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We consider the problem of verifying safety when running a Bayesian neural network policy in a feedback loop with infinite time horizon systems. Compared to the existing sampling-based approaches, which are inapplicable to the infinite time horizon setting, we train a separate deterministic neural network that serves as an infinite time horizon safety certificate. In particular, we show that the certificate network guarantees the safety of the system over a subset of the BNN weight posterior's support. Our method first computes a safe weight set and then alters the BNN's weight posterior to reject samples outside this set. Moreover, we show how to extend our approach to a safe-exploration reinforcement learning setting, in order to avoid unsafe trajectories during the training of the policy. We evaluate our approach on a series of reinforcement learning benchmarks, including non-Lyapunovian safety specifications."}],"oa_version":"Published Version","related_material":{"record":[{"relation":"dissertation_contains","id":"11362","status":"public"}]},"ec_funded":1,"license":"https://creativecommons.org/licenses/by-nc-nd/3.0/","publication_status":"published","file":[{"success":1,"checksum":"0fc0f852525c10dda9cc9ffea07fb4e4","file_id":"10682","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"infinite_time_horizon_safety_o.pdf","date_created":"2022-01-26T07:39:59Z","creator":"mlechner","file_size":452492,"date_updated":"2022-01-26T07:39:59Z"}],"language":[{"iso":"eng"}],"project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385"},{"grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020"},{"name":"The Wittgenstein Prize","grant_number":"Z211","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"author":[{"full_name":"Lechner, Mathias","last_name":"Lechner","id":"3DC22916-F248-11E8-B48F-1D18A9856A87","first_name":"Mathias"},{"last_name":"Žikelić","full_name":"Žikelić, Ðorđe","first_name":"Ðorđe"},{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724"}],"external_id":{"arxiv":["2111.03165"]},"article_processing_charge":"No","title":"Infinite time horizon safety of Bayesian neural networks","citation":{"ista":"Lechner M, Žikelić Ð, Chatterjee K, Henzinger TA. 2021. Infinite time horizon safety of Bayesian neural networks. 35th Conference on Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, .","chicago":"Lechner, Mathias, Ðorđe Žikelić, Krishnendu Chatterjee, and Thomas A Henzinger. “Infinite Time Horizon Safety of Bayesian Neural Networks.” In 35th Conference on Neural Information Processing Systems, 2021. https://doi.org/10.48550/arXiv.2111.03165.","ieee":"M. Lechner, Ð. Žikelić, K. Chatterjee, and T. A. Henzinger, “Infinite time horizon safety of Bayesian neural networks,” in 35th Conference on Neural Information Processing Systems, Virtual, 2021.","short":"M. Lechner, Ð. Žikelić, K. Chatterjee, T.A. Henzinger, in:, 35th Conference on Neural Information Processing Systems, 2021.","apa":"Lechner, M., Žikelić, Ð., Chatterjee, K., & Henzinger, T. A. (2021). Infinite time horizon safety of Bayesian neural networks. 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Boosting expensive synchronizing heuristics. Expert Systems with Applications. 167(4), 114203.","chicago":"Sarac, Naci E, Ömer Faruk Altun, Kamil Tolga Atam, Sertac Karahoda, Kamer Kaya, and Hüsnü Yenigün. “Boosting Expensive Synchronizing Heuristics.” Expert Systems with Applications. Elsevier, 2021. https://doi.org/10.1016/j.eswa.2020.114203.","apa":"Sarac, N. E., Altun, Ö. F., Atam, K. T., Karahoda, S., Kaya, K., & Yenigün, H. (2021). Boosting expensive synchronizing heuristics. Expert Systems with Applications. Elsevier. https://doi.org/10.1016/j.eswa.2020.114203","ama":"Sarac NE, Altun ÖF, Atam KT, Karahoda S, Kaya K, Yenigün H. Boosting expensive synchronizing heuristics. Expert Systems with Applications. 2021;167(4). doi:10.1016/j.eswa.2020.114203","ieee":"N. E. Sarac, Ö. F. Altun, K. T. Atam, S. Karahoda, K. Kaya, and H. Yenigün, “Boosting expensive synchronizing heuristics,” Expert Systems with Applications, vol. 167, no. 4. Elsevier, 2021.","short":"N.E. Sarac, Ö.F. Altun, K.T. Atam, S. Karahoda, K. Kaya, H. Yenigün, Expert Systems with Applications 167 (2021).","mla":"Sarac, Naci E., et al. “Boosting Expensive Synchronizing Heuristics.” Expert Systems with Applications, vol. 167, no. 4, 114203, Elsevier, 2021, doi:10.1016/j.eswa.2020.114203."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","quality_controlled":"1","publisher":"Elsevier","oa":1,"acknowledgement":"This work was supported by The Scientific and Technological Research Council of Turkey (TUBITAK) [grant number 114E569]. This research was supported in part by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award). We would like to thank the authors of (Roman & Szykula, 2015) for providing their heuristics implementations, which we used to compare our SynchroP implementation as given in Table 11.","doi":"10.1016/j.eswa.2020.114203","date_published":"2021-04-01T00:00:00Z","date_created":"2020-12-02T13:34:25Z","isi":1,"has_accepted_license":"1","year":"2021","day":"01","publication":"Expert Systems with Applications","article_type":"original","type":"journal_article","status":"public","_id":"8912","department":[{"_id":"ToHe"}],"file_date_updated":"2020-12-02T13:33:51Z","date_updated":"2023-08-04T11:19:00Z","ddc":["000"],"scopus_import":"1","month":"04","intvolume":" 167","abstract":[{"text":"For automata, synchronization, the problem of bringing an automaton to a particular state regardless of its initial state, is important. It has several applications in practice and is related to a fifty-year-old conjecture on the length of the shortest synchronizing word. Although using shorter words increases the effectiveness in practice, finding a shortest one (which is not necessarily unique) is NP-hard. For this reason, there exist various heuristics in the literature. However, high-quality heuristics such as SynchroP producing relatively shorter sequences are very expensive and can take hours when the automaton has tens of thousands of states. The SynchroP heuristic has been frequently used as a benchmark to evaluate the performance of the new heuristics. In this work, we first improve the runtime of SynchroP and its variants by using algorithmic techniques. We then focus on adapting SynchroP for many-core architectures,\r\nand overall, we obtain more than 1000× speedup on GPUs compared to naive sequential implementation that has been frequently used as a benchmark to evaluate new heuristics in the literature. We also propose two SynchroP variants and evaluate their performance.","lang":"eng"}],"oa_version":"Submitted Version","issue":"4","volume":167,"publication_identifier":{"issn":["09574174"]},"publication_status":"published","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"8913","checksum":"600c2f81bc898a725bcfa7cf26ff4fed","creator":"esarac","file_size":634967,"date_updated":"2020-12-02T13:33:51Z","file_name":"synchroPaperRevised.pdf","date_created":"2020-12-02T13:33:51Z"}],"language":[{"iso":"eng"}]},{"title":"Synthesis of hybrid automata with affine dynamics from time-series data","author":[{"id":"4B3207F6-F248-11E8-B48F-1D18A9856A87","first_name":"Miriam","orcid":"0000-0003-2936-5719","full_name":"Garcia Soto, Miriam","last_name":"Garcia Soto"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger","orcid":"0000-0002-2985-7724","full_name":"Henzinger, Thomas A"},{"full_name":"Schilling, Christian","orcid":"0000-0003-3658-1065","last_name":"Schilling","first_name":"Christian","id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","external_id":{"arxiv":["2102.12734"],"isi":["000932821700028"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Garcia Soto, Miriam, Thomas A Henzinger, and Christian Schilling. “Synthesis of Hybrid Automata with Affine Dynamics from Time-Series Data.” In HSCC ’21: Proceedings of the 24th International Conference on Hybrid Systems: Computation and Control, 2102.12734. Association for Computing Machinery, 2021. https://doi.org/10.1145/3447928.3456704.","ista":"Garcia Soto M, Henzinger TA, Schilling C. 2021. Synthesis of hybrid automata with affine dynamics from time-series data. HSCC ’21: Proceedings of the 24th International Conference on Hybrid Systems: Computation and Control. HSCC: International Conference on Hybrid Systems Computation and Control, 2102.12734.","mla":"Garcia Soto, Miriam, et al. “Synthesis of Hybrid Automata with Affine Dynamics from Time-Series Data.” HSCC ’21: Proceedings of the 24th International Conference on Hybrid Systems: Computation and Control, Association for Computing Machinery, 2021, p. 2102.12734, doi:10.1145/3447928.3456704.","apa":"Garcia Soto, M., Henzinger, T. A., & Schilling, C. (2021). Synthesis of hybrid automata with affine dynamics from time-series data. In HSCC ’21: Proceedings of the 24th International Conference on Hybrid Systems: Computation and Control (p. 2102.12734). Nashville, TN, United States: Association for Computing Machinery. https://doi.org/10.1145/3447928.3456704","ama":"Garcia Soto M, Henzinger TA, Schilling C. Synthesis of hybrid automata with affine dynamics from time-series data. In: HSCC ’21: Proceedings of the 24th International Conference on Hybrid Systems: Computation and Control. Association for Computing Machinery; 2021:2102.12734. doi:10.1145/3447928.3456704","ieee":"M. Garcia Soto, T. A. Henzinger, and C. Schilling, “Synthesis of hybrid automata with affine dynamics from time-series data,” in HSCC ’21: Proceedings of the 24th International Conference on Hybrid Systems: Computation and Control, Nashville, TN, United States, 2021, p. 2102.12734.","short":"M. Garcia Soto, T.A. Henzinger, C. Schilling, in:, HSCC ’21: Proceedings of the 24th International Conference on Hybrid Systems: Computation and Control, Association for Computing Machinery, 2021, p. 2102.12734."},"project":[{"call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","grant_number":"Z211"},{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"date_published":"2021-05-01T00:00:00Z","doi":"10.1145/3447928.3456704","date_created":"2021-02-26T16:30:39Z","page":"2102.12734","day":"01","publication":"HSCC '21: Proceedings of the 24th International Conference on Hybrid Systems: Computation and Control","isi":1,"has_accepted_license":"1","year":"2021","quality_controlled":"1","publisher":"Association for Computing Machinery","oa":1,"acknowledgement":"This research was supported in part by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award) and the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 754411.","file_date_updated":"2021-05-25T13:53:22Z","department":[{"_id":"ToHe"}],"ddc":["000"],"date_updated":"2023-08-07T13:49:33Z","status":"public","keyword":["hybrid automaton","membership","system identification"],"type":"conference","conference":{"start_date":"2021-05-19","end_date":"2021-05-21","location":"Nashville, TN, United States","name":"HSCC: International Conference on Hybrid Systems Computation and Control"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"9200","ec_funded":1,"file":[{"file_size":1474786,"date_updated":"2021-05-25T13:53:22Z","creator":"kschuh","file_name":"2021_HSCC_Soto.pdf","date_created":"2021-05-25T13:53:22Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"4c1202c1abf71384c3ee6fea88c2f80e","file_id":"9424"}],"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9781450383394"]},"publication_status":"published","month":"05","scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"Formal design of embedded and cyber-physical systems relies on mathematical modeling. In this paper, we consider the model class of hybrid automata whose dynamics are defined by affine differential equations. Given a set of time-series data, we present an algorithmic approach to synthesize a hybrid automaton exhibiting behavior that is close to the data, up to a specified precision, and changes in synchrony with the data. A fundamental problem in our synthesis algorithm is to check membership of a time series in a hybrid automaton. Our solution integrates reachability and optimization techniques for affine dynamical systems to obtain both a sufficient and a necessary condition for membership, combined in a refinement framework. The algorithm processes one time series at a time and hence can be interrupted, provide an intermediate result, and be resumed. We report experimental results demonstrating the applicability of our synthesis approach.","lang":"eng"}]},{"title":"Bidding mechanisms in graph games","article_processing_charge":"No","external_id":{"arxiv":["1905.03835"],"isi":["000634149800009"]},"author":[{"orcid":"0000-0001-5588-8287","full_name":"Avni, Guy","last_name":"Avni","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","first_name":"Guy"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","orcid":"0000-0002-2985-7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger"},{"last_name":"Žikelić","full_name":"Žikelić, Đorđe","first_name":"Đorđe"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Avni, Guy, Thomas A Henzinger, and Đorđe Žikelić. “Bidding Mechanisms in Graph Games.” Journal of Computer and System Sciences. Elsevier, 2021. https://doi.org/10.1016/j.jcss.2021.02.008.","ista":"Avni G, Henzinger TA, Žikelić Đ. 2021. Bidding mechanisms in graph games. Journal of Computer and System Sciences. 119(8), 133–144.","mla":"Avni, Guy, et al. “Bidding Mechanisms in Graph Games.” Journal of Computer and System Sciences, vol. 119, no. 8, Elsevier, 2021, pp. 133–44, doi:10.1016/j.jcss.2021.02.008.","ieee":"G. Avni, T. A. Henzinger, and Đ. Žikelić, “Bidding mechanisms in graph games,” Journal of Computer and System Sciences, vol. 119, no. 8. Elsevier, pp. 133–144, 2021.","short":"G. Avni, T.A. Henzinger, Đ. Žikelić, Journal of Computer and System Sciences 119 (2021) 133–144.","apa":"Avni, G., Henzinger, T. A., & Žikelić, Đ. (2021). Bidding mechanisms in graph games. Journal of Computer and System Sciences. Elsevier. https://doi.org/10.1016/j.jcss.2021.02.008","ama":"Avni G, Henzinger TA, Žikelić Đ. Bidding mechanisms in graph games. Journal of Computer and System Sciences. 2021;119(8):133-144. doi:10.1016/j.jcss.2021.02.008"},"date_created":"2021-03-14T23:01:32Z","doi":"10.1016/j.jcss.2021.02.008","date_published":"2021-03-03T00:00:00Z","page":"133-144","publication":"Journal of Computer and System Sciences","day":"03","year":"2021","isi":1,"oa":1,"publisher":"Elsevier","quality_controlled":"1","department":[{"_id":"ToHe"}],"date_updated":"2023-08-07T14:08:34Z","status":"public","type":"journal_article","article_type":"original","_id":"9239","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"6884"}]},"volume":119,"issue":"8","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1090-2724"],"issn":["0022-0000"]},"intvolume":" 119","month":"03","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.1905.03835","open_access":"1"}],"scopus_import":"1","oa_version":"Preprint","abstract":[{"lang":"eng","text":"A graph game proceeds as follows: two players move a token through a graph to produce a finite or infinite path, which determines the payoff of the game. We study bidding games in which in each turn, an auction determines which player moves the token. Bidding games were largely studied in combination with two variants of first-price auctions called “Richman” and “poorman” bidding. We study taxman bidding, which span the spectrum between the two. The game is parameterized by a constant : portion τ of the winning bid is paid to the other player, and portion to the bank. While finite-duration (reachability) taxman games have been studied before, we present, for the first time, results on infinite-duration taxman games: we unify, generalize, and simplify previous equivalences between bidding games and a class of stochastic games called random-turn games."}]},{"_id":"9356","conference":{"name":"LICS: Symposium on Logic in Computer Science","location":"Online","end_date":"2021-07-02","start_date":"2021-06-29"},"type":"conference","status":"public","date_updated":"2023-08-08T13:52:56Z","ddc":["000"],"file_date_updated":"2021-06-16T08:23:54Z","department":[{"_id":"GradSch"},{"_id":"ToHe"}],"abstract":[{"lang":"eng","text":"In runtime verification, a monitor watches a trace of a system and, if possible, decides after observing each finite prefix whether or not the unknown infinite trace satisfies a given specification. We generalize the theory of runtime verification to monitors that attempt to estimate numerical values of quantitative trace properties (instead of attempting to conclude boolean values of trace specifications), such as maximal or average response time along a trace. Quantitative monitors are approximate: with every finite prefix, they can improve their estimate of the infinite trace's unknown property value. Consequently, quantitative monitors can be compared with regard to a precision-cost trade-off: better approximations of the property value require more monitor resources, such as states (in the case of finite-state monitors) or registers, and additional resources yield better approximations. We introduce a formal framework for quantitative and approximate monitoring, show how it conservatively generalizes the classical boolean setting for monitoring, and give several precision-cost trade-offs for monitors. For example, we prove that there are quantitative properties for which every additional register improves monitoring precision."}],"oa_version":"Published Version","scopus_import":"1","month":"06","publication_status":"published","language":[{"iso":"eng"}],"file":[{"date_created":"2021-06-16T08:23:54Z","file_name":"qam.pdf","date_updated":"2021-06-16T08:23:54Z","file_size":641990,"creator":"esarac","checksum":"6e4cba3f72775f479c5b1b75d1a4a0c4","file_id":"9557","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"article_number":"9470547","project":[{"name":"The Wittgenstein Prize","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"citation":{"chicago":"Henzinger, Thomas A, and Naci E Sarac. “Quantitative and Approximate Monitoring.” In Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science. Institute of Electrical and Electronics Engineers, 2021. https://doi.org/10.1109/LICS52264.2021.9470547.","ista":"Henzinger TA, Sarac NE. 2021. Quantitative and approximate monitoring. Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science. LICS: Symposium on Logic in Computer Science, 9470547.","mla":"Henzinger, Thomas A., and Naci E. Sarac. “Quantitative and Approximate Monitoring.” Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science, 9470547, Institute of Electrical and Electronics Engineers, 2021, doi:10.1109/LICS52264.2021.9470547.","apa":"Henzinger, T. A., & Sarac, N. E. (2021). Quantitative and approximate monitoring. In Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science. Online: Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/LICS52264.2021.9470547","ama":"Henzinger TA, Sarac NE. Quantitative and approximate monitoring. In: Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science. Institute of Electrical and Electronics Engineers; 2021. doi:10.1109/LICS52264.2021.9470547","short":"T.A. Henzinger, N.E. Sarac, in:, Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science, Institute of Electrical and Electronics Engineers, 2021.","ieee":"T. A. Henzinger and N. E. Sarac, “Quantitative and approximate monitoring,” in Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science, Online, 2021."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000947350400021"],"arxiv":["2105.08353"]},"article_processing_charge":"No","author":[{"last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"},{"first_name":"Naci E","id":"8C6B42F8-C8E6-11E9-A03A-F2DCE5697425","last_name":"Sarac","full_name":"Sarac, Naci E"}],"title":"Quantitative and approximate monitoring","acknowledgement":"We thank the anonymous reviewers for their helpful comments. This research was supported in part by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award).","oa":1,"quality_controlled":"1","publisher":"Institute of Electrical and Electronics Engineers","year":"2021","isi":1,"has_accepted_license":"1","publication":"Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science","day":"29","date_created":"2021-04-30T17:30:47Z","date_published":"2021-06-29T00:00:00Z","doi":"10.1109/LICS52264.2021.9470547"},{"page":"1-16","doi":"10.1016/j.tcs.2021.05.023","date_published":"2021-06-04T00:00:00Z","date_created":"2021-07-11T22:01:18Z","isi":1,"has_accepted_license":"1","year":"2021","day":"04","publication":"Theoretical Computer Science","quality_controlled":"1","publisher":"Elsevier","oa":1,"acknowledgement":"Tatjana Petrov’s research was supported in part by SNSF Advanced Postdoctoral Mobility Fellowship grant number P300P2 161067, the Ministry of Science, Research and the Arts of the state of Baden-Wurttemberg, and the DFG Centre of Excellence 2117 ‘Centre for the Advanced Study of Collective Behaviour’ (ID: 422037984). Claudia Igler is the recipient of a DOC Fellowship of the Austrian Academy of Sciences. Thomas A. Henzinger’s research was supported in part by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award).","author":[{"first_name":"Tatjana","last_name":"Petrov","full_name":"Petrov, Tatjana"},{"first_name":"Claudia","id":"46613666-F248-11E8-B48F-1D18A9856A87","last_name":"Igler","full_name":"Igler, Claudia"},{"id":"4C7638DA-F248-11E8-B48F-1D18A9856A87","first_name":"Ali","full_name":"Sezgin, Ali","last_name":"Sezgin"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724"},{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C","last_name":"Guet","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C"}],"external_id":{"isi":["000710180500002"]},"article_processing_charge":"No","title":"Long lived transients in gene regulation","citation":{"ista":"Petrov T, Igler C, Sezgin A, Henzinger TA, Guet CC. 2021. Long lived transients in gene regulation. Theoretical Computer Science. 893, 1–16.","chicago":"Petrov, Tatjana, Claudia Igler, Ali Sezgin, Thomas A Henzinger, and Calin C Guet. “Long Lived Transients in Gene Regulation.” Theoretical Computer Science. Elsevier, 2021. https://doi.org/10.1016/j.tcs.2021.05.023.","ieee":"T. Petrov, C. Igler, A. Sezgin, T. A. Henzinger, and C. C. Guet, “Long lived transients in gene regulation,” Theoretical Computer Science, vol. 893. Elsevier, pp. 1–16, 2021.","short":"T. Petrov, C. Igler, A. Sezgin, T.A. Henzinger, C.C. Guet, Theoretical Computer Science 893 (2021) 1–16.","ama":"Petrov T, Igler C, Sezgin A, Henzinger TA, Guet CC. Long lived transients in gene regulation. Theoretical Computer Science. 2021;893:1-16. doi:10.1016/j.tcs.2021.05.023","apa":"Petrov, T., Igler, C., Sezgin, A., Henzinger, T. A., & Guet, C. C. (2021). Long lived transients in gene regulation. Theoretical Computer Science. Elsevier. https://doi.org/10.1016/j.tcs.2021.05.023","mla":"Petrov, Tatjana, et al. “Long Lived Transients in Gene Regulation.” Theoretical Computer Science, vol. 893, Elsevier, 2021, pp. 1–16, doi:10.1016/j.tcs.2021.05.023."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"grant_number":"Z211","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"volume":893,"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","publication_identifier":{"issn":["0304-3975"]},"publication_status":"published","file":[{"file_name":"2021_TheoreticalComputerScience_Petrov.pdf","date_created":"2022-05-12T12:13:27Z","file_size":2566504,"date_updated":"2022-05-12T12:13:27Z","creator":"dernst","success":1,"checksum":"d3aef34cfb13e53bba4cf44d01680793","file_id":"11364","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"06","intvolume":" 893","abstract":[{"text":"Gene expression is regulated by the set of transcription factors (TFs) that bind to the promoter. The ensuing regulating function is often represented as a combinational logic circuit, where output (gene expression) is determined by current input values (promoter bound TFs) only. However, the simultaneous arrival of TFs is a strong assumption, since transcription and translation of genes introduce intrinsic time delays and there is no global synchronisation among the arrival times of different molecular species at their targets. We present an experimentally implementable genetic circuit with two inputs and one output, which in the presence of small delays in input arrival, exhibits qualitatively distinct population-level phenotypes, over timescales that are longer than typical cell doubling times. From a dynamical systems point of view, these phenotypes represent long-lived transients: although they converge to the same value eventually, they do so after a very long time span. The key feature of this toy model genetic circuit is that, despite having only two inputs and one output, it is regulated by twenty-three distinct DNA-TF configurations, two of which are more stable than others (DNA looped states), one promoting and another blocking the expression of the output gene. Small delays in input arrival time result in a majority of cells in the population quickly reaching the stable state associated with the first input, while exiting of this stable state occurs at a slow timescale. In order to mechanistically model the behaviour of this genetic circuit, we used a rule-based modelling language, and implemented a grid-search to find parameter combinations giving rise to long-lived transients. Our analysis shows that in the absence of feedback, there exist path-dependent gene regulatory mechanisms based on the long timescale of transients. The behaviour of this toy model circuit suggests that gene regulatory networks can exploit event timing to create phenotypes, and it opens the possibility that they could use event timing to memorise events, without regulatory feedback. The model reveals the importance of (i) mechanistically modelling the transitions between the different DNA-TF states, and (ii) employing transient analysis thereof.","lang":"eng"}],"oa_version":"Published Version","department":[{"_id":"ToHe"},{"_id":"CaGu"}],"file_date_updated":"2022-05-12T12:13:27Z","date_updated":"2023-08-10T14:11:19Z","ddc":["004"],"article_type":"original","type":"journal_article","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"status":"public","_id":"9647"},{"oa":1,"quality_controlled":"1","publisher":"Springer Nature","acknowledgement":"The authors would like to thank Borzoo Bonakdarpour, Derek Dreyer, Adrian Francalanza, Owolabi Legunsen, Mae Milano, Manuel Rigger, Cesar Sanchez, and the members of the IST Verification Seminar for their helpful comments and insights on various stages of this work, as well as the reviewers of RV’21 for their helpful suggestions on the actual paper.","page":"231-243","date_created":"2021-10-07T23:30:10Z","date_published":"2021-10-06T00:00:00Z","doi":"10.1007/978-3-030-88494-9_12","year":"2021","has_accepted_license":"1","isi":1,"publication":"International Conference on Runtime Verification","day":"06","project":[{"grant_number":"Z211","name":"The Wittgenstein Prize","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"article_processing_charge":"No","external_id":{"isi":["000719383800012"]},"author":[{"id":"6395C5F6-89DF-11E9-9C97-6BDFE5697425","first_name":"Fabian","last_name":"Mühlböck","orcid":"0000-0003-1548-0177","full_name":"Mühlböck, Fabian"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger","orcid":"0000-0002-2985-7724","full_name":"Henzinger, Thomas A"}],"title":"Differential monitoring","citation":{"ieee":"F. Mühlböck and T. A. Henzinger, “Differential monitoring,” in International Conference on Runtime Verification, Virtual, 2021, vol. 12974, pp. 231–243.","short":"F. Mühlböck, T.A. Henzinger, in:, International Conference on Runtime Verification, Springer Nature, Cham, 2021, pp. 231–243.","apa":"Mühlböck, F., & Henzinger, T. A. (2021). Differential monitoring. In International Conference on Runtime Verification (Vol. 12974, pp. 231–243). Cham: Springer Nature. https://doi.org/10.1007/978-3-030-88494-9_12","ama":"Mühlböck F, Henzinger TA. Differential monitoring. In: International Conference on Runtime Verification. Vol 12974. Cham: Springer Nature; 2021:231-243. doi:10.1007/978-3-030-88494-9_12","mla":"Mühlböck, Fabian, and Thomas A. Henzinger. “Differential Monitoring.” International Conference on Runtime Verification, vol. 12974, Springer Nature, 2021, pp. 231–43, doi:10.1007/978-3-030-88494-9_12.","ista":"Mühlböck F, Henzinger TA. 2021. Differential monitoring. International Conference on Runtime Verification. RV: Runtime Verification, LNCS, vol. 12974, 231–243.","chicago":"Mühlböck, Fabian, and Thomas A Henzinger. “Differential Monitoring.” In International Conference on Runtime Verification, 12974:231–43. Cham: Springer Nature, 2021. https://doi.org/10.1007/978-3-030-88494-9_12."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","scopus_import":"1","alternative_title":["LNCS"],"intvolume":" 12974","month":"10","place":"Cham","abstract":[{"text":"We argue that the time is ripe to investigate differential monitoring, in which the specification of a program's behavior is implicitly given by a second program implementing the same informal specification. Similar ideas have been proposed before, and are currently implemented in restricted form for testing and specialized run-time analyses, aspects of which we combine. We discuss the challenges of implementing differential monitoring as a general-purpose, black-box run-time monitoring framework, and present promising results of a preliminary implementation, showing low monitoring overheads for diverse programs.","lang":"eng"}],"oa_version":"Preprint","related_material":{"record":[{"relation":"extended_version","id":"9946","status":"public"}]},"volume":12974,"publication_status":"published","publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["978-3-030-88493-2"],"eisbn":["978-3-030-88494-9"]},"language":[{"iso":"eng"}],"file":[{"file_id":"10109","checksum":"554c7fdb259eda703a8b6328a6dad55a","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2021-10-07T23:32:18Z","file_name":"differentialmonitoring-cameraready-openaccess.pdf","creator":"fmuehlbo","date_updated":"2021-10-07T23:32:18Z","file_size":350632}],"conference":{"name":"RV: Runtime Verification","start_date":"2021-10-11","end_date":"2021-10-14","location":"Virtual"},"type":"conference","keyword":["run-time verification","software engineering","implicit specification"],"status":"public","_id":"10108","department":[{"_id":"ToHe"}],"file_date_updated":"2021-10-07T23:32:18Z","date_updated":"2023-08-14T07:20:30Z","ddc":["005"]},{"author":[{"id":"6395C5F6-89DF-11E9-9C97-6BDFE5697425","first_name":"Fabian","orcid":"0000-0003-1548-0177","full_name":"Mühlböck, Fabian","last_name":"Mühlböck"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724","last_name":"Henzinger"}],"article_processing_charge":"No","title":"Differential monitoring","citation":{"ista":"Mühlböck F, Henzinger TA. 2021. Differential monitoring, IST Austria, 17p.","chicago":"Mühlböck, Fabian, and Thomas A Henzinger. Differential Monitoring. IST Austria, 2021. https://doi.org/10.15479/AT:ISTA:9946.","short":"F. Mühlböck, T.A. Henzinger, Differential Monitoring, IST Austria, 2021.","ieee":"F. Mühlböck and T. A. Henzinger, Differential monitoring. IST Austria, 2021.","ama":"Mühlböck F, Henzinger TA. Differential Monitoring. IST Austria; 2021. doi:10.15479/AT:ISTA:9946","apa":"Mühlböck, F., & Henzinger, T. A. (2021). Differential monitoring. IST Austria. https://doi.org/10.15479/AT:ISTA:9946","mla":"Mühlböck, Fabian, and Thomas A. Henzinger. Differential Monitoring. IST Austria, 2021, doi:10.15479/AT:ISTA:9946."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","project":[{"grant_number":"Z211","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"page":"17","date_published":"2021-09-01T00:00:00Z","doi":"10.15479/AT:ISTA:9946","date_created":"2021-08-20T20:00:37Z","has_accepted_license":"1","year":"2021","day":"01","publisher":"IST Austria","oa":1,"acknowledgement":"The authors would like to thank Borzoo Bonakdarpour, Derek Dreyer, Adrian Francalanza, Owolabi Legunsen, Matthew Milano, Manuel Rigger, Cesar Sanchez, and the members of the IST Verification Seminar for their helpful comments and insights on various stages of this work, as well as the reviewers of RV’21 for their helpful suggestions on the actual paper.","department":[{"_id":"ToHe"}],"file_date_updated":"2021-09-03T12:34:28Z","date_updated":"2023-08-14T07:20:29Z","ddc":["005"],"type":"technical_report","status":"public","keyword":["run-time verification","software engineering","implicit specification"],"_id":"9946","related_material":{"record":[{"status":"public","id":"9281","relation":"other"},{"relation":"shorter_version","id":"10108","status":"public"}]},"publication_identifier":{"issn":["2664-1690"]},"publication_status":"published","file":[{"date_created":"2021-08-20T19:59:44Z","file_name":"differentialmonitoring-techreport.pdf","date_updated":"2021-09-03T12:34:28Z","file_size":"320453","creator":"fmuehlbo","file_id":"9948","checksum":"0f9aafd59444cb6bdca6925d163ab946","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"alternative_title":["IST Austria Technical Report"],"month":"09","abstract":[{"lang":"eng","text":"We argue that the time is ripe to investigate differential monitoring, in which the specification of a program's behavior is implicitly given by a second program implementing the same informal specification. Similar ideas have been proposed before, and are currently implemented in restricted form for testing and specialized run-time analyses, aspects of which we combine. We discuss the challenges of implementing differential monitoring as a general-purpose, black-box run-time monitoring framework, and present promising results of a preliminary implementation, showing low monitoring overheads for diverse programs."}],"oa_version":"Published Version"},{"project":[{"name":"The Wittgenstein Prize","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"citation":{"ista":"Sietzen S, Lechner M, Borowski J, Hasani R, Waldner M. 2021. Interactive analysis of CNN robustness. Computer Graphics Forum. 40(7), 253–264.","chicago":"Sietzen, Stefan, Mathias Lechner, Judy Borowski, Ramin Hasani, and Manuela Waldner. “Interactive Analysis of CNN Robustness.” Computer Graphics Forum. Wiley, 2021. https://doi.org/10.1111/cgf.14418.","short":"S. Sietzen, M. Lechner, J. Borowski, R. Hasani, M. Waldner, Computer Graphics Forum 40 (2021) 253–264.","ieee":"S. Sietzen, M. Lechner, J. Borowski, R. Hasani, and M. Waldner, “Interactive analysis of CNN robustness,” Computer Graphics Forum, vol. 40, no. 7. Wiley, pp. 253–264, 2021.","ama":"Sietzen S, Lechner M, Borowski J, Hasani R, Waldner M. Interactive analysis of CNN robustness. Computer Graphics Forum. 2021;40(7):253-264. doi:10.1111/cgf.14418","apa":"Sietzen, S., Lechner, M., Borowski, J., Hasani, R., & Waldner, M. (2021). Interactive analysis of CNN robustness. Computer Graphics Forum. Wiley. https://doi.org/10.1111/cgf.14418","mla":"Sietzen, Stefan, et al. “Interactive Analysis of CNN Robustness.” Computer Graphics Forum, vol. 40, no. 7, Wiley, 2021, pp. 253–64, doi:10.1111/cgf.14418."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Sietzen, Stefan","last_name":"Sietzen","first_name":"Stefan"},{"last_name":"Lechner","full_name":"Lechner, Mathias","first_name":"Mathias","id":"3DC22916-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Judy","full_name":"Borowski, Judy","last_name":"Borowski"},{"last_name":"Hasani","full_name":"Hasani, Ramin","first_name":"Ramin"},{"first_name":"Manuela","last_name":"Waldner","full_name":"Waldner, Manuela"}],"external_id":{"arxiv":["2110.07667"],"isi":["000722952000024"]},"article_processing_charge":"No","title":"Interactive analysis of CNN robustness","acknowledgement":"We thank Robert Geirhos and Roland Zimmermann for their participation in the case study and valuable feedback, Chris Olah and Nick Cammarata for valuable discussions in the early phase of the project, as well as the Distill Slack workspace as a platform for discussions. M.L. is supported in part by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award). J.B. is supported by the German Federal Ministry of Education and Research\r\n(BMBF) through the Competence Center for Machine Learning (TUE.AI, FKZ 01IS18039A) and the International Max Planck Research School for Intelligent Systems (IMPRS-IS). R.H. is partially supported by Boeing and Horizon-2020 ECSEL (grant 783163, iDev40).\r\n","publisher":"Wiley","quality_controlled":"1","oa":1,"isi":1,"year":"2021","day":"27","publication":"Computer Graphics Forum","page":"253-264","doi":"10.1111/cgf.14418","date_published":"2021-11-27T00:00:00Z","date_created":"2021-12-05T23:01:40Z","_id":"10404","article_type":"original","type":"journal_article","status":"public","date_updated":"2023-08-14T13:11:42Z","department":[{"_id":"ToHe"}],"abstract":[{"text":"While convolutional neural networks (CNNs) have found wide adoption as state-of-the-art models for image-related tasks, their predictions are often highly sensitive to small input perturbations, which the human vision is robust against. This paper presents Perturber, a web-based application that allows users to instantaneously explore how CNN activations and predictions evolve when a 3D input scene is interactively perturbed. Perturber offers a large variety of scene modifications, such as camera controls, lighting and shading effects, background modifications, object morphing, as well as adversarial attacks, to facilitate the discovery of potential vulnerabilities. Fine-tuned model versions can be directly compared for qualitative evaluation of their robustness. Case studies with machine learning experts have shown that Perturber helps users to quickly generate hypotheses about model vulnerabilities and to qualitatively compare model behavior. Using quantitative analyses, we could replicate users’ insights with other CNN architectures and input images, yielding new insights about the vulnerability of adversarially trained models.","lang":"eng"}],"oa_version":"Preprint","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/2110.07667","open_access":"1"}],"month":"11","intvolume":" 40","publication_identifier":{"eissn":["1467-8659"],"issn":["0167-7055"]},"publication_status":"published","language":[{"iso":"eng"}],"issue":"7","volume":40},{"type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","keyword":["computer science","computer science and game theory","logic in computer science"],"_id":"10674","file_date_updated":"2022-01-26T08:04:50Z","department":[{"_id":"ToHe"}],"date_updated":"2023-08-17T06:56:42Z","ddc":["510"],"scopus_import":"1","month":"02","intvolume":" 17","abstract":[{"text":"In two-player games on graphs, the players move a token through a graph to produce an infinite path, which determines the winner of the game. Such games are central in formal methods since they model the interaction between a non-terminating system and its environment. In bidding games the players bid for the right to move the token: in each round, the players simultaneously submit bids, and the higher bidder moves the token and pays the other player. Bidding games are known to have a clean and elegant mathematical structure that relies on the ability of the players to submit arbitrarily small bids. Many applications, however, require a fixed granularity for the bids, which can represent, for example, the monetary value expressed in cents. We study, for the first time, the combination of discrete-bidding and infinite-duration games. Our most important result proves that these games form a large determined subclass of concurrent games, where determinacy is the strong property that there always exists exactly one player who can guarantee winning the game. In particular, we show that, in contrast to non-discrete bidding games, the mechanism with which tied bids are resolved plays an important role in discrete-bidding games. We study several natural tie-breaking mechanisms and show that, while some do not admit determinacy, most natural mechanisms imply determinacy for every pair of initial budgets.","lang":"eng"}],"oa_version":"Published Version","volume":17,"issue":"1","publication_identifier":{"eissn":["1860-5974"]},"publication_status":"published","file":[{"creator":"alisjak","date_updated":"2022-01-26T08:04:50Z","file_size":819878,"date_created":"2022-01-26T08:04:50Z","file_name":"2021_LMCS_AGHAJOHAR.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"10690","checksum":"b35586a50ed1ca8f44767de116d18d81","success":1}],"language":[{"iso":"eng"}],"project":[{"name":"Formal Methods meets Algorithmic Game Theory","grant_number":"M02369","_id":"264B3912-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"FWF","_id":"25F2ACDE-B435-11E9-9278-68D0E5697425","grant_number":"S11402-N23","name":"Rigorous Systems Engineering"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z211","name":"The Wittgenstein Prize"}],"author":[{"full_name":"Aghajohari, Milad","last_name":"Aghajohari","first_name":"Milad"},{"id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","first_name":"Guy","last_name":"Avni","full_name":"Avni, Guy","orcid":"0000-0001-5588-8287"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2985-7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger"}],"article_processing_charge":"No","external_id":{"arxiv":["1905.03588"],"isi":["000658724600010"]},"title":"Determinacy in discrete-bidding infinite-duration games","citation":{"ama":"Aghajohari M, Avni G, Henzinger TA. Determinacy in discrete-bidding infinite-duration games. Logical Methods in Computer Science. 2021;17(1):10:1-10:23. doi:10.23638/LMCS-17(1:10)2021","apa":"Aghajohari, M., Avni, G., & Henzinger, T. A. (2021). Determinacy in discrete-bidding infinite-duration games. Logical Methods in Computer Science. International Federation for Computational Logic. https://doi.org/10.23638/LMCS-17(1:10)2021","short":"M. Aghajohari, G. Avni, T.A. Henzinger, Logical Methods in Computer Science 17 (2021) 10:1-10:23.","ieee":"M. Aghajohari, G. Avni, and T. A. Henzinger, “Determinacy in discrete-bidding infinite-duration games,” Logical Methods in Computer Science, vol. 17, no. 1. International Federation for Computational Logic, p. 10:1-10:23, 2021.","mla":"Aghajohari, Milad, et al. “Determinacy in Discrete-Bidding Infinite-Duration Games.” Logical Methods in Computer Science, vol. 17, no. 1, International Federation for Computational Logic, 2021, p. 10:1-10:23, doi:10.23638/LMCS-17(1:10)2021.","ista":"Aghajohari M, Avni G, Henzinger TA. 2021. Determinacy in discrete-bidding infinite-duration games. Logical Methods in Computer Science. 17(1), 10:1-10:23.","chicago":"Aghajohari, Milad, Guy Avni, and Thomas A Henzinger. “Determinacy in Discrete-Bidding Infinite-Duration Games.” Logical Methods in Computer Science. International Federation for Computational Logic, 2021. https://doi.org/10.23638/LMCS-17(1:10)2021."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"International Federation for Computational Logic","quality_controlled":"1","oa":1,"acknowledgement":"This research was supported in part by the Austrian Science Fund (FWF) under grants S11402-N23 (RiSE/SHiNE), Z211-N23 (Wittgenstein Award), and M 2369-N33 (Meitner fellowship).\r\n","page":"10:1-10:23","date_published":"2021-02-03T00:00:00Z","doi":"10.23638/LMCS-17(1:10)2021","date_created":"2022-01-25T16:32:13Z","has_accepted_license":"1","isi":1,"year":"2021","day":"03","publication":"Logical Methods in Computer Science"}]