[{"scopus_import":1,"month":"09","intvolume":" 10","abstract":[{"text":"A fundamental question in biology is the following: what is the time scale that is needed for evolutionary innovations? There are many results that characterize single steps in terms of the fixation time of new mutants arising in populations of certain size and structure. But here we ask a different question, which is concerned with the much longer time scale of evolutionary trajectories: how long does it take for a population exploring a fitness landscape to find target sequences that encode new biological functions? Our key variable is the length, (Formula presented.) of the genetic sequence that undergoes adaptation. In computer science there is a crucial distinction between problems that require algorithms which take polynomial or exponential time. The latter are considered to be intractable. Here we develop a theoretical approach that allows us to estimate the time of evolution as function of (Formula presented.) We show that adaptation on many fitness landscapes takes time that is exponential in (Formula presented.) even if there are broad selection gradients and many targets uniformly distributed in sequence space. These negative results lead us to search for specific mechanisms that allow evolution to work on polynomial time scales. We study a regeneration process and show that it enables evolution to work in polynomial time.","lang":"eng"}],"oa_version":"Published Version","issue":"9","related_material":{"record":[{"status":"public","id":"9739","relation":"research_data"}]},"volume":10,"license":"https://creativecommons.org/licenses/by/4.0/","ec_funded":1,"publication_status":"published","file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"4890","checksum":"712d4c5787ddf97809cfc962507f0738","creator":"system","date_updated":"2020-07-14T12:45:26Z","file_size":1399093,"date_created":"2018-12-12T10:11:35Z","file_name":"IST-2016-440-v1+1_journal.pcbi.1003818.pdf"}],"language":[{"iso":"eng"}],"type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","pubrep_id":"440","_id":"2039","file_date_updated":"2020-07-14T12:45:26Z","department":[{"_id":"KrCh"}],"date_updated":"2023-02-23T14:06:36Z","ddc":["510"],"publisher":"Public Library of Science","quality_controlled":"1","oa":1,"date_published":"2014-09-11T00:00:00Z","doi":"10.1371/journal.pcbi.1003818","date_created":"2018-12-11T11:55:22Z","has_accepted_license":"1","year":"2014","day":"11","publication":"PLoS Computational Biology","project":[{"grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","grant_number":"S11407"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"article_number":"7p","publist_id":"5012","author":[{"last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"id":"49704004-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas","orcid":"0000-0002-8943-0722","full_name":"Pavlogiannis, Andreas","last_name":"Pavlogiannis"},{"full_name":"Adlam, Ben","last_name":"Adlam","first_name":"Ben"},{"first_name":"Martin","full_name":"Nowak, Martin","last_name":"Nowak"}],"title":"The time scale of evolutionary innovation","citation":{"ista":"Chatterjee K, Pavlogiannis A, Adlam B, Nowak M. 2014. The time scale of evolutionary innovation. PLoS Computational Biology. 10(9), 7p.","chicago":"Chatterjee, Krishnendu, Andreas Pavlogiannis, Ben Adlam, and Martin Nowak. “The Time Scale of Evolutionary Innovation.” PLoS Computational Biology. Public Library of Science, 2014. https://doi.org/10.1371/journal.pcbi.1003818.","apa":"Chatterjee, K., Pavlogiannis, A., Adlam, B., & Nowak, M. (2014). The time scale of evolutionary innovation. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1003818","ama":"Chatterjee K, Pavlogiannis A, Adlam B, Nowak M. The time scale of evolutionary innovation. PLoS Computational Biology. 2014;10(9). doi:10.1371/journal.pcbi.1003818","short":"K. Chatterjee, A. Pavlogiannis, B. Adlam, M. Nowak, PLoS Computational Biology 10 (2014).","ieee":"K. Chatterjee, A. Pavlogiannis, B. Adlam, and M. Nowak, “The time scale of evolutionary innovation,” PLoS Computational Biology, vol. 10, no. 9. Public Library of Science, 2014.","mla":"Chatterjee, Krishnendu, et al. “The Time Scale of Evolutionary Innovation.” PLoS Computational Biology, vol. 10, no. 9, 7p, Public Library of Science, 2014, doi:10.1371/journal.pcbi.1003818."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87"},{"type":"research_data_reference","status":"public","_id":"9739","article_processing_charge":"No","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"},{"first_name":"Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","full_name":"Pavlogiannis, Andreas","orcid":"0000-0002-8943-0722","last_name":"Pavlogiannis"},{"last_name":"Adlam","full_name":"Adlam, Ben","first_name":"Ben"},{"first_name":"Martin","full_name":"Novak, Martin","last_name":"Novak"}],"title":"Detailed proofs for “The time scale of evolutionary innovation”","department":[{"_id":"KrCh"}],"citation":{"chicago":"Chatterjee, Krishnendu, Andreas Pavlogiannis, Ben Adlam, and Martin Novak. “Detailed Proofs for ‘The Time Scale of Evolutionary Innovation.’” Public Library of Science, 2014. https://doi.org/10.1371/journal.pcbi.1003818.s001.","ista":"Chatterjee K, Pavlogiannis A, Adlam B, Novak M. 2014. Detailed proofs for “The time scale of evolutionary innovation”, Public Library of Science, 10.1371/journal.pcbi.1003818.s001.","mla":"Chatterjee, Krishnendu, et al. Detailed Proofs for “The Time Scale of Evolutionary Innovation.” Public Library of Science, 2014, doi:10.1371/journal.pcbi.1003818.s001.","short":"K. Chatterjee, A. Pavlogiannis, B. Adlam, M. Novak, (2014).","ieee":"K. Chatterjee, A. Pavlogiannis, B. Adlam, and M. Novak, “Detailed proofs for ‘The time scale of evolutionary innovation.’” Public Library of Science, 2014.","ama":"Chatterjee K, Pavlogiannis A, Adlam B, Novak M. Detailed proofs for “The time scale of evolutionary innovation.” 2014. doi:10.1371/journal.pcbi.1003818.s001","apa":"Chatterjee, K., Pavlogiannis, A., Adlam, B., & Novak, M. (2014). Detailed proofs for “The time scale of evolutionary innovation.” Public Library of Science. https://doi.org/10.1371/journal.pcbi.1003818.s001"},"date_updated":"2023-02-23T10:25:37Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","publisher":"Public Library of Science","month":"09","oa_version":"Published Version","date_created":"2021-07-28T08:13:57Z","doi":"10.1371/journal.pcbi.1003818.s001","date_published":"2014-09-11T00:00:00Z","related_material":{"record":[{"id":"2039","status":"public","relation":"used_in_publication"}]},"year":"2014","day":"11"},{"day":"01","publication":"Algorithmica","year":"2014","doi":"10.1007/s00453-013-9843-7","date_published":"2014-11-01T00:00:00Z","date_created":"2018-12-11T11:47:01Z","page":"457 - 492","publisher":"Springer","quality_controlled":"1","oa":1,"user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","citation":{"ista":"Chatterjee K, Henzinger MH, Krinninger S, Nanongkai D. 2014. Polynomial-time algorithms for energy games with special weight structures. Algorithmica. 70(3), 457–492.","chicago":"Chatterjee, Krishnendu, Monika H Henzinger, Sebastian Krinninger, and Danupon Nanongkai. “Polynomial-Time Algorithms for Energy Games with Special Weight Structures.” Algorithmica. Springer, 2014. https://doi.org/10.1007/s00453-013-9843-7.","ieee":"K. Chatterjee, M. H. Henzinger, S. Krinninger, and D. Nanongkai, “Polynomial-time algorithms for energy games with special weight structures,” Algorithmica, vol. 70, no. 3. Springer, pp. 457–492, 2014.","short":"K. Chatterjee, M.H. Henzinger, S. Krinninger, D. Nanongkai, Algorithmica 70 (2014) 457–492.","apa":"Chatterjee, K., Henzinger, M. H., Krinninger, S., & Nanongkai, D. (2014). Polynomial-time algorithms for energy games with special weight structures. Algorithmica. Springer. https://doi.org/10.1007/s00453-013-9843-7","ama":"Chatterjee K, Henzinger MH, Krinninger S, Nanongkai D. Polynomial-time algorithms for energy games with special weight structures. Algorithmica. 2014;70(3):457-492. doi:10.1007/s00453-013-9843-7","mla":"Chatterjee, Krishnendu, et al. “Polynomial-Time Algorithms for Energy Games with Special Weight Structures.” Algorithmica, vol. 70, no. 3, Springer, 2014, pp. 457–92, doi:10.1007/s00453-013-9843-7."},"title":"Polynomial-time algorithms for energy games with special weight structures","publist_id":"7282","author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"first_name":"Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","last_name":"Henzinger","full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530"},{"first_name":"Sebastian","full_name":"Krinninger, Sebastian","last_name":"Krinninger"},{"first_name":"Danupon","full_name":"Nanongkai, Danupon","last_name":"Nanongkai"}],"external_id":{"arxiv":["1604.08234"]},"article_processing_charge":"No","project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S11407","name":"Game Theory"},{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"language":[{"iso":"eng"}],"publication_status":"published","issue":"3","related_material":{"record":[{"status":"public","id":"10905","relation":"earlier_version"}]},"volume":70,"ec_funded":1,"oa_version":"Preprint","abstract":[{"lang":"eng","text":"Energy games belong to a class of turn-based two-player infinite-duration games played on a weighted directed graph. It is one of the rare and intriguing combinatorial problems that lie in NP∩co-NP, but are not known to be in P. The existence of polynomial-time algorithms has been a major open problem for decades and apart from pseudopolynomial algorithms there is no algorithm that solves any non-trivial subclass in polynomial time. In this paper, we give several results based on the weight structures of the graph. First, we identify a notion of penalty and present a polynomial-time algorithm when the penalty is large. Our algorithm is the first polynomial-time algorithm on a large class of weighted graphs. It includes several worst-case instances on which previous algorithms, such as value iteration and random facet algorithms, require at least sub-exponential time. Our main technique is developing the first non-trivial approximation algorithm and showing how to convert it to an exact algorithm. Moreover, we show that in a practical case in verification where weights are clustered around a constant number of values, the energy game problem can be solved in polynomial time. We also show that the problem is still as hard as in general when the clique-width is bounded or the graph is strongly ergodic, suggesting that restricting the graph structure does not necessarily help."}],"month":"11","intvolume":" 70","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1604.08234","open_access":"1"}],"date_updated":"2023-09-05T14:09:29Z","department":[{"_id":"KrCh"}],"_id":"535","status":"public","article_type":"original","type":"journal_article"},{"_id":"2063","project":[{"call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","name":"Game Theory"},{"name":"Moderne Concurrency Paradigms","grant_number":"S11402-N23","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"},{"grant_number":"267989","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"status":"public","type":"conference","conference":{"end_date":"2014-07-22","location":"Vienna, Austria","start_date":"2014-07-18","name":"CAV: Computer Aided Verification"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-09-07T11:58:33Z","citation":{"short":"K. Chatterjee, M. Chmelik, P. Daca, in:, Springer, 2014, pp. 473–490.","ieee":"K. Chatterjee, M. Chmelik, and P. Daca, “CEGAR for qualitative analysis of probabilistic systems,” presented at the CAV: Computer Aided Verification, Vienna, Austria, 2014, vol. 8559, pp. 473–490.","ama":"Chatterjee K, Chmelik M, Daca P. CEGAR for qualitative analysis of probabilistic systems. In: Vol 8559. Springer; 2014:473-490. doi:10.1007/978-3-319-08867-9_31","apa":"Chatterjee, K., Chmelik, M., & Daca, P. (2014). CEGAR for qualitative analysis of probabilistic systems (Vol. 8559, pp. 473–490). Presented at the CAV: Computer Aided Verification, Vienna, Austria: Springer. https://doi.org/10.1007/978-3-319-08867-9_31","mla":"Chatterjee, Krishnendu, et al. CEGAR for Qualitative Analysis of Probabilistic Systems. Vol. 8559, Springer, 2014, pp. 473–90, doi:10.1007/978-3-319-08867-9_31.","ista":"Chatterjee K, Chmelik M, Daca P. 2014. CEGAR for qualitative analysis of probabilistic systems. CAV: Computer Aided Verification, LNCS, vol. 8559, 473–490.","chicago":"Chatterjee, Krishnendu, Martin Chmelik, and Przemyslaw Daca. “CEGAR for Qualitative Analysis of Probabilistic Systems,” 8559:473–90. Springer, 2014. https://doi.org/10.1007/978-3-319-08867-9_31."},"department":[{"_id":"KrCh"},{"_id":"ToHe"}],"title":"CEGAR for qualitative analysis of probabilistic systems","author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"last_name":"Chmelik","full_name":"Chmelik, Martin","id":"3624234E-F248-11E8-B48F-1D18A9856A87","first_name":"Martin"},{"last_name":"Daca","full_name":"Daca, Przemyslaw","id":"49351290-F248-11E8-B48F-1D18A9856A87","first_name":"Przemyslaw"}],"publist_id":"4978","oa_version":"None","abstract":[{"text":"We consider Markov decision processes (MDPs) which are a standard model for probabilistic systems.We focus on qualitative properties forMDPs that can express that desired behaviors of the system arise almost-surely (with probability 1) or with positive probability. We introduce a new simulation relation to capture the refinement relation ofMDPs with respect to qualitative properties, and present discrete graph theoretic algorithms with quadratic complexity to compute the simulation relation.We present an automated technique for assume-guarantee style reasoning for compositional analysis ofMDPs with qualitative properties by giving a counterexample guided abstraction-refinement approach to compute our new simulation relation. We have implemented our algorithms and show that the compositional analysis leads to significant improvements.","lang":"eng"}],"month":"07","intvolume":" 8559","publisher":"Springer","alternative_title":["LNCS"],"quality_controlled":"1","day":"01","language":[{"iso":"eng"}],"year":"2014","publication_status":"published","volume":8559,"doi":"10.1007/978-3-319-08867-9_31","date_published":"2014-07-01T00:00:00Z","related_material":{"record":[{"id":"5412","status":"public","relation":"earlier_version"},{"id":"5413","status":"public","relation":"earlier_version"},{"relation":"earlier_version","status":"public","id":"5414"},{"relation":"dissertation_contains","status":"public","id":"1155"}]},"ec_funded":1,"date_created":"2018-12-11T11:55:30Z","page":"473 - 490"},{"ddc":["004"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Chatterjee, Krishnendu, et al. Quantitative Fair Simulation Games. IST Austria, 2014, doi:10.15479/AT:IST-2014-315-v1-1.","apa":"Chatterjee, K., Henzinger, T. A., Otop, J., & Velner, Y. (2014). Quantitative fair simulation games. IST Austria. https://doi.org/10.15479/AT:IST-2014-315-v1-1","ama":"Chatterjee K, Henzinger TA, Otop J, Velner Y. Quantitative Fair Simulation Games. IST Austria; 2014. doi:10.15479/AT:IST-2014-315-v1-1","short":"K. Chatterjee, T.A. Henzinger, J. Otop, Y. Velner, Quantitative Fair Simulation Games, IST Austria, 2014.","ieee":"K. Chatterjee, T. A. Henzinger, J. Otop, and Y. Velner, Quantitative fair simulation games. IST Austria, 2014.","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, Jan Otop, and Yaron Velner. Quantitative Fair Simulation Games. IST Austria, 2014. https://doi.org/10.15479/AT:IST-2014-315-v1-1.","ista":"Chatterjee K, Henzinger TA, Otop J, Velner Y. 2014. Quantitative fair simulation games, IST Austria, 26p."},"date_updated":"2023-09-20T12:07:48Z","file_date_updated":"2020-07-14T12:46:52Z","title":"Quantitative fair simulation games","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger"},{"first_name":"Jan","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","full_name":"Otop, Jan","last_name":"Otop"},{"first_name":"Yaron","full_name":"Velner, Yaron","last_name":"Velner"}],"_id":"5428","pubrep_id":"315","status":"public","type":"technical_report","language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"5521","checksum":"b1d573bc04365625ff9974880c0aa807","creator":"system","file_size":531046,"date_updated":"2020-07-14T12:46:52Z","file_name":"IST-2014-315-v1+1_report.pdf","date_created":"2018-12-12T11:53:59Z"}],"day":"05","year":"2014","publication_status":"published","publication_identifier":{"issn":["2664-1690"]},"has_accepted_license":"1","date_created":"2018-12-12T11:39:16Z","doi":"10.15479/AT:IST-2014-315-v1-1","related_material":{"record":[{"status":"public","id":"1066","relation":"later_version"}]},"date_published":"2014-12-05T00:00:00Z","page":"26","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Simulation is an attractive alternative for language inclusion for automata as it is an under-approximation of language inclusion, but usually has much lower complexity. For non-deterministic automata, while language inclusion is PSPACE-complete, simulation can be computed in polynomial time. Simulation has also been extended in two orthogonal directions, namely, (1) fair simulation, for simulation over specified set of infinite runs; and (2) quantitative simulation, for simulation between weighted automata. Again, while fair trace inclusion is PSPACE-complete, fair simulation can be computed in polynomial time. For weighted automata, the (quantitative) language inclusion problem is undecidable for mean-payoff automata and the decidability is open for discounted-sum automata, whereas the (quantitative) simulation reduce to mean-payoff games and discounted-sum games, which admit pseudo-polynomial time algorithms.\r\n\r\nIn this work, we study (quantitative) simulation for weighted automata with Büchi acceptance conditions, i.e., we generalize fair simulation from non-weighted automata to weighted automata. We show that imposing Büchi acceptance conditions on weighted automata changes many fundamental properties of the simulation games. For example, whereas for mean-payoff and discounted-sum games, the players do not need memory to play optimally; we show in contrast that for simulation games with Büchi acceptance conditions, (i) for mean-payoff objectives, optimal strategies for both players require infinite memory in general, and (ii) for discounted-sum objectives, optimal strategies need not exist for both players. While the simulation games with Büchi acceptance conditions are more complicated (e.g., due to infinite-memory requirements for mean-payoff objectives) as compared to their counterpart without Büchi acceptance conditions, we still present pseudo-polynomial time algorithms to solve simulation games with Büchi acceptance conditions for both weighted mean-payoff and weighted discounted-sum automata."}],"month":"12","oa":1,"alternative_title":["IST Austria Technical Report"],"publisher":"IST Austria"}]