[{"abstract":[{"lang":"eng","text":"We present a new dynamic partial-order reduction method for stateless model checking of concurrent programs. A common approach for exploring program behaviors relies on enumerating the traces of the program, without storing the visited states (aka stateless exploration). As the number of distinct traces grows exponentially, dynamic partial-order reduction (DPOR) techniques have been successfully used to partition the space of traces into equivalence classes (Mazurkiewicz partitioning), with the goal of exploring only few representative traces from each class.\r\nWe introduce a new equivalence on traces under sequential consistency semantics, which we call the observation equivalence. Two traces are observationally equivalent if every read event observes the same write event in both traces. While the traditional Mazurkiewicz equivalence is control-centric, our new definition is data-centric. We show that our observation equivalence is coarser than the Mazurkiewicz equivalence, and in many cases even exponentially coarser. We devise a DPOR exploration of the trace space, called data-centric DPOR, based on the observation equivalence.\r\n1. For acyclic architectures, our algorithm is guaranteed to explore exactly one representative trace from each observation class, while spending polynomial time per class. Hence, our algorithm is optimal wrt the observation equivalence, and in several cases explores exponentially fewer traces than any enumerative method based on the Mazurkiewicz equivalence.\r\n2. For cyclic architectures, we consider an equivalence between traces which is finer than the observation equivalence; but coarser than the Mazurkiewicz equivalence, and in some cases is exponentially coarser. Our data-centric DPOR algorithm remains optimal under this trace equivalence. \r\nFinally, we perform a basic experimental comparison between the existing Mazurkiewicz-based DPOR and our data-centric DPOR on a set of academic benchmarks. Our results show a significant reduction in both running time and the number of explored equivalence classes."}],"pubrep_id":"872","related_material":{"record":[{"id":"5448","relation":"earlier_version","status":"public"},{"id":"10417","status":"public","relation":"later_version"}]},"doi":"10.15479/AT:IST-2017-872-v1-1","file":[{"relation":"main_file","file_id":"5487","creator":"system","file_name":"IST-2017-872-v1+1_main.pdf","file_size":910347,"checksum":"d2635c4cf013000f0a1b09e80f9e4ab7","access_level":"open_access","content_type":"application/pdf","date_updated":"2020-07-14T12:46:59Z","date_created":"2018-12-12T11:53:26Z"}],"publication_status":"published","oa_version":"Published Version","page":"36","alternative_title":["IST Austria Technical Report"],"fulldoi":"https://doi.org/10.15479/AT:IST-2017-872-v1-1","type":"technical_report","publisher":"IST Austria","author":[{"last_name":"Chalupa","first_name":"Marek","full_name":"Chalupa, Marek"},{"last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"full_name":"Pavlogiannis, Andreas","orcid":"0000-0002-8943-0722","first_name":"Andreas","last_name":"Pavlogiannis","id":"49704004-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Sinha","first_name":"Nishant","full_name":"Sinha, Nishant"},{"first_name":"Kapil","last_name":"Vaidya","full_name":"Vaidya, Kapil"}],"oa":1,"has_accepted_license":"1","month":"10","department":[{"_id":"KrCh"}],"citation":{"mla":"Chalupa, Marek, et al. <i>Data-Centric Dynamic Partial Order Reduction</i>. IST Austria, 2017, doi:<a href=\"https://doi.org/10.15479/AT:IST-2017-872-v1-1\">10.15479/AT:IST-2017-872-v1-1</a>.","ama":"Chalupa M, Chatterjee K, Pavlogiannis A, Sinha N, Vaidya K. <i>Data-Centric Dynamic Partial Order Reduction</i>. IST Austria; 2017. doi:<a href=\"https://doi.org/10.15479/AT:IST-2017-872-v1-1\">10.15479/AT:IST-2017-872-v1-1</a>","short":"M. Chalupa, K. Chatterjee, A. Pavlogiannis, N. Sinha, K. Vaidya, Data-Centric Dynamic Partial Order Reduction, IST Austria, 2017.","apa":"Chalupa, M., Chatterjee, K., Pavlogiannis, A., Sinha, N., &#38; Vaidya, K. (2017). <i>Data-centric dynamic partial order reduction</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2017-872-v1-1\">https://doi.org/10.15479/AT:IST-2017-872-v1-1</a>","chicago":"Chalupa, Marek, Krishnendu Chatterjee, Andreas Pavlogiannis, Nishant Sinha, and Kapil Vaidya. <i>Data-Centric Dynamic Partial Order Reduction</i>. IST Austria, 2017. <a href=\"https://doi.org/10.15479/AT:IST-2017-872-v1-1\">https://doi.org/10.15479/AT:IST-2017-872-v1-1</a>.","ista":"Chalupa M, Chatterjee K, Pavlogiannis A, Sinha N, Vaidya K. 2017. Data-centric dynamic partial order reduction, IST Austria, 36p.","ieee":"M. Chalupa, K. Chatterjee, A. Pavlogiannis, N. Sinha, and K. Vaidya, <i>Data-centric dynamic partial order reduction</i>. IST Austria, 2017."},"date_created":"2018-12-12T11:39:26Z","year":"2017","status":"public","day":"23","_id":"5456","language":[{"iso":"eng"}],"title":"Data-centric dynamic partial order reduction","date_updated":"2025-05-20T09:45:08Z","date_published":"2017-10-23T00:00:00Z","ddc":["000"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2020-07-14T12:46:59Z","publication_identifier":{"issn":["2664-1690"]}},{"status":"public","date_created":"2018-12-11T11:47:06Z","citation":{"ista":"De Martino D. 2017. Maximum entropy modeling of metabolic networks by constraining growth-rate moments predicts coexistence of phenotypes. Physical Review E. 96(6), 060401.","chicago":"De Martino, Daniele. “Maximum Entropy Modeling of Metabolic Networks by Constraining Growth-Rate Moments Predicts Coexistence of Phenotypes.” <i>Physical Review E</i>. American Physical Society, 2017. <a href=\"https://doi.org/10.1103/PhysRevE.96.060401\">https://doi.org/10.1103/PhysRevE.96.060401</a>.","ieee":"D. De Martino, “Maximum entropy modeling of metabolic networks by constraining growth-rate moments predicts coexistence of phenotypes,” <i>Physical Review E</i>, vol. 96, no. 6. American Physical Society, 2017.","ama":"De Martino D. Maximum entropy modeling of metabolic networks by constraining growth-rate moments predicts coexistence of phenotypes. <i>Physical Review E</i>. 2017;96(6). doi:<a href=\"https://doi.org/10.1103/PhysRevE.96.060401\">10.1103/PhysRevE.96.060401</a>","short":"D. De Martino, Physical Review E 96 (2017).","apa":"De Martino, D. (2017). Maximum entropy modeling of metabolic networks by constraining growth-rate moments predicts coexistence of phenotypes. <i>Physical Review E</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevE.96.060401\">https://doi.org/10.1103/PhysRevE.96.060401</a>","mla":"De Martino, Daniele. “Maximum Entropy Modeling of Metabolic Networks by Constraining Growth-Rate Moments Predicts Coexistence of Phenotypes.” <i>Physical Review E</i>, vol. 96, no. 6, 060401, American Physical Society, 2017, doi:<a href=\"https://doi.org/10.1103/PhysRevE.96.060401\">10.1103/PhysRevE.96.060401</a>."},"year":"2017","department":[{"_id":"GaTk"}],"external_id":{"isi":["000418574400001"],"arxiv":["1707.00320"]},"month":"12","oa":1,"author":[{"full_name":"De Martino, Daniele","orcid":"0000-0002-5214-4706","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","last_name":"De Martino","first_name":"Daniele"}],"publication_identifier":{"issn":["2470-0045"]},"intvolume":"        96","date_updated":"2025-09-18T09:41:11Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2017-12-21T00:00:00Z","title":"Maximum entropy modeling of metabolic networks by constraining growth-rate moments predicts coexistence of phenotypes","publist_id":"7266","arxiv":1,"_id":"548","language":[{"iso":"eng"}],"day":"21","isi":1,"issue":"6","doi":"10.1103/PhysRevE.96.060401","quality_controlled":"1","article_processing_charge":"No","publication":"Physical Review E","project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"abstract":[{"lang":"eng","text":"In this work maximum entropy distributions in the space of steady states of metabolic networks are considered upon constraining the first and second moments of the growth rate. Coexistence of fast and slow phenotypes, with bimodal flux distributions, emerges upon considering control on the average growth (optimization) and its fluctuations (heterogeneity). This is applied to the carbon catabolic core of Escherichia coli where it quantifies the metabolic activity of slow growing phenotypes and it provides a quantitative map with metabolic fluxes, opening the possibility to detect coexistence from flux data. A preliminary analysis on data for E. coli cultures in standard conditions shows degeneracy for the inferred parameters that extend in the coexistence region."}],"publisher":"American Physical Society","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1707.00320","open_access":"1"}],"ec_funded":1,"fulldoi":"https://doi.org/10.1103/PhysRevE.96.060401","type":"journal_article","article_number":"060401","alternative_title":["Rapid Communications"],"volume":96,"corr_author":"1","publication_status":"published","oa_version":"Submitted Version"},{"pubrep_id":"925","project":[{"name":"Moderne Concurrency Paradigms","grant_number":"S11402-N23","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","name":"Formal methods for the design and analysis of complex systems","call_identifier":"FWF"}],"publication":"Electronic Proceedings in Theoretical Computer Science","abstract":[{"text":"Model checking is usually based on a comprehensive traversal of the state space. Causality-based model checking is a radically different approach that instead analyzes the cause-effect relationships in a program. We give an overview on a new class of model checking algorithms that capture the causal relationships in a special data structure called concurrent traces. Concurrent traces identify key events in an execution history and link them through their cause-effect relationships. The model checker builds a tableau of concurrent traces, where the case splits represent different causal explanations of a hypothetical error. Causality-based model checking has been implemented in the ARCTOR tool, and applied to previously intractable multi-threaded benchmarks.","lang":"eng"}],"quality_controlled":"1","article_processing_charge":"No","doi":"10.4204/EPTCS.259.3","file":[{"access_level":"open_access","content_type":"application/pdf","date_updated":"2020-07-14T12:47:00Z","date_created":"2018-12-12T10:12:21Z","relation":"main_file","file_id":"4939","file_name":"IST-2018-925-v1+1_1710.03391v1.pdf","file_size":209294,"checksum":"6274f6c0da3376a7b079180d81568518","creator":"system"}],"corr_author":"1","oa_version":"Submitted Version","publication_status":"published","volume":259,"alternative_title":["EPTCS"],"page":"31 - 38","type":"conference","fulldoi":"https://doi.org/10.4204/EPTCS.259.3","publisher":"Open Publishing Association","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1710.03391","open_access":"1"}],"oa":1,"has_accepted_license":"1","author":[{"full_name":"Finkbeiner, Bernd","first_name":"Bernd","last_name":"Finkbeiner"},{"id":"2C311BF8-F248-11E8-B48F-1D18A9856A87","last_name":"Kupriyanov","first_name":"Andrey","full_name":"Kupriyanov, Andrey"}],"conference":{"end_date":"2017-04-29","name":"CREST: Causal Reasoning for Embedded and Safety-Critical Systems Technologies","location":"Uppsala, Sweden","start_date":"2017-04-29"},"external_id":{"isi":["000439358700004"],"arxiv":["1710.03391"]},"month":"10","year":"2017","date_created":"2018-12-11T11:47:07Z","citation":{"mla":"Finkbeiner, Bernd, and Andrey Kupriyanov. “Causality-Based Model Checking.” <i>Electronic Proceedings in Theoretical Computer Science</i>, vol. 259, Open Publishing Association, 2017, pp. 31–38, doi:<a href=\"https://doi.org/10.4204/EPTCS.259.3\">10.4204/EPTCS.259.3</a>.","short":"B. Finkbeiner, A. Kupriyanov, in:, Electronic Proceedings in Theoretical Computer Science, Open Publishing Association, 2017, pp. 31–38.","apa":"Finkbeiner, B., &#38; Kupriyanov, A. (2017). Causality-based model checking. In <i>Electronic Proceedings in Theoretical Computer Science</i> (Vol. 259, pp. 31–38). Uppsala, Sweden: Open Publishing Association. <a href=\"https://doi.org/10.4204/EPTCS.259.3\">https://doi.org/10.4204/EPTCS.259.3</a>","ama":"Finkbeiner B, Kupriyanov A. Causality-based model checking. In: <i>Electronic Proceedings in Theoretical Computer Science</i>. Vol 259. Open Publishing Association; 2017:31-38. doi:<a href=\"https://doi.org/10.4204/EPTCS.259.3\">10.4204/EPTCS.259.3</a>","ieee":"B. Finkbeiner and A. Kupriyanov, “Causality-based model checking,” in <i>Electronic Proceedings in Theoretical Computer Science</i>, Uppsala, Sweden, 2017, vol. 259, pp. 31–38.","chicago":"Finkbeiner, Bernd, and Andrey Kupriyanov. “Causality-Based Model Checking.” In <i>Electronic Proceedings in Theoretical Computer Science</i>, 259:31–38. Open Publishing Association, 2017. <a href=\"https://doi.org/10.4204/EPTCS.259.3\">https://doi.org/10.4204/EPTCS.259.3</a>.","ista":"Finkbeiner B, Kupriyanov A. 2017. Causality-based model checking. Electronic Proceedings in Theoretical Computer Science. CREST: Causal Reasoning for Embedded and Safety-Critical Systems Technologies, EPTCS, vol. 259, 31–38."},"department":[{"_id":"ToHe"}],"status":"public","language":[{"iso":"eng"}],"_id":"549","isi":1,"day":"10","title":"Causality-based model checking","arxiv":1,"publist_id":"7264","ddc":["004"],"date_published":"2017-10-10T00:00:00Z","date_updated":"2025-09-18T09:38:35Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","intvolume":"       259","publication_identifier":{"issn":["2075-2180"]},"file_date_updated":"2020-07-14T12:47:00Z"},{"has_accepted_license":"1","oa":1,"author":[{"full_name":"Alt, Johannes","id":"36D3D8B6-F248-11E8-B48F-1D18A9856A87","last_name":"Alt","first_name":"Johannes"}],"external_id":{"isi":["000416389200001"]},"month":"11","date_created":"2018-12-11T11:47:07Z","citation":{"chicago":"Alt, Johannes. “Singularities of the Density of States of Random Gram Matrices.” <i>Electronic Communications in Probability</i>. Institute of Mathematical Statistics, 2017. <a href=\"https://doi.org/10.1214/17-ECP97\">https://doi.org/10.1214/17-ECP97</a>.","ista":"Alt J. 2017. Singularities of the density of states of random Gram matrices. Electronic Communications in Probability. 22, 63.","ieee":"J. Alt, “Singularities of the density of states of random Gram matrices,” <i>Electronic Communications in Probability</i>, vol. 22. Institute of Mathematical Statistics, 2017.","mla":"Alt, Johannes. “Singularities of the Density of States of Random Gram Matrices.” <i>Electronic Communications in Probability</i>, vol. 22, 63, Institute of Mathematical Statistics, 2017, doi:<a href=\"https://doi.org/10.1214/17-ECP97\">10.1214/17-ECP97</a>.","ama":"Alt J. Singularities of the density of states of random Gram matrices. <i>Electronic Communications in Probability</i>. 2017;22. doi:<a href=\"https://doi.org/10.1214/17-ECP97\">10.1214/17-ECP97</a>","apa":"Alt, J. (2017). Singularities of the density of states of random Gram matrices. <i>Electronic Communications in Probability</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/17-ECP97\">https://doi.org/10.1214/17-ECP97</a>","short":"J. Alt, Electronic Communications in Probability 22 (2017)."},"year":"2017","department":[{"_id":"LaEr"}],"status":"public","language":[{"iso":"eng"}],"_id":"550","day":"21","isi":1,"title":"Singularities of the density of states of random Gram matrices","publist_id":"7265","ddc":["539"],"date_published":"2017-11-21T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2026-04-08T14:11:36Z","file_date_updated":"2020-07-14T12:47:00Z","intvolume":"        22","publication_identifier":{"issn":["1083-589X"]},"publication":"Electronic Communications in Probability","project":[{"_id":"258DCDE6-B435-11E9-9278-68D0E5697425","name":"Random matrices, universality and disordered quantum systems","grant_number":"338804","call_identifier":"FP7"}],"pubrep_id":"926","abstract":[{"text":"For large random matrices X with independent, centered entries but not necessarily identical variances, the eigenvalue density of XX* is well-approximated by a deterministic measure on ℝ. We show that the density of this measure has only square and cubic-root singularities away from zero. We also extend the bulk local law in [5] to the vicinity of these singularities.","lang":"eng"}],"quality_controlled":"1","article_processing_charge":"No","doi":"10.1214/17-ECP97","related_material":{"record":[{"id":"149","relation":"dissertation_contains","status":"public"}]},"file":[{"file_id":"4663","file_size":470876,"file_name":"IST-2018-926-v1+1_euclid.ecp.1511233247.pdf","creator":"system","checksum":"0ec05303a0de190de145654237984c79","relation":"main_file","date_updated":"2020-07-14T12:47:00Z","date_created":"2018-12-12T10:08:04Z","access_level":"open_access","content_type":"application/pdf"}],"corr_author":"1","publication_status":"published","oa_version":"Published Version","article_number":"63","volume":22,"ec_funded":1,"fulldoi":"https://doi.org/10.1214/17-ECP97","type":"journal_article","license":"https://creativecommons.org/licenses/by/4.0/","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publisher":"Institute of Mathematical Statistics","scopus_import":"1"},{"publication":"Leibniz International Proceedings in Informatics","pubrep_id":"924","abstract":[{"lang":"eng","text":"Evolutionary graph theory studies the evolutionary dynamics in a population structure given as a connected graph. Each node of the graph represents an individual of the population, and edges determine how offspring are placed. We consider the classical birth-death Moran process where there are two types of individuals, namely, the residents with fitness 1 and mutants with fitness r. The fitness indicates the reproductive strength. The evolutionary dynamics happens as follows: in the initial step, in a population of all resident individuals a mutant is introduced, and then at each step, an individual is chosen proportional to the fitness of its type to reproduce, and the offspring replaces a neighbor uniformly at random. The process stops when all individuals are either residents or mutants. The probability that all individuals in the end are mutants is called the fixation probability, which is a key factor in the rate of evolution. We consider the problem of approximating the fixation probability. The class of algorithms that is extremely relevant for approximation of the fixation probabilities is the Monte-Carlo simulation of the process. Previous results present a polynomial-time Monte-Carlo algorithm for undirected graphs when r is given in unary. First, we present a simple modification: instead of simulating each step, we discard ineffective steps, where no node changes type (i.e., either residents replace residents, or mutants replace mutants). Using the above simple modification and our result that the number of effective steps is concentrated around the expected number of effective steps, we present faster polynomial-time Monte-Carlo algorithms for undirected graphs. Our algorithms are always at least a factor O(n2/ log n) faster as compared to the previous algorithms, where n is the number of nodes, and is polynomial even if r is given in binary. We also present lower bounds showing that the upper bound on the expected number of effective steps we present is asymptotically tight for undirected graphs. "}],"quality_controlled":"1","article_processing_charge":"No","doi":"10.4230/LIPIcs.MFCS.2017.61","file":[{"access_level":"open_access","content_type":"application/pdf","date_updated":"2020-07-14T12:47:00Z","date_created":"2018-12-12T10:18:04Z","relation":"main_file","file_id":"5322","checksum":"2eed5224c0e4e259484a1d71acb8ba6a","file_size":535077,"file_name":"IST-2018-924-v1+1_LIPIcs-MFCS-2017-61.pdf","creator":"system"}],"corr_author":"1","publication_status":"published","oa_version":"Published Version","article_number":"61","alternative_title":["LIPIcs"],"volume":83,"fulldoi":"https://doi.org/10.4230/LIPIcs.MFCS.2017.61","type":"conference","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","scopus_import":"1","has_accepted_license":"1","oa":1,"conference":{"start_date":"2017-08-21","location":"Aalborg, Denmark","end_date":"2017-08-25","name":"MFCS: Mathematical Foundations of Computer Science"},"author":[{"first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"first_name":"Rasmus","id":"3B699956-F248-11E8-B48F-1D18A9856A87","last_name":"Ibsen-Jensen","full_name":"Ibsen-Jensen, Rasmus","orcid":"0000-0003-4783-0389"},{"full_name":"Nowak, Martin","first_name":"Martin","last_name":"Nowak"}],"month":"11","citation":{"mla":"Chatterjee, Krishnendu, et al. “Faster Monte Carlo Algorithms for Fixation Probability of the Moran Process on Undirected Graphs.” <i>Leibniz International Proceedings in Informatics</i>, vol. 83, 61, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:<a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2017.61\">10.4230/LIPIcs.MFCS.2017.61</a>.","ama":"Chatterjee K, Ibsen-Jensen R, Nowak M. Faster Monte Carlo algorithms for fixation probability of the Moran process on undirected graphs. In: <i>Leibniz International Proceedings in Informatics</i>. Vol 83. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:<a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2017.61\">10.4230/LIPIcs.MFCS.2017.61</a>","apa":"Chatterjee, K., Ibsen-Jensen, R., &#38; Nowak, M. (2017). Faster Monte Carlo algorithms for fixation probability of the Moran process on undirected graphs. In <i>Leibniz International Proceedings in Informatics</i> (Vol. 83). Aalborg, Denmark: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2017.61\">https://doi.org/10.4230/LIPIcs.MFCS.2017.61</a>","short":"K. Chatterjee, R. Ibsen-Jensen, M. Nowak, in:, Leibniz International Proceedings in Informatics, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017.","chicago":"Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Martin Nowak. “Faster Monte Carlo Algorithms for Fixation Probability of the Moran Process on Undirected Graphs.” In <i>Leibniz International Proceedings in Informatics</i>, Vol. 83. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. <a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2017.61\">https://doi.org/10.4230/LIPIcs.MFCS.2017.61</a>.","ista":"Chatterjee K, Ibsen-Jensen R, Nowak M. 2017. Faster Monte Carlo algorithms for fixation probability of the Moran process on undirected graphs. Leibniz International Proceedings in Informatics. MFCS: Mathematical Foundations of Computer Science, LIPIcs, vol. 83, 61.","ieee":"K. Chatterjee, R. Ibsen-Jensen, and M. Nowak, “Faster Monte Carlo algorithms for fixation probability of the Moran process on undirected graphs,” in <i>Leibniz International Proceedings in Informatics</i>, Aalborg, Denmark, 2017, vol. 83."},"date_created":"2018-12-11T11:47:08Z","year":"2017","department":[{"_id":"KrCh"}],"status":"public","language":[{"iso":"eng"}],"_id":"551","day":"01","title":"Faster Monte Carlo algorithms for fixation probability of the Moran process on undirected graphs","publist_id":"7263","ddc":["004"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2025-07-10T11:52:51Z","date_published":"2017-11-01T00:00:00Z","file_date_updated":"2020-07-14T12:47:00Z","publication_identifier":{"isbn":["978-395977046-0"]},"intvolume":"        83"},{"doi":"10.4230/LIPIcs.MFCS.2017.39","file":[{"access_level":"open_access","content_type":"application/pdf","date_created":"2018-12-12T10:16:57Z","date_updated":"2020-07-14T12:47:00Z","relation":"main_file","file_id":"5248","file_size":610339,"creator":"system","file_name":"IST-2018-923-v1+1_LIPIcs-MFCS-2017-39.pdf","checksum":"c67f4866ddbfd555afef1f63ae9a8fc7"}],"publication":"Leibniz International Proceedings in Informatics","project":[{"call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","name":"Game Theory"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"}],"pubrep_id":"923","abstract":[{"lang":"eng","text":"Graph games provide the foundation for modeling and synthesis of reactive processes. Such games are played over graphs where the vertices are controlled by two adversarial players. We consider graph games where the objective of the first player is the conjunction of a qualitative objective (specified as a parity condition) and a quantitative objective (specified as a meanpayoff condition). There are two variants of the problem, namely, the threshold problem where the quantitative goal is to ensure that the mean-payoff value is above a threshold, and the value problem where the quantitative goal is to ensure the optimal mean-payoff value; in both cases ensuring the qualitative parity objective. The previous best-known algorithms for game graphs with n vertices, m edges, parity objectives with d priorities, and maximal absolute reward value W for mean-payoff objectives, are as follows: O(nd+1 . m . w) for the threshold problem, and O(nd+2 · m · W) for the value problem. Our main contributions are faster algorithms, and the running times of our algorithms are as follows: O(nd-1 · m ·W) for the threshold problem, and O(nd · m · W · log(n · W)) for the value problem. For mean-payoff parity objectives with two priorities, our algorithms match the best-known bounds of the algorithms for mean-payoff games (without conjunction with parity objectives). Our results are relevant in synthesis of reactive systems with both functional requirement (given as a qualitative objective) and performance requirement (given as a quantitative objective)."}],"quality_controlled":"1","article_processing_charge":"No","ec_funded":1,"fulldoi":"https://doi.org/10.4230/LIPIcs.MFCS.2017.39","type":"conference","license":"https://creativecommons.org/licenses/by/3.0/","tmp":{"short":"CC BY (3.0)","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode"},"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","scopus_import":"1","corr_author":"1","publication_status":"published","oa_version":"Published Version","article_number":"39","volume":83,"alternative_title":["LIPIcs"],"date_created":"2018-12-11T11:47:08Z","citation":{"ista":"Chatterjee K, Henzinger M, Svozil A. 2017. Faster algorithms for mean-payoff parity games. Leibniz International Proceedings in Informatics. MFCS: Mathematical Foundations of Computer Science, LIPIcs, vol. 83, 39.","chicago":"Chatterjee, Krishnendu, Monika Henzinger, and Alexander Svozil. “Faster Algorithms for Mean-Payoff Parity Games.” In <i>Leibniz International Proceedings in Informatics</i>, Vol. 83. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. <a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2017.39\">https://doi.org/10.4230/LIPIcs.MFCS.2017.39</a>.","ieee":"K. Chatterjee, M. Henzinger, and A. Svozil, “Faster algorithms for mean-payoff parity games,” in <i>Leibniz International Proceedings in Informatics</i>, Aalborg, Denmark, 2017, vol. 83.","ama":"Chatterjee K, Henzinger M, Svozil A. Faster algorithms for mean-payoff parity games. In: <i>Leibniz International Proceedings in Informatics</i>. Vol 83. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:<a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2017.39\">10.4230/LIPIcs.MFCS.2017.39</a>","short":"K. Chatterjee, M. Henzinger, A. Svozil, in:, Leibniz International Proceedings in Informatics, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017.","apa":"Chatterjee, K., Henzinger, M., &#38; Svozil, A. (2017). Faster algorithms for mean-payoff parity games. In <i>Leibniz International Proceedings in Informatics</i> (Vol. 83). Aalborg, Denmark: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2017.39\">https://doi.org/10.4230/LIPIcs.MFCS.2017.39</a>","mla":"Chatterjee, Krishnendu, et al. “Faster Algorithms for Mean-Payoff Parity Games.” <i>Leibniz International Proceedings in Informatics</i>, vol. 83, 39, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:<a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2017.39\">10.4230/LIPIcs.MFCS.2017.39</a>."},"year":"2017","department":[{"_id":"KrCh"}],"status":"public","has_accepted_license":"1","oa":1,"conference":{"location":"Aalborg, Denmark","name":"MFCS: Mathematical Foundations of Computer Science","end_date":"2017-08-25","start_date":"2017-08-21"},"author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"last_name":"Henzinger","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","first_name":"Monika H","full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530"},{"last_name":"Svozil","first_name":"Alexander","full_name":"Svozil, Alexander"}],"month":"11","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2025-07-10T11:52:52Z","ddc":["004"],"date_published":"2017-11-01T00:00:00Z","file_date_updated":"2020-07-14T12:47:00Z","intvolume":"        83","publication_identifier":{"isbn":["978-395977046-0"]},"language":[{"iso":"eng"}],"_id":"552","day":"01","title":"Faster algorithms for mean-payoff parity games","publist_id":"7262"},{"status":"public","department":[{"_id":"KrCh"}],"year":"2017","date_created":"2018-12-11T11:47:08Z","citation":{"ieee":"K. Chatterjee, K. Hansen, and R. Ibsen-Jensen, “Strategy complexity of concurrent safety games,” in <i>Leibniz International Proceedings in Informatics</i>, Aalborg, Denmark, 2017, vol. 83.","chicago":"Chatterjee, Krishnendu, Kristofer Hansen, and Rasmus Ibsen-Jensen. “Strategy Complexity of Concurrent Safety Games.” In <i>Leibniz International Proceedings in Informatics</i>, Vol. 83. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. <a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2017.55\">https://doi.org/10.4230/LIPIcs.MFCS.2017.55</a>.","ista":"Chatterjee K, Hansen K, Ibsen-Jensen R. 2017. Strategy complexity of concurrent safety games. Leibniz International Proceedings in Informatics. MFCS: Mathematical Foundations of Computer Science, LIPIcs, vol. 83, 55.","mla":"Chatterjee, Krishnendu, et al. “Strategy Complexity of Concurrent Safety Games.” <i>Leibniz International Proceedings in Informatics</i>, vol. 83, 55, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:<a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2017.55\">10.4230/LIPIcs.MFCS.2017.55</a>.","short":"K. Chatterjee, K. Hansen, R. Ibsen-Jensen, in:, Leibniz International Proceedings in Informatics, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017.","apa":"Chatterjee, K., Hansen, K., &#38; Ibsen-Jensen, R. (2017). Strategy complexity of concurrent safety games. In <i>Leibniz International Proceedings in Informatics</i> (Vol. 83). Aalborg, Denmark: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2017.55\">https://doi.org/10.4230/LIPIcs.MFCS.2017.55</a>","ama":"Chatterjee K, Hansen K, Ibsen-Jensen R. Strategy complexity of concurrent safety games. In: <i>Leibniz International Proceedings in Informatics</i>. Vol 83. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:<a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2017.55\">10.4230/LIPIcs.MFCS.2017.55</a>"},"month":"11","external_id":{"arxiv":["1506.02434"]},"author":[{"first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"full_name":"Hansen, Kristofer","last_name":"Hansen","first_name":"Kristofer"},{"full_name":"Ibsen-Jensen, Rasmus","orcid":"0000-0003-4783-0389","first_name":"Rasmus","last_name":"Ibsen-Jensen","id":"3B699956-F248-11E8-B48F-1D18A9856A87"}],"conference":{"location":"Aalborg, Denmark","end_date":"2017-08-25","name":"MFCS: Mathematical Foundations of Computer Science","start_date":"2017-08-21"},"has_accepted_license":"1","oa":1,"intvolume":"        83","publication_identifier":{"isbn":["978-395977046-0"]},"file_date_updated":"2020-07-14T12:47:00Z","ddc":["004"],"date_published":"2017-11-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2025-06-04T09:37:06Z","arxiv":1,"publist_id":"7261","title":"Strategy complexity of concurrent safety games","day":"01","_id":"553","language":[{"iso":"eng"}],"file":[{"file_name":"IST-2018-922-v1+1_LIPIcs-MFCS-2017-55.pdf","creator":"system","file_size":549967,"checksum":"7101facb56ade363205c695d72dbd173","file_id":"4753","relation":"main_file","date_created":"2018-12-12T10:09:29Z","date_updated":"2020-07-14T12:47:00Z","content_type":"application/pdf","access_level":"open_access"}],"doi":"10.4230/LIPIcs.MFCS.2017.55","article_processing_charge":"No","quality_controlled":"1","abstract":[{"lang":"eng","text":"We consider two player, zero-sum, finite-state concurrent reachability games, played for an infinite number of rounds, where in every round, each player simultaneously and independently of the other players chooses an action, whereafter the successor state is determined by a probability distribution given by the current state and the chosen actions. Player 1 wins iff a designated goal state is eventually visited. We are interested in the complexity of stationary strategies measured by their patience, which is defined as the inverse of the smallest non-zero probability employed. Our main results are as follows: We show that: (i) the optimal bound on the patience of optimal and -optimal strategies, for both players is doubly exponential; and (ii) even in games with a single non-absorbing state exponential (in the number of actions) patience is necessary. "}],"pubrep_id":"922","publication":"Leibniz International Proceedings in Informatics","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1506.02434"}],"scopus_import":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"type":"conference","fulldoi":"https://doi.org/10.4230/LIPIcs.MFCS.2017.55","alternative_title":["LIPIcs"],"volume":83,"article_number":"55","oa_version":"Published Version","publication_status":"published","corr_author":"1"},{"title":"Strong amplifiers of natural selection","keyword":["natural selection"],"_id":"5559","day":"02","oa_version":"Published Version","publisher":"Institute of Science and Technology Austria","file_date_updated":"2020-07-14T12:47:02Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2025-04-15T08:12:19Z","datarep_id":"51","date_published":"2017-01-02T00:00:00Z","ddc":["519"],"ec_funded":1,"fulldoi":"https://doi.org/10.15479/AT:ISTA:51","type":"research_data","article_processing_charge":"No","month":"01","oa":1,"has_accepted_license":"1","project":[{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"}],"author":[{"orcid":"0000-0002-8943-0722","full_name":"Pavlogiannis, Andreas","first_name":"Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","last_name":"Pavlogiannis"},{"first_name":"Josef","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","last_name":"Tkadlec","orcid":"0000-0002-1097-9684","full_name":"Tkadlec, Josef"},{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee"},{"full_name":"Nowak , Martin","first_name":"Martin","last_name":"Nowak "}],"abstract":[{"lang":"eng","text":"Strong amplifiers of natural selection"}],"file":[{"content_type":"video/mp4","access_level":"open_access","date_updated":"2020-07-14T12:47:02Z","date_created":"2018-12-12T13:05:18Z","relation":"main_file","file_name":"IST-2017-51-v1+2_illustration.mp4","file_size":32987015,"creator":"system","checksum":"b427dd46a30096a1911b245640c47af8","file_id":"5644"}],"status":"public","date_created":"2018-12-12T12:31:32Z","citation":{"mla":"Pavlogiannis, Andreas, et al. <i>Strong Amplifiers of Natural Selection</i>. Institute of Science and Technology Austria, 2017, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:51\">10.15479/AT:ISTA:51</a>.","ama":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak  M. Strong amplifiers of natural selection. 2017. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:51\">10.15479/AT:ISTA:51</a>","apa":"Pavlogiannis, A., Tkadlec, J., Chatterjee, K., &#38; Nowak , M. (2017). Strong amplifiers of natural selection. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:51\">https://doi.org/10.15479/AT:ISTA:51</a>","short":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, M. Nowak , (2017).","chicago":"Pavlogiannis, Andreas, Josef Tkadlec, Krishnendu Chatterjee, and Martin Nowak . “Strong Amplifiers of Natural Selection.” Institute of Science and Technology Austria, 2017. <a href=\"https://doi.org/10.15479/AT:ISTA:51\">https://doi.org/10.15479/AT:ISTA:51</a>.","ista":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak  M. 2017. Strong amplifiers of natural selection, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:51\">10.15479/AT:ISTA:51</a>.","ieee":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, and M. Nowak , “Strong amplifiers of natural selection.” Institute of Science and Technology Austria, 2017."},"doi":"10.15479/AT:ISTA:51","year":"2017","related_material":{"record":[{"id":"5452","status":"public","relation":"research_paper"},{"id":"5751","relation":"research_paper","status":"public"}]},"department":[{"_id":"KrCh"}]},{"status":"public","file":[{"content_type":"application/zip","access_level":"open_access","date_created":"2018-12-12T13:02:38Z","date_updated":"2020-07-14T12:47:03Z","relation":"main_file","file_size":6773204,"checksum":"d77859af757ac8025c50c7b12b52eaf3","creator":"system","file_name":"IST-2017-53-v1+1_Data_MDE.zip","file_id":"5603"}],"related_material":{"record":[{"status":"public","relation":"research_paper","id":"665"}]},"department":[{"_id":"CaGu"},{"_id":"GaTk"},{"_id":"Bio"}],"year":"2017","date_created":"2018-12-12T12:31:32Z","citation":{"mla":"Bergmiller, Tobias, et al. <i>Biased Partitioning of the Multi-Drug Efflux Pump AcrAB-TolC Underlies Long-Lived Phenotypic Heterogeneity</i>. Institute of Science and Technology Austria, 2017, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:53\">10.15479/AT:ISTA:53</a>.","apa":"Bergmiller, T., Andersson, A. M., Tomasek, K., Balleza, E., Kiviet, D., Hauschild, R., … Guet, C. C. (2017). Biased partitioning of the multi-drug efflux pump AcrAB-TolC underlies long-lived phenotypic heterogeneity. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:53\">https://doi.org/10.15479/AT:ISTA:53</a>","short":"T. Bergmiller, A.M. Andersson, K. Tomasek, E. Balleza, D. Kiviet, R. Hauschild, G. Tkačik, C.C. Guet, (2017).","ama":"Bergmiller T, Andersson AM, Tomasek K, et al. Biased partitioning of the multi-drug efflux pump AcrAB-TolC underlies long-lived phenotypic heterogeneity. 2017. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:53\">10.15479/AT:ISTA:53</a>","ieee":"T. Bergmiller <i>et al.</i>, “Biased partitioning of the multi-drug efflux pump AcrAB-TolC underlies long-lived phenotypic heterogeneity.” Institute of Science and Technology Austria, 2017.","ista":"Bergmiller T, Andersson AM, Tomasek K, Balleza E, Kiviet D, Hauschild R, Tkačik G, Guet CC. 2017. Biased partitioning of the multi-drug efflux pump AcrAB-TolC underlies long-lived phenotypic heterogeneity, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:53\">10.15479/AT:ISTA:53</a>.","chicago":"Bergmiller, Tobias, Anna M Andersson, Kathrin Tomasek, Enrique Balleza, Daniel Kiviet, Robert Hauschild, Gašper Tkačik, and Calin C Guet. “Biased Partitioning of the Multi-Drug Efflux Pump AcrAB-TolC Underlies Long-Lived Phenotypic Heterogeneity.” Institute of Science and Technology Austria, 2017. <a href=\"https://doi.org/10.15479/AT:ISTA:53\">https://doi.org/10.15479/AT:ISTA:53</a>."},"doi":"10.15479/AT:ISTA:53","month":"03","article_processing_charge":"No","abstract":[{"lang":"eng","text":"This repository contains the data collected for the manuscript \"Biased partitioning of the multi-drug efflux pump AcrAB-TolC underlies long-lived phenotypic heterogeneity\".\r\nThe data is compressed into a single archive. Within the archive, different folders correspond to figures of the main text and the SI of the related publication.\r\nData is saved as plain text, with each folder containing a separate readme file describing the format. Typically, the data is from fluorescence microscopy measurements of single cells growing in a microfluidic \"mother machine\" device, and consists of relevant values (primarily arbitrary unit or normalized fluorescence measurements, and division times / growth rates) after raw microscopy images have been processed, segmented, and their features extracted, as described in the methods section of the related publication."}],"author":[{"id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","last_name":"Bergmiller","first_name":"Tobias","orcid":"0000-0001-5396-4346","full_name":"Bergmiller, Tobias"},{"id":"2B8A40DA-F248-11E8-B48F-1D18A9856A87","last_name":"Andersson","first_name":"Anna M","full_name":"Andersson, Anna M","orcid":"0000-0003-2912-6769"},{"id":"3AEC8556-F248-11E8-B48F-1D18A9856A87","last_name":"Tomasek","first_name":"Kathrin","full_name":"Tomasek, Kathrin","orcid":"0000-0003-3768-877X"},{"first_name":"Enrique","last_name":"Balleza","full_name":"Balleza, Enrique"},{"full_name":"Kiviet, Daniel","last_name":"Kiviet","first_name":"Daniel"},{"full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522","first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","last_name":"Hauschild"},{"first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkacik","full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455"},{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","first_name":"Calin C","full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052"}],"has_accepted_license":"1","oa":1,"file_date_updated":"2020-07-14T12:47:03Z","publisher":"Institute of Science and Technology Austria","tmp":{"short":"CC0 (1.0)","name":"Creative Commons Public Domain Dedication (CC0 1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode"},"type":"research_data","license":"https://creativecommons.org/publicdomain/zero/1.0/","fulldoi":"https://doi.org/10.15479/AT:ISTA:53","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["571"],"datarep_id":"53","date_updated":"2025-09-11T07:05:03Z","date_published":"2017-03-10T00:00:00Z","keyword":["single cell microscopy","mother machine microfluidic device","AcrAB-TolC pump","multi-drug efflux","Escherichia coli"],"title":"Biased partitioning of the multi-drug efflux pump AcrAB-TolC underlies long-lived phenotypic heterogeneity","oa_version":"Published Version","day":"10","_id":"5560"},{"acknowledgement":"We thank Vladimir Kolmogorov and Stephan Saalfeld forinspiring discussions.","department":[{"_id":"VlKo"}],"year":"2017","date_created":"2018-12-12T12:31:32Z","citation":{"chicago":"Kainmueller, Dagmar, Florian Jug, Carsten Rother, and Gene Meyers. “Graph Matching Problems for Annotating C. Elegans.” Institute of Science and Technology Austria, 2017. <a href=\"https://doi.org/10.15479/AT:ISTA:57\">https://doi.org/10.15479/AT:ISTA:57</a>.","ista":"Kainmueller D, Jug F, Rother C, Meyers G. 2017. Graph matching problems for annotating C. Elegans, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:57\">10.15479/AT:ISTA:57</a>.","ieee":"D. Kainmueller, F. Jug, C. Rother, and G. Meyers, “Graph matching problems for annotating C. Elegans.” Institute of Science and Technology Austria, 2017.","mla":"Kainmueller, Dagmar, et al. <i>Graph Matching Problems for Annotating C. Elegans</i>. Institute of Science and Technology Austria, 2017, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:57\">10.15479/AT:ISTA:57</a>.","ama":"Kainmueller D, Jug F, Rother C, Meyers G. Graph matching problems for annotating C. Elegans. 2017. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:57\">10.15479/AT:ISTA:57</a>","apa":"Kainmueller, D., Jug, F., Rother, C., &#38; Meyers, G. (2017). Graph matching problems for annotating C. Elegans. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:57\">https://doi.org/10.15479/AT:ISTA:57</a>","short":"D. Kainmueller, F. Jug, C. Rother, G. Meyers, (2017)."},"doi":"10.15479/AT:ISTA:57","file":[{"relation":"main_file","file_name":"IST-2017-57-v1+1_wormMatchingProblems.zip","checksum":"3dc3e1306a66028a34181ebef2923139","file_size":327042819,"creator":"system","file_id":"5614","content_type":"application/zip","access_level":"open_access","date_created":"2018-12-12T13:02:54Z","date_updated":"2020-07-14T12:47:03Z"}],"status":"public","author":[{"full_name":"Kainmueller, Dagmar","first_name":"Dagmar","last_name":"Kainmueller"},{"first_name":"Florian","last_name":"Jug","full_name":"Jug, Florian"},{"first_name":"Carsten","last_name":"Rother","full_name":"Rother, Carsten"},{"last_name":"Meyers","first_name":"Gene","full_name":"Meyers, Gene"}],"abstract":[{"lang":"eng","text":"Graph matching problems as described in \"Active Graph Matching for Automatic Joint Segmentation and Annotation of C. Elegans.\" by Kainmueller, Dagmar and Jug, Florian and Rother, Carsten and Myers, Gene, MICCAI 2014. Problems are in OpenGM2 hdf5 format (see http://hciweb2.iwr.uni-heidelberg.de/opengm/) and a custom text format used by the feature matching solver described in \"Feature Correspondence via Graph Matching: Models and Global Optimization.\" by Lorenzo Torresani, Vladimir Kolmogorov and Carsten Rother, ECCV 2008, code at http://pub.ist.ac.at/~vnk/software/GraphMatching-v1.02.src.zip. 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It consists of preprocessed multi-electrode array recording from 160 salamander retinal ganglion cells responding to 297 repeats of a 19 s natural movie. The data is available in two formats: (1) a .mat file containing an array with dimensions “number of repeats” x “number of neurons” x “time in a repeat”; (2) a zipped .txt file containing the same data represented as an array with dimensions “number of neurons” x “number of samples”, where the number of samples is equal to the product of the number of repeats and timebins within a repeat. The time dimension is divided into 20 ms time windows, and the array is binary indicating whether a given cell elicited at least one spike in a given time window during a particular repeat. See the reference below for details regarding collection and preprocessing:\r\n\r\n[1] Tkačik G, Marre O, Amodei D, Schneidman E, Bialek W, Berry MJ II. Searching for Collective Behavior in a Large Network of Sensory Neurons. 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Lukacisin, “MATLAB analysis code for ‘Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.’” Institute of Science and Technology Austria, 2017.","chicago":"Lukacisin, Martin. “MATLAB Analysis Code for ‘Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.’” Institute of Science and Technology Austria, 2017. <a href=\"https://doi.org/10.15479/AT:ISTA:64\">https://doi.org/10.15479/AT:ISTA:64</a>.","ista":"Lukacisin M. 2017. MATLAB analysis code for ‘Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:64\">10.15479/AT:ISTA:64</a>.","mla":"Lukacisin, Martin. <i>MATLAB Analysis Code for “Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.”</i> Institute of Science and Technology Austria, 2017, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:64\">10.15479/AT:ISTA:64</a>.","short":"M. Lukacisin, (2017).","apa":"Lukacisin, M. (2017). MATLAB analysis code for “Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:64\">https://doi.org/10.15479/AT:ISTA:64</a>","ama":"Lukacisin M. 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Fastq files for “Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:65\">https://doi.org/10.15479/AT:ISTA:65</a>"},"date_created":"2018-12-12T12:31:33Z","related_material":{"record":[{"relation":"research_paper","status":"public","id":"704"}]},"department":[{"_id":"CaGu"}],"month":"04","article_processing_charge":"No","oa":1,"has_accepted_license":"1","abstract":[{"text":"Compressed Fastq files with whole-genome sequencing data of IS-wt strain D and clones from four evolved populations (A11, C08, C10, D08). Information on this data collection is available in the Methods Section of the primary publication.","lang":"eng"}],"author":[{"last_name":"Steinrück","id":"2C023F40-F248-11E8-B48F-1D18A9856A87","first_name":"Magdalena","orcid":"0000-0003-1229-9719","full_name":"Steinrück, Magdalena"},{"orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","first_name":"Calin C"}]},{"fulldoi":"https://doi.org/10.15479/AT:ISTA:69","type":"research_data","datarep_id":"69","date_published":"2017-07-21T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"date_updated":"2025-04-15T07:48:05Z","file_date_updated":"2020-07-14T12:47:04Z","tmp":{"short":"CC BY-SA (4.0)","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)","image":"/images/cc_by_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode"},"publisher":"Institute of Science and Technology Austria","day":"21","oa_version":"Published Version","_id":"5566","keyword":["tool","tracking","confocal microscopy"],"title":"Live tracking of moving samples in confocal microscopy for vertically grown roots","related_material":{"record":[{"status":"public","relation":"research_paper","id":"946"}]},"department":[{"_id":"Bio"}],"date_created":"2018-12-12T12:31:34Z","doi":"10.15479/AT:ISTA:69","citation":{"ieee":"R. 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Vertebrate immune memory is highly specific due to antibody responses. On the other hand, some invertebrates show immune priming, i.e. improved survival after secondary exposure to a previously encountered pathogen. Until now, specificity of priming has only been demonstrated via the septic infection route or when live pathogens were used for priming. Therefore, we tested for specificity in the oral priming route in the red flour beetle, Tribolium castaneum. For priming, we used pathogen-free supernatants derived from three different strains of the entomopathogen, Bacillus thuringiensis, which express different Cry toxin variants known for their toxicity against this beetle. Subsequent exposure to the infective spores showed that oral priming was specific for two naturally occurring strains, while a third engineered strain did not induce any priming effect. Our data demonstrate that oral immune priming with a non-infectious bacterial agent can be specific, but the priming effect is not universal across all bacterial strains.","lang":"eng"}],"article_type":"original","publication_identifier":{"issn":["1744-9561"]},"intvolume":"        13","date_published":"2017-12-01T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2025-09-11T08:07:58Z","title":"Specificity of oral immune priming in the red flour beetle Tribolium castaneum","publist_id":"7255","language":[{"iso":"eng"}],"_id":"558","isi":1,"pmid":1,"issue":"12","day":"01","status":"public","year":"2017","date_created":"2018-12-11T11:47:10Z","citation":{"ista":"Futo M, Sell M, Kutzer M, Kurtz J. 2017. Specificity of oral immune priming in the red flour beetle Tribolium castaneum. Biology Letters. 13(12), 0632.","chicago":"Futo, Momir, Marie Sell, Megan Kutzer, and Joachim Kurtz. “Specificity of Oral Immune Priming in the Red Flour Beetle Tribolium Castaneum.” <i>Biology Letters</i>. The Royal Society, 2017. <a href=\"https://doi.org/10.1098/rsbl.2017.0632\">https://doi.org/10.1098/rsbl.2017.0632</a>.","ieee":"M. Futo, M. Sell, M. Kutzer, and J. Kurtz, “Specificity of oral immune priming in the red flour beetle Tribolium castaneum,” <i>Biology Letters</i>, vol. 13, no. 12. The Royal Society, 2017.","mla":"Futo, Momir, et al. “Specificity of Oral Immune Priming in the Red Flour Beetle Tribolium Castaneum.” <i>Biology Letters</i>, vol. 13, no. 12, 0632, The Royal Society, 2017, doi:<a href=\"https://doi.org/10.1098/rsbl.2017.0632\">10.1098/rsbl.2017.0632</a>.","ama":"Futo M, Sell M, Kutzer M, Kurtz J. Specificity of oral immune priming in the red flour beetle Tribolium castaneum. <i>Biology Letters</i>. 2017;13(12). doi:<a href=\"https://doi.org/10.1098/rsbl.2017.0632\">10.1098/rsbl.2017.0632</a>","short":"M. Futo, M. Sell, M. Kutzer, J. Kurtz, Biology Letters 13 (2017).","apa":"Futo, M., Sell, M., Kutzer, M., &#38; Kurtz, J. (2017). Specificity of oral immune priming in the red flour beetle Tribolium castaneum. <i>Biology Letters</i>. The Royal Society. <a href=\"https://doi.org/10.1098/rsbl.2017.0632\">https://doi.org/10.1098/rsbl.2017.0632</a>"},"department":[{"_id":"SyCr"}],"external_id":{"isi":["000418695400010"],"pmid":["29237813"]},"month":"12","author":[{"full_name":"Futo, Momir","first_name":"Momir","last_name":"Futo"},{"full_name":"Sell, Marie","last_name":"Sell","first_name":"Marie"},{"first_name":"Megan","id":"29D0B332-F248-11E8-B48F-1D18A9856A87","last_name":"Kutzer","full_name":"Kutzer, Megan","orcid":"0000-0002-8696-6978"},{"full_name":"Kurtz, Joachim","last_name":"Kurtz","first_name":"Joachim"}]},{"external_id":{"isi":["000416736700003"],"arxiv":["1702.03229"]},"month":"11","oa":1,"author":[{"last_name":"Gerencser","id":"44ECEDF2-F248-11E8-B48F-1D18A9856A87","first_name":"Mate","full_name":"Gerencser, Mate"},{"last_name":"Jentzen","first_name":"Arnulf","full_name":"Jentzen, Arnulf"},{"full_name":"Salimova, Diyora","first_name":"Diyora","last_name":"Salimova"}],"status":"public","citation":{"chicago":"Gerencser, Mate, Arnulf Jentzen, and Diyora Salimova. “On Stochastic Differential Equations with Arbitrarily Slow Convergence Rates for Strong Approximation in Two Space Dimensions.” <i>Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences</i>. Royal Society of London, 2017. <a href=\"https://doi.org/10.1098/rspa.2017.0104\">https://doi.org/10.1098/rspa.2017.0104</a>.","ista":"Gerencser M, Jentzen A, Salimova D. 2017. On stochastic differential equations with arbitrarily slow convergence rates for strong approximation in two space dimensions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. 473(2207), 0104.","ieee":"M. Gerencser, A. Jentzen, and D. Salimova, “On stochastic differential equations with arbitrarily slow convergence rates for strong approximation in two space dimensions,” <i>Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences</i>, vol. 473, no. 2207. Royal Society of London, 2017.","mla":"Gerencser, Mate, et al. “On Stochastic Differential Equations with Arbitrarily Slow Convergence Rates for Strong Approximation in Two Space Dimensions.” <i>Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences</i>, vol. 473, no. 2207, 0104, Royal Society of London, 2017, doi:<a href=\"https://doi.org/10.1098/rspa.2017.0104\">10.1098/rspa.2017.0104</a>.","ama":"Gerencser M, Jentzen A, Salimova D. On stochastic differential equations with arbitrarily slow convergence rates for strong approximation in two space dimensions. <i>Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences</i>. 2017;473(2207). doi:<a href=\"https://doi.org/10.1098/rspa.2017.0104\">10.1098/rspa.2017.0104</a>","apa":"Gerencser, M., Jentzen, A., &#38; Salimova, D. (2017). On stochastic differential equations with arbitrarily slow convergence rates for strong approximation in two space dimensions. <i>Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences</i>. Royal Society of London. <a href=\"https://doi.org/10.1098/rspa.2017.0104\">https://doi.org/10.1098/rspa.2017.0104</a>","short":"M. Gerencser, A. Jentzen, D. Salimova, Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 473 (2017)."},"date_created":"2018-12-11T11:47:11Z","year":"2017","department":[{"_id":"JaMa"}],"title":"On stochastic differential equations with arbitrarily slow convergence rates for strong approximation in two space dimensions","arxiv":1,"publist_id":"7256","language":[{"iso":"eng"}],"_id":"560","day":"01","issue":"2207","isi":1,"publication_identifier":{"issn":["1364-5021"]},"intvolume":"       473","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2025-09-18T07:33:24Z","date_published":"2017-11-01T00:00:00Z","quality_controlled":"1","article_processing_charge":"No","project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"publication":"Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences","abstract":[{"lang":"eng","text":"In a recent article (Jentzen et al. 2016 Commun. Math. Sci. 14, 1477–1500 (doi:10.4310/CMS.2016.v14. n6.a1)), it has been established that, for every arbitrarily slow convergence speed and every natural number d ? {4, 5, . . .}, there exist d-dimensional stochastic differential equations with infinitely often differentiable and globally bounded coefficients such that no approximation method based on finitely many observations of the driving Brownian motion can converge in absolute mean to the solution faster than the given speed of convergence. In this paper, we strengthen the above result by proving that this slow convergence phenomenon also arises in two (d = 2) and three (d = 3) space dimensions."}],"doi":"10.1098/rspa.2017.0104","article_number":"0104","volume":473,"publication_status":"published","oa_version":"Submitted Version","publisher":"Royal Society of London","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1702.03229","open_access":"1"}],"fulldoi":"https://doi.org/10.1098/rspa.2017.0104","ec_funded":1,"type":"journal_article"}]