--- _id: '4243' abstract: - lang: eng text: We investigate a new model for populations evolving in a spatial continuum. This model can be thought of as a spatial version of the Lambda-Fleming-Viot process. It explicitly incorporates both small scale reproduction events and large scale extinction-recolonisation events. The lineages ancestral to a sample from a population evolving according to this model can be described in terms of a spatial version of the Lambda-coalescent. Using a technique of Evans (1997), we prove existence and uniqueness in law for the model. We then investigate the asymptotic behaviour of the genealogy of a finite number of individuals sampled uniformly at random (or more generally `far enough apart') from a two-dimensional torus of sidelength L as L tends to infinity. Under appropriate conditions (and on a suitable timescale) we can obtain as limiting genealogical processes a Kingman coalescent, a more general Lambda-coalescent or a system of coalescing Brownian motions (with a non-local coalescence mechanism). article_processing_charge: No author: - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Alison full_name: Etheridge, Alison last_name: Etheridge - first_name: Amandine full_name: Véber, Amandine last_name: Véber citation: ama: Barton NH, Etheridge A, Véber A. A new model for evolution in a spatial continuum. Electronic Journal of Probability. 2010;15(7):162-216. doi:10.1214/EJP.v15-741 apa: Barton, N. H., Etheridge, A., & Véber, A. (2010). A new model for evolution in a spatial continuum. Electronic Journal of Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/EJP.v15-741 chicago: Barton, Nicholas H, Alison Etheridge, and Amandine Véber. “A New Model for Evolution in a Spatial Continuum.” Electronic Journal of Probability. Institute of Mathematical Statistics, 2010. https://doi.org/10.1214/EJP.v15-741. ieee: N. H. Barton, A. Etheridge, and A. Véber, “A new model for evolution in a spatial continuum,” Electronic Journal of Probability, vol. 15, no. 7. Institute of Mathematical Statistics, pp. 162–216, 2010. ista: Barton NH, Etheridge A, Véber A. 2010. A new model for evolution in a spatial continuum. Electronic Journal of Probability. 15(7), 162–216. mla: Barton, Nicholas H., et al. “A New Model for Evolution in a Spatial Continuum.” Electronic Journal of Probability, vol. 15, no. 7, Institute of Mathematical Statistics, 2010, pp. 162–216, doi:10.1214/EJP.v15-741. short: N.H. Barton, A. Etheridge, A. Véber, Electronic Journal of Probability 15 (2010) 162–216. date_created: 2018-12-11T12:07:48Z date_published: 2010-02-03T00:00:00Z date_updated: 2025-09-30T09:28:54Z day: '03' ddc: - '576' department: - _id: NiBa doi: 10.1214/EJP.v15-741 external_id: isi: - '000274822400001' file: - access_level: open_access checksum: bab577546dd4e8f882e9a9dd645cd01e content_type: application/pdf creator: system date_created: 2018-12-12T10:15:21Z date_updated: 2020-07-14T12:46:26Z file_id: '5140' file_name: IST-2015-369-v1+1_741-2535-1-PB.pdf file_size: 450171 relation: main_file file_date_updated: 2020-07-14T12:46:26Z fulldoi: https://doi.org/10.1214/EJP.v15-741 has_accepted_license: '1' intvolume: ' 15' isi: 1 issue: '7' language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: 162 - 216 publication: Electronic Journal of Probability publication_status: published publisher: Institute of Mathematical Statistics publist_id: '1863' pubrep_id: '369' quality_controlled: '1' scopus_import: '1' status: public title: A new model for evolution in a spatial continuum 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: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 15 year: '2010' ... --- _id: '3867' abstract: - lang: eng text: Weighted automata are nondeterministic automata with numerical weights on transitions. They can define quantitative languages L that assign to each word w a real number L(w). In the case of infinite words, the value of a run is naturally computed as the maximum, limsup, liminf, limit-average, or discounted-sum of the transition weights. The value of a word w is the supremum of the values of the runs over w. We study expressiveness and closure questions about these quantitative languages. We first show that the set of words with value greater than a threshold can be omega-regular for deterministic limit-average and discounted-sum automata, while this set is always omega-regular when the threshold is isolated (i.e., some neighborhood around the threshold contains no word). In the latter case, we prove that the omega-regular language is robust against small perturbations of the transition weights. We next consider automata with transition weights 0 or 1 and show that they are as expressive as general weighted automata in the limit-average case, but not in the discounted-sum case. Third, for quantitative languages L-1 and L-2, we consider the operations max(L-1, L-2), min(L-1, L-2), and 1 - L-1, which generalize the boolean operations on languages, as well as the sum L-1 + L-2. We establish the closure properties of all classes of quantitative languages with respect to these four operations. 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: Laurent full_name: Doyen, Laurent last_name: Doyen - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 citation: ama: Chatterjee K, Doyen L, Henzinger TA. Expressiveness and closure properties for quantitative languages. Logical Methods in Computer Science. 2010;6(3):1-23. doi:10.2168/LMCS-6(3:10)2010 apa: Chatterjee, K., Doyen, L., & Henzinger, T. A. (2010). Expressiveness and closure properties for quantitative languages. Logical Methods in Computer Science. International Federation for Computational Logic. https://doi.org/10.2168/LMCS-6(3:10)2010 chicago: Chatterjee, Krishnendu, Laurent Doyen, and Thomas A Henzinger. “Expressiveness and Closure Properties for Quantitative Languages.” Logical Methods in Computer Science. International Federation for Computational Logic, 2010. https://doi.org/10.2168/LMCS-6(3:10)2010. ieee: K. Chatterjee, L. Doyen, and T. A. Henzinger, “Expressiveness and closure properties for quantitative languages,” Logical Methods in Computer Science, vol. 6, no. 3. International Federation for Computational Logic, pp. 1–23, 2010. ista: Chatterjee K, Doyen L, Henzinger TA. 2010. Expressiveness and closure properties for quantitative languages. Logical Methods in Computer Science. 6(3), 1–23. mla: Chatterjee, Krishnendu, et al. “Expressiveness and Closure Properties for Quantitative Languages.” Logical Methods in Computer Science, vol. 6, no. 3, International Federation for Computational Logic, 2010, pp. 1–23, doi:10.2168/LMCS-6(3:10)2010. short: K. Chatterjee, L. Doyen, T.A. Henzinger, Logical Methods in Computer Science 6 (2010) 1–23. corr_author: '1' das_tickbox: '1' date_created: 2018-12-11T12:05:36Z date_published: 2010-08-30T00:00:00Z date_updated: 2026-07-06T13:24:40Z day: '30' ddc: - '000' - '004' department: - _id: KrCh - _id: ToHe doi: 10.2168/LMCS-6(3:10)2010 ec_funded: 1 external_id: isi: - '000282653500010' file: - access_level: open_access checksum: 0243da726476817f2ea33b48b78be696 content_type: application/pdf creator: system date_created: 2018-12-12T10:17:54Z date_updated: 2020-07-14T12:46:19Z file_id: '5312' file_name: IST-2012-55-v1+1_Expressiveness_Closure_Properties_Quantitative_Languages.pdf file_size: 216598 relation: main_file - access_level: open_access checksum: 5e512b8503a9cb263de26331c4ee9cf2 content_type: application/pdf creator: system date_created: 2018-12-12T10:17:55Z date_updated: 2020-07-14T12:46:19Z file_id: '5313' file_name: IST-2016-55-v2+1_1007.4018.pdf file_size: 302416 relation: main_file file_date_updated: 2020-07-14T12:46:19Z fulldoi: https://doi.org/10.2168/LMCS-6(3:10)2010 has_accepted_license: '1' intvolume: ' 6' isi: 1 issue: '3' language: - iso: eng month: '08' oa: 1 oa_version: Published Version page: 1 - 23 project: - _id: 25F1337C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '214373' name: Design for Embedded Systems - _id: 25EFB36C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '215543' name: COMponent-Based Embedded Systems design Techniques publication: Logical Methods in Computer Science publication_status: published publisher: International Federation for Computational Logic publist_id: '2311' pubrep_id: '504' quality_controlled: '1' related_material: record: - id: '4540' relation: earlier_version status: public scopus_import: '1' status: public title: Expressiveness and closure properties for quantitative languages tmp: image: /image/cc_by_nd.png legal_code_url: https://creativecommons.org/licenses/by-nd/4.0/legalcode name: Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0) short: CC BY-ND (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 6 year: '2010' ... --- _id: '3868' abstract: - lang: eng text: Simulation and bisimulation metrics for stochastic systems provide a quantitative generalization of the classical simulation and bisimulation relations. These metrics capture the similarity of states with respect to quantitative specifications written in the quantitative mu-calculus and related probabilistic logics. We first show that the metrics provide a bound for the difference in long-run average and discounted average behavior across states, indicating that the metrics can be used both in system verification, and in performance evaluation. For turn-based games and MDPs, we provide a polynomial-time algorithm for the computation of the one-step metric distance between states. The algorithm is based on linear programming; it improves on the previous known exponential-time algorithm based on a reduction to the theory of reals. We then present PSPACE algorithms for both the decision problem and the problem of approximating the metric distance between two states, matching the best known algorithms for Markov chains. For the bisimulation kernel of the metric our algorithm works in time O(n(4)) for both turn-based games and MDPs; improving the previously best known O(n(9).log(n)) time algorithm for MDPs. For a concurrent game G, we show that computing the exact distance be tween states is at least as hard as computing the value of concurrent reachability games and the square-root-sum problem in computational geometry. We show that checking whether the metric distance is bounded by a rational r, can be done via a reduction to the theory of real closed fields, involving a formula with three quantifier alternations, yielding O(vertical bar G vertical bar(O(vertical bar G vertical bar 5))) time complexity, improving the previously known reduction, which yielded O(vertical bar G vertical bar(O(vertical bar G vertical bar 7))) time complexity. These algorithms can be iterated to approximate the metrics using binary search 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: Luca full_name: De Alfaro, Luca last_name: De Alfaro - first_name: Ritankar full_name: Majumdar, Ritankar last_name: Majumdar - first_name: Vishwanath full_name: Raman, Vishwanath last_name: Raman citation: ama: Chatterjee K, De Alfaro L, Majumdar R, Raman V. Algorithms for game metrics. Logical Methods in Computer Science. 2010;6(3):1-27. doi:10.2168/LMCS-6(3:13)2010 apa: Chatterjee, K., De Alfaro, L., Majumdar, R., & Raman, V. (2010). Algorithms for game metrics. Logical Methods in Computer Science. International Federation for Computational Logic. https://doi.org/10.2168/LMCS-6(3:13)2010 chicago: Chatterjee, Krishnendu, Luca De Alfaro, Ritankar Majumdar, and Vishwanath Raman. “Algorithms for Game Metrics.” Logical Methods in Computer Science. International Federation for Computational Logic, 2010. https://doi.org/10.2168/LMCS-6(3:13)2010. ieee: K. Chatterjee, L. De Alfaro, R. Majumdar, and V. Raman, “Algorithms for game metrics,” Logical Methods in Computer Science, vol. 6, no. 3. International Federation for Computational Logic, pp. 1–27, 2010. ista: Chatterjee K, De Alfaro L, Majumdar R, Raman V. 2010. Algorithms for game metrics. Logical Methods in Computer Science. 6(3), 1–27. mla: Chatterjee, Krishnendu, et al. “Algorithms for Game Metrics.” Logical Methods in Computer Science, vol. 6, no. 3, International Federation for Computational Logic, 2010, pp. 1–27, doi:10.2168/LMCS-6(3:13)2010. short: K. Chatterjee, L. De Alfaro, R. Majumdar, V. Raman, Logical Methods in Computer Science 6 (2010) 1–27. corr_author: '1' das_tickbox: '1' date_created: 2018-12-11T12:05:36Z date_published: 2010-09-01T00:00:00Z date_updated: 2026-07-06T13:25:11Z day: '01' ddc: - '000' department: - _id: KrCh doi: 10.2168/LMCS-6(3:13)2010 external_id: isi: - '000282653500013' file: - access_level: open_access checksum: a18988135fef3016c93808ecb15b55f5 content_type: application/pdf creator: system date_created: 2018-12-12T10:08:11Z date_updated: 2020-07-14T12:46:19Z file_id: '4671' file_name: IST-2015-370-v1+1_0809.4326.pdf file_size: 346527 relation: main_file file_date_updated: 2020-07-14T12:46:19Z fulldoi: https://doi.org/10.2168/LMCS-6(3:13)2010 has_accepted_license: '1' intvolume: ' 6' isi: 1 issue: '3' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: 1 - 27 publication: Logical Methods in Computer Science publication_status: published publisher: International Federation for Computational Logic publist_id: '2312' pubrep_id: '370' quality_controlled: '1' related_material: record: - id: '3504' relation: earlier_version status: public scopus_import: '1' status: public title: Algorithms for game metrics tmp: image: /image/cc_by_nd.png legal_code_url: https://creativecommons.org/licenses/by-nd/4.0/legalcode name: Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0) short: CC BY-ND (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 6 year: '2010' ... --- _id: '3782' abstract: - lang: eng text: In cortex surface segmentation, the extracted surface is required to have a particular topology, namely, a two-sphere. We present a new method for removing topology noise of a curve or surface within the level set framework, and thus produce a cortical surface with correct topology. We define a new energy term which quantifies topology noise. We then show how to minimize this term by computing its functional derivative with respect to the level set function. This method differs from existing methods in that it is inherently continuous and not digital; and in the way that our energy directly relates to the topology of the underlying curve or surface, versus existing knot-based measures which are related in a more indirect fashion. The proposed flow is validated empirically. acknowledgement: "Partially supported by the Austri an Science Fund unde r grant P20134-N13.\r\nWe thank Helena Molina-Abril for very helpful discussion. We thank anonymous reviewers for helpful comments." alternative_title: - LNCS article_processing_charge: No author: - first_name: Chao full_name: Chen, Chao id: 3E92416E-F248-11E8-B48F-1D18A9856A87 last_name: Chen - first_name: Daniel full_name: Freedman, Daniel last_name: Freedman citation: ama: 'Chen C, Freedman D. Topology noise removal for curve  and surface evolution. In: Conference Proceedings MCV 2010. Vol 6533. Springer; 2010:31-42. doi:10.1007/978-3-642-18421-5_4' apa: 'Chen, C., & Freedman, D. (2010). Topology noise removal for curve  and surface evolution. In Conference proceedings MCV 2010 (Vol. 6533, pp. 31–42). Beijing, China: Springer. https://doi.org/10.1007/978-3-642-18421-5_4' chicago: Chen, Chao, and Daniel Freedman. “Topology Noise Removal for Curve  and Surface Evolution.” In Conference Proceedings MCV 2010, 6533:31–42. Springer, 2010. https://doi.org/10.1007/978-3-642-18421-5_4. ieee: C. Chen and D. Freedman, “Topology noise removal for curve  and surface evolution,” in Conference proceedings MCV 2010, Beijing, China, 2010, vol. 6533, pp. 31–42. ista: 'Chen C, Freedman D. 2010. Topology noise removal for curve  and surface evolution. Conference proceedings MCV 2010. MCV: Medical Computer Vision, LNCS, vol. 6533, 31–42.' mla: Chen, Chao, and Daniel Freedman. “Topology Noise Removal for Curve  and Surface Evolution.” Conference Proceedings MCV 2010, vol. 6533, Springer, 2010, pp. 31–42, doi:10.1007/978-3-642-18421-5_4. short: C. Chen, D. Freedman, in:, Conference Proceedings MCV 2010, Springer, 2010, pp. 31–42. conference: end_date: 2010-09-20 location: Beijing, China name: 'MCV: Medical Computer Vision' start_date: 2010-09-20 date_created: 2018-12-11T12:05:08Z date_published: 2010-12-31T00:00:00Z date_updated: 2026-07-07T13:07:08Z day: '31' department: - _id: HeEd doi: 10.1007/978-3-642-18421-5_4 fulldoi: https://doi.org/10.1007/978-3-642-18421-5_4 intvolume: ' 6533' language: - iso: eng month: '12' oa_version: None page: 31 - 42 publication: Conference proceedings MCV 2010 publication_status: published publisher: Springer publist_id: '2445' quality_controlled: '1' scopus_import: '1' status: public title: Topology noise removal for curve and surface evolution type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 6533 year: '2010' ... --- OA_place: publisher OA_type: free access _id: '3789' abstract: - lang: eng text: 'The development of multicellular organisms is dependent on the tight coordination between tissue growth and morphogenesis. The stereotypical orientation of cell divisions has been proposed to be a fundamental mechanism by which proliferating and growing tissues take shape. However, the actual contribution of stereotypical division orientation (SDO) to tissue morphogenesis is unclear. In zebrafish, cell divisions with stereotypical orientation have been implicated in both body-axis elongation and neural rod formation [1, 2], although there is little direct evidence for a critical function of SDO in either of these processes. Here we show that SDO is required for formation of the neural rod midline during neurulation but dispensable for elongation of the body axis during gastrulation. Our data indicate that SDO during both gastrulation and neurulation is dependent on the noncanonical Wnt receptor Frizzled 7 (Fz7) and that interfering with cell division orientation leads to severe defects in neural rod midline formation but not body-axis elongation. These findings suggest a novel function for Fz7-controlled cell division orientation in neural rod midline formation during neurulation. ' acknowledgement: "This work was supported by grants from the Fundacion Caja Madrid to E.Q.H. and the Institute of Science and Technology Austria, the Max-Planck-Society, and the Deutsche Forschungsgemeinschaft to C.P.H.\r\nWe are grateful to Jon Clarke, Andy Oates, and Garrett Greenan for reading earlier versions of this manuscript. We thank J. Peychl, H. Ibarra, and P. Pitrone for excellent assistance and advice in multi-photon microscopy and D. White for assistance during the image-processing steps. We also thank D. Panhans for technical assistance, the whole Heisenberg laboratory for useful comments and discussions, and E. Lehmann, J. Hückmann, and G. Junghans for excellent fish care. " article_processing_charge: No article_type: original author: - first_name: Elena full_name: Quesada-Hernández, Elena id: EA35229E-E909-11E9-8DF8-C90C5D5AF86E last_name: Quesada-Hernández - first_name: Luca full_name: Caneparo, Luca last_name: Caneparo - first_name: Sylvia full_name: Schneider, Sylvia id: 1FAC36B0-E90A-11E9-9D2F-EF31CE0C9C2F last_name: Schneider - first_name: Sylke full_name: Winkler, Sylke last_name: Winkler - first_name: Michael full_name: Liebling, Michael last_name: Liebling - first_name: Scott full_name: Fraser, Scott last_name: Fraser - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 citation: ama: Quesada-Hernández E, Caneparo L, Schneider S, et al. Stereotypical cell division orientation controls neural rod midline formation in zebrafish. Current Biology. 2010;20(21):1966-1972. doi:10.1016/j.cub.2010.10.009 apa: Quesada-Hernández, E., Caneparo, L., Schneider, S., Winkler, S., Liebling, M., Fraser, S., & Heisenberg, C.-P. J. (2010). Stereotypical cell division orientation controls neural rod midline formation in zebrafish. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2010.10.009 chicago: Quesada-Hernández, Elena, Luca Caneparo, Sylvia Schneider, Sylke Winkler, Michael Liebling, Scott Fraser, and Carl-Philipp J Heisenberg. “Stereotypical Cell Division Orientation Controls Neural Rod Midline Formation in Zebrafish.” Current Biology. Cell Press, 2010. https://doi.org/10.1016/j.cub.2010.10.009. ieee: E. Quesada-Hernández et al., “Stereotypical cell division orientation controls neural rod midline formation in zebrafish,” Current Biology, vol. 20, no. 21. Cell Press, pp. 1966–1972, 2010. ista: Quesada-Hernández E, Caneparo L, Schneider S, Winkler S, Liebling M, Fraser S, Heisenberg C-PJ. 2010. Stereotypical cell division orientation controls neural rod midline formation in zebrafish. Current Biology. 20(21), 1966–1972. mla: Quesada-Hernández, Elena, et al. “Stereotypical Cell Division Orientation Controls Neural Rod Midline Formation in Zebrafish.” Current Biology, vol. 20, no. 21, Cell Press, 2010, pp. 1966–72, doi:10.1016/j.cub.2010.10.009. short: E. Quesada-Hernández, L. Caneparo, S. Schneider, S. Winkler, M. Liebling, S. Fraser, C.-P.J. Heisenberg, Current Biology 20 (2010) 1966–1972. corr_author: '1' das_tickbox: '1' date_created: 2018-12-11T12:05:11Z date_published: 2010-11-09T00:00:00Z date_updated: 2026-07-28T08:03:47Z day: '09' department: - _id: CaHe doi: 10.1016/j.cub.2010.10.009 external_id: isi: - '000284193900032' fulldoi: https://doi.org/10.1016/j.cub.2010.10.009 intvolume: ' 20' isi: 1 issue: '21' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.cub.2010.10.009 month: '11' oa: 1 oa_version: Published Version page: 1966 - 1972 publication: Current Biology publication_status: published publisher: Cell Press publist_id: '2438' quality_controlled: '1' scopus_import: '1' status: public title: Stereotypical cell division orientation controls neural rod midline formation in zebrafish type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 20 year: '2010' ... --- _id: '4542' abstract: - lang: eng 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." 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. 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: Laurent full_name: Doyen, Laurent last_name: Doyen - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 citation: ama: 'Chatterjee K, Doyen L, Henzinger TA. Alternating weighted automata. In: Vol 5699. Springer; 2009:3-13. doi:10.1007/978-3-642-03409-1_2' apa: 'Chatterjee, K., Doyen, L., & Henzinger, T. A. (2009). Alternating weighted automata (Vol. 5699, pp. 3–13). Presented at the FCT: Fundamentals of Computation Theory, Wroclaw, Poland: Springer. https://doi.org/10.1007/978-3-642-03409-1_2' chicago: Chatterjee, Krishnendu, Laurent Doyen, and Thomas A Henzinger. “Alternating Weighted Automata,” 5699:3–13. Springer, 2009. https://doi.org/10.1007/978-3-642-03409-1_2. 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. Alternating Weighted Automata. Vol. 5699, Springer, 2009, pp. 3–13, doi:10.1007/978-3-642-03409-1_2. short: K. Chatterjee, L. Doyen, T.A. Henzinger, in:, Springer, 2009, pp. 3–13. conference: end_date: 2009-09-04 location: Wroclaw, Poland name: 'FCT: Fundamentals of Computation Theory' start_date: 2009-09-02 corr_author: '1' date_created: 2018-12-11T12:09:23Z date_published: 2009-09-10T00:00:00Z date_updated: 2024-10-09T20:53:55Z day: '10' ddc: - '004' department: - _id: KrCh doi: 10.1007/978-3-642-03409-1_2 ec_funded: 1 file: - access_level: open_access checksum: e8f53abb63579de3f2bff58b2a1188e2 content_type: application/pdf creator: system date_created: 2018-12-12T10:15:09Z date_updated: 2020-07-14T12:46:31Z file_id: '5126' file_name: IST-2012-39-v1+1_Alternating_Weighted_Automata.pdf file_size: 164428 relation: main_file file_date_updated: 2020-07-14T12:46:31Z fulldoi: https://doi.org/10.1007/978-3-642-03409-1_2 has_accepted_license: '1' intvolume: ' 5699' language: - iso: eng month: '09' oa: 1 oa_version: Submitted Version page: 3 - 13 project: - _id: 25F1337C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '214373' name: Design for Embedded Systems - _id: 25EFB36C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '215543' name: COMponent-Based Embedded Systems design Techniques publication_status: published publisher: Springer publist_id: '180' pubrep_id: '39' quality_controlled: '1' scopus_import: 1 status: public title: Alternating weighted automata type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 5699 year: '2009' ... --- _id: '4543' abstract: - lang: eng text: The synthesis of a reactive system with respect to all omega-regular specification requires the solution of a graph game. Such games have been extended in two natural ways. First, a game graph can be equipped with probabilistic choices between alternative transitions, thus allowing the, modeling of uncertain behaviour. These are called stochastic games. Second, a liveness specification can he strengthened to require satisfaction within all unknown but bounded amount of time. These are called finitary objectives. We study. for the first time, the, combination of Stochastic games and finitary objectives. We characterize the requirements on optimal strategies and provide algorithms for Computing the maximal achievable probability of winning stochastic games with finitary parity or Street, objectives. Most notably the set of state's from which a player can win with probability . for a finitary parity objective can he computed in polynomial time even though no polynomial-time algorithm is known in the nonfinitary case. 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), and by the European project Combest. 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: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Florian full_name: Horn, Florian id: 37327ACE-F248-11E8-B48F-1D18A9856A87 last_name: Horn citation: ama: 'Chatterjee K, Henzinger TA, Horn F. Stochastic games with finitary objectives. In: Vol 5734. Springer; 2009:34-54. doi:10.1007/978-3-642-03816-7_4' apa: 'Chatterjee, K., Henzinger, T. A., & Horn, F. (2009). Stochastic games with finitary objectives (Vol. 5734, pp. 34–54). Presented at the MFCS: Mathematical Foundations of Computer Science, High Tatras, Slovakia: Springer. https://doi.org/10.1007/978-3-642-03816-7_4' chicago: Chatterjee, Krishnendu, Thomas A Henzinger, and Florian Horn. “Stochastic Games with Finitary Objectives,” 5734:34–54. Springer, 2009. https://doi.org/10.1007/978-3-642-03816-7_4. ieee: 'K. Chatterjee, T. A. Henzinger, and F. Horn, “Stochastic games with finitary objectives,” presented at the MFCS: Mathematical Foundations of Computer Science, High Tatras, Slovakia, 2009, vol. 5734, pp. 34–54.' ista: 'Chatterjee K, Henzinger TA, Horn F. 2009. Stochastic games with finitary objectives. MFCS: Mathematical Foundations of Computer Science, LNCS, vol. 5734, 34–54.' mla: Chatterjee, Krishnendu, et al. Stochastic Games with Finitary Objectives. Vol. 5734, Springer, 2009, pp. 34–54, doi:10.1007/978-3-642-03816-7_4. short: K. Chatterjee, T.A. Henzinger, F. Horn, in:, Springer, 2009, pp. 34–54. conference: end_date: 2009-08-28 location: High Tatras, Slovakia name: 'MFCS: Mathematical Foundations of Computer Science' start_date: 2009-08-24 corr_author: '1' date_created: 2018-12-11T12:09:24Z date_published: 2009-08-01T00:00:00Z date_updated: 2024-10-09T20:53:54Z day: '01' department: - _id: KrCh doi: 10.1007/978-3-642-03816-7_4 ec_funded: 1 fulldoi: https://doi.org/10.1007/978-3-642-03816-7_4 intvolume: ' 5734' language: - iso: eng month: '08' oa_version: None page: 34 - 54 project: - _id: 25EFB36C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '215543' name: COMponent-Based Embedded Systems design Techniques - _id: 25F1337C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '214373' name: Design for Embedded Systems publication_status: published publisher: Springer publist_id: '178' quality_controlled: '1' scopus_import: 1 status: public title: Stochastic games with finitary objectives type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 5734 year: '2009' ... --- _id: '4545' abstract: - lang: eng 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. ' 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. 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: Laurent full_name: Doyen, Laurent last_name: Doyen - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 citation: 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:10.1007/978-3-642-02930-1_1' apa: 'Chatterjee, K., Doyen, L., & 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. https://doi.org/10.1007/978-3-642-02930-1_1' chicago: Chatterjee, Krishnendu, Laurent Doyen, and Thomas A Henzinger. “A Survey of Stochastic Games with Limsup and Liminf Objectives,” 5556:1–15. Springer, 2009. https://doi.org/10.1007/978-3-642-02930-1_1. 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.' 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.' mla: Chatterjee, Krishnendu, et al. A Survey of Stochastic Games with Limsup and Liminf Objectives. Vol. 5556, Springer, 2009, pp. 1–15, doi:10.1007/978-3-642-02930-1_1. short: K. Chatterjee, L. Doyen, T.A. Henzinger, in:, Springer, 2009, pp. 1–15. conference: end_date: 2009-07-12 location: Rhodos, Greece name: 'ICALP: Automata, Languages and Programming' start_date: 2009-07-05 corr_author: '1' date_created: 2018-12-11T12:09:24Z date_published: 2009-06-24T00:00:00Z date_updated: 2024-10-09T20:53:54Z day: '24' ddc: - '000' - '005' department: - _id: KrCh doi: 10.1007/978-3-642-02930-1_1 ec_funded: 1 file: - access_level: open_access checksum: dabb6d24428a000254c95493d9c492e6 content_type: application/pdf creator: system date_created: 2018-12-12T10:13:11Z date_updated: 2020-07-14T12:46:31Z file_id: '4992' file_name: IST-2012-38-v1+1_A_survey_of_stochastic_games_with_limsup_and_liminf_objectives.pdf file_size: 187419 relation: main_file file_date_updated: 2020-07-14T12:46:31Z fulldoi: https://doi.org/10.1007/978-3-642-02930-1_1 has_accepted_license: '1' intvolume: ' 5556' language: - iso: eng month: '06' oa: 1 oa_version: Submitted Version page: 1 - 15 project: - _id: 25EFB36C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '215543' name: COMponent-Based Embedded Systems design Techniques publication_status: published publisher: Springer publist_id: '177' pubrep_id: '38' quality_controlled: '1' scopus_import: 1 status: public title: A survey of stochastic games with limsup and liminf objectives type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 5556 year: '2009' ... --- _id: '4569' abstract: - lang: eng 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." 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. alternative_title: - LNCS arxiv: 1 author: - first_name: Roderick full_name: Bloem, Roderick last_name: Bloem - 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: Barbara full_name: Jobstmann, Barbara last_name: Jobstmann 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:10.1007/978-3-642-02658-4_14' apa: 'Bloem, R., Chatterjee, K., Henzinger, T. A., & 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. https://doi.org/10.1007/978-3-642-02658-4_14' chicago: Bloem, Roderick, Krishnendu Chatterjee, Thomas A Henzinger, and Barbara Jobstmann. “Better Quality in Synthesis through Quantitative Objectives,” 5643:140–56. Springer, 2009. https://doi.org/10.1007/978-3-642-02658-4_14. 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.' mla: Bloem, Roderick, et al. Better Quality in Synthesis through Quantitative Objectives. Vol. 5643, Springer, 2009, pp. 140–56, doi:10.1007/978-3-642-02658-4_14. short: R. Bloem, K. Chatterjee, T.A. Henzinger, B. Jobstmann, in:, Springer, 2009, pp. 140–156. conference: end_date: 2009-07-02 location: Grenoble, France name: 'CAV: Computer Aided Verification' start_date: 2009-06-26 date_created: 2018-12-11T12:09:31Z date_published: 2009-06-19T00:00:00Z date_updated: 2024-10-21T06:03:07Z day: '19' department: - _id: KrCh doi: 10.1007/978-3-642-02658-4_14 ec_funded: 1 external_id: arxiv: - '0904.2638' fulldoi: https://doi.org/10.1007/978-3-642-02658-4_14 intvolume: ' 5643' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/0904.2638 month: '06' oa: 1 oa_version: Preprint page: 140 - 156 project: - _id: 25EFB36C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '215543' name: COMponent-Based Embedded Systems design Techniques publication_status: published publisher: Springer publist_id: '141' quality_controlled: '1' scopus_import: '1' status: public title: Better quality in synthesis through quantitative objectives type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 5643 year: '2009' ... --- _id: '5392' abstract: - lang: eng text: We consider probabilistic automata on infinite words with acceptance defined by safety, reachability, Büchi, coBüchi and limit-average conditions. We consider quantitative and qualitative decision problems. We present extensions and adaptations of proofs of [GO09] and present a precise characterization of the decidability and undecidability frontier of the quantitative and qualitative decision problems. 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 citation: ama: 'Chatterjee K. Probabilistic Automata on Infinite Words: Decidability and Undecidability Results. IST Austria; 2009. doi:10.15479/AT:IST-2009-0004' apa: 'Chatterjee, K. (2009). Probabilistic automata on infinite words: Decidability and undecidability results. IST Austria. https://doi.org/10.15479/AT:IST-2009-0004' chicago: 'Chatterjee, Krishnendu. Probabilistic Automata on Infinite Words: Decidability and Undecidability Results. IST Austria, 2009. https://doi.org/10.15479/AT:IST-2009-0004.' ieee: 'K. Chatterjee, Probabilistic automata on infinite words: Decidability and undecidability results. IST Austria, 2009.' ista: 'Chatterjee K. 2009. Probabilistic automata on infinite words: Decidability and undecidability results, IST Austria, 17p.' mla: 'Chatterjee, Krishnendu. Probabilistic Automata on Infinite Words: Decidability and Undecidability Results. IST Austria, 2009, doi:10.15479/AT:IST-2009-0004.' short: 'K. Chatterjee, Probabilistic Automata on Infinite Words: Decidability and Undecidability Results, IST Austria, 2009.' corr_author: '1' date_created: 2018-12-12T11:39:04Z date_published: 2009-11-02T00:00:00Z date_updated: 2025-04-14T13:37:25Z day: '02' ddc: - '005' department: - _id: KrCh doi: 10.15479/AT:IST-2009-0004 file: - access_level: open_access checksum: fb7563150231325b00b1718d956f687b content_type: application/pdf creator: system date_created: 2018-12-12T11:54:08Z date_updated: 2020-07-14T12:46:43Z file_id: '5530' file_name: IST-2009-0004_IST-2009-0004.pdf file_size: 311065 relation: main_file file_date_updated: 2020-07-14T12:46:43Z fulldoi: https://doi.org/10.15479/AT:IST-2009-0004 has_accepted_license: '1' language: - iso: eng month: '11' oa: 1 oa_version: Published Version page: '17' publication_identifier: issn: - 2664-1690 publication_status: published publisher: IST Austria pubrep_id: '28' related_material: record: - id: '3857' relation: later_version status: public status: public title: 'Probabilistic automata on infinite words: Decidability and undecidability results' type: technical_report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2009' ... --- _id: '5393' abstract: - lang: eng text: Gist is a tool that (a) solves the qualitative analysis problem of turn-based probabilistic games with ω-regular objectives; and (b) synthesizes reasonable environment assumptions for synthesis of unrealizable specifications. Our tool provides efficient implementations of several reduction based techniques to solve turn-based probabilistic games, and uses the analysis of turn-based probabilistic games for synthesizing environment assumptions for unrealizable specifications. 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: Barbara full_name: Jobstmann, Barbara last_name: Jobstmann - first_name: Arjun full_name: Radhakrishna, Arjun id: 3B51CAC4-F248-11E8-B48F-1D18A9856A87 last_name: Radhakrishna citation: ama: 'Chatterjee K, Henzinger TA, Jobstmann B, Radhakrishna A. Gist: A Solver for Probabilistic Games. IST Austria; 2009. doi:10.15479/AT:IST-2009-0003' apa: 'Chatterjee, K., Henzinger, T. A., Jobstmann, B., & Radhakrishna, A. (2009). Gist: A solver for probabilistic games. IST Austria. https://doi.org/10.15479/AT:IST-2009-0003' chicago: 'Chatterjee, Krishnendu, Thomas A Henzinger, Barbara Jobstmann, and Arjun Radhakrishna. Gist: A Solver for Probabilistic Games. IST Austria, 2009. https://doi.org/10.15479/AT:IST-2009-0003.' ieee: 'K. Chatterjee, T. A. Henzinger, B. Jobstmann, and A. Radhakrishna, Gist: A solver for probabilistic games. IST Austria, 2009.' ista: 'Chatterjee K, Henzinger TA, Jobstmann B, Radhakrishna A. 2009. Gist: A solver for probabilistic games, IST Austria, 12p.' mla: 'Chatterjee, Krishnendu, et al. Gist: A Solver for Probabilistic Games. IST Austria, 2009, doi:10.15479/AT:IST-2009-0003.' short: 'K. Chatterjee, T.A. Henzinger, B. Jobstmann, A. Radhakrishna, Gist: A Solver for Probabilistic Games, IST Austria, 2009.' corr_author: '1' date_created: 2018-12-12T11:39:05Z date_published: 2009-10-09T00:00:00Z date_updated: 2025-04-14T13:37:27Z day: '09' ddc: - '000' - '005' department: - _id: KrCh - _id: ToHe doi: 10.15479/AT:IST-2009-0003 file: - access_level: open_access checksum: 49551ac552915b17593a14c993845274 content_type: application/pdf creator: system date_created: 2018-12-12T11:52:58Z date_updated: 2020-07-14T12:46:43Z file_id: '5459' file_name: IST-2009-0003_IST-2009-0003.pdf file_size: 386866 relation: main_file file_date_updated: 2020-07-14T12:46:43Z fulldoi: https://doi.org/10.15479/AT:IST-2009-0003 has_accepted_license: '1' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: '12' publication_identifier: issn: - 2664-1690 publication_status: published publisher: IST Austria pubrep_id: '29' related_material: record: - id: '4388' relation: later_version status: public status: public title: 'Gist: A solver for probabilistic games' type: technical_report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2009' ... --- _id: '5394' abstract: - lang: eng text: We consider two-player games played on graphs with request-response and finitary Streett objectives. We show these games are PSPACE-hard, improving the previous known NP-hardness. We also improve the lower bounds on memory required by the winning strategies for the players. 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: Florian full_name: Horn, Florian id: 37327ACE-F248-11E8-B48F-1D18A9856A87 last_name: Horn citation: ama: Chatterjee K, Henzinger TA, Horn F. Improved Lower Bounds for Request-Response and Finitary Streett Games. IST Austria; 2009. doi:10.15479/AT:IST-2009-0002 apa: Chatterjee, K., Henzinger, T. A., & Horn, F. (2009). Improved lower bounds for request-response and finitary Streett games. IST Austria. https://doi.org/10.15479/AT:IST-2009-0002 chicago: Chatterjee, Krishnendu, Thomas A Henzinger, and Florian Horn. Improved Lower Bounds for Request-Response and Finitary Streett Games. IST Austria, 2009. https://doi.org/10.15479/AT:IST-2009-0002. ieee: K. Chatterjee, T. A. Henzinger, and F. Horn, Improved lower bounds for request-response and finitary Streett games. IST Austria, 2009. ista: Chatterjee K, Henzinger TA, Horn F. 2009. Improved lower bounds for request-response and finitary Streett games, IST Austria, 11p. mla: Chatterjee, Krishnendu, et al. Improved Lower Bounds for Request-Response and Finitary Streett Games. IST Austria, 2009, doi:10.15479/AT:IST-2009-0002. short: K. Chatterjee, T.A. Henzinger, F. Horn, Improved Lower Bounds for Request-Response and Finitary Streett Games, IST Austria, 2009. corr_author: '1' date_created: 2018-12-12T11:39:05Z date_published: 2009-09-09T00:00:00Z date_updated: 2024-10-09T21:08:23Z day: '09' ddc: - '004' department: - _id: KrCh - _id: ToHe doi: 10.15479/AT:IST-2009-0002 file: - access_level: open_access checksum: 1c50a9723fbae1b2c46d18138968efb3 content_type: application/pdf creator: system date_created: 2018-12-12T11:53:50Z date_updated: 2020-07-14T12:46:43Z file_id: '5511' file_name: IST-2009-0002_IST-2009-0002.pdf file_size: 238091 relation: main_file file_date_updated: 2020-07-14T12:46:43Z fulldoi: https://doi.org/10.15479/AT:IST-2009-0002 has_accepted_license: '1' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: '11' publication_identifier: issn: - 2664-1690 publication_status: published publisher: IST Austria pubrep_id: '30' status: public title: Improved lower bounds for request-response and finitary Streett games type: technical_report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2009' ... --- _id: '5395' abstract: - lang: eng text: 'We study observation-based strategies for partially-observable Markov decision processes (POMDPs) with omega-regular objectives. An observation-based strategy relies on partial information about the history of a play, namely, on the past sequence of observa- tions. We consider the qualitative analysis problem: given a POMDP with an omega-regular objective, whether there is an observation-based strategy to achieve the objective with probability 1 (almost-sure winning), or with positive probability (positive winning). Our main results are twofold. First, we present a complete picture of the computational complexity of the qualitative analysis of POMDPs with parity objectives (a canonical form to express omega-regular objectives) and its subclasses. Our contribution consists in establishing several upper and lower bounds that were not known in literature. Second, we present optimal bounds (matching upper and lower bounds) on the memory required by pure and randomized observation-based strategies for the qualitative analysis of POMDPs with parity objectives and its subclasses.' 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: Laurent full_name: Doyen, Laurent last_name: Doyen - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 citation: ama: Chatterjee K, Doyen L, Henzinger TA. Qualitative Analysis of Partially-Observable Markov Decision Processes. IST Austria; 2009. doi:10.15479/AT:IST-2009-0001 apa: Chatterjee, K., Doyen, L., & Henzinger, T. A. (2009). Qualitative analysis of partially-observable Markov decision processes. IST Austria. https://doi.org/10.15479/AT:IST-2009-0001 chicago: Chatterjee, Krishnendu, Laurent Doyen, and Thomas A Henzinger. Qualitative Analysis of Partially-Observable Markov Decision Processes. IST Austria, 2009. https://doi.org/10.15479/AT:IST-2009-0001. ieee: K. Chatterjee, L. Doyen, and T. A. Henzinger, Qualitative analysis of partially-observable Markov decision processes. IST Austria, 2009. ista: Chatterjee K, Doyen L, Henzinger TA. 2009. Qualitative analysis of partially-observable Markov decision processes, IST Austria, 20p. mla: Chatterjee, Krishnendu, et al. Qualitative Analysis of Partially-Observable Markov Decision Processes. IST Austria, 2009, doi:10.15479/AT:IST-2009-0001. short: K. Chatterjee, L. Doyen, T.A. Henzinger, Qualitative Analysis of Partially-Observable Markov Decision Processes, IST Austria, 2009. corr_author: '1' date_created: 2018-12-12T11:39:05Z date_published: 2009-09-09T00:00:00Z date_updated: 2025-04-14T13:37:25Z day: '09' ddc: - '005' department: - _id: KrCh - _id: ToHe doi: 10.15479/AT:IST-2009-0001 file: - access_level: open_access checksum: 04d9cc065cc19598a4e8631c47f1a562 content_type: application/pdf creator: system date_created: 2018-12-12T11:53:25Z date_updated: 2020-07-14T12:46:43Z file_id: '5486' file_name: IST-2009-0001_IST-2009-0001.pdf file_size: 342088 relation: main_file file_date_updated: 2020-07-14T12:46:43Z fulldoi: https://doi.org/10.15479/AT:IST-2009-0001 has_accepted_license: '1' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: '20' publication_identifier: issn: - 2664-1690 publication_status: published publisher: IST Austria pubrep_id: '31' related_material: record: - id: '3855' relation: later_version status: public status: public title: Qualitative analysis of partially-observable Markov decision processes type: technical_report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2009' ... --- _id: '9453' abstract: - lang: eng text: Parent-of-origin-specific (imprinted) gene expression is regulated in Arabidopsis thaliana endosperm by cytosine demethylation of the maternal genome mediated by the DNA glycosylase DEMETER, but the extent of the methylation changes is not known. Here, we show that virtually the entire endosperm genome is demethylated, coupled with extensive local non-CG hypermethylation of small interfering RNA–targeted sequences. Mutation of DEMETER partially restores endosperm CG methylation to levels found in other tissues, indicating that CG demethylation is specific to maternal sequences. Endosperm demethylation is accompanied by CHH hypermethylation of embryo transposable elements. Our findings demonstrate extensive reconfiguration of the endosperm methylation landscape that likely reinforces transposon silencing in the embryo. article_processing_charge: No article_type: original author: - first_name: Tzung-Fu full_name: Hsieh, Tzung-Fu last_name: Hsieh - first_name: Christian A. full_name: Ibarra, Christian A. last_name: Ibarra - first_name: Pedro full_name: Silva, Pedro last_name: Silva - first_name: Assaf full_name: Zemach, Assaf last_name: Zemach - first_name: Leor full_name: Eshed-Williams, Leor last_name: Eshed-Williams - first_name: Robert L. full_name: Fischer, Robert L. last_name: Fischer - first_name: Daniel full_name: Zilberman, Daniel id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1 last_name: Zilberman orcid: 0000-0002-0123-8649 citation: ama: Hsieh T-F, Ibarra CA, Silva P, et al. Genome-wide demethylation of Arabidopsis endosperm. Science. 2009;324(5933):1451-1454. doi:10.1126/science.1172417 apa: Hsieh, T.-F., Ibarra, C. A., Silva, P., Zemach, A., Eshed-Williams, L., Fischer, R. L., & Zilberman, D. (2009). Genome-wide demethylation of Arabidopsis endosperm. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1172417 chicago: Hsieh, Tzung-Fu, Christian A. Ibarra, Pedro Silva, Assaf Zemach, Leor Eshed-Williams, Robert L. Fischer, and Daniel Zilberman. “Genome-Wide Demethylation of Arabidopsis Endosperm.” Science. American Association for the Advancement of Science, 2009. https://doi.org/10.1126/science.1172417. ieee: T.-F. Hsieh et al., “Genome-wide demethylation of Arabidopsis endosperm,” Science, vol. 324, no. 5933. American Association for the Advancement of Science, pp. 1451–1454, 2009. ista: Hsieh T-F, Ibarra CA, Silva P, Zemach A, Eshed-Williams L, Fischer RL, Zilberman D. 2009. Genome-wide demethylation of Arabidopsis endosperm. Science. 324(5933), 1451–1454. mla: Hsieh, Tzung-Fu, et al. “Genome-Wide Demethylation of Arabidopsis Endosperm.” Science, vol. 324, no. 5933, American Association for the Advancement of Science, 2009, pp. 1451–54, doi:10.1126/science.1172417. short: T.-F. Hsieh, C.A. Ibarra, P. Silva, A. Zemach, L. Eshed-Williams, R.L. Fischer, D. Zilberman, Science 324 (2009) 1451–1454. date_created: 2021-06-04T08:55:41Z date_published: 2009-06-12T00:00:00Z date_updated: 2021-12-14T08:53:26Z day: '12' department: - _id: DaZi doi: 10.1126/science.1172417 extern: '1' external_id: pmid: - '19520962' fulldoi: https://doi.org/10.1126/science.1172417 intvolume: ' 324' issue: '5933' keyword: - Multidisciplinary language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4044190/ month: '06' oa: 1 oa_version: Submitted Version page: 1451-1454 pmid: 1 publication: Science publication_identifier: eissn: - 1095-9203 issn: - 0036-8075 publication_status: published publisher: American Association for the Advancement of Science quality_controlled: '1' scopus_import: '1' status: public title: Genome-wide demethylation of Arabidopsis endosperm type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 324 year: '2009' ... --- _id: '3675' abstract: - lang: eng text: "Sex and recombination have long been seen as adaptations that facilitate natural selection by generating favorable variations. If recombination is to aid selection, there must be negative linkage disequilibria—favorable alleles must be found together less often than expected by chance. These negative linkage disequilibria can be generated directly by selection, but this must involve negative epistasis of just the right strength, which is not expected, from either experiment or theory. Random drift provides a more general source of negative associations: Favorable mutations almost always arise on different genomes, and negative associations tend to persist, precisely because they shield variation from selection.\r\n\r\nWe can understand how recombination aids adaptation by determining the maximum possible rate of adaptation. With unlinked loci, this rate increases only logarithmically with the influx of favorable mutations. With a linear genome, a scaling argument shows that in a large population, the rate of adaptive substitution depends only on the expected rate in the absence of interference, divided by the total rate of recombination. A two-locus approximation predicts an upper bound on the rate of substitution, proportional to recombination rate.\r\n\r\nIf associations between linked loci do impede adaptation, there can be substantial selection for modifiers that increase recombination. Whether this can account for the maintenance of high rates of sex and recombination depends on the extent of selection. It is clear that the rate of species-wide substitutions is typically far too low to generate appreciable selection for recombination. However, local sweeps within a subdivided population may be effective." acknowledgement: Royal Society and the Engineering and Physical Sciences for support (GR/ T11753/01) article_processing_charge: No author: - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: 'Barton NH. Why sex and recombination? In: Cold Spring Harbor Symposia on Quantitative Biology. Vol 74. Cold Spring Harbor Laboratory Press; 2009:187-195. doi:10.1101/sqb.2009.74.030' apa: Barton, N. H. (2009). Why sex and recombination? In Cold Spring Harbor Symposia on Quantitative Biology (Vol. 74, pp. 187–195). Cold Spring Harbor Laboratory Press. https://doi.org/10.1101/sqb.2009.74.030 chicago: Barton, Nicholas H. “Why Sex and Recombination?” In Cold Spring Harbor Symposia on Quantitative Biology, 74:187–95. Cold Spring Harbor Laboratory Press, 2009. https://doi.org/10.1101/sqb.2009.74.030. ieee: N. H. Barton, “Why sex and recombination?,” in Cold Spring Harbor Symposia on Quantitative Biology, vol. 74, Cold Spring Harbor Laboratory Press, 2009, pp. 187–195. ista: 'Barton NH. 2009.Why sex and recombination? In: Cold Spring Harbor Symposia on Quantitative Biology. vol. 74, 187–195.' mla: Barton, Nicholas H. “Why Sex and Recombination?” Cold Spring Harbor Symposia on Quantitative Biology, vol. 74, Cold Spring Harbor Laboratory Press, 2009, pp. 187–95, doi:10.1101/sqb.2009.74.030. short: N.H. Barton, in:, Cold Spring Harbor Symposia on Quantitative Biology, Cold Spring Harbor Laboratory Press, 2009, pp. 187–195. corr_author: '1' date_created: 2018-12-11T12:04:33Z date_published: 2009-11-10T00:00:00Z date_updated: 2025-09-30T09:56:29Z day: '10' department: - _id: NiBa doi: 10.1101/sqb.2009.74.030 external_id: isi: - '000578380600022' fulldoi: https://doi.org/10.1101/sqb.2009.74.030 intvolume: ' 74' isi: 1 language: - iso: eng month: '11' oa_version: None page: 187 - 195 publication: Cold Spring Harbor Symposia on Quantitative Biology publication_status: published publisher: Cold Spring Harbor Laboratory Press publist_id: '2708' quality_controlled: '1' scopus_import: '1' status: public title: Why sex and recombination? type: book_chapter user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 74 year: '2009' ... --- _id: '3775' abstract: - lang: eng 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. 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." article_processing_charge: No author: - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Jason full_name: Coe, Jason last_name: Coe citation: ama: Barton NH, Coe J. On the application of statistical physics to evolutionary biology. Journal of Theoretical Biology. 2009;259(2):317-324. doi:10.1016/j.jtbi.2009.03.019 apa: Barton, N. H., & Coe, J. (2009). On the application of statistical physics to evolutionary biology. Journal of Theoretical Biology. Elsevier. https://doi.org/10.1016/j.jtbi.2009.03.019 chicago: Barton, Nicholas H, and Jason Coe. “On the Application of Statistical Physics to Evolutionary Biology.” Journal of Theoretical Biology. Elsevier, 2009. https://doi.org/10.1016/j.jtbi.2009.03.019. ieee: N. H. Barton and J. Coe, “On the application of statistical physics to evolutionary biology,” Journal of Theoretical Biology, 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.” Journal of Theoretical Biology, vol. 259, no. 2, Elsevier, 2009, pp. 317–24, doi:10.1016/j.jtbi.2009.03.019. short: N.H. Barton, J. Coe, Journal of Theoretical Biology 259 (2009) 317–324. corr_author: '1' date_created: 2018-12-11T12:05:06Z date_published: 2009-07-21T00:00:00Z date_updated: 2025-09-30T09:56:01Z day: '21' department: - _id: NiBa doi: 10.1016/j.jtbi.2009.03.019 external_id: isi: - '000267176100013' fulldoi: https://doi.org/10.1016/j.jtbi.2009.03.019 intvolume: ' 259' isi: 1 issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://hal.archives-ouvertes.fr/hal-00554594/document month: '07' oa: 1 oa_version: Submitted Version page: 317 - 324 publication: Journal of Theoretical Biology publication_status: published publisher: Elsevier publist_id: '2452' quality_controlled: '1' scopus_import: '1' status: public title: On the application of statistical physics to evolutionary biology type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 259 year: '2009' ... --- _id: '3780' 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 (< 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. 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. article_processing_charge: No author: - first_name: Angus full_name: Davison, Angus last_name: Davison - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Bryan full_name: Clarke, Bryan last_name: Clarke 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. Journal of Evolutionary Biology. 2009;22(8):1624-1635. doi:10.1111/j.1420-9101.2009.01770.x' apa: 'Davison, A., Barton, N. H., & 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. Wiley. https://doi.org/10.1111/j.1420-9101.2009.01770.x' 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.” Journal of Evolutionary Biology. Wiley, 2009. https://doi.org/10.1111/j.1420-9101.2009.01770.x.' 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,” Journal of Evolutionary Biology, 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.' 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.” Journal of Evolutionary Biology, vol. 22, no. 8, Wiley, 2009, pp. 1624–35, doi:10.1111/j.1420-9101.2009.01770.x.' short: A. Davison, N.H. Barton, B. Clarke, Journal of Evolutionary Biology 22 (2009) 1624–1635. date_created: 2018-12-11T12:05:08Z date_published: 2009-08-01T00:00:00Z date_updated: 2025-09-30T09:55:32Z day: '01' ddc: - '570' department: - _id: NiBa doi: 10.1111/j.1420-9101.2009.01770.x external_id: isi: - '000268029800006' file: - access_level: open_access checksum: f70c15c6ab9306121d4153a3be0d2346 content_type: application/pdf creator: dernst date_created: 2019-02-22T09:21:44Z date_updated: 2020-07-14T12:46:15Z file_id: '6044' file_name: Davison_JEB_v31_2009.pdf file_size: 2583812 relation: main_file file_date_updated: 2020-07-14T12:46:15Z fulldoi: https://doi.org/10.1111/j.1420-9101.2009.01770.x has_accepted_license: '1' intvolume: ' 22' isi: 1 issue: '8' language: - iso: eng month: '08' oa: 1 oa_version: Submitted Version page: 1624 - 1635 publication: Journal of Evolutionary Biology publication_status: published publisher: Wiley publist_id: '2447' pubrep_id: '553' quality_controlled: '1' scopus_import: '1' status: public 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' type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 22 year: '2009' ... --- _id: '3837' 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. 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. ' author: - first_name: Stavros full_name: Tripakis, Stavros last_name: Tripakis - first_name: Ben full_name: Lickly, Ben last_name: Lickly - 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: Edward full_name: Lee, Edward last_name: Lee citation: ama: 'Tripakis S, Lickly B, Henzinger TA, Lee E. On relational interfaces. In: EMSOFT ’09 Proceedings of the Seventh ACM International Conference on Embedded Software. ACM; 2009:67-76. doi:10.1145/1629335.1629346' apa: 'Tripakis, S., Lickly, B., Henzinger, T. A., & Lee, E. (2009). On relational interfaces. In EMSOFT ’09 Proceedings of the seventh ACM international conference on Embedded software (pp. 67–76). Grenoble, France: ACM. https://doi.org/10.1145/1629335.1629346' chicago: Tripakis, Stavros, Ben Lickly, Thomas A Henzinger, and Edward Lee. “On Relational Interfaces.” In EMSOFT ’09 Proceedings of the Seventh ACM International Conference on Embedded Software, 67–76. ACM, 2009. https://doi.org/10.1145/1629335.1629346. ieee: S. Tripakis, B. Lickly, T. A. Henzinger, and E. Lee, “On relational interfaces,” in EMSOFT ’09 Proceedings of the seventh ACM international conference on Embedded software, 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.” EMSOFT ’09 Proceedings of the Seventh ACM International Conference on Embedded Software, ACM, 2009, pp. 67–76, doi:10.1145/1629335.1629346. 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. conference: end_date: 2009-10-16 location: Grenoble, France name: 'EMSOFT: Embedded Software ' start_date: 2009-10-12 date_created: 2018-12-11T12:05:26Z date_published: 2009-01-01T00:00:00Z date_updated: 2024-10-21T06:03:06Z day: '01' ddc: - '004' department: - _id: ToHe doi: 10.1145/1629335.1629346 ec_funded: 1 file: - access_level: open_access checksum: 3a70e21527dfaad2f198549ae5710786 content_type: application/pdf creator: system date_created: 2018-12-12T10:13:57Z date_updated: 2020-07-14T12:46:16Z file_id: '5045' file_name: IST-2012-70-v1+1_On_Relational_Interfaces.pdf file_size: 310902 relation: main_file file_date_updated: 2020-07-14T12:46:16Z fulldoi: https://doi.org/10.1145/1629335.1629346 has_accepted_license: '1' language: - iso: eng month: '01' oa: 1 oa_version: Submitted Version page: 67 - 76 project: - _id: 25EFB36C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '215543' name: COMponent-Based Embedded Systems design Techniques - _id: 25F1337C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '214373' name: Design for Embedded Systems publication: EMSOFT '09 Proceedings of the seventh ACM international conference on Embedded software publication_status: published publisher: ACM publist_id: '2360' pubrep_id: '70' quality_controlled: '1' scopus_import: '1' status: public title: On relational interfaces type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2009' ... --- _id: '3841' abstract: - lang: eng 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. ' acknowledgement: This research was supported in part by the Excellence Cluster on Multimodal Computing and Interaction and the Swiss National Science Foundation. alternative_title: - LNCS author: - 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: Barbara full_name: Jobstmann, Barbara last_name: Jobstmann - first_name: Verena full_name: Wolf, Verena last_name: Wolf citation: ama: 'Henzinger TA, Jobstmann B, Wolf V. Formalisms for specifying Markovian population models. In: Vol 5797. Springer; 2009:3-23. doi:10.1007/978-3-642-04420-5_2' apa: 'Henzinger, T. A., Jobstmann, B., & Wolf, V. (2009). Formalisms for specifying Markovian population models (Vol. 5797, pp. 3–23). Presented at the RP: Reachability Problems, Palaiseau, France: Springer. https://doi.org/10.1007/978-3-642-04420-5_2' chicago: Henzinger, Thomas A, Barbara Jobstmann, and Verena Wolf. “Formalisms for Specifying Markovian Population Models,” 5797:3–23. Springer, 2009. https://doi.org/10.1007/978-3-642-04420-5_2. 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.' ista: 'Henzinger TA, Jobstmann B, Wolf V. 2009. Formalisms for specifying Markovian population models. RP: Reachability Problems, LNCS, vol. 5797, 3–23.' mla: Henzinger, Thomas A., et al. Formalisms for Specifying Markovian Population Models. Vol. 5797, Springer, 2009, pp. 3–23, doi:10.1007/978-3-642-04420-5_2. short: T.A. Henzinger, B. Jobstmann, V. Wolf, in:, Springer, 2009, pp. 3–23. conference: end_date: 2009-09-25 location: Palaiseau, France name: 'RP: Reachability Problems' start_date: 2009-09-23 date_created: 2018-12-11T12:05:28Z date_published: 2009-09-07T00:00:00Z date_updated: 2025-09-30T08:49:00Z day: '07' ddc: - '005' department: - _id: ToHe doi: 10.1007/978-3-642-04420-5_2 file: - access_level: open_access checksum: df88431872586c773fbcfea37d7b36a2 content_type: application/pdf creator: system date_created: 2018-12-12T10:08:41Z date_updated: 2020-07-14T12:46:16Z file_id: '4702' file_name: IST-2012-67-v1+1_Formalisms_for_specifying_Markovian_population_models.pdf file_size: 222840 relation: main_file file_date_updated: 2020-07-14T12:46:16Z fulldoi: https://doi.org/10.1007/978-3-642-04420-5_2 has_accepted_license: '1' intvolume: ' 5797' language: - iso: eng month: '09' oa: 1 oa_version: Submitted Version page: 3 - 23 publication_status: published publisher: Springer publist_id: '2352' pubrep_id: '67' quality_controlled: '1' related_material: record: - id: '3381' relation: later_version status: public scopus_import: 1 status: public title: Formalisms for specifying Markovian population models type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 5797 year: '2009' ... --- _id: '3843' 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." 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. article_processing_charge: No author: - first_name: Frédéric full_name: Didier, Frédéric last_name: Didier - 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: Maria full_name: Mateescu, Maria id: 3B43276C-F248-11E8-B48F-1D18A9856A87 last_name: Mateescu - first_name: Verena full_name: Wolf, Verena last_name: Wolf citation: 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:10.1109/HiBi.2009.23' apa: 'Didier, F., Henzinger, T. A., Mateescu, M., & 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. https://doi.org/10.1109/HiBi.2009.23' chicago: Didier, Frédéric, Thomas A Henzinger, Maria Mateescu, and Verena Wolf. “Fast Adaptive Uniformization of the Chemical Master Equation,” 4:118–27. IEEE, 2009. https://doi.org/10.1109/HiBi.2009.23. 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. Fast Adaptive Uniformization of the Chemical Master Equation. Vol. 4, no. 6, IEEE, 2009, pp. 118–27, doi:10.1109/HiBi.2009.23. short: F. Didier, T.A. Henzinger, M. Mateescu, V. Wolf, in:, IEEE, 2009, pp. 118–127. conference: end_date: 2009-10-16 location: Trento, Italy name: 'HIBI: High-Performance Computational Systems Biology' start_date: 2009-10-14 date_created: 2018-12-11T12:05:28Z date_published: 2009-10-30T00:00:00Z date_updated: 2025-09-30T09:54:51Z day: '30' ddc: - '000' department: - _id: ToHe - _id: CaGu doi: 10.1109/HiBi.2009.23 external_id: isi: - '000275038300017' file: - access_level: open_access checksum: 9a3bde48f43203991a0b3c6a277c2f5b content_type: application/pdf creator: dernst date_created: 2020-05-19T16:33:55Z date_updated: 2020-07-14T12:46:17Z file_id: '7874' file_name: 2009_HIBI_Didier.pdf file_size: 222890 relation: main_file file_date_updated: 2020-07-14T12:46:17Z fulldoi: https://doi.org/10.1109/HiBi.2009.23 has_accepted_license: '1' intvolume: ' 4' isi: 1 issue: '6' language: - iso: eng month: '10' oa: 1 oa_version: Submitted Version page: 118 - 127 publication_status: published publisher: IEEE publist_id: '2348' quality_controlled: '1' related_material: record: - id: '3842' relation: later_version status: public scopus_import: '1' status: public title: Fast adaptive uniformization of the chemical master equation type: conference user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 4 year: '2009' ...