[{"department":[{"_id":"NiBa"}],"author":[{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton"},{"first_name":"Jason","last_name":"Coe","full_name":"Coe, Jason"}],"publication":"Journal of Theoretical Biology","issue":"2","type":"journal_article","_id":"3775","oa_version":"Submitted Version","date_created":"2018-12-11T12:05:06Z","status":"public","title":"On the application of statistical physics to evolutionary biology","volume":259,"day":"21","scopus_import":1,"main_file_link":[{"url":"https://hal.archives-ouvertes.fr/hal-00554594/document","open_access":"1"}],"publist_id":"2452","date_updated":"2021-01-12T07:52:06Z","publisher":"Elsevier","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"07","date_published":"2009-07-21T00:00:00Z","acknowledgement":"This work was supported by a Royal Society/Wolfson Award, and by grants EP/T11753/01, EP/C546318/01 from the EPSRC.\r\nWe are grateful to M. Cates, H.P. de Vladar and G. Sella, and to two anonymous referees, for their helpful comments.","quality_controlled":"1","doi":"10.1016/j.jtbi.2009.03.019","citation":{"ieee":"N. H. Barton and J. Coe, “On the application of statistical physics to evolutionary biology,” <i>Journal of Theoretical Biology</i>, vol. 259, no. 2. Elsevier, pp. 317–324, 2009.","ista":"Barton NH, Coe J. 2009. On the application of statistical physics to evolutionary biology. Journal of Theoretical Biology. 259(2), 317–324.","mla":"Barton, Nicholas H., and Jason Coe. “On the Application of Statistical Physics to Evolutionary Biology.” <i>Journal of Theoretical Biology</i>, vol. 259, no. 2, Elsevier, 2009, pp. 317–24, doi:<a href=\"https://doi.org/10.1016/j.jtbi.2009.03.019\">10.1016/j.jtbi.2009.03.019</a>.","apa":"Barton, N. H., &#38; Coe, J. (2009). On the application of statistical physics to evolutionary biology. <i>Journal of Theoretical Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jtbi.2009.03.019\">https://doi.org/10.1016/j.jtbi.2009.03.019</a>","short":"N.H. Barton, J. Coe, Journal of Theoretical Biology 259 (2009) 317–324.","chicago":"Barton, Nicholas H, and Jason Coe. “On the Application of Statistical Physics to Evolutionary Biology.” <i>Journal of Theoretical Biology</i>. Elsevier, 2009. <a href=\"https://doi.org/10.1016/j.jtbi.2009.03.019\">https://doi.org/10.1016/j.jtbi.2009.03.019</a>.","ama":"Barton NH, Coe J. On the application of statistical physics to evolutionary biology. <i>Journal of Theoretical Biology</i>. 2009;259(2):317-324. doi:<a href=\"https://doi.org/10.1016/j.jtbi.2009.03.019\">10.1016/j.jtbi.2009.03.019</a>"},"intvolume":"       259","language":[{"iso":"eng"}],"year":"2009","page":"317 - 324","abstract":[{"text":"There is a close analogy between statistical thermodynamics and the evolution of allele frequencies under mutation, selection and random drift. Wright's formula for the stationary distribution of allele frequencies is analogous to the Boltzmann distribution in statistical physics. Population size, 2N, plays the role of the inverse temperature, 1/kT, and determines the magnitude of random fluctuations. Log mean fitness, View the MathML source, tends to increase under selection, and is analogous to a (negative) energy; a potential function, U, increases under mutation in a similar way. An entropy, SH, can be defined which measures the deviation from the distribution of allele frequencies expected under random drift alone; the sum View the MathML source gives a free fitness that increases as the population evolves towards its stationary distribution. Usually, we observe the distribution of a few quantitative traits that depend on the frequencies of very many alleles. The mean and variance of such traits are analogous to observable quantities in statistical thermodynamics. Thus, we can define an entropy, SΩ, which measures the volume of allele frequency space that is consistent with the observed trait distribution. The stationary distribution of the traits is View the MathML source; this applies with arbitrary epistasis and dominance. The entropies SΩ, SH are distinct, but converge when there are so many alleles that traits fluctuate close to their expectations. Populations tend to evolve towards states that can be realised in many ways (i.e., large SΩ), which may lead to a substantial drop below the adaptive peak; we illustrate this point with a simple model of genetic redundancy. This analogy with statistical thermodynamics brings together previous ideas in a general framework, and justifies a maximum entropy approximation to the dynamics of quantitative traits.","lang":"eng"}],"oa":1},{"has_accepted_license":"1","intvolume":"        22","year":"2009","language":[{"iso":"eng"}],"acknowledgement":"We owe a great debt to Jim Murray for his many contributions to the study of Partula, in the field, in the laboratory, in the interpretation of data, and in generating new ideas about evolution. With pleasure and respect we dedicate this paper to him. Jim Murray played a leading role in making the collections used here. We are very grateful also to Ann Clarke and Elizabeth Murray for help with collecting, to Lorna Stewart for snail dissections, to Joris Koene for the gift of snails, to Natasha Constant for entering the data, and Takahiro Asami, Edmund Gittenberger and Gerhard Falkner for establishing the sinistral stock of L. stagnalis. Comments from an anonymous referee, A. Richard Palmer and the editorial board improved the manuscript. Work in the field was supported by the Royal Society, The Carnegie Trust, the Percy Sladen Trust and the National Science Foundation. The Science Research Council (B/SR/4144), the National Science Foundation (GB-4188), the Royal Society and the University of Nottingham supported work in the laboratory.","doi":"10.1111/j.1420-9101.2009.01770.x","citation":{"ama":"Davison A, Barton NH, Clarke B. The effect of chirality phenotype and genotype on the fecundity and viability of Partula suturalis and Lymnaea stagnalis: Implications for the evolution of sinistral snails. <i>Journal of Evolutionary Biology</i>. 2009;22(8):1624-1635. doi:<a href=\"https://doi.org/10.1111/j.1420-9101.2009.01770.x\">10.1111/j.1420-9101.2009.01770.x</a>","chicago":"Davison, Angus, Nicholas H Barton, and Bryan Clarke. “The Effect of Chirality Phenotype and Genotype on the Fecundity and Viability of Partula Suturalis and Lymnaea Stagnalis: Implications for the Evolution of Sinistral Snails.” <i>Journal of Evolutionary Biology</i>. Wiley, 2009. <a href=\"https://doi.org/10.1111/j.1420-9101.2009.01770.x\">https://doi.org/10.1111/j.1420-9101.2009.01770.x</a>.","short":"A. Davison, N.H. Barton, B. Clarke, Journal of Evolutionary Biology 22 (2009) 1624–1635.","apa":"Davison, A., Barton, N. H., &#38; Clarke, B. (2009). The effect of chirality phenotype and genotype on the fecundity and viability of Partula suturalis and Lymnaea stagnalis: Implications for the evolution of sinistral snails. <i>Journal of Evolutionary Biology</i>. Wiley. <a href=\"https://doi.org/10.1111/j.1420-9101.2009.01770.x\">https://doi.org/10.1111/j.1420-9101.2009.01770.x</a>","mla":"Davison, Angus, et al. “The Effect of Chirality Phenotype and Genotype on the Fecundity and Viability of Partula Suturalis and Lymnaea Stagnalis: Implications for the Evolution of Sinistral Snails.” <i>Journal of Evolutionary Biology</i>, vol. 22, no. 8, Wiley, 2009, pp. 1624–35, doi:<a href=\"https://doi.org/10.1111/j.1420-9101.2009.01770.x\">10.1111/j.1420-9101.2009.01770.x</a>.","ieee":"A. Davison, N. H. Barton, and B. Clarke, “The effect of chirality phenotype and genotype on the fecundity and viability of Partula suturalis and Lymnaea stagnalis: Implications for the evolution of sinistral snails,” <i>Journal of Evolutionary Biology</i>, vol. 22, no. 8. Wiley, pp. 1624–1635, 2009.","ista":"Davison A, Barton NH, Clarke B. 2009. The effect of chirality phenotype and genotype on the fecundity and viability of Partula suturalis and Lymnaea stagnalis: Implications for the evolution of sinistral snails. Journal of Evolutionary Biology. 22(8), 1624–1635."},"quality_controlled":"1","oa":1,"ddc":["570"],"abstract":[{"lang":"eng","text":"Why are sinistral snails so rare? Two main hypotheses are that selection acts against the establishment of new coiling morphs, because dextral and sinistral snails have trouble mating, or else a developmental constraint prevents the establishment of sinistrals. We therefore used an isolate of the snail Lymnaea stagnalis, in which sinistrals are rare, and populations of Partula suturalis, in which sinistrals are common, as well as a mathematical model, to understand the circumstances by which new morphs evolve. The main finding is that the sinistral genotype is associated with reduced egg viability in L. stagnalis, but in P. suturalis individuals of sinistral and dextral genotype appear equally fecund, implying a lack of a constraint. As positive frequency-dependent selection against the rare chiral morph in P. suturalis also operates over a narrow range (&lt; 3%), the results suggest a model for chiral evolution in snails in which weak positive frequency-dependent selection may be overcome by a negative frequency-dependent selection, such as reproductive character displacement. In snails, there is not always a developmental constraint. As the direction of cleavage, and thus the directional asymmetry of the entire body, does not generally vary in other Spiralia (annelids, echiurans, vestimentiferans, sipunculids and nemerteans), it remains an open question as to whether this is because of a constraint and/or because most taxa do not have a conspicuous external asymmetry (like a shell) upon which selection can act."}],"file":[{"date_updated":"2020-07-14T12:46:15Z","checksum":"f70c15c6ab9306121d4153a3be0d2346","file_size":2583812,"creator":"dernst","content_type":"application/pdf","relation":"main_file","file_name":"Davison_JEB_v31_2009.pdf","file_id":"6044","date_created":"2019-02-22T09:21:44Z","access_level":"open_access"}],"page":"1624 - 1635","title":"The effect of chirality phenotype and genotype on the fecundity and viability of Partula suturalis and Lymnaea stagnalis: Implications for the evolution of sinistral snails","volume":22,"status":"public","day":"01","author":[{"full_name":"Davison, Angus","last_name":"Davison","first_name":"Angus"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"},{"first_name":"Bryan","last_name":"Clarke","full_name":"Clarke, Bryan"}],"department":[{"_id":"NiBa"}],"pubrep_id":"553","oa_version":"Submitted Version","date_created":"2018-12-11T12:05:08Z","issue":"8","_id":"3780","type":"journal_article","publication":"Journal of Evolutionary Biology","file_date_updated":"2020-07-14T12:46:15Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","publisher":"Wiley","publist_id":"2447","date_updated":"2021-01-12T07:52:09Z","month":"08","date_published":"2009-08-01T00:00:00Z","scopus_import":1},{"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"2360","date_updated":"2021-01-12T07:52:33Z","publisher":"ACM","date_published":"2009-01-01T00:00:00Z","month":"01","author":[{"full_name":"Tripakis, Stavros","first_name":"Stavros","last_name":"Tripakis"},{"full_name":"Lickly, Ben","last_name":"Lickly","first_name":"Ben"},{"last_name":"Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"},{"full_name":"Lee, Edward","first_name":"Edward","last_name":"Lee"}],"department":[{"_id":"ToHe"}],"pubrep_id":"70","oa_version":"Submitted Version","date_created":"2018-12-11T12:05:26Z","project":[{"name":"COMponent-Based Embedded Systems design Techniques","_id":"25EFB36C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"215543"},{"_id":"25F1337C-B435-11E9-9278-68D0E5697425","name":"Design for Embedded Systems","grant_number":"214373","call_identifier":"FP7"}],"publication":"EMSOFT '09 Proceedings of the seventh ACM international conference on Embedded software","file_date_updated":"2020-07-14T12:46:16Z","_id":"3837","type":"conference","title":"On relational interfaces","status":"public","day":"01","page":"67 - 76","abstract":[{"lang":"eng","text":"In this paper we extend the work of Alfaro, Henzinger et al. on interface theories for component-based design. Existing interface theories often fail to capture functional relations between the inputs and outputs of an interface. For example, a simple synchronous interface that takes as input a number n ≥ 0 and returns, at the same time, as output n + 1, cannot be expressed in existing theories. In this paper we provide a theory of relational interfaces, where such input-output relations can be captured. Our theory supports synchronous interfaces, both stateless and stateful. It includes explicit notions of environments and pluggability, and satisfies fundamental properties such as preservation of refinement by composition, and characterization of pluggability by refinement. We achieve these properties by making reasonable restrictions on feedback loops in interface compositions."}],"ddc":["004"],"oa":1,"file":[{"file_name":"IST-2012-70-v1+1_On_Relational_Interfaces.pdf","relation":"main_file","content_type":"application/pdf","date_created":"2018-12-12T10:13:57Z","access_level":"open_access","file_id":"5045","date_updated":"2020-07-14T12:46:16Z","creator":"system","file_size":310902,"checksum":"3a70e21527dfaad2f198549ae5710786"}],"acknowledgement":"This work is supported by the Center for Hybrid and Embedded Software Systems (CHESS) at UC Berkeley, which receives support from the National Science Foundation (NSF awards #0720882 (CSR-EHS: PRET) and #0720841 (CSR-CPS)), the U.S. Army Research Office (ARO #W911NF-07-2-0019), the U.S. Air Force Office of Scientific Research (MURI #FA9550-06-0312), the Air Force Research Lab (AFRL), the State of California Micro Program, and the following companies: Agilent, Bosch, Lockheed-Martin, National Instruments, Thales and Toyota. This work is also supported by the COMBEST and ArtistDesign projects of the European Union, and the Swiss National Science Foundation. ","conference":{"location":"Grenoble, France","start_date":"2009-10-12","end_date":"2009-10-16","name":"EMSOFT: Embedded Software "},"quality_controlled":"1","ec_funded":1,"citation":{"apa":"Tripakis, S., Lickly, B., Henzinger, T. A., &#38; Lee, E. (2009). On relational interfaces. In <i>EMSOFT ’09 Proceedings of the seventh ACM international conference on Embedded software</i> (pp. 67–76). Grenoble, France: ACM. <a href=\"https://doi.org/10.1145/1629335.1629346\">https://doi.org/10.1145/1629335.1629346</a>","short":"S. Tripakis, B. Lickly, T.A. Henzinger, E. Lee, in:, EMSOFT ’09 Proceedings of the Seventh ACM International Conference on Embedded Software, ACM, 2009, pp. 67–76.","chicago":"Tripakis, Stavros, Ben Lickly, Thomas A Henzinger, and Edward Lee. “On Relational Interfaces.” In <i>EMSOFT ’09 Proceedings of the Seventh ACM International Conference on Embedded Software</i>, 67–76. ACM, 2009. <a href=\"https://doi.org/10.1145/1629335.1629346\">https://doi.org/10.1145/1629335.1629346</a>.","ieee":"S. Tripakis, B. Lickly, T. A. Henzinger, and E. Lee, “On relational interfaces,” in <i>EMSOFT ’09 Proceedings of the seventh ACM international conference on Embedded software</i>, Grenoble, France, 2009, pp. 67–76.","ista":"Tripakis S, Lickly B, Henzinger TA, Lee E. 2009. On relational interfaces. EMSOFT ’09 Proceedings of the seventh ACM international conference on Embedded software. EMSOFT: Embedded Software , 67–76.","mla":"Tripakis, Stavros, et al. “On Relational Interfaces.” <i>EMSOFT ’09 Proceedings of the Seventh ACM International Conference on Embedded Software</i>, ACM, 2009, pp. 67–76, doi:<a href=\"https://doi.org/10.1145/1629335.1629346\">10.1145/1629335.1629346</a>.","ama":"Tripakis S, Lickly B, Henzinger TA, Lee E. On relational interfaces. In: <i>EMSOFT ’09 Proceedings of the Seventh ACM International Conference on Embedded Software</i>. ACM; 2009:67-76. doi:<a href=\"https://doi.org/10.1145/1629335.1629346\">10.1145/1629335.1629346</a>"},"doi":"10.1145/1629335.1629346","has_accepted_license":"1","year":"2009","language":[{"iso":"eng"}]},{"intvolume":"      5797","has_accepted_license":"1","language":[{"iso":"eng"}],"year":"2009","conference":{"name":"RP: Reachability Problems","start_date":"2009-09-23","end_date":"2009-09-25","location":"Palaiseau, France"},"acknowledgement":"This research was supported in part by the Excellence Cluster on Multimodal Computing and Interaction and the Swiss National Science Foundation.","related_material":{"record":[{"relation":"later_version","status":"public","id":"3381"}]},"citation":{"ista":"Henzinger TA, Jobstmann B, Wolf V. 2009. Formalisms for specifying Markovian population models. RP: Reachability Problems, LNCS, vol. 5797, 3–23.","ieee":"T. A. Henzinger, B. Jobstmann, and V. Wolf, “Formalisms for specifying Markovian population models,” presented at the RP: Reachability Problems, Palaiseau, France, 2009, vol. 5797, pp. 3–23.","mla":"Henzinger, Thomas A., et al. <i>Formalisms for Specifying Markovian Population Models</i>. Vol. 5797, Springer, 2009, pp. 3–23, doi:<a href=\"https://doi.org/10.1007/978-3-642-04420-5_2\">10.1007/978-3-642-04420-5_2</a>.","apa":"Henzinger, T. A., Jobstmann, B., &#38; Wolf, V. (2009). Formalisms for specifying Markovian population models (Vol. 5797, pp. 3–23). Presented at the RP: Reachability Problems, Palaiseau, France: Springer. <a href=\"https://doi.org/10.1007/978-3-642-04420-5_2\">https://doi.org/10.1007/978-3-642-04420-5_2</a>","short":"T.A. Henzinger, B. Jobstmann, V. Wolf, in:, Springer, 2009, pp. 3–23.","chicago":"Henzinger, Thomas A, Barbara Jobstmann, and Verena Wolf. “Formalisms for Specifying Markovian Population Models,” 5797:3–23. Springer, 2009. <a href=\"https://doi.org/10.1007/978-3-642-04420-5_2\">https://doi.org/10.1007/978-3-642-04420-5_2</a>.","ama":"Henzinger TA, Jobstmann B, Wolf V. Formalisms for specifying Markovian population models. In: Vol 5797. Springer; 2009:3-23. doi:<a href=\"https://doi.org/10.1007/978-3-642-04420-5_2\">10.1007/978-3-642-04420-5_2</a>"},"doi":"10.1007/978-3-642-04420-5_2","quality_controlled":"1","file":[{"creator":"system","checksum":"df88431872586c773fbcfea37d7b36a2","file_size":222840,"date_updated":"2020-07-14T12:46:16Z","access_level":"open_access","date_created":"2018-12-12T10:08:41Z","file_id":"4702","file_name":"IST-2012-67-v1+1_Formalisms_for_specifying_Markovian_population_models.pdf","relation":"main_file","content_type":"application/pdf"}],"oa":1,"ddc":["005"],"abstract":[{"text":"We compare several languages for specifying Markovian population models such as queuing networks and chemical reaction networks. These languages —matrix descriptions, stochastic Petri nets, stoichiometric equations, stochastic process algebras, and guarded command models— all describe continuous-time Markov chains, but they differ according to important properties, such as compositionality, expressiveness and succinctness, executability, ease of use, and the support they provide for checking the well-formedness of a model and for analyzing a model. ","lang":"eng"}],"page":"3 - 23","alternative_title":["LNCS"],"status":"public","volume":5797,"title":"Formalisms for specifying Markovian population models","day":"07","department":[{"_id":"ToHe"}],"author":[{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"},{"full_name":"Jobstmann, Barbara","first_name":"Barbara","last_name":"Jobstmann"},{"last_name":"Wolf","first_name":"Verena","full_name":"Wolf, Verena"}],"type":"conference","_id":"3841","file_date_updated":"2020-07-14T12:46:16Z","oa_version":"Submitted Version","date_created":"2018-12-11T12:05:28Z","pubrep_id":"67","publisher":"Springer","date_updated":"2023-02-23T11:24:49Z","publist_id":"2352","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","date_published":"2009-09-07T00:00:00Z","month":"09","scopus_import":1},{"year":"2009","language":[{"iso":"eng"}],"has_accepted_license":"1","intvolume":"         4","quality_controlled":"1","doi":"10.1109/HiBi.2009.23","citation":{"apa":"Didier, F., Henzinger, T. A., Mateescu, M., &#38; Wolf, V. (2009). Fast adaptive uniformization of the chemical master equation (Vol. 4, pp. 118–127). Presented at the HIBI: High-Performance Computational Systems Biology, Trento, Italy: IEEE. <a href=\"https://doi.org/10.1109/HiBi.2009.23\">https://doi.org/10.1109/HiBi.2009.23</a>","short":"F. Didier, T.A. Henzinger, M. Mateescu, V. Wolf, in:, IEEE, 2009, pp. 118–127.","chicago":"Didier, Frédéric, Thomas A Henzinger, Maria Mateescu, and Verena Wolf. “Fast Adaptive Uniformization of the Chemical Master Equation,” 4:118–27. IEEE, 2009. <a href=\"https://doi.org/10.1109/HiBi.2009.23\">https://doi.org/10.1109/HiBi.2009.23</a>.","ieee":"F. Didier, T. A. Henzinger, M. Mateescu, and V. Wolf, “Fast adaptive uniformization of the chemical master equation,” presented at the HIBI: High-Performance Computational Systems Biology, Trento, Italy, 2009, vol. 4, no. 6, pp. 118–127.","ista":"Didier F, Henzinger TA, Mateescu M, Wolf V. 2009. Fast adaptive uniformization of the chemical master equation. HIBI: High-Performance Computational Systems Biology vol. 4, 118–127.","mla":"Didier, Frédéric, et al. <i>Fast Adaptive Uniformization of the Chemical Master Equation</i>. Vol. 4, no. 6, IEEE, 2009, pp. 118–27, doi:<a href=\"https://doi.org/10.1109/HiBi.2009.23\">10.1109/HiBi.2009.23</a>.","ama":"Didier F, Henzinger TA, Mateescu M, Wolf V. Fast adaptive uniformization of the chemical master equation. In: Vol 4. IEEE; 2009:118-127. doi:<a href=\"https://doi.org/10.1109/HiBi.2009.23\">10.1109/HiBi.2009.23</a>"},"related_material":{"record":[{"status":"public","id":"3842","relation":"later_version"}]},"acknowledgement":"This research has been partially funded by the Swiss National Science Foundation under grant 205321-111840 and by the Cluster of Excellence on Multimodal Computing and Interaction at Saarland University.","conference":{"name":"HIBI: High-Performance Computational Systems Biology","end_date":"2009-10-16","start_date":"2009-10-14","location":"Trento, Italy"},"abstract":[{"lang":"eng","text":"Within systems biology there is an increasing interest in the stochastic behavior of biochemical reaction networks. An appropriate stochastic description is provided by the chemical master equation, which represents a continuous- time Markov chain (CTMC).\r\nStandard Uniformization (SU) is an efficient method for the transient analysis of CTMCs. For systems with very different time scales, such as biochemical reaction networks, SU is computationally expensive. In these cases, a variant of SU, called adaptive uniformization (AU), is known to reduce the large number of iterations needed by SU. The additional difficulty of AU is that it requires the solution of a birth process.\r\nIn this paper we present an on-the-fly variant of AU, where we improve the original algorithm for AU at the cost of a small approximation error. By means of several examples, we show that our approach is particularly well-suited for biochemical reaction networks."}],"ddc":["000"],"oa":1,"file":[{"date_created":"2020-05-19T16:33:55Z","access_level":"open_access","file_id":"7874","relation":"main_file","file_name":"2009_HIBI_Didier.pdf","content_type":"application/pdf","creator":"dernst","checksum":"9a3bde48f43203991a0b3c6a277c2f5b","file_size":222890,"date_updated":"2020-07-14T12:46:17Z"}],"page":"118 - 127","day":"30","title":"Fast adaptive uniformization of the chemical master equation","volume":4,"status":"public","oa_version":"Submitted Version","date_created":"2018-12-11T12:05:28Z","file_date_updated":"2020-07-14T12:46:17Z","_id":"3843","article_processing_charge":"No","issue":"6","type":"conference","author":[{"first_name":"Frédéric","last_name":"Didier","full_name":"Didier, Frédéric"},{"orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger"},{"full_name":"Mateescu, Maria","last_name":"Mateescu","first_name":"Maria","id":"3B43276C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Wolf","first_name":"Verena","full_name":"Wolf, Verena"}],"department":[{"_id":"ToHe"},{"_id":"CaGu"}],"month":"10","date_published":"2009-10-30T00:00:00Z","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"2348","date_updated":"2023-02-23T11:45:05Z","publisher":"IEEE","scopus_import":1},{"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"2346","date_updated":"2021-01-12T07:52:36Z","publisher":"IEEE","date_published":"2009-01-01T00:00:00Z","month":"01","title":"Distributed, modular HTL","status":"public","day":"01","author":[{"full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"},{"first_name":"Christoph","last_name":"Kirsch","full_name":"Kirsch, Christoph"},{"last_name":"Marques","first_name":"Eduardo","full_name":"Marques, Eduardo"},{"last_name":"Sokolova","first_name":"Ana","full_name":"Sokolova, Ana"}],"department":[{"_id":"ToHe"}],"date_created":"2018-12-11T12:05:28Z","pubrep_id":"65","oa_version":"Submitted Version","project":[{"_id":"25F1337C-B435-11E9-9278-68D0E5697425","name":"Design for Embedded Systems","call_identifier":"FP7","grant_number":"214373"},{"call_identifier":"FP7","grant_number":"215543","_id":"25EFB36C-B435-11E9-9278-68D0E5697425","name":"COMponent-Based Embedded Systems design Techniques"}],"file_date_updated":"2020-07-14T12:46:17Z","_id":"3844","type":"conference","abstract":[{"text":"The Hierarchical Timing Language (HTL) is a real-time coordination language for distributed control systems. HTL programs must be checked for well-formedness, race freedom, transmission safety (schedulability of inter-host communication), and time safety (schedulability of host computation). We present a modular abstract syntax and semantics for HTL, modular checks of well-formedness, race freedom, and transmission safety, and modular code distribution. Our contributions here complement previous results on HTL time safety and modular code generation. Modularity in HTL can be utilized in easy program composition as well as fast program analysis and code generation, but also in so-called runtime patching, where program components may be modified at runtime.","lang":"eng"}],"oa":1,"ddc":["000"],"file":[{"file_id":"4655","access_level":"open_access","date_created":"2018-12-12T10:07:56Z","content_type":"application/pdf","relation":"main_file","file_name":"IST-2012-65-v1+1_Distributed_modular_Htl.pdf","file_size":526458,"checksum":"b2b15a5ef71eb50d62eaa5aea7efd8c4","creator":"system","date_updated":"2020-07-14T12:46:17Z"}],"page":"171 - 180","has_accepted_license":"1","year":"2009","language":[{"iso":"eng"}],"acknowledgement":"Supported by the EU ArtistDesign Network of Excellence on Embedded Systems Design, the EU project COMBEST, the Austrian Science Funds P18913-N15 and V00125, and Fundacao para a Ciencia e Tecnologia funds SFRH/BD/29461/2006 and PTDC/EIA/71462/2006","conference":{"location":"Washington, DC, United States","end_date":"2009-12-04","start_date":"2009-12-01","name":"RTSS: Real-Time Systems Symposium"},"ec_funded":1,"quality_controlled":"1","doi":"10.1109/RTSS.2009.9","citation":{"apa":"Henzinger, T. A., Kirsch, C., Marques, E., &#38; Sokolova, A. (2009). Distributed, modular HTL (pp. 171–180). Presented at the RTSS: Real-Time Systems Symposium, Washington, DC, United States: IEEE. <a href=\"https://doi.org/10.1109/RTSS.2009.9\">https://doi.org/10.1109/RTSS.2009.9</a>","short":"T.A. Henzinger, C. Kirsch, E. Marques, A. Sokolova, in:, IEEE, 2009, pp. 171–180.","chicago":"Henzinger, Thomas A, Christoph Kirsch, Eduardo Marques, and Ana Sokolova. “Distributed, Modular HTL,” 171–80. IEEE, 2009. <a href=\"https://doi.org/10.1109/RTSS.2009.9\">https://doi.org/10.1109/RTSS.2009.9</a>.","ista":"Henzinger TA, Kirsch C, Marques E, Sokolova A. 2009. Distributed, modular HTL. RTSS: Real-Time Systems Symposium, 171–180.","ieee":"T. A. Henzinger, C. Kirsch, E. Marques, and A. Sokolova, “Distributed, modular HTL,” presented at the RTSS: Real-Time Systems Symposium, Washington, DC, United States, 2009, pp. 171–180.","mla":"Henzinger, Thomas A., et al. <i>Distributed, Modular HTL</i>. IEEE, 2009, pp. 171–80, doi:<a href=\"https://doi.org/10.1109/RTSS.2009.9\">10.1109/RTSS.2009.9</a>.","ama":"Henzinger TA, Kirsch C, Marques E, Sokolova A. Distributed, modular HTL. In: IEEE; 2009:171-180. doi:<a href=\"https://doi.org/10.1109/RTSS.2009.9\">10.1109/RTSS.2009.9</a>"}},{"department":[{"_id":"KrCh"}],"author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee"},{"orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger"},{"last_name":"Horn","id":"37327ACE-F248-11E8-B48F-1D18A9856A87","first_name":"Florian","full_name":"Horn, Florian"}],"issue":"1","_id":"3870","type":"journal_article","file_date_updated":"2020-07-14T12:46:20Z","publication":"ACM Transactions on Computational Logic (TOCL)","project":[{"call_identifier":"FP7","grant_number":"215543","_id":"25EFB36C-B435-11E9-9278-68D0E5697425","name":"COMponent-Based Embedded Systems design Techniques"}],"oa_version":"Submitted Version","pubrep_id":"53","date_created":"2018-12-11T12:05:37Z","article_number":"1","status":"public","title":"Finitary winning in omega-regular games","volume":11,"day":"01","scopus_import":1,"publisher":"ACM","date_updated":"2021-01-12T07:52:50Z","publist_id":"2309","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","month":"10","date_published":"2009-10-01T00:00:00Z","acknowledgement":"This research was supported in part by the AFOSR MURI grant F49620-00-1-0327, the NSF grants CCR-0132780, CNS-0720884, and CCR- 225610, by the Swiss National Science Foundation, by the COMBEST project of the European Union, and EU-TMR network Games.\r\nWe thank anonymous reviewers for useful comments.","doi":"10.1145/1614431.1614432","citation":{"ama":"Chatterjee K, Henzinger TA, Horn F. Finitary winning in omega-regular games. <i>ACM Transactions on Computational Logic (TOCL)</i>. 2009;11(1). doi:<a href=\"https://doi.org/10.1145/1614431.1614432\">10.1145/1614431.1614432</a>","mla":"Chatterjee, Krishnendu, et al. “Finitary Winning in Omega-Regular Games.” <i>ACM Transactions on Computational Logic (TOCL)</i>, vol. 11, no. 1, 1, ACM, 2009, doi:<a href=\"https://doi.org/10.1145/1614431.1614432\">10.1145/1614431.1614432</a>.","ista":"Chatterjee K, Henzinger TA, Horn F. 2009. Finitary winning in omega-regular games. ACM Transactions on Computational Logic (TOCL). 11(1), 1.","ieee":"K. Chatterjee, T. A. Henzinger, and F. Horn, “Finitary winning in omega-regular games,” <i>ACM Transactions on Computational Logic (TOCL)</i>, vol. 11, no. 1. ACM, 2009.","short":"K. Chatterjee, T.A. Henzinger, F. Horn, ACM Transactions on Computational Logic (TOCL) 11 (2009).","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, and Florian Horn. “Finitary Winning in Omega-Regular Games.” <i>ACM Transactions on Computational Logic (TOCL)</i>. ACM, 2009. <a href=\"https://doi.org/10.1145/1614431.1614432\">https://doi.org/10.1145/1614431.1614432</a>.","apa":"Chatterjee, K., Henzinger, T. A., &#38; Horn, F. (2009). Finitary winning in omega-regular games. <i>ACM Transactions on Computational Logic (TOCL)</i>. ACM. <a href=\"https://doi.org/10.1145/1614431.1614432\">https://doi.org/10.1145/1614431.1614432</a>"},"quality_controlled":"1","ec_funded":1,"intvolume":"        11","has_accepted_license":"1","language":[{"iso":"eng"}],"year":"2009","file":[{"file_id":"5125","date_created":"2018-12-12T10:15:08Z","access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_name":"IST-2012-53-v1+1_Finitary_winning_in_omega-regular_games.pdf","file_size":180082,"checksum":"139c4586d24f11e5da31fb3a0cf96ef4","creator":"system","date_updated":"2020-07-14T12:46:20Z"}],"ddc":["004"],"oa":1,"abstract":[{"lang":"eng","text":"Games on graphs with omega-regular objectives provide a model for the control and synthesis of reactive systems. Every omega-regular objective can be decomposed into a safety part and a liveness part. The liveness part ensures that something good happens “eventually.” Two main strengths of the classical, infinite-limit formulation of liveness are robustness (independence from the granularity of transitions) and simplicity (abstraction of complicated time bounds). However, the classical liveness formulation suffers from the drawback that the time until something good happens may be unbounded. A stronger formulation of liveness, so-called finitary liveness, overcomes this drawback, while still retaining robustness and simplicity. Finitary liveness requires that there exists an unknown, fixed bound b such that something good happens within b transitions. While for one-shot liveness (reachability) objectives, classical and finitary liveness coincide, for repeated liveness (Buchi) objectives, the finitary formulation is strictly stronger. In this work we study games with finitary parity and Streett objectives. We prove the determinacy of these games, present algorithms for solving these games, and characterize the memory requirements of winning strategies. We show that finitary parity games can be solved in polynomial time, which is not known for infinitary parity games. For finitary Streett games, we give an EXPTIME algorithm and show that the problem is NP-hard. Our algorithms can be used, for example, for synthesizing controllers that do not let the response time of a system increase without bound."}]},{"conference":{"location":"Bologna, Italy","start_date":"2009-09-01","end_date":"2009-09-04","name":"CONCUR: Concurrency Theory"},"acknowledgement":"This research was supported in part by the Swiss National Science Foundation under the Indo-Swiss Joint Research Programme, by the European Network of Excellence on Embedded Systems Design (ArtistDesign), by the European projects Combest, Quasimodo, and Gasics, by the PAI program Moves funded by the Belgian Federal Government, and by the CFV (Federated Center in Verification ) funded by the F.R.S.-FNRS.","citation":{"ama":"Chatterjee K, Doyen L, Henzinger TA. Probabilistic weighted automata. In: Vol 5710. Springer; 2009:244-258. doi:<a href=\"https://doi.org/10.1007/978-3-642-04081-8_17\">10.1007/978-3-642-04081-8_17</a>","apa":"Chatterjee, K., Doyen, L., &#38; Henzinger, T. A. (2009). Probabilistic weighted automata (Vol. 5710, pp. 244–258). Presented at the CONCUR: Concurrency Theory, Bologna, Italy: Springer. <a href=\"https://doi.org/10.1007/978-3-642-04081-8_17\">https://doi.org/10.1007/978-3-642-04081-8_17</a>","short":"K. Chatterjee, L. Doyen, T.A. Henzinger, in:, Springer, 2009, pp. 244–258.","chicago":"Chatterjee, Krishnendu, Laurent Doyen, and Thomas A Henzinger. “Probabilistic Weighted Automata,” 5710:244–58. Springer, 2009. <a href=\"https://doi.org/10.1007/978-3-642-04081-8_17\">https://doi.org/10.1007/978-3-642-04081-8_17</a>.","ieee":"K. Chatterjee, L. Doyen, and T. A. Henzinger, “Probabilistic weighted automata,” presented at the CONCUR: Concurrency Theory, Bologna, Italy, 2009, vol. 5710, pp. 244–258.","ista":"Chatterjee K, Doyen L, Henzinger TA. 2009. Probabilistic weighted automata. CONCUR: Concurrency Theory, LNCS, vol. 5710, 244–258.","mla":"Chatterjee, Krishnendu, et al. <i>Probabilistic Weighted Automata</i>. Vol. 5710, Springer, 2009, pp. 244–58, doi:<a href=\"https://doi.org/10.1007/978-3-642-04081-8_17\">10.1007/978-3-642-04081-8_17</a>."},"doi":"10.1007/978-3-642-04081-8_17","ec_funded":1,"quality_controlled":"1","intvolume":"      5710","has_accepted_license":"1","language":[{"iso":"eng"}],"year":"2009","page":"244 - 258","alternative_title":["LNCS"],"file":[{"date_created":"2018-12-12T10:09:46Z","access_level":"open_access","file_id":"4771","relation":"main_file","file_name":"IST-2012-52-v1+1_Probabilistic_Weighted_Automata.pdf","content_type":"application/pdf","creator":"system","file_size":200161,"checksum":"af973ddbcf131b8810c6bff2c055ff56","date_updated":"2020-07-14T12:46:20Z"}],"oa":1,"ddc":["000","005"],"abstract":[{"text":"Nondeterministic weighted automata are finite automata with numerical weights oil transitions. They define quantitative languages 1, that assign to each word v; a real number L(w). The value of ail infinite word w is computed as the maximal value of all runs over w, and the value of a run as the supremum, limsup liminf, limit average, or discounted sum of the transition weights. We introduce probabilistic weighted antomata, in which the transitions are chosen in a randomized (rather than nondeterministic) fashion. Under almost-sure semantics (resp. positive semantics), the value of a word v) is the largest real v such that the runs over w have value at least v with probability I (resp. positive probability). We study the classical questions of automata theory for probabilistic weighted automata: emptiness and universality, expressiveness, and closure under various operations oil languages. For quantitative languages, emptiness university axe defined as whether the value of some (resp. every) word exceeds a given threshold. We prove some, of these questions to he decidable, and others undecidable. Regarding expressive power, we show that probabilities allow its to define a wide variety of new classes of quantitative languages except for discounted-sum automata, where probabilistic choice is no more expressive than nondeterminism. Finally we live ail almost complete picture of the closure of various classes of probabilistic weighted automata for the following, provide, is operations oil quantitative languages: maximum, sum. and numerical complement.","lang":"eng"}],"department":[{"_id":"KrCh"}],"author":[{"last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"first_name":"Laurent","last_name":"Doyen","full_name":"Doyen, Laurent"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724"}],"_id":"3871","type":"conference","file_date_updated":"2020-07-14T12:46:20Z","project":[{"_id":"25F1337C-B435-11E9-9278-68D0E5697425","name":"Design for Embedded Systems","grant_number":"214373","call_identifier":"FP7"},{"call_identifier":"FP7","grant_number":"215543","name":"COMponent-Based Embedded Systems design Techniques","_id":"25EFB36C-B435-11E9-9278-68D0E5697425"}],"date_created":"2018-12-11T12:05:37Z","oa_version":"Submitted Version","pubrep_id":"52","status":"public","volume":5710,"title":"Probabilistic weighted automata","day":"01","scopus_import":1,"publisher":"Springer","date_updated":"2021-01-12T07:52:50Z","publist_id":"2304","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","date_published":"2009-09-01T00:00:00Z","month":"09"},{"day":"12","year":"2009","language":[{"iso":"eng"}],"volume":364,"title":"Analogies in the evolution of individual and social immunity","intvolume":"       364","status":"public","oa_version":"None","date_created":"2018-12-11T12:06:02Z","doi":"10.1098/rstb.2008.0166","citation":{"ama":"Cremer S, Sixt MK. Analogies in the evolution of individual and social immunity. <i>Philosophical Transactions of the Royal Society of London Series B, Biological Sciences</i>. 2009;364(1513):129-142. doi:<a href=\"https://doi.org/10.1098/rstb.2008.0166\">10.1098/rstb.2008.0166</a>","short":"S. Cremer, M.K. Sixt, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 364 (2009) 129–142.","chicago":"Cremer, Sylvia, and Michael K Sixt. “Analogies in the Evolution of Individual and Social Immunity.” <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>. Royal Society, The, 2009. <a href=\"https://doi.org/10.1098/rstb.2008.0166\">https://doi.org/10.1098/rstb.2008.0166</a>.","apa":"Cremer, S., &#38; Sixt, M. K. (2009). Analogies in the evolution of individual and social immunity. <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>. Royal Society, The. <a href=\"https://doi.org/10.1098/rstb.2008.0166\">https://doi.org/10.1098/rstb.2008.0166</a>","mla":"Cremer, Sylvia, and Michael K. Sixt. “Analogies in the Evolution of Individual and Social Immunity.” <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>, vol. 364, no. 1513, Royal Society, The, 2009, pp. 129–42, doi:<a href=\"https://doi.org/10.1098/rstb.2008.0166\">10.1098/rstb.2008.0166</a>.","ieee":"S. Cremer and M. K. Sixt, “Analogies in the evolution of individual and social immunity,” <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>, vol. 364, no. 1513. Royal Society, The, pp. 129–142, 2009.","ista":"Cremer S, Sixt MK. 2009. Analogies in the evolution of individual and social immunity. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 364(1513), 129–142."},"extern":"1","publication":"Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences","_id":"3946","issue":"1513","type":"journal_article","author":[{"last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia","full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868"},{"full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K"}],"abstract":[{"lang":"eng","text":"We compare anti-parasite defences at the level of multicellular organisms and insect societies, and find that selection by parasites at these two organisational levels is often very similar and has created a number of parallel evolutionary solutions in the host's immune response. The defence mechanisms of both individuals and insect colonies start with border defences to prevent parasite intake and are followed by soma defences that prevent the establishment and spread of the parasite between the body's cells or the social insect workers. Lastly, germ line defences are employed to inhibit infection of the reproductive tissue of organisms or the reproductive individuals in colonies. We further find sophisticated self/non-self-recognition systems operating at both levels, which appear to be vital in maintaining the integrity of the body or colony as a reproductive entity. We then expand on the regulation of immune responses and end with a contemplation of how evolution may shape the different immune components, both within and between levels. The aim of this review is to highlight common evolutionary principles acting in disease defence at the level of both individual organisms and societies, thereby linking the fields of physiological and ecological immunology."}],"oa":1,"month":"01","date_published":"2009-01-12T00:00:00Z","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"2181","date_updated":"2021-01-12T07:53:23Z","publisher":"Royal Society, The","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2666697/"}],"page":"129 - 142"},{"year":"2009","language":[{"iso":"eng"}],"has_accepted_license":"1","intvolume":"      5903","quality_controlled":"1","doi":"10.1007/978-3-642-10470-1_4","citation":{"ama":"Edelsbrunner H, Harer J. The persistent Morse complex segmentation of a 3-manifold. In: Vol 5903. Springer; 2009:36-50. doi:<a href=\"https://doi.org/10.1007/978-3-642-10470-1_4\">10.1007/978-3-642-10470-1_4</a>","ista":"Edelsbrunner H, Harer J. 2009. The persistent Morse complex segmentation of a 3-manifold. 3DPH: Modelling the Physiological Human, LNCS, vol. 5903, 36–50.","ieee":"H. Edelsbrunner and J. Harer, “The persistent Morse complex segmentation of a 3-manifold,” presented at the 3DPH: Modelling the Physiological Human, Zermatt, Switzerland, 2009, vol. 5903, pp. 36–50.","mla":"Edelsbrunner, Herbert, and John Harer. <i>The Persistent Morse Complex Segmentation of a 3-Manifold</i>. Vol. 5903, Springer, 2009, pp. 36–50, doi:<a href=\"https://doi.org/10.1007/978-3-642-10470-1_4\">10.1007/978-3-642-10470-1_4</a>.","apa":"Edelsbrunner, H., &#38; Harer, J. (2009). The persistent Morse complex segmentation of a 3-manifold (Vol. 5903, pp. 36–50). Presented at the 3DPH: Modelling the Physiological Human, Zermatt, Switzerland: Springer. <a href=\"https://doi.org/10.1007/978-3-642-10470-1_4\">https://doi.org/10.1007/978-3-642-10470-1_4</a>","chicago":"Edelsbrunner, Herbert, and John Harer. “The Persistent Morse Complex Segmentation of a 3-Manifold,” 5903:36–50. Springer, 2009. <a href=\"https://doi.org/10.1007/978-3-642-10470-1_4\">https://doi.org/10.1007/978-3-642-10470-1_4</a>.","short":"H. Edelsbrunner, J. Harer, in:, Springer, 2009, pp. 36–50."},"acknowledgement":"This research was partially supported by Geomagic, Inc., and by the Defense Advanced Research Projects Agency (DARPA) under grants HR0011-05-1-0007 and HR0011-05-1-0057.","conference":{"end_date":"2009-12-02","start_date":"2009-11-29","location":"Zermatt, Switzerland","name":"3DPH: Modelling the Physiological Human"},"abstract":[{"text":"We describe an algorithm for segmenting three-dimensional medical imaging data modeled as a continuous function on a 3-manifold. It is related to watershed algorithms developed in image processing but is closer to its mathematical roots, which are Morse theory and homological algebra. It allows for the implicit treatment of an underlying mesh, thus combining the structural integrity of its mathematical foundations with the computational efficiency of image processing.","lang":"eng"}],"ddc":["000"],"oa":1,"file":[{"date_updated":"2020-07-14T12:46:21Z","creator":"system","file_size":165090,"checksum":"11fc85bcc19bab1f020e706a4b8a4660","relation":"main_file","file_name":"IST-2016-535-v1+1_2009-P-04-3ManifoldSegmentation.pdf","content_type":"application/pdf","access_level":"open_access","date_created":"2018-12-12T10:08:33Z","file_id":"4694"}],"page":"36 - 50","alternative_title":["LNCS"],"day":"17","title":"The persistent Morse complex segmentation of a 3-manifold","volume":5903,"status":"public","oa_version":"Submitted Version","date_created":"2018-12-11T12:06:10Z","pubrep_id":"535","file_date_updated":"2020-07-14T12:46:21Z","type":"conference","_id":"3968","author":[{"last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert","full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833"},{"full_name":"Harer, John","first_name":"John","last_name":"Harer"}],"department":[{"_id":"HeEd"}],"month":"11","date_published":"2009-11-17T00:00:00Z","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T07:53:32Z","publist_id":"2160","publisher":"Springer","scopus_import":1},{"month":"11","date_published":"2009-11-05T00:00:00Z","article_type":"original","publisher":"University of Chicago Press","date_updated":"2021-01-12T07:54:46Z","publist_id":"1986","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","main_file_link":[{"open_access":"1","url":"https://www.doi.org/10.1086/605958"}],"scopus_import":1,"day":"05","status":"public","volume":174,"title":"Species' range: Adaptation in space and time","_id":"4136","type":"journal_article","issue":"5","article_processing_charge":"No","publication":"American Naturalist","pubrep_id":"552","date_created":"2018-12-11T12:07:09Z","oa_version":"Published Version","department":[{"_id":"NiBa"}],"author":[{"orcid":"0000-0003-0951-3112","full_name":"Polechova, Jitka","last_name":"Polechova","first_name":"Jitka","id":"3BBFB084-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"},{"full_name":"Marion, Glenn","last_name":"Marion","first_name":"Glenn"}],"oa":1,"ddc":["570"],"abstract":[{"text":"Populations living in a spatially and temporally changing environment can adapt to the changing optimum and/or migrate toward favorable habitats. Here we extend previous analyses with a static optimum to allow the environment to vary in time as well as in space. The model follows both population dynamics and the trait mean under stabilizing selection, and the outcomes can be understood by comparing the loads due to genetic variance, dispersal, and temporal change. With fixed genetic variance, we obtain two regimes: (1) adaptation that is uniform along the environmental gradient and that responds to the moving optimum as expected for panmictic populations and when the spatial gradient is sufficiently steep, and (2) a population with limited range that adapts more slowly than the environmental optimum changes in both time and space; the population therefore becomes locally extinct and migrates toward suitable habitat. We also use a population‐genetic model with many loci to allow genetic variance to evolve, and we show that the only solution now has uniform adaptation.","lang":"eng"}],"external_id":{"pmid":[" 19788353"]},"page":"E186 - E204","language":[{"iso":"eng"}],"year":"2009","pmid":1,"intvolume":"       174","citation":{"ama":"Polechova J, Barton NH, Marion G. Species’ range: Adaptation in space and time. <i>American Naturalist</i>. 2009;174(5):E186-E204. doi:<a href=\"https://doi.org/10.1086/605958\">10.1086/605958</a>","mla":"Polechova, Jitka, et al. “Species’ Range: Adaptation in Space and Time.” <i>American Naturalist</i>, vol. 174, no. 5, University of Chicago Press, 2009, pp. E186–204, doi:<a href=\"https://doi.org/10.1086/605958\">10.1086/605958</a>.","ista":"Polechova J, Barton NH, Marion G. 2009. Species’ range: Adaptation in space and time. American Naturalist. 174(5), E186–E204.","ieee":"J. Polechova, N. H. Barton, and G. Marion, “Species’ range: Adaptation in space and time,” <i>American Naturalist</i>, vol. 174, no. 5. University of Chicago Press, pp. E186–E204, 2009.","short":"J. Polechova, N.H. Barton, G. Marion, American Naturalist 174 (2009) E186–E204.","chicago":"Polechova, Jitka, Nicholas H Barton, and Glenn Marion. “Species’ Range: Adaptation in Space and Time.” <i>American Naturalist</i>. University of Chicago Press, 2009. <a href=\"https://doi.org/10.1086/605958\">https://doi.org/10.1086/605958</a>.","apa":"Polechova, J., Barton, N. H., &#38; Marion, G. (2009). Species’ range: Adaptation in space and time. <i>American Naturalist</i>. University of Chicago Press. <a href=\"https://doi.org/10.1086/605958\">https://doi.org/10.1086/605958</a>"},"doi":"10.1086/605958","quality_controlled":"1","related_material":{"link":[{"url":"https://doi.org/10.1086/659642","relation":"erratum"}]}},{"oa_version":"Submitted Version","date_created":"2018-12-11T12:07:48Z","pubrep_id":"551","_id":"4242","type":"journal_article","issue":"5","file_date_updated":"2020-07-14T12:46:25Z","publication":"Evolution; International Journal of Organic Evolution","author":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"},{"full_name":"De Cara, Maria","last_name":"De Cara","first_name":"Maria"}],"department":[{"_id":"NiBa"}],"day":"01","title":"The evolution of strong reproductive isolation","volume":63,"status":"public","scopus_import":1,"date_published":"2009-05-01T00:00:00Z","month":"05","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","publisher":"Wiley","publist_id":"1866","date_updated":"2021-01-12T07:55:33Z","doi":"10.1111/j.1558-5646.2009.00622.x","citation":{"mla":"Barton, Nicholas H., and Maria De Cara. “The Evolution of Strong Reproductive Isolation.” <i>Evolution; International Journal of Organic Evolution</i>, vol. 63, no. 5, Wiley, 2009, pp. 1171–90, doi:<a href=\"https://doi.org/10.1111/j.1558-5646.2009.00622.x\">10.1111/j.1558-5646.2009.00622.x</a>.","ista":"Barton NH, De Cara M. 2009. The evolution of strong reproductive isolation. Evolution; International Journal of Organic Evolution. 63(5), 1171–1190.","ieee":"N. H. Barton and M. De Cara, “The evolution of strong reproductive isolation,” <i>Evolution; International Journal of Organic Evolution</i>, vol. 63, no. 5. Wiley, pp. 1171–1190, 2009.","short":"N.H. Barton, M. De Cara, Evolution; International Journal of Organic Evolution 63 (2009) 1171–1190.","chicago":"Barton, Nicholas H, and Maria De Cara. “The Evolution of Strong Reproductive Isolation.” <i>Evolution; International Journal of Organic Evolution</i>. Wiley, 2009. <a href=\"https://doi.org/10.1111/j.1558-5646.2009.00622.x\">https://doi.org/10.1111/j.1558-5646.2009.00622.x</a>.","apa":"Barton, N. H., &#38; De Cara, M. (2009). The evolution of strong reproductive isolation. <i>Evolution; International Journal of Organic Evolution</i>. Wiley. <a href=\"https://doi.org/10.1111/j.1558-5646.2009.00622.x\">https://doi.org/10.1111/j.1558-5646.2009.00622.x</a>","ama":"Barton NH, De Cara M. The evolution of strong reproductive isolation. <i>Evolution; International Journal of Organic Evolution</i>. 2009;63(5):1171-1190. doi:<a href=\"https://doi.org/10.1111/j.1558-5646.2009.00622.x\">10.1111/j.1558-5646.2009.00622.x</a>"},"quality_controlled":"1","acknowledgement":"This work was supported by a Royal Society/Wolfson Research Merit award, and by a grant from the Natural Environment Research Council.\r\nWe are very grateful for insightful comments from S. P. Otto, and for helpful suggestions from the referees and the Associate Editor, Maria Servedio.","year":"2009","language":[{"iso":"eng"}],"has_accepted_license":"1","intvolume":"        63","page":"1171 - 1190","oa":1,"ddc":["570"],"abstract":[{"lang":"eng","text":"Felsenstein distinguished two ways by which selection can directly strengthen isolation. First, a modifier that strengthens prezygotic isolation can be favored everywhere. This fits with the traditional view of reinforcement as an adaptation to reduce deleterious hybridization by strengthening assortative mating. Second, selection can favor association between different incompatibilities, despite recombination. We generalize this “two allele” model to follow associations among any number of incompatibilities, which may include both assortment and hybrid inviability. Our key argument is that this process, of coupling between incompatibilities, may be quite different from the usual view of reinforcement: strong isolation can evolve through the coupling of any kind of incompatibility, whether prezygotic or postzygotic. Single locus incompatibilities become coupled because associations between them increase the variance in compatibility, which in turn increases mean fitness if there is positive epistasis. Multiple incompatibilities, each maintained by epistasis, can become coupled in the same way. In contrast, a single-locus incompatibility can become coupled with loci that reduce the viability of haploid hybrids because this reduces harmful recombination. We obtain simple approximations for the limits of tight linkage, and strong assortment, and show how assortment alleles can invade through associations with other components of reproductive isolation."}],"file":[{"content_type":"application/pdf","relation":"main_file","file_name":"IST-2016-551-v1+1_BartonDeCaraRevNew.pdf","file_id":"4903","access_level":"open_access","date_created":"2018-12-12T10:11:46Z","date_updated":"2020-07-14T12:46:25Z","file_size":720913,"checksum":"1920d2e25ef335833764256c1a47bbfb","creator":"system"},{"relation":"main_file","file_name":"IST-2016-551-v1+2_BartonDeCaraRevNewSI.pdf","content_type":"application/pdf","access_level":"open_access","date_created":"2018-12-12T10:11:47Z","file_id":"4904","date_updated":"2020-07-14T12:46:25Z","creator":"system","file_size":290160,"checksum":"c1c51bbc10d4f328fc96fc5b0e5dc25d"}]},{"title":"Software transactional memory on relaxed memory models","volume":5643,"intvolume":"      5643","status":"public","day":"19","year":"2009","author":[{"last_name":"Guerraoui","first_name":"Rachid","full_name":"Guerraoui, Rachid"},{"full_name":"Thomas Henzinger","orcid":"0000−0002−2985−7724","last_name":"Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Vasu","id":"4DAE2708-F248-11E8-B48F-1D18A9856A87","last_name":"Singh","full_name":"Vasu Singh"}],"conference":{"name":"CAV: Computer Aided Verification"},"acknowledgement":"This research was supported by the Swiss National Science Foundation.","citation":{"short":"R. Guerraoui, T.A. Henzinger, V. Singh, in:, Springer, 2009, pp. 321–336.","chicago":"Guerraoui, Rachid, Thomas A Henzinger, and Vasu Singh. “Software Transactional Memory on Relaxed Memory Models,” 5643:321–36. Springer, 2009. <a href=\"https://doi.org/10.1007/978-3-642-02658-4_26\">https://doi.org/10.1007/978-3-642-02658-4_26</a>.","apa":"Guerraoui, R., Henzinger, T. A., &#38; Singh, V. (2009). Software transactional memory on relaxed memory models (Vol. 5643, pp. 321–336). Presented at the CAV: Computer Aided Verification, Springer. <a href=\"https://doi.org/10.1007/978-3-642-02658-4_26\">https://doi.org/10.1007/978-3-642-02658-4_26</a>","mla":"Guerraoui, Rachid, et al. <i>Software Transactional Memory on Relaxed Memory Models</i>. Vol. 5643, Springer, 2009, pp. 321–36, doi:<a href=\"https://doi.org/10.1007/978-3-642-02658-4_26\">10.1007/978-3-642-02658-4_26</a>.","ieee":"R. Guerraoui, T. A. Henzinger, and V. Singh, “Software transactional memory on relaxed memory models,” presented at the CAV: Computer Aided Verification, 2009, vol. 5643, pp. 321–336.","ista":"Guerraoui R, Henzinger TA, Singh V. 2009. Software transactional memory on relaxed memory models. CAV: Computer Aided Verification, LNCS, vol. 5643, 321–336.","ama":"Guerraoui R, Henzinger TA, Singh V. Software transactional memory on relaxed memory models. In: Vol 5643. Springer; 2009:321-336. doi:<a href=\"https://doi.org/10.1007/978-3-642-02658-4_26\">10.1007/978-3-642-02658-4_26</a>"},"doi":"10.1007/978-3-642-02658-4_26","quality_controlled":0,"pubrep_id":"45","date_created":"2018-12-11T12:08:34Z","type":"conference","_id":"4383","extern":1,"file_date_updated":"2020-07-14T12:46:28Z","publication_status":"published","publisher":"Springer","publist_id":"1074","date_updated":"2021-01-12T07:56:34Z","oa":1,"abstract":[{"text":"Pseudo-code descriptions of STMs assume sequentially consistent program execution and atomicity of high-level STM operations like read, write, and commit. These assumptions are often violated in realistic settings, as STM implementations run on relaxed memory models, with the atomicity of operations as provided by the hardware. This paper presents the first approach to verify STMs under relaxed memory models with atomicity of 32 bit loads and stores, and read-modify-write operations. We present RML, a new high-level language for expressing concurrent algorithms with a hardware-level atomicity of instructions, and whose semantics is parametrized by various relaxed memory models. We then present our tool, FOIL, which takes as input the RML description of an STM algorithm and the description of a memory model, and automatically determines the locations of fences, which if inserted, ensure the correctness of the STM algorithm under the given memory model. We use FOIL to verify DSTM, TL2, and McRT STM under the memory models of sequential consistency, total store order, partial store order, and relaxed memory order.","lang":"eng"}],"date_published":"2009-06-19T00:00:00Z","month":"06","file":[{"file_id":"5105","access_level":"open_access","date_created":"2018-12-12T10:14:50Z","content_type":"application/pdf","file_name":"IST-2012-45-v1+1_Software_transactional_memory_on_relaxed_memory_models.pdf","relation":"main_file","checksum":"df3c3e6306afd3f630a9146f91642f0a","file_size":265763,"creator":"system","date_updated":"2020-07-14T12:46:28Z"}],"page":"321 - 336","alternative_title":["LNCS"]},{"extern":"1","type":"conference","_id":"4403","quality_controlled":"1","date_created":"2018-12-11T12:08:40Z","oa_version":"Submitted Version","citation":{"short":"R. Alur, P. Cerny, S. Weinstein, in:, Springer, 2009, pp. 86–101.","chicago":"Alur, Rajeev, Pavol Cerny, and Scott Weinstein. “Algorithmic Analysis of Array-Accessing Programs,” 5771:86–101. Springer, 2009. <a href=\"https://doi.org/10.1007/978-3-642-04027-6_9\">https://doi.org/10.1007/978-3-642-04027-6_9</a>.","apa":"Alur, R., Cerny, P., &#38; Weinstein, S. (2009). Algorithmic analysis of array-accessing programs (Vol. 5771, pp. 86–101). Presented at the CSL: Computer Science Logic, Coimbra, Portugal: Springer. <a href=\"https://doi.org/10.1007/978-3-642-04027-6_9\">https://doi.org/10.1007/978-3-642-04027-6_9</a>","mla":"Alur, Rajeev, et al. <i>Algorithmic Analysis of Array-Accessing Programs</i>. Vol. 5771, Springer, 2009, pp. 86–101, doi:<a href=\"https://doi.org/10.1007/978-3-642-04027-6_9\">10.1007/978-3-642-04027-6_9</a>.","ieee":"R. Alur, P. Cerny, and S. Weinstein, “Algorithmic analysis of array-accessing programs,” presented at the CSL: Computer Science Logic, Coimbra, Portugal, 2009, vol. 5771, pp. 86–101.","ista":"Alur R, Cerny P, Weinstein S. 2009. Algorithmic analysis of array-accessing programs. CSL: Computer Science Logic, LNCS, vol. 5771, 86–101.","ama":"Alur R, Cerny P, Weinstein S. Algorithmic analysis of array-accessing programs. In: Vol 5771. Springer; 2009:86-101. doi:<a href=\"https://doi.org/10.1007/978-3-642-04027-6_9\">10.1007/978-3-642-04027-6_9</a>"},"doi":"10.1007/978-3-642-04027-6_9","conference":{"location":"Coimbra, Portugal","start_date":"2009-09-07","end_date":"2009-09-11","name":"CSL: Computer Science Logic"},"author":[{"first_name":"Rajeev","last_name":"Alur","full_name":"Alur, Rajeev"},{"full_name":"Cerny, Pavol","id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87","first_name":"Pavol","last_name":"Cerny"},{"last_name":"Weinstein","first_name":"Scott","full_name":"Weinstein, Scott"}],"related_material":{"record":[{"id":"2967","status":"public","relation":"later_version"}]},"language":[{"iso":"eng"}],"year":"2009","day":"01","status":"public","intvolume":"      5771","volume":5771,"title":"Algorithmic analysis of array-accessing programs","main_file_link":[{"open_access":"1","url":"http://repository.upenn.edu/cis_reports/894/"}],"page":"86 - 101","alternative_title":["LNCS"],"month":"09","date_published":"2009-09-01T00:00:00Z","abstract":[{"lang":"eng","text":"For programs whose data variables range over boolean or finite domains, program verification is decidable, and this forms the basis of recent tools for software model checking. In this paper, we consider algorithmic verification of programs that use boolean variables, and in addition, access a single read-only array whose length is potentially unbounded, and whose elements range over a potentially unbounded data domain. We show that the reachability problem, while undecidable in general, is (1) Pspace-complete for programs in which the array-accessing for-loops are not nested, (2) decidable for a restricted class of programs with doubly-nested loops. The second result establishes connections to automata and logics defining languages over data words."}],"oa":1,"date_updated":"2023-02-23T11:06:20Z","publist_id":"1056","publisher":"Springer","publication_status":"published","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87"},{"abstract":[{"lang":"eng","text":"We present an on-the-fly abstraction technique for infinite-state continuous -time Markov chains. We consider Markov chains that are specified by a finite set of transition classes. Such models naturally represent biochemical reactions and therefore play an important role in the stochastic modeling of biological systems. We approximate the transient probability distributions at various time instances by solving a sequence of dynamically constructed abstract models, each depending on the previous one. Each abstract model is a finite Markov chain that represents the behavior of the original, infinite chain during a specific time interval. Our approach provides complete information about probability distributions, not just about individual parameters like the mean. The error of each abstraction can be computed, and the precision of the abstraction refined when desired. We implemented the algorithm and demonstrate its usefulness and efficiency on several case studies from systems biology."}],"oa":1,"file":[{"file_name":"IST-2012-40-v1+1_Sliding-window_abstraction_for_infinite_markov_chains.pdf","relation":"main_file","content_type":"application/pdf","date_created":"2018-12-12T10:12:20Z","access_level":"open_access","file_id":"4938","date_updated":"2020-07-14T12:46:30Z","creator":"system","file_size":804295,"checksum":"36b974111521ea534aae294166e93a63"}],"month":"01","date_published":"2009-01-01T00:00:00Z","publication_status":"published","date_updated":"2021-01-12T07:57:04Z","publist_id":"278","publisher":"Springer","main_file_link":[{"url":"http://pub.ist.ac.at/%7Etah/Publications/sliding-window_abstraction_for_infinite_markov_chains.pdf","open_access":"0"}],"alternative_title":["LNCS"],"page":"337 - 352","year":"2009","day":"01","volume":5643,"title":"Sliding-window abstraction for infinite Markov chains","status":"public","intvolume":"      5643","date_created":"2018-12-11T12:08:55Z","quality_controlled":0,"pubrep_id":"40","citation":{"ama":"Henzinger TA, Mateescu M, Wolf V. Sliding-window abstraction for infinite Markov chains. In: Vol 5643. Springer; 2009:337-352. doi:<a href=\"https://doi.org/10.1007/978-3-642-02658-4_27\">10.1007/978-3-642-02658-4_27</a>","mla":"Henzinger, Thomas A., et al. <i>Sliding-Window Abstraction for Infinite Markov Chains</i>. Vol. 5643, Springer, 2009, pp. 337–52, doi:<a href=\"https://doi.org/10.1007/978-3-642-02658-4_27\">10.1007/978-3-642-02658-4_27</a>.","ista":"Henzinger TA, Mateescu M, Wolf V. 2009. Sliding-window abstraction for infinite Markov chains. CAV: Computer Aided Verification, LNCS, vol. 5643, 337–352.","ieee":"T. A. Henzinger, M. Mateescu, and V. Wolf, “Sliding-window abstraction for infinite Markov chains,” presented at the CAV: Computer Aided Verification, 2009, vol. 5643, pp. 337–352.","chicago":"Henzinger, Thomas A, Maria Mateescu, and Verena Wolf. “Sliding-Window Abstraction for Infinite Markov Chains,” 5643:337–52. Springer, 2009. <a href=\"https://doi.org/10.1007/978-3-642-02658-4_27\">https://doi.org/10.1007/978-3-642-02658-4_27</a>.","short":"T.A. Henzinger, M. Mateescu, V. Wolf, in:, Springer, 2009, pp. 337–352.","apa":"Henzinger, T. A., Mateescu, M., &#38; Wolf, V. (2009). Sliding-window abstraction for infinite Markov chains (Vol. 5643, pp. 337–352). Presented at the CAV: Computer Aided Verification, Springer. <a href=\"https://doi.org/10.1007/978-3-642-02658-4_27\">https://doi.org/10.1007/978-3-642-02658-4_27</a>"},"doi":"10.1007/978-3-642-02658-4_27","file_date_updated":"2020-07-14T12:46:30Z","extern":1,"type":"conference","_id":"4453","author":[{"orcid":"0000−0002−2985−7724","full_name":"Thomas Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger"},{"first_name":"Maria","id":"3B43276C-F248-11E8-B48F-1D18A9856A87","last_name":"Mateescu","full_name":"Maria Mateescu"},{"full_name":"Wolf, Verena","first_name":"Verena","last_name":"Wolf"}],"acknowledgement":"The research has been partially funded by the Swiss National Science Foundation under grant 205321-111840.","conference":{"name":"CAV: Computer Aided Verification"}},{"file":[{"file_name":"IST-2012-39-v1+1_Alternating_Weighted_Automata.pdf","relation":"main_file","content_type":"application/pdf","date_created":"2018-12-12T10:15:09Z","access_level":"open_access","file_id":"5126","date_updated":"2020-07-14T12:46:31Z","creator":"system","file_size":164428,"checksum":"e8f53abb63579de3f2bff58b2a1188e2"}],"ddc":["004"],"oa":1,"abstract":[{"text":"Weighted automata are finite automata with numerical weights on transitions. Nondeterministic weighted automata define quantitative languages L that assign to each word w a real number L(w) computed as the maximal value of all runs over w, and the value of a run r is a function of the sequence of weights that appear along r. There are several natural functions to consider such as Sup, LimSup, LimInf, limit average, and discounted sum of transition weights.\r\nWe introduce alternating weighted automata in which the transitions of the runs are chosen by two players in a turn-based fashion. Each word is assigned the maximal value of a run that the first player can enforce regardless of the choices made by the second player. We survey the results about closure properties, expressiveness, and decision problems for nondeterministic weighted automata, and we extend these results to alternating weighted automata.\r\nFor quantitative languages L 1 and L 2, we consider the pointwise operations max(L 1,L 2), min(L 1,L 2), 1 − L 1, and the sum L 1 + L 2. We establish the closure properties of all classes of alternating weighted automata with respect to these four operations.\r\nWe next compare the expressive power of the various classes of alternating and nondeterministic weighted automata over infinite words. In particular, for limit average and discounted sum, we show that alternation brings more expressive power than nondeterminism.\r\nFinally, we present decidability results and open questions for the quantitative extension of the classical decision problems in automata theory: emptiness, universality, language inclusion, and language equivalence.","lang":"eng"}],"page":"3 - 13","alternative_title":["LNCS"],"intvolume":"      5699","has_accepted_license":"1","language":[{"iso":"eng"}],"year":"2009","conference":{"name":"FCT: Fundamentals of Computation Theory","location":"Wroclaw, Poland","start_date":"2009-09-02","end_date":"2009-09-04"},"acknowledgement":"This research was supported in part by the Swiss National Science Foundation under the Indo-Swiss Joint Research Programme, by the European Network of Excellence on Embedded Systems Design (ArtistDesign), by the European Combest, Quasimodo, and Gasics projects, by the PAI program Moves funded by the Belgian Federal Government, and by the CFV (Federated Center in Verification) funded by the F.R.S.-FNRS.","doi":"10.1007/978-3-642-03409-1_2","citation":{"apa":"Chatterjee, K., Doyen, L., &#38; Henzinger, T. A. (2009). Alternating weighted automata (Vol. 5699, pp. 3–13). Presented at the FCT: Fundamentals of Computation Theory, Wroclaw, Poland: Springer. <a href=\"https://doi.org/10.1007/978-3-642-03409-1_2\">https://doi.org/10.1007/978-3-642-03409-1_2</a>","chicago":"Chatterjee, Krishnendu, Laurent Doyen, and Thomas A Henzinger. “Alternating Weighted Automata,” 5699:3–13. Springer, 2009. <a href=\"https://doi.org/10.1007/978-3-642-03409-1_2\">https://doi.org/10.1007/978-3-642-03409-1_2</a>.","short":"K. Chatterjee, L. Doyen, T.A. Henzinger, in:, Springer, 2009, pp. 3–13.","ieee":"K. Chatterjee, L. Doyen, and T. A. Henzinger, “Alternating weighted automata,” presented at the FCT: Fundamentals of Computation Theory, Wroclaw, Poland, 2009, vol. 5699, pp. 3–13.","ista":"Chatterjee K, Doyen L, Henzinger TA. 2009. Alternating weighted automata. FCT: Fundamentals of Computation Theory, LNCS, vol. 5699, 3–13.","mla":"Chatterjee, Krishnendu, et al. <i>Alternating Weighted Automata</i>. Vol. 5699, Springer, 2009, pp. 3–13, doi:<a href=\"https://doi.org/10.1007/978-3-642-03409-1_2\">10.1007/978-3-642-03409-1_2</a>.","ama":"Chatterjee K, Doyen L, Henzinger TA. Alternating weighted automata. In: Vol 5699. Springer; 2009:3-13. doi:<a href=\"https://doi.org/10.1007/978-3-642-03409-1_2\">10.1007/978-3-642-03409-1_2</a>"},"ec_funded":1,"quality_controlled":"1","publisher":"Springer","publist_id":"180","date_updated":"2021-01-12T07:59:34Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","month":"09","date_published":"2009-09-10T00:00:00Z","scopus_import":1,"status":"public","volume":5699,"title":"Alternating weighted automata","day":"10","department":[{"_id":"KrCh"}],"author":[{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Doyen, Laurent","last_name":"Doyen","first_name":"Laurent"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"}],"type":"conference","_id":"4542","file_date_updated":"2020-07-14T12:46:31Z","project":[{"_id":"25F1337C-B435-11E9-9278-68D0E5697425","name":"Design for Embedded Systems","call_identifier":"FP7","grant_number":"214373"},{"grant_number":"215543","call_identifier":"FP7","_id":"25EFB36C-B435-11E9-9278-68D0E5697425","name":"COMponent-Based Embedded Systems design Techniques"}],"date_created":"2018-12-11T12:09:23Z","pubrep_id":"39","oa_version":"Submitted Version"},{"day":"01","year":"2009","status":"public","title":"Termination criteria for solving concurrent safety and reachability games","type":"conference","_id":"4544","extern":1,"file_date_updated":"2020-07-14T12:46:31Z","doi":"10.1137/1.9781611973068.23","citation":{"apa":"Chatterjee, K., De Alfaro, L., &#38; Henzinger, T. A. (2009). Termination criteria for solving concurrent safety and reachability games (pp. 197–206). Presented at the SODA: Symposium on Discrete Algorithms, SIAM. <a href=\"https://doi.org/10.1137/1.9781611973068.23\">https://doi.org/10.1137/1.9781611973068.23</a>","chicago":"Chatterjee, Krishnendu, Luca De Alfaro, and Thomas A Henzinger. “Termination Criteria for Solving Concurrent Safety and Reachability Games,” 197–206. SIAM, 2009. <a href=\"https://doi.org/10.1137/1.9781611973068.23\">https://doi.org/10.1137/1.9781611973068.23</a>.","short":"K. Chatterjee, L. De Alfaro, T.A. Henzinger, in:, SIAM, 2009, pp. 197–206.","ista":"Chatterjee K, De Alfaro L, Henzinger TA. 2009. Termination criteria for solving concurrent safety and reachability games. SODA: Symposium on Discrete Algorithms, 197–206.","ieee":"K. Chatterjee, L. De Alfaro, and T. A. Henzinger, “Termination criteria for solving concurrent safety and reachability games,” presented at the SODA: Symposium on Discrete Algorithms, 2009, pp. 197–206.","mla":"Chatterjee, Krishnendu, et al. <i>Termination Criteria for Solving Concurrent Safety and Reachability Games</i>. SIAM, 2009, pp. 197–206, doi:<a href=\"https://doi.org/10.1137/1.9781611973068.23\">10.1137/1.9781611973068.23</a>.","ama":"Chatterjee K, De Alfaro L, Henzinger TA. Termination criteria for solving concurrent safety and reachability games. In: SIAM; 2009:197-206. doi:<a href=\"https://doi.org/10.1137/1.9781611973068.23\">10.1137/1.9781611973068.23</a>"},"quality_controlled":0,"date_created":"2018-12-11T12:09:24Z","pubrep_id":"37","conference":{"name":"SODA: Symposium on Discrete Algorithms"},"author":[{"full_name":"Krishnendu Chatterjee","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee"},{"full_name":"de Alfaro, Luca","first_name":"Luca","last_name":"De Alfaro"},{"orcid":"0000−0002−2985−7724","full_name":"Thomas Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger"}],"month":"01","date_published":"2009-01-01T00:00:00Z","file":[{"date_created":"2018-12-12T10:08:03Z","access_level":"open_access","file_id":"4662","relation":"main_file","file_name":"IST-2012-37-v1+1_Termination_criteria_for_solving_concurrent_safety_and_reachability_games.pdf","content_type":"application/pdf","creator":"system","file_size":212369,"checksum":"ce7dc1667502e26b23c07a767ac41ae6","date_updated":"2020-07-14T12:46:31Z"}],"oa":1,"abstract":[{"text":"We consider concurrent games played on graphs. At every round of a game, each player simultaneously and independently selects a move; the moves jointly determine the transition to a successor state. Two basic objectives are the safety objective to stay forever in a given set of states, and its dual, the reachability objective to reach a given set of states. We present in this paper a strategy improvement algorithm for computing the value of a concurrent safety game, that is, the maximal probability with which player 1 can enforce the safety objective. The algorithm yields a sequence of player-1 strategies which ensure probabilities of winning that converge monotonically to the value of the safety game. Our result is significant because the strategy improvement algorithm provides, for the first time, a way to approximate the value of a concurrent safety game from below. Since a value iteration algorithm, or a strategy improvement algorithm for reachability games, can be used to approximate the same value from above, the combination of both algorithms yields a method for computing a converging sequence of upper and lower bounds for the values of concurrent reachability and safety games. Previous methods could approximate the values of these games only from one direction, and as no rates of convergence are known, they did not provide a practical way to solve these games.","lang":"eng"}],"publisher":"SIAM","publist_id":"176","date_updated":"2021-01-12T07:59:35Z","publication_status":"published","main_file_link":[{"open_access":"1","url":"https://repository.ist.ac.at/id/eprint/37"}],"page":"197 - 206"},{"pubrep_id":"38","oa_version":"Submitted Version","date_created":"2018-12-11T12:09:24Z","project":[{"_id":"25EFB36C-B435-11E9-9278-68D0E5697425","name":"COMponent-Based Embedded Systems design Techniques","call_identifier":"FP7","grant_number":"215543"}],"file_date_updated":"2020-07-14T12:46:31Z","type":"conference","_id":"4545","author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"full_name":"Doyen, Laurent","first_name":"Laurent","last_name":"Doyen"},{"last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724"}],"department":[{"_id":"KrCh"}],"day":"24","title":"A survey of stochastic games with limsup and liminf objectives","volume":5556,"status":"public","scopus_import":1,"date_published":"2009-06-24T00:00:00Z","month":"06","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T07:59:35Z","publist_id":"177","publisher":"Springer","quality_controlled":"1","ec_funded":1,"doi":"10.1007/978-3-642-02930-1_1","citation":{"apa":"Chatterjee, K., Doyen, L., &#38; Henzinger, T. A. (2009). A survey of stochastic games with limsup and liminf objectives (Vol. 5556, pp. 1–15). Presented at the ICALP: Automata, Languages and Programming, Rhodos, Greece: Springer. <a href=\"https://doi.org/10.1007/978-3-642-02930-1_1\">https://doi.org/10.1007/978-3-642-02930-1_1</a>","short":"K. Chatterjee, L. Doyen, T.A. Henzinger, in:, Springer, 2009, pp. 1–15.","chicago":"Chatterjee, Krishnendu, Laurent Doyen, and Thomas A Henzinger. “A Survey of Stochastic Games with Limsup and Liminf Objectives,” 5556:1–15. Springer, 2009. <a href=\"https://doi.org/10.1007/978-3-642-02930-1_1\">https://doi.org/10.1007/978-3-642-02930-1_1</a>.","ista":"Chatterjee K, Doyen L, Henzinger TA. 2009. A survey of stochastic games with limsup and liminf objectives. ICALP: Automata, Languages and Programming, LNCS, vol. 5556, 1–15.","ieee":"K. Chatterjee, L. Doyen, and T. A. Henzinger, “A survey of stochastic games with limsup and liminf objectives,” presented at the ICALP: Automata, Languages and Programming, Rhodos, Greece, 2009, vol. 5556, pp. 1–15.","mla":"Chatterjee, Krishnendu, et al. <i>A Survey of Stochastic Games with Limsup and Liminf Objectives</i>. Vol. 5556, Springer, 2009, pp. 1–15, doi:<a href=\"https://doi.org/10.1007/978-3-642-02930-1_1\">10.1007/978-3-642-02930-1_1</a>.","ama":"Chatterjee K, Doyen L, Henzinger TA. A survey of stochastic games with limsup and liminf objectives. In: Vol 5556. Springer; 2009:1-15. doi:<a href=\"https://doi.org/10.1007/978-3-642-02930-1_1\">10.1007/978-3-642-02930-1_1</a>"},"acknowledgement":"This research was supported in part by the Swiss National Science Foundation under the Indo-Swiss Joint Research Programme, by the European Network of Excellence on Embedded Systems Design (ArtistDesign), by the European projects COMBEST, Quasimodo, Gasics, by the PAI program Moves funded by the Belgian Federal Government, and by the CFV (Federated Center in Verification) funded by the F.R.S.-FNRS.","conference":{"name":"ICALP: Automata, Languages and Programming","location":"Rhodos, Greece","end_date":"2009-07-12","start_date":"2009-07-05"},"year":"2009","language":[{"iso":"eng"}],"has_accepted_license":"1","intvolume":"      5556","alternative_title":["LNCS"],"page":"1 - 15","abstract":[{"text":"A stochastic game is a two-player game played oil a graph, where in each state the successor is chosen either by One of the players, or according to a probability distribution. We Survey Stochastic games with limsup and liminf objectives. A real-valued re-ward is assigned to each state, and the value of all infinite path is the limsup (resp. liminf) of all rewards along the path. The value of a stochastic game is the maximal expected value of an infinite path that call he achieved by resolving the decisions of the first player. We present the complexity of computing values of Stochastic games and their subclasses, and the complexity, of optimal strategies in such games. ","lang":"eng"}],"oa":1,"ddc":["000","005"],"file":[{"file_size":187419,"checksum":"dabb6d24428a000254c95493d9c492e6","creator":"system","date_updated":"2020-07-14T12:46:31Z","file_id":"4992","access_level":"open_access","date_created":"2018-12-12T10:13:11Z","content_type":"application/pdf","relation":"main_file","file_name":"IST-2012-38-v1+1_A_survey_of_stochastic_games_with_limsup_and_liminf_objectives.pdf"}]},{"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"141","date_updated":"2021-01-12T07:59:46Z","publisher":"Springer","month":"06","date_published":"2009-06-19T00:00:00Z","main_file_link":[{"url":"http://arxiv.org/abs/0904.2638","open_access":"1"}],"volume":5643,"title":"Better quality in synthesis through quantitative objectives","status":"public","day":"19","author":[{"last_name":"Bloem","first_name":"Roderick","full_name":"Bloem, Roderick"},{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee"},{"orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger"},{"full_name":"Jobstmann, Barbara","last_name":"Jobstmann","first_name":"Barbara"}],"department":[{"_id":"KrCh"}],"oa_version":"Preprint","date_created":"2018-12-11T12:09:31Z","project":[{"grant_number":"215543","call_identifier":"FP7","_id":"25EFB36C-B435-11E9-9278-68D0E5697425","name":"COMponent-Based Embedded Systems design Techniques"}],"type":"conference","_id":"4569","abstract":[{"text":"Most specification languages express only qualitative constraints. However, among two implementations that satisfy a given specification, one may be preferred to another. For example, if a specification asks that every request is followed by a response, one may prefer an implementation that generates responses quickly but does not generate unnecessary responses. We use quantitative properties to measure the “goodness” of an implementation. Using games with corresponding quantitative objectives, we can synthesize “optimal” implementations, which are preferred among the set of possible implementations that satisfy a given specification.\r\nIn particular, we show how automata with lexicographic mean-payoff conditions can be used to express many interesting quantitative properties for reactive systems. In this framework, the synthesis of optimal implementations requires the solution of lexicographic mean-payoff games (for safety requirements), and the solution of games with both lexicographic mean-payoff and parity objectives (for liveness requirements). We present algorithms for solving both kinds of novel graph games.","lang":"eng"}],"oa":1,"alternative_title":["LNCS"],"page":"140 - 156","external_id":{"arxiv":["0904.2638"]},"intvolume":"      5643","arxiv":1,"year":"2009","language":[{"iso":"eng"}],"acknowledgement":"This research was supported by the Swiss National Science Foundation (Indo-Swiss Research Program and NCCR MICS) and the European Union projects COMBEST and COCONUT.","conference":{"name":"CAV: Computer Aided Verification","location":"Grenoble, France","end_date":"2009-07-02","start_date":"2009-06-26"},"ec_funded":1,"quality_controlled":"1","citation":{"ama":"Bloem R, Chatterjee K, Henzinger TA, Jobstmann B. Better quality in synthesis through quantitative objectives. In: Vol 5643. Springer; 2009:140-156. doi:<a href=\"https://doi.org/10.1007/978-3-642-02658-4_14\">10.1007/978-3-642-02658-4_14</a>","mla":"Bloem, Roderick, et al. <i>Better Quality in Synthesis through Quantitative Objectives</i>. Vol. 5643, Springer, 2009, pp. 140–56, doi:<a href=\"https://doi.org/10.1007/978-3-642-02658-4_14\">10.1007/978-3-642-02658-4_14</a>.","ieee":"R. Bloem, K. Chatterjee, T. A. Henzinger, and B. Jobstmann, “Better quality in synthesis through quantitative objectives,” presented at the CAV: Computer Aided Verification, Grenoble, France, 2009, vol. 5643, pp. 140–156.","ista":"Bloem R, Chatterjee K, Henzinger TA, Jobstmann B. 2009. Better quality in synthesis through quantitative objectives. CAV: Computer Aided Verification, LNCS, vol. 5643, 140–156.","chicago":"Bloem, Roderick, Krishnendu Chatterjee, Thomas A Henzinger, and Barbara Jobstmann. “Better Quality in Synthesis through Quantitative Objectives,” 5643:140–56. Springer, 2009. <a href=\"https://doi.org/10.1007/978-3-642-02658-4_14\">https://doi.org/10.1007/978-3-642-02658-4_14</a>.","short":"R. Bloem, K. Chatterjee, T.A. Henzinger, B. Jobstmann, in:, Springer, 2009, pp. 140–156.","apa":"Bloem, R., Chatterjee, K., Henzinger, T. A., &#38; Jobstmann, B. (2009). Better quality in synthesis through quantitative objectives (Vol. 5643, pp. 140–156). Presented at the CAV: Computer Aided Verification, Grenoble, France: Springer. <a href=\"https://doi.org/10.1007/978-3-642-02658-4_14\">https://doi.org/10.1007/978-3-642-02658-4_14</a>"},"doi":"10.1007/978-3-642-02658-4_14"},{"publication_status":"published","publisher":"Springer","date_updated":"2021-01-12T07:59:52Z","publist_id":"127","oa":1,"abstract":[{"lang":"eng","text":"Alpaga is a solver for two-player parity games with imperfect information. Given the description of a game, it determines whether the first player can ensure to win and, if so, it constructs a winning strategy. The tool provides a symbolic implementation of a recent algorithm based on antichains."}],"date_published":"2009-03-09T00:00:00Z","month":"03","file":[{"date_created":"2018-12-12T10:15:45Z","access_level":"open_access","file_id":"5168","relation":"main_file","file_name":"IST-2012-35-v1+1_Alpaga_-_A_tool_for_solving_parity_games_with_imperfect_information.pdf","content_type":"application/pdf","creator":"system","checksum":"d52b55a10a47b3e3b0e016ea9bf85c41","file_size":212180,"date_updated":"2020-07-14T12:46:32Z"}],"alternative_title":["LNCS"],"page":"58 - 61","main_file_link":[{"url":"https://repository.ist.ac.at/35/","open_access":"1"}],"title":"Alpaga: A tool for solving parity games with imperfect information","volume":5505,"status":"public","intvolume":"      5505","year":"2009","day":"09","author":[{"full_name":"Berwanger, Dietmar","last_name":"Berwanger","first_name":"Dietmar"},{"last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Krishnendu Chatterjee","orcid":"0000-0002-4561-241X"},{"full_name":"De Wulf, Martin","first_name":"Martin","last_name":"De Wulf"},{"first_name":"Laurent","last_name":"Doyen","full_name":"Doyen, Laurent"},{"last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","orcid":"0000−0002−2985−7724","full_name":"Thomas Henzinger"}],"conference":{"name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems"},"doi":"10.1007/978-3-642-00768-2_7","citation":{"ama":"Berwanger D, Chatterjee K, De Wulf M, Doyen L, Henzinger TA. Alpaga: A tool for solving parity games with imperfect information. In: Vol 5505. Springer; 2009:58-61. doi:<a href=\"https://doi.org/10.1007/978-3-642-00768-2_7\">10.1007/978-3-642-00768-2_7</a>","apa":"Berwanger, D., Chatterjee, K., De Wulf, M., Doyen, L., &#38; Henzinger, T. A. (2009). Alpaga: A tool for solving parity games with imperfect information (Vol. 5505, pp. 58–61). Presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, Springer. <a href=\"https://doi.org/10.1007/978-3-642-00768-2_7\">https://doi.org/10.1007/978-3-642-00768-2_7</a>","short":"D. Berwanger, K. Chatterjee, M. De Wulf, L. Doyen, T.A. Henzinger, in:, Springer, 2009, pp. 58–61.","chicago":"Berwanger, Dietmar, Krishnendu Chatterjee, Martin De Wulf, Laurent Doyen, and Thomas A Henzinger. “Alpaga: A Tool for Solving Parity Games with Imperfect Information,” 5505:58–61. Springer, 2009. <a href=\"https://doi.org/10.1007/978-3-642-00768-2_7\">https://doi.org/10.1007/978-3-642-00768-2_7</a>.","ista":"Berwanger D, Chatterjee K, De Wulf M, Doyen L, Henzinger TA. 2009. Alpaga: A tool for solving parity games with imperfect information. TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 5505, 58–61.","ieee":"D. Berwanger, K. Chatterjee, M. De Wulf, L. Doyen, and T. A. Henzinger, “Alpaga: A tool for solving parity games with imperfect information,” presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, 2009, vol. 5505, pp. 58–61.","mla":"Berwanger, Dietmar, et al. <i>Alpaga: A Tool for Solving Parity Games with Imperfect Information</i>. Vol. 5505, Springer, 2009, pp. 58–61, doi:<a href=\"https://doi.org/10.1007/978-3-642-00768-2_7\">10.1007/978-3-642-00768-2_7</a>."},"date_created":"2018-12-11T12:09:35Z","pubrep_id":"35","quality_controlled":0,"type":"conference","_id":"4580","extern":1,"file_date_updated":"2020-07-14T12:46:32Z"}]