bs.mcb.2016.03.036","publication_status":"published","project":[{"grant_number":"ALTF 2015-1163","_id":"2596EAB6-B435-11E9-9278-68D0E5697425","name":"Synthesis of bacterial cell wall"},{"grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"alternative_title":["Methods in Cell Biology"],"abstract":[{"lang":"eng","text":"Bacterial cytokinesis is commonly initiated by the Z-ring, a dynamic cytoskeletal structure that assembles at the site of division. Its primary component is FtsZ, a tubulin-like GTPase, that like its eukaryotic relative forms protein filaments in the presence of GTP. Since the discovery of the Z-ring 25 years ago, various models for the role of FtsZ have been suggested. However, important information about the architecture and dynamics of FtsZ filaments during cytokinesis is still missing. One reason for this lack of knowledge has been the small size of bacteria, which has made it difficult to resolve the orientation and dynamics of individual FtsZ filaments in the Z-ring. While superresolution microscopy experiments have helped to gain more information about the organization of the Z-ring in the dividing cell, they were not yet able to elucidate a mechanism of how FtsZ filaments reorganize during assembly and disassembly of the Z-ring. In this chapter, we explain how to use an in vitro reconstitution approach to investigate the self-organization of FtsZ filaments recruited to a biomimetic lipid bilayer by its membrane anchor FtsA. We show how to perform single-molecule experiments to study the behavior of individual FtsZ monomers during the constant reorganization of the FtsZ-FtsA filament network. We describe how to analyze the dynamics of single molecules and explain why this information can help to shed light onto possible mechanism of Z-ring constriction. We believe that similar experimental approaches will be useful to study the mechanism of membrane-based polymerization of other cytoskeletal systems, not only from prokaryotic but also eukaryotic origin."}],"month":"12","title":"Single-molecule measurements to study polymerization dynamics of FtsZ-FtsA copolymers","date_updated":"2025-07-10T11:50:24Z","publication_identifier":{"issn":["0091-679X"]},"date_published":"2017-12-01T00:00:00Z","editor":[{"full_name":"Echard, Arnaud ","first_name":"Arnaud ","last_name":"Echard"}],"day":"01","date_created":"2018-12-11T11:50:45Z","_id":"1213","author":[{"last_name":"Baranova","id":"38661662-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3086-9124","full_name":"Baranova, Natalia","first_name":"Natalia"},{"last_name":"Loose","id":"462D4284-F248-11E8-B48F-1D18A9856A87","full_name":"Loose, Martin","first_name":"Martin","orcid":"0000-0001-7309-9724"}],"page":"355 - 370","volume":137,"quality_controlled":"1","citation":{"short":"N.S. Baranova, M. Loose, in:, A. Echard (Ed.), Cytokinesis, Academic Press, 2017, pp. 355–370.","apa":"Baranova, N. S., &#38; Loose, M. (2017). Single-molecule measurements to study polymerization dynamics of FtsZ-FtsA copolymers. In A. Echard (Ed.), <i>Cytokinesis</i> (Vol. 137, pp. 355–370). Academic Press. <a href=\"https://doi.org/10.1016/bs.mcb.2016.03.036\">https://doi.org/10.1016/bs.mcb.2016.03.036</a>","ista":"Baranova NS, Loose M. 2017.Single-molecule measurements to study polymerization dynamics of FtsZ-FtsA copolymers. In: Cytokinesis. Methods in Cell Biology, vol. 137, 355–370.","chicago":"Baranova, Natalia S., and Martin Loose. “Single-Molecule Measurements to Study Polymerization Dynamics of FtsZ-FtsA Copolymers.” In <i>Cytokinesis</i>, edited by Arnaud  Echard, 137:355–70. Academic Press, 2017. <a href=\"https://doi.org/10.1016/bs.mcb.2016.03.036\">https://doi.org/10.1016/bs.mcb.2016.03.036</a>.","ama":"Baranova NS, Loose M. Single-molecule measurements to study polymerization dynamics of FtsZ-FtsA copolymers. In: Echard A, ed. <i>Cytokinesis</i>. Vol 137. Academic Press; 2017:355-370. doi:<a href=\"https://doi.org/10.1016/bs.mcb.2016.03.036\">10.1016/bs.mcb.2016.03.036</a>","mla":"Baranova, Natalia S., and Martin Loose. “Single-Molecule Measurements to Study Polymerization Dynamics of FtsZ-FtsA Copolymers.” <i>Cytokinesis</i>, edited by Arnaud  Echard, vol. 137, Academic Press, 2017, pp. 355–70, doi:<a href=\"https://doi.org/10.1016/bs.mcb.2016.03.036\">10.1016/bs.mcb.2016.03.036</a>.","ieee":"N. S. Baranova and M. Loose, “Single-molecule measurements to study polymerization dynamics of FtsZ-FtsA copolymers,” in <i>Cytokinesis</i>, vol. 137, A. Echard, Ed. Academic Press, 2017, pp. 355–370."},"publication":"Cytokinesis","status":"public","external_id":{"isi":["000403542900022"]},"ec_funded":1,"scopus_import":"1","department":[{"_id":"MaLo"}],"article_processing_charge":"No","intvolume":"       137","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"acknowledgement":"Natalia Baranova is supported by an EMBO Long-Term Fellowship (EMBO ALTF 1163-2015) and Martin Loose by an ERC Starting Grant (ERCStG-2015-SelfOrganiCell).","acknowledged_ssus":[{"_id":"Bio"}],"year":"2017","publisher":"Academic Press"},{"oa":1,"abstract":[{"text":"We consider the problem of estimating the partition function Z(β)=∑xexp(−β(H(x)) of a Gibbs distribution with a Hamilton H(⋅), or more precisely the logarithm of the ratio q=lnZ(0)/Z(β). It has been recently shown how to approximate q with high probability assuming the existence of an oracle that produces samples from the Gibbs distribution for a given parameter value in [0,β]. The current best known approach due to Huber [9] uses O(qlnn⋅[lnq+lnlnn+ε−2]) oracle calls on average where ε is the desired accuracy of approximation and H(⋅) is assumed to lie in {0}∪[1,n]. We improve the complexity to O(qlnn⋅ε−2) oracle calls. We also show that the same complexity can be achieved if exact oracles are replaced with approximate sampling oracles that are within O(ε2qlnn) variation distance from exact oracles. Finally, we prove a lower bound of Ω(q⋅ε−2) oracle calls under a natural model of computation.","lang":"eng"}],"month":"12","file":[{"content_type":"application/pdf","file_name":"2018_PMLR_Kolmogorov.pdf","file_id":"7820","date_updated":"2020-07-14T12:45:45Z","creator":"dernst","date_created":"2020-05-12T09:23:27Z","checksum":"89db06a0e8083524449cb59b56bf4e5b","access_level":"open_access","file_size":408974,"relation":"main_file"}],"title":"A faster approximation algorithm for the Gibbs partition function","date_updated":"2024-11-04T13:52:32Z","date_published":"2017-12-27T00:00:00Z","oa_version":"Published Version","type":"conference","has_accepted_license":"1","publication_status":"published","file_date_updated":"2020-07-14T12:45:45Z","publist_id":"7628","arxiv":1,"ddc":["510"],"project":[{"grant_number":"616160","call_identifier":"FP7","name":"Discrete Optimization in Computer Vision: Theory and Practice","_id":"25FBA906-B435-11E9-9278-68D0E5697425"}],"conference":{"start_date":"2018-07-06","name":"COLT: Annual Conference on Learning Theory ","end_date":"2018-07-09"},"quality_controlled":"1","citation":{"apa":"Kolmogorov, V. (2017). A faster approximation algorithm for the Gibbs partition function. In <i>Proceedings of the 31st Conference On Learning Theory</i> (Vol. 75, pp. 228–249). ML Research Press.","short":"V. Kolmogorov, in:, Proceedings of the 31st Conference On Learning Theory, ML Research Press, 2017, pp. 228–249.","chicago":"Kolmogorov, Vladimir. “A Faster Approximation Algorithm for the Gibbs Partition Function.” In <i>Proceedings of the 31st Conference On Learning Theory</i>, 75:228–49. ML Research Press, 2017.","ista":"Kolmogorov V. 2017. A faster approximation algorithm for the Gibbs partition function. Proceedings of the 31st Conference On Learning Theory. COLT: Annual Conference on Learning Theory  vol. 75, 228–249.","ama":"Kolmogorov V. A faster approximation algorithm for the Gibbs partition function. In: <i>Proceedings of the 31st Conference On Learning Theory</i>. Vol 75. ML Research Press; 2017:228-249.","ieee":"V. Kolmogorov, “A faster approximation algorithm for the Gibbs partition function,” in <i>Proceedings of the 31st Conference On Learning Theory</i>, 2017, vol. 75, pp. 228–249.","mla":"Kolmogorov, Vladimir. “A Faster Approximation Algorithm for the Gibbs Partition Function.” <i>Proceedings of the 31st Conference On Learning Theory</i>, vol. 75, ML Research Press, 2017, pp. 228–49."},"publication":"Proceedings of the 31st Conference On Learning Theory","status":"public","external_id":{"arxiv":["1608.04223"]},"ec_funded":1,"department":[{"_id":"VlKo"}],"article_processing_charge":"No","intvolume":"        75","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"publisher":"ML Research Press","year":"2017","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"day":"27","date_created":"2018-12-11T11:45:33Z","_id":"274","page":"228-249","author":[{"first_name":"Vladimir","full_name":"Kolmogorov, Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","last_name":"Kolmogorov"}],"volume":75},{"publication_identifier":{"eissn":["1546-1718"],"issn":["1061-4036"]},"date_updated":"2026-03-19T10:51:18Z","date_published":"2017-12-18T00:00:00Z","article_type":"original","title":"Sexual-lineage-specific DNA methylation regulates meiosis in Arabidopsis","pmid":1,"month":"12","oa":1,"abstract":[{"lang":"eng","text":"DNA methylation regulates eukaryotic gene expression and is extensively reprogrammed during animal development. However, whether developmental methylation reprogramming during the sporophytic life cycle of flowering plants regulates genes is presently unknown. Here we report a distinctive gene-targeted RNA-directed DNA methylation (RdDM) activity in the Arabidopsis thaliana male sexual lineage that regulates gene expression in meiocytes. Loss of sexual-lineage-specific RdDM causes mis-splicing of the MPS1 gene (also known as PRD2), thereby disrupting meiosis. Our results establish a regulatory paradigm in which de novo methylation creates a cell-lineage-specific epigenetic signature that controls gene expression and contributes to cellular function in flowering plants."}],"extern":"1","keyword":["Genetics"],"publication_status":"published","doi":"10.1038/s41588-017-0008-5","type":"journal_article","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7611288/"}],"oa_version":"Submitted Version","issue":"1","publisher":"Nature Research","year":"2017","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"We thank Daniel Zilberman for intellectual contributions to this work and assistance with manuscript preparation. We also thank Caroline Dean, Kirsten Bomblies, Vinod Kumar, Siobhan Brady and Sophien Kamoun for comments on the manuscript, Hugh Dickinson and Josephine Hellberg for developing the meiocyte isolation method, Giles Oldroyd for the pGWB13-Bar vector, Elisa Fiume for the pMDC107-NTF vector, Matthew Hartley, Matthew Couchman and Tjelvar Sten Gunnar Olsson for bioinformatics support, and the John Innes Centre Bioimaging Facility (Elaine Barclay and Grant Calder) for their assistance with microscopy. This work was funded by a Biotechnology and Biological Sciences Research Council (BBSRC) David Phillips Fellowship (BBL0250431) to X.F., a BBSRC grant (BBM01973X1) to J.H., and a Sainsbury PhD Studentship to J.W.","language":[{"iso":"eng"}],"intvolume":"        50","OA_place":"repository","article_processing_charge":"No","scopus_import":"1","department":[{"_id":"XiFe"}],"external_id":{"pmid":["29255257"]},"quality_controlled":"1","citation":{"ama":"Walker J, Gao H, Zhang J, et al. Sexual-lineage-specific DNA methylation regulates meiosis in Arabidopsis. <i>Nature Genetics</i>. 2017;50(1):130-137. doi:<a href=\"https://doi.org/10.1038/s41588-017-0008-5\">10.1038/s41588-017-0008-5</a>","ieee":"J. Walker <i>et al.</i>, “Sexual-lineage-specific DNA methylation regulates meiosis in Arabidopsis,” <i>Nature Genetics</i>, vol. 50, no. 1. Nature Research, pp. 130–137, 2017.","mla":"Walker, James, et al. “Sexual-Lineage-Specific DNA Methylation Regulates Meiosis in Arabidopsis.” <i>Nature Genetics</i>, vol. 50, no. 1, Nature Research, 2017, pp. 130–37, doi:<a href=\"https://doi.org/10.1038/s41588-017-0008-5\">10.1038/s41588-017-0008-5</a>.","short":"J. Walker, H. Gao, J. Zhang, B. Aldridge, M. Vickers, J.D. Higgins, X. Feng, Nature Genetics 50 (2017) 130–137.","apa":"Walker, J., Gao, H., Zhang, J., Aldridge, B., Vickers, M., Higgins, J. D., &#38; Feng, X. (2017). Sexual-lineage-specific DNA methylation regulates meiosis in Arabidopsis. <i>Nature Genetics</i>. Nature Research. <a href=\"https://doi.org/10.1038/s41588-017-0008-5\">https://doi.org/10.1038/s41588-017-0008-5</a>","chicago":"Walker, James, Hongbo Gao, Jingyi Zhang, Billy Aldridge, Martin Vickers, James D. Higgins, and Xiaoqi Feng. “Sexual-Lineage-Specific DNA Methylation Regulates Meiosis in Arabidopsis.” <i>Nature Genetics</i>. Nature Research, 2017. <a href=\"https://doi.org/10.1038/s41588-017-0008-5\">https://doi.org/10.1038/s41588-017-0008-5</a>.","ista":"Walker J, Gao H, Zhang J, Aldridge B, Vickers M, Higgins JD, Feng X. 2017. Sexual-lineage-specific DNA methylation regulates meiosis in Arabidopsis. Nature Genetics. 50(1), 130–137."},"OA_type":"green","publication":"Nature Genetics","status":"public","volume":50,"_id":"12193","page":"130-137","author":[{"last_name":"Walker","full_name":"Walker, James","first_name":"James"},{"last_name":"Gao","first_name":"Hongbo","full_name":"Gao, Hongbo"},{"first_name":"Jingyi","full_name":"Zhang, Jingyi","last_name":"Zhang"},{"last_name":"Aldridge","first_name":"Billy","full_name":"Aldridge, Billy"},{"last_name":"Vickers","first_name":"Martin","full_name":"Vickers, Martin"},{"full_name":"Higgins, James D.","first_name":"James D.","last_name":"Higgins"},{"orcid":"0000-0002-4008-1234","first_name":"Xiaoqi","full_name":"Feng, Xiaoqi","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","last_name":"Feng"}],"date_created":"2023-01-16T09:18:05Z","day":"18"},{"date_created":"2018-12-11T11:50:50Z","_id":"1228","author":[{"full_name":"Sauerzopf, Ulrich","first_name":"Ulrich","last_name":"Sauerzopf"},{"last_name":"Sacco","id":"42C9F57E-F248-11E8-B48F-1D18A9856A87","first_name":"Roberto","full_name":"Sacco, Roberto"},{"orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia","first_name":"Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino"},{"full_name":"Niello, Marco","first_name":"Marco","last_name":"Niello"},{"first_name":"Ana","full_name":"Weidenauer, Ana","last_name":"Weidenauer"},{"last_name":"Praschak Rieder","first_name":"Nicole","full_name":"Praschak Rieder, Nicole"},{"first_name":"Harald","full_name":"Sitte, Harald","last_name":"Sitte"},{"first_name":"Matthaeus","full_name":"Willeit, Matthaeus","last_name":"Willeit"}],"page":"45 - 57","volume":45,"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"day":"01","intvolume":"        45","article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","language":[{"iso":"eng"}],"acknowledgement":"This work was supported by grants of the Austrian Science Fund (FWF) P23585B09 to M.W. and F3506 to H.H.S. and the “Wiener Wissenschafts-, Forschungs- und Technologiefonds” (Vienna Science and Technology Fund; WWTF) CS15-033 to M.W.","year":"2017","publisher":"Wiley-Blackwell","issue":"1","citation":{"ieee":"U. Sauerzopf <i>et al.</i>, “Are reprogrammed cells a useful tool for studying dopamine dysfunction in psychotic disorders? A review of the current evidence,” <i>European Journal of Neuroscience</i>, vol. 45, no. 1. Wiley-Blackwell, pp. 45–57, 2017.","mla":"Sauerzopf, Ulrich, et al. “Are Reprogrammed Cells a Useful Tool for Studying Dopamine Dysfunction in Psychotic Disorders? A Review of the Current Evidence.” <i>European Journal of Neuroscience</i>, vol. 45, no. 1, Wiley-Blackwell, 2017, pp. 45–57, doi:<a href=\"https://doi.org/10.1111/ejn.13418\">10.1111/ejn.13418</a>.","ama":"Sauerzopf U, Sacco R, Novarino G, et al. Are reprogrammed cells a useful tool for studying dopamine dysfunction in psychotic disorders? A review of the current evidence. <i>European Journal of Neuroscience</i>. 2017;45(1):45-57. doi:<a href=\"https://doi.org/10.1111/ejn.13418\">10.1111/ejn.13418</a>","ista":"Sauerzopf U, Sacco R, Novarino G, Niello M, Weidenauer A, Praschak Rieder N, Sitte H, Willeit M. 2017. Are reprogrammed cells a useful tool for studying dopamine dysfunction in psychotic disorders? A review of the current evidence. European Journal of Neuroscience. 45(1), 45–57.","chicago":"Sauerzopf, Ulrich, Roberto Sacco, Gaia Novarino, Marco Niello, Ana Weidenauer, Nicole Praschak Rieder, Harald Sitte, and Matthaeus Willeit. “Are Reprogrammed Cells a Useful Tool for Studying Dopamine Dysfunction in Psychotic Disorders? A Review of the Current Evidence.” <i>European Journal of Neuroscience</i>. Wiley-Blackwell, 2017. <a href=\"https://doi.org/10.1111/ejn.13418\">https://doi.org/10.1111/ejn.13418</a>.","apa":"Sauerzopf, U., Sacco, R., Novarino, G., Niello, M., Weidenauer, A., Praschak Rieder, N., … Willeit, M. (2017). Are reprogrammed cells a useful tool for studying dopamine dysfunction in psychotic disorders? A review of the current evidence. <i>European Journal of Neuroscience</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/ejn.13418\">https://doi.org/10.1111/ejn.13418</a>","short":"U. Sauerzopf, R. Sacco, G. Novarino, M. Niello, A. Weidenauer, N. Praschak Rieder, H. Sitte, M. Willeit, European Journal of Neuroscience 45 (2017) 45–57."},"quality_controlled":"1","publication":"European Journal of Neuroscience","status":"public","external_id":{"isi":["000392487100005"],"pmid":["27690184"]},"scopus_import":"1","department":[{"_id":"GaNo"}],"ddc":["616"],"oa_version":"Published Version","type":"journal_article","isi":1,"publication_status":"published","doi":"10.1111/ejn.13418","file_date_updated":"2020-07-14T12:44:39Z","publist_id":"6106","has_accepted_license":"1","month":"01","file":[{"checksum":"c572cf02be8fbb7020cfcfb892182e4c","relation":"main_file","access_level":"open_access","file_size":169145,"file_id":"4838","file_name":"IST-2017-738-v1+1_Sauerzopf_et_al-2017-European_Journal_of_Neuroscience.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:44:39Z","creator":"system","date_created":"2018-12-12T10:10:48Z"}],"title":"Are reprogrammed cells a useful tool for studying dopamine dysfunction in psychotic disorders? A review of the current evidence","pmid":1,"date_updated":"2023-09-20T11:16:01Z","article_type":"review","date_published":"2017-01-01T00:00:00Z","pubrep_id":"738","oa":1,"abstract":[{"text":"Since 2006, reprogrammed cells have increasingly been used as a biomedical research technique in addition to neuro-psychiatric methods. These rapidly evolving techniques allow for the generation of neuronal sub-populations, and have sparked interest not only in monogenetic neuro-psychiatric diseases, but also in poly-genetic and poly-aetiological disorders such as schizophrenia (SCZ) and bipolar disorder (BPD). This review provides a summary of 19 publications on reprogrammed adult somatic cells derived from patients with SCZ, and five publications using this technique in patients with BPD. As both disorders are complex and heterogeneous, there is a plurality of hypotheses to be tested in vitro. In SCZ, data on alterations of dopaminergic transmission in vitro are sparse, despite the great explanatory power of the so-called DA hypothesis of SCZ. Some findings correspond to perturbations of cell energy metabolism, and observations in reprogrammed cells suggest neuro-developmental alterations. Some studies also report on the efficacy of medicinal compounds to revert alterations observed in cellular models. However, due to the paucity of replication studies, no comprehensive conclusions can be drawn from studies using reprogrammed cells at the present time. In the future, findings from cell culture methods need to be integrated with clinical, epidemiological, pharmacological and imaging data in order to generate a more comprehensive picture of SCZ and BPD.","lang":"eng"}]},{"intvolume":"        84","article_processing_charge":"No","language":[{"iso":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Elsevier","year":"2017","publication":"Journal of Computer and System Sciences","status":"public","citation":{"ama":"Brázdil T, Chatterjee K, Forejt V, Kučera A. Trading performance for stability in Markov decision processes. <i>Journal of Computer and System Sciences</i>. 2017;84:144-170. doi:<a href=\"https://doi.org/10.1016/j.jcss.2016.09.009\">10.1016/j.jcss.2016.09.009</a>","ieee":"T. Brázdil, K. Chatterjee, V. Forejt, and A. Kučera, “Trading performance for stability in Markov decision processes,” <i>Journal of Computer and System Sciences</i>, vol. 84. Elsevier, pp. 144–170, 2017.","mla":"Brázdil, Tomáš, et al. “Trading Performance for Stability in Markov Decision Processes.” <i>Journal of Computer and System Sciences</i>, vol. 84, Elsevier, 2017, pp. 144–70, doi:<a href=\"https://doi.org/10.1016/j.jcss.2016.09.009\">10.1016/j.jcss.2016.09.009</a>.","short":"T. Brázdil, K. Chatterjee, V. Forejt, A. Kučera, Journal of Computer and System Sciences 84 (2017) 144–170.","apa":"Brázdil, T., Chatterjee, K., Forejt, V., &#38; Kučera, A. (2017). Trading performance for stability in Markov decision processes. <i>Journal of Computer and System Sciences</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jcss.2016.09.009\">https://doi.org/10.1016/j.jcss.2016.09.009</a>","chicago":"Brázdil, Tomáš, Krishnendu Chatterjee, Vojtěch Forejt, and Antonín Kučera. “Trading Performance for Stability in Markov Decision Processes.” <i>Journal of Computer and System Sciences</i>. Elsevier, 2017. <a href=\"https://doi.org/10.1016/j.jcss.2016.09.009\">https://doi.org/10.1016/j.jcss.2016.09.009</a>.","ista":"Brázdil T, Chatterjee K, Forejt V, Kučera A. 2017. Trading performance for stability in Markov decision processes. Journal of Computer and System Sciences. 84, 144–170."},"quality_controlled":"1","external_id":{"isi":["000388430000011"]},"ec_funded":1,"department":[{"_id":"KrCh"}],"scopus_import":"1","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"2305"}]},"date_created":"2018-12-11T11:51:12Z","page":"144 - 170","author":[{"last_name":"Brázdil","first_name":"Tomáš","full_name":"Brázdil, Tomáš"},{"last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu"},{"last_name":"Forejt","first_name":"Vojtěch","full_name":"Forejt, Vojtěch"},{"last_name":"Kučera","first_name":"Antonín","full_name":"Kučera, Antonín"}],"_id":"1294","volume":84,"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"day":"01","file":[{"file_name":"IST-2016-717-v1+1_1-s2.0-S0022000016300897-main.pdf","content_type":"application/pdf","file_id":"4885","date_updated":"2020-07-14T12:44:42Z","creator":"system","date_created":"2018-12-12T10:11:30Z","checksum":"91271b23cf884d7c06d33bef0cd623b1","file_size":708657,"access_level":"open_access","relation":"main_file"}],"month":"03","title":"Trading performance for stability in Markov decision processes","pubrep_id":"717","date_published":"2017-03-01T00:00:00Z","date_updated":"2025-09-29T14:16:56Z","abstract":[{"lang":"eng","text":"We study controller synthesis problems for finite-state Markov decision processes, where the objective is to optimize the expected mean-payoff performance and stability (also known as variability in the literature). We argue that the basic notion of expressing the stability using the statistical variance of the mean payoff is sometimes insufficient, and propose an alternative definition. We show that a strategy ensuring both the expected mean payoff and the variance below given bounds requires randomization and memory, under both the above definitions. We then show that the problem of finding such a strategy can be expressed as a set of constraints."}],"oa":1,"ddc":["004","006"],"project":[{"call_identifier":"FWF","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","grant_number":"S11407","name":"Game Theory","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","call_identifier":"FP7"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"oa_version":"Published Version","type":"journal_article","isi":1,"has_accepted_license":"1","publication_status":"published","doi":"10.1016/j.jcss.2016.09.009","publist_id":"6009","file_date_updated":"2020-07-14T12:44:42Z"},{"external_id":{"isi":["000440734900026"],"arxiv":["1701.05738"]},"status":"public","publication":"Tools and Algorithms for the Construction and Analysis of Systems","quality_controlled":"1","citation":{"ieee":"J. Kretinsky, T. Meggendorfer, C. Waldmann, and M. Weininger, “Index appearance record for transforming Rabin automata into parity automata,” in <i>Tools and Algorithms for the Construction and Analysis of Systems</i>, Uppsala, Sweden, 2017, vol. 10205, pp. 443–460.","mla":"Kretinsky, Jan, et al. “Index Appearance Record for Transforming Rabin Automata into Parity Automata.” <i>Tools and Algorithms for the Construction and Analysis of Systems</i>, vol. 10205, Springer, 2017, pp. 443–60, doi:<a href=\"https://doi.org/10.1007/978-3-662-54577-5_26\">10.1007/978-3-662-54577-5_26</a>.","ama":"Kretinsky J, Meggendorfer T, Waldmann C, Weininger M. Index appearance record for transforming Rabin automata into parity automata. In: <i>Tools and Algorithms for the Construction and Analysis of Systems</i>. Vol 10205. Springer; 2017:443-460. doi:<a href=\"https://doi.org/10.1007/978-3-662-54577-5_26\">10.1007/978-3-662-54577-5_26</a>","chicago":"Kretinsky, Jan, Tobias Meggendorfer, Clara Waldmann, and Maximilian Weininger. “Index Appearance Record for Transforming Rabin Automata into Parity Automata.” In <i>Tools and Algorithms for the Construction and Analysis of Systems</i>, 10205:443–60. Springer, 2017. <a href=\"https://doi.org/10.1007/978-3-662-54577-5_26\">https://doi.org/10.1007/978-3-662-54577-5_26</a>.","ista":"Kretinsky J, Meggendorfer T, Waldmann C, Weininger M. 2017. Index appearance record for transforming Rabin automata into parity automata. Tools and Algorithms for the Construction and Analysis of Systems. TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 10205, 443–460.","apa":"Kretinsky, J., Meggendorfer, T., Waldmann, C., &#38; Weininger, M. (2017). Index appearance record for transforming Rabin automata into parity automata. In <i>Tools and Algorithms for the Construction and Analysis of Systems</i> (Vol. 10205, pp. 443–460). Uppsala, Sweden: Springer. <a href=\"https://doi.org/10.1007/978-3-662-54577-5_26\">https://doi.org/10.1007/978-3-662-54577-5_26</a>","short":"J. Kretinsky, T. Meggendorfer, C. Waldmann, M. Weininger, in:, Tools and Algorithms for the Construction and Analysis of Systems, Springer, 2017, pp. 443–460."},"department":[{"_id":"KrCh"}],"language":[{"iso":"eng"}],"acknowledgement":"This work is partially funded by the DFG project “Verified Model Checkers” and by the Czech Science Foundation, grant No. P202/12/G061.","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","intvolume":"     10205","article_processing_charge":"No","year":"2017","publisher":"Springer","day":"31","corr_author":"1","page":"443-460","author":[{"last_name":"Kretinsky","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8122-2881","first_name":"Jan","full_name":"Kretinsky, Jan"},{"last_name":"Meggendorfer","id":"b21b0c15-30a2-11eb-80dc-f13ca25802e1","orcid":"0000-0002-1712-2165","full_name":"Meggendorfer, Tobias","first_name":"Tobias"},{"last_name":"Waldmann","full_name":"Waldmann, Clara","first_name":"Clara"},{"last_name":"Weininger","first_name":"Maximilian","full_name":"Weininger, Maximilian"}],"_id":"13160","date_created":"2023-06-21T13:21:14Z","volume":10205,"abstract":[{"text":"Transforming deterministic ω\r\n-automata into deterministic parity automata is traditionally done using variants of appearance records. We present a more efficient variant of this approach, tailored to Rabin automata, and several optimizations applicable to all appearance records. We compare the methods experimentally and find out that our method produces smaller automata than previous approaches. Moreover, the experiments demonstrate the potential of our method for LTL synthesis, using LTL-to-Rabin translators. It leads to significantly smaller parity automata when compared to state-of-the-art approaches on complex formulae.","lang":"eng"}],"oa":1,"month":"03","date_published":"2017-03-31T00:00:00Z","date_updated":"2025-09-18T10:42:48Z","publication_identifier":{"eissn":["1611-3349"],"issn":["0302-9743"],"isbn":["9783662545768"],"eisbn":["9783662545775"]},"title":"Index appearance record for transforming Rabin automata into parity automata","type":"conference","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.1701.05738"}],"isi":1,"oa_version":"Preprint","arxiv":1,"doi":"10.1007/978-3-662-54577-5_26","publication_status":"published","conference":{"name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems","start_date":"2017-04-22","location":"Uppsala, Sweden","end_date":"2017-04-29"},"alternative_title":["LNCS"]},{"scopus_import":"1","department":[{"_id":"NiBa"},{"_id":"CaGu"}],"ec_funded":1,"external_id":{"isi":["000400379500013"]},"citation":{"ama":"Paixao T, Pérez Heredia J, Sudholt D, Trubenova B. Towards a runtime comparison of natural and artificial evolution. <i>Algorithmica</i>. 2017;78(2):681-713. doi:<a href=\"https://doi.org/10.1007/s00453-016-0212-1\">10.1007/s00453-016-0212-1</a>","ieee":"T. Paixao, J. Pérez Heredia, D. Sudholt, and B. Trubenova, “Towards a runtime comparison of natural and artificial evolution,” <i>Algorithmica</i>, vol. 78, no. 2. Springer, pp. 681–713, 2017.","mla":"Paixao, Tiago, et al. “Towards a Runtime Comparison of Natural and Artificial Evolution.” <i>Algorithmica</i>, vol. 78, no. 2, Springer, 2017, pp. 681–713, doi:<a href=\"https://doi.org/10.1007/s00453-016-0212-1\">10.1007/s00453-016-0212-1</a>.","apa":"Paixao, T., Pérez Heredia, J., Sudholt, D., &#38; Trubenova, B. (2017). Towards a runtime comparison of natural and artificial evolution. <i>Algorithmica</i>. Springer. <a href=\"https://doi.org/10.1007/s00453-016-0212-1\">https://doi.org/10.1007/s00453-016-0212-1</a>","short":"T. Paixao, J. Pérez Heredia, D. Sudholt, B. Trubenova, Algorithmica 78 (2017) 681–713.","chicago":"Paixao, Tiago, Jorge Pérez Heredia, Dirk Sudholt, and Barbora Trubenova. “Towards a Runtime Comparison of Natural and Artificial Evolution.” <i>Algorithmica</i>. Springer, 2017. <a href=\"https://doi.org/10.1007/s00453-016-0212-1\">https://doi.org/10.1007/s00453-016-0212-1</a>.","ista":"Paixao T, Pérez Heredia J, Sudholt D, Trubenova B. 2017. Towards a runtime comparison of natural and artificial evolution. Algorithmica. 78(2), 681–713."},"quality_controlled":"1","publication":"Algorithmica","status":"public","issue":"2","publisher":"Springer","year":"2017","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","language":[{"iso":"eng"}],"intvolume":"        78","article_processing_charge":"No","day":"01","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"volume":78,"_id":"1336","page":"681 - 713","author":[{"id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","last_name":"Paixao","full_name":"Paixao, Tiago","first_name":"Tiago","orcid":"0000-0003-2361-3953"},{"first_name":"Jorge","full_name":"Pérez Heredia, Jorge","last_name":"Pérez Heredia"},{"first_name":"Dirk","full_name":"Sudholt, Dirk","last_name":"Sudholt"},{"id":"42302D54-F248-11E8-B48F-1D18A9856A87","last_name":"Trubenova","full_name":"Trubenova, Barbora","first_name":"Barbora","orcid":"0000-0002-6873-2967"}],"date_created":"2018-12-11T11:51:27Z","oa":1,"abstract":[{"text":"Evolutionary algorithms (EAs) form a popular optimisation paradigm inspired by natural evolution. In recent years the field of evolutionary computation has developed a rigorous analytical theory to analyse the runtimes of EAs on many illustrative problems. Here we apply this theory to a simple model of natural evolution. In the Strong Selection Weak Mutation (SSWM) evolutionary regime the time between occurrences of new mutations is much longer than the time it takes for a mutated genotype to take over the population. In this situation, the population only contains copies of one genotype and evolution can be modelled as a stochastic process evolving one genotype by means of mutation and selection between the resident and the mutated genotype. The probability of accepting the mutated genotype then depends on the change in fitness. We study this process, SSWM, from an algorithmic perspective, quantifying its expected optimisation time for various parameters and investigating differences to a similar evolutionary algorithm, the well-known (1+1) EA. We show that SSWM can have a moderate advantage over the (1+1) EA at crossing fitness valleys and study an example where SSWM outperforms the (1+1) EA by taking advantage of information on the fitness gradient.","lang":"eng"}],"publication_identifier":{"issn":["0178-4617"]},"date_updated":"2026-04-16T09:55:33Z","date_published":"2017-06-01T00:00:00Z","pubrep_id":"658","title":"Towards a runtime comparison of natural and artificial evolution","month":"06","file":[{"checksum":"7873f665a0c598ac747c908f34cb14b9","relation":"main_file","file_size":710206,"access_level":"open_access","file_name":"IST-2016-658-v1+1_s00453-016-0212-1.pdf","file_id":"4805","date_updated":"2020-07-14T12:44:44Z","content_type":"application/pdf","date_created":"2018-12-12T10:10:19Z","creator":"system"}],"publist_id":"5931","doi":"10.1007/s00453-016-0212-1","has_accepted_license":"1","file_date_updated":"2020-07-14T12:44:44Z","publication_status":"published","isi":1,"type":"journal_article","oa_version":"Published Version","project":[{"grant_number":"618091","call_identifier":"FP7","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425"}],"ddc":["576"]},{"year":"2017","publisher":"Springer","issue":"3-4","article_processing_charge":"Yes (via OA deal)","intvolume":"       169","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria).  ","language":[{"iso":"eng"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","ec_funded":1,"department":[{"_id":"LaEr"}],"scopus_import":"1","status":"public","publication":"Probability Theory and Related Fields","quality_controlled":"1","citation":{"mla":"Ajanki, Oskari H., et al. “Universality for General Wigner-Type Matrices.” <i>Probability Theory and Related Fields</i>, vol. 169, no. 3–4, Springer, 2017, pp. 667–727, doi:<a href=\"https://doi.org/10.1007/s00440-016-0740-2\">10.1007/s00440-016-0740-2</a>.","ieee":"O. H. Ajanki, L. Erdös, and T. H. Krüger, “Universality for general Wigner-type matrices,” <i>Probability Theory and Related Fields</i>, vol. 169, no. 3–4. Springer, pp. 667–727, 2017.","ama":"Ajanki OH, Erdös L, Krüger TH. Universality for general Wigner-type matrices. <i>Probability Theory and Related Fields</i>. 2017;169(3-4):667-727. doi:<a href=\"https://doi.org/10.1007/s00440-016-0740-2\">10.1007/s00440-016-0740-2</a>","chicago":"Ajanki, Oskari H, László Erdös, and Torben H Krüger. “Universality for General Wigner-Type Matrices.” <i>Probability Theory and Related Fields</i>. Springer, 2017. <a href=\"https://doi.org/10.1007/s00440-016-0740-2\">https://doi.org/10.1007/s00440-016-0740-2</a>.","ista":"Ajanki OH, Erdös L, Krüger TH. 2017. Universality for general Wigner-type matrices. Probability Theory and Related Fields. 169(3–4), 667–727.","apa":"Ajanki, O. H., Erdös, L., &#38; Krüger, T. H. (2017). Universality for general Wigner-type matrices. <i>Probability Theory and Related Fields</i>. Springer. <a href=\"https://doi.org/10.1007/s00440-016-0740-2\">https://doi.org/10.1007/s00440-016-0740-2</a>","short":"O.H. Ajanki, L. Erdös, T.H. Krüger, Probability Theory and Related Fields 169 (2017) 667–727."},"external_id":{"isi":["000414358400002"]},"volume":169,"date_created":"2018-12-11T11:51:27Z","page":"667 - 727","author":[{"first_name":"Oskari H","full_name":"Ajanki, Oskari H","last_name":"Ajanki","id":"36F2FB7E-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-5366-9603","first_name":"László","full_name":"Erdös, László","last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Krüger","id":"3020C786-F248-11E8-B48F-1D18A9856A87","first_name":"Torben H","full_name":"Krüger, Torben H","orcid":"0000-0002-4821-3297"}],"_id":"1337","day":"01","corr_author":"1","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"title":"Universality for general Wigner-type matrices","pubrep_id":"657","date_published":"2017-12-01T00:00:00Z","date_updated":"2026-04-16T09:55:44Z","publication_identifier":{"issn":["0178-8051"]},"file":[{"creator":"system","date_created":"2018-12-12T10:08:25Z","file_name":"IST-2017-657-v1+2_s00440-016-0740-2.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:44:44Z","file_id":"4686","checksum":"29f5a72c3f91e408aeb9e78344973803","access_level":"open_access","relation":"main_file","file_size":988843}],"month":"12","abstract":[{"text":"We consider the local eigenvalue distribution of large self-adjoint N×N random matrices H=H∗ with centered independent entries. In contrast to previous works the matrix of variances sij=\\mathbbmE|hij|2 is not assumed to be stochastic. Hence the density of states is not the Wigner semicircle law. Its possible shapes are described in the companion paper (Ajanki et al. in Quadratic Vector Equations on the Complex Upper Half Plane. arXiv:1506.05095). We show that as N grows, the resolvent, G(z)=(H−z)−1, converges to a diagonal matrix, diag(m(z)), where m(z)=(m1(z),…,mN(z)) solves the vector equation −1/mi(z)=z+∑jsijmj(z) that has been analyzed in Ajanki et al. (Quadratic Vector Equations on the Complex Upper Half Plane. arXiv:1506.05095). We prove a local law down to the smallest spectral resolution scale, and bulk universality for both real symmetric and complex hermitian symmetry classes.","lang":"eng"}],"oa":1,"ddc":["510","530"],"project":[{"name":"Random matrices, universality and disordered quantum systems","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804","call_identifier":"FP7"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"doi":"10.1007/s00440-016-0740-2","publist_id":"5930","publication_status":"published","file_date_updated":"2020-07-14T12:44:44Z","has_accepted_license":"1","oa_version":"Published Version","isi":1,"type":"journal_article"},{"ddc":["000"],"project":[{"name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","call_identifier":"FP7"},{"call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"grant_number":"Z211","call_identifier":"FWF","name":"Formal methods for the design and analysis of complex systems","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"oa_version":"Published Version","type":"journal_article","isi":1,"doi":"10.1007/s10703-016-0256-5","file_date_updated":"2020-07-14T12:44:44Z","publist_id":"5929","has_accepted_license":"1","publication_status":"published","month":"06","file":[{"file_id":"4985","content_type":"application/pdf","file_name":"IST-2016-656-v1+1_s10703-016-0256-5.pdf","date_updated":"2020-07-14T12:44:44Z","date_created":"2018-12-12T10:13:05Z","creator":"system","access_level":"open_access","relation":"main_file","file_size":1416170,"checksum":"1163dfd997e8212c789525d4178b1653"}],"title":"From non-preemptive to preemptive scheduling using synchronization synthesis","pmid":1,"date_updated":"2025-09-23T08:54:01Z","pubrep_id":"656","date_published":"2017-06-01T00:00:00Z","oa":1,"abstract":[{"text":"We present a computer-aided programming approach to concurrency. The approach allows programmers to program assuming a friendly, non-preemptive scheduler, and our synthesis procedure inserts synchronization to ensure that the final program works even with a preemptive scheduler. The correctness specification is implicit, inferred from the non-preemptive behavior. Let us consider sequences of calls that the program makes to an external interface. The specification requires that any such sequence produced under a preemptive scheduler should be included in the set of sequences produced under a non-preemptive scheduler. We guarantee that our synthesis does not introduce deadlocks and that the synchronization inserted is optimal w.r.t. a given objective function. The solution is based on a finitary abstraction, an algorithm for bounded language inclusion modulo an independence relation, and generation of a set of global constraints over synchronization placements. Each model of the global constraints set corresponds to a correctness-ensuring synchronization placement. The placement that is optimal w.r.t. the given objective function is chosen as the synchronization solution. We apply the approach to device-driver programming, where the driver threads call the software interface of the device and the API provided by the operating system. Our experiments demonstrate that our synthesis method is precise and efficient. The implicit specification helped us find one concurrency bug previously missed when model-checking using an explicit, user-provided specification. We implemented objective functions for coarse-grained and fine-grained locking and observed that different synchronization placements are produced for our experiments, favoring a minimal number of synchronization operations or maximum concurrency, respectively.","lang":"eng"}],"date_created":"2018-12-11T11:51:27Z","related_material":{"record":[{"id":"1729","status":"public","relation":"earlier_version"}]},"_id":"1338","author":[{"id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87","last_name":"Cerny","first_name":"Pavol","full_name":"Cerny, Pavol"},{"last_name":"Clarke","full_name":"Clarke, Edmund","first_name":"Edmund"},{"orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger"},{"full_name":"Radhakrishna, Arjun","first_name":"Arjun","id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87","last_name":"Radhakrishna"},{"last_name":"Ryzhyk","full_name":"Ryzhyk, Leonid","first_name":"Leonid"},{"last_name":"Samanta","id":"3D2AAC08-F248-11E8-B48F-1D18A9856A87","full_name":"Samanta, Roopsha","first_name":"Roopsha"},{"first_name":"Thorsten","full_name":"Tarrach, Thorsten","orcid":"0000-0003-4409-8487","last_name":"Tarrach","id":"3D6E8F2C-F248-11E8-B48F-1D18A9856A87"}],"page":"97 - 139","volume":50,"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"corr_author":"1","day":"01","article_processing_charge":"No","intvolume":"        50","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"year":"2017","publisher":"Springer","issue":"2-3","quality_controlled":"1","citation":{"short":"P. Cerny, E. Clarke, T.A. Henzinger, A. Radhakrishna, L. Ryzhyk, R. Samanta, T. Tarrach, Formal Methods in System Design 50 (2017) 97–139.","apa":"Cerny, P., Clarke, E., Henzinger, T. A., Radhakrishna, A., Ryzhyk, L., Samanta, R., &#38; Tarrach, T. (2017). From non-preemptive to preemptive scheduling using synchronization synthesis. <i>Formal Methods in System Design</i>. Springer. <a href=\"https://doi.org/10.1007/s10703-016-0256-5\">https://doi.org/10.1007/s10703-016-0256-5</a>","ista":"Cerny P, Clarke E, Henzinger TA, Radhakrishna A, Ryzhyk L, Samanta R, Tarrach T. 2017. From non-preemptive to preemptive scheduling using synchronization synthesis. Formal Methods in System Design. 50(2–3), 97–139.","chicago":"Cerny, Pavol, Edmund Clarke, Thomas A Henzinger, Arjun Radhakrishna, Leonid Ryzhyk, Roopsha Samanta, and Thorsten Tarrach. “From Non-Preemptive to Preemptive Scheduling Using Synchronization Synthesis.” <i>Formal Methods in System Design</i>. Springer, 2017. <a href=\"https://doi.org/10.1007/s10703-016-0256-5\">https://doi.org/10.1007/s10703-016-0256-5</a>.","ama":"Cerny P, Clarke E, Henzinger TA, et al. From non-preemptive to preemptive scheduling using synchronization synthesis. <i>Formal Methods in System Design</i>. 2017;50(2-3):97-139. doi:<a href=\"https://doi.org/10.1007/s10703-016-0256-5\">10.1007/s10703-016-0256-5</a>","ieee":"P. Cerny <i>et al.</i>, “From non-preemptive to preemptive scheduling using synchronization synthesis,” <i>Formal Methods in System Design</i>, vol. 50, no. 2–3. Springer, pp. 97–139, 2017.","mla":"Cerny, Pavol, et al. “From Non-Preemptive to Preemptive Scheduling Using Synchronization Synthesis.” <i>Formal Methods in System Design</i>, vol. 50, no. 2–3, Springer, 2017, pp. 97–139, doi:<a href=\"https://doi.org/10.1007/s10703-016-0256-5\">10.1007/s10703-016-0256-5</a>."},"status":"public","publication":"Formal Methods in System Design","external_id":{"isi":["000399888900001"],"pmid":["28490835"]},"ec_funded":1,"scopus_import":"1","department":[{"_id":"ToHe"}]},{"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"day":"01","corr_author":"1","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"1835"}]},"date_created":"2018-12-11T11:51:32Z","author":[{"id":"3444EA5E-F248-11E8-B48F-1D18A9856A87","last_name":"Giacobbe","orcid":"0000-0001-8180-0904","full_name":"Giacobbe, Mirco","first_name":"Mirco"},{"last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","first_name":"Calin C"},{"first_name":"Ashutosh","full_name":"Gupta, Ashutosh","last_name":"Gupta","id":"335E5684-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger"},{"first_name":"Tiago","full_name":"Paixao, Tiago","orcid":"0000-0003-2361-3953","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","last_name":"Paixao"},{"orcid":"0000-0002-9041-0905","first_name":"Tatjana","full_name":"Petrov, Tatjana","id":"3D5811FC-F248-11E8-B48F-1D18A9856A87","last_name":"Petrov"}],"page":"765 - 787","_id":"1351","volume":54,"status":"public","publication":"Acta Informatica","quality_controlled":"1","citation":{"apa":"Giacobbe, M., Guet, C. C., Gupta, A., Henzinger, T. A., Paixao, T., &#38; Petrov, T. (2017). Model checking the evolution of gene regulatory networks. <i>Acta Informatica</i>. Springer. <a href=\"https://doi.org/10.1007/s00236-016-0278-x\">https://doi.org/10.1007/s00236-016-0278-x</a>","short":"M. Giacobbe, C.C. Guet, A. Gupta, T.A. Henzinger, T. Paixao, T. Petrov, Acta Informatica 54 (2017) 765–787.","chicago":"Giacobbe, Mirco, Calin C Guet, Ashutosh Gupta, Thomas A Henzinger, Tiago Paixao, and Tatjana Petrov. “Model Checking the Evolution of Gene Regulatory Networks.” <i>Acta Informatica</i>. Springer, 2017. <a href=\"https://doi.org/10.1007/s00236-016-0278-x\">https://doi.org/10.1007/s00236-016-0278-x</a>.","ista":"Giacobbe M, Guet CC, Gupta A, Henzinger TA, Paixao T, Petrov T. 2017. Model checking the evolution of gene regulatory networks. Acta Informatica. 54(8), 765–787.","ama":"Giacobbe M, Guet CC, Gupta A, Henzinger TA, Paixao T, Petrov T. Model checking the evolution of gene regulatory networks. <i>Acta Informatica</i>. 2017;54(8):765-787. doi:<a href=\"https://doi.org/10.1007/s00236-016-0278-x\">10.1007/s00236-016-0278-x</a>","ieee":"M. Giacobbe, C. C. Guet, A. Gupta, T. A. Henzinger, T. Paixao, and T. Petrov, “Model checking the evolution of gene regulatory networks,” <i>Acta Informatica</i>, vol. 54, no. 8. Springer, pp. 765–787, 2017.","mla":"Giacobbe, Mirco, et al. “Model Checking the Evolution of Gene Regulatory Networks.” <i>Acta Informatica</i>, vol. 54, no. 8, Springer, 2017, pp. 765–87, doi:<a href=\"https://doi.org/10.1007/s00236-016-0278-x\">10.1007/s00236-016-0278-x</a>."},"external_id":{"isi":["000414343200003"]},"ec_funded":1,"department":[{"_id":"ToHe"},{"_id":"CaGu"},{"_id":"NiBa"}],"scopus_import":"1","intvolume":"        54","article_processing_charge":"No","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Springer","year":"2017","issue":"8","oa_version":"Published Version","type":"journal_article","isi":1,"file_date_updated":"2020-07-14T12:44:46Z","doi":"10.1007/s00236-016-0278-x","publication_status":"published","has_accepted_license":"1","publist_id":"5898","ddc":["006","576"],"project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","grant_number":"267989","call_identifier":"FP7"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","call_identifier":"FWF"},{"name":"Formal methods for the design and analysis of complex systems","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z211"},{"_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","grant_number":"618091","call_identifier":"FP7"},{"grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7","grant_number":"250152"}],"abstract":[{"text":"The behaviour of gene regulatory networks (GRNs) is typically analysed using simulation-based statistical testing-like methods. In this paper, we demonstrate that we can replace this approach by a formal verification-like method that gives higher assurance and scalability. We focus on Wagner’s weighted GRN model with varying weights, which is used in evolutionary biology. In the model, weight parameters represent the gene interaction strength that may change due to genetic mutations. For a property of interest, we synthesise the constraints over the parameter space that represent the set of GRNs satisfying the property. We experimentally show that our parameter synthesis procedure computes the mutational robustness of GRNs—an important problem of interest in evolutionary biology—more efficiently than the classical simulation method. We specify the property in linear temporal logic. We employ symbolic bounded model checking and SMT solving to compute the space of GRNs that satisfy the property, which amounts to synthesizing a set of linear constraints on the weights.","lang":"eng"}],"oa":1,"file":[{"date_created":"2019-01-17T15:57:29Z","creator":"dernst","date_updated":"2020-07-14T12:44:46Z","file_name":"2017_ActaInformatica_Giacobbe.pdf","content_type":"application/pdf","file_id":"5841","file_size":755241,"access_level":"open_access","relation":"main_file","checksum":"4e661d9135d7f8c342e8e258dee76f3e"}],"month":"12","title":"Model checking the evolution of gene regulatory networks","pubrep_id":"649","date_published":"2017-12-01T00:00:00Z","date_updated":"2025-07-10T11:50:42Z","publication_identifier":{"issn":["0001-5903"]}}]