[{"date_published":"2014-04-01T00:00:00Z","status":"public","publist_id":"7345","publication":"Electronic Proceedings in Theoretical Computer Science, EPTCS","abstract":[{"lang":"eng","text":"First cycle games (FCG) are played on a finite graph by two players who push a token along the edges until a vertex is repeated, and a simple cycle is formed. The winner is determined by some fixed property Y of the sequence of labels of the edges (or nodes) forming this cycle. These games are traditionally of interest because of their connection with infinite-duration games such as parity and mean-payoff games. We study the memory requirements for winning strategies of FCGs and certain associated infinite duration games. We exhibit a simple FCG that is not memoryless determined (this corrects a mistake in Memoryless determinacy of parity and mean payoff games: a simple proof by Bj⋯orklund, Sandberg, Vorobyov (2004) that claims that FCGs for which Y is closed under cyclic permutations are memoryless determined). We show that θ (n)! memory (where n is the number of nodes in the graph), which is always sufficient, may be necessary to win some FCGs. On the other hand, we identify easy to check conditions on Y (i.e., Y is closed under cyclic permutations, and both Y and its complement are closed under concatenation) that are sufficient to ensure that the corresponding FCGs and their associated infinite duration games are memoryless determined. We demonstrate that many games considered in the literature, such as mean-payoff, parity, energy, etc., satisfy these conditions. On the complexity side, we show (for efficiently computable Y) that while solving FCGs is in PSPACE, solving some families of FCGs is PSPACE-hard. "}],"intvolume":"       146","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","date_created":"2018-12-11T11:46:41Z","alternative_title":["EPTCS"],"scopus_import":1,"volume":146,"type":"conference","project":[{"call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23"},{"call_identifier":"FWF","grant_number":"S11402-N23","name":"Moderne Concurrency Paradigms","_id":"25F5A88A-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory"},{"call_identifier":"FP7","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification","_id":"25892FC0-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","department":[{"_id":"KrCh"}],"publisher":"Open Publishing Association","publication_status":"published","page":"83 - 90","pubrep_id":"952","_id":"475","language":[{"iso":"eng"}],"month":"04","file_date_updated":"2020-07-14T12:46:35Z","file":[{"file_name":"IST-2018-952-v1+1_2014_Rubin_First_cycle.pdf","relation":"main_file","checksum":"4d7b4ab82980cca2b96ac7703992a8c8","creator":"system","content_type":"application/pdf","access_level":"open_access","date_created":"2018-12-12T10:17:08Z","date_updated":"2020-07-14T12:46:35Z","file_size":100115,"file_id":"5260"}],"author":[{"last_name":"Aminof","first_name":"Benjamin","id":"4A55BD00-F248-11E8-B48F-1D18A9856A87","full_name":"Aminof, Benjamin"},{"id":"2EC51194-F248-11E8-B48F-1D18A9856A87","first_name":"Sasha","last_name":"Rubin","full_name":"Rubin, Sasha"}],"citation":{"short":"B. Aminof, S. Rubin, in:, Electronic Proceedings in Theoretical Computer Science, EPTCS, Open Publishing Association, 2014, pp. 83–90.","mla":"Aminof, Benjamin, and Sasha Rubin. “First Cycle Games.” <i>Electronic Proceedings in Theoretical Computer Science, EPTCS</i>, vol. 146, Open Publishing Association, 2014, pp. 83–90, doi:<a href=\"https://doi.org/10.4204/EPTCS.146.11\">10.4204/EPTCS.146.11</a>.","chicago":"Aminof, Benjamin, and Sasha Rubin. “First Cycle Games.” In <i>Electronic Proceedings in Theoretical Computer Science, EPTCS</i>, 146:83–90. Open Publishing Association, 2014. <a href=\"https://doi.org/10.4204/EPTCS.146.11\">https://doi.org/10.4204/EPTCS.146.11</a>.","ieee":"B. Aminof and S. Rubin, “First cycle games,” in <i>Electronic Proceedings in Theoretical Computer Science, EPTCS</i>, Grenoble, France, 2014, vol. 146, pp. 83–90.","ista":"Aminof B, Rubin S. 2014. First cycle games. Electronic Proceedings in Theoretical Computer Science, EPTCS. SR: Strategic Reasoning, EPTCS, vol. 146, 83–90.","apa":"Aminof, B., &#38; Rubin, S. (2014). First cycle games. In <i>Electronic Proceedings in Theoretical Computer Science, EPTCS</i> (Vol. 146, pp. 83–90). Grenoble, France: Open Publishing Association. <a href=\"https://doi.org/10.4204/EPTCS.146.11\">https://doi.org/10.4204/EPTCS.146.11</a>","ama":"Aminof B, Rubin S. First cycle games. In: <i>Electronic Proceedings in Theoretical Computer Science, EPTCS</i>. Vol 146. Open Publishing Association; 2014:83-90. doi:<a href=\"https://doi.org/10.4204/EPTCS.146.11\">10.4204/EPTCS.146.11</a>"},"ddc":["004"],"ec_funded":1,"year":"2014","has_accepted_license":"1","conference":{"name":"SR: Strategic Reasoning","location":"Grenoble, France","end_date":"2014-04-06","start_date":"2014-04-05"},"oa":1,"title":"First cycle games","doi":"10.4204/EPTCS.146.11","date_updated":"2021-01-12T08:00:53Z","day":"01"},{"article_type":"original","arxiv":1,"citation":{"ieee":"K. Chatterjee, M. H. Henzinger, S. Krinninger, and D. Nanongkai, “Polynomial-time algorithms for energy games with special weight structures,” <i>Algorithmica</i>, vol. 70, no. 3. Springer, pp. 457–492, 2014.","chicago":"Chatterjee, Krishnendu, Monika H Henzinger, Sebastian Krinninger, and Danupon Nanongkai. “Polynomial-Time Algorithms for Energy Games with Special Weight Structures.” <i>Algorithmica</i>. Springer, 2014. <a href=\"https://doi.org/10.1007/s00453-013-9843-7\">https://doi.org/10.1007/s00453-013-9843-7</a>.","mla":"Chatterjee, Krishnendu, et al. “Polynomial-Time Algorithms for Energy Games with Special Weight Structures.” <i>Algorithmica</i>, vol. 70, no. 3, Springer, 2014, pp. 457–92, doi:<a href=\"https://doi.org/10.1007/s00453-013-9843-7\">10.1007/s00453-013-9843-7</a>.","short":"K. Chatterjee, M.H. Henzinger, S. Krinninger, D. Nanongkai, Algorithmica 70 (2014) 457–492.","ama":"Chatterjee K, Henzinger MH, Krinninger S, Nanongkai D. Polynomial-time algorithms for energy games with special weight structures. <i>Algorithmica</i>. 2014;70(3):457-492. doi:<a href=\"https://doi.org/10.1007/s00453-013-9843-7\">10.1007/s00453-013-9843-7</a>","apa":"Chatterjee, K., Henzinger, M. H., Krinninger, S., &#38; Nanongkai, D. (2014). Polynomial-time algorithms for energy games with special weight structures. <i>Algorithmica</i>. Springer. <a href=\"https://doi.org/10.1007/s00453-013-9843-7\">https://doi.org/10.1007/s00453-013-9843-7</a>","ista":"Chatterjee K, Henzinger MH, Krinninger S, Nanongkai D. 2014. Polynomial-time algorithms for energy games with special weight structures. Algorithmica. 70(3), 457–492."},"month":"11","author":[{"first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H","first_name":"Monika H","last_name":"Henzinger","id":"540c9bbd-f2de-11ec-812d-d04a5be85630"},{"first_name":"Sebastian","last_name":"Krinninger","full_name":"Krinninger, Sebastian"},{"last_name":"Nanongkai","first_name":"Danupon","full_name":"Nanongkai, Danupon"}],"_id":"535","language":[{"iso":"eng"}],"page":"457 - 492","issue":"3","day":"01","date_updated":"2023-09-05T14:09:29Z","title":"Polynomial-time algorithms for energy games with special weight structures","doi":"10.1007/s00453-013-9843-7","external_id":{"arxiv":["1604.08234"]},"oa":1,"article_processing_charge":"No","related_material":{"record":[{"relation":"earlier_version","id":"10905","status":"public"}]},"ec_funded":1,"year":"2014","scopus_import":"1","date_created":"2018-12-11T11:47:01Z","oa_version":"Preprint","user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","intvolume":"        70","abstract":[{"lang":"eng","text":"Energy games belong to a class of turn-based two-player infinite-duration games played on a weighted directed graph. It is one of the rare and intriguing combinatorial problems that lie in NP∩co-NP, but are not known to be in P. The existence of polynomial-time algorithms has been a major open problem for decades and apart from pseudopolynomial algorithms there is no algorithm that solves any non-trivial subclass in polynomial time. In this paper, we give several results based on the weight structures of the graph. First, we identify a notion of penalty and present a polynomial-time algorithm when the penalty is large. Our algorithm is the first polynomial-time algorithm on a large class of weighted graphs. It includes several worst-case instances on which previous algorithms, such as value iteration and random facet algorithms, require at least sub-exponential time. Our main technique is developing the first non-trivial approximation algorithm and showing how to convert it to an exact algorithm. Moreover, we show that in a practical case in verification where weights are clustered around a constant number of values, the energy game problem can be solved in polynomial time. We also show that the problem is still as hard as in general when the clique-width is bounded or the graph is strongly ergodic, suggesting that restricting the graph structure does not necessarily help."}],"status":"public","date_published":"2014-11-01T00:00:00Z","publist_id":"7282","publication":"Algorithmica","publication_status":"published","publisher":"Springer","department":[{"_id":"KrCh"}],"project":[{"call_identifier":"FWF","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","call_identifier":"FWF"},{"name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","call_identifier":"FP7"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"quality_controlled":"1","volume":70,"type":"journal_article","main_file_link":[{"url":"https://arxiv.org/abs/1604.08234","open_access":"1"}]},{"date_created":"2018-12-11T11:47:02Z","scopus_import":1,"oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"intvolume":"         4","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Ecology and Evolution","publist_id":"7280","status":"public","date_published":"2014-07-19T00:00:00Z","abstract":[{"lang":"eng","text":"Transgenerational effects are broader than only parental relationships. Despite mounting evidence that multigenerational effects alter phenotypic and life-history traits, our understanding of how they combine to determine fitness is not well developed because of the added complexity necessary to study them. Here, we derive a quantitative genetic model of adaptation to an extraordinary new environment by an additive genetic component, phenotypic plasticity, maternal and grandmaternal effects. We show how, at equilibrium, negative maternal and negative grandmaternal effects maximize expected population mean fitness. We define negative transgenerational effects as those that have a negative effect on trait expression in the subsequent generation, that is, they slow, or potentially reverse, the expected evolutionary dynamic. When maternal effects are positive, negative grandmaternal effects are preferred. As expected under Mendelian inheritance, the grandmaternal effects have a lower impact on fitness than the maternal effects, but this dual inheritance model predicts a more complex relationship between maternal and grandmaternal effects to constrain phenotypic variance and so maximize expected population mean fitness in the offspring."}],"publisher":"Wiley-Blackwell","publication_status":"published","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"type":"journal_article","volume":4,"ddc":["530","571"],"citation":{"ama":"Prizak R, Ezard T, Hoyle R. Fitness consequences of maternal and grandmaternal effects. <i>Ecology and Evolution</i>. 2014;4(15):3139-3145. doi:<a href=\"https://doi.org/10.1002/ece3.1150\">10.1002/ece3.1150</a>","ista":"Prizak R, Ezard T, Hoyle R. 2014. Fitness consequences of maternal and grandmaternal effects. Ecology and Evolution. 4(15), 3139–3145.","apa":"Prizak, R., Ezard, T., &#38; Hoyle, R. (2014). Fitness consequences of maternal and grandmaternal effects. <i>Ecology and Evolution</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1002/ece3.1150\">https://doi.org/10.1002/ece3.1150</a>","chicago":"Prizak, Roshan, Thomas Ezard, and Rebecca Hoyle. “Fitness Consequences of Maternal and Grandmaternal Effects.” <i>Ecology and Evolution</i>. Wiley-Blackwell, 2014. <a href=\"https://doi.org/10.1002/ece3.1150\">https://doi.org/10.1002/ece3.1150</a>.","ieee":"R. Prizak, T. Ezard, and R. Hoyle, “Fitness consequences of maternal and grandmaternal effects,” <i>Ecology and Evolution</i>, vol. 4, no. 15. Wiley-Blackwell, pp. 3139–3145, 2014.","mla":"Prizak, Roshan, et al. “Fitness Consequences of Maternal and Grandmaternal Effects.” <i>Ecology and Evolution</i>, vol. 4, no. 15, Wiley-Blackwell, 2014, pp. 3139–45, doi:<a href=\"https://doi.org/10.1002/ece3.1150\">10.1002/ece3.1150</a>.","short":"R. Prizak, T. Ezard, R. Hoyle, Ecology and Evolution 4 (2014) 3139–3145."},"file":[{"content_type":"application/pdf","relation":"main_file","file_name":"IST-2018-934-v1+1_Prizak_et_al-2014-Ecology_and_Evolution.pdf","checksum":"e32abf75a248e7a11811fd7f60858769","creator":"system","file_size":621582,"file_id":"4886","access_level":"open_access","date_created":"2018-12-12T10:11:31Z","date_updated":"2020-07-14T12:46:38Z"}],"author":[{"id":"4456104E-F248-11E8-B48F-1D18A9856A87","last_name":"Prizak","first_name":"Roshan","full_name":"Prizak, Roshan"},{"first_name":"Thomas","last_name":"Ezard","full_name":"Ezard, Thomas"},{"last_name":"Hoyle","first_name":"Rebecca","full_name":"Hoyle, Rebecca"}],"file_date_updated":"2020-07-14T12:46:38Z","month":"07","_id":"537","language":[{"iso":"eng"}],"pubrep_id":"934","issue":"15","page":"3139 - 3145","date_updated":"2021-01-12T08:01:30Z","day":"19","doi":"10.1002/ece3.1150","title":"Fitness consequences of maternal and grandmaternal effects","oa":1,"year":"2014","has_accepted_license":"1"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"intvolume":"         4","abstract":[{"text":"As sessile organisms, plants have to be able to adapt to a continuously changing environment. Plants that perceive some of these changes as stress signals activate signaling pathways to modulate their development and to enable them to survive. The complex responses to environmental cues are to a large extent mediated by plant hormones that together orchestrate the final plant response. The phytohormone cytokinin is involved in many plant developmental processes. Recently, it has been established that cytokinin plays an important role in stress responses, but does not act alone. Indeed, the hormonal control of plant development and stress adaptation is the outcome of a complex network of multiple synergistic and antagonistic interactions between various hormones. Here, we review the recent findings on the cytokinin function as part of this hormonal network. We focus on the importance of the crosstalk between cytokinin and other hormones, such as abscisic acid, jasmonate, salicylic acid, ethylene, and auxin in the modulation of plant development and stress adaptation. Finally, the impact of the current research in the biotechnological industry will be discussed.","lang":"eng"}],"date_published":"2013-11-19T00:00:00Z","status":"public","publist_id":"6821","publication":"Frontiers in Plant Science","scopus_import":1,"date_created":"2018-12-11T11:48:43Z","oa_version":"Published Version","volume":4,"type":"journal_article","publication_status":"published","publisher":"Frontiers Research Foundation","department":[{"_id":"EvBe"}],"project":[{"call_identifier":"FP7","_id":"253FCA6A-B435-11E9-9278-68D0E5697425","name":"Hormonal cross-talk in plant organogenesis","grant_number":"207362"}],"quality_controlled":"1","language":[{"iso":"eng"}],"_id":"827","citation":{"ama":"O’Brien J, Benková E. Cytokinin cross talking during biotic and abiotic stress responses. <i>Frontiers in Plant Science</i>. 2013;4. doi:<a href=\"https://doi.org/10.3389/fpls.2013.00451\">10.3389/fpls.2013.00451</a>","apa":"O’Brien, J., &#38; Benková, E. (2013). Cytokinin cross talking during biotic and abiotic stress responses. <i>Frontiers in Plant Science</i>. Frontiers Research Foundation. <a href=\"https://doi.org/10.3389/fpls.2013.00451\">https://doi.org/10.3389/fpls.2013.00451</a>","ista":"O’Brien J, Benková E. 2013. Cytokinin cross talking during biotic and abiotic stress responses. Frontiers in Plant Science. 4, 451.","ieee":"J. O’Brien and E. Benková, “Cytokinin cross talking during biotic and abiotic stress responses,” <i>Frontiers in Plant Science</i>, vol. 4. Frontiers Research Foundation, 2013.","chicago":"O’Brien, José, and Eva Benková. “Cytokinin Cross Talking during Biotic and Abiotic Stress Responses.” <i>Frontiers in Plant Science</i>. Frontiers Research Foundation, 2013. <a href=\"https://doi.org/10.3389/fpls.2013.00451\">https://doi.org/10.3389/fpls.2013.00451</a>.","short":"J. O’Brien, E. Benková, Frontiers in Plant Science 4 (2013).","mla":"O’Brien, José, and Eva Benková. “Cytokinin Cross Talking during Biotic and Abiotic Stress Responses.” <i>Frontiers in Plant Science</i>, vol. 4, 451, Frontiers Research Foundation, 2013, doi:<a href=\"https://doi.org/10.3389/fpls.2013.00451\">10.3389/fpls.2013.00451</a>."},"ddc":["580"],"file_date_updated":"2020-07-14T12:48:11Z","article_number":"451","month":"11","author":[{"full_name":"O'Brien, José","last_name":"O'Brien","first_name":"José"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková","first_name":"Eva","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva"}],"file":[{"relation":"main_file","file_name":"2013_FrontiersPlant_OBrien.pdf","creator":"dernst","checksum":"fdc25ddd1bf9a99b99f662cdbafeddd4","content_type":"application/pdf","access_level":"open_access","date_updated":"2020-07-14T12:48:11Z","date_created":"2019-01-31T10:40:38Z","file_size":953299,"file_id":"5903"}],"oa":1,"has_accepted_license":"1","ec_funded":1,"year":"2013","day":"19","date_updated":"2021-01-12T08:17:50Z","title":"Cytokinin cross talking during biotic and abiotic stress responses","doi":"10.3389/fpls.2013.00451"},{"oa_version":"Published Version","date_created":"2018-12-11T11:48:43Z","scopus_import":1,"publication":"Frontiers in Plant Science","publist_id":"6820","status":"public","date_published":"2013-12-26T00:00:00Z","abstract":[{"lang":"eng","text":"The plant root system is essential for providing anchorage to the soil, supplying minerals and water, and synthesizing metabolites. It is a dynamic organ modulated by external cues such as environmental signals, water and nutrients availability, salinity and others. Lateral roots (LRs) are initiated from the primary root post-embryonically, after which they progress through discrete developmental stages which can be independently controlled, providing a high level of plasticity during root system formation. Within this review, main contributions are presented, from the classical forward genetic screens to the more recent high-throughput approaches, combined with computer model predictions, dissecting how LRs and thereby root system architecture is established and developed."}],"intvolume":"         4","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","project":[{"name":"Hormonal cross-talk in plant organogenesis","_id":"253FCA6A-B435-11E9-9278-68D0E5697425","grant_number":"207362","call_identifier":"FP7"}],"department":[{"_id":"EvBe"}],"publisher":"Frontiers Research Foundation","publication_status":"published","type":"journal_article","volume":4,"file":[{"relation":"main_file","file_name":"2013_FrontiersPlant_Cuesta.pdf","checksum":"0185b3c4d7df9a94bd3ce5a66d213506","creator":"dernst","content_type":"application/pdf","access_level":"open_access","date_created":"2019-01-31T10:36:43Z","date_updated":"2020-07-14T12:48:11Z","file_size":710835,"file_id":"5902"}],"author":[{"orcid":"0000-0003-1923-2410","full_name":"Cuesta, Candela","id":"33A3C818-F248-11E8-B48F-1D18A9856A87","first_name":"Candela","last_name":"Cuesta"},{"full_name":"Wabnik, Krzysztof T","orcid":"0000-0001-7263-0560","id":"4DE369A4-F248-11E8-B48F-1D18A9856A87","last_name":"Wabnik","first_name":"Krzysztof T"},{"orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","last_name":"Benková"}],"article_number":"537","month":"12","file_date_updated":"2020-07-14T12:48:11Z","ddc":["580"],"citation":{"ama":"Cuesta C, Wabnik KT, Benková E. Systems approaches to study root architecture dynamics. <i>Frontiers in Plant Science</i>. 2013;4. doi:<a href=\"https://doi.org/10.3389/fpls.2013.00537\">10.3389/fpls.2013.00537</a>","apa":"Cuesta, C., Wabnik, K. T., &#38; Benková, E. (2013). Systems approaches to study root architecture dynamics. <i>Frontiers in Plant Science</i>. Frontiers Research Foundation. <a href=\"https://doi.org/10.3389/fpls.2013.00537\">https://doi.org/10.3389/fpls.2013.00537</a>","ista":"Cuesta C, Wabnik KT, Benková E. 2013. Systems approaches to study root architecture dynamics. Frontiers in Plant Science. 4, 537.","ieee":"C. Cuesta, K. T. Wabnik, and E. Benková, “Systems approaches to study root architecture dynamics,” <i>Frontiers in Plant Science</i>, vol. 4. Frontiers Research Foundation, 2013.","chicago":"Cuesta, Candela, Krzysztof T Wabnik, and Eva Benková. “Systems Approaches to Study Root Architecture Dynamics.” <i>Frontiers in Plant Science</i>. Frontiers Research Foundation, 2013. <a href=\"https://doi.org/10.3389/fpls.2013.00537\">https://doi.org/10.3389/fpls.2013.00537</a>.","mla":"Cuesta, Candela, et al. “Systems Approaches to Study Root Architecture Dynamics.” <i>Frontiers in Plant Science</i>, vol. 4, 537, Frontiers Research Foundation, 2013, doi:<a href=\"https://doi.org/10.3389/fpls.2013.00537\">10.3389/fpls.2013.00537</a>.","short":"C. Cuesta, K.T. Wabnik, E. Benková, Frontiers in Plant Science 4 (2013)."},"language":[{"iso":"eng"}],"_id":"828","doi":"10.3389/fpls.2013.00537","title":"Systems approaches to study root architecture dynamics","date_updated":"2021-01-12T08:17:52Z","day":"26","ec_funded":1,"year":"2013","has_accepted_license":"1","oa":1},{"date_updated":"2023-09-07T11:40:43Z","day":"01","external_id":{"arxiv":["1303.5251"]},"title":"TTP: Tool for tumor progression","doi":"10.1007/978-3-642-39799-8_6","oa":1,"year":"2013","ec_funded":1,"series_title":"Lecture Notes in Computer Science","related_material":{"record":[{"id":"5399","relation":"earlier_version","status":"public"},{"status":"public","id":"1400","relation":"dissertation_contains"}]},"conference":{"end_date":"2013-07-19","start_date":"2013-07-13","name":"CAV: Computer Aided Verification","location":"St. Petersburg, Russia"},"citation":{"chicago":"Reiter, Johannes, Ivana Božić, Krishnendu Chatterjee, and Martin Nowak. “TTP: Tool for Tumor Progression.” In <i>Proceedings of 25th Int. Conf. on Computer Aided Verification</i>, 8044:101–6. Lecture Notes in Computer Science. Springer, 2013. <a href=\"https://doi.org/10.1007/978-3-642-39799-8_6\">https://doi.org/10.1007/978-3-642-39799-8_6</a>.","ieee":"J. Reiter, I. Božić, K. Chatterjee, and M. Nowak, “TTP: Tool for tumor progression,” in <i>Proceedings of 25th Int. Conf. on Computer Aided Verification</i>, St. Petersburg, Russia, 2013, vol. 8044, pp. 101–106.","short":"J. Reiter, I. Božić, K. Chatterjee, M. Nowak, in:, Proceedings of 25th Int. Conf. on Computer Aided Verification, Springer, 2013, pp. 101–106.","mla":"Reiter, Johannes, et al. “TTP: Tool for Tumor Progression.” <i>Proceedings of 25th Int. Conf. on Computer Aided Verification</i>, vol. 8044, Springer, 2013, pp. 101–06, doi:<a href=\"https://doi.org/10.1007/978-3-642-39799-8_6\">10.1007/978-3-642-39799-8_6</a>.","ama":"Reiter J, Božić I, Chatterjee K, Nowak M. TTP: Tool for tumor progression. In: <i>Proceedings of 25th Int. Conf. on Computer Aided Verification</i>. Vol 8044. Lecture Notes in Computer Science. Springer; 2013:101-106. doi:<a href=\"https://doi.org/10.1007/978-3-642-39799-8_6\">10.1007/978-3-642-39799-8_6</a>","ista":"Reiter J, Božić I, Chatterjee K, Nowak M. 2013. TTP: Tool for tumor progression. Proceedings of 25th Int. Conf. on Computer Aided Verification. CAV: Computer Aided VerificationLecture Notes in Computer Science, LNCS, vol. 8044, 101–106.","apa":"Reiter, J., Božić, I., Chatterjee, K., &#38; Nowak, M. (2013). TTP: Tool for tumor progression. In <i>Proceedings of 25th Int. Conf. on Computer Aided Verification</i> (Vol. 8044, pp. 101–106). St. Petersburg, Russia: Springer. <a href=\"https://doi.org/10.1007/978-3-642-39799-8_6\">https://doi.org/10.1007/978-3-642-39799-8_6</a>"},"arxiv":1,"month":"01","author":[{"full_name":"Reiter, Johannes","orcid":"0000-0002-0170-7353","id":"4A918E98-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes","last_name":"Reiter"},{"full_name":"Božić, Ivana","last_name":"Božić","first_name":"Ivana"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"last_name":"Nowak","first_name":"Martin","full_name":"Nowak, Martin"}],"_id":"2000","language":[{"iso":"eng"}],"page":"101 - 106","publisher":"Springer","publication_status":"published","project":[{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","call_identifier":"FWF"},{"call_identifier":"FWF","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","department":[{"_id":"KrCh"}],"volume":8044,"type":"conference","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1303.5251"}],"date_created":"2018-12-11T11:55:08Z","alternative_title":["LNCS"],"scopus_import":1,"oa_version":"Preprint","intvolume":"      8044","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2013-01-01T00:00:00Z","status":"public","publist_id":"5077","publication":"Proceedings of 25th Int. Conf. on Computer Aided Verification","abstract":[{"lang":"eng","text":"In this work we present a flexible tool for tumor progression, which simulates the evolutionary dynamics of cancer. Tumor progression implements a multi-type branching process where the key parameters are the fitness landscape, the mutation rate, and the average time of cell division. The fitness of a cancer cell depends on the mutations it has accumulated. The input to our tool could be any fitness landscape, mutation rate, and cell division time, and the tool produces the growth dynamics and all relevant statistics."}]},{"year":"2013","main_file_link":[{"url":"http://repository.cmu.edu/jpc/vol5/iss1/6","open_access":"1"}],"article_processing_charge":"No","oa":1,"type":"journal_article","volume":5,"quality_controlled":"1","doi":"10.29012/jpc.v5i1.629","title":"Privacy-preserving data sharing for genome-wide association studies","department":[{"_id":"CaUh"}],"date_updated":"2021-01-12T06:54:41Z","publisher":"Carnegie Mellon University","day":"01","publication_status":"published","publication":"Journal of Privacy and Confidentiality ","issue":"1","publist_id":"5067","date_published":"2013-08-01T00:00:00Z","status":"public","page":"137 - 166","abstract":[{"text":"Traditional statistical methods for confidentiality protection of statistical databases do not scale well to deal with GWAS databases especially in terms of guarantees regarding protection from linkage to external information. The more recent concept of differential privacy, introduced by the cryptographic community, is an approach which provides a rigorous definition of privacy with meaningful privacy guarantees in the presence of arbitrary external information, although the guarantees may come at a serious price in terms of data utility. Building on such notions, we propose new methods to release aggregate GWAS data without compromising an individual’s privacy. We present methods for releasing differentially private minor allele frequencies, chi-square statistics and p-values. We compare these approaches on simulated data and on a GWAS study of canine hair length involving 685 dogs. We also propose a privacy-preserving method for finding genome-wide associations based on a differentially-private approach to penalized logistic regression.","lang":"eng"}],"language":[{"iso":"eng"}],"_id":"2009","intvolume":"         5","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","last_name":"Uhler","first_name":"Caroline","orcid":"0000-0002-7008-0216","full_name":"Uhler, Caroline"},{"first_name":"Aleksandra","last_name":"Slavkovic","full_name":"Slavkovic, Aleksandra"},{"full_name":"Fienberg, Stephen","last_name":"Fienberg","first_name":"Stephen"}],"oa_version":"Published Version","month":"08","citation":{"ama":"Uhler C, Slavkovic A, Fienberg S. Privacy-preserving data sharing for genome-wide association studies. <i>Journal of Privacy and Confidentiality </i>. 2013;5(1):137-166. doi:<a href=\"https://doi.org/10.29012/jpc.v5i1.629\">10.29012/jpc.v5i1.629</a>","ista":"Uhler C, Slavkovic A, Fienberg S. 2013. Privacy-preserving data sharing for genome-wide association studies. Journal of Privacy and Confidentiality . 5(1), 137–166.","apa":"Uhler, C., Slavkovic, A., &#38; Fienberg, S. (2013). Privacy-preserving data sharing for genome-wide association studies. <i>Journal of Privacy and Confidentiality </i>. Carnegie Mellon University. <a href=\"https://doi.org/10.29012/jpc.v5i1.629\">https://doi.org/10.29012/jpc.v5i1.629</a>","chicago":"Uhler, Caroline, Aleksandra Slavkovic, and Stephen Fienberg. “Privacy-Preserving Data Sharing for Genome-Wide Association Studies.” <i>Journal of Privacy and Confidentiality </i>. Carnegie Mellon University, 2013. <a href=\"https://doi.org/10.29012/jpc.v5i1.629\">https://doi.org/10.29012/jpc.v5i1.629</a>.","ieee":"C. Uhler, A. Slavkovic, and S. Fienberg, “Privacy-preserving data sharing for genome-wide association studies,” <i>Journal of Privacy and Confidentiality </i>, vol. 5, no. 1. Carnegie Mellon University, pp. 137–166, 2013.","short":"C. Uhler, A. Slavkovic, S. Fienberg, Journal of Privacy and Confidentiality  5 (2013) 137–166.","mla":"Uhler, Caroline, et al. “Privacy-Preserving Data Sharing for Genome-Wide Association Studies.” <i>Journal of Privacy and Confidentiality </i>, vol. 5, no. 1, Carnegie Mellon University, 2013, pp. 137–66, doi:<a href=\"https://doi.org/10.29012/jpc.v5i1.629\">10.29012/jpc.v5i1.629</a>."},"date_created":"2018-12-11T11:55:11Z"},{"external_id":{"arxiv":["1207.0547"]},"title":"Geometry of the faithfulness assumption in causal inference","doi":"10.1214/12-AOS1080","date_updated":"2021-01-12T06:54:42Z","day":"01","year":"2013","oa":1,"month":"04","author":[{"full_name":"Uhler, Caroline","orcid":"0000-0002-7008-0216","last_name":"Uhler","first_name":"Caroline","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Raskutti, Garvesh","first_name":"Garvesh","last_name":"Raskutti"},{"first_name":"Peter","last_name":"Bühlmann","full_name":"Bühlmann, Peter"},{"last_name":"Yu","first_name":"Bin","full_name":"Yu, Bin"}],"citation":{"ieee":"C. Uhler, G. Raskutti, P. Bühlmann, and B. Yu, “Geometry of the faithfulness assumption in causal inference,” <i>The Annals of Statistics</i>, vol. 41, no. 2. Institute of Mathematical Statistics, pp. 436–463, 2013.","chicago":"Uhler, Caroline, Garvesh Raskutti, Peter Bühlmann, and Bin Yu. “Geometry of the Faithfulness Assumption in Causal Inference.” <i>The Annals of Statistics</i>. Institute of Mathematical Statistics, 2013. <a href=\"https://doi.org/10.1214/12-AOS1080\">https://doi.org/10.1214/12-AOS1080</a>.","mla":"Uhler, Caroline, et al. “Geometry of the Faithfulness Assumption in Causal Inference.” <i>The Annals of Statistics</i>, vol. 41, no. 2, Institute of Mathematical Statistics, 2013, pp. 436–63, doi:<a href=\"https://doi.org/10.1214/12-AOS1080\">10.1214/12-AOS1080</a>.","short":"C. Uhler, G. Raskutti, P. Bühlmann, B. Yu, The Annals of Statistics 41 (2013) 436–463.","ama":"Uhler C, Raskutti G, Bühlmann P, Yu B. Geometry of the faithfulness assumption in causal inference. <i>The Annals of Statistics</i>. 2013;41(2):436-463. doi:<a href=\"https://doi.org/10.1214/12-AOS1080\">10.1214/12-AOS1080</a>","apa":"Uhler, C., Raskutti, G., Bühlmann, P., &#38; Yu, B. (2013). Geometry of the faithfulness assumption in causal inference. <i>The Annals of Statistics</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/12-AOS1080\">https://doi.org/10.1214/12-AOS1080</a>","ista":"Uhler C, Raskutti G, Bühlmann P, Yu B. 2013. Geometry of the faithfulness assumption in causal inference. The Annals of Statistics. 41(2), 436–463."},"arxiv":1,"issue":"2","page":"436 - 463","_id":"2010","language":[{"iso":"eng"}],"quality_controlled":"1","department":[{"_id":"CaUh"}],"publisher":"Institute of Mathematical Statistics","publication_status":"published","main_file_link":[{"url":"www.doi.org/10.1214/12-AOS1080","open_access":"1"}],"volume":41,"type":"journal_article","oa_version":"Published Version","date_created":"2018-12-11T11:55:11Z","scopus_import":1,"date_published":"2013-04-01T00:00:00Z","status":"public","publist_id":"5066","publication":"The Annals of Statistics","abstract":[{"text":"Many algorithms for inferring causality rely heavily on the faithfulness assumption. The main justification for imposing this assumption is that the set of unfaithful distributions has Lebesgue measure zero, since it can be seen as a collection of hypersurfaces in a hypercube. However, due to sampling error the faithfulness condition alone is not sufficient for statistical estimation, and strong-faithfulness has been proposed and assumed to achieve uniform or high-dimensional consistency. In contrast to the plain faithfulness assumption, the set of distributions that is not strong-faithful has nonzero Lebesgue measure and in fact, can be surprisingly large as we show in this paper. We study the strong-faithfulness condition from a geometric and combinatorial point of view and give upper and lower bounds on the Lebesgue measure of strong-faithful distributions for various classes of directed acyclic graphs. Our results imply fundamental limitations for the PC-algorithm and potentially also for other algorithms based on partial correlation testing in the Gaussian case.","lang":"eng"}],"intvolume":"        41","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"pubrep_id":"624","_id":"1374","language":[{"iso":"eng"}],"page":"181 - 196","ddc":["000"],"citation":{"ieee":"K. Chatterjee and N. Fijalkow, “Infinite-state games with finitary conditions,” in <i>22nd EACSL Annual Conference on Computer Science Logic</i>, Torino, Italy, 2013, vol. 23, pp. 181–196.","chicago":"Chatterjee, Krishnendu, and Nathanaël Fijalkow. “Infinite-State Games with Finitary Conditions.” In <i>22nd EACSL Annual Conference on Computer Science Logic</i>, 23:181–96. Leibniz International Proceedings in Informatics. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2013. <a href=\"https://doi.org/10.4230/LIPIcs.CSL.2013.181\">https://doi.org/10.4230/LIPIcs.CSL.2013.181</a>.","short":"K. Chatterjee, N. Fijalkow, in:, 22nd EACSL Annual Conference on Computer Science Logic, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2013, pp. 181–196.","mla":"Chatterjee, Krishnendu, and Nathanaël Fijalkow. “Infinite-State Games with Finitary Conditions.” <i>22nd EACSL Annual Conference on Computer Science Logic</i>, vol. 23, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2013, pp. 181–96, doi:<a href=\"https://doi.org/10.4230/LIPIcs.CSL.2013.181\">10.4230/LIPIcs.CSL.2013.181</a>.","ama":"Chatterjee K, Fijalkow N. Infinite-state games with finitary conditions. In: <i>22nd EACSL Annual Conference on Computer Science Logic</i>. Vol 23. Leibniz International Proceedings in Informatics. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2013:181-196. doi:<a href=\"https://doi.org/10.4230/LIPIcs.CSL.2013.181\">10.4230/LIPIcs.CSL.2013.181</a>","apa":"Chatterjee, K., &#38; Fijalkow, N. (2013). Infinite-state games with finitary conditions. In <i>22nd EACSL Annual Conference on Computer Science Logic</i> (Vol. 23, pp. 181–196). Torino, Italy: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.CSL.2013.181\">https://doi.org/10.4230/LIPIcs.CSL.2013.181</a>","ista":"Chatterjee K, Fijalkow N. 2013. Infinite-state games with finitary conditions. 22nd EACSL Annual Conference on Computer Science Logic. CSL: Computer Science LogicLeibniz International Proceedings in Informatics, LIPIcs, vol. 23, 181–196."},"file":[{"relation":"main_file","file_name":"IST-2016-624-v1+1_ChKr_Infinite-state_games_2013_17.pdf","checksum":"b7091a3866db573c0db5ec486952255e","creator":"system","content_type":"application/pdf","access_level":"open_access","date_created":"2018-12-12T10:13:38Z","date_updated":"2020-07-14T12:44:47Z","file_size":547296,"file_id":"5023"}],"author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"full_name":"Fijalkow, Nathanaël","first_name":"Nathanaël","last_name":"Fijalkow"}],"file_date_updated":"2020-07-14T12:44:47Z","month":"09","oa":1,"conference":{"name":"CSL: Computer Science Logic","location":"Torino, Italy","end_date":"2013-09-05","start_date":"203-09-02"},"has_accepted_license":"1","series_title":"Leibniz International Proceedings in Informatics","year":"2013","ec_funded":1,"day":"01","date_updated":"2021-01-12T06:50:14Z","doi":"10.4230/LIPIcs.CSL.2013.181","title":"Infinite-state games with finitary conditions","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"        23","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"abstract":[{"text":"We study two-player zero-sum games over infinite-state graphs equipped with ωB and finitary conditions. Our first contribution is about the strategy complexity, i.e the memory required for winning strategies: we prove that over general infinite-state graphs, memoryless strategies are sufficient for finitary Büchi, and finite-memory suffices for finitary parity games. We then study pushdown games with boundedness conditions, with two contributions. First we prove a collapse result for pushdown games with ωB-conditions, implying the decidability of solving these games. Second we consider pushdown games with finitary parity along with stack boundedness conditions, and show that solving these games is EXPTIME-complete.","lang":"eng"}],"publication":"22nd EACSL Annual Conference on Computer Science Logic","publist_id":"5837","status":"public","date_published":"2013-09-01T00:00:00Z","scopus_import":1,"alternative_title":["LIPIcs"],"date_created":"2018-12-11T11:51:39Z","oa_version":"Published Version","type":"conference","volume":23,"publication_status":"published","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"KrCh"}],"quality_controlled":"1","project":[{"grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF"},{"call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","grant_number":"S11407"},{"call_identifier":"FP7","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}]},{"type":"conference","conference":{"location":"Portland, OR, United States","name":"FMCAD: Formal Methods in Computer-Aided Design","start_date":"2013-10-20","end_date":"2013-10-23"},"related_material":{"record":[{"status":"public","id":"5406","relation":"earlier_version"}]},"ec_funded":1,"year":"2013","day":"11","publication_status":"published","date_updated":"2023-02-23T12:24:53Z","publisher":"IEEE","doi":"10.1109/FMCAD.2013.6679386","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"title":"Distributed synthesis for LTL fragments","quality_controlled":"1","project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","call_identifier":"FWF"},{"call_identifier":"FWF","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","grant_number":"267989","call_identifier":"FP7"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1376","language":[{"iso":"eng"}],"page":"18 - 25","abstract":[{"lang":"eng","text":"We consider the distributed synthesis problem for temporal logic specifications. Traditionally, the problem has been studied for LTL, and the previous results show that the problem is decidable iff there is no information fork in the architecture. We consider the problem for fragments of LTL and our main results are as follows: (1) We show that the problem is undecidable for architectures with information forks even for the fragment of LTL with temporal operators restricted to next and eventually. (2) For specifications restricted to globally along with non-nested next operators, we establish decidability (in EXPSPACE) for star architectures where the processes receive disjoint inputs, whereas we establish undecidability for architectures containing an information fork-meet structure. (3) Finally, we consider LTL without the next operator, and establish decidability (NEXPTIME-complete) for all architectures for a fragment that consists of a set of safety assumptions, and a set of guarantees where each guarantee is a safety, reachability, or liveness condition."}],"publication":"13th International Conference on Formal Methods in Computer-Aided Design","publist_id":"5835","date_published":"2013-12-11T00:00:00Z","status":"public","citation":{"mla":"Chatterjee, Krishnendu, et al. “Distributed Synthesis for LTL Fragments.” <i>13th International Conference on Formal Methods in Computer-Aided Design</i>, IEEE, 2013, pp. 18–25, doi:<a href=\"https://doi.org/10.1109/FMCAD.2013.6679386\">10.1109/FMCAD.2013.6679386</a>.","short":"K. Chatterjee, T.A. Henzinger, J. Otop, A. Pavlogiannis, in:, 13th International Conference on Formal Methods in Computer-Aided Design, IEEE, 2013, pp. 18–25.","ieee":"K. Chatterjee, T. A. Henzinger, J. Otop, and A. Pavlogiannis, “Distributed synthesis for LTL fragments,” in <i>13th International Conference on Formal Methods in Computer-Aided Design</i>, Portland, OR, United States, 2013, pp. 18–25.","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, Jan Otop, and Andreas Pavlogiannis. “Distributed Synthesis for LTL Fragments.” In <i>13th International Conference on Formal Methods in Computer-Aided Design</i>, 18–25. IEEE, 2013. <a href=\"https://doi.org/10.1109/FMCAD.2013.6679386\">https://doi.org/10.1109/FMCAD.2013.6679386</a>.","apa":"Chatterjee, K., Henzinger, T. A., Otop, J., &#38; Pavlogiannis, A. (2013). Distributed synthesis for LTL fragments. In <i>13th International Conference on Formal Methods in Computer-Aided Design</i> (pp. 18–25). Portland, OR, United States: IEEE. <a href=\"https://doi.org/10.1109/FMCAD.2013.6679386\">https://doi.org/10.1109/FMCAD.2013.6679386</a>","ista":"Chatterjee K, Henzinger TA, Otop J, Pavlogiannis A. 2013. Distributed synthesis for LTL fragments. 13th International Conference on Formal Methods in Computer-Aided Design. FMCAD: Formal Methods in Computer-Aided Design, 18–25.","ama":"Chatterjee K, Henzinger TA, Otop J, Pavlogiannis A. Distributed synthesis for LTL fragments. In: <i>13th International Conference on Formal Methods in Computer-Aided Design</i>. IEEE; 2013:18-25. doi:<a href=\"https://doi.org/10.1109/FMCAD.2013.6679386\">10.1109/FMCAD.2013.6679386</a>"},"date_created":"2018-12-11T11:51:40Z","oa_version":"None","author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"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":"Otop, Jan","first_name":"Jan","last_name":"Otop","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87"},{"id":"49704004-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas","last_name":"Pavlogiannis","full_name":"Pavlogiannis, Andreas","orcid":"0000-0002-8943-0722"}],"month":"12"},{"external_id":{"arxiv":["1308.4767"]},"doi":"10.1109/FMCAD.2013.6679394","title":"Synthesizing multiple boolean functions using interpolation on a single proof","date_updated":"2021-01-12T06:50:19Z","day":"11","ec_funded":1,"year":"2013","conference":{"end_date":"2013-10-23","start_date":"2013-10-20","name":"FMCAD: Formal Methods in Computer-Aided Design","location":"Portland, OR, United States"},"oa":1,"author":[{"full_name":"Hofferek, Georg","first_name":"Georg","last_name":"Hofferek"},{"id":"335E5684-F248-11E8-B48F-1D18A9856A87","first_name":"Ashutosh","last_name":"Gupta","full_name":"Gupta, Ashutosh"},{"first_name":"Bettina","last_name":"Könighofer","full_name":"Könighofer, Bettina"},{"full_name":"Jiang, Jie","last_name":"Jiang","first_name":"Jie"},{"first_name":"Roderick","last_name":"Bloem","full_name":"Bloem, Roderick"}],"month":"12","arxiv":1,"citation":{"apa":"Hofferek, G., Gupta, A., Könighofer, B., Jiang, J., &#38; Bloem, R. (2013). Synthesizing multiple boolean functions using interpolation on a single proof. In <i>2013 Formal Methods in Computer-Aided Design</i> (pp. 77–84). Portland, OR, United States: IEEE. <a href=\"https://doi.org/10.1109/FMCAD.2013.6679394\">https://doi.org/10.1109/FMCAD.2013.6679394</a>","ista":"Hofferek G, Gupta A, Könighofer B, Jiang J, Bloem R. 2013. Synthesizing multiple boolean functions using interpolation on a single proof. 2013 Formal Methods in Computer-Aided Design. FMCAD: Formal Methods in Computer-Aided Design, 77–84.","ama":"Hofferek G, Gupta A, Könighofer B, Jiang J, Bloem R. Synthesizing multiple boolean functions using interpolation on a single proof. In: <i>2013 Formal Methods in Computer-Aided Design</i>. IEEE; 2013:77-84. doi:<a href=\"https://doi.org/10.1109/FMCAD.2013.6679394\">10.1109/FMCAD.2013.6679394</a>","short":"G. Hofferek, A. Gupta, B. Könighofer, J. Jiang, R. Bloem, in:, 2013 Formal Methods in Computer-Aided Design, IEEE, 2013, pp. 77–84.","mla":"Hofferek, Georg, et al. “Synthesizing Multiple Boolean Functions Using Interpolation on a Single Proof.” <i>2013 Formal Methods in Computer-Aided Design</i>, IEEE, 2013, pp. 77–84, doi:<a href=\"https://doi.org/10.1109/FMCAD.2013.6679394\">10.1109/FMCAD.2013.6679394</a>.","ieee":"G. Hofferek, A. Gupta, B. Könighofer, J. Jiang, and R. Bloem, “Synthesizing multiple boolean functions using interpolation on a single proof,” in <i>2013 Formal Methods in Computer-Aided Design</i>, Portland, OR, United States, 2013, pp. 77–84.","chicago":"Hofferek, Georg, Ashutosh Gupta, Bettina Könighofer, Jie Jiang, and Roderick Bloem. “Synthesizing Multiple Boolean Functions Using Interpolation on a Single Proof.” In <i>2013 Formal Methods in Computer-Aided Design</i>, 77–84. IEEE, 2013. <a href=\"https://doi.org/10.1109/FMCAD.2013.6679394\">https://doi.org/10.1109/FMCAD.2013.6679394</a>."},"page":"77 - 84","_id":"1385","language":[{"iso":"eng"}],"acknowledgement":"This research was supported by the European Commission through project\r\nDIAMOND  (FP7-2009-IST-4-248613), and  QUAINT  (I774-N23),  ","quality_controlled":"1","project":[{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"FP7","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling"}],"department":[{"_id":"ToHe"}],"publisher":"IEEE","publication_status":"published","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1308.4767"}],"type":"conference","oa_version":"Preprint","date_created":"2018-12-11T11:51:43Z","publist_id":"5825","publication":"2013 Formal Methods in Computer-Aided Design","date_published":"2013-12-11T00:00:00Z","status":"public","abstract":[{"lang":"eng","text":"It is often difficult to correctly implement a Boolean controller for a complex system, especially when concurrency is involved. Yet, it may be easy to formally specify a controller. For instance, for a pipelined processor it suffices to state that the visible behavior of the pipelined system should be identical to a non-pipelined reference system (Burch-Dill paradigm). We present a novel procedure to efficiently synthesize multiple Boolean control signals from a specification given as a quantified first-order formula (with a specific quantifier structure). Our approach uses uninterpreted functions to abstract details of the design. We construct an unsatisfiable SMT formula from the given specification. Then, from just one proof of unsatisfiability, we use a variant of Craig interpolation to compute multiple coordinated interpolants that implement the Boolean control signals. Our method avoids iterative learning and back-substitution of the control functions. We applied our approach to synthesize a controller for a simple two-stage pipelined processor, and present first experimental results."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"conference":{"location":"Riga, Latvia","name":"ICALP: Automata, Languages and Programming","start_date":"2013-07-08","end_date":"2013-07-12"},"series_title":"Lecture Notes in Computer Science","has_accepted_license":"1","ec_funded":1,"year":"2013","oa":1,"article_processing_charge":"No","doi":"10.1007/978-3-642-39212-2_11","title":"Nondeterminism in the presence of a diverse or unknown future","day":"01","date_updated":"2020-08-11T10:09:09Z","page":"89 - 100","issue":"PART 2","_id":"1387","language":[{"iso":"eng"}],"acknowledgement":"and ERC Grant QUALITY.","file":[{"content_type":"application/pdf","relation":"main_file","file_name":"2013_ICALP_Boker.pdf","checksum":"98bc02e3793072e279ec8d364b381ff3","creator":"dernst","file_size":276982,"file_id":"7857","access_level":"open_access","date_created":"2020-05-15T11:05:50Z","date_updated":"2020-07-14T12:44:48Z"}],"author":[{"full_name":"Boker, Udi","last_name":"Boker","first_name":"Udi","id":"31E297B6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Denis","last_name":"Kuperberg","full_name":"Kuperberg, Denis"},{"full_name":"Kupferman, Orna","last_name":"Kupferman","first_name":"Orna"},{"last_name":"Skrzypczak","first_name":"Michał","full_name":"Skrzypczak, Michał"}],"month":"07","file_date_updated":"2020-07-14T12:44:48Z","ddc":["000"],"citation":{"ama":"Boker U, Kuperberg D, Kupferman O, Skrzypczak M. Nondeterminism in the presence of a diverse or unknown future. 2013;7966(PART 2):89-100. doi:<a href=\"https://doi.org/10.1007/978-3-642-39212-2_11\">10.1007/978-3-642-39212-2_11</a>","ista":"Boker U, Kuperberg D, Kupferman O, Skrzypczak M. 2013. Nondeterminism in the presence of a diverse or unknown future. 7966(PART 2), 89–100.","apa":"Boker, U., Kuperberg, D., Kupferman, O., &#38; Skrzypczak, M. (2013). Nondeterminism in the presence of a diverse or unknown future. Presented at the ICALP: Automata, Languages and Programming, Riga, Latvia: Springer. <a href=\"https://doi.org/10.1007/978-3-642-39212-2_11\">https://doi.org/10.1007/978-3-642-39212-2_11</a>","chicago":"Boker, Udi, Denis Kuperberg, Orna Kupferman, and Michał Skrzypczak. “Nondeterminism in the Presence of a Diverse or Unknown Future.” Lecture Notes in Computer Science. Springer, 2013. <a href=\"https://doi.org/10.1007/978-3-642-39212-2_11\">https://doi.org/10.1007/978-3-642-39212-2_11</a>.","ieee":"U. Boker, D. Kuperberg, O. Kupferman, and M. Skrzypczak, “Nondeterminism in the presence of a diverse or unknown future,” vol. 7966, no. PART 2. Springer, pp. 89–100, 2013.","short":"U. Boker, D. Kuperberg, O. Kupferman, M. Skrzypczak, 7966 (2013) 89–100.","mla":"Boker, Udi, et al. <i>Nondeterminism in the Presence of a Diverse or Unknown Future</i>. Vol. 7966, no. PART 2, Springer, 2013, pp. 89–100, doi:<a href=\"https://doi.org/10.1007/978-3-642-39212-2_11\">10.1007/978-3-642-39212-2_11</a>."},"type":"conference","volume":7966,"department":[{"_id":"ToHe"}],"quality_controlled":"1","project":[{"call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","call_identifier":"FP7"}],"publication_status":"published","publisher":"Springer","abstract":[{"text":"Choices made by nondeterministic word automata depend on both the past (the prefix of the word read so far) and the future (the suffix yet to be read). In several applications, most notably synthesis, the future is diverse or unknown, leading to algorithms that are based on deterministic automata. Hoping to retain some of the advantages of nondeterministic automata, researchers have studied restricted classes of nondeterministic automata. Three such classes are nondeterministic automata that are good for trees (GFT; i.e., ones that can be expanded to tree automata accepting the derived tree languages, thus whose choices should satisfy diverse futures), good for games (GFG; i.e., ones whose choices depend only on the past), and determinizable by pruning (DBP; i.e., ones that embody equivalent deterministic automata). The theoretical properties and relative merits of the different classes are still open, having vagueness on whether they really differ from deterministic automata. In particular, while DBP ⊆ GFG ⊆ GFT, it is not known whether every GFT automaton is GFG and whether every GFG automaton is DBP. Also open is the possible succinctness of GFG and GFT automata compared to deterministic automata. We study these problems for ω-regular automata with all common acceptance conditions. We show that GFT=GFG⊃DBP, and describe a determinization construction for GFG automata.","lang":"eng"}],"publist_id":"5823","date_published":"2013-07-01T00:00:00Z","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"      7966","oa_version":"Submitted Version","scopus_import":1,"alternative_title":["LNCS"],"date_created":"2018-12-11T11:51:44Z"},{"oa_version":"Published Version","date_created":"2018-12-11T11:51:50Z","alternative_title":["ISTA Thesis"],"date_published":"2013-09-05T00:00:00Z","status":"public","publist_id":"5802","abstract":[{"lang":"eng","text":"Motivated by the analysis of highly dynamic message-passing systems, i.e. unbounded thread creation, mobility, etc. we present a framework for the analysis of depth-bounded systems. Depth-bounded systems are one of the most expressive known fragment of the π-calculus for which interesting verification problems are still decidable. Even though they are infinite state systems depth-bounded systems are well-structured, thus can be analyzed algorithmically. We give an interpretation of depth-bounded systems as graph-rewriting systems. This gives more flexibility and ease of use to apply depth-bounded systems to other type of systems like shared memory concurrency.\r\n\r\nFirst, we develop an adequate domain of limits for depth-bounded systems, a prerequisite for the effective representation of downward-closed sets. Downward-closed sets are needed by forward saturation-based algorithms to represent potentially infinite sets of states. Then, we present an abstract interpretation framework to compute the covering set of well-structured transition systems. Because, in general, the covering set is not computable, our abstraction over-approximates the actual covering set. Our abstraction captures the essence of acceleration based-algorithms while giving up enough precision to ensure convergence. We have implemented the analysis in the PICASSO tool and show that it is accurate in practice. Finally, we build some further analyses like termination using the covering set as starting point."}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF"},{"call_identifier":"FP7","grant_number":"267989","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425"}],"department":[{"_id":"ToHe"},{"_id":"GradSch"}],"supervisor":[{"orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","main_file_link":[{"url":"http://dzufferey.github.io/files/2013_thesis.pdf"}],"type":"dissertation","month":"09","file_date_updated":"2021-11-17T13:47:58Z","author":[{"full_name":"Zufferey, Damien","orcid":"0000-0002-3197-8736","first_name":"Damien","last_name":"Zufferey","id":"4397AC76-F248-11E8-B48F-1D18A9856A87"}],"file":[{"content_type":"application/pdf","file_name":"2013_Zufferey_thesis_final.pdf","relation":"main_file","creator":"dernst","checksum":"ed2d7b52933d134e8dc69d569baa284e","file_size":1514906,"file_id":"9176","success":1,"access_level":"open_access","date_created":"2021-02-22T11:28:36Z","date_updated":"2021-02-22T11:28:36Z"},{"file_id":"10298","file_size":1378313,"date_created":"2021-11-16T14:42:52Z","date_updated":"2021-11-17T13:47:58Z","access_level":"closed","content_type":"application/pdf","creator":"cchlebak","checksum":"cecc4c4b14225bee973d32e3dba91a55","relation":"main_file","file_name":"2013_Zufferey_thesis_final_pdfa.pdf"}],"citation":{"short":"D. Zufferey, Analysis of Dynamic Message Passing Programs, Institute of Science and Technology Austria, 2013.","mla":"Zufferey, Damien. <i>Analysis of Dynamic Message Passing Programs</i>. Institute of Science and Technology Austria, 2013, doi:<a href=\"https://doi.org/10.15479/at:ista:1405\">10.15479/at:ista:1405</a>.","chicago":"Zufferey, Damien. “Analysis of Dynamic Message Passing Programs.” Institute of Science and Technology Austria, 2013. <a href=\"https://doi.org/10.15479/at:ista:1405\">https://doi.org/10.15479/at:ista:1405</a>.","ieee":"D. Zufferey, “Analysis of dynamic message passing programs,” Institute of Science and Technology Austria, 2013.","ista":"Zufferey D. 2013. Analysis of dynamic message passing programs. Institute of Science and Technology Austria.","apa":"Zufferey, D. (2013). <i>Analysis of dynamic message passing programs</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:1405\">https://doi.org/10.15479/at:ista:1405</a>","ama":"Zufferey D. Analysis of dynamic message passing programs. 2013. doi:<a href=\"https://doi.org/10.15479/at:ista:1405\">10.15479/at:ista:1405</a>"},"ddc":["000"],"page":"134","acknowledgement":"This work was supported in part by the Austrian Science Fund NFN RiSE (Rigorous Systems Engineering) and by the ERC Advanced Grant QUAREM (Quantitative Reactve Modeling).\r\nChapter 2, 3, and 4 are joint work with Thomas A. Henzinger and Thomas Wies. Chapter 2 was published in FoSSaCS 2010 as “Forward Analysis of Depth-Bounded Processes” [112]. Chapter 3 was published in VMCAI 2012 as “Ideal Abstractions for Well-Structured Transition Systems” [114]. Chap- ter 5.1 is joint work with Kshitij Bansal, Eric Koskinen, and Thomas Wies. It was published in TACAS 2013 as “Structural Counter Abstraction” [13]. The author’s contribution in this part is mostly related to the implementation. The theory required to understand the method and its implementation is quickly recalled to make the thesis self-contained, but should not be considered as a contribution. For the details of the methods, we refer the reader to the orig- inal publication [13] and the corresponding technical report [14]. Chapter 5.2 is ongoing work with Shahram Esmaeilsabzali, Rupak Majumdar, and Thomas Wies. I also would like to thank the people who supported over the past 4 years. My advisor Thomas A. Henzinger who gave me a lot of freedom to work on projects I was interested in. My collaborators, especially Thomas Wies with whom I worked since the beginning. The members of my thesis committee, Viktor Kun- cak and Rupak Majumdar, who also agreed to advise me. Simon Aeschbacher, Pavol Cerny, Cezara Dragoi, Arjun Radhakrishna, my family, friends and col- leagues who created an enjoyable environment. ","language":[{"iso":"eng"}],"_id":"1405","degree_awarded":"PhD","title":"Analysis of dynamic message passing programs","doi":"10.15479/at:ista:1405","date_updated":"2023-09-07T11:36:37Z","publication_identifier":{"issn":["2663-337X"]},"day":"05","year":"2013","ec_funded":1,"has_accepted_license":"1","related_material":{"record":[{"status":"public","id":"2847","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"3251"},{"status":"public","relation":"part_of_dissertation","id":"4361"}]},"article_processing_charge":"No","oa":1},{"month":"10","author":[{"orcid":"0000-0002-8526-5416","full_name":"Campinho, Pedro","id":"3AFBBC42-F248-11E8-B48F-1D18A9856A87","first_name":"Pedro","last_name":"Campinho"}],"oa_version":"None","alternative_title":["ISTA Thesis"],"date_created":"2018-12-11T11:51:50Z","citation":{"ieee":"P. Campinho, “Mechanics of zebrafish epiboly: Tension-oriented cell divisions limit anisotropic tissue tension in epithelial spreading,” Institute of Science and Technology Austria, 2013.","chicago":"Campinho, Pedro. “Mechanics of Zebrafish Epiboly: Tension-Oriented Cell Divisions Limit Anisotropic Tissue Tension in Epithelial Spreading.” Institute of Science and Technology Austria, 2013.","mla":"Campinho, Pedro. <i>Mechanics of Zebrafish Epiboly: Tension-Oriented Cell Divisions Limit Anisotropic Tissue Tension in Epithelial Spreading</i>. Institute of Science and Technology Austria, 2013.","short":"P. Campinho, Mechanics of Zebrafish Epiboly: Tension-Oriented Cell Divisions Limit Anisotropic Tissue Tension in Epithelial Spreading, Institute of Science and Technology Austria, 2013.","ama":"Campinho P. Mechanics of zebrafish epiboly: Tension-oriented cell divisions limit anisotropic tissue tension in epithelial spreading. 2013.","apa":"Campinho, P. (2013). <i>Mechanics of zebrafish epiboly: Tension-oriented cell divisions limit anisotropic tissue tension in epithelial spreading</i>. Institute of Science and Technology Austria.","ista":"Campinho P. 2013. Mechanics of zebrafish epiboly: Tension-oriented cell divisions limit anisotropic tissue tension in epithelial spreading. Institute of Science and Technology Austria."},"abstract":[{"text":"Epithelial spreading is a critical part of various developmental and wound repair processes. Here we use zebrafish epiboly as a model system to study the cellular and molecular mechanisms underlying the spreading of epithelial sheets. During zebrafish epiboly the enveloping cell layer (EVL), a simple squamous epithelium, spreads over the embryo to eventually cover the entire yolk cell by the end of gastrulation. The EVL leading edge is anchored through tight junctions to the yolk syncytial layer (YSL), where directly adjacent to the EVL margin a contractile actomyosin ring is formed that is thought to drive EVL epiboly. The prevalent view in the field was that the contractile ring exerts a pulling force on the EVL margin, which pulls the EVL towards the vegetal pole. However, how this force is generated and how it affects EVL morphology still remains elusive. Moreover, the cellular mechanisms mediating the increase in EVL surface area, while maintaining tissue integrity and function are still unclear. Here we show that the YSL actomyosin ring pulls on the EVL margin by two distinct force-generating mechanisms. One mechanism is based on contraction of the ring around its circumference, as previously proposed. The second mechanism is based on actomyosin retrogade flows, generating force through resistance against the substrate. The latter can function at any epiboly stage even in situations where the contraction-based mechanism is unproductive. Additionally, we demonstrate that during epiboly the EVL is subjected to anisotropic tension, which guides the orientation of EVL cell division along the main axis (animal-vegetal) of tension. The influence of tension in cell division orientation involves cell elongation and requires myosin-2 activity for proper spindle alignment. Strikingly, we reveal that tension-oriented cell divisions release anisotropic tension within the EVL and that in the absence of such divisions, EVL cells undergo ectopic fusions. We conclude that forces applied to the EVL by the action of the YSL actomyosin ring generate a tension anisotropy in the EVL that orients cell divisions, which in turn limit tissue tension increase thereby facilitating tissue spreading.","lang":"eng"}],"page":"123","date_published":"2013-10-01T00:00:00Z","status":"public","publist_id":"5801","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","degree_awarded":"PhD","language":[{"iso":"eng"}],"_id":"1406","title":"Mechanics of zebrafish epiboly: Tension-oriented cell divisions limit anisotropic tissue tension in epithelial spreading","department":[{"_id":"CaHe"}],"supervisor":[{"full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","first_name":"Carl-Philipp J"}],"publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","day":"01","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"publisher":"Institute of Science and Technology Austria","date_updated":"2023-09-07T11:36:07Z","year":"2013","type":"dissertation","article_processing_charge":"No"},{"year":"2013","related_material":{"record":[{"relation":"later_version","id":"2000","status":"public"}]},"has_accepted_license":"1","oa":1,"type":"technical_report","department":[{"_id":"KrCh"}],"title":"TTP: Tool for Tumor Progression","doi":"10.15479/AT:IST-2013-104-v1-1","publisher":"IST Austria","date_updated":"2023-02-23T10:23:57Z","publication_identifier":{"issn":["2664-1690"]},"publication_status":"published","day":"11","date_published":"2013-01-11T00:00:00Z","status":"public","abstract":[{"lang":"eng","text":"In this work we present a flexible tool for tumor progression, which simulates the evolutionary dynamics of cancer. Tumor progression implements a multi-type branching process where the key parameters are the fitness landscape, the mutation rate, and the average time of cell division. The fitness of a cancer cell depends on the mutations it has accumulated. The input to our tool could be any fitness landscape, mutation rate, and cell division time, and the tool produces the growth dynamics and all relevant statistics."}],"page":"17","pubrep_id":"104","_id":"5399","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"01","file_date_updated":"2020-07-14T12:46:44Z","file":[{"file_id":"5542","file_size":1471954,"date_updated":"2020-07-14T12:46:44Z","date_created":"2018-12-12T11:54:20Z","access_level":"open_access","content_type":"application/pdf","creator":"system","checksum":"2cc8c6e157eca1271128db80bb3dec80","relation":"main_file","file_name":"IST-2013-104-v1+1_tumortool.pdf"}],"author":[{"last_name":"Reiter","first_name":"Johannes","id":"4A918E98-F248-11E8-B48F-1D18A9856A87","full_name":"Reiter, Johannes","orcid":"0000-0002-0170-7353"},{"full_name":"Bozic, Ivana","first_name":"Ivana","last_name":"Bozic"},{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Nowak, Martin","last_name":"Nowak","first_name":"Martin"}],"oa_version":"Published Version","date_created":"2018-12-12T11:39:07Z","citation":{"ama":"Reiter J, Bozic I, Chatterjee K, Nowak M. <i>TTP: Tool for Tumor Progression</i>. IST Austria; 2013. doi:<a href=\"https://doi.org/10.15479/AT:IST-2013-104-v1-1\">10.15479/AT:IST-2013-104-v1-1</a>","apa":"Reiter, J., Bozic, I., Chatterjee, K., &#38; Nowak, M. (2013). <i>TTP: Tool for Tumor Progression</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2013-104-v1-1\">https://doi.org/10.15479/AT:IST-2013-104-v1-1</a>","ista":"Reiter J, Bozic I, Chatterjee K, Nowak M. 2013. TTP: Tool for Tumor Progression, IST Austria, 17p.","ieee":"J. Reiter, I. Bozic, K. Chatterjee, and M. Nowak, <i>TTP: Tool for Tumor Progression</i>. IST Austria, 2013.","chicago":"Reiter, Johannes, Ivana Bozic, Krishnendu Chatterjee, and Martin Nowak. <i>TTP: Tool for Tumor Progression</i>. IST Austria, 2013. <a href=\"https://doi.org/10.15479/AT:IST-2013-104-v1-1\">https://doi.org/10.15479/AT:IST-2013-104-v1-1</a>.","short":"J. Reiter, I. Bozic, K. Chatterjee, M. Nowak, TTP: Tool for Tumor Progression, IST Austria, 2013.","mla":"Reiter, Johannes, et al. <i>TTP: Tool for Tumor Progression</i>. IST Austria, 2013, doi:<a href=\"https://doi.org/10.15479/AT:IST-2013-104-v1-1\">10.15479/AT:IST-2013-104-v1-1</a>."},"ddc":["000"],"alternative_title":["IST Austria Technical Report"]},{"title":"What is decidable about partially observable Markov decision processes with ω-regular objectives","department":[{"_id":"KrCh"}],"doi":"10.15479/AT:IST-2013-109-v1-1","publisher":"IST Austria","date_updated":"2023-02-23T10:36:45Z","publication_identifier":{"issn":["2664-1690"]},"publication_status":"published","day":"20","year":"2013","has_accepted_license":"1","related_material":{"record":[{"relation":"later_version","id":"1477","status":"public"},{"id":"2295","relation":"later_version","status":"public"}]},"oa":1,"type":"technical_report","month":"02","file_date_updated":"2020-07-14T12:46:44Z","author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Chmelik, Martin","first_name":"Martin","last_name":"Chmelik","id":"3624234E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Tracol, Mathieu","last_name":"Tracol","first_name":"Mathieu","id":"3F54FA38-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"Published Version","file":[{"access_level":"open_access","date_updated":"2020-07-14T12:46:44Z","date_created":"2018-12-12T11:53:06Z","file_size":483407,"file_id":"5467","relation":"main_file","file_name":"IST-2013-109-v1+1_What_is_Decidable_about_Partially_Observable_Markov_Decision_Processes_with_ω-Regular_Objectives.pdf","creator":"system","checksum":"cbba40210788a1b22c6cf06433b5ed6f","content_type":"application/pdf"}],"citation":{"ama":"Chatterjee K, Chmelik M, Tracol M. <i>What Is Decidable about Partially Observable Markov Decision Processes with ω-Regular Objectives</i>. IST Austria; 2013. doi:<a href=\"https://doi.org/10.15479/AT:IST-2013-109-v1-1\">10.15479/AT:IST-2013-109-v1-1</a>","apa":"Chatterjee, K., Chmelik, M., &#38; Tracol, M. (2013). <i>What is decidable about partially observable Markov decision processes with ω-regular objectives</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2013-109-v1-1\">https://doi.org/10.15479/AT:IST-2013-109-v1-1</a>","ista":"Chatterjee K, Chmelik M, Tracol M. 2013. What is decidable about partially observable Markov decision processes with ω-regular objectives, IST Austria, 41p.","ieee":"K. Chatterjee, M. Chmelik, and M. Tracol, <i>What is decidable about partially observable Markov decision processes with ω-regular objectives</i>. IST Austria, 2013.","chicago":"Chatterjee, Krishnendu, Martin Chmelik, and Mathieu Tracol. <i>What Is Decidable about Partially Observable Markov Decision Processes with ω-Regular Objectives</i>. IST Austria, 2013. <a href=\"https://doi.org/10.15479/AT:IST-2013-109-v1-1\">https://doi.org/10.15479/AT:IST-2013-109-v1-1</a>.","short":"K. Chatterjee, M. Chmelik, M. Tracol, What Is Decidable about Partially Observable Markov Decision Processes with ω-Regular Objectives, IST Austria, 2013.","mla":"Chatterjee, Krishnendu, et al. <i>What Is Decidable about Partially Observable Markov Decision Processes with ω-Regular Objectives</i>. IST Austria, 2013, doi:<a href=\"https://doi.org/10.15479/AT:IST-2013-109-v1-1\">10.15479/AT:IST-2013-109-v1-1</a>."},"date_created":"2018-12-12T11:39:07Z","ddc":["000","005"],"alternative_title":["IST Austria Technical Report"],"status":"public","date_published":"2013-02-20T00:00:00Z","abstract":[{"lang":"eng","text":"We consider partially observable Markov decision processes (POMDPs) with ω-regular conditions specified as parity objectives. The class of ω-regular languages extends regular languages to infinite strings and provides a robust specification language to express all properties used in verification, and parity objectives are canonical forms to express ω-regular conditions. The qualitative analysis problem given a POMDP and a parity objective asks whether there is a strategy to ensure that the objective is satis- fied with probability 1 (resp. positive probability). While the qualitative analysis problems are known to be undecidable even for very special cases of parity objectives, we establish decidability (with optimal complexity) of the qualitative analysis problems for POMDPs with all parity objectives under finite- memory strategies. We establish asymptotically optimal (exponential) memory bounds and EXPTIME- completeness of the qualitative analysis problems under finite-memory strategies for POMDPs with parity objectives."}],"page":"41","language":[{"iso":"eng"}],"_id":"5400","pubrep_id":"109","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"day":"20","publication_status":"published","date_updated":"2020-07-14T23:04:47Z","publisher":"IST Austria","department":[{"_id":"E-Lib"}],"title":"Initiatives and projects related to RD","type":"report","oa":1,"has_accepted_license":"1","year":"2013","ddc":["020"],"citation":{"ieee":"J. Porsche, <i>Initiatives and projects related to RD</i>. IST Austria, 2013.","chicago":"Porsche, Jana. <i>Initiatives and Projects Related to RD</i>. IST Austria, 2013.","mla":"Porsche, Jana. <i>Initiatives and Projects Related to RD</i>. IST Austria, 2013.","short":"J. Porsche, Initiatives and Projects Related to RD, IST Austria, 2013.","ama":"Porsche J. <i>Initiatives and Projects Related to RD</i>. IST Austria; 2013.","apa":"Porsche, J. (2013). <i>Initiatives and projects related to RD</i>. IST Austria.","ista":"Porsche J. 2013. Initiatives and projects related to RD, IST Austria,p."},"date_created":"2018-12-12T11:39:07Z","oa_version":"Published Version","author":[{"full_name":"Porsche, Jana","id":"3252EDC2-F248-11E8-B48F-1D18A9856A87","first_name":"Jana","last_name":"Porsche"}],"file":[{"content_type":"application/pdf","creator":"system","checksum":"d68712db838432ecdacf9ffb1de8f8a6","file_name":"IST-2013-113-v1+1_Initiatives_and_projects_related_to_RD.pdf","relation":"main_file","file_id":"5536","file_size":151208,"date_updated":"2020-07-14T12:46:45Z","date_created":"2018-12-12T11:54:14Z","access_level":"open_access"}],"month":"03","file_date_updated":"2020-07-14T12:46:45Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"_id":"5401","pubrep_id":"113","abstract":[{"text":"This document is created as a part of the project “Repository for Research Data at IST Austria”. It summarises the actual initiatives, projects and standards related to the project. It supports the preparation of standards and specifications for the project, which should be considered and followed to ensure interoperability and visibility of the uploaded data.","lang":"eng"}],"status":"public","date_published":"2013-03-20T00:00:00Z"},{"abstract":[{"text":"Linearizability requires that the outcome of calls by competing threads to a concurrent data structure is the same as some sequential execution where each thread has exclusive access to the data structure. In an ordered data structure, such as a queue or a stack, linearizability is ensured by requiring threads commit in the order dictated by the sequential semantics of the data structure; e.g., in a concurrent queue implementation a dequeue can only remove the oldest element. \r\nIn this paper, we investigate the impact of this strict ordering, by comparing what linearizability allows to what existing implementations do. We first give an operational definition for linearizability which allows us to build the most general linearizable implementation as a transition system for any given sequential specification. We then use this operational definition to categorize linearizable implementations based on whether they are bound or free. In a bound implementation, whenever all threads observe the same logical state, the updates to the logical state and the temporal order of commits coincide. All existing queue implementations we know of are bound. We then proceed to present, to the best of our knowledge, the first ever free queue implementation. Our experiments show that free implementations have the potential for better performance by suffering less from contention.","lang":"eng"}],"page":"16","status":"public","date_published":"2013-06-12T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"_id":"5402","pubrep_id":"123","file_date_updated":"2020-07-14T12:46:45Z","month":"06","oa_version":"Published Version","author":[{"last_name":"Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724"},{"first_name":"Ali","last_name":"Sezgin","id":"4C7638DA-F248-11E8-B48F-1D18A9856A87","full_name":"Sezgin, Ali"}],"file":[{"checksum":"ce580605ae9756a8c99d7b403ebb8eed","creator":"system","relation":"main_file","file_name":"IST-2013-123-v1+1_main-concur2013.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:46:45Z","date_created":"2018-12-12T11:53:19Z","access_level":"open_access","file_id":"5480","file_size":249790}],"alternative_title":["IST Austria Technical Report"],"date_created":"2018-12-12T11:39:07Z","citation":{"ama":"Henzinger TA, Sezgin A. <i>How Free Is Your Linearizable Concurrent Data Structure?</i> IST Austria; 2013. doi:<a href=\"https://doi.org/10.15479/AT:IST-2013-123-v1-1\">10.15479/AT:IST-2013-123-v1-1</a>","ista":"Henzinger TA, Sezgin A. 2013. How free is your linearizable concurrent data structure?, IST Austria, 16p.","apa":"Henzinger, T. A., &#38; Sezgin, A. (2013). <i>How free is your linearizable concurrent data structure?</i> IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2013-123-v1-1\">https://doi.org/10.15479/AT:IST-2013-123-v1-1</a>","chicago":"Henzinger, Thomas A, and Ali Sezgin. <i>How Free Is Your Linearizable Concurrent Data Structure?</i> IST Austria, 2013. <a href=\"https://doi.org/10.15479/AT:IST-2013-123-v1-1\">https://doi.org/10.15479/AT:IST-2013-123-v1-1</a>.","ieee":"T. A. Henzinger and A. Sezgin, <i>How free is your linearizable concurrent data structure?</i> IST Austria, 2013.","short":"T.A. Henzinger, A. Sezgin, How Free Is Your Linearizable Concurrent Data Structure?, IST Austria, 2013.","mla":"Henzinger, Thomas A., and Ali Sezgin. <i>How Free Is Your Linearizable Concurrent Data Structure?</i> IST Austria, 2013, doi:<a href=\"https://doi.org/10.15479/AT:IST-2013-123-v1-1\">10.15479/AT:IST-2013-123-v1-1</a>."},"ddc":["000","004"],"has_accepted_license":"1","year":"2013","type":"technical_report","oa":1,"department":[{"_id":"ToHe"}],"title":"How free is your linearizable concurrent data structure?","doi":"10.15479/AT:IST-2013-123-v1-1","publication_identifier":{"issn":["2664-1690"]},"publication_status":"published","day":"12","publisher":"IST Austria","date_updated":"2020-07-14T23:04:47Z"},{"has_accepted_license":"1","related_material":{"record":[{"id":"524","relation":"later_version","status":"public"}]},"year":"2013","type":"technical_report","oa":1,"department":[{"_id":"KrCh"}],"title":"Qualitative analysis of concurrent mean-payoff games","doi":"10.15479/AT:IST-2013-126-v1-1","publication_status":"published","publication_identifier":{"issn":["2664-1690"]},"day":"03","publisher":"IST Austria","date_updated":"2023-02-23T12:22:53Z","abstract":[{"lang":"eng","text":"We consider concurrent games played by two-players on a finite state graph, where in every round the players simultaneously choose a move, and the current state along with the joint moves determine the successor state. We study the most fundamental objective for concurrent games, namely, mean-payoff or limit-average objective, where a reward is associated to every transition, and the goal of player 1 is to maximize the long-run average of the rewards, and the objective of player 2 is strictly the opposite (i.e., the games are zero-sum). The path constraint for player 1 could be qualitative, i.e., the mean-payoff is the maximal reward, or arbitrarily close to it; or quantitative, i.e., a given threshold between the minimal and maximal reward. We consider the computation of the almost-sure (resp. positive) winning sets, where player 1 can ensure that the path constraint is satisfied with probability 1 (resp. positive probability). Almost-sure winning with qualitative constraint exactly corresponds to the question whether there exists a strategy to ensure that the payoff is the maximal reward of the game. Our main results for qualitative path constraints are as follows: (1) we establish qualitative determinacy results that show for every state either player 1 has a strategy to ensure almost-sure (resp. positive) winning against all player-2 strategies or player 2 has a spoiling strategy to falsify almost-sure (resp. positive) winning against all player-1 strategies; (2) we present optimal strategy complexity results that precisely characterize the classes of strategies required for almost-sure and positive winning for both players; and (3) we present quadratic time algorithms to compute the almost-sure and the positive winning sets, matching the best known bound of the algorithms for much simpler problems (such as reachability objectives). For quantitative constraints we show that a polynomial time solution for the almost-sure or the positive winning set would imply a solution to a long-standing open problem (of solving the value problem of mean-payoff games) that is not known to be in polynomial time."}],"page":"33","date_published":"2013-07-03T00:00:00Z","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"5403","language":[{"iso":"eng"}],"pubrep_id":"126","file_date_updated":"2020-07-14T12:46:45Z","month":"07","oa_version":"Published Version","author":[{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"},{"full_name":"Ibsen-Jensen, Rasmus","orcid":"0000-0003-4783-0389","first_name":"Rasmus","last_name":"Ibsen-Jensen","id":"3B699956-F248-11E8-B48F-1D18A9856A87"}],"file":[{"file_id":"5510","file_size":434523,"date_created":"2018-12-12T11:53:49Z","date_updated":"2020-07-14T12:46:45Z","access_level":"open_access","content_type":"application/pdf","checksum":"063868c665beec37bf28160e2a695746","creator":"system","relation":"main_file","file_name":"IST-2013-126-v1+1_soda_full.pdf"}],"alternative_title":["IST Austria Technical Report"],"date_created":"2018-12-12T11:39:08Z","citation":{"ama":"Chatterjee K, Ibsen-Jensen R. <i>Qualitative Analysis of Concurrent Mean-Payoff Games</i>. IST Austria; 2013. doi:<a href=\"https://doi.org/10.15479/AT:IST-2013-126-v1-1\">10.15479/AT:IST-2013-126-v1-1</a>","ista":"Chatterjee K, Ibsen-Jensen R. 2013. Qualitative analysis of concurrent mean-payoff games, IST Austria, 33p.","apa":"Chatterjee, K., &#38; Ibsen-Jensen, R. (2013). <i>Qualitative analysis of concurrent mean-payoff games</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2013-126-v1-1\">https://doi.org/10.15479/AT:IST-2013-126-v1-1</a>","chicago":"Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. <i>Qualitative Analysis of Concurrent Mean-Payoff Games</i>. IST Austria, 2013. <a href=\"https://doi.org/10.15479/AT:IST-2013-126-v1-1\">https://doi.org/10.15479/AT:IST-2013-126-v1-1</a>.","ieee":"K. Chatterjee and R. Ibsen-Jensen, <i>Qualitative analysis of concurrent mean-payoff games</i>. IST Austria, 2013.","mla":"Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. <i>Qualitative Analysis of Concurrent Mean-Payoff Games</i>. IST Austria, 2013, doi:<a href=\"https://doi.org/10.15479/AT:IST-2013-126-v1-1\">10.15479/AT:IST-2013-126-v1-1</a>.","short":"K. Chatterjee, R. Ibsen-Jensen, Qualitative Analysis of Concurrent Mean-Payoff Games, IST Austria, 2013."},"ddc":["000","005"]},{"oa":1,"type":"technical_report","year":"2013","has_accepted_license":"1","related_material":{"record":[{"id":"2162","relation":"later_version","status":"public"}]},"date_updated":"2023-02-23T10:30:55Z","publisher":"IST Austria","day":"03","publication_identifier":{"issn":["2664-1690"]},"publication_status":"published","doi":"10.15479/AT:IST-2013-127-v1-1","department":[{"_id":"KrCh"}],"title":"The complexity of ergodic games","_id":"5404","language":[{"iso":"eng"}],"pubrep_id":"127","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","date_published":"2013-07-03T00:00:00Z","page":"29","abstract":[{"text":"We study finite-state two-player (zero-sum) concurrent mean-payoff games played on a graph. We focus on the important sub-class of ergodic games where all states are visited infinitely often with probability 1. The algorithmic study of ergodic games was initiated in a seminal work of Hoffman and Karp in 1966, but all basic complexity questions have remained unresolved. Our main results for ergodic games are as follows: We establish (1) an optimal exponential bound on the patience of stationary strategies (where patience of a distribution is the inverse of the smallest positive probability and represents a complexity measure of a stationary strategy); (2) the approximation problem lie in FNP; (3) the approximation problem is at least as hard as the decision problem for simple stochastic games (for which NP and coNP is the long-standing best known bound). We show that the exact value can be expressed in the existential theory of the reals, and also establish square-root sum hardness for a related class of games.","lang":"eng"}],"ddc":["000","005"],"citation":{"mla":"Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. <i>The Complexity of Ergodic Games</i>. IST Austria, 2013, doi:<a href=\"https://doi.org/10.15479/AT:IST-2013-127-v1-1\">10.15479/AT:IST-2013-127-v1-1</a>.","short":"K. Chatterjee, R. Ibsen-Jensen, The Complexity of Ergodic Games, IST Austria, 2013.","chicago":"Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. <i>The Complexity of Ergodic Games</i>. IST Austria, 2013. <a href=\"https://doi.org/10.15479/AT:IST-2013-127-v1-1\">https://doi.org/10.15479/AT:IST-2013-127-v1-1</a>.","ieee":"K. Chatterjee and R. Ibsen-Jensen, <i>The complexity of ergodic games</i>. IST Austria, 2013.","ista":"Chatterjee K, Ibsen-Jensen R. 2013. The complexity of ergodic games, IST Austria, 29p.","apa":"Chatterjee, K., &#38; Ibsen-Jensen, R. (2013). <i>The complexity of ergodic games</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2013-127-v1-1\">https://doi.org/10.15479/AT:IST-2013-127-v1-1</a>","ama":"Chatterjee K, Ibsen-Jensen R. <i>The Complexity of Ergodic Games</i>. IST Austria; 2013. doi:<a href=\"https://doi.org/10.15479/AT:IST-2013-127-v1-1\">10.15479/AT:IST-2013-127-v1-1</a>"},"date_created":"2018-12-12T11:39:08Z","alternative_title":["IST Austria Technical Report"],"oa_version":"Published Version","file":[{"content_type":"application/pdf","creator":"system","checksum":"79ee5e677a82611ce06e0360c69d494a","file_name":"IST-2013-127-v1+1_ergodic.pdf","relation":"main_file","file_id":"5496","file_size":517275,"date_created":"2018-12-12T11:53:35Z","date_updated":"2020-07-14T12:46:45Z","access_level":"open_access"}],"author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"},{"orcid":"0000-0003-4783-0389","full_name":"Ibsen-Jensen, Rasmus","first_name":"Rasmus","last_name":"Ibsen-Jensen","id":"3B699956-F248-11E8-B48F-1D18A9856A87"}],"month":"07","file_date_updated":"2020-07-14T12:46:45Z"}]