[{"related_material":{"record":[{"relation":"earlier_version","id":"5421","status":"public"},{"id":"5432","relation":"earlier_version","status":"public"}]},"date_created":"2018-12-12T11:39:21Z","month":"06","pubrep_id":"338","publication_status":"published","language":[{"iso":"eng"}],"department":[{"_id":"KrCh"}],"page":"18","type":"technical_report","doi":"10.15479/AT:IST-2015-323-v2-2","oa":1,"title":"The complexity of evolutionary games on graphs","publication_identifier":{"issn":["2664-1690"]},"author":[{"first_name":"Krishnendu","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Rasmus","orcid":"0000-0003-4783-0389","id":"3B699956-F248-11E8-B48F-1D18A9856A87","last_name":"Ibsen-Jensen","full_name":"Ibsen-Jensen, Rasmus"},{"last_name":"Nowak","full_name":"Nowak, Martin","first_name":"Martin"}],"file":[{"file_name":"IST-2015-323-v2+2_main.pdf","file_size":466161,"date_created":"2018-12-12T11:53:23Z","file_id":"5484","date_updated":"2020-07-14T12:46:56Z","content_type":"application/pdf","creator":"system","relation":"main_file","checksum":"66aace7d367032af97c15e35c9be9636","access_level":"open_access"}],"publisher":"IST Austria","year":"2015","citation":{"chicago":"Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Martin Nowak. <i>The Complexity of Evolutionary Games on Graphs</i>. IST Austria, 2015. <a href=\"https://doi.org/10.15479/AT:IST-2015-323-v2-2\">https://doi.org/10.15479/AT:IST-2015-323-v2-2</a>.","short":"K. Chatterjee, R. Ibsen-Jensen, M. Nowak, The Complexity of Evolutionary Games on Graphs, IST Austria, 2015.","mla":"Chatterjee, Krishnendu, et al. <i>The Complexity of Evolutionary Games on Graphs</i>. IST Austria, 2015, doi:<a href=\"https://doi.org/10.15479/AT:IST-2015-323-v2-2\">10.15479/AT:IST-2015-323-v2-2</a>.","ista":"Chatterjee K, Ibsen-Jensen R, Nowak M. 2015. The complexity of evolutionary games on graphs, IST Austria, 18p.","ama":"Chatterjee K, Ibsen-Jensen R, Nowak M. <i>The Complexity of Evolutionary Games on Graphs</i>. IST Austria; 2015. doi:<a href=\"https://doi.org/10.15479/AT:IST-2015-323-v2-2\">10.15479/AT:IST-2015-323-v2-2</a>","ieee":"K. Chatterjee, R. Ibsen-Jensen, and M. Nowak, <i>The complexity of evolutionary games on graphs</i>. IST Austria, 2015.","apa":"Chatterjee, K., Ibsen-Jensen, R., &#38; Nowak, M. (2015). <i>The complexity of evolutionary games on graphs</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2015-323-v2-2\">https://doi.org/10.15479/AT:IST-2015-323-v2-2</a>"},"day":"16","oa_version":"Published Version","_id":"5440","status":"public","fulldoi":"https://doi.org/10.15479/AT:IST-2015-323-v2-2","date_published":"2015-06-16T00:00:00Z","has_accepted_license":"1","ddc":["005","576"],"abstract":[{"lang":"eng","text":"Evolution occurs in populations of reproducing individuals. The structure of the population affects the outcome of the evolutionary process. Evolutionary graph theory is a powerful approach to study this phenomenon. There are two graphs. The interaction graph specifies who interacts with whom for payoff in the context of evolution. The replacement graph specifies who competes with whom for reproduction. The vertices of the two graphs are the same, and each vertex corresponds to an individual of the population. The fitness (or the reproductive rate) is a non-negative number, and depends on the payoff. A key quantity is the fixation probability of a new mutant. It is defined as the probability that a newly introduced mutant (on a single vertex) generates a lineage of offspring which eventually takes over the entire population of resident individuals. The basic computational questions are as follows: (i) the qualitative question asks whether the fixation probability is positive; and (ii) the quantitative approximation question asks for an approximation of the fixation probability. Our main results are as follows: First, we consider a special case of the general problem, where the residents do not reproduce. We show that the qualitative question is NP-complete, and the quantitative approximation question is #P-complete, and the hardness results hold even in the special case where the interaction and the replacement graphs coincide. Second, we show that in general both the qualitative and the quantitative approximation questions are PSPACE-complete. The PSPACE-hardness result for quantitative approximation holds even when the fitness is always positive."}],"file_date_updated":"2020-07-14T12:46:56Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","alternative_title":["IST Austria Technical Report"],"date_updated":"2023-02-23T12:26:10Z"},{"alternative_title":["IST Austria Technical Report"],"date_updated":"2025-04-15T08:11:48Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2020-07-14T12:46:56Z","abstract":[{"text":"We study algorithmic questions for concurrent systems where the transitions are labeled from a complete, closed semiring, and path properties are algebraic with semiring operations. The algebraic path properties can model dataflow analysis problems, the shortest path problem, and many other natural problems that arise in program analysis. We consider that each component of the concurrent system is a graph with constant treewidth, a property satisfied by the controlflow graphs of most programs. We allow for multiple possible queries, which arise naturally in demand driven dataflow analysis. The study of multiple queries allows us to consider the tradeoff between the resource usage of the one-time preprocessing and for each individual query. The traditional approach constructs the product graph of all components and applies the best-known graph algorithm on the product. In this approach, even the answer to a single query requires the transitive closure (i.e., the results of all possible queries), which provides no room for tradeoff between preprocessing and query time. Our main contributions are algorithms that significantly improve the worst-case running time of the traditional approach, and provide various tradeoffs depending on the number of queries. For example, in a concurrent system of two components, the traditional approach requires hexic time in the worst case for answering one query as well as computing the transitive closure, whereas we show that with one-time preprocessing in almost cubic time, each subsequent query can be answered in at most linear time, and even the transitive closure can be computed in almost quartic time. Furthermore, we establish conditional optimality results showing that the worst-case running time of our algorithms cannot be improved without achieving major breakthroughs in graph algorithms (i.e., improving the worst-case bound for the shortest path problem in general graphs). Preliminary experimental results show that our algorithms perform favorably on several benchmarks.","lang":"eng"}],"ddc":["000"],"date_published":"2015-07-11T00:00:00Z","has_accepted_license":"1","fulldoi":"https://doi.org/10.15479/AT:IST-2015-340-v1-1","_id":"5441","status":"public","oa_version":"Published Version","day":"11","citation":{"ama":"Chatterjee K, Ibsen-Jensen R, Goharshady AK, Pavlogiannis A. <i>Algorithms for Algebraic Path Properties in Concurrent Systems of Constant Treewidth Components</i>. IST Austria; 2015. doi:<a href=\"https://doi.org/10.15479/AT:IST-2015-340-v1-1\">10.15479/AT:IST-2015-340-v1-1</a>","ista":"Chatterjee K, Ibsen-Jensen R, Goharshady AK, Pavlogiannis A. 2015. Algorithms for algebraic path properties in concurrent systems of constant treewidth components, IST Austria, 24p.","ieee":"K. Chatterjee, R. Ibsen-Jensen, A. K. Goharshady, and A. Pavlogiannis, <i>Algorithms for algebraic path properties in concurrent systems of constant treewidth components</i>. IST Austria, 2015.","apa":"Chatterjee, K., Ibsen-Jensen, R., Goharshady, A. K., &#38; Pavlogiannis, A. (2015). <i>Algorithms for algebraic path properties in concurrent systems of constant treewidth components</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2015-340-v1-1\">https://doi.org/10.15479/AT:IST-2015-340-v1-1</a>","chicago":"Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, Amir Kafshdar Goharshady, and Andreas Pavlogiannis. <i>Algorithms for Algebraic Path Properties in Concurrent Systems of Constant Treewidth Components</i>. IST Austria, 2015. <a href=\"https://doi.org/10.15479/AT:IST-2015-340-v1-1\">https://doi.org/10.15479/AT:IST-2015-340-v1-1</a>.","mla":"Chatterjee, Krishnendu, et al. <i>Algorithms for Algebraic Path Properties in Concurrent Systems of Constant Treewidth Components</i>. IST Austria, 2015, doi:<a href=\"https://doi.org/10.15479/AT:IST-2015-340-v1-1\">10.15479/AT:IST-2015-340-v1-1</a>.","short":"K. Chatterjee, R. Ibsen-Jensen, A.K. Goharshady, A. Pavlogiannis, Algorithms for Algebraic Path Properties in Concurrent Systems of Constant Treewidth Components, IST Austria, 2015."},"year":"2015","publisher":"IST Austria","file":[{"date_updated":"2020-07-14T12:46:56Z","content_type":"application/pdf","creator":"system","relation":"main_file","checksum":"df383dc62c94d7b2ea639aba088a76c6","access_level":"open_access","file_name":"IST-2015-340-v1+1_main.pdf","file_size":861396,"date_created":"2018-12-12T11:54:09Z","file_id":"5531"}],"author":[{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X"},{"last_name":"Ibsen-Jensen","id":"3B699956-F248-11E8-B48F-1D18A9856A87","full_name":"Ibsen-Jensen, Rasmus","first_name":"Rasmus","orcid":"0000-0003-4783-0389"},{"first_name":"Amir","orcid":"0000-0003-1702-6584","id":"391365CE-F248-11E8-B48F-1D18A9856A87","last_name":"Goharshady","full_name":"Goharshady, Amir"},{"full_name":"Pavlogiannis, Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","last_name":"Pavlogiannis","first_name":"Andreas","orcid":"0000-0002-8943-0722"}],"publication_identifier":{"issn":["2664-1690"]},"oa":1,"title":"Algorithms for algebraic path properties in concurrent systems of constant treewidth components","doi":"10.15479/AT:IST-2015-340-v1-1","type":"technical_report","page":"24","language":[{"iso":"eng"}],"department":[{"_id":"KrCh"}],"publication_status":"published","pubrep_id":"340","month":"07","date_created":"2018-12-12T11:39:21Z","related_material":{"record":[{"relation":"earlier_version","id":"5442","status":"public"},{"id":"6009","relation":"later_version","status":"public"},{"status":"public","relation":"later_version","id":"1437"}]}},{"file":[{"creator":"system","date_updated":"2020-07-14T12:46:57Z","content_type":"application/pdf","checksum":"f0fa31ad8161ed655137e94012123ef9","access_level":"open_access","relation":"main_file","file_size":412379,"date_created":"2018-12-12T11:53:05Z","file_name":"IST-2015-325-v2+1_main.pdf","file_id":"5466"}],"publisher":"IST Austria","year":"2015","citation":{"ieee":"K. Chatterjee, M. Chmelik, and J. Davies, <i>A symbolic SAT-based algorithm for almost-sure reachability with small strategies in POMDPs</i>. IST Austria, 2015.","apa":"Chatterjee, K., Chmelik, M., &#38; Davies, J. (2015). <i>A symbolic SAT-based algorithm for almost-sure reachability with small strategies in POMDPs</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2015-325-v2-1\">https://doi.org/10.15479/AT:IST-2015-325-v2-1</a>","ista":"Chatterjee K, Chmelik M, Davies J. 2015. A symbolic SAT-based algorithm for almost-sure reachability with small strategies in POMDPs, IST Austria, 23p.","ama":"Chatterjee K, Chmelik M, Davies J. <i>A Symbolic SAT-Based Algorithm for Almost-Sure Reachability with Small Strategies in POMDPs</i>. IST Austria; 2015. doi:<a href=\"https://doi.org/10.15479/AT:IST-2015-325-v2-1\">10.15479/AT:IST-2015-325-v2-1</a>","mla":"Chatterjee, Krishnendu, et al. <i>A Symbolic SAT-Based Algorithm for Almost-Sure Reachability with Small Strategies in POMDPs</i>. IST Austria, 2015, doi:<a href=\"https://doi.org/10.15479/AT:IST-2015-325-v2-1\">10.15479/AT:IST-2015-325-v2-1</a>.","short":"K. Chatterjee, M. Chmelik, J. Davies, A Symbolic SAT-Based Algorithm for Almost-Sure Reachability with Small Strategies in POMDPs, IST Austria, 2015.","chicago":"Chatterjee, Krishnendu, Martin Chmelik, and Jessica Davies. <i>A Symbolic SAT-Based Algorithm for Almost-Sure Reachability with Small Strategies in POMDPs</i>. IST Austria, 2015. <a href=\"https://doi.org/10.15479/AT:IST-2015-325-v2-1\">https://doi.org/10.15479/AT:IST-2015-325-v2-1</a>."},"day":"06","oa_version":"Published Version","status":"public","_id":"5443","fulldoi":"https://doi.org/10.15479/AT:IST-2015-325-v2-1","has_accepted_license":"1","date_published":"2015-11-06T00:00:00Z","ddc":["000"],"file_date_updated":"2020-07-14T12:46:57Z","abstract":[{"lang":"eng","text":"POMDPs are standard models for probabilistic planning problems, where an agent interacts with an uncertain environment. We study the problem of almost-sure reachability, where given a set of target states, the question is to decide whether there is a policy to ensure that the target set is reached with probability 1 (almost-surely). While in general the problem is EXPTIME-complete, in many practical cases policies with a small amount of memory suffice. Moreover, the existing solution to the problem is explicit, which first requires to construct explicitly an exponential reduction to a belief-support MDP. In this work, we first study the existence of observation-stationary strategies, which is NP-complete, and then small-memory strategies. We present a symbolic algorithm by an efficient encoding to SAT and using a SAT solver for the problem. We report experimental results demonstrating the scalability of our symbolic (SAT-based) approach."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2025-06-25T11:52:13Z","alternative_title":["IST Austria Technical Report"],"related_material":{"record":[{"status":"public","relation":"later_version","id":"1166"}]},"date_created":"2018-12-12T11:39:22Z","month":"11","publication_status":"published","pubrep_id":"362","department":[{"_id":"KrCh"}],"language":[{"iso":"eng"}],"page":"23","type":"technical_report","doi":"10.15479/AT:IST-2015-325-v2-1","title":"A symbolic SAT-based algorithm for almost-sure reachability with small strategies in POMDPs","oa":1,"publication_identifier":{"issn":["2664-1690"]},"author":[{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X"},{"first_name":"Martin","full_name":"Chmelik, Martin","id":"3624234E-F248-11E8-B48F-1D18A9856A87","last_name":"Chmelik"},{"id":"378E0060-F248-11E8-B48F-1D18A9856A87","last_name":"Davies","full_name":"Davies, Jessica","first_name":"Jessica"}]},{"status":"public","_id":"5444","page":"25","department":[{"_id":"KrCh"}],"language":[{"iso":"eng"}],"publication_status":"published","pubrep_id":"399","oa_version":"Published Version","day":"30","month":"12","citation":{"apa":"Reiter, J., Makohon-Moore, A., Gerold, J., Bozic, I., Chatterjee, K., Iacobuzio-Donahue, C., … Nowak, M. (2015). <i>Reconstructing robust phylogenies of metastatic cancers</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2015-399-v1-1\">https://doi.org/10.15479/AT:IST-2015-399-v1-1</a>","ieee":"J. Reiter <i>et al.</i>, <i>Reconstructing robust phylogenies of metastatic cancers</i>. IST Austria, 2015.","ista":"Reiter J, Makohon-Moore A, Gerold J, Bozic I, Chatterjee K, Iacobuzio-Donahue C, Vogelstein B, Nowak M. 2015. Reconstructing robust phylogenies of metastatic cancers, IST Austria, 25p.","ama":"Reiter J, Makohon-Moore A, Gerold J, et al. <i>Reconstructing Robust Phylogenies of Metastatic Cancers</i>. IST Austria; 2015. doi:<a href=\"https://doi.org/10.15479/AT:IST-2015-399-v1-1\">10.15479/AT:IST-2015-399-v1-1</a>","short":"J. Reiter, A. Makohon-Moore, J. Gerold, I. Bozic, K. Chatterjee, C. Iacobuzio-Donahue, B. Vogelstein, M. Nowak, Reconstructing Robust Phylogenies of Metastatic Cancers, IST Austria, 2015.","mla":"Reiter, Johannes, et al. <i>Reconstructing Robust Phylogenies of Metastatic Cancers</i>. IST Austria, 2015, doi:<a href=\"https://doi.org/10.15479/AT:IST-2015-399-v1-1\">10.15479/AT:IST-2015-399-v1-1</a>.","chicago":"Reiter, Johannes, Alvin Makohon-Moore, Jeffrey Gerold, Ivana Bozic, Krishnendu Chatterjee, Christine Iacobuzio-Donahue, Bert Vogelstein, and Martin Nowak. <i>Reconstructing Robust Phylogenies of Metastatic Cancers</i>. IST Austria, 2015. <a href=\"https://doi.org/10.15479/AT:IST-2015-399-v1-1\">https://doi.org/10.15479/AT:IST-2015-399-v1-1</a>."},"year":"2015","publisher":"IST Austria","date_created":"2018-12-12T11:39:22Z","file":[{"file_id":"5485","file_name":"IST-2015-399-v1+1_treeomics.pdf","date_created":"2018-12-12T11:53:24Z","file_size":3533200,"access_level":"open_access","checksum":"c47d33bdda06181753c0af36f16e7b5d","relation":"main_file","content_type":"application/pdf","date_updated":"2020-07-14T12:46:58Z","creator":"system"}],"date_updated":"2020-07-14T23:05:07Z","alternative_title":["IST Austria Technical Report"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2020-07-14T12:46:58Z","author":[{"first_name":"Johannes","orcid":"0000-0002-0170-7353","full_name":"Reiter, Johannes","last_name":"Reiter","id":"4A918E98-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Makohon-Moore, Alvin","last_name":"Makohon-Moore","first_name":"Alvin"},{"last_name":"Gerold","full_name":"Gerold, Jeffrey","first_name":"Jeffrey"},{"last_name":"Bozic","full_name":"Bozic, Ivana","first_name":"Ivana"},{"orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"last_name":"Iacobuzio-Donahue","full_name":"Iacobuzio-Donahue, Christine","first_name":"Christine"},{"last_name":"Vogelstein","full_name":"Vogelstein, Bert","first_name":"Bert"},{"full_name":"Nowak, Martin","last_name":"Nowak","first_name":"Martin"}],"abstract":[{"text":"A comprehensive understanding of the clonal evolution of cancer is critical for understanding neoplasia. Genome-wide sequencing data enables evolutionary studies at unprecedented depth. However, classical phylogenetic methods often struggle with noisy sequencing data of impure DNA samples and fail to detect subclones that have different evolutionary trajectories. We have developed a tool, called Treeomics, that allows us to reconstruct the phylogeny of a cancer with commonly available sequencing technologies. Using Bayesian inference and Integer Linear Programming, robust phylogenies consistent with the biological processes underlying cancer evolution were obtained for pancreatic, ovarian, and prostate cancers. Furthermore, Treeomics correctly identified sequencing artifacts such as those resulting from low statistical power; nearly 7% of variants were misclassified by conventional statistical methods. These artifacts can skew phylogenies by creating illusory tumor heterogeneity among distinct samples. Importantly, we show that the evolutionary trees generated with Treeomics are mathematically optimal.","lang":"eng"}],"ddc":["000","576"],"publication_identifier":{"issn":["2664-1690"]},"has_accepted_license":"1","oa":1,"title":"Reconstructing robust phylogenies of metastatic cancers","date_published":"2015-12-30T00:00:00Z","doi":"10.15479/AT:IST-2015-399-v1-1","fulldoi":"https://doi.org/10.15479/AT:IST-2015-399-v1-1","type":"technical_report"},{"file":[{"access_level":"open_access","checksum":"b8bcb43c0893023cda66c1b69c16ac62","relation":"main_file","creator":"system","date_updated":"2020-07-14T12:47:00Z","content_type":"application/zip","file_id":"5597","date_created":"2018-12-12T13:02:31Z","file_size":49557109,"file_name":"IST-2015-28-v1+2_Fellner_DataRep.zip"}],"citation":{"ista":"Fellner A. 2015. Experimental part of CAV 2015 publication: Counterexample Explanation by Learning Small Strategies in Markov Decision Processes, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:28\">10.15479/AT:ISTA:28</a>.","ama":"Fellner A. Experimental part of CAV 2015 publication: Counterexample Explanation by Learning Small Strategies in Markov Decision Processes. 2015. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:28\">10.15479/AT:ISTA:28</a>","ieee":"A. Fellner, “Experimental part of CAV 2015 publication: Counterexample Explanation by Learning Small Strategies in Markov Decision Processes.” Institute of Science and Technology Austria, 2015.","apa":"Fellner, A. (2015). Experimental part of CAV 2015 publication: Counterexample Explanation by Learning Small Strategies in Markov Decision Processes. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:28\">https://doi.org/10.15479/AT:ISTA:28</a>","chicago":"Fellner, Andreas. “Experimental Part of CAV 2015 Publication: Counterexample Explanation by Learning Small Strategies in Markov Decision Processes.” Institute of Science and Technology Austria, 2015. <a href=\"https://doi.org/10.15479/AT:ISTA:28\">https://doi.org/10.15479/AT:ISTA:28</a>.","short":"A. Fellner, (2015).","mla":"Fellner, Andreas. <i>Experimental Part of CAV 2015 Publication: Counterexample Explanation by Learning Small Strategies in Markov Decision Processes</i>. Institute of Science and Technology Austria, 2015, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:28\">10.15479/AT:ISTA:28</a>."},"year":"2015","publisher":"Institute of Science and Technology Austria","day":"13","oa_version":"Published Version","status":"public","_id":"5549","fulldoi":"https://doi.org/10.15479/AT:ISTA:28","keyword":["Markov Decision Process","Decision Tree","Probabilistic Verification","Counterexample Explanation"],"tmp":{"short":"CC0 (1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","image":"/images/cc_0.png"},"ddc":["004"],"date_published":"2015-08-13T00:00:00Z","has_accepted_license":"1","file_date_updated":"2020-07-14T12:47:00Z","ec_funded":1,"abstract":[{"text":"This repository contains the experimental part of the CAV 2015 publication Counterexample Explanation by Learning Small Strategies in Markov Decision Processes.\r\nWe extended the probabilistic model checker PRISM to represent strategies of Markov Decision Processes as Decision Trees.\r\nThe archive contains a java executable version of the extended tool (prism_dectree.jar) together with a few examples of the PRISM benchmark library.\r\nTo execute the program, please have a look at the README.txt, which provides instructions and further information on the archive.\r\nThe archive contains scripts that (if run often enough) reproduces the data presented in the publication.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"5564","date_updated":"2025-09-23T08:23:15Z","related_material":{"record":[{"status":"public","relation":"popular_science","id":"1603"}]},"project":[{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"date_created":"2018-12-12T12:31:29Z","datarep_id":"28","article_processing_charge":"No","license":"https://creativecommons.org/publicdomain/zero/1.0/","month":"08","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"contributor":[{"first_name":"Jan","last_name":"Kretinsky","id":"44CEF464-F248-11E8-B48F-1D18A9856A87"}],"doi":"10.15479/AT:ISTA:28","type":"research_data","oa":1,"title":"Experimental part of CAV 2015 publication: Counterexample Explanation by Learning Small Strategies in Markov Decision Processes","author":[{"last_name":"Fellner","id":"42BABFB4-F248-11E8-B48F-1D18A9856A87","full_name":"Fellner, Andreas","first_name":"Andreas"}]},{"publication_identifier":{"isbn":["978-1-4503-3300-9"]},"oa":1,"title":"Succinct representation of concurrent trace sets","doi":"10.1145/2676726.2677008","type":"conference","author":[{"first_name":"Ashutosh","last_name":"Gupta","id":"335E5684-F248-11E8-B48F-1D18A9856A87","full_name":"Gupta, Ashutosh"},{"full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","orcid":"0000−0002−2985−7724","first_name":"Thomas A"},{"id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87","last_name":"Radhakrishna","full_name":"Radhakrishna, Arjun","first_name":"Arjun"},{"full_name":"Samanta, Roopsha","id":"3D2AAC08-F248-11E8-B48F-1D18A9856A87","last_name":"Samanta","first_name":"Roopsha"},{"full_name":"Tarrach, Thorsten","id":"3D6E8F2C-F248-11E8-B48F-1D18A9856A87","last_name":"Tarrach","orcid":"0000-0003-4409-8487","first_name":"Thorsten"}],"conference":{"end_date":"2015-01-17","name":"POPL: Principles of Programming Languages","location":"Mumbai, India","start_date":"2015-01-15"},"scopus_import":"1","quality_controlled":"1","date_created":"2018-12-11T11:55:05Z","article_processing_charge":"No","month":"01","page":"433 - 444","language":[{"iso":"eng"}],"department":[{"_id":"ToHe"}],"pubrep_id":"317","publication_status":"published","ddc":["005"],"has_accepted_license":"1","date_published":"2015-01-15T00:00:00Z","fulldoi":"https://doi.org/10.1145/2676726.2677008","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"We present a method and a tool for generating succinct representations of sets of concurrent traces. We focus on trace sets that contain all correct or all incorrect permutations of events from a given trace. We represent trace sets as HB-Formulas that are Boolean combinations of happens-before constraints between events. To generate a representation of incorrect interleavings, our method iteratively explores interleavings that violate the specification and gathers generalizations of the discovered interleavings into an HB-Formula; its complement yields a representation of correct interleavings.\r\n\r\nWe claim that our trace set representations can drive diverse verification, fault localization, repair, and synthesis techniques for concurrent programs. We demonstrate this by using our tool in three case studies involving synchronization synthesis, bug summarization, and abstraction refinement based verification. In each case study, our initial experimental results have been promising.\r\n\r\nIn the first case study, we present an algorithm for inferring missing synchronization from an HB-Formula representing correct interleavings of a given trace. The algorithm applies rules to rewrite specific patterns in the HB-Formula into locks, barriers, and wait-notify constructs. In the second case study, we use an HB-Formula representing incorrect interleavings for bug summarization. While the HB-Formula itself is a concise counterexample summary, we present additional inference rules to help identify specific concurrency bugs such as data races, define-use order violations, and two-stage access bugs. In the final case study, we present a novel predicate learning procedure that uses HB-Formulas representing abstract counterexamples to accelerate counterexample-guided abstraction refinement (CEGAR). In each iteration of the CEGAR loop, the procedure refines the abstraction to eliminate multiple spurious abstract counterexamples drawn from the HB-Formula.","lang":"eng"}],"file_date_updated":"2020-07-14T12:45:22Z","publist_id":"5091","date_updated":"2025-03-07T08:44:29Z","file":[{"creator":"system","content_type":"application/pdf","date_updated":"2020-07-14T12:45:22Z","access_level":"open_access","checksum":"f0d4395b600f410a191256ac0b73af32","relation":"main_file","date_created":"2018-12-12T10:17:56Z","file_size":399462,"file_name":"IST-2015-317-v1+1_author_version.pdf","file_id":"5314"}],"day":"15","citation":{"chicago":"Gupta, Ashutosh, Thomas A Henzinger, Arjun Radhakrishna, Roopsha Samanta, and Thorsten Tarrach. “Succinct Representation of Concurrent Trace Sets,” 433–44. ACM, 2015. <a href=\"https://doi.org/10.1145/2676726.2677008\">https://doi.org/10.1145/2676726.2677008</a>.","mla":"Gupta, Ashutosh, et al. <i>Succinct Representation of Concurrent Trace Sets</i>. ACM, 2015, pp. 433–44, doi:<a href=\"https://doi.org/10.1145/2676726.2677008\">10.1145/2676726.2677008</a>.","short":"A. Gupta, T.A. Henzinger, A. Radhakrishna, R. Samanta, T. Tarrach, in:, ACM, 2015, pp. 433–444.","ama":"Gupta A, Henzinger TA, Radhakrishna A, Samanta R, Tarrach T. Succinct representation of concurrent trace sets. In: ACM; 2015:433-444. doi:<a href=\"https://doi.org/10.1145/2676726.2677008\">10.1145/2676726.2677008</a>","ista":"Gupta A, Henzinger TA, Radhakrishna A, Samanta R, Tarrach T. 2015. Succinct representation of concurrent trace sets. POPL: Principles of Programming Languages, 433–444.","ieee":"A. Gupta, T. A. Henzinger, A. Radhakrishna, R. Samanta, and T. Tarrach, “Succinct representation of concurrent trace sets,” presented at the POPL: Principles of Programming Languages, Mumbai, India, 2015, pp. 433–444.","apa":"Gupta, A., Henzinger, T. A., Radhakrishna, A., Samanta, R., &#38; Tarrach, T. (2015). Succinct representation of concurrent trace sets (pp. 433–444). Presented at the POPL: Principles of Programming Languages, Mumbai, India: ACM. <a href=\"https://doi.org/10.1145/2676726.2677008\">https://doi.org/10.1145/2676726.2677008</a>"},"year":"2015","publisher":"ACM","_id":"1992","status":"public","oa_version":"Submitted Version"},{"date_created":"2018-12-11T11:55:06Z","article_processing_charge":"No","quality_controlled":"1","related_material":{"record":[{"id":"9740","relation":"research_data","status":"public"}]},"project":[{"grant_number":"243071","name":"Social Vaccination in Ant Colonies: from Individual Mechanisms to Society Effects","_id":"25DC711C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"grant_number":"CR-118/3-1","_id":"25DAF0B2-B435-11E9-9278-68D0E5697425","name":"Host-Parasite Coevolution"}],"volume":282,"language":[{"iso":"eng"}],"department":[{"_id":"SyCr"}],"publication_status":"published","month":"01","doi":"10.1098/rspb.2014.1976","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4286035/"}],"type":"journal_article","publication_identifier":{"eissn":["1471-2954"],"issn":["0962-8452"]},"pmid":1,"title":"Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host","oa":1,"article_number":"20141976","scopus_import":"1","corr_author":"1","author":[{"full_name":"Konrad, Matthias","id":"46528076-F248-11E8-B48F-1D18A9856A87","last_name":"Konrad","first_name":"Matthias"},{"first_name":"Anna V","id":"406F989C-F248-11E8-B48F-1D18A9856A87","last_name":"Grasse","full_name":"Grasse, Anna V"},{"first_name":"Simon","id":"35A7A418-F248-11E8-B48F-1D18A9856A87","last_name":"Tragust","full_name":"Tragust, Simon"},{"last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868","first_name":"Sylvia"}],"publication":"Proceedings of the Royal Society of London Series B Biological Sciences","acknowledged_ssus":[{"_id":"EM-Fac"}],"intvolume":"       282","external_id":{"isi":["000345624600008"],"pmid":["25473011"]},"issue":"1799","oa_version":"Submitted Version","_id":"1993","status":"public","acknowledgement":"Funding was obtained by the German Research Foundation (CR 118–2) and an ERC StG (243071) by the European Research Council (both to S.C.).\r\nWe thank Line V. Ugelvig for help with ant collection and statistical discussion, Xavier Espadaler for detailed information on the ant collection site, Birgit Lautenschläger for the electron microscopy images and Eva Sixt for ant drawings. We further thank Jørgen Eilenberg for the fungal strain, Meghan L. Vyleta for genetic strain characterization and immune gene primer development, Paul Schmid-Hempel for discussion, and Line V. Ugelvig, Xavier Espadaler and Christopher D. Pull for comments on the manuscript. S.C., M.K. and S.T. conceived the study; M.K. and A.V.G. performed the experiments; M.K. performed the statistical analysis; S.C. and M.K. wrote the manuscript with intense contributions of A.V.G. and S.T.; all authors approved the manuscript.","citation":{"ista":"Konrad M, Grasse AV, Tragust S, Cremer S. 2015. Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host. Proceedings of the Royal Society of London Series B Biological Sciences. 282(1799), 20141976.","ama":"Konrad M, Grasse AV, Tragust S, Cremer S. Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host. <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>. 2015;282(1799). doi:<a href=\"https://doi.org/10.1098/rspb.2014.1976\">10.1098/rspb.2014.1976</a>","apa":"Konrad, M., Grasse, A. V., Tragust, S., &#38; Cremer, S. (2015). Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host. <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>. The Royal Society. <a href=\"https://doi.org/10.1098/rspb.2014.1976\">https://doi.org/10.1098/rspb.2014.1976</a>","ieee":"M. Konrad, A. V. Grasse, S. Tragust, and S. Cremer, “Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host,” <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>, vol. 282, no. 1799. The Royal Society, 2015.","chicago":"Konrad, Matthias, Anna V Grasse, Simon Tragust, and Sylvia Cremer. “Anti-Pathogen Protection versus Survival Costs Mediated by an Ectosymbiont in an Ant Host.” <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>. The Royal Society, 2015. <a href=\"https://doi.org/10.1098/rspb.2014.1976\">https://doi.org/10.1098/rspb.2014.1976</a>.","short":"M. Konrad, A.V. Grasse, S. Tragust, S. Cremer, Proceedings of the Royal Society of London Series B Biological Sciences 282 (2015).","mla":"Konrad, Matthias, et al. “Anti-Pathogen Protection versus Survival Costs Mediated by an Ectosymbiont in an Ant Host.” <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>, vol. 282, no. 1799, 20141976, The Royal Society, 2015, doi:<a href=\"https://doi.org/10.1098/rspb.2014.1976\">10.1098/rspb.2014.1976</a>."},"year":"2015","publisher":"The Royal Society","day":"22","isi":1,"article_type":"original","fulldoi":"https://doi.org/10.1098/rspb.2014.1976","date_published":"2015-01-22T00:00:00Z","publist_id":"5090","date_updated":"2025-09-23T07:55:03Z","ec_funded":1,"abstract":[{"lang":"eng","text":"The fitness effects of symbionts on their hosts can be context-dependent, with usually benign symbionts causing detrimental effects when their hosts are stressed, or typically parasitic symbionts providing protection towards their hosts (e.g. against pathogen infection). Here, we studied the novel association between the invasive garden ant Lasius neglectus and its fungal ectosymbiont Laboulbenia formicarum for potential costs and benefits. We tested ants with different Laboulbenia levels for their survival and immunity under resource limitation and exposure to the obligate killing entomopathogen Metarhizium brunneum. While survival of L. neglectus workers under starvation was significantly decreased with increasing Laboulbenia levels, host survival under Metarhizium exposure increased with higher levels of the ectosymbiont, suggesting a symbiont-mediated anti-pathogen protection, which seems to be driven mechanistically by both improved sanitary behaviours and an upregulated immune system. Ants with high Laboulbenia levels showed significantly longer self-grooming and elevated expression of immune genes relevant for wound repair and antifungal responses (β-1,3-glucan binding protein, Prophenoloxidase), compared with ants carrying low Laboulbenia levels. This suggests that the ectosymbiont Laboulbenia formicarum weakens its ant host by either direct resource exploitation or the costs of an upregulated behavioural and immunological response, which, however, provides a prophylactic protection upon later exposure to pathogens. "}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345"},{"date_published":"2015-05-01T00:00:00Z","fulldoi":"https://doi.org/10.1016/j.jsc.2014.09.014","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","abstract":[{"lang":"eng","text":"We prove that the three-state toric homogeneous Markov chain model has Markov degree two. In algebraic terminology this means, that a certain class of toric ideals is generated by quadratic binomials. This was conjectured by Haws, Martin del Campo, Takemura and Yoshida, who proved that they are generated by degree six binomials."}],"publist_id":"5082","date_updated":"2025-09-23T14:17:34Z","issue":"May-June","external_id":{"isi":["000347767600016"],"arxiv":["1207.0077"]},"isi":1,"day":"01","arxiv":1,"publisher":"Elsevier","citation":{"apa":"Noren, P. (2015). The three-state toric homogeneous Markov chain model has Markov degree two. <i>Journal of Symbolic Computation</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jsc.2014.09.014\">https://doi.org/10.1016/j.jsc.2014.09.014</a>","ieee":"P. Noren, “The three-state toric homogeneous Markov chain model has Markov degree two,” <i>Journal of Symbolic Computation</i>, vol. 68/Part 2, no. May-June. Elsevier, pp. 285–296, 2015.","ama":"Noren P. The three-state toric homogeneous Markov chain model has Markov degree two. <i>Journal of Symbolic Computation</i>. 2015;68/Part 2(May-June):285-296. doi:<a href=\"https://doi.org/10.1016/j.jsc.2014.09.014\">10.1016/j.jsc.2014.09.014</a>","ista":"Noren P. 2015. The three-state toric homogeneous Markov chain model has Markov degree two. Journal of Symbolic Computation. 68/Part 2(May-June), 285–296.","mla":"Noren, Patrik. “The Three-State Toric Homogeneous Markov Chain Model Has Markov Degree Two.” <i>Journal of Symbolic Computation</i>, vol. 68/Part 2, no. May-June, Elsevier, 2015, pp. 285–96, doi:<a href=\"https://doi.org/10.1016/j.jsc.2014.09.014\">10.1016/j.jsc.2014.09.014</a>.","short":"P. Noren, Journal of Symbolic Computation 68/Part 2 (2015) 285–296.","chicago":"Noren, Patrik. “The Three-State Toric Homogeneous Markov Chain Model Has Markov Degree Two.” <i>Journal of Symbolic Computation</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.jsc.2014.09.014\">https://doi.org/10.1016/j.jsc.2014.09.014</a>."},"year":"2015","status":"public","_id":"1997","oa_version":"Preprint","title":"The three-state toric homogeneous Markov chain model has Markov degree two","oa":1,"type":"journal_article","main_file_link":[{"url":"http://arxiv.org/abs/1207.0077","open_access":"1"}],"doi":"10.1016/j.jsc.2014.09.014","publication":"Journal of Symbolic Computation","author":[{"full_name":"Noren, Patrik","id":"46870C74-F248-11E8-B48F-1D18A9856A87","last_name":"Noren","first_name":"Patrik"}],"corr_author":"1","scopus_import":"1","quality_controlled":"1","article_processing_charge":"No","date_created":"2018-12-11T11:55:07Z","month":"05","page":"285 - 296","publication_status":"published","language":[{"iso":"eng"}],"department":[{"_id":"CaUh"}],"volume":"68/Part 2"},{"external_id":{"isi":["000356873900001"],"arxiv":["1109.3436"]},"issue":"3","intvolume":"        24","arxiv":1,"day":"23","isi":1,"year":"2015","citation":{"ieee":"N. Hein, C. Hillar, A. Martin del Campo Sanchez, F. Sottile, and Z. Teitler, “The monotone secant conjecture in the real Schubert calculus,” <i>Experimental Mathematics</i>, vol. 24, no. 3. Taylor &#38; Francis, pp. 261–269, 2015.","apa":"Hein, N., Hillar, C., Martin del Campo Sanchez, A., Sottile, F., &#38; Teitler, Z. (2015). The monotone secant conjecture in the real Schubert calculus. <i>Experimental Mathematics</i>. Taylor &#38; Francis. <a href=\"https://doi.org/10.1080/10586458.2014.980044\">https://doi.org/10.1080/10586458.2014.980044</a>","ista":"Hein N, Hillar C, Martin del Campo Sanchez A, Sottile F, Teitler Z. 2015. The monotone secant conjecture in the real Schubert calculus. Experimental Mathematics. 24(3), 261–269.","ama":"Hein N, Hillar C, Martin del Campo Sanchez A, Sottile F, Teitler Z. The monotone secant conjecture in the real Schubert calculus. <i>Experimental Mathematics</i>. 2015;24(3):261-269. doi:<a href=\"https://doi.org/10.1080/10586458.2014.980044\">10.1080/10586458.2014.980044</a>","mla":"Hein, Nicolas, et al. “The Monotone Secant Conjecture in the Real Schubert Calculus.” <i>Experimental Mathematics</i>, vol. 24, no. 3, Taylor &#38; Francis, 2015, pp. 261–69, doi:<a href=\"https://doi.org/10.1080/10586458.2014.980044\">10.1080/10586458.2014.980044</a>.","short":"N. Hein, C. Hillar, A. Martin del Campo Sanchez, F. Sottile, Z. Teitler, Experimental Mathematics 24 (2015) 261–269.","chicago":"Hein, Nicolas, Christopher Hillar, Abraham Martin del Campo Sanchez, Frank Sottile, and Zach Teitler. “The Monotone Secant Conjecture in the Real Schubert Calculus.” <i>Experimental Mathematics</i>. Taylor &#38; Francis, 2015. <a href=\"https://doi.org/10.1080/10586458.2014.980044\">https://doi.org/10.1080/10586458.2014.980044</a>."},"publisher":"Taylor & Francis","status":"public","_id":"2006","oa_version":"Preprint","date_published":"2015-06-23T00:00:00Z","fulldoi":"https://doi.org/10.1080/10586458.2014.980044","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","abstract":[{"text":"The monotone secant conjecture posits a rich class of polynomial systems, all of whose solutions are real. These systems come from the Schubert calculus on flag manifolds, and the monotone secant conjecture is a compelling generalization of the Shapiro conjecture for Grassmannians (Theorem of Mukhin, Tarasov, and Varchenko). We present some theoretical evidence for this conjecture, as well as computational evidence obtained by 1.9 teraHertz-years of computing, and we discuss some of the phenomena we observed in our data. ","lang":"eng"}],"publist_id":"5070","date_updated":"2025-09-23T14:07:49Z","quality_controlled":"1","date_created":"2018-12-11T11:55:10Z","article_processing_charge":"No","month":"06","page":"261 - 269","department":[{"_id":"CaUh"}],"volume":24,"language":[{"iso":"eng"}],"publication_status":"published","oa":1,"title":"The monotone secant conjecture in the real Schubert calculus","doi":"10.1080/10586458.2014.980044","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1109.3436"}],"type":"journal_article","publication":"Experimental Mathematics","author":[{"last_name":"Hein","full_name":"Hein, Nicolas","first_name":"Nicolas"},{"first_name":"Christopher","last_name":"Hillar","full_name":"Hillar, Christopher"},{"first_name":"Abraham","full_name":"Martin Del Campo Sanchez, Abraham","last_name":"Martin Del Campo Sanchez","id":"4CF47F6A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Frank","last_name":"Sottile","full_name":"Sottile, Frank"},{"first_name":"Zach","full_name":"Teitler, Zach","last_name":"Teitler"}],"scopus_import":"1"},{"publisher":"Wiley","acknowledgement":"Part of the material presented here was contained in the PhD thesis of the first author to which the second author and Thomas Richardson were advisers. The authors wish to thank him for several comments and suggestions. We also thank the reviewers and the Associate Editor for helpful comments. The proof of Proposition 1 uses the idea of Olga Klimova, to whom the authors are also indebted. The second author was supported in part by Grant K-106154 from the Hungarian National Scientific Research Fund (OTKA).","year":"2015","citation":{"apa":"Klimova, A., &#38; Rudas, T. (2015). Iterative scaling in curved exponential families. <i>Scandinavian Journal of Statistics</i>. Wiley. <a href=\"https://doi.org/10.1111/sjos.12139\">https://doi.org/10.1111/sjos.12139</a>","ieee":"A. Klimova and T. Rudas, “Iterative scaling in curved exponential families,” <i>Scandinavian Journal of Statistics</i>, vol. 42, no. 3. Wiley, pp. 832–847, 2015.","ista":"Klimova A, Rudas T. 2015. Iterative scaling in curved exponential families. Scandinavian Journal of Statistics. 42(3), 832–847.","ama":"Klimova A, Rudas T. Iterative scaling in curved exponential families. <i>Scandinavian Journal of Statistics</i>. 2015;42(3):832-847. doi:<a href=\"https://doi.org/10.1111/sjos.12139\">10.1111/sjos.12139</a>","short":"A. Klimova, T. Rudas, Scandinavian Journal of Statistics 42 (2015) 832–847.","mla":"Klimova, Anna, and Tamás Rudas. “Iterative Scaling in Curved Exponential Families.” <i>Scandinavian Journal of Statistics</i>, vol. 42, no. 3, Wiley, 2015, pp. 832–47, doi:<a href=\"https://doi.org/10.1111/sjos.12139\">10.1111/sjos.12139</a>.","chicago":"Klimova, Anna, and Tamás Rudas. “Iterative Scaling in Curved Exponential Families.” <i>Scandinavian Journal of Statistics</i>. Wiley, 2015. <a href=\"https://doi.org/10.1111/sjos.12139\">https://doi.org/10.1111/sjos.12139</a>."},"isi":1,"day":"01","arxiv":1,"oa_version":"Preprint","status":"public","_id":"2008","intvolume":"        42","issue":"3","external_id":{"isi":["000360077100012"],"arxiv":["1307.3282"]},"abstract":[{"lang":"eng","text":"The paper describes a generalized iterative proportional fitting procedure that can be used for maximum likelihood estimation in a special class of the general log-linear model. The models in this class, called relational, apply to multivariate discrete sample spaces that do not necessarily have a Cartesian product structure and may not contain an overall effect. When applied to the cell probabilities, the models without the overall effect are curved exponential families and the values of the sufficient statistics are reproduced by the MLE only up to a constant of proportionality. The paper shows that Iterative Proportional Fitting, Generalized Iterative Scaling, and Improved Iterative Scaling fail to work for such models. The algorithm proposed here is based on iterated Bregman projections. As a by-product, estimates of the multiplicative parameters are also obtained. An implementation of the algorithm is available as an R-package."}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2025-09-23T09:25:01Z","publist_id":"5068","fulldoi":"https://doi.org/10.1111/sjos.12139","date_published":"2015-09-01T00:00:00Z","month":"09","publication_status":"published","volume":42,"language":[{"iso":"eng"}],"department":[{"_id":"CaUh"}],"page":"832 - 847","quality_controlled":"1","article_processing_charge":"No","date_created":"2018-12-11T11:55:11Z","author":[{"first_name":"Anna","last_name":"Klimova","id":"31934120-F248-11E8-B48F-1D18A9856A87","full_name":"Klimova, Anna"},{"first_name":"Tamás","last_name":"Rudas","full_name":"Rudas, Tamás"}],"publication":"Scandinavian Journal of Statistics","scopus_import":"1","type":"journal_article","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1307.3282"}],"doi":"10.1111/sjos.12139","title":"Iterative scaling in curved exponential families","oa":1},{"publist_id":"5062","date_updated":"2025-09-23T08:45:54Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","abstract":[{"text":"The concepts of faithfulness and strong-faithfulness are important for statistical learning of graphical models. Graphs are not sufficient for describing the association structure of a discrete distribution. Hypergraphs representing hierarchical log-linear models are considered instead, and the concept of parametric (strong-) faithfulness with respect to a hypergraph is introduced. Strong-faithfulness ensures the existence of uniformly consistent parameter estimators and enables building uniformly consistent procedures for a hypergraph search. The strength of association in a discrete distribution can be quantified with various measures, leading to different concepts of strong-faithfulness. Lower and upper bounds for the proportions of distributions that do not satisfy strong-faithfulness are computed for different parameterizations and measures of association.","lang":"eng"}],"date_published":"2015-07-01T00:00:00Z","fulldoi":"https://doi.org/10.1016/j.csda.2015.01.017","_id":"2014","status":"public","oa_version":"Preprint","isi":1,"arxiv":1,"day":"01","publisher":"Elsevier","year":"2015","citation":{"ieee":"A. Klimova, C. Uhler, and T. Rudas, “Faithfulness and learning hypergraphs from discrete distributions,” <i>Computational Statistics &#38; Data Analysis</i>, vol. 87, no. 7. Elsevier, pp. 57–72, 2015.","apa":"Klimova, A., Uhler, C., &#38; Rudas, T. (2015). Faithfulness and learning hypergraphs from discrete distributions. <i>Computational Statistics &#38; Data Analysis</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.csda.2015.01.017\">https://doi.org/10.1016/j.csda.2015.01.017</a>","ista":"Klimova A, Uhler C, Rudas T. 2015. Faithfulness and learning hypergraphs from discrete distributions. Computational Statistics &#38; Data Analysis. 87(7), 57–72.","ama":"Klimova A, Uhler C, Rudas T. Faithfulness and learning hypergraphs from discrete distributions. <i>Computational Statistics &#38; Data Analysis</i>. 2015;87(7):57-72. doi:<a href=\"https://doi.org/10.1016/j.csda.2015.01.017\">10.1016/j.csda.2015.01.017</a>","mla":"Klimova, Anna, et al. “Faithfulness and Learning Hypergraphs from Discrete Distributions.” <i>Computational Statistics &#38; Data Analysis</i>, vol. 87, no. 7, Elsevier, 2015, pp. 57–72, doi:<a href=\"https://doi.org/10.1016/j.csda.2015.01.017\">10.1016/j.csda.2015.01.017</a>.","short":"A. Klimova, C. Uhler, T. Rudas, Computational Statistics &#38; Data Analysis 87 (2015) 57–72.","chicago":"Klimova, Anna, Caroline Uhler, and Tamás Rudas. “Faithfulness and Learning Hypergraphs from Discrete Distributions.” <i>Computational Statistics &#38; Data Analysis</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.csda.2015.01.017\">https://doi.org/10.1016/j.csda.2015.01.017</a>."},"issue":"7","external_id":{"arxiv":["1404.6617"],"isi":["000352661000005"]},"intvolume":"        87","corr_author":"1","scopus_import":"1","publication":"Computational Statistics & Data Analysis","author":[{"first_name":"Anna","id":"31934120-F248-11E8-B48F-1D18A9856A87","last_name":"Klimova","full_name":"Klimova, Anna"},{"orcid":"0000-0002-7008-0216","first_name":"Caroline","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","last_name":"Uhler","full_name":"Uhler, Caroline"},{"first_name":"Tamás","last_name":"Rudas","full_name":"Rudas, Tamás"}],"title":"Faithfulness and learning hypergraphs from discrete distributions","oa":1,"type":"journal_article","doi":"10.1016/j.csda.2015.01.017","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1404.6617"}],"page":"57 - 72","publication_status":"published","department":[{"_id":"CaUh"}],"language":[{"iso":"eng"}],"volume":87,"month":"07","article_processing_charge":"No","date_created":"2018-12-11T11:55:13Z","quality_controlled":"1"},{"date_published":"2015-01-01T00:00:00Z","has_accepted_license":"1","ddc":["570"],"tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"fulldoi":"https://doi.org/10.1016/j.bbamcr.2014.10.009","publist_id":"5047","date_updated":"2025-09-23T14:51:55Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","abstract":[{"lang":"eng","text":"Small GTP-binding proteins of the Ras superfamily play diverse roles in intracellular trafficking. Among them, the Rab, Arf, and Rho families function in successive steps of vesicle transport, in forming vesicles from donor membranes, directing vesicle trafficking toward target membranes and docking vesicles onto target membranes. These proteins act as molecular switches that are controlled by a cycle of GTP binding and hydrolysis regulated by guanine nucleotide exchange factors (GEFs) and GTPase-activating proteins (GAPs). In this study we explored the role of GAPs in the regulation of the endocytic pathway using fluorescently labeled yeast mating pheromone α-factor. Among 25 non-essential GAP mutants, we found that deletion of the GLO3 gene, encoding Arf-GAP protein, caused defective internalization of fluorescently labeled α-factor. Quantitative analysis revealed that glo3Δ cells show defective α-factor binding to the cell surface. Interestingly, Ste2p, the α-factor receptor, was mis-localized from the plasma membrane to the vacuole in glo3Δ cells. Domain deletion mutants of Glo3p revealed that a GAP-independent function, as well as the GAP activity, of Glo3p is important for both α-factor binding and Ste2p localization at the cell surface. Additionally, we found that deletion of the GLO3 gene affects the size and number of Arf1p-residing Golgi compartments and causes a defect in transport from the TGN to the plasma membrane. Furthermore, we demonstrated that glo3Δ cells were defective in the late endosome-to-TGN transport pathway, but not in the early endosome-to-TGN transport pathway. These findings suggest novel roles for Arf-GAP Glo3p in endocytic recycling of cell surface proteins."}],"file_date_updated":"2020-07-14T12:45:25Z","issue":"1","external_id":{"isi":["000347598100014"]},"intvolume":"      1853","file":[{"file_name":"IST-2016-615-v1+1_BBAMCR.pdf","date_created":"2018-12-12T10:12:18Z","file_size":926685,"file_id":"4936","content_type":"application/pdf","date_updated":"2020-07-14T12:45:25Z","creator":"system","relation":"main_file","access_level":"open_access","checksum":"5bb328edebb6a91337cadd7d63f961b7"}],"_id":"2025","status":"public","oa_version":"Submitted Version","isi":1,"day":"01","publisher":"Elsevier","year":"2015","citation":{"ieee":"D. Kawada <i>et al.</i>, “The yeast Arf-GAP Glo3p is required for the endocytic recycling of cell surface proteins,” <i>Biochimica et Biophysica Acta - Molecular Cell Research</i>, vol. 1853, no. 1. Elsevier, pp. 144–156, 2015.","apa":"Kawada, D., Kobayashi, H., Tomita, T., Nakata, E., Nagano, M., Siekhaus, D. E., … Toshimaa, J. (2015). The yeast Arf-GAP Glo3p is required for the endocytic recycling of cell surface proteins. <i>Biochimica et Biophysica Acta - Molecular Cell Research</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.bbamcr.2014.10.009\">https://doi.org/10.1016/j.bbamcr.2014.10.009</a>","ista":"Kawada D, Kobayashi H, Tomita T, Nakata E, Nagano M, Siekhaus DE, Toshima J, Toshimaa J. 2015. The yeast Arf-GAP Glo3p is required for the endocytic recycling of cell surface proteins. Biochimica et Biophysica Acta - Molecular Cell Research. 1853(1), 144–156.","ama":"Kawada D, Kobayashi H, Tomita T, et al. The yeast Arf-GAP Glo3p is required for the endocytic recycling of cell surface proteins. <i>Biochimica et Biophysica Acta - Molecular Cell Research</i>. 2015;1853(1):144-156. doi:<a href=\"https://doi.org/10.1016/j.bbamcr.2014.10.009\">10.1016/j.bbamcr.2014.10.009</a>","mla":"Kawada, Daiki, et al. “The Yeast Arf-GAP Glo3p Is Required for the Endocytic Recycling of Cell Surface Proteins.” <i>Biochimica et Biophysica Acta - Molecular Cell Research</i>, vol. 1853, no. 1, Elsevier, 2015, pp. 144–56, doi:<a href=\"https://doi.org/10.1016/j.bbamcr.2014.10.009\">10.1016/j.bbamcr.2014.10.009</a>.","short":"D. Kawada, H. Kobayashi, T. Tomita, E. Nakata, M. Nagano, D.E. Siekhaus, J. Toshima, J. Toshimaa, Biochimica et Biophysica Acta - Molecular Cell Research 1853 (2015) 144–156.","chicago":"Kawada, Daiki, Hiromu Kobayashi, Tsuyoshi Tomita, Eisuke Nakata, Makoto Nagano, Daria E Siekhaus, Junko Toshima, and Jiro Toshimaa. “The Yeast Arf-GAP Glo3p Is Required for the Endocytic Recycling of Cell Surface Proteins.” <i>Biochimica et Biophysica Acta - Molecular Cell Research</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.bbamcr.2014.10.009\">https://doi.org/10.1016/j.bbamcr.2014.10.009</a>."},"title":"The yeast Arf-GAP Glo3p is required for the endocytic recycling of cell surface proteins","oa":1,"type":"journal_article","doi":"10.1016/j.bbamcr.2014.10.009","scopus_import":"1","publication":"Biochimica et Biophysica Acta - Molecular Cell Research","author":[{"first_name":"Daiki","last_name":"Kawada","full_name":"Kawada, Daiki"},{"last_name":"Kobayashi","full_name":"Kobayashi, Hiromu","first_name":"Hiromu"},{"last_name":"Tomita","full_name":"Tomita, Tsuyoshi","first_name":"Tsuyoshi"},{"last_name":"Nakata","full_name":"Nakata, Eisuke","first_name":"Eisuke"},{"first_name":"Makoto","last_name":"Nagano","full_name":"Nagano, Makoto"},{"orcid":"0000-0001-8323-8353","first_name":"Daria E","full_name":"Siekhaus, Daria E","last_name":"Siekhaus","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Junko","full_name":"Toshima, Junko","last_name":"Toshima"},{"full_name":"Toshimaa, Jiro","last_name":"Toshimaa","first_name":"Jiro"}],"article_processing_charge":"No","date_created":"2018-12-11T11:55:17Z","quality_controlled":"1","page":"144 - 156","pubrep_id":"615","publication_status":"published","department":[{"_id":"DaSi"}],"language":[{"iso":"eng"}],"volume":1853,"month":"01"},{"_id":"2030","status":"public","oa_version":"Preprint","day":"01","arxiv":1,"isi":1,"year":"2015","citation":{"chicago":"Shi, Liang, Markus Rampp, Björn Hof, and Marc Avila. “A Hybrid MPI-OpenMP Parallel Implementation for Pseudospectral Simulations with Application to Taylor-Couette Flow.” <i>Computers and Fluids</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.compfluid.2014.09.021\">https://doi.org/10.1016/j.compfluid.2014.09.021</a>.","mla":"Shi, Liang, et al. “A Hybrid MPI-OpenMP Parallel Implementation for Pseudospectral Simulations with Application to Taylor-Couette Flow.” <i>Computers and Fluids</i>, vol. 106, no. 1, Elsevier, 2015, pp. 1–11, doi:<a href=\"https://doi.org/10.1016/j.compfluid.2014.09.021\">10.1016/j.compfluid.2014.09.021</a>.","short":"L. Shi, M. Rampp, B. Hof, M. Avila, Computers and Fluids 106 (2015) 1–11.","ama":"Shi L, Rampp M, Hof B, Avila M. A hybrid MPI-OpenMP parallel implementation for pseudospectral simulations with application to Taylor-Couette flow. <i>Computers and Fluids</i>. 2015;106(1):1-11. doi:<a href=\"https://doi.org/10.1016/j.compfluid.2014.09.021\">10.1016/j.compfluid.2014.09.021</a>","ista":"Shi L, Rampp M, Hof B, Avila M. 2015. A hybrid MPI-OpenMP parallel implementation for pseudospectral simulations with application to Taylor-Couette flow. Computers and Fluids. 106(1), 1–11.","ieee":"L. Shi, M. Rampp, B. Hof, and M. Avila, “A hybrid MPI-OpenMP parallel implementation for pseudospectral simulations with application to Taylor-Couette flow,” <i>Computers and Fluids</i>, vol. 106, no. 1. Elsevier, pp. 1–11, 2015.","apa":"Shi, L., Rampp, M., Hof, B., &#38; Avila, M. (2015). A hybrid MPI-OpenMP parallel implementation for pseudospectral simulations with application to Taylor-Couette flow. <i>Computers and Fluids</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.compfluid.2014.09.021\">https://doi.org/10.1016/j.compfluid.2014.09.021</a>"},"publisher":"Elsevier","external_id":{"isi":["000346213200001"],"arxiv":["1311.2481"]},"issue":"1","intvolume":"       106","date_updated":"2025-09-22T14:31:33Z","publist_id":"5042","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","abstract":[{"text":"A hybrid-parallel direct-numerical-simulation method with application to turbulent Taylor-Couette flow is presented. The Navier-Stokes equations are discretized in cylindrical coordinates with the spectral Fourier-Galerkin method in the axial and azimuthal directions, and high-order finite differences in the radial direction. Time is advanced by a second-order, semi-implicit projection scheme, which requires the solution of five Helmholtz/Poisson equations, avoids staggered grids and renders very small slip velocities. Nonlinear terms are evaluated with the pseudospectral method. The code is parallelized using a hybrid MPI-OpenMP strategy, which, compared with a flat MPI parallelization, is simpler to implement, allows to reduce inter-node communications and MPI overhead that become relevant at high processor-core counts, and helps to contain the memory footprint. A strong scaling study shows that the hybrid code maintains scalability up to more than 20,000 processor cores and thus allows to perform simulations at higher resolutions than previously feasible. In particular, it opens up the possibility to simulate turbulent Taylor-Couette flows at Reynolds numbers up to O(105). This enables to probe hydrodynamic turbulence in Keplerian flows in experimentally relevant regimes.","lang":"eng"}],"date_published":"2015-01-01T00:00:00Z","fulldoi":"https://doi.org/10.1016/j.compfluid.2014.09.021","page":"1 - 11","department":[{"_id":"BjHo"}],"volume":106,"language":[{"iso":"eng"}],"publication_status":"published","month":"01","date_created":"2018-12-11T11:55:18Z","article_processing_charge":"No","quality_controlled":"1","scopus_import":"1","publication":"Computers and Fluids","author":[{"first_name":"Liang","full_name":"Shi, Liang","id":"374A3F1A-F248-11E8-B48F-1D18A9856A87","last_name":"Shi"},{"first_name":"Markus","last_name":"Rampp","full_name":"Rampp, Markus"},{"id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof","full_name":"Hof, Björn","orcid":"0000-0003-2057-2754","first_name":"Björn"},{"first_name":"Marc","last_name":"Avila","full_name":"Avila, Marc"}],"oa":1,"title":"A hybrid MPI-OpenMP parallel implementation for pseudospectral simulations with application to Taylor-Couette flow","doi":"10.1016/j.compfluid.2014.09.021","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1311.2481"}],"type":"journal_article"},{"issue":"5","external_id":{"isi":["000360862900004"]},"intvolume":"        15","file":[{"content_type":"application/pdf","date_updated":"2020-07-14T12:45:26Z","creator":"system","relation":"main_file","checksum":"3566f3a8b0c1bc550e62914a88c584ff","access_level":"open_access","file_name":"IST-2016-486-v1+1_s10208-014-9223-y.pdf","date_created":"2018-12-12T10:08:10Z","file_size":1317546,"file_id":"4670"}],"status":"public","_id":"2035","oa_version":"Published Version","isi":1,"day":"01","publisher":"Springer","year":"2015","acknowledgement":"This research is partially supported by the Toposys project FP7-ICT-318493-STREP, by ESF under the ACAT Research Network Programme, by the Russian Government under mega project 11.G34.31.0053, and by the Polish National Science Center under Grant No. N201 419639.","citation":{"mla":"Edelsbrunner, Herbert, et al. “The Persistent Homology of a Self-Map.” <i>Foundations of Computational Mathematics</i>, vol. 15, no. 5, Springer, 2015, pp. 1213–44, doi:<a href=\"https://doi.org/10.1007/s10208-014-9223-y\">10.1007/s10208-014-9223-y</a>.","short":"H. Edelsbrunner, G. Jablonski, M. Mrozek, Foundations of Computational Mathematics 15 (2015) 1213–1244.","chicago":"Edelsbrunner, Herbert, Grzegorz Jablonski, and Marian Mrozek. “The Persistent Homology of a Self-Map.” <i>Foundations of Computational Mathematics</i>. Springer, 2015. <a href=\"https://doi.org/10.1007/s10208-014-9223-y\">https://doi.org/10.1007/s10208-014-9223-y</a>.","ieee":"H. Edelsbrunner, G. Jablonski, and M. Mrozek, “The persistent homology of a self-map,” <i>Foundations of Computational Mathematics</i>, vol. 15, no. 5. Springer, pp. 1213–1244, 2015.","apa":"Edelsbrunner, H., Jablonski, G., &#38; Mrozek, M. (2015). The persistent homology of a self-map. <i>Foundations of Computational Mathematics</i>. Springer. <a href=\"https://doi.org/10.1007/s10208-014-9223-y\">https://doi.org/10.1007/s10208-014-9223-y</a>","ista":"Edelsbrunner H, Jablonski G, Mrozek M. 2015. The persistent homology of a self-map. Foundations of Computational Mathematics. 15(5), 1213–1244.","ama":"Edelsbrunner H, Jablonski G, Mrozek M. The persistent homology of a self-map. <i>Foundations of Computational Mathematics</i>. 2015;15(5):1213-1244. doi:<a href=\"https://doi.org/10.1007/s10208-014-9223-y\">10.1007/s10208-014-9223-y</a>"},"has_accepted_license":"1","date_published":"2015-10-01T00:00:00Z","ddc":["000"],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"fulldoi":"https://doi.org/10.1007/s10208-014-9223-y","publist_id":"5022","date_updated":"2025-09-23T14:08:54Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","file_date_updated":"2020-07-14T12:45:26Z","ec_funded":1,"abstract":[{"lang":"eng","text":"Considering a continuous self-map and the induced endomorphism on homology, we study the eigenvalues and eigenspaces of the latter. Taking a filtration of representations, we define the persistence of the eigenspaces, effectively introducing a hierarchical organization of the map. The algorithm that computes this information for a finite sample is proved to be stable, and to give the correct answer for a sufficiently dense sample. Results computed with an implementation of the algorithm provide evidence of its practical utility.\r\n"}],"article_processing_charge":"No","date_created":"2018-12-11T11:55:20Z","project":[{"_id":"255D761E-B435-11E9-9278-68D0E5697425","name":"Topological Complex Systems","call_identifier":"FP7","grant_number":"318493"}],"quality_controlled":"1","page":"1213 - 1244","pubrep_id":"486","publication_status":"published","language":[{"iso":"eng"}],"department":[{"_id":"HeEd"}],"volume":15,"month":"10","oa":1,"title":"The persistent homology of a self-map","type":"journal_article","doi":"10.1007/s10208-014-9223-y","scopus_import":"1","publication":"Foundations of Computational Mathematics","author":[{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert","first_name":"Herbert","orcid":"0000-0002-9823-6833"},{"first_name":"Grzegorz","orcid":"0000-0002-3536-9866","full_name":"Jablonski, Grzegorz","id":"4483EF78-F248-11E8-B48F-1D18A9856A87","last_name":"Jablonski"},{"first_name":"Marian","full_name":"Mrozek, Marian","last_name":"Mrozek"}]},{"publication":"Frontiers in Environmental Science","author":[{"first_name":"Francesca","last_name":"Parise","full_name":"Parise, Francesca"},{"last_name":"Lygeros","full_name":"Lygeros, John","first_name":"John"},{"first_name":"Jakob","orcid":"0000-0003-1615-3282","id":"4A245D00-F248-11E8-B48F-1D18A9856A87","last_name":"Ruess","full_name":"Ruess, Jakob"}],"corr_author":"1","scopus_import":"1","article_number":"42","oa":1,"title":"Bayesian inference for stochastic individual-based models of ecological systems: a pest control simulation study","publication_identifier":{"issn":["2296-665X"]},"type":"journal_article","doi":"10.3389/fenvs.2015.00042","month":"06","publication_status":"published","language":[{"iso":"eng"}],"department":[{"_id":"ToHe"},{"_id":"GaTk"}],"volume":3,"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734"}],"quality_controlled":"1","article_processing_charge":"No","date_created":"2022-02-25T11:42:25Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2022-02-25T11:55:26Z","abstract":[{"lang":"eng","text":"Mathematical models are of fundamental importance in the understanding of complex population dynamics. For instance, they can be used to predict the population evolution starting from different initial conditions or to test how a system responds to external perturbations. For this analysis to be meaningful in real applications, however, it is of paramount importance to choose an appropriate model structure and to infer the model parameters from measured data. While many parameter inference methods are available for models based on deterministic ordinary differential equations, the same does not hold for more detailed individual-based models. Here we consider, in particular, stochastic models in which the time evolution of the species abundances is described by a continuous-time Markov chain. These models are governed by a master equation that is typically difficult to solve. Consequently, traditional inference methods that rely on iterative evaluation of parameter likelihoods are computationally intractable. The aim of this paper is to present recent advances in parameter inference for continuous-time Markov chain models, based on a moment closure approximation of the parameter likelihood, and to investigate how these results can help in understanding, and ultimately controlling, complex systems in ecology. Specifically, we illustrate through an agricultural pest case study how parameters of a stochastic individual-based model can be identified from measured data and how the resulting model can be used to solve an optimal control problem in a stochastic setting. In particular, we show how the matter of determining the optimal combination of two different pest control methods can be formulated as a chance constrained optimization problem where the control action is modeled as a state reset, leading to a hybrid system formulation."}],"ec_funded":1,"date_updated":"2025-04-15T06:50:01Z","has_accepted_license":"1","date_published":"2015-06-10T00:00:00Z","ddc":["000","570"],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"keyword":["General Environmental Science"],"article_type":"original","fulldoi":"https://doi.org/10.3389/fenvs.2015.00042","day":"10","publisher":"Frontiers","year":"2015","acknowledgement":"The authors would like to acknowledge contributions from Baptiste Mottet who performed preliminary analysis regarding parameter inference for the considered case study in a student project (Mottet, 2014/2015).\r\nThe research leading to these results has received funding from the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007-2013) under REA grant agreement No. [291734] and from SystemsX under the project SignalX.","citation":{"apa":"Parise, F., Lygeros, J., &#38; Ruess, J. (2015). Bayesian inference for stochastic individual-based models of ecological systems: a pest control simulation study. <i>Frontiers in Environmental Science</i>. Frontiers. <a href=\"https://doi.org/10.3389/fenvs.2015.00042\">https://doi.org/10.3389/fenvs.2015.00042</a>","ieee":"F. Parise, J. Lygeros, and J. Ruess, “Bayesian inference for stochastic individual-based models of ecological systems: a pest control simulation study,” <i>Frontiers in Environmental Science</i>, vol. 3. Frontiers, 2015.","ista":"Parise F, Lygeros J, Ruess J. 2015. Bayesian inference for stochastic individual-based models of ecological systems: a pest control simulation study. Frontiers in Environmental Science. 3, 42.","ama":"Parise F, Lygeros J, Ruess J. Bayesian inference for stochastic individual-based models of ecological systems: a pest control simulation study. <i>Frontiers in Environmental Science</i>. 2015;3. doi:<a href=\"https://doi.org/10.3389/fenvs.2015.00042\">10.3389/fenvs.2015.00042</a>","mla":"Parise, Francesca, et al. “Bayesian Inference for Stochastic Individual-Based Models of Ecological Systems: A Pest Control Simulation Study.” <i>Frontiers in Environmental Science</i>, vol. 3, 42, Frontiers, 2015, doi:<a href=\"https://doi.org/10.3389/fenvs.2015.00042\">10.3389/fenvs.2015.00042</a>.","short":"F. Parise, J. Lygeros, J. Ruess, Frontiers in Environmental Science 3 (2015).","chicago":"Parise, Francesca, John Lygeros, and Jakob Ruess. “Bayesian Inference for Stochastic Individual-Based Models of Ecological Systems: A Pest Control Simulation Study.” <i>Frontiers in Environmental Science</i>. Frontiers, 2015. <a href=\"https://doi.org/10.3389/fenvs.2015.00042\">https://doi.org/10.3389/fenvs.2015.00042</a>."},"_id":"10794","status":"public","oa_version":"Published Version","intvolume":"         3","file":[{"file_name":"2015_FrontiersEnvironmScience_Parise.pdf","date_created":"2022-02-25T11:55:26Z","file_size":1371201,"file_id":"10795","success":1,"content_type":"application/pdf","date_updated":"2022-02-25T11:55:26Z","creator":"dernst","relation":"main_file","checksum":"26c222487564e1be02a11d688d6f769d","access_level":"open_access"}]},{"oa_version":"Preprint","status":"public","_id":"10796","year":"2015","citation":{"apa":"Chatterjee, K., &#38; Ibsen-Jensen, R. (2015). The value 1 problem under finite-memory strategies for concurrent mean-payoff games. In <i>Proceedings of the Twenty-Sixth Annual ACM-SIAM Symposium on Discrete Algorithms</i> (Vol. 2015, pp. 1018–1029). San Diego, CA, United States: SIAM. <a href=\"https://doi.org/10.1137/1.9781611973730.69\">https://doi.org/10.1137/1.9781611973730.69</a>","ieee":"K. Chatterjee and R. Ibsen-Jensen, “The value 1 problem under finite-memory strategies for concurrent mean-payoff games,” in <i>Proceedings of the Twenty-Sixth Annual ACM-SIAM Symposium on Discrete Algorithms</i>, San Diego, CA, United States, 2015, vol. 2015, no. 1, pp. 1018–1029.","ista":"Chatterjee K, Ibsen-Jensen R. 2015. The value 1 problem under finite-memory strategies for concurrent mean-payoff games. Proceedings of the Twenty-Sixth Annual ACM-SIAM Symposium on Discrete Algorithms. SODA: Symposium on Discrete Algorithms vol. 2015, 1018–1029.","ama":"Chatterjee K, Ibsen-Jensen R. The value 1 problem under finite-memory strategies for concurrent mean-payoff games. In: <i>Proceedings of the Twenty-Sixth Annual ACM-SIAM Symposium on Discrete Algorithms</i>. Vol 2015. SIAM; 2015:1018-1029. doi:<a href=\"https://doi.org/10.1137/1.9781611973730.69\">10.1137/1.9781611973730.69</a>","mla":"Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. “The Value 1 Problem under Finite-Memory Strategies for Concurrent Mean-Payoff Games.” <i>Proceedings of the Twenty-Sixth Annual ACM-SIAM Symposium on Discrete Algorithms</i>, vol. 2015, no. 1, SIAM, 2015, pp. 1018–29, doi:<a href=\"https://doi.org/10.1137/1.9781611973730.69\">10.1137/1.9781611973730.69</a>.","short":"K. Chatterjee, R. Ibsen-Jensen, in:, Proceedings of the Twenty-Sixth Annual ACM-SIAM Symposium on Discrete Algorithms, SIAM, 2015, pp. 1018–1029.","chicago":"Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. “The Value 1 Problem under Finite-Memory Strategies for Concurrent Mean-Payoff Games.” In <i>Proceedings of the Twenty-Sixth Annual ACM-SIAM Symposium on Discrete Algorithms</i>, 2015:1018–29. SIAM, 2015. <a href=\"https://doi.org/10.1137/1.9781611973730.69\">https://doi.org/10.1137/1.9781611973730.69</a>."},"acknowledgement":"The research was partly supported by FWF Grant No P 23499-N23, FWF NFN Grant\r\nNo S11407-N23 (RiSE), ERC Start grant (279307: Graph Games), and Microsoft faculty fellows award.","publisher":"SIAM","arxiv":1,"day":"01","intvolume":"      2015","external_id":{"arxiv":["1409.6690"]},"issue":"1","date_updated":"2025-06-26T06:54:08Z","ec_funded":1,"abstract":[{"text":"We consider concurrent mean-payoff games, a very well-studied class of two-player (player 1 vs player 2) zero-sum games on finite-state graphs where every transition is assigned a reward between 0 and 1, and the payoff function is the long-run average of the rewards. The value is the maximal expected payoff that player 1 can guarantee against all strategies of player 2. We consider the computation of the set of states with value 1 under finite-memory strategies for player 1, and our main results for the problem are as follows: (1) we present a polynomial-time algorithm; (2) we show that whenever there is a finite-memory strategy, there is a stationary strategy that does not need memory at all; and (3) we present an optimal bound (which is double exponential) 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).","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","fulldoi":"https://doi.org/10.1137/1.9781611973730.69","OA_type":"green","date_published":"2015-01-01T00:00:00Z","OA_place":"publisher","volume":2015,"language":[{"iso":"eng"}],"department":[{"_id":"KrCh"}],"publication_status":"published","page":"1018-1029","month":"01","date_created":"2022-02-25T12:18:43Z","article_processing_charge":"No","quality_controlled":"1","project":[{"grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","call_identifier":"FWF"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","grant_number":"279307"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"scopus_import":"1","corr_author":"1","conference":{"start_date":"2015-01-04","end_date":"2015-01-06","name":"SODA: Symposium on Discrete Algorithms","location":"San Diego, CA, United States"},"author":[{"last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","orcid":"0000-0002-4561-241X"},{"first_name":"Rasmus","orcid":"0000-0003-4783-0389","last_name":"Ibsen-Jensen","id":"3B699956-F248-11E8-B48F-1D18A9856A87","full_name":"Ibsen-Jensen, Rasmus"}],"publication":"Proceedings of the Twenty-Sixth Annual ACM-SIAM Symposium on Discrete Algorithms","doi":"10.1137/1.9781611973730.69","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.1409.6690"}],"type":"conference","publication_identifier":{"isbn":["978-161197374-7"]},"oa":1,"title":"The value 1 problem under finite-memory strategies for concurrent mean-payoff games"},{"external_id":{"isi":["000368443700010"],"pmid":["26306635"]},"issue":"12","intvolume":"        25","day":"01","isi":1,"citation":{"mla":"Engel, Jakob, et al. “Characterization of an N-Acetylglucosaminyltransferase Involved in Aspergillus Fumigatus Zwitterionic Glycoinositolphosphoceramide Biosynthesis.” <i>Glycobiology</i>, vol. 25, no. 12, Oxford University Press, 2015, pp. 1423–30, doi:<a href=\"https://doi.org/10.1093/glycob/cwv059\">10.1093/glycob/cwv059</a>.","short":"J. Engel, P.S. Schmalhorst, A. Kruger, C. Muller, F. Buettner, F. Routier, Glycobiology 25 (2015) 1423–1430.","chicago":"Engel, Jakob, Philipp S Schmalhorst, Anke Kruger, Christina Muller, Falk Buettner, and Françoise Routier. “Characterization of an N-Acetylglucosaminyltransferase Involved in Aspergillus Fumigatus Zwitterionic Glycoinositolphosphoceramide Biosynthesis.” <i>Glycobiology</i>. Oxford University Press, 2015. <a href=\"https://doi.org/10.1093/glycob/cwv059\">https://doi.org/10.1093/glycob/cwv059</a>.","ieee":"J. Engel, P. S. Schmalhorst, A. Kruger, C. Muller, F. Buettner, and F. Routier, “Characterization of an N-acetylglucosaminyltransferase involved in Aspergillus fumigatus zwitterionic glycoinositolphosphoceramide biosynthesis,” <i>Glycobiology</i>, vol. 25, no. 12. Oxford University Press, pp. 1423–1430, 2015.","apa":"Engel, J., Schmalhorst, P. S., Kruger, A., Muller, C., Buettner, F., &#38; Routier, F. (2015). Characterization of an N-acetylglucosaminyltransferase involved in Aspergillus fumigatus zwitterionic glycoinositolphosphoceramide biosynthesis. <i>Glycobiology</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/glycob/cwv059\">https://doi.org/10.1093/glycob/cwv059</a>","ama":"Engel J, Schmalhorst PS, Kruger A, Muller C, Buettner F, Routier F. Characterization of an N-acetylglucosaminyltransferase involved in Aspergillus fumigatus zwitterionic glycoinositolphosphoceramide biosynthesis. <i>Glycobiology</i>. 2015;25(12):1423-1430. doi:<a href=\"https://doi.org/10.1093/glycob/cwv059\">10.1093/glycob/cwv059</a>","ista":"Engel J, Schmalhorst PS, Kruger A, Muller C, Buettner F, Routier F. 2015. Characterization of an N-acetylglucosaminyltransferase involved in Aspergillus fumigatus zwitterionic glycoinositolphosphoceramide biosynthesis. Glycobiology. 25(12), 1423–1430."},"year":"2015","publisher":"Oxford University Press","_id":"802","status":"public","oa_version":"None","date_published":"2015-12-01T00:00:00Z","fulldoi":"https://doi.org/10.1093/glycob/cwv059","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","abstract":[{"lang":"eng","text":"Glycoinositolphosphoceramides (GIPCs) are complex sphingolipids present at the plasma membrane of various eukaryotes with the important exception of mammals. In fungi, these glycosphingolipids commonly contain an alpha-mannose residue (Man) linked at position 2 of the inositol. However, several pathogenic fungi additionally synthesize zwitterionic GIPCs carrying an alpha-glucosamine residue (GlcN) at this position. In the human pathogen Aspergillus fumigatus, the GlcNalpha1,2IPC core (where IPC is inositolphosphoceramide) is elongated to Manalpha1,3Manalpha1,6GlcNalpha1,2IPC, which is the most abundant GIPC synthesized by this fungus. In this study, we identified an A. fumigatus N-acetylglucosaminyltransferase, named GntA, and demonstrate its involvement in the initiation of zwitterionic GIPC biosynthesis. Targeted deletion of the gene encoding GntA in A. fumigatus resulted in complete absence of zwitterionic GIPC; a phenotype that could be reverted by episomal expression of GntA in the mutant. The N-acetylhexosaminyltransferase activity of GntA was substantiated by production of N-acetylhexosamine-IPC in the yeast Saccharomyces cerevisiae upon GntA expression. Using an in vitro assay, GntA was furthermore shown to use UDP-N-acetylglucosamine as donor substrate to generate a glycolipid product resistant to saponification and to digestion by phosphatidylinositol-phospholipase C as expected for GlcNAcalpha1,2IPC. Finally, as the enzymes involved in mannosylation of IPC, GntA was localized to the Golgi apparatus, the site of IPC synthesis."}],"publist_id":"6851","date_updated":"2025-09-23T08:14:24Z","quality_controlled":"1","date_created":"2018-12-11T11:48:35Z","article_processing_charge":"No","month":"12","page":"1423 - 1430","volume":25,"department":[{"_id":"CaHe"}],"language":[{"iso":"eng"}],"publication_status":"published","pmid":1,"title":"Characterization of an N-acetylglucosaminyltransferase involved in Aspergillus fumigatus zwitterionic glycoinositolphosphoceramide biosynthesis","doi":"10.1093/glycob/cwv059","type":"journal_article","publication":"Glycobiology","author":[{"first_name":"Jakob","full_name":"Engel, Jakob","last_name":"Engel"},{"last_name":"Schmalhorst","id":"309D50DA-F248-11E8-B48F-1D18A9856A87","full_name":"Schmalhorst, Philipp S","orcid":"0000-0002-5795-0133","first_name":"Philipp S"},{"full_name":"Kruger, Anke","last_name":"Kruger","first_name":"Anke"},{"full_name":"Muller, Christina","last_name":"Muller","first_name":"Christina"},{"last_name":"Buettner","full_name":"Buettner, Falk","first_name":"Falk"},{"full_name":"Routier, Françoise","last_name":"Routier","first_name":"Françoise"}],"scopus_import":"1"},{"external_id":{"arxiv":["1511.03501"]},"related_material":{"record":[{"id":"9308","relation":"later_version","status":"public"},{"status":"public","id":"10220","relation":"later_version"},{"status":"public","id":"8156","relation":"dissertation_contains"}]},"article_processing_charge":"No","date_created":"2020-07-30T10:45:19Z","month":"11","arxiv":1,"day":"15","acknowledgement":"We would like to thank A. Klyachko, V. Krushkal, S. Melikhov, M. Tancer, P. Teichner and anonymous referees for helpful discussions.","citation":{"mla":"Avvakumov, Sergey, et al. “Eliminating Higher-Multiplicity Intersections, III. Codimension 2.” <i>ArXiv</i>, 1511.03501, doi:<a href=\"https://doi.org/10.48550/arXiv.1511.03501\">10.48550/arXiv.1511.03501</a>.","short":"S. Avvakumov, I. Mabillard, A. Skopenkov, U. Wagner, ArXiv (n.d.).","chicago":"Avvakumov, Sergey, Isaac Mabillard, A. Skopenkov, and Uli Wagner. “Eliminating Higher-Multiplicity Intersections, III. Codimension 2.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.1511.03501\">https://doi.org/10.48550/arXiv.1511.03501</a>.","apa":"Avvakumov, S., Mabillard, I., Skopenkov, A., &#38; Wagner, U. (n.d.). Eliminating higher-multiplicity intersections, III. Codimension 2. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.1511.03501\">https://doi.org/10.48550/arXiv.1511.03501</a>","ieee":"S. Avvakumov, I. Mabillard, A. Skopenkov, and U. Wagner, “Eliminating higher-multiplicity intersections, III. Codimension 2,” <i>arXiv</i>. .","ista":"Avvakumov S, Mabillard I, Skopenkov A, Wagner U. Eliminating higher-multiplicity intersections, III. Codimension 2. arXiv, 1511.03501.","ama":"Avvakumov S, Mabillard I, Skopenkov A, Wagner U. Eliminating higher-multiplicity intersections, III. Codimension 2. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.1511.03501\">10.48550/arXiv.1511.03501</a>"},"year":"2015","status":"public","_id":"8183","publication_status":"draft","oa_version":"Preprint","department":[{"_id":"UlWa"}],"language":[{"iso":"eng"}],"article_number":"1511.03501","title":"Eliminating higher-multiplicity intersections, III. Codimension 2","oa":1,"date_published":"2015-11-15T00:00:00Z","type":"preprint","fulldoi":"https://doi.org/10.48550/arXiv.1511.03501","doi":"10.48550/arXiv.1511.03501","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1511.03501"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"arXiv","abstract":[{"text":"We study conditions under which a finite simplicial complex $K$ can be mapped to $\\mathbb R^d$ without higher-multiplicity intersections. An almost $r$-embedding is a map $f: K\\to \\mathbb R^d$ such that the images of any $r$\r\npairwise disjoint simplices of $K$ do not have a common point. We show that if $r$ is not a prime power and $d\\geq 2r+1$, then there is a counterexample to the topological Tverberg conjecture, i.e., there is an almost $r$-embedding of\r\nthe $(d+1)(r-1)$-simplex in $\\mathbb R^d$. This improves on previous constructions of counterexamples (for $d\\geq 3r$) based on a series of papers by M. \\\"Ozaydin, M. Gromov, P. Blagojevi\\'c, F. Frick, G. Ziegler, and the second and fourth present authors. The counterexamples are obtained by proving the following algebraic criterion in codimension 2: If $r\\ge3$ and if $K$ is a finite $2(r-1)$-complex then there exists an almost $r$-embedding $K\\to \\mathbb R^{2r}$ if and only if there exists a general position PL map $f:K\\to \\mathbb R^{2r}$ such that the algebraic intersection number of the $f$-images of any $r$ pairwise disjoint simplices of $K$ is zero. This result can be restated in terms of cohomological obstructions or equivariant maps, and extends an analogous codimension 3 criterion by the second and fourth authors. As another application we classify ornaments $f:S^3 \\sqcup S^3\\sqcup S^3\\to \\mathbb R^5$ up to ornament\r\nconcordance. It follows from work of M. Freedman, V. Krushkal and P. Teichner that the analogous criterion for $r=2$ is false. We prove a lemma on singular higher-dimensional Borromean rings, yielding an elementary proof of the counterexample.","lang":"eng"}],"author":[{"first_name":"Sergey","orcid":"0000-0002-7840-5062","id":"3827DAC8-F248-11E8-B48F-1D18A9856A87","last_name":"Avvakumov","full_name":"Avvakumov, Sergey"},{"first_name":"Isaac","id":"32BF9DAA-F248-11E8-B48F-1D18A9856A87","last_name":"Mabillard","full_name":"Mabillard, Isaac"},{"first_name":"A.","last_name":"Skopenkov","full_name":"Skopenkov, A."},{"last_name":"Wagner","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","full_name":"Wagner, Uli","orcid":"0000-0002-1494-0568","first_name":"Uli"}],"date_updated":"2026-04-08T07:25:54Z","corr_author":"1"},{"date_created":"2021-06-08T09:56:24Z","article_processing_charge":"No","quality_controlled":"1","volume":29,"department":[{"_id":"DaZi"}],"language":[{"iso":"eng"}],"publication_status":"published","page":"2517–2531","month":"12","doi":"10.1101/gad.269902.115","type":"journal_article","pmid":1,"publication_identifier":{"issn":["0890-9369"],"eissn":["1549-5477"]},"title":"Evolution and function of genomic imprinting in plants","oa":1,"extern":"1","scopus_import":"1","author":[{"full_name":"Rodrigues, Jessica A.","last_name":"Rodrigues","first_name":"Jessica A."},{"first_name":"Daniel","orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel","last_name":"Zilberman","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1"}],"publication":"Genes and Development","file":[{"relation":"main_file","access_level":"open_access","checksum":"086a88cfca4677646da26ed960cb02e9","date_updated":"2021-06-08T09:55:10Z","content_type":"application/pdf","creator":"asandaue","file_id":"9533","success":1,"file_name":"2015_GenesAndDevelopment_Rodrigues.pdf","file_size":1116846,"date_created":"2021-06-08T09:55:10Z"}],"intvolume":"        29","external_id":{"pmid":["26680300"]},"issue":"24","oa_version":"Published Version","_id":"9532","status":"public","citation":{"ama":"Rodrigues JA, Zilberman D. Evolution and function of genomic imprinting in plants. <i>Genes and Development</i>. 2015;29(24):2517–2531. doi:<a href=\"https://doi.org/10.1101/gad.269902.115\">10.1101/gad.269902.115</a>","ista":"Rodrigues JA, Zilberman D. 2015. Evolution and function of genomic imprinting in plants. Genes and Development. 29(24), 2517–2531.","apa":"Rodrigues, J. A., &#38; Zilberman, D. (2015). Evolution and function of genomic imprinting in plants. <i>Genes and Development</i>. Cold Spring Harbor Laboratory Press. <a href=\"https://doi.org/10.1101/gad.269902.115\">https://doi.org/10.1101/gad.269902.115</a>","ieee":"J. A. Rodrigues and D. Zilberman, “Evolution and function of genomic imprinting in plants,” <i>Genes and Development</i>, vol. 29, no. 24. Cold Spring Harbor Laboratory Press, pp. 2517–2531, 2015.","chicago":"Rodrigues, Jessica A., and Daniel Zilberman. “Evolution and Function of Genomic Imprinting in Plants.” <i>Genes and Development</i>. Cold Spring Harbor Laboratory Press, 2015. <a href=\"https://doi.org/10.1101/gad.269902.115\">https://doi.org/10.1101/gad.269902.115</a>.","mla":"Rodrigues, Jessica A., and Daniel Zilberman. “Evolution and Function of Genomic Imprinting in Plants.” <i>Genes and Development</i>, vol. 29, no. 24, Cold Spring Harbor Laboratory Press, 2015, pp. 2517–2531, doi:<a href=\"https://doi.org/10.1101/gad.269902.115\">10.1101/gad.269902.115</a>.","short":"J.A. Rodrigues, D. Zilberman, Genes and Development 29 (2015) 2517–2531."},"year":"2015","publisher":"Cold Spring Harbor Laboratory Press","day":"15","article_type":"review","fulldoi":"https://doi.org/10.1101/gad.269902.115","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png"},"ddc":["570"],"has_accepted_license":"1","date_published":"2015-12-15T00:00:00Z","date_updated":"2021-12-14T07:58:15Z","file_date_updated":"2021-06-08T09:55:10Z","abstract":[{"text":"Genomic imprinting, an inherently epigenetic phenomenon defined by parent of origin-dependent gene expression, is observed in mammals and flowering plants. Genome-scale surveys of imprinted expression and the underlying differential epigenetic marks have led to the discovery of hundreds of imprinted plant genes and confirmed DNA and histone methylation as key regulators of plant imprinting. However, the biological roles of the vast majority of imprinted plant genes are unknown, and the evolutionary forces shaping plant imprinting remain rather opaque. Here, we review the mechanisms of plant genomic imprinting and discuss theories of imprinting evolution and biological significance in light of recent findings.","lang":"eng"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9"},{"related_material":{"record":[{"relation":"used_in_publication","id":"1619","status":"public"}]},"article_processing_charge":"No","date_created":"2021-07-23T11:53:50Z","month":"11","day":"18","publisher":"Public Library of Science","citation":{"apa":"Chevereau, G., Lukacisinova, M., Batur, T., Guvenek, A., Ayhan, D. H., Toprak, E., &#38; Bollenbach, M. T. (2015). Excel file containing the raw data for all figures. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.1002299.s001\">https://doi.org/10.1371/journal.pbio.1002299.s001</a>","ieee":"G. Chevereau <i>et al.</i>, “Excel file containing the raw data for all figures.” Public Library of Science, 2015.","ista":"Chevereau G, Lukacisinova M, Batur T, Guvenek A, Ayhan DH, Toprak E, Bollenbach MT. 2015. Excel file containing the raw data for all figures, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pbio.1002299.s001\">10.1371/journal.pbio.1002299.s001</a>.","ama":"Chevereau G, Lukacisinova M, Batur T, et al. Excel file containing the raw data for all figures. 2015. doi:<a href=\"https://doi.org/10.1371/journal.pbio.1002299.s001\">10.1371/journal.pbio.1002299.s001</a>","mla":"Chevereau, Guillaume, et al. <i>Excel File Containing the Raw Data for All Figures</i>. Public Library of Science, 2015, doi:<a href=\"https://doi.org/10.1371/journal.pbio.1002299.s001\">10.1371/journal.pbio.1002299.s001</a>.","short":"G. Chevereau, M. Lukacisinova, T. Batur, A. Guvenek, D.H. Ayhan, E. Toprak, M.T. Bollenbach, (2015).","chicago":"Chevereau, Guillaume, Marta Lukacisinova, Tugce Batur, Aysegul Guvenek, Dilay Hazal Ayhan, Erdal Toprak, and Mark Tobias Bollenbach. “Excel File Containing the Raw Data for All Figures.” Public Library of Science, 2015. <a href=\"https://doi.org/10.1371/journal.pbio.1002299.s001\">https://doi.org/10.1371/journal.pbio.1002299.s001</a>."},"year":"2015","_id":"9711","status":"public","oa_version":"Published Version","department":[{"_id":"ToBo"}],"date_published":"2015-11-18T00:00:00Z","title":"Excel file containing the raw data for all figures","type":"research_data_reference","doi":"10.1371/journal.pbio.1002299.s001","fulldoi":"https://doi.org/10.1371/journal.pbio.1002299.s001","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","author":[{"first_name":"Guillaume","last_name":"Chevereau","id":"424D78A0-F248-11E8-B48F-1D18A9856A87","full_name":"Chevereau, Guillaume"},{"orcid":"0000-0002-2519-8004","first_name":"Marta","full_name":"Lukacisinova, Marta","last_name":"Lukacisinova","id":"4342E402-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Tugce","last_name":"Batur","full_name":"Batur, Tugce"},{"first_name":"Aysegul","last_name":"Guvenek","full_name":"Guvenek, Aysegul"},{"first_name":"Dilay Hazal","full_name":"Ayhan, Dilay Hazal","last_name":"Ayhan"},{"full_name":"Toprak, Erdal","last_name":"Toprak","first_name":"Erdal"},{"last_name":"Bollenbach","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","full_name":"Bollenbach, Mark Tobias","orcid":"0000-0003-4398-476X","first_name":"Mark Tobias"}],"date_updated":"2025-09-23T09:58:54Z"}]