--- _id: '2039' abstract: - lang: eng 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.' article_number: 7p author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Andreas full_name: Pavlogiannis, Andreas id: 49704004-F248-11E8-B48F-1D18A9856A87 last_name: Pavlogiannis orcid: 0000-0002-8943-0722 - first_name: Ben full_name: Adlam, Ben last_name: Adlam - first_name: Martin full_name: Nowak, Martin last_name: Nowak citation: 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 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 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. 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. ista: Chatterjee K, Pavlogiannis A, Adlam B, Nowak M. 2014. The time scale of evolutionary innovation. PLoS Computational Biology. 10(9), 7p. 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. short: K. Chatterjee, A. Pavlogiannis, B. Adlam, M. Nowak, PLoS Computational Biology 10 (2014). date_created: 2018-12-11T11:55:22Z date_published: 2014-09-11T00:00:00Z date_updated: 2023-02-23T14:06:36Z day: '11' ddc: - '510' department: - _id: KrCh doi: 10.1371/journal.pcbi.1003818 ec_funded: 1 file: - access_level: open_access checksum: 712d4c5787ddf97809cfc962507f0738 content_type: application/pdf creator: system date_created: 2018-12-12T10:11:35Z date_updated: 2020-07-14T12:45:26Z file_id: '4890' file_name: IST-2016-440-v1+1_journal.pcbi.1003818.pdf file_size: 1399093 relation: main_file file_date_updated: 2020-07-14T12:45:26Z has_accepted_license: '1' intvolume: ' 10' issue: '9' language: - iso: eng month: '09' oa: 1 oa_version: Published Version project: - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication: PLoS Computational Biology publication_status: published publisher: Public Library of Science publist_id: '5012' pubrep_id: '440' quality_controlled: '1' related_material: record: - id: '9739' relation: research_data status: public scopus_import: 1 status: public title: The time scale of evolutionary innovation tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 10 year: '2014' ... --- _id: '9739' article_processing_charge: No author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Andreas full_name: Pavlogiannis, Andreas id: 49704004-F248-11E8-B48F-1D18A9856A87 last_name: Pavlogiannis orcid: 0000-0002-8943-0722 - first_name: Ben full_name: Adlam, Ben last_name: Adlam - first_name: Martin full_name: Novak, Martin last_name: Novak citation: 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 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. ieee: K. Chatterjee, A. Pavlogiannis, B. Adlam, and M. Novak, “Detailed proofs for ‘The time scale of evolutionary innovation.’” Public Library of Science, 2014. 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). date_created: 2021-07-28T08:13:57Z date_published: 2014-09-11T00:00:00Z date_updated: 2023-02-23T10:25:37Z day: '11' department: - _id: KrCh doi: 10.1371/journal.pcbi.1003818.s001 month: '09' oa_version: Published Version publisher: Public Library of Science related_material: record: - id: '2039' relation: used_in_publication status: public status: public title: Detailed proofs for “The time scale of evolutionary innovation” type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2014' ... --- _id: '535' 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. article_processing_charge: No article_type: original author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger 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 citation: 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 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 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. 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. 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. short: K. Chatterjee, M.H. Henzinger, S. Krinninger, D. Nanongkai, Algorithmica 70 (2014) 457–492. date_created: 2018-12-11T11:47:01Z date_published: 2014-11-01T00:00:00Z date_updated: 2023-09-05T14:09:29Z day: '01' department: - _id: KrCh doi: 10.1007/s00453-013-9843-7 ec_funded: 1 external_id: arxiv: - '1604.08234' intvolume: ' 70' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1604.08234 month: '11' oa: 1 oa_version: Preprint page: 457 - 492 project: - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication: Algorithmica publication_status: published publisher: Springer publist_id: '7282' quality_controlled: '1' related_material: record: - id: '10905' relation: earlier_version status: public scopus_import: '1' status: public title: Polynomial-time algorithms for energy games with special weight structures type: journal_article user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd volume: 70 year: '2014' ... --- _id: '2063' abstract: - lang: eng 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. alternative_title: - LNCS author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Martin full_name: Chmelik, Martin id: 3624234E-F248-11E8-B48F-1D18A9856A87 last_name: Chmelik - first_name: Przemyslaw full_name: Daca, Przemyslaw id: 49351290-F248-11E8-B48F-1D18A9856A87 last_name: Daca citation: 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' 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. 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.' ista: 'Chatterjee K, Chmelik M, Daca P. 2014. CEGAR for qualitative analysis of probabilistic systems. CAV: Computer Aided Verification, LNCS, vol. 8559, 473–490.' 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. short: K. Chatterjee, M. Chmelik, P. Daca, in:, Springer, 2014, pp. 473–490. conference: end_date: 2014-07-22 location: Vienna, Austria name: 'CAV: Computer Aided Verification' start_date: 2014-07-18 date_created: 2018-12-11T11:55:30Z date_published: 2014-07-01T00:00:00Z date_updated: 2023-09-07T11:58:33Z day: '01' department: - _id: KrCh - _id: ToHe doi: 10.1007/978-3-319-08867-9_31 ec_funded: 1 intvolume: ' 8559' language: - iso: eng month: '07' oa_version: None page: 473 - 490 project: - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory - _id: 25F5A88A-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11402-N23 name: Moderne Concurrency Paradigms - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling publication_status: published publisher: Springer publist_id: '4978' quality_controlled: '1' related_material: record: - id: '5412' relation: earlier_version status: public - id: '5413' relation: earlier_version status: public - id: '5414' relation: earlier_version status: public - id: '1155' relation: dissertation_contains status: public status: public title: CEGAR for qualitative analysis of probabilistic systems type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8559 year: '2014' ... --- _id: '5428' 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." alternative_title: - IST Austria Technical Report author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Jan full_name: Otop, Jan id: 2FC5DA74-F248-11E8-B48F-1D18A9856A87 last_name: Otop - first_name: Yaron full_name: Velner, Yaron last_name: Velner citation: 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 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 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. ieee: K. Chatterjee, T. A. Henzinger, J. Otop, and Y. Velner, Quantitative fair simulation games. IST Austria, 2014. ista: Chatterjee K, Henzinger TA, Otop J, Velner Y. 2014. Quantitative fair simulation games, IST Austria, 26p. mla: Chatterjee, Krishnendu, et al. 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. date_created: 2018-12-12T11:39:16Z date_published: 2014-12-05T00:00:00Z date_updated: 2023-09-20T12:07:48Z day: '05' ddc: - '004' department: - _id: ToHe - _id: KrCh doi: 10.15479/AT:IST-2014-315-v1-1 file: - access_level: open_access checksum: b1d573bc04365625ff9974880c0aa807 content_type: application/pdf creator: system date_created: 2018-12-12T11:53:59Z date_updated: 2020-07-14T12:46:52Z file_id: '5521' file_name: IST-2014-315-v1+1_report.pdf file_size: 531046 relation: main_file file_date_updated: 2020-07-14T12:46:52Z has_accepted_license: '1' language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: '26' publication_identifier: issn: - 2664-1690 publication_status: published publisher: IST Austria pubrep_id: '315' related_material: record: - id: '1066' relation: later_version status: public status: public title: Quantitative fair simulation games type: technical_report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2014' ...