[{"scopus_import":"1","day":"01","article_processing_charge":"No","has_accepted_license":"1","citation":{"ieee":"M. Aghajohari, G. Avni, and T. A. Henzinger, “Determinacy in discrete-bidding infinite-duration games,” presented at the CONCUR: International Conference on Concurrency Theory, Amsterdam, Netherlands, 2019, vol. 140.","apa":"Aghajohari, M., Avni, G., & Henzinger, T. A. (2019). Determinacy in discrete-bidding infinite-duration games (Vol. 140). Presented at the CONCUR: International Conference on Concurrency Theory, Amsterdam, Netherlands: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.CONCUR.2019.20","ista":"Aghajohari M, Avni G, Henzinger TA. 2019. Determinacy in discrete-bidding infinite-duration games. CONCUR: International Conference on Concurrency Theory, LIPIcs, vol. 140, 20.","ama":"Aghajohari M, Avni G, Henzinger TA. Determinacy in discrete-bidding infinite-duration games. In: Vol 140. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2019. doi:10.4230/LIPICS.CONCUR.2019.20","chicago":"Aghajohari, Milad, Guy Avni, and Thomas A Henzinger. “Determinacy in Discrete-Bidding Infinite-Duration Games,” Vol. 140. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. https://doi.org/10.4230/LIPICS.CONCUR.2019.20.","short":"M. Aghajohari, G. Avni, T.A. Henzinger, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019.","mla":"Aghajohari, Milad, et al. Determinacy in Discrete-Bidding Infinite-Duration Games. Vol. 140, 20, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, doi:10.4230/LIPICS.CONCUR.2019.20."},"date_published":"2019-08-01T00:00:00Z","type":"conference","alternative_title":["LIPIcs"],"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"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"6886","title":"Determinacy in discrete-bidding infinite-duration games","ddc":["000"],"status":"public","intvolume":" 140","oa_version":"Published Version","file":[{"file_size":741425,"content_type":"application/pdf","creator":"kschuh","file_name":"2019_LIPIcs_Aghajohari.pdf","access_level":"open_access","date_updated":"2020-07-14T12:47:43Z","date_created":"2019-09-27T12:21:38Z","checksum":"4df6d3575c506edb17215adada03cc8e","relation":"main_file","file_id":"6915"}],"month":"08","external_id":{"arxiv":["1905.03588"]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","short":"CC BY (3.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","project":[{"grant_number":"S11402-N23","_id":"25F2ACDE-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"call_identifier":"FWF","name":"Formal Methods meets Algorithmic Game Theory","grant_number":"M02369","_id":"264B3912-B435-11E9-9278-68D0E5697425"}],"conference":{"location":"Amsterdam, Netherlands","start_date":"2019-08-27","end_date":"2019-08-30","name":"CONCUR: International Conference on Concurrency Theory"},"doi":"10.4230/LIPICS.CONCUR.2019.20","language":[{"iso":"eng"}],"article_number":"20","file_date_updated":"2020-07-14T12:47:43Z","license":"https://creativecommons.org/licenses/by/3.0/","year":"2019","publication_status":"published","department":[{"_id":"ToHe"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","author":[{"full_name":"Aghajohari, Milad","last_name":"Aghajohari","first_name":"Milad"},{"id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5588-8287","first_name":"Guy","last_name":"Avni","full_name":"Avni, Guy"},{"full_name":"Henzinger, Thomas A","first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724"}],"date_updated":"2022-01-26T08:27:10Z","date_created":"2019-09-18T08:06:58Z","volume":140},{"scopus_import":1,"has_accepted_license":"1","day":"01","citation":{"mla":"Chatterjee, Krishnendu, et al. Long-Run Average Behavior of Vector Addition Systems with States. Vol. 140, 27, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, doi:10.4230/LIPICS.CONCUR.2019.27.","short":"K. Chatterjee, T.A. Henzinger, J. Otop, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019.","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. “Long-Run Average Behavior of Vector Addition Systems with States,” Vol. 140. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. https://doi.org/10.4230/LIPICS.CONCUR.2019.27.","ama":"Chatterjee K, Henzinger TA, Otop J. Long-run average behavior of vector addition systems with states. In: Vol 140. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2019. doi:10.4230/LIPICS.CONCUR.2019.27","ista":"Chatterjee K, Henzinger TA, Otop J. 2019. Long-run average behavior of vector addition systems with states. CONCUR: International Conference on Concurrency Theory, LIPIcs, vol. 140, 27.","ieee":"K. Chatterjee, T. A. Henzinger, and J. Otop, “Long-run average behavior of vector addition systems with states,” presented at the CONCUR: International Conference on Concurrency Theory, Amsterdam, Netherlands, 2019, vol. 140.","apa":"Chatterjee, K., Henzinger, T. A., & Otop, J. (2019). Long-run average behavior of vector addition systems with states (Vol. 140). Presented at the CONCUR: International Conference on Concurrency Theory, Amsterdam, Netherlands: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.CONCUR.2019.27"},"date_published":"2019-08-01T00:00:00Z","type":"conference","alternative_title":["LIPIcs"],"abstract":[{"text":"A vector addition system with states (VASS) consists of a finite set of states and counters. A configuration is a state and a value for each counter; a transition changes the state and each counter is incremented, decremented, or left unchanged. While qualitative properties such as state and configuration reachability have been studied for VASS, we consider the long-run average cost of infinite computations of VASS. The cost of a configuration is for each state, a linear combination of the counter values. In the special case of uniform cost functions, the linear combination is the same for all states. The (regular) long-run emptiness problem is, given a VASS, a cost function, and a threshold value, if there is a (lasso-shaped) computation such that the long-run average value of the cost function does not exceed the threshold. For uniform cost functions, we show that the regular long-run emptiness problem is (a) decidable in polynomial time for integer-valued VASS, and (b) decidable but nonelementarily hard for natural-valued VASS (i.e., nonnegative counters). For general cost functions, we show that the problem is (c) NP-complete for integer-valued VASS, and (d) undecidable for natural-valued VASS. Our most interesting result is for (c) integer-valued VASS with general cost functions, where we establish a connection between the regular long-run emptiness problem and quadratic Diophantine inequalities. The general (nonregular) long-run emptiness problem is equally hard as the regular problem in all cases except (c), where it remains open. ","lang":"eng"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"6885","intvolume":" 140","status":"public","title":"Long-run average behavior of vector addition systems with states","ddc":["000"],"file":[{"content_type":"application/pdf","file_size":538120,"creator":"kschuh","access_level":"open_access","file_name":"2019_LIPIcs_Chatterjee.pdf","checksum":"4985e26e1572d1575d64d38acabd71d6","date_created":"2019-09-27T12:09:35Z","date_updated":"2020-07-14T12:47:43Z","relation":"main_file","file_id":"6914"}],"oa_version":"Published Version","month":"08","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"project":[{"name":"Game Theory","call_identifier":"FWF","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"_id":"25F2ACDE-B435-11E9-9278-68D0E5697425","grant_number":"S11402-N23","name":"Rigorous Systems Engineering","call_identifier":"FWF"}],"quality_controlled":"1","doi":"10.4230/LIPICS.CONCUR.2019.27","conference":{"start_date":"2019-08-27","location":"Amsterdam, Netherlands","end_date":"2019-08-30","name":"CONCUR: International Conference on Concurrency Theory"},"language":[{"iso":"eng"}],"article_number":"27","file_date_updated":"2020-07-14T12:47:43Z","license":"https://creativecommons.org/licenses/by/4.0/","year":"2019","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"publication_status":"published","author":[{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A"},{"full_name":"Otop, Jan","first_name":"Jan","last_name":"Otop"}],"volume":140,"date_created":"2019-09-18T08:06:14Z","date_updated":"2021-01-12T08:09:27Z"},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","project":[{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","call_identifier":"FWF","name":"Game Theory"},{"name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425"}],"conference":{"name":"CONCUR: International Conference on Concurrency Theory","start_date":"2019-08-27","location":"Amsterdam, Netherlands","end_date":"2019-08-30"},"doi":"10.4230/LIPICS.CONCUR.2019.6","language":[{"iso":"eng"}],"month":"08","year":"2019","publication_status":"published","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"KrCh"}],"author":[{"first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"last_name":"Piterman","first_name":"Nir","full_name":"Piterman, Nir"}],"date_updated":"2021-01-12T08:09:28Z","date_created":"2019-09-18T08:11:43Z","volume":140,"article_number":"6","file_date_updated":"2020-07-14T12:47:43Z","citation":{"chicago":"Chatterjee, Krishnendu, and Nir Piterman. “Combinations of Qualitative Winning for Stochastic Parity Games,” Vol. 140. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. https://doi.org/10.4230/LIPICS.CONCUR.2019.6.","mla":"Chatterjee, Krishnendu, and Nir Piterman. Combinations of Qualitative Winning for Stochastic Parity Games. Vol. 140, 6, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, doi:10.4230/LIPICS.CONCUR.2019.6.","short":"K. Chatterjee, N. Piterman, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019.","ista":"Chatterjee K, Piterman N. 2019. Combinations of Qualitative Winning for Stochastic Parity Games. CONCUR: International Conference on Concurrency Theory, LIPIcs, vol. 140, 6.","apa":"Chatterjee, K., & Piterman, N. (2019). Combinations of Qualitative Winning for Stochastic Parity Games (Vol. 140). Presented at the CONCUR: International Conference on Concurrency Theory, Amsterdam, Netherlands: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.CONCUR.2019.6","ieee":"K. Chatterjee and N. Piterman, “Combinations of Qualitative Winning for Stochastic Parity Games,” presented at the CONCUR: International Conference on Concurrency Theory, Amsterdam, Netherlands, 2019, vol. 140.","ama":"Chatterjee K, Piterman N. Combinations of Qualitative Winning for Stochastic Parity Games. In: Vol 140. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2019. doi:10.4230/LIPICS.CONCUR.2019.6"},"date_published":"2019-08-01T00:00:00Z","scopus_import":1,"day":"01","has_accepted_license":"1","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"6889","ddc":["000"],"title":"Combinations of Qualitative Winning for Stochastic Parity Games","status":"public","intvolume":" 140","file":[{"checksum":"7b2ecfd4d9d02360308c0ca986fc10a7","date_updated":"2020-07-14T12:47:43Z","date_created":"2019-10-01T08:49:45Z","relation":"main_file","file_id":"6923","file_size":509163,"content_type":"application/pdf","creator":"kschuh","access_level":"open_access","file_name":"2019_LIPIcs_Chatterjee.pdf"}],"oa_version":"Published Version","type":"conference","alternative_title":["LIPIcs"],"abstract":[{"lang":"eng","text":"We study Markov decision processes and turn-based stochastic games with parity conditions. There are three qualitative winning criteria, namely, sure winning, which requires all paths to satisfy the condition, almost-sure winning, which requires the condition to be satisfied with probability 1, and limit-sure winning, which requires the condition to be satisfied with probability arbitrarily close to 1. We study the combination of two of these criteria for parity conditions, e.g., there are two parity conditions one of which must be won surely, and the other almost-surely. The problem has been studied recently by Berthon et al. for MDPs with combination of sure and almost-sure winning, under infinite-memory strategies, and the problem has been established to be in NP cap co-NP. Even in MDPs there is a difference between finite-memory and infinite-memory strategies. Our main results for combination of sure and almost-sure winning are as follows: (a) we show that for MDPs with finite-memory strategies the problem is in NP cap co-NP; (b) we show that for turn-based stochastic games the problem is co-NP-complete, both for finite-memory and infinite-memory strategies; and (c) we present algorithmic results for the finite-memory case, both for MDPs and turn-based stochastic games, by reduction to non-stochastic parity games. In addition we show that all the above complexity results also carry over to combination of sure and limit-sure winning, and results for all other combinations can be derived from existing results in the literature. Thus we present a complete picture for the study of combinations of two qualitative winning criteria for parity conditions in MDPs and turn-based stochastic games. "}]},{"page":"29:1--29:17","publication":"33rd International Symposium on Distributed Computing","citation":{"chicago":"Nowak, Thomas, and Joel Rybicki. “Byzantine Approximate Agreement on Graphs.” In 33rd International Symposium on Distributed Computing, 146:29:1--29:17. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. https://doi.org/10.4230/LIPICS.DISC.2019.29.","mla":"Nowak, Thomas, and Joel Rybicki. “Byzantine Approximate Agreement on Graphs.” 33rd International Symposium on Distributed Computing, vol. 146, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, p. 29:1--29:17, doi:10.4230/LIPICS.DISC.2019.29.","short":"T. Nowak, J. Rybicki, in:, 33rd International Symposium on Distributed Computing, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, p. 29:1--29:17.","ista":"Nowak T, Rybicki J. 2019. Byzantine approximate agreement on graphs. 33rd International Symposium on Distributed Computing. DISC: International Symposium on Distributed Computing, LIPIcs, vol. 146, 29:1--29:17.","ieee":"T. Nowak and J. Rybicki, “Byzantine approximate agreement on graphs,” in 33rd International Symposium on Distributed Computing, Budapest, Hungary, 2019, vol. 146, p. 29:1--29:17.","apa":"Nowak, T., & Rybicki, J. (2019). Byzantine approximate agreement on graphs. In 33rd International Symposium on Distributed Computing (Vol. 146, p. 29:1--29:17). Budapest, Hungary: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.DISC.2019.29","ama":"Nowak T, Rybicki J. Byzantine approximate agreement on graphs. In: 33rd International Symposium on Distributed Computing. Vol 146. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2019:29:1--29:17. doi:10.4230/LIPICS.DISC.2019.29"},"date_published":"2019-01-01T00:00:00Z","keyword":["consensus","approximate agreement","Byzantine faults","chordal graphs","lattice agreement"],"scopus_import":1,"has_accepted_license":"1","article_processing_charge":"No","ddc":["004"],"title":"Byzantine approximate agreement on graphs","status":"public","intvolume":" 146","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"6931","file":[{"date_updated":"2020-07-14T12:47:44Z","date_created":"2019-10-08T12:47:19Z","checksum":"2d2202f90c6ac991e50876451627c4b5","file_id":"6934","relation":"main_file","creator":"jrybicki","content_type":"application/pdf","file_size":639378,"file_name":"LIPIcs-DISC-2019-29.pdf","access_level":"open_access"}],"oa_version":"Published Version","alternative_title":["LIPIcs"],"type":"conference","abstract":[{"lang":"eng","text":"Consider a distributed system with n processors out of which f can be Byzantine faulty. In the\r\napproximate agreement task, each processor i receives an input value xi and has to decide on an\r\noutput value yi such that\r\n1. the output values are in the convex hull of the non-faulty processors’ input values,\r\n2. the output values are within distance d of each other.\r\n\r\n\r\nClassically, the values are assumed to be from an m-dimensional Euclidean space, where m ≥ 1.\r\nIn this work, we study the task in a discrete setting, where input values with some structure\r\nexpressible as a graph. Namely, the input values are vertices of a finite graph G and the goal is to\r\noutput vertices that are within distance d of each other in G, but still remain in the graph-induced\r\nconvex hull of the input values. For d = 0, the task reduces to consensus and cannot be solved with\r\na deterministic algorithm in an asynchronous system even with a single crash fault. For any d ≥ 1,\r\nwe show that the task is solvable in asynchronous systems when G is chordal and n > (ω + 1)f,\r\nwhere ω is the clique number of G. In addition, we give the first Byzantine-tolerant algorithm for a\r\nvariant of lattice agreement. For synchronous systems, we show tight resilience bounds for the exact\r\nvariants of these and related tasks over a large class of combinatorial structures."}],"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["1908.02743"]},"oa":1,"language":[{"iso":"eng"}],"conference":{"end_date":"2019-10-18","start_date":"2019-10-14","location":"Budapest, Hungary","name":"DISC: International Symposium on Distributed Computing"},"doi":"10.4230/LIPICS.DISC.2019.29","publication_identifier":{"eisbn":["978-3-95977-126-9"]},"publication_status":"published","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"DaAl"}],"year":"2019","date_updated":"2021-01-12T08:09:38Z","date_created":"2019-10-08T12:41:38Z","volume":146,"author":[{"full_name":"Nowak, Thomas","first_name":"Thomas","last_name":"Nowak"},{"orcid":"0000-0002-6432-6646","id":"334EFD2E-F248-11E8-B48F-1D18A9856A87","last_name":"Rybicki","first_name":"Joel","full_name":"Rybicki, Joel"}],"file_date_updated":"2020-07-14T12:47:44Z","ec_funded":1},{"status":"public","publication_status":"published","title":"Response characterization for auditing cell dynamics in long short-term memory networks","publisher":"IEEE","department":[{"_id":"ToHe"}],"year":"2019","_id":"6985","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:11:19Z","date_created":"2019-11-04T15:59:58Z","oa_version":"Preprint","author":[{"full_name":"Hasani, Ramin","first_name":"Ramin","last_name":"Hasani"},{"last_name":"Amini","first_name":"Alexander","full_name":"Amini, Alexander"},{"id":"3DC22916-F248-11E8-B48F-1D18A9856A87","last_name":"Lechner","first_name":"Mathias","full_name":"Lechner, Mathias"},{"full_name":"Naser, Felix","first_name":"Felix","last_name":"Naser"},{"full_name":"Grosu, Radu","last_name":"Grosu","first_name":"Radu"},{"full_name":"Rus, Daniela","last_name":"Rus","first_name":"Daniela"}],"article_number":"8851954","type":"conference","abstract":[{"text":"In this paper, we introduce a novel method to interpret recurrent neural networks (RNNs), particularly long short-term memory networks (LSTMs) at the cellular level. We propose a systematic pipeline for interpreting individual hidden state dynamics within the network using response characterization methods. The ranked contribution of individual cells to the network's output is computed by analyzing a set of interpretable metrics of their decoupled step and sinusoidal responses. As a result, our method is able to uniquely identify neurons with insightful dynamics, quantify relationships between dynamical properties and test accuracy through ablation analysis, and interpret the impact of network capacity on a network's dynamical distribution. Finally, we demonstrate the generalizability and scalability of our method by evaluating a series of different benchmark sequential datasets.","lang":"eng"}],"quality_controlled":"1","publication":"Proceedings of the International Joint Conference on Neural Networks","oa":1,"external_id":{"arxiv":["1809.03864"]},"citation":{"chicago":"Hasani, Ramin, Alexander Amini, Mathias Lechner, Felix Naser, Radu Grosu, and Daniela Rus. “Response Characterization for Auditing Cell Dynamics in Long Short-Term Memory Networks.” In Proceedings of the International Joint Conference on Neural Networks. IEEE, 2019. https://doi.org/10.1109/ijcnn.2019.8851954.","short":"R. Hasani, A. Amini, M. Lechner, F. Naser, R. Grosu, D. Rus, in:, Proceedings of the International Joint Conference on Neural Networks, IEEE, 2019.","mla":"Hasani, Ramin, et al. “Response Characterization for Auditing Cell Dynamics in Long Short-Term Memory Networks.” Proceedings of the International Joint Conference on Neural Networks, 8851954, IEEE, 2019, doi:10.1109/ijcnn.2019.8851954.","apa":"Hasani, R., Amini, A., Lechner, M., Naser, F., Grosu, R., & Rus, D. (2019). Response characterization for auditing cell dynamics in long short-term memory networks. In Proceedings of the International Joint Conference on Neural Networks. Budapest, Hungary: IEEE. https://doi.org/10.1109/ijcnn.2019.8851954","ieee":"R. Hasani, A. Amini, M. Lechner, F. Naser, R. Grosu, and D. Rus, “Response characterization for auditing cell dynamics in long short-term memory networks,” in Proceedings of the International Joint Conference on Neural Networks, Budapest, Hungary, 2019.","ista":"Hasani R, Amini A, Lechner M, Naser F, Grosu R, Rus D. 2019. Response characterization for auditing cell dynamics in long short-term memory networks. Proceedings of the International Joint Conference on Neural Networks. IJCNN: International Joint Conference on Neural Networks, 8851954.","ama":"Hasani R, Amini A, Lechner M, Naser F, Grosu R, Rus D. Response characterization for auditing cell dynamics in long short-term memory networks. In: Proceedings of the International Joint Conference on Neural Networks. IEEE; 2019. doi:10.1109/ijcnn.2019.8851954"},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1809.03864"}],"language":[{"iso":"eng"}],"conference":{"name":"IJCNN: International Joint Conference on Neural Networks","start_date":"2019-07-14","location":"Budapest, Hungary","end_date":"2019-07-19"},"date_published":"2019-09-30T00:00:00Z","doi":"10.1109/ijcnn.2019.8851954","scopus_import":1,"day":"30","month":"09","publication_identifier":{"isbn":["9781728119854"]}},{"doi":"10.3390/a12100218","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"arxiv":["1801.03153"]},"quality_controlled":"1","publication_identifier":{"issn":["1999-4893"]},"month":"10","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"6675"}]},"author":[{"last_name":"Mondelli","first_name":"Marco","orcid":"0000-0002-3242-7020","id":"27EB676C-8706-11E9-9510-7717E6697425","full_name":"Mondelli, Marco"},{"full_name":"Hassani, S. Hamed","first_name":"S. Hamed","last_name":"Hassani"},{"last_name":"Urbanke","first_name":"Rüdiger","full_name":"Urbanke, Rüdiger"}],"volume":12,"date_updated":"2023-02-23T12:49:28Z","date_created":"2019-11-12T14:46:19Z","year":"2019","department":[{"_id":"MaMo"}],"publisher":"MDPI","publication_status":"published","file_date_updated":"2020-07-14T12:47:47Z","article_number":"218","date_published":"2019-10-18T00:00:00Z","citation":{"apa":"Mondelli, M., Hassani, S. H., & Urbanke, R. (2019). A new coding paradigm for the primitive relay channel. Algorithms. MDPI. https://doi.org/10.3390/a12100218","ieee":"M. Mondelli, S. H. Hassani, and R. Urbanke, “A new coding paradigm for the primitive relay channel,” Algorithms, vol. 12, no. 10. MDPI, 2019.","ista":"Mondelli M, Hassani SH, Urbanke R. 2019. A new coding paradigm for the primitive relay channel. Algorithms. 12(10), 218.","ama":"Mondelli M, Hassani SH, Urbanke R. A new coding paradigm for the primitive relay channel. Algorithms. 2019;12(10). doi:10.3390/a12100218","chicago":"Mondelli, Marco, S. Hamed Hassani, and Rüdiger Urbanke. “A New Coding Paradigm for the Primitive Relay Channel.” Algorithms. MDPI, 2019. https://doi.org/10.3390/a12100218.","short":"M. Mondelli, S.H. Hassani, R. Urbanke, Algorithms 12 (2019).","mla":"Mondelli, Marco, et al. “A New Coding Paradigm for the Primitive Relay Channel.” Algorithms, vol. 12, no. 10, 218, MDPI, 2019, doi:10.3390/a12100218."},"publication":"Algorithms","article_type":"original","has_accepted_license":"1","day":"18","scopus_import":1,"file":[{"creator":"dernst","file_size":696791,"content_type":"application/pdf","file_name":"2019_Algorithms_Mondelli.pdf","access_level":"open_access","date_created":"2019-11-12T14:48:45Z","date_updated":"2020-07-14T12:47:47Z","checksum":"267756d8f9db572f496cd1663c89d59a","file_id":"7008","relation":"main_file"}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7007","intvolume":" 12","ddc":["510"],"title":"A new coding paradigm for the primitive relay channel","status":"public","issue":"10","abstract":[{"text":"We consider the primitive relay channel, where the source sends a message to the relay and to the destination, and the relay helps the communication by transmitting an additional message to the destination via a separate channel. Two well-known coding techniques have been introduced for this setting: decode-and-forward and compress-and-forward. In decode-and-forward, the relay completely decodes the message and sends some information to the destination; in compress-and-forward, the relay does not decode, and it sends a compressed version of the received signal to the destination using Wyner–Ziv coding. In this paper, we present a novel coding paradigm that provides an improved achievable rate for the primitive relay channel. The idea is to combine compress-and-forward and decode-and-forward via a chaining construction. We transmit over pairs of blocks: in the first block, we use compress-and-forward; and, in the second block, we use decode-and-forward. More specifically, in the first block, the relay does not decode, it compresses the received signal via Wyner–Ziv, and it sends only part of the compression to the destination. In the second block, the relay completely decodes the message, it sends some information to the destination, and it also sends the remaining part of the compression coming from the first block. By doing so, we are able to strictly outperform both compress-and-forward and decode-and-forward. Note that the proposed coding scheme can be implemented with polar codes. As such, it has the typical attractive properties of polar coding schemes, namely, quasi-linear encoding and decoding complexity, and error probability that decays at super-polynomial speed. As a running example, we take into account the special case of the erasure relay channel, and we provide a comparison between the rates achievable by our proposed scheme and the existing upper and lower bounds.","lang":"eng"}],"type":"journal_article"},{"page":"34-41","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"http://www.kurims.kyoto-u.ac.jp/~kyodo/kokyuroku/contents/2125.html"}],"oa":1,"citation":{"ama":"Geher GP, Titkos T, Virosztek D. Dirac masses and isometric rigidity. In: Kyoto RIMS Kôkyûroku. Vol 2125. Research Institute for Mathematical Sciences, Kyoto University; 2019:34-41.","ista":"Geher GP, Titkos T, Virosztek D. 2019. Dirac masses and isometric rigidity. Kyoto RIMS Kôkyûroku. Research on isometries as preserver problems and related topics vol. 2125, 34–41.","ieee":"G. P. Geher, T. Titkos, and D. Virosztek, “Dirac masses and isometric rigidity,” in Kyoto RIMS Kôkyûroku, Kyoto, Japan, 2019, vol. 2125, pp. 34–41.","apa":"Geher, G. P., Titkos, T., & Virosztek, D. (2019). Dirac masses and isometric rigidity. In Kyoto RIMS Kôkyûroku (Vol. 2125, pp. 34–41). Kyoto, Japan: Research Institute for Mathematical Sciences, Kyoto University.","mla":"Geher, Gyorgy Pal, et al. “Dirac Masses and Isometric Rigidity.” Kyoto RIMS Kôkyûroku, vol. 2125, Research Institute for Mathematical Sciences, Kyoto University, 2019, pp. 34–41.","short":"G.P. Geher, T. Titkos, D. Virosztek, in:, Kyoto RIMS Kôkyûroku, Research Institute for Mathematical Sciences, Kyoto University, 2019, pp. 34–41.","chicago":"Geher, Gyorgy Pal, Tamas Titkos, and Daniel Virosztek. “Dirac Masses and Isometric Rigidity.” In Kyoto RIMS Kôkyûroku, 2125:34–41. Research Institute for Mathematical Sciences, Kyoto University, 2019."},"publication":"Kyoto RIMS Kôkyûroku","language":[{"iso":"eng"}],"date_published":"2019-01-30T00:00:00Z","conference":{"end_date":"2019-01-30","start_date":"2019-01-28","location":"Kyoto, Japan","name":"Research on isometries as preserver problems and related topics"},"article_processing_charge":"No","month":"01","day":"30","publisher":"Research Institute for Mathematical Sciences, Kyoto University","intvolume":" 2125","department":[{"_id":"LaEr"}],"status":"public","title":"Dirac masses and isometric rigidity","publication_status":"published","year":"2019","_id":"7035","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","volume":2125,"date_created":"2019-11-18T15:39:53Z","date_updated":"2021-01-12T08:11:33Z","author":[{"last_name":"Geher","first_name":"Gyorgy Pal","full_name":"Geher, Gyorgy Pal"},{"full_name":"Titkos, Tamas","first_name":"Tamas","last_name":"Titkos"},{"full_name":"Virosztek, Daniel","last_name":"Virosztek","first_name":"Daniel","orcid":"0000-0003-1109-5511","id":"48DB45DA-F248-11E8-B48F-1D18A9856A87"}],"type":"conference","abstract":[{"text":"The aim of this short note is to expound one particular issue that was discussed during the talk [10] given at the symposium ”Researches on isometries as preserver problems and related topics” at Kyoto RIMS. That is, the role of Dirac masses by describing the isometry group of various metric spaces of probability measures. This article is of survey character, and it does not contain any essentially new results.From an isometric point of view, in some cases, metric spaces of measures are similar to C(K)-type function spaces. Similarity means here that their isometries are driven by some nice transformations of the underlying space. Of course, it depends on the particular choice of the metric how nice these transformations should be. Sometimes, as we will see, being a homeomorphism is enough to generate an isometry. But sometimes we need more: the transformation must preserve the underlying distance as well. Statements claiming that isometries in questions are necessarily induced by homeomorphisms are called Banach-Stone-type results, while results asserting that the underlying transformation is necessarily an isometry are termed as isometric rigidity results.As Dirac masses can be considered as building bricks of the set of all Borel measures, a natural question arises:Is it enough to understand how an isometry acts on the set of Dirac masses? Does this action extend uniquely to all measures?In what follows, we will thoroughly investigate this question.","lang":"eng"}]},{"quality_controlled":"1","page":"XIV, 245","citation":{"mla":"Kersting, Kristian, et al., editors. Wie Maschinen Lernen: Künstliche Intelligenz Verständlich Erklärt. 1st ed., Springer Nature, 2019, doi:10.1007/978-3-658-26763-6.","short":"K. Kersting, C. Lampert, C. Rothkopf, eds., Wie Maschinen Lernen: Künstliche Intelligenz Verständlich Erklärt, 1st ed., Springer Nature, Wiesbaden, 2019.","chicago":"Kersting, Kristian, Christoph Lampert, and Constantin Rothkopf, eds. Wie Maschinen Lernen: Künstliche Intelligenz Verständlich Erklärt. 1st ed. Wiesbaden: Springer Nature, 2019. https://doi.org/10.1007/978-3-658-26763-6.","ama":"Kersting K, Lampert C, Rothkopf C, eds. Wie Maschinen Lernen: Künstliche Intelligenz Verständlich Erklärt. 1st ed. Wiesbaden: Springer Nature; 2019. doi:10.1007/978-3-658-26763-6","ista":"Kersting K, Lampert C, Rothkopf C eds. 2019. Wie Maschinen Lernen: Künstliche Intelligenz Verständlich Erklärt 1st ed., Wiesbaden: Springer Nature, XIV, 245p.","ieee":"K. Kersting, C. Lampert, and C. Rothkopf, Eds., Wie Maschinen Lernen: Künstliche Intelligenz Verständlich Erklärt, 1st ed. Wiesbaden: Springer Nature, 2019.","apa":"Kersting, K., Lampert, C., & Rothkopf, C. (Eds.). (2019). Wie Maschinen Lernen: Künstliche Intelligenz Verständlich Erklärt (1st ed.). Wiesbaden: Springer Nature. https://doi.org/10.1007/978-3-658-26763-6"},"language":[{"iso":"ger"}],"doi":"10.1007/978-3-658-26763-6","date_published":"2019-10-30T00:00:00Z","day":"30","month":"10","publication_identifier":{"eisbn":["978-3-658-26763-6"],"isbn":["978-3-658-26762-9"]},"article_processing_charge":"No","publication_status":"published","title":"Wie Maschinen Lernen: Künstliche Intelligenz Verständlich Erklärt","status":"public","department":[{"_id":"ChLa"}],"editor":[{"last_name":"Kersting","first_name":"Kristian","full_name":"Kersting, Kristian"},{"full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert","first_name":"Christoph"},{"last_name":"Rothkopf","first_name":"Constantin","full_name":"Rothkopf, Constantin"}],"publisher":"Springer Nature","_id":"7171","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","year":"2019","date_created":"2019-12-11T14:15:56Z","date_updated":"2021-12-22T14:40:58Z","oa_version":"None","related_material":{"link":[{"url":"https://ist.ac.at/en/news/book-release-how-machines-learn/","description":"News on IST Website","relation":"press_release"}]},"edition":"1","place":"Wiesbaden","type":"book_editor","abstract":[{"lang":"ger","text":"Wissen Sie, was sich hinter künstlicher Intelligenz und maschinellem Lernen verbirgt? \r\nDieses Sachbuch erklärt Ihnen leicht verständlich und ohne komplizierte Formeln die grundlegenden Methoden und Vorgehensweisen des maschinellen Lernens. Mathematisches Vorwissen ist dafür nicht nötig. Kurzweilig und informativ illustriert Lisa, die Protagonistin des Buches, diese anhand von Alltagssituationen. \r\nEin Buch für alle, die in Diskussionen über Chancen und Risiken der aktuellen Entwicklung der künstlichen Intelligenz und des maschinellen Lernens mit Faktenwissen punkten möchten. Auch für Schülerinnen und Schüler geeignet!"}]},{"file_date_updated":"2020-07-14T12:47:57Z","article_number":"39","author":[{"orcid":"0000-0001-8485-1774","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","last_name":"Fulek","first_name":"Radoslav","full_name":"Fulek, Radoslav"},{"first_name":"Jan","last_name":"Kyncl","full_name":"Kyncl, Jan"}],"volume":129,"date_created":"2020-01-29T16:17:05Z","date_updated":"2021-01-12T08:13:24Z","year":"2019","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"UlWa"}],"publication_status":"published","publication_identifier":{"isbn":["978-3-95977-104-7"],"issn":["1868-8969"]},"month":"06","doi":"10.4230/LIPICS.SOCG.2019.39","conference":{"start_date":"2019-06-18","location":"Portland, OR, United States","end_date":"2019-06-21","name":"SoCG: Symposium on Computational Geometry"},"language":[{"iso":"eng"}],"external_id":{"arxiv":["1903.08637"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"project":[{"_id":"261FA626-B435-11E9-9278-68D0E5697425","grant_number":"M02281","name":"Eliminating intersections in drawings of graphs","call_identifier":"FWF"}],"quality_controlled":"1","abstract":[{"lang":"eng","text":"The genus g(G) of a graph G is the minimum g such that G has an embedding on the orientable surface M_g of genus g. A drawing of a graph on a surface is independently even if every pair of nonadjacent edges in the drawing crosses an even number of times. The Z_2-genus of a graph G, denoted by g_0(G), is the minimum g such that G has an independently even drawing on M_g. By a result of Battle, Harary, Kodama and Youngs from 1962, the graph genus is additive over 2-connected blocks. In 2013, Schaefer and Stefankovic proved that the Z_2-genus of a graph is additive over 2-connected blocks as well, and asked whether this result can be extended to so-called 2-amalgamations, as an analogue of results by Decker, Glover, Huneke, and Stahl for the genus. We give the following partial answer. If G=G_1 cup G_2, G_1 and G_2 intersect in two vertices u and v, and G-u-v has k connected components (among which we count the edge uv if present), then |g_0(G)-(g_0(G_1)+g_0(G_2))|<=k+1. For complete bipartite graphs K_{m,n}, with n >= m >= 3, we prove that g_0(K_{m,n})/g(K_{m,n})=1-O(1/n). Similar results are proved also for the Euler Z_2-genus. We express the Z_2-genus of a graph using the minimum rank of partial symmetric matrices over Z_2; a problem that might be of independent interest. "}],"type":"conference","alternative_title":["LIPIcs"],"file":[{"date_updated":"2020-07-14T12:47:57Z","date_created":"2020-02-04T09:14:31Z","checksum":"aac37b09118cc0ab58cf77129e691f8c","file_id":"7445","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":628347,"file_name":"2019_LIPIcs_Fulek.pdf","access_level":"open_access"}],"oa_version":"Published Version","_id":"7401","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 129","ddc":["000"],"status":"public","title":"Z_2-Genus of graphs and minimum rank of partial symmetric matrices","article_processing_charge":"No","has_accepted_license":"1","day":"01","scopus_import":1,"date_published":"2019-06-01T00:00:00Z","citation":{"apa":"Fulek, R., & Kyncl, J. (2019). Z_2-Genus of graphs and minimum rank of partial symmetric matrices. In 35th International Symposium on Computational Geometry (SoCG 2019) (Vol. 129). Portland, OR, United States: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.SOCG.2019.39","ieee":"R. Fulek and J. Kyncl, “Z_2-Genus of graphs and minimum rank of partial symmetric matrices,” in 35th International Symposium on Computational Geometry (SoCG 2019), Portland, OR, United States, 2019, vol. 129.","ista":"Fulek R, Kyncl J. 2019. Z_2-Genus of graphs and minimum rank of partial symmetric matrices. 35th International Symposium on Computational Geometry (SoCG 2019). SoCG: Symposium on Computational Geometry, LIPIcs, vol. 129, 39.","ama":"Fulek R, Kyncl J. Z_2-Genus of graphs and minimum rank of partial symmetric matrices. In: 35th International Symposium on Computational Geometry (SoCG 2019). Vol 129. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2019. doi:10.4230/LIPICS.SOCG.2019.39","chicago":"Fulek, Radoslav, and Jan Kyncl. “Z_2-Genus of Graphs and Minimum Rank of Partial Symmetric Matrices.” In 35th International Symposium on Computational Geometry (SoCG 2019), Vol. 129. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. https://doi.org/10.4230/LIPICS.SOCG.2019.39.","short":"R. Fulek, J. Kyncl, in:, 35th International Symposium on Computational Geometry (SoCG 2019), Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019.","mla":"Fulek, Radoslav, and Jan Kyncl. “Z_2-Genus of Graphs and Minimum Rank of Partial Symmetric Matrices.” 35th International Symposium on Computational Geometry (SoCG 2019), vol. 129, 39, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, doi:10.4230/LIPICS.SOCG.2019.39."},"publication":"35th International Symposium on Computational Geometry (SoCG 2019)"},{"month":"10","publication_identifier":{"eissn":["0302-9743"],"isbn":["9783319919072"],"issn":["1611-3349"],"eisbn":["9783319919089"]},"main_file_link":[{"url":"https://doi.org/10.1007/978-3-319-91908-9_22","open_access":"1"}],"oa":1,"quality_controlled":"1","project":[{"_id":"25F2ACDE-B435-11E9-9278-68D0E5697425","grant_number":"S11402-N23","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"name":"The Wittgenstein Prize","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211"}],"doi":"10.1007/978-3-319-91908-9_22","language":[{"iso":"eng"}],"year":"2019","acknowledgement":"This research was supported in part by the Austrian Science Fund (FWF) under grants S11402-N23(RiSE/SHiNE) and Z211-N23 (Wittgenstein Award). This research has received funding from the Sino-Danish Basic Research Centre, IDEA4CPS, funded by the Danish National Research Foundation and the National Science Foundation, China, the Innovation Fund Denmark centre DiCyPS, as well as the ERC Advanced Grant LASSO.","publication_status":"published","department":[{"_id":"ToHe"}],"editor":[{"full_name":"Steffen, Bernhard","first_name":"Bernhard","last_name":"Steffen"},{"full_name":"Woeginger, Gerhard","first_name":"Gerhard","last_name":"Woeginger"}],"publisher":"Springer Nature","author":[{"first_name":"Rajeev","last_name":"Alur","full_name":"Alur, Rajeev"},{"full_name":"Giacobbe, Mirco","last_name":"Giacobbe","first_name":"Mirco","orcid":"0000-0001-8180-0904","id":"3444EA5E-F248-11E8-B48F-1D18A9856A87"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","first_name":"Thomas A","last_name":"Henzinger","full_name":"Henzinger, Thomas A"},{"full_name":"Larsen, Kim G.","last_name":"Larsen","first_name":"Kim G."},{"full_name":"Mikučionis, Marius","first_name":"Marius","last_name":"Mikučionis"}],"date_created":"2020-02-05T10:51:44Z","date_updated":"2022-09-06T08:25:52Z","volume":10000,"scopus_import":"1","series_title":"LNCS","day":"05","article_processing_charge":"No","publication":"Computing and Software Science","citation":{"ista":"Alur R, Giacobbe M, Henzinger TA, Larsen KG, Mikučionis M. 2019.Continuous-time models for system design and analysis. In: Computing and Software Science. Lecture Notes in Computer Science, vol. 10000, 452–477.","apa":"Alur, R., Giacobbe, M., Henzinger, T. A., Larsen, K. G., & Mikučionis, M. (2019). Continuous-time models for system design and analysis. In B. Steffen & G. Woeginger (Eds.), Computing and Software Science (Vol. 10000, pp. 452–477). Springer Nature. https://doi.org/10.1007/978-3-319-91908-9_22","ieee":"R. Alur, M. Giacobbe, T. A. Henzinger, K. G. Larsen, and M. Mikučionis, “Continuous-time models for system design and analysis,” in Computing and Software Science, vol. 10000, B. Steffen and G. Woeginger, Eds. Springer Nature, 2019, pp. 452–477.","ama":"Alur R, Giacobbe M, Henzinger TA, Larsen KG, Mikučionis M. Continuous-time models for system design and analysis. In: Steffen B, Woeginger G, eds. Computing and Software Science. Vol 10000. LNCS. Springer Nature; 2019:452-477. doi:10.1007/978-3-319-91908-9_22","chicago":"Alur, Rajeev, Mirco Giacobbe, Thomas A Henzinger, Kim G. Larsen, and Marius Mikučionis. “Continuous-Time Models for System Design and Analysis.” In Computing and Software Science, edited by Bernhard Steffen and Gerhard Woeginger, 10000:452–77. LNCS. Springer Nature, 2019. https://doi.org/10.1007/978-3-319-91908-9_22.","mla":"Alur, Rajeev, et al. “Continuous-Time Models for System Design and Analysis.” Computing and Software Science, edited by Bernhard Steffen and Gerhard Woeginger, vol. 10000, Springer Nature, 2019, pp. 452–77, doi:10.1007/978-3-319-91908-9_22.","short":"R. Alur, M. Giacobbe, T.A. Henzinger, K.G. Larsen, M. Mikučionis, in:, B. Steffen, G. Woeginger (Eds.), Computing and Software Science, Springer Nature, 2019, pp. 452–477."},"page":"452-477","date_published":"2019-10-05T00:00:00Z","type":"book_chapter","alternative_title":["Lecture Notes in Computer Science"],"abstract":[{"lang":"eng","text":"We illustrate the ingredients of the state-of-the-art of model-based approach for the formal design and verification of cyber-physical systems. To capture the interaction between a discrete controller and its continuously evolving environment, we use the formal models of timed and hybrid automata. We explain the steps of modeling and verification in the tools Uppaal and SpaceEx using a case study based on a dual-chamber implantable pacemaker monitoring a human heart. We show how to design a model as a composition of components, how to construct models at varying levels of detail, how to establish that one model is an abstraction of another, how to specify correctness requirements using temporal logic, and how to verify that a model satisfies a logical requirement."}],"_id":"7453","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Continuous-time models for system design and analysis","status":"public","intvolume":" 10000","oa_version":"Published Version"},{"issue":"2","abstract":[{"text":"We consider an optimal control problem for an abstract nonlinear dissipative evolution equation. The differential constraint is penalized by augmenting the target functional by a nonnegative global-in-time functional which is null-minimized in the evolution equation is satisfied. Different variational settings are presented, leading to the convergence of the penalization method for gradient flows, noncyclic and semimonotone flows, doubly nonlinear evolutions, and GENERIC systems. ","lang":"eng"}],"type":"journal_article","oa_version":"Preprint","_id":"7550","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 28","title":"Penalization via global functionals of optimal-control problems for dissipative evolution","status":"public","article_processing_charge":"No","day":"22","date_published":"2019-10-22T00:00:00Z","citation":{"short":"L. Portinale, U. Stefanelli, Advances in Mathematical Sciences and Applications 28 (2019) 425–447.","mla":"Portinale, Lorenzo, and Ulisse Stefanelli. “Penalization via Global Functionals of Optimal-Control Problems for Dissipative Evolution.” Advances in Mathematical Sciences and Applications, vol. 28, no. 2, Gakko Tosho, 2019, pp. 425–47.","chicago":"Portinale, Lorenzo, and Ulisse Stefanelli. “Penalization via Global Functionals of Optimal-Control Problems for Dissipative Evolution.” Advances in Mathematical Sciences and Applications. Gakko Tosho, 2019.","ama":"Portinale L, Stefanelli U. Penalization via global functionals of optimal-control problems for dissipative evolution. Advances in Mathematical Sciences and Applications. 2019;28(2):425-447.","ieee":"L. Portinale and U. Stefanelli, “Penalization via global functionals of optimal-control problems for dissipative evolution,” Advances in Mathematical Sciences and Applications, vol. 28, no. 2. Gakko Tosho, pp. 425–447, 2019.","apa":"Portinale, L., & Stefanelli, U. (2019). Penalization via global functionals of optimal-control problems for dissipative evolution. Advances in Mathematical Sciences and Applications. Gakko Tosho.","ista":"Portinale L, Stefanelli U. 2019. Penalization via global functionals of optimal-control problems for dissipative evolution. Advances in Mathematical Sciences and Applications. 28(2), 425–447."},"publication":"Advances in Mathematical Sciences and Applications","page":"425-447","article_type":"original","author":[{"full_name":"Portinale, Lorenzo","last_name":"Portinale","first_name":"Lorenzo","id":"30AD2CBC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ulisse","last_name":"Stefanelli","full_name":"Stefanelli, Ulisse"}],"volume":28,"date_updated":"2022-06-17T07:52:41Z","date_created":"2020-02-28T10:54:41Z","year":"2019","acknowledgement":"This work is supported by Vienna Science and Technology Fund (WWTF) through Project MA14-009 and by the Austrian Science Fund (FWF) projects F 65 and I 2375.","publisher":"Gakko Tosho","department":[{"_id":"JaMa"}],"publication_status":"published","publication_identifier":{"issn":["1343-4373"]},"month":"10","language":[{"iso":"eng"}],"external_id":{"arxiv":["1910.10050"]},"oa":1,"main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.1910.10050"}],"project":[{"grant_number":"F6504","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","name":"Taming Complexity in Partial Differential Systems"}],"quality_controlled":"1"},{"abstract":[{"lang":"eng","text":"There is increasing evidence that protein binding to specific sites along DNA can activate the reading out of genetic information without coming into direct physical contact with the gene. There also is evidence that these distant but interacting sites are embedded in a liquid droplet of proteins which condenses out of the surrounding solution. We argue that droplet-mediated interactions can account for crucial features of gene regulation only if the droplet is poised at a non-generic point in its phase diagram. We explore a minimal model that embodies this idea, show that this model has a natural mechanism for self-tuning, and suggest direct experimental tests. "}],"type":"preprint","date_created":"2020-02-28T10:57:08Z","date_updated":"2021-01-12T08:14:09Z","oa_version":"Preprint","author":[{"last_name":"Bialek","first_name":"William","full_name":"Bialek, William"},{"full_name":"Gregor, Thomas","last_name":"Gregor","first_name":"Thomas"},{"full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","first_name":"Gašper"}],"status":"public","publication_status":"submitted","title":"Action at a distance in transcriptional regulation","department":[{"_id":"GaTk"}],"publisher":"ArXiv","_id":"7552","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2019","day":"18","month":"12","article_processing_charge":"No","language":[{"iso":"eng"}],"date_published":"2019-12-18T00:00:00Z","page":"5","project":[{"call_identifier":"FWF","name":"Biophysics of information processing in gene regulation","grant_number":"P28844-B27","_id":"254E9036-B435-11E9-9278-68D0E5697425"}],"publication":"arXiv:1912.08579","oa":1,"citation":{"ama":"Bialek W, Gregor T, Tkačik G. Action at a distance in transcriptional regulation. arXiv:191208579.","ieee":"W. Bialek, T. Gregor, and G. Tkačik, “Action at a distance in transcriptional regulation,” arXiv:1912.08579. ArXiv.","apa":"Bialek, W., Gregor, T., & Tkačik, G. (n.d.). Action at a distance in transcriptional regulation. arXiv:1912.08579. ArXiv.","ista":"Bialek W, Gregor T, Tkačik G. Action at a distance in transcriptional regulation. arXiv:1912.08579, .","short":"W. Bialek, T. Gregor, G. Tkačik, ArXiv:1912.08579 (n.d.).","mla":"Bialek, William, et al. “Action at a Distance in Transcriptional Regulation.” ArXiv:1912.08579, ArXiv.","chicago":"Bialek, William, Thomas Gregor, and Gašper Tkačik. “Action at a Distance in Transcriptional Regulation.” ArXiv:1912.08579. ArXiv, n.d."},"main_file_link":[{"url":"https://arxiv.org/abs/1912.08579","open_access":"1"}],"external_id":{"arxiv":["1912.08579"]}},{"language":[{"iso":"eng"}],"doi":"10.29007/m75b","conference":{"start_date":"2019-04-15","location":"Montreal, Canada","end_date":"2019-04-15","name":"ARCH: International Workshop on Applied Verification on Continuous and Hybrid Systems"},"quality_controlled":"1","oa":1,"publication_identifier":{"eissn":["23987340"]},"month":"05","volume":61,"date_created":"2020-03-08T23:00:49Z","date_updated":"2021-01-12T08:14:17Z","author":[{"full_name":"Immler, Fabian","first_name":"Fabian","last_name":"Immler"},{"last_name":"Althoff","first_name":"Matthias","full_name":"Althoff, Matthias"},{"last_name":"Benet","first_name":"Luis","full_name":"Benet, Luis"},{"full_name":"Chapoutot, Alexandre","last_name":"Chapoutot","first_name":"Alexandre"},{"last_name":"Chen","first_name":"Xin","full_name":"Chen, Xin"},{"last_name":"Forets","first_name":"Marcelo","full_name":"Forets, Marcelo"},{"last_name":"Geretti","first_name":"Luca","full_name":"Geretti, Luca"},{"first_name":"Niklas","last_name":"Kochdumper","full_name":"Kochdumper, Niklas"},{"last_name":"Sanders","first_name":"David P.","full_name":"Sanders, David P."},{"orcid":"0000-0003-3658-1065","id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87","last_name":"Schilling","first_name":"Christian","full_name":"Schilling, Christian"}],"department":[{"_id":"ToHe"}],"publisher":"EasyChair Publications","publication_status":"published","year":"2019","file_date_updated":"2020-07-14T12:48:00Z","date_published":"2019-05-25T00:00:00Z","page":"41-61","citation":{"apa":"Immler, F., Althoff, M., Benet, L., Chapoutot, A., Chen, X., Forets, M., … Schilling, C. (2019). ARCH-COMP19 Category Report: Continuous and hybrid systems with nonlinear dynamics. In EPiC Series in Computing (Vol. 61, pp. 41–61). Montreal, Canada: EasyChair Publications. https://doi.org/10.29007/m75b","ieee":"F. Immler et al., “ARCH-COMP19 Category Report: Continuous and hybrid systems with nonlinear dynamics,” in EPiC Series in Computing, Montreal, Canada, 2019, vol. 61, pp. 41–61.","ista":"Immler F, Althoff M, Benet L, Chapoutot A, Chen X, Forets M, Geretti L, Kochdumper N, Sanders DP, Schilling C. 2019. ARCH-COMP19 Category Report: Continuous and hybrid systems with nonlinear dynamics. EPiC Series in Computing. ARCH: International Workshop on Applied Verification on Continuous and Hybrid Systems vol. 61, 41–61.","ama":"Immler F, Althoff M, Benet L, et al. ARCH-COMP19 Category Report: Continuous and hybrid systems with nonlinear dynamics. In: EPiC Series in Computing. Vol 61. EasyChair Publications; 2019:41-61. doi:10.29007/m75b","chicago":"Immler, Fabian, Matthias Althoff, Luis Benet, Alexandre Chapoutot, Xin Chen, Marcelo Forets, Luca Geretti, Niklas Kochdumper, David P. Sanders, and Christian Schilling. “ARCH-COMP19 Category Report: Continuous and Hybrid Systems with Nonlinear Dynamics.” In EPiC Series in Computing, 61:41–61. EasyChair Publications, 2019. https://doi.org/10.29007/m75b.","short":"F. Immler, M. Althoff, L. Benet, A. Chapoutot, X. Chen, M. Forets, L. Geretti, N. Kochdumper, D.P. Sanders, C. Schilling, in:, EPiC Series in Computing, EasyChair Publications, 2019, pp. 41–61.","mla":"Immler, Fabian, et al. “ARCH-COMP19 Category Report: Continuous and Hybrid Systems with Nonlinear Dynamics.” EPiC Series in Computing, vol. 61, EasyChair Publications, 2019, pp. 41–61, doi:10.29007/m75b."},"publication":"EPiC Series in Computing","article_processing_charge":"No","has_accepted_license":"1","day":"25","scopus_import":1,"oa_version":"Published Version","file":[{"creator":"dernst","content_type":"application/pdf","file_size":1934830,"access_level":"open_access","file_name":"2019_ARCH19_Immler.pdf","checksum":"9138977a06fcd6a95976eb4bca875f0c","date_updated":"2020-07-14T12:48:00Z","date_created":"2020-03-24T07:36:36Z","file_id":"7617","relation":"main_file"}],"intvolume":" 61","ddc":["000"],"title":"ARCH-COMP19 Category Report: Continuous and hybrid systems with nonlinear dynamics","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7576","abstract":[{"text":"We present the results of a friendly competition for formal verification of continuous and hybrid systems with nonlinear continuous dynamics. The friendly competition took place as part of the workshop Applied Verification for Continuous and Hybrid Systems (ARCH) in 2019. In this year, 6 tools Ariadne, CORA, DynIbex, Flow*, Isabelle/HOL, and JuliaReach (in alphabetic order) participated. They are applied to solve reachability analysis problems on four benchmark problems, one of them with hybrid dynamics. We do not rank the tools based on the results, but show the current status and discover the potential advantages of different tools.","lang":"eng"}],"type":"conference"},{"publisher":"Formal Power Series and Algebraic Combinatorics","department":[{"_id":"LaEr"}],"publication_status":"published","acknowledgement":"D.B. is especially grateful to Patrik Ferrari for suggesting simplifications in Section 3 and\r\nto Alessandra Occelli for suggesting the name for the models of Section 2.\r\n","year":"2019","date_created":"2020-07-26T22:01:04Z","date_updated":"2021-01-12T08:17:18Z","author":[{"full_name":"Betea, Dan","last_name":"Betea","first_name":"Dan"},{"full_name":"Bouttier, Jérémie","first_name":"Jérémie","last_name":"Bouttier"},{"id":"4BF426E2-F248-11E8-B48F-1D18A9856A87","first_name":"Peter","last_name":"Nejjar","full_name":"Nejjar, Peter"},{"full_name":"Vuletíc, Mirjana","last_name":"Vuletíc","first_name":"Mirjana"}],"article_number":"34","ec_funded":1,"project":[{"grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7"},{"call_identifier":"H2020","name":"Optimal Transport and Stochastic Dynamics","_id":"256E75B8-B435-11E9-9278-68D0E5697425","grant_number":"716117"}],"quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1902.08750","open_access":"1"}],"external_id":{"arxiv":["1902.08750"]},"oa":1,"language":[{"iso":"eng"}],"conference":{"end_date":"2019-07-05","start_date":"2019-07-01","location":"Ljubljana, Slovenia","name":"FPSAC: International Conference on Formal Power Series and Algebraic Combinatorics"},"month":"07","title":"New edge asymptotics of skew Young diagrams via free boundaries","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8175","oa_version":"Preprint","type":"conference","abstract":[{"lang":"eng","text":"We study edge asymptotics of poissonized Plancherel-type measures on skew Young diagrams (integer partitions). These measures can be seen as generalizations of those studied by Baik--Deift--Johansson and Baik--Rains in resolving Ulam's problem on longest increasing subsequences of random permutations and the last passage percolation (corner growth) discrete versions thereof. Moreover they interpolate between said measures and the uniform measure on partitions. In the new KPZ-like 1/3 exponent edge scaling limit with logarithmic corrections, we find new probability distributions generalizing the classical Tracy--Widom GUE, GOE and GSE distributions from the theory of random matrices."}],"citation":{"ama":"Betea D, Bouttier J, Nejjar P, Vuletíc M. New edge asymptotics of skew Young diagrams via free boundaries. In: Proceedings on the 31st International Conference on Formal Power Series and Algebraic Combinatorics. Formal Power Series and Algebraic Combinatorics; 2019.","ista":"Betea D, Bouttier J, Nejjar P, Vuletíc M. 2019. New edge asymptotics of skew Young diagrams via free boundaries. Proceedings on the 31st International Conference on Formal Power Series and Algebraic Combinatorics. FPSAC: International Conference on Formal Power Series and Algebraic Combinatorics, 34.","apa":"Betea, D., Bouttier, J., Nejjar, P., & Vuletíc, M. (2019). New edge asymptotics of skew Young diagrams via free boundaries. In Proceedings on the 31st International Conference on Formal Power Series and Algebraic Combinatorics. Ljubljana, Slovenia: Formal Power Series and Algebraic Combinatorics.","ieee":"D. Betea, J. Bouttier, P. Nejjar, and M. Vuletíc, “New edge asymptotics of skew Young diagrams via free boundaries,” in Proceedings on the 31st International Conference on Formal Power Series and Algebraic Combinatorics, Ljubljana, Slovenia, 2019.","mla":"Betea, Dan, et al. “New Edge Asymptotics of Skew Young Diagrams via Free Boundaries.” Proceedings on the 31st International Conference on Formal Power Series and Algebraic Combinatorics, 34, Formal Power Series and Algebraic Combinatorics, 2019.","short":"D. Betea, J. Bouttier, P. Nejjar, M. Vuletíc, in:, Proceedings on the 31st International Conference on Formal Power Series and Algebraic Combinatorics, Formal Power Series and Algebraic Combinatorics, 2019.","chicago":"Betea, Dan, Jérémie Bouttier, Peter Nejjar, and Mirjana Vuletíc. “New Edge Asymptotics of Skew Young Diagrams via Free Boundaries.” In Proceedings on the 31st International Conference on Formal Power Series and Algebraic Combinatorics. Formal Power Series and Algebraic Combinatorics, 2019."},"publication":"Proceedings on the 31st International Conference on Formal Power Series and Algebraic Combinatorics","date_published":"2019-07-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"01"},{"article_processing_charge":"No","publication_identifier":{"eissn":["23987340"]},"day":"25","month":"05","oa":1,"citation":{"ama":"Althoff M, Bak S, Forets M, et al. ARCH-COMP19 Category Report: Continuous and hybrid systems with linear continuous dynamics. In: EPiC Series in Computing. Vol 61. EasyChair; 2019:14-40. doi:10.29007/bj1w","ista":"Althoff M, Bak S, Forets M, Frehse G, Kochdumper N, Ray R, Schilling C, Schupp S. 2019. ARCH-COMP19 Category Report: Continuous and hybrid systems with linear continuous dynamics. EPiC Series in Computing. ARCH: International Workshop on Applied Verification on Continuous and Hybrid Systems vol. 61, 14–40.","apa":"Althoff, M., Bak, S., Forets, M., Frehse, G., Kochdumper, N., Ray, R., … Schupp, S. (2019). ARCH-COMP19 Category Report: Continuous and hybrid systems with linear continuous dynamics. In EPiC Series in Computing (Vol. 61, pp. 14–40). Montreal, Canada: EasyChair. https://doi.org/10.29007/bj1w","ieee":"M. Althoff et al., “ARCH-COMP19 Category Report: Continuous and hybrid systems with linear continuous dynamics,” in EPiC Series in Computing, Montreal, Canada, 2019, vol. 61, pp. 14–40.","mla":"Althoff, Matthias, et al. “ARCH-COMP19 Category Report: Continuous and Hybrid Systems with Linear Continuous Dynamics.” EPiC Series in Computing, vol. 61, EasyChair, 2019, pp. 14–40, doi:10.29007/bj1w.","short":"M. Althoff, S. Bak, M. Forets, G. Frehse, N. Kochdumper, R. Ray, C. Schilling, S. Schupp, in:, EPiC Series in Computing, EasyChair, 2019, pp. 14–40.","chicago":"Althoff, Matthias, Stanley Bak, Marcelo Forets, Goran Frehse, Niklas Kochdumper, Rajarshi Ray, Christian Schilling, and Stefan Schupp. “ARCH-COMP19 Category Report: Continuous and Hybrid Systems with Linear Continuous Dynamics.” In EPiC Series in Computing, 61:14–40. EasyChair, 2019. https://doi.org/10.29007/bj1w."},"main_file_link":[{"url":"https://easychair.org/publications/open/1gbP","open_access":"1"}],"publication":"EPiC Series in Computing","page":"14-40","quality_controlled":"1","date_published":"2019-05-25T00:00:00Z","doi":"10.29007/bj1w","conference":{"name":"ARCH: International Workshop on Applied Verification on Continuous and Hybrid Systems","start_date":"2019-04-15","location":"Montreal, Canada","end_date":"2019-04-15"},"language":[{"iso":"eng"}],"type":"conference","abstract":[{"lang":"eng","text":"This report presents the results of a friendly competition for formal verification of continuous and hybrid systems with linear continuous dynamics. The friendly competition took place as part of the workshop Applied Verification for Continuous and Hybrid Systems (ARCH) in 2019. In its third edition, seven tools have been applied to solve six different benchmark problems in the category for linear continuous dynamics (in alphabetical order): CORA, CORA/SX, HyDRA, Hylaa, JuliaReach, SpaceEx, and XSpeed. This report is a snapshot of the current landscape of tools and the types of benchmarks they are particularly suited for. Due to the diversity of problems, we are not ranking tools, yet the presented results provide one of the most complete assessments of tools for the safety verification of continuous and hybrid systems with linear continuous dynamics up to this date."}],"year":"2019","_id":"8570","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"ToHe"}],"publisher":"EasyChair","intvolume":" 61","status":"public","publication_status":"published","title":"ARCH-COMP19 Category Report: Continuous and hybrid systems with linear continuous dynamics","author":[{"full_name":"Althoff, Matthias","last_name":"Althoff","first_name":"Matthias"},{"full_name":"Bak, Stanley","last_name":"Bak","first_name":"Stanley"},{"last_name":"Forets","first_name":"Marcelo","full_name":"Forets, Marcelo"},{"full_name":"Frehse, Goran","last_name":"Frehse","first_name":"Goran"},{"first_name":"Niklas","last_name":"Kochdumper","full_name":"Kochdumper, Niklas"},{"last_name":"Ray","first_name":"Rajarshi","full_name":"Ray, Rajarshi"},{"first_name":"Christian","last_name":"Schilling","id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3658-1065","full_name":"Schilling, Christian"},{"full_name":"Schupp, Stefan","first_name":"Stefan","last_name":"Schupp"}],"oa_version":"Published Version","volume":61,"date_created":"2020-09-26T14:23:54Z","date_updated":"2021-01-12T08:20:05Z"},{"citation":{"ama":"Kim MY, Ono A, Scholten S, et al. DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm. Proceedings of the National Academy of Sciences. 2019;116(19):9652-9657. doi:10.1073/pnas.1821435116","ista":"Kim MY, Ono A, Scholten S, Kinoshita T, Zilberman D, Okamoto T, Fischer RL. 2019. DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm. Proceedings of the National Academy of Sciences. 116(19), 9652–9657.","apa":"Kim, M. Y., Ono, A., Scholten, S., Kinoshita, T., Zilberman, D., Okamoto, T., & Fischer, R. L. (2019). DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1821435116","ieee":"M. Y. Kim et al., “DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm,” Proceedings of the National Academy of Sciences, vol. 116, no. 19. National Academy of Sciences, pp. 9652–9657, 2019.","mla":"Kim, M. Yvonne, et al. “DNA Demethylation by ROS1a in Rice Vegetative Cells Promotes Methylation in Sperm.” Proceedings of the National Academy of Sciences, vol. 116, no. 19, National Academy of Sciences, 2019, pp. 9652–57, doi:10.1073/pnas.1821435116.","short":"M.Y. Kim, A. Ono, S. Scholten, T. Kinoshita, D. Zilberman, T. Okamoto, R.L. Fischer, Proceedings of the National Academy of Sciences 116 (2019) 9652–9657.","chicago":"Kim, M. Yvonne, Akemi Ono, Stefan Scholten, Tetsu Kinoshita, Daniel Zilberman, Takashi Okamoto, and Robert L. Fischer. “DNA Demethylation by ROS1a in Rice Vegetative Cells Promotes Methylation in Sperm.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2019. https://doi.org/10.1073/pnas.1821435116."},"publication":"Proceedings of the National Academy of Sciences","page":"9652-9657","article_type":"original","date_published":"2019-05-07T00:00:00Z","scopus_import":"1","keyword":["Multidisciplinary"],"has_accepted_license":"1","article_processing_charge":"No","day":"07","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"9460","intvolume":" 116","ddc":["580"],"title":"DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm","status":"public","oa_version":"Published Version","file":[{"file_name":"2019_PNAS_Kim.pdf","access_level":"open_access","content_type":"application/pdf","file_size":1142540,"creator":"asandaue","relation":"main_file","file_id":"9461","date_updated":"2021-06-04T12:50:47Z","date_created":"2021-06-04T12:50:47Z","checksum":"5b0ae3779b8b21b5223bd2d3cceede3a","success":1}],"type":"journal_article","issue":"19","abstract":[{"lang":"eng","text":"Epigenetic reprogramming is required for proper regulation of gene expression in eukaryotic organisms. In Arabidopsis, active DNA demethylation is crucial for seed viability, pollen function, and successful reproduction. The DEMETER (DME) DNA glycosylase initiates localized DNA demethylation in vegetative and central cells, so-called companion cells that are adjacent to sperm and egg gametes, respectively. In rice, the central cell genome displays local DNA hypomethylation, suggesting that active DNA demethylation also occurs in rice; however, the enzyme responsible for this process is unknown. One candidate is the rice REPRESSOR OF SILENCING 1a (ROS1a) gene, which is related to DME and is essential for rice seed viability and pollen function. Here, we report genome-wide analyses of DNA methylation in wild-type and ros1a mutant sperm and vegetative cells. We find that the rice vegetative cell genome is locally hypomethylated compared with sperm by a process that requires ROS1a activity. We show that many ROS1a target sequences in the vegetative cell are hypomethylated in the rice central cell, suggesting that ROS1a also demethylates the central cell genome. Similar to Arabidopsis, we show that sperm non-CG methylation is indirectly promoted by DNA demethylation in the vegetative cell. These results reveal that DNA glycosylase-mediated DNA demethylation processes are conserved in Arabidopsis and rice, plant species that diverged 150 million years ago. Finally, although global non-CG methylation levels of sperm and egg differ, the maternal and paternal embryo genomes show similar non-CG methylation levels, suggesting that rice gamete genomes undergo dynamic DNA methylation reprogramming after cell fusion."}],"oa":1,"tmp":{"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","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"external_id":{"pmid":["31000601"]},"quality_controlled":"1","doi":"10.1073/pnas.1821435116","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"month":"05","pmid":1,"year":"2019","publisher":"National Academy of Sciences","department":[{"_id":"DaZi"}],"publication_status":"published","author":[{"last_name":"Kim","first_name":"M. Yvonne","full_name":"Kim, M. Yvonne"},{"first_name":"Akemi","last_name":"Ono","full_name":"Ono, Akemi"},{"full_name":"Scholten, Stefan","first_name":"Stefan","last_name":"Scholten"},{"full_name":"Kinoshita, Tetsu","last_name":"Kinoshita","first_name":"Tetsu"},{"full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","last_name":"Zilberman","first_name":"Daniel"},{"last_name":"Okamoto","first_name":"Takashi","full_name":"Okamoto, Takashi"},{"first_name":"Robert L.","last_name":"Fischer","full_name":"Fischer, Robert L."}],"volume":116,"date_created":"2021-06-04T12:38:20Z","date_updated":"2021-12-14T07:52:30Z","file_date_updated":"2021-06-04T12:50:47Z","extern":"1"},{"month":"08","publication_identifier":{"eissn":["1756-0500"]},"doi":"10.1186/s13104-019-4534-3","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"pmid":["31395095"]},"quality_controlled":"1","file_date_updated":"2020-07-14T12:47:40Z","article_number":"494","author":[{"first_name":"Michael N.","last_name":"Antoniou","full_name":"Antoniou, Michael N."},{"first_name":"Armel","last_name":"Nicolas","id":"2A103192-F248-11E8-B48F-1D18A9856A87","full_name":"Nicolas, Armel"},{"last_name":"Mesnage","first_name":"Robin","full_name":"Mesnage, Robin"},{"first_name":"Martina","last_name":"Biserni","full_name":"Biserni, Martina"},{"first_name":"Francesco V.","last_name":"Rao","full_name":"Rao, Francesco V."},{"full_name":"Martin, Cristina Vazquez","last_name":"Martin","first_name":"Cristina Vazquez"}],"related_material":{"record":[{"id":"9784","status":"public","relation":"research_data"}]},"date_created":"2019-08-18T22:00:39Z","date_updated":"2023-02-23T14:08:14Z","volume":12,"year":"2019","pmid":1,"publication_status":"published","department":[{"_id":"LifeSc"}],"publisher":"BioMed Central","day":"08","article_processing_charge":"No","has_accepted_license":"1","scopus_import":1,"date_published":"2019-08-08T00:00:00Z","publication":"BMC Research Notes","citation":{"short":"M.N. Antoniou, A. Nicolas, R. Mesnage, M. Biserni, F.V. Rao, C.V. Martin, BMC Research Notes 12 (2019).","mla":"Antoniou, Michael N., et al. “Glyphosate Does Not Substitute for Glycine in Proteins of Actively Dividing Mammalian Cells.” BMC Research Notes, vol. 12, 494, BioMed Central, 2019, doi:10.1186/s13104-019-4534-3.","chicago":"Antoniou, Michael N., Armel Nicolas, Robin Mesnage, Martina Biserni, Francesco V. Rao, and Cristina Vazquez Martin. “Glyphosate Does Not Substitute for Glycine in Proteins of Actively Dividing Mammalian Cells.” BMC Research Notes. BioMed Central, 2019. https://doi.org/10.1186/s13104-019-4534-3.","ama":"Antoniou MN, Nicolas A, Mesnage R, Biserni M, Rao FV, Martin CV. Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells. BMC Research Notes. 2019;12. doi:10.1186/s13104-019-4534-3","apa":"Antoniou, M. N., Nicolas, A., Mesnage, R., Biserni, M., Rao, F. V., & Martin, C. V. (2019). Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells. BMC Research Notes. BioMed Central. https://doi.org/10.1186/s13104-019-4534-3","ieee":"M. N. Antoniou, A. Nicolas, R. Mesnage, M. Biserni, F. V. Rao, and C. V. Martin, “Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells,” BMC Research Notes, vol. 12. BioMed Central, 2019.","ista":"Antoniou MN, Nicolas A, Mesnage R, Biserni M, Rao FV, Martin CV. 2019. Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells. BMC Research Notes. 12, 494."},"abstract":[{"lang":"eng","text":"Glyphosate (N-phosphonomethyl glycine) and its commercial herbicide formulations have been shown to exert toxicity via various mechanisms. It has been asserted that glyphosate substitutes for glycine in polypeptide chains leading to protein misfolding and toxicity. However, as no direct evidence exists for glycine to glyphosate substitution in proteins, including in mammalian organisms, we tested this claim by conducting a proteomics analysis of MDA-MB-231 human breast cancer cells grown in the presence of 100 mg/L glyphosate for 6 days. Protein extracts from three treated and three untreated cell cultures were analysed as one TMT-6plex labelled sample, to highlight a specific pattern (+/+/+/−/−/−) of reporter intensities for peptides bearing true glyphosate treatment induced-post translational modifications as well as allowing an investigation of the total proteome."}],"type":"journal_article","file":[{"content_type":"application/pdf","file_size":1177482,"creator":"dernst","access_level":"open_access","file_name":"2019_BMC_Antoniou.pdf","checksum":"4a2bb7994b7f2c432bf44f5127ea3102","date_created":"2019-08-23T11:10:35Z","date_updated":"2020-07-14T12:47:40Z","relation":"main_file","file_id":"6829"}],"oa_version":"Published Version","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"6819","title":"Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells","status":"public","ddc":["570"],"intvolume":" 12"},{"status":"public","title":"MOESM1 of Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells","publisher":"Springer Nature","department":[{"_id":"LifeSc"}],"year":"2019","_id":"9784","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_created":"2021-08-06T08:14:05Z","date_updated":"2023-02-23T12:52:29Z","oa_version":"Published Version","author":[{"first_name":"Michael N.","last_name":"Antoniou","full_name":"Antoniou, Michael N."},{"id":"2A103192-F248-11E8-B48F-1D18A9856A87","first_name":"Armel","last_name":"Nicolas","full_name":"Nicolas, Armel"},{"last_name":"Mesnage","first_name":"Robin","full_name":"Mesnage, Robin"},{"first_name":"Martina","last_name":"Biserni","full_name":"Biserni, Martina"},{"last_name":"Rao","first_name":"Francesco V.","full_name":"Rao, Francesco V."},{"full_name":"Martin, Cristina Vazquez","first_name":"Cristina Vazquez","last_name":"Martin"}],"related_material":{"record":[{"id":"6819","status":"public","relation":"used_in_publication"}]},"type":"research_data_reference","abstract":[{"text":"Additional file 1: Table S1. Kinetics of MDA-MB-231 cell growth in either the presence or absence of 100Â mg/L glyphosate. Cell counts are given at day-1 of seeding flasks and following 6-days of continuous culture. Note: no differences in cell numbers were observed between negative control and glyphosate treated cultures.","lang":"eng"}],"citation":{"mla":"Antoniou, Michael N., et al. MOESM1 of Glyphosate Does Not Substitute for Glycine in Proteins of Actively Dividing Mammalian Cells. Springer Nature, 2019, doi:10.6084/m9.figshare.9411761.v1.","short":"M.N. Antoniou, A. Nicolas, R. Mesnage, M. Biserni, F.V. Rao, C.V. Martin, (2019).","chicago":"Antoniou, Michael N., Armel Nicolas, Robin Mesnage, Martina Biserni, Francesco V. Rao, and Cristina Vazquez Martin. “MOESM1 of Glyphosate Does Not Substitute for Glycine in Proteins of Actively Dividing Mammalian Cells.” Springer Nature, 2019. https://doi.org/10.6084/m9.figshare.9411761.v1.","ama":"Antoniou MN, Nicolas A, Mesnage R, Biserni M, Rao FV, Martin CV. MOESM1 of Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells. 2019. doi:10.6084/m9.figshare.9411761.v1","ista":"Antoniou MN, Nicolas A, Mesnage R, Biserni M, Rao FV, Martin CV. 2019. MOESM1 of Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells, Springer Nature, 10.6084/m9.figshare.9411761.v1.","ieee":"M. N. Antoniou, A. Nicolas, R. Mesnage, M. Biserni, F. V. Rao, and C. V. Martin, “MOESM1 of Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells.” Springer Nature, 2019.","apa":"Antoniou, M. N., Nicolas, A., Mesnage, R., Biserni, M., Rao, F. V., & Martin, C. V. (2019). MOESM1 of Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells. Springer Nature. https://doi.org/10.6084/m9.figshare.9411761.v1"},"oa":1,"main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.9411761.v1","open_access":"1"}],"date_published":"2019-08-09T00:00:00Z","doi":"10.6084/m9.figshare.9411761.v1","day":"09","month":"08","article_processing_charge":"No"},{"day":"22","month":"06","article_processing_charge":"No","citation":{"ista":"Polechova J. 2019. Data from: Is the sky the limit? On the expansion threshold of a species’ range, Dryad, 10.5061/dryad.5vv37.","ieee":"J. Polechova, “Data from: Is the sky the limit? On the expansion threshold of a species’ range.” Dryad, 2019.","apa":"Polechova, J. (2019). Data from: Is the sky the limit? On the expansion threshold of a species’ range. Dryad. https://doi.org/10.5061/dryad.5vv37","ama":"Polechova J. Data from: Is the sky the limit? On the expansion threshold of a species’ range. 2019. doi:10.5061/dryad.5vv37","chicago":"Polechova, Jitka. “Data from: Is the Sky the Limit? On the Expansion Threshold of a Species’ Range.” Dryad, 2019. https://doi.org/10.5061/dryad.5vv37.","mla":"Polechova, Jitka. Data from: Is the Sky the Limit? On the Expansion Threshold of a Species’ Range. Dryad, 2019, doi:10.5061/dryad.5vv37.","short":"J. Polechova, (2019)."},"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.5vv37"}],"doi":"10.5061/dryad.5vv37","date_published":"2019-06-22T00:00:00Z","type":"research_data_reference","abstract":[{"text":"More than 100 years after Grigg’s influential analysis of species’ borders, the causes of limits to species’ ranges still represent a puzzle that has never been understood with clarity. The topic has become especially important recently as many scientists have become interested in the potential for species’ ranges to shift in response to climate change—and yet nearly all of those studies fail to recognise or incorporate evolutionary genetics in a way that relates to theoretical developments. I show that range margins can be understood based on just two measurable parameters: (i) the fitness cost of dispersal—a measure of environmental heterogeneity—and (ii) the strength of genetic drift, which reduces genetic diversity. Together, these two parameters define an ‘expansion threshold’: adaptation fails when genetic drift reduces genetic diversity below that required for adaptation to a heterogeneous environment. When the key parameters drop below this expansion threshold locally, a sharp range margin forms. When they drop below this threshold throughout the species’ range, adaptation collapses everywhere, resulting in either extinction or formation of a fragmented metapopulation. Because the effects of dispersal differ fundamentally with dimension, the second parameter—the strength of genetic drift—is qualitatively different compared to a linear habitat. In two-dimensional habitats, genetic drift becomes effectively independent of selection. It decreases with ‘neighbourhood size’—the number of individuals accessible by dispersal within one generation. Moreover, in contrast to earlier predictions, which neglected evolution of genetic variance and/or stochasticity in two dimensions, dispersal into small marginal populations aids adaptation. This is because the reduction of both genetic and demographic stochasticity has a stronger effect than the cost of dispersal through increased maladaptation. The expansion threshold thus provides a novel, theoretically justified, and testable prediction for formation of the range margin and collapse of the species’ range.","lang":"eng"}],"_id":"9839","year":"2019","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","status":"public","title":"Data from: Is the sky the limit? On the expansion threshold of a species' range","publisher":"Dryad","department":[{"_id":"NiBa"}],"author":[{"full_name":"Polechova, Jitka","last_name":"Polechova","first_name":"Jitka","orcid":"0000-0003-0951-3112","id":"3BBFB084-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"id":"315","status":"public","relation":"used_in_publication"}]},"date_created":"2021-08-09T13:07:28Z","date_updated":"2023-02-23T11:14:30Z","oa_version":"Published Version"},{"day":"10","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2019-10-10T00:00:00Z","publication":"Epigenetics and Chromatin","citation":{"ama":"Harris KD, Lloyd JPB, Domb K, Zilberman D, Zemach A. DNA methylation is maintained with high fidelity in the honey bee germline and exhibits global non-functional fluctuations during somatic development. Epigenetics and Chromatin. 2019;12. doi:10.1186/s13072-019-0307-4","ista":"Harris KD, Lloyd JPB, Domb K, Zilberman D, Zemach A. 2019. DNA methylation is maintained with high fidelity in the honey bee germline and exhibits global non-functional fluctuations during somatic development. Epigenetics and Chromatin. 12, 62.","apa":"Harris, K. D., Lloyd, J. P. B., Domb, K., Zilberman, D., & Zemach, A. (2019). DNA methylation is maintained with high fidelity in the honey bee germline and exhibits global non-functional fluctuations during somatic development. Epigenetics and Chromatin. Springer Nature. https://doi.org/10.1186/s13072-019-0307-4","ieee":"K. D. Harris, J. P. B. Lloyd, K. Domb, D. Zilberman, and A. Zemach, “DNA methylation is maintained with high fidelity in the honey bee germline and exhibits global non-functional fluctuations during somatic development,” Epigenetics and Chromatin, vol. 12. Springer Nature, 2019.","mla":"Harris, Keith D., et al. “DNA Methylation Is Maintained with High Fidelity in the Honey Bee Germline and Exhibits Global Non-Functional Fluctuations during Somatic Development.” Epigenetics and Chromatin, vol. 12, 62, Springer Nature, 2019, doi:10.1186/s13072-019-0307-4.","short":"K.D. Harris, J.P.B. Lloyd, K. Domb, D. Zilberman, A. Zemach, Epigenetics and Chromatin 12 (2019).","chicago":"Harris, Keith D., James P. B. Lloyd, Katherine Domb, Daniel Zilberman, and Assaf Zemach. “DNA Methylation Is Maintained with High Fidelity in the Honey Bee Germline and Exhibits Global Non-Functional Fluctuations during Somatic Development.” Epigenetics and Chromatin. Springer Nature, 2019. https://doi.org/10.1186/s13072-019-0307-4."},"article_type":"original","abstract":[{"text":"Background\r\nDNA methylation of active genes, also known as gene body methylation, is found in many animal and plant genomes. Despite this, the transcriptional and developmental role of such methylation remains poorly understood. Here, we explore the dynamic range of DNA methylation in honey bee, a model organism for gene body methylation.\r\n\r\nResults\r\nOur data show that CG methylation in gene bodies globally fluctuates during honey bee development. However, these changes cause no gene expression alterations. Intriguingly, despite the global alterations, tissue-specific CG methylation patterns of complete genes or exons are rare, implying robust maintenance of genic methylation during development. Additionally, we show that CG methylation maintenance fluctuates in somatic cells, while reaching maximum fidelity in sperm cells. Finally, unlike universally present CG methylation, we discovered non-CG methylation specifically in bee heads that resembles such methylation in mammalian brain tissue.\r\n\r\nConclusions\r\nBased on these results, we propose that gene body CG methylation can oscillate during development if it is kept to a level adequate to preserve function. Additionally, our data suggest that heightened non-CG methylation is a conserved regulator of animal nervous systems.","lang":"eng"}],"type":"journal_article","file":[{"file_name":"2019_EpigeneticsAndChromatin_Harris.pdf","access_level":"open_access","content_type":"application/pdf","file_size":3221067,"creator":"asandaue","relation":"main_file","file_id":"9531","date_updated":"2021-06-08T09:29:19Z","date_created":"2021-06-08T09:29:19Z","checksum":"86ff50a7517891511af2733c76c81b67","success":1}],"oa_version":"Published Version","_id":"9530","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","status":"public","ddc":["570"],"title":"DNA methylation is maintained with high fidelity in the honey bee germline and exhibits global non-functional fluctuations during somatic development","intvolume":" 12","month":"10","publication_identifier":{"eissn":["1756-8935"]},"doi":"10.1186/s13072-019-0307-4","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["31601251"]},"quality_controlled":"1","file_date_updated":"2021-06-08T09:29:19Z","extern":"1","article_number":"62","author":[{"last_name":"Harris","first_name":"Keith D.","full_name":"Harris, Keith D."},{"last_name":"Lloyd","first_name":"James P. B.","full_name":"Lloyd, James P. B."},{"last_name":"Domb","first_name":"Katherine","full_name":"Domb, Katherine"},{"first_name":"Daniel","last_name":"Zilberman","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel"},{"full_name":"Zemach, Assaf","first_name":"Assaf","last_name":"Zemach"}],"date_updated":"2021-12-14T07:53:00Z","date_created":"2021-06-08T09:21:51Z","volume":12,"year":"2019","pmid":1,"publication_status":"published","department":[{"_id":"DaZi"}],"publisher":"Springer Nature"}]