[{"volume":82,"ddc":["004"],"tmp":{"short":"CC BY (3.0)","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","image":"/images/cc_by.png"},"date_created":"2019-06-04T12:42:43Z","status":"public","day":"01","doi":"10.4230/LIPICS.CSL.2017.18","oa_version":"Published Version","ec_funded":1,"intvolume":"        82","month":"08","date_published":"2017-08-01T00:00:00Z","article_number":"18","date_updated":"2025-06-02T08:53:46Z","oa":1,"conference":{"name":"CSL: Conference on Computer Science Logic","start_date":"2017-08-20","end_date":"2017-08-24","location":"Stockholm, Sweden"},"year":"2017","citation":{"chicago":"Chatterjee, Krishnendu, Wolfgang Dvorák, Monika H Henzinger, and Veronika Loitzenbauer. “Improved Set-Based Symbolic Algorithms for Parity Games,” Vol. 82. Schloss Dagstuhl -Leibniz-Zentrum fuer Informatik, 2017. <a href=\"https://doi.org/10.4230/LIPICS.CSL.2017.18\">https://doi.org/10.4230/LIPICS.CSL.2017.18</a>.","ieee":"K. Chatterjee, W. Dvorák, M. H. Henzinger, and V. Loitzenbauer, “Improved set-based symbolic algorithms for parity games,” presented at the CSL: Conference on Computer Science Logic, Stockholm, Sweden, 2017, vol. 82.","ista":"Chatterjee K, Dvorák W, Henzinger MH, Loitzenbauer V. 2017. Improved set-based symbolic algorithms for parity games. CSL: Conference on Computer Science Logic vol. 82, 18.","short":"K. Chatterjee, W. Dvorák, M.H. Henzinger, V. Loitzenbauer, in:, Schloss Dagstuhl -Leibniz-Zentrum fuer Informatik, 2017.","ama":"Chatterjee K, Dvorák W, Henzinger MH, Loitzenbauer V. Improved set-based symbolic algorithms for parity games. In: Vol 82. Schloss Dagstuhl -Leibniz-Zentrum fuer Informatik; 2017. doi:<a href=\"https://doi.org/10.4230/LIPICS.CSL.2017.18\">10.4230/LIPICS.CSL.2017.18</a>","mla":"Chatterjee, Krishnendu, et al. <i>Improved Set-Based Symbolic Algorithms for Parity Games</i>. Vol. 82, 18, Schloss Dagstuhl -Leibniz-Zentrum fuer Informatik, 2017, doi:<a href=\"https://doi.org/10.4230/LIPICS.CSL.2017.18\">10.4230/LIPICS.CSL.2017.18</a>.","apa":"Chatterjee, K., Dvorák, W., Henzinger, M. H., &#38; Loitzenbauer, V. (2017). Improved set-based symbolic algorithms for parity games (Vol. 82). Presented at the CSL: Conference on Computer Science Logic, Stockholm, Sweden: Schloss Dagstuhl -Leibniz-Zentrum fuer Informatik. <a href=\"https://doi.org/10.4230/LIPICS.CSL.2017.18\">https://doi.org/10.4230/LIPICS.CSL.2017.18</a>"},"type":"conference","file_date_updated":"2020-07-14T12:47:33Z","abstract":[{"text":"Graph games with omega-regular winning conditions provide a mathematical framework to analyze a wide range of problems in the analysis of reactive systems and programs (such as the synthesis of reactive systems, program repair, and the verification of branching time properties). Parity conditions are canonical forms to specify omega-regular winning conditions. Graph games with parity conditions are equivalent to mu-calculus model checking, and thus a very important algorithmic problem. Symbolic algorithms are of great significance because they provide scalable algorithms for the analysis of large finite-state systems, as well as algorithms for the analysis of infinite-state systems with finite quotient. A set-based symbolic algorithm uses the basic set operations and the one-step predecessor operators. We consider graph games with n vertices and parity conditions with c priorities (equivalently, a mu-calculus formula with c alternations of least and greatest fixed points). While many explicit algorithms exist for graph games with parity conditions, for set-based symbolic algorithms there are only two algorithms (notice that we use space to refer to the number of sets stored by a symbolic algorithm): (a) the basic algorithm that requires O(n^c) symbolic operations and linear space; and (b) an improved algorithm that requires O(n^{c/2+1}) symbolic operations but also O(n^{c/2+1}) space (i.e., exponential space). In this work we present two set-based symbolic algorithms for parity games: (a) our first algorithm requires O(n^{c/2+1}) symbolic operations and only requires linear space; and (b) developing on our first algorithm, we present an algorithm that requires O(n^{c/3+1}) symbolic operations and only linear space. We also present the first linear space set-based symbolic algorithm for parity games that requires at most a sub-exponential number of symbolic operations. ","lang":"eng"}],"scopus_import":"1","_id":"6519","quality_controlled":"1","project":[{"name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF"},{"grant_number":"279307","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications"},{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003"}],"publication_status":"published","has_accepted_license":"1","publisher":"Schloss Dagstuhl -Leibniz-Zentrum fuer Informatik","file":[{"file_name":"2017_LIPIcs-Chatterjee.pdf","date_updated":"2020-07-14T12:47:33Z","date_created":"2019-06-04T12:56:52Z","file_size":710185,"creator":"kschuh","content_type":"application/pdf","file_id":"6520","checksum":"7c2c9d09970af79026d7e37d9b632ef8","relation":"main_file","access_level":"open_access"}],"title":"Improved set-based symbolic algorithms for parity games","author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"last_name":"Dvorák","first_name":"Wolfgang","full_name":"Dvorák, Wolfgang"},{"id":"540c9bbd-f2de-11ec-812d-d04a5be85630","first_name":"Monika H","orcid":"0000-0002-5008-6530","last_name":"Henzinger","full_name":"Henzinger, Monika H"},{"full_name":"Loitzenbauer, Veronika","first_name":"Veronika","last_name":"Loitzenbauer"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","department":[{"_id":"KrCh"}],"language":[{"iso":"eng"}]},{"conference":{"location":"Cergy-Pontoise, France","name":"ICDL EpiRob: International Conference on Development and Learning and Epigenetic Robotics ","end_date":"2016-09-22","start_date":"2016-09-19"},"publist_id":"7100","department":[{"_id":"ChLa"},{"_id":"GaTk"}],"language":[{"iso":"eng"}],"year":"2017","date_published":"2017-02-07T00:00:00Z","month":"02","article_number":"7846789","publisher":"IEEE","date_updated":"2021-01-12T08:07:51Z","author":[{"full_name":"Der, Ralf","last_name":"Der","first_name":"Ralf"},{"full_name":"Martius, Georg S","first_name":"Georg S","id":"3A276B68-F248-11E8-B48F-1D18A9856A87","last_name":"Martius"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"Dynamical self consistency leads to behavioral development and emergent social interactions in robots","doi":"10.1109/DEVLRN.2016.7846789","publication_status":"published","oa_version":"None","publication_identifier":{"isbn":["978-150905069-7"]},"citation":{"chicago":"Der, Ralf, and Georg S Martius. “Dynamical Self Consistency Leads to Behavioral Development and Emergent Social Interactions in Robots.” IEEE, 2017. <a href=\"https://doi.org/10.1109/DEVLRN.2016.7846789\">https://doi.org/10.1109/DEVLRN.2016.7846789</a>.","ama":"Der R, Martius GS. Dynamical self consistency leads to behavioral development and emergent social interactions in robots. In: IEEE; 2017. doi:<a href=\"https://doi.org/10.1109/DEVLRN.2016.7846789\">10.1109/DEVLRN.2016.7846789</a>","short":"R. Der, G.S. Martius, in:, IEEE, 2017.","ista":"Der R, Martius GS. 2017. Dynamical self consistency leads to behavioral development and emergent social interactions in robots. ICDL EpiRob: International Conference on Development and Learning and Epigenetic Robotics , 7846789.","ieee":"R. Der and G. S. Martius, “Dynamical self consistency leads to behavioral development and emergent social interactions in robots,” presented at the ICDL EpiRob: International Conference on Development and Learning and Epigenetic Robotics , Cergy-Pontoise, France, 2017.","mla":"Der, Ralf, and Georg S. Martius. <i>Dynamical Self Consistency Leads to Behavioral Development and Emergent Social Interactions in Robots</i>. 7846789, IEEE, 2017, doi:<a href=\"https://doi.org/10.1109/DEVLRN.2016.7846789\">10.1109/DEVLRN.2016.7846789</a>.","apa":"Der, R., &#38; Martius, G. S. (2017). Dynamical self consistency leads to behavioral development and emergent social interactions in robots. Presented at the ICDL EpiRob: International Conference on Development and Learning and Epigenetic Robotics , Cergy-Pontoise, France: IEEE. <a href=\"https://doi.org/10.1109/DEVLRN.2016.7846789\">https://doi.org/10.1109/DEVLRN.2016.7846789</a>"},"scopus_import":1,"abstract":[{"lang":"eng","text":"We present an approach that enables robots to self-organize their sensorimotor behavior from scratch without providing specific information about neither the robot nor its environment. This is achieved by a simple neural control law that increases the consistency between external sensor dynamics and internal neural dynamics of the utterly simple controller. In this way, the embodiment and the agent-environment coupling are the only source of individual development. We show how an anthropomorphic tendon driven arm-shoulder system develops different behaviors depending on that coupling. For instance: Given a bottle half-filled with water, the arm starts to shake it, driven by the physical response of the water. When attaching a brush, the arm can be manipulated into wiping a table, and when connected to a revolvable wheel it finds out how to rotate it. Thus, the robot may be said to discover the affordances of the world. When allowing two (simulated) humanoid robots to interact physically, they engage into a joint behavior development leading to, for instance, spontaneous cooperation. More social effects are observed if the robots can visually perceive each other. Although, as an observer, it is tempting to attribute an apparent intentionality, there is nothing of the kind put in. As a conclusion, we argue that emergent behavior may be much less rooted in explicit intentions, internal motivations, or specific reward systems than is commonly believed."}],"type":"conference","date_created":"2018-12-11T11:47:43Z","_id":"652","quality_controlled":"1","day":"07","status":"public"},{"publisher":"IEEE","title":"On the complexity of estimating Rènyi divergences","author":[{"last_name":"Skórski","first_name":"Maciej","id":"EC09FA6A-02D0-11E9-8223-86B7C91467DD","full_name":"Skórski, Maciej"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"KrPi"}],"language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"This paper studies the complexity of estimating Rényi divergences of discrete distributions: p observed from samples and the baseline distribution q known a priori. Extending the results of Acharya et al. (SODA'15) on estimating Rényi entropy, we present improved estimation techniques together with upper and lower bounds on the sample complexity. We show that, contrarily to estimating Rényi entropy where a sublinear (in the alphabet size) number of samples suffices, the sample complexity is heavily dependent on events occurring unlikely in q, and is unbounded in general (no matter what an estimation technique is used). For any divergence of integer order bigger than 1, we provide upper and lower bounds on the number of samples dependent on probabilities of p and q (the lower bounds hold for non-integer orders as well). We conclude that the worst-case sample complexity is polynomial in the alphabet size if and only if the probabilities of q are non-negligible. This gives theoretical insights into heuristics used in the applied literature to handle numerical instability, which occurs for small probabilities of q. Our result shows that they should be handled with care not only because of numerical issues, but also because of a blow up in the sample complexity."}],"arxiv":1,"scopus_import":1,"type":"conference","publication_identifier":{"isbn":["9781509040964"]},"citation":{"mla":"Skórski, Maciej. “On the Complexity of Estimating Rènyi Divergences.” <i>2017 IEEE International Symposium on Information Theory (ISIT)</i>, 8006529, IEEE, 2017, doi:<a href=\"https://doi.org/10.1109/isit.2017.8006529\">10.1109/isit.2017.8006529</a>.","apa":"Skórski, M. (2017). On the complexity of estimating Rènyi divergences. In <i>2017 IEEE International Symposium on Information Theory (ISIT)</i>. Aachen, Germany: IEEE. <a href=\"https://doi.org/10.1109/isit.2017.8006529\">https://doi.org/10.1109/isit.2017.8006529</a>","chicago":"Skórski, Maciej. “On the Complexity of Estimating Rènyi Divergences.” In <i>2017 IEEE International Symposium on Information Theory (ISIT)</i>. IEEE, 2017. <a href=\"https://doi.org/10.1109/isit.2017.8006529\">https://doi.org/10.1109/isit.2017.8006529</a>.","short":"M. Skórski, in:, 2017 IEEE International Symposium on Information Theory (ISIT), IEEE, 2017.","ista":"Skórski M. 2017. On the complexity of estimating Rènyi divergences. 2017 IEEE International Symposium on Information Theory (ISIT). ISIT: International Symposium on Information Theory, 8006529.","ieee":"M. Skórski, “On the complexity of estimating Rènyi divergences,” in <i>2017 IEEE International Symposium on Information Theory (ISIT)</i>, Aachen, Germany, 2017.","ama":"Skórski M. On the complexity of estimating Rènyi divergences. In: <i>2017 IEEE International Symposium on Information Theory (ISIT)</i>. IEEE; 2017. doi:<a href=\"https://doi.org/10.1109/isit.2017.8006529\">10.1109/isit.2017.8006529</a>"},"quality_controlled":"1","_id":"6526","publication_status":"published","project":[{"grant_number":"682815","call_identifier":"H2020","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","name":"Teaching Old Crypto New Tricks"}],"article_number":"8006529","date_published":"2017-08-09T00:00:00Z","month":"08","oa":1,"date_updated":"2021-01-12T08:07:53Z","conference":{"location":"Aachen, Germany","end_date":"2017-06-30","start_date":"2017-06-25","name":"ISIT: International Symposium on Information Theory"},"external_id":{"arxiv":["1702.01666"]},"year":"2017","day":"09","status":"public","date_created":"2019-06-06T12:53:09Z","publication":"2017 IEEE International Symposium on Information Theory (ISIT)","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1702.01666"}],"doi":"10.1109/isit.2017.8006529","oa_version":"Preprint","ec_funded":1},{"title":"Practical graphs for optimal side-channel resistant memory-hard functions","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Alwen, Joel F","first_name":"Joel F","id":"2A8DFA8C-F248-11E8-B48F-1D18A9856A87","last_name":"Alwen"},{"full_name":"Blocki, Jeremiah","last_name":"Blocki","first_name":"Jeremiah"},{"full_name":"Harsha, Ben","last_name":"Harsha","first_name":"Ben"}],"date_updated":"2021-01-12T08:07:53Z","publisher":"ACM Press","month":"10","date_published":"2017-10-30T00:00:00Z","year":"2017","language":[{"iso":"eng"}],"conference":{"location":"Dallas, TX, USA","name":"CCS: Conference on Computer and Communications Security","start_date":"2017-10-30","end_date":"2017-11-03"},"department":[{"_id":"KrPi"}],"page":"1001-1017","status":"public","day":"30","quality_controlled":"1","_id":"6527","date_created":"2019-06-06T13:21:29Z","type":"conference","abstract":[{"lang":"eng","text":"A memory-hard function (MHF) ƒn with parameter n can be computed in sequential time and space n. Simultaneously, a high amortized parallel area-time complexity (aAT) is incurred per evaluation. In practice, MHFs are used to limit the rate at which an adversary (using a custom computational device) can evaluate a security sensitive function that still occasionally needs to be evaluated by honest users (using an off-the-shelf general purpose device). The most prevalent examples of such sensitive functions are Key Derivation Functions (KDFs) and password hashing algorithms where rate limits help mitigate off-line dictionary attacks. As the honest users' inputs to these functions are often (low-entropy) passwords special attention is given to a class of side-channel resistant MHFs called iMHFs.\r\n\r\nEssentially all iMHFs can be viewed as some mode of operation (making n calls to some round function) given by a directed acyclic graph (DAG) with very low indegree. Recently, a combinatorial property of a DAG has been identified (called \"depth-robustness\") which results in good provable security for an iMHF based on that DAG. Depth-robust DAGs have also proven useful in other cryptographic applications. Unfortunately, up till now, all known very depth-robust DAGs are impractically complicated and little is known about their exact (i.e. non-asymptotic) depth-robustness both in theory and in practice.\r\n\r\nIn this work we build and analyze (both formally and empirically) several exceedingly simple and efficient to navigate practical DAGs for use in iMHFs and other applications. For each DAG we:\r\n*Prove that their depth-robustness is asymptotically maximal.\r\n*Prove bounds of at least 3 orders of magnitude better on their exact depth-robustness compared to known bounds for other practical iMHF.\r\n*Implement and empirically evaluate their depth-robustness and aAT against a variety of state-of-the art (and several new) depth-reduction and low aAT attacks. \r\nWe find that, against all attacks, the new DAGs perform significantly better in practice than Argon2i, the most widely deployed iMHF in practice.\r\n\r\nAlong the way we also improve the best known empirical attacks on the aAT of Argon2i by implementing and testing several heuristic versions of a (hitherto purely theoretical) depth-reduction attack. Finally, we demonstrate practicality of our constructions by modifying the Argon2i code base to use one of the new high aAT DAGs. Experimental benchmarks on a standard off-the-shelf CPU show that the new modifications do not adversely affect the impressive throughput of Argon2i (despite seemingly enjoying significantly higher aAT).\r\n"}],"scopus_import":1,"publication_identifier":{"isbn":["9781450349468"]},"citation":{"short":"J.F. Alwen, J. Blocki, B. Harsha, in:, Proceedings of the 2017 ACM SIGSAC Conference on Computer and Communications Security, ACM Press, 2017, pp. 1001–1017.","ieee":"J. F. Alwen, J. Blocki, and B. Harsha, “Practical graphs for optimal side-channel resistant memory-hard functions,” in <i>Proceedings of the 2017 ACM SIGSAC Conference on Computer and Communications Security</i>, Dallas, TX, USA, 2017, pp. 1001–1017.","ista":"Alwen JF, Blocki J, Harsha B. 2017. Practical graphs for optimal side-channel resistant memory-hard functions. Proceedings of the 2017 ACM SIGSAC Conference on Computer and Communications Security. CCS: Conference on Computer and Communications Security, 1001–1017.","ama":"Alwen JF, Blocki J, Harsha B. Practical graphs for optimal side-channel resistant memory-hard functions. In: <i>Proceedings of the 2017 ACM SIGSAC Conference on Computer and Communications Security</i>. ACM Press; 2017:1001-1017. doi:<a href=\"https://doi.org/10.1145/3133956.3134031\">10.1145/3133956.3134031</a>","chicago":"Alwen, Joel F, Jeremiah Blocki, and Ben Harsha. “Practical Graphs for Optimal Side-Channel Resistant Memory-Hard Functions.” In <i>Proceedings of the 2017 ACM SIGSAC Conference on Computer and Communications Security</i>, 1001–17. ACM Press, 2017. <a href=\"https://doi.org/10.1145/3133956.3134031\">https://doi.org/10.1145/3133956.3134031</a>.","apa":"Alwen, J. F., Blocki, J., &#38; Harsha, B. (2017). Practical graphs for optimal side-channel resistant memory-hard functions. In <i>Proceedings of the 2017 ACM SIGSAC Conference on Computer and Communications Security</i> (pp. 1001–1017). Dallas, TX, USA: ACM Press. <a href=\"https://doi.org/10.1145/3133956.3134031\">https://doi.org/10.1145/3133956.3134031</a>","mla":"Alwen, Joel F., et al. “Practical Graphs for Optimal Side-Channel Resistant Memory-Hard Functions.” <i>Proceedings of the 2017 ACM SIGSAC Conference on Computer and Communications Security</i>, ACM Press, 2017, pp. 1001–17, doi:<a href=\"https://doi.org/10.1145/3133956.3134031\">10.1145/3133956.3134031</a>."},"ec_funded":1,"oa_version":"Submitted Version","publication_status":"published","doi":"10.1145/3133956.3134031","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2017/443"}],"publication":"Proceedings of the 2017 ACM SIGSAC Conference on Computer and Communications Security","project":[{"_id":"258AA5B2-B435-11E9-9278-68D0E5697425","name":"Teaching Old Crypto New Tricks","grant_number":"682815","call_identifier":"H2020"}]},{"file":[{"creator":"dernst","file_size":908099,"file_id":"7050","content_type":"application/pdf","relation":"main_file","checksum":"e442dc3b7420a36ec805e9bb45cc1a2e","access_level":"open_access","file_name":"2017_NatureGenetics_Makohon.pdf","date_updated":"2020-07-14T12:47:33Z","date_created":"2019-11-19T08:13:50Z"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Makohon Moore","first_name":"Alvin","full_name":"Makohon Moore, Alvin"},{"full_name":"Zhang, Ming","first_name":"Ming","last_name":"Zhang"},{"id":"4A918E98-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes","orcid":"0000-0002-0170-7353","last_name":"Reiter","full_name":"Reiter, Johannes"},{"last_name":"Božić","first_name":"Ivana","full_name":"Božić, Ivana"},{"full_name":"Allen, Benjamin","last_name":"Allen","first_name":"Benjamin"},{"full_name":"Kundu, Deepanjan","last_name":"Kundu","first_name":"Deepanjan","id":"1d4c0f4f-e8a3-11ec-a351-e36772758c45"},{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"full_name":"Wong, Fay","first_name":"Fay","last_name":"Wong"},{"full_name":"Jiao, Yuchen","first_name":"Yuchen","last_name":"Jiao"},{"last_name":"Kohutek","first_name":"Zachary","full_name":"Kohutek, Zachary"},{"first_name":"Jungeui","last_name":"Hong","full_name":"Hong, Jungeui"},{"full_name":"Attiyeh, Marc","last_name":"Attiyeh","first_name":"Marc"},{"full_name":"Javier, Breanna","first_name":"Breanna","last_name":"Javier"},{"last_name":"Wood","first_name":"Laura","full_name":"Wood, Laura"},{"last_name":"Hruban","first_name":"Ralph","full_name":"Hruban, Ralph"},{"last_name":"Nowak","first_name":"Martin","full_name":"Nowak, Martin"},{"full_name":"Papadopoulos, Nickolas","last_name":"Papadopoulos","first_name":"Nickolas"},{"full_name":"Kinzler, Kenneth","last_name":"Kinzler","first_name":"Kenneth"},{"full_name":"Vogelstein, Bert","last_name":"Vogelstein","first_name":"Bert"},{"last_name":"Iacobuzio Donahue","first_name":"Christine","full_name":"Iacobuzio Donahue, Christine"}],"title":"Limited heterogeneity of known driver gene mutations among the metastases of individual patients with pancreatic cancer","publisher":"Nature Publishing Group","has_accepted_license":"1","article_type":"original","language":[{"iso":"eng"}],"publist_id":"7092","department":[{"_id":"KrCh"}],"article_processing_charge":"No","quality_controlled":"1","_id":"653","file_date_updated":"2020-07-14T12:47:33Z","type":"journal_article","scopus_import":"1","abstract":[{"text":"The extent of heterogeneity among driver gene mutations present in naturally occurring metastases - that is, treatment-naive metastatic disease - is largely unknown. To address this issue, we carried out 60× whole-genome sequencing of 26 metastases from four patients with pancreatic cancer. We found that identical mutations in known driver genes were present in every metastatic lesion for each patient studied. Passenger gene mutations, which do not have known or predicted functional consequences, accounted for all intratumoral heterogeneity. Even with respect to these passenger mutations, our analysis suggests that the genetic similarity among the founding cells of metastases was higher than that expected for any two cells randomly taken from a normal tissue. The uniformity of known driver gene mutations among metastases in the same patient has critical and encouraging implications for the success of future targeted therapies in advanced-stage disease.","lang":"eng"}],"citation":{"mla":"Makohon Moore, Alvin, et al. “Limited Heterogeneity of Known Driver Gene Mutations among the Metastases of Individual Patients with Pancreatic Cancer.” <i>Nature Genetics</i>, vol. 49, no. 3, Nature Publishing Group, 2017, pp. 358–66, doi:<a href=\"https://doi.org/10.1038/ng.3764\">10.1038/ng.3764</a>.","apa":"Makohon Moore, A., Zhang, M., Reiter, J., Božić, I., Allen, B., Kundu, D., … Iacobuzio Donahue, C. (2017). Limited heterogeneity of known driver gene mutations among the metastases of individual patients with pancreatic cancer. <i>Nature Genetics</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ng.3764\">https://doi.org/10.1038/ng.3764</a>","chicago":"Makohon Moore, Alvin, Ming Zhang, Johannes Reiter, Ivana Božić, Benjamin Allen, Deepanjan Kundu, Krishnendu Chatterjee, et al. “Limited Heterogeneity of Known Driver Gene Mutations among the Metastases of Individual Patients with Pancreatic Cancer.” <i>Nature Genetics</i>. Nature Publishing Group, 2017. <a href=\"https://doi.org/10.1038/ng.3764\">https://doi.org/10.1038/ng.3764</a>.","ista":"Makohon Moore A, Zhang M, Reiter J, Božić I, Allen B, Kundu D, Chatterjee K, Wong F, Jiao Y, Kohutek Z, Hong J, Attiyeh M, Javier B, Wood L, Hruban R, Nowak M, Papadopoulos N, Kinzler K, Vogelstein B, Iacobuzio Donahue C. 2017. Limited heterogeneity of known driver gene mutations among the metastases of individual patients with pancreatic cancer. Nature Genetics. 49(3), 358–366.","ieee":"A. Makohon Moore <i>et al.</i>, “Limited heterogeneity of known driver gene mutations among the metastases of individual patients with pancreatic cancer,” <i>Nature Genetics</i>, vol. 49, no. 3. Nature Publishing Group, pp. 358–366, 2017.","short":"A. Makohon Moore, M. Zhang, J. Reiter, I. Božić, B. Allen, D. Kundu, K. Chatterjee, F. Wong, Y. Jiao, Z. Kohutek, J. Hong, M. Attiyeh, B. Javier, L. Wood, R. Hruban, M. Nowak, N. Papadopoulos, K. Kinzler, B. Vogelstein, C. Iacobuzio Donahue, Nature Genetics 49 (2017) 358–366.","ama":"Makohon Moore A, Zhang M, Reiter J, et al. Limited heterogeneity of known driver gene mutations among the metastases of individual patients with pancreatic cancer. <i>Nature Genetics</i>. 2017;49(3):358-366. doi:<a href=\"https://doi.org/10.1038/ng.3764\">10.1038/ng.3764</a>"},"publication_identifier":{"issn":["10614036"]},"publication_status":"published","project":[{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","call_identifier":"FP7"},{"grant_number":"P 23499-N23","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"grant_number":"S11407","call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory"}],"issue":"3","oa":1,"date_updated":"2022-06-10T09:55:08Z","acknowledgement":"We thank the Memorial Sloan Kettering Cancer Center Molecular Cytology core facility for immunohistochemistry staining. This work was supported by Office of Naval Research grant N00014-16-1-2914, the Bill and Melinda Gates Foundation (OPP1148627), and a gift from B. Wu and E. Larson (M.A.N.), National Institutes of Health grants CA179991 (C.A.I.-D. and I.B.), F31 CA180682 (A.P.M.-M.), CA43460 (B.V.), and P50 CA62924, the Monastra Foundation, the Virginia and D.K. Ludwig Fund for Cancer Research, the Lustgarten Foundation for Pancreatic Cancer Research, the Sol Goldman Center for Pancreatic Cancer Research, the Sol Goldman Sequencing Center, ERC Start grant 279307: Graph Games (J.G.R., D.K., and C.K.), Austrian Science Fund (FWF) grant P23499-N23 (J.G.R., D.K., and C.K.), and FWF NFN grant S11407-N23 RiSE/SHiNE (J.G.R., D.K., and C.K.).","month":"03","intvolume":"        49","date_published":"2017-03-01T00:00:00Z","year":"2017","page":"358 - 366","external_id":{"pmid":["28092682"]},"day":"01","status":"public","date_created":"2018-12-11T11:47:43Z","ddc":["000"],"pmid":1,"volume":49,"ec_funded":1,"oa_version":"Submitted Version","doi":"10.1038/ng.3764","publication":"Nature Genetics"},{"publist_id":"7089","department":[{"_id":"AnKi"}],"pubrep_id":"987","language":[{"iso":"eng"}],"publisher":"Company of Biologists","has_accepted_license":"1","title":"Creating to understand – developmental biology meets engineering in Paris","author":[{"full_name":"Kicheva, Anna","orcid":"0000-0003-4509-4998","last_name":"Kicheva","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","first_name":"Anna"},{"full_name":"Rivron, Nicolas","last_name":"Rivron","first_name":"Nicolas"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"file_name":"IST-2018-987-v1+1_2017_KichevaRivron__Creating_to.pdf","date_updated":"2020-07-14T12:47:33Z","date_created":"2018-12-12T10:15:20Z","file_id":"5139","content_type":"application/pdf","file_size":228206,"creator":"system","access_level":"open_access","relation":"main_file","checksum":"eef22a0f42a55b232cb2d1188a2322cb"}],"publication_status":"published","project":[{"call_identifier":"H2020","grant_number":"680037","_id":"B6FC0238-B512-11E9-945C-1524E6697425","name":"Coordination of Patterning And Growth In the Spinal Cord"}],"abstract":[{"text":"In November 2016, developmental biologists, synthetic biologists and engineers gathered in Paris for a meeting called ‘Engineering the embryo’. The participants shared an interest in exploring how synthetic systems can reveal new principles of embryonic development, and how the in vitro manipulation and modeling of development using stem cells can be used to integrate ideas and expertise from physics, developmental biology and tissue engineering. As we review here, the conference pinpointed some of the challenges arising at the intersection of these fields, along with great enthusiasm for finding new approaches and collaborations.","lang":"eng"}],"scopus_import":1,"file_date_updated":"2020-07-14T12:47:33Z","type":"journal_article","citation":{"short":"A. Kicheva, N. Rivron, Development 144 (2017) 733–736.","ieee":"A. Kicheva and N. Rivron, “Creating to understand – developmental biology meets engineering in Paris,” <i>Development</i>, vol. 144, no. 5. Company of Biologists, pp. 733–736, 2017.","ista":"Kicheva A, Rivron N. 2017. Creating to understand – developmental biology meets engineering in Paris. Development. 144(5), 733–736.","ama":"Kicheva A, Rivron N. Creating to understand – developmental biology meets engineering in Paris. <i>Development</i>. 2017;144(5):733-736. doi:<a href=\"https://doi.org/10.1242/dev.144915\">10.1242/dev.144915</a>","chicago":"Kicheva, Anna, and Nicolas Rivron. “Creating to Understand – Developmental Biology Meets Engineering in Paris.” <i>Development</i>. Company of Biologists, 2017. <a href=\"https://doi.org/10.1242/dev.144915\">https://doi.org/10.1242/dev.144915</a>.","apa":"Kicheva, A., &#38; Rivron, N. (2017). Creating to understand – developmental biology meets engineering in Paris. <i>Development</i>. Company of Biologists. <a href=\"https://doi.org/10.1242/dev.144915\">https://doi.org/10.1242/dev.144915</a>","mla":"Kicheva, Anna, and Nicolas Rivron. “Creating to Understand – Developmental Biology Meets Engineering in Paris.” <i>Development</i>, vol. 144, no. 5, Company of Biologists, 2017, pp. 733–36, doi:<a href=\"https://doi.org/10.1242/dev.144915\">10.1242/dev.144915</a>."},"publication_identifier":{"issn":["09501991"]},"quality_controlled":"1","_id":"654","page":"733 - 736","year":"2017","date_published":"2017-03-01T00:00:00Z","intvolume":"       144","month":"03","oa":1,"issue":"5","date_updated":"2021-01-12T08:07:54Z","publication":"Development","doi":"10.1242/dev.144915","ec_funded":1,"oa_version":"Submitted Version","volume":144,"status":"public","day":"01","ddc":["571"],"date_created":"2018-12-11T11:47:44Z"},{"publication_status":"published","quality_controlled":"1","_id":"655","scopus_import":1,"abstract":[{"lang":"eng","text":"The bacterial flagellum is a self-assembling nanomachine. The external flagellar filament, several times longer than a bacterial cell body, is made of a few tens of thousands subunits of a single protein: flagellin. A fundamental problem concerns the molecular mechanism of how the flagellum grows outside the cell, where no discernible energy source is available. Here, we monitored the dynamic assembly of individual flagella using in situ labelling and real-time immunostaining of elongating flagellar filaments. We report that the rate of flagellum growth, initially ~1,700 amino acids per second, decreases with length and that the previously proposed chain mechanism does not contribute to the filament elongation dynamics. Inhibition of the proton motive force-dependent export apparatus revealed a major contribution of substrate injection in driving filament elongation. The combination of experimental and mathematical evidence demonstrates that a simple, injection-diffusion mechanism controls bacterial flagella growth outside the cell."}],"file_date_updated":"2020-07-14T12:47:33Z","type":"journal_article","publication_identifier":{"issn":["2050084X"]},"citation":{"apa":"Renault, T., Abraham, A., Bergmiller, T., Paradis, G., Rainville, S., Charpentier, E., … Erhardt, M. (2017). Bacterial flagella grow through an injection diffusion mechanism. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.23136\">https://doi.org/10.7554/eLife.23136</a>","mla":"Renault, Thibaud, et al. “Bacterial Flagella Grow through an Injection Diffusion Mechanism.” <i>ELife</i>, vol. 6, e23136, eLife Sciences Publications, 2017, doi:<a href=\"https://doi.org/10.7554/eLife.23136\">10.7554/eLife.23136</a>.","ieee":"T. Renault <i>et al.</i>, “Bacterial flagella grow through an injection diffusion mechanism,” <i>eLife</i>, vol. 6. eLife Sciences Publications, 2017.","short":"T. Renault, A. Abraham, T. Bergmiller, G. Paradis, S. Rainville, E. Charpentier, C.C. Guet, Y. Tu, K. Namba, J. Keener, T. Minamino, M. Erhardt, ELife 6 (2017).","ista":"Renault T, Abraham A, Bergmiller T, Paradis G, Rainville S, Charpentier E, Guet CC, Tu Y, Namba K, Keener J, Minamino T, Erhardt M. 2017. Bacterial flagella grow through an injection diffusion mechanism. eLife. 6, e23136.","ama":"Renault T, Abraham A, Bergmiller T, et al. Bacterial flagella grow through an injection diffusion mechanism. <i>eLife</i>. 2017;6. doi:<a href=\"https://doi.org/10.7554/eLife.23136\">10.7554/eLife.23136</a>","chicago":"Renault, Thibaud, Anthony Abraham, Tobias Bergmiller, Guillaume Paradis, Simon Rainville, Emmanuelle Charpentier, Calin C Guet, et al. “Bacterial Flagella Grow through an Injection Diffusion Mechanism.” <i>ELife</i>. eLife Sciences Publications, 2017. <a href=\"https://doi.org/10.7554/eLife.23136\">https://doi.org/10.7554/eLife.23136</a>."},"pubrep_id":"904","language":[{"iso":"eng"}],"publist_id":"7082","department":[{"_id":"CaGu"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Thibaud","last_name":"Renault","full_name":"Renault, Thibaud"},{"first_name":"Anthony","last_name":"Abraham","full_name":"Abraham, Anthony"},{"id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","first_name":"Tobias","last_name":"Bergmiller","orcid":"0000-0001-5396-4346","full_name":"Bergmiller, Tobias"},{"full_name":"Paradis, Guillaume","first_name":"Guillaume","last_name":"Paradis"},{"last_name":"Rainville","first_name":"Simon","full_name":"Rainville, Simon"},{"last_name":"Charpentier","first_name":"Emmanuelle","full_name":"Charpentier, Emmanuelle"},{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C","orcid":"0000-0001-6220-2052","last_name":"Guet","full_name":"Guet, Calin C"},{"full_name":"Tu, Yuhai","first_name":"Yuhai","last_name":"Tu"},{"full_name":"Namba, Keiichi","last_name":"Namba","first_name":"Keiichi"},{"full_name":"Keener, James","first_name":"James","last_name":"Keener"},{"full_name":"Minamino, Tohru","first_name":"Tohru","last_name":"Minamino"},{"full_name":"Erhardt, Marc","first_name":"Marc","last_name":"Erhardt"}],"title":"Bacterial flagella grow through an injection diffusion mechanism","file":[{"file_name":"IST-2017-904-v1+1_elife-23136-v2.pdf","date_created":"2018-12-12T10:08:53Z","date_updated":"2020-07-14T12:47:33Z","file_id":"4716","content_type":"application/pdf","creator":"system","file_size":5520359,"access_level":"open_access","checksum":"39e1c3e82ddac83a30422fa72fa1a383","relation":"main_file"},{"file_size":11242920,"creator":"system","content_type":"application/pdf","file_id":"4717","relation":"main_file","checksum":"a6d542253028f52e00aa29739ddffe8f","access_level":"open_access","file_name":"IST-2017-904-v1+2_elife-23136-figures-v2.pdf","date_created":"2018-12-12T10:08:54Z","date_updated":"2020-07-14T12:47:33Z"}],"publisher":"eLife Sciences Publications","has_accepted_license":"1","oa_version":"Published Version","publication":"eLife","doi":"10.7554/eLife.23136","day":"06","status":"public","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["579"],"date_created":"2018-12-11T11:47:44Z","volume":6,"year":"2017","oa":1,"date_updated":"2021-01-12T08:07:55Z","article_number":"e23136","date_published":"2017-03-06T00:00:00Z","intvolume":"         6","month":"03"},{"oa_version":"None","doi":"10.1126/scitranslmed.aam9867","publication_status":"published","publication":"Science Translational Medicine","status":"public","day":"15","quality_controlled":"1","date_created":"2018-12-11T11:47:45Z","_id":"656","type":"journal_article","scopus_import":1,"abstract":[{"lang":"eng","text":"Human neurons transplanted into a mouse model for Alzheimer’s disease show human-specific vulnerability to β-amyloid plaques and may help to identify new therapeutic targets."}],"publication_identifier":{"issn":["19466234"]},"citation":{"mla":"Novarino, Gaia. “Modeling Alzheimer’s Disease in Mice with Human Neurons.” <i>Science Translational Medicine</i>, vol. 9, no. 381, eaam9867, American Association for the Advancement of Science, 2017, doi:<a href=\"https://doi.org/10.1126/scitranslmed.aam9867\">10.1126/scitranslmed.aam9867</a>.","apa":"Novarino, G. (2017). Modeling Alzheimer’s disease in mice with human neurons. <i>Science Translational Medicine</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/scitranslmed.aam9867\">https://doi.org/10.1126/scitranslmed.aam9867</a>","chicago":"Novarino, Gaia. “Modeling Alzheimer’s Disease in Mice with Human Neurons.” <i>Science Translational Medicine</i>. American Association for the Advancement of Science, 2017. <a href=\"https://doi.org/10.1126/scitranslmed.aam9867\">https://doi.org/10.1126/scitranslmed.aam9867</a>.","ista":"Novarino G. 2017. Modeling Alzheimer’s disease in mice with human neurons. Science Translational Medicine. 9(381), eaam9867.","short":"G. Novarino, Science Translational Medicine 9 (2017).","ieee":"G. Novarino, “Modeling Alzheimer’s disease in mice with human neurons,” <i>Science Translational Medicine</i>, vol. 9, no. 381. American Association for the Advancement of Science, 2017.","ama":"Novarino G. Modeling Alzheimer’s disease in mice with human neurons. <i>Science Translational Medicine</i>. 2017;9(381). doi:<a href=\"https://doi.org/10.1126/scitranslmed.aam9867\">10.1126/scitranslmed.aam9867</a>"},"volume":9,"year":"2017","language":[{"iso":"eng"}],"department":[{"_id":"GaNo"}],"publist_id":"7079","issue":"381","author":[{"full_name":"Novarino, Gaia","last_name":"Novarino","orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","title":"Modeling Alzheimer's disease in mice with human neurons","date_updated":"2021-01-12T08:07:59Z","article_number":"eaam9867","publisher":"American Association for the Advancement of Science","month":"03","intvolume":"         9","date_published":"2017-03-15T00:00:00Z"},{"date_updated":"2021-01-12T08:08:02Z","issue":"12","oa":1,"month":"03","intvolume":"       114","date_published":"2017-03-21T00:00:00Z","year":"2017","external_id":{"pmid":["28265057"]},"page":"E2533 - E2539","date_created":"2018-12-11T11:47:45Z","day":"21","status":"public","pmid":1,"volume":114,"oa_version":"Submitted Version","doi":"10.1073/pnas.1616493114","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5373392/","open_access":"1"}],"publication":"PNAS","title":"Auxin response cell autonomously controls ground tissue initiation in the early arabidopsis embryo","author":[{"full_name":"Möller, Barbara","last_name":"Möller","first_name":"Barbara"},{"full_name":"Ten Hove, Colette","first_name":"Colette","last_name":"Ten Hove"},{"last_name":"Xiang","first_name":"Daoquan","full_name":"Xiang, Daoquan"},{"full_name":"Williams, Nerys","last_name":"Williams","first_name":"Nerys"},{"first_name":"Lorena","last_name":"López","full_name":"López, Lorena"},{"last_name":"Yoshida","first_name":"Saiko","id":"2E46069C-F248-11E8-B48F-1D18A9856A87","full_name":"Yoshida, Saiko"},{"full_name":"Smit, Margot","first_name":"Margot","last_name":"Smit"},{"full_name":"Datla, Raju","first_name":"Raju","last_name":"Datla"},{"last_name":"Weijers","first_name":"Dolf","full_name":"Weijers, Dolf"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"National Academy of Sciences","language":[{"iso":"eng"}],"publist_id":"7076","department":[{"_id":"JiFr"}],"_id":"657","quality_controlled":"1","publication_identifier":{"issn":["00278424"]},"citation":{"ista":"Möller B, Ten Hove C, Xiang D, Williams N, López L, Yoshida S, Smit M, Datla R, Weijers D. 2017. Auxin response cell autonomously controls ground tissue initiation in the early arabidopsis embryo. PNAS. 114(12), E2533–E2539.","short":"B. Möller, C. Ten Hove, D. Xiang, N. Williams, L. López, S. Yoshida, M. Smit, R. Datla, D. Weijers, PNAS 114 (2017) E2533–E2539.","ieee":"B. Möller <i>et al.</i>, “Auxin response cell autonomously controls ground tissue initiation in the early arabidopsis embryo,” <i>PNAS</i>, vol. 114, no. 12. National Academy of Sciences, pp. E2533–E2539, 2017.","ama":"Möller B, Ten Hove C, Xiang D, et al. Auxin response cell autonomously controls ground tissue initiation in the early arabidopsis embryo. <i>PNAS</i>. 2017;114(12):E2533-E2539. doi:<a href=\"https://doi.org/10.1073/pnas.1616493114\">10.1073/pnas.1616493114</a>","chicago":"Möller, Barbara, Colette Ten Hove, Daoquan Xiang, Nerys Williams, Lorena López, Saiko Yoshida, Margot Smit, Raju Datla, and Dolf Weijers. “Auxin Response Cell Autonomously Controls Ground Tissue Initiation in the Early Arabidopsis Embryo.” <i>PNAS</i>. National Academy of Sciences, 2017. <a href=\"https://doi.org/10.1073/pnas.1616493114\">https://doi.org/10.1073/pnas.1616493114</a>.","apa":"Möller, B., Ten Hove, C., Xiang, D., Williams, N., López, L., Yoshida, S., … Weijers, D. (2017). Auxin response cell autonomously controls ground tissue initiation in the early arabidopsis embryo. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1616493114\">https://doi.org/10.1073/pnas.1616493114</a>","mla":"Möller, Barbara, et al. “Auxin Response Cell Autonomously Controls Ground Tissue Initiation in the Early Arabidopsis Embryo.” <i>PNAS</i>, vol. 114, no. 12, National Academy of Sciences, 2017, pp. E2533–39, doi:<a href=\"https://doi.org/10.1073/pnas.1616493114\">10.1073/pnas.1616493114</a>."},"type":"journal_article","scopus_import":1,"abstract":[{"lang":"eng","text":"Plant organs are typically organized into three main tissue layers. The middle ground tissue layer comprises the majority of the plant body and serves a wide range of functions, including photosynthesis, selective nutrient uptake and storage, and gravity sensing. Ground tissue patterning and maintenance in Arabidopsis are controlled by a well-established gene network revolving around the key regulator SHORT-ROOT (SHR). In contrast, it is completely unknown how ground tissue identity is first specified from totipotent precursor cells in the embryo. The plant signaling molecule auxin, acting through AUXIN RESPONSE FACTOR (ARF) transcription factors, is critical for embryo patterning. The auxin effector ARF5/MONOPTEROS (MP) acts both cell-autonomously and noncell-autonomously to control embryonic vascular tissue formation and root initiation, respectively. Here we show that auxin response and ARF activity cell-autonomously control the asymmetric division of the first ground tissue cells. By identifying embryonic target genes, we show that MP transcriptionally initiates the ground tissue lineage and acts upstream of the regulatory network that controls ground tissue patterning and maintenance. Strikingly, whereas the SHR network depends on MP, this MP function is, at least in part, SHR independent. Our study therefore identifies auxin response as a regulator of ground tissue specification in the embryonic root, and reveals that ground tissue initiation and maintenance use different regulators and mechanisms. Moreover, our data provide a framework for the simultaneous formation of multiple cell types by the same transcriptional regulator."}],"publication_status":"published"},{"publication_status":"published","project":[{"call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme"}],"quality_controlled":"1","_id":"658","type":"journal_article","file_date_updated":"2020-07-14T12:47:33Z","abstract":[{"text":"With the accelerated development of robot technologies, control becomes one of the central themes of research. In traditional approaches, the controller, by its internal functionality, finds appropriate actions on the basis of specific objectives for the task at hand. While very successful in many applications, self-organized control schemes seem to be favored in large complex systems with unknown dynamics or which are difficult to model. Reasons are the expected scalability, robustness, and resilience of self-organizing systems. The paper presents a self-learning neurocontroller based on extrinsic differential plasticity introduced recently, applying it to an anthropomorphic musculoskeletal robot arm with attached objects of unknown physical dynamics. The central finding of the paper is the following effect: by the mere feedback through the internal dynamics of the object, the robot is learning to relate each of the objects with a very specific sensorimotor pattern. Specifically, an attached pendulum pilots the arm into a circular motion, a half-filled bottle produces axis oriented shaking behavior, a wheel is getting rotated, and wiping patterns emerge automatically in a table-plus-brush setting. By these object-specific dynamical patterns, the robot may be said to recognize the object's identity, or in other words, it discovers dynamical affordances of objects. Furthermore, when including hand coordinates obtained from a camera, a dedicated hand-eye coordination self-organizes spontaneously. These phenomena are discussed from a specific dynamical system perspective. Central is the dedicated working regime at the border to instability with its potentially infinite reservoir of (limit cycle) attractors &quot;waiting&quot; to be excited. Besides converging toward one of these attractors, variate behavior is also arising from a self-induced attractor morphing driven by the learning rule. We claim that experimental investigations with this anthropomorphic, self-learning robot not only generate interesting and potentially useful behaviors, but may also help to better understand what subjective human muscle feelings are, how they can be rooted in sensorimotor patterns, and how these concepts may feed back on robotics.","lang":"eng"}],"scopus_import":1,"citation":{"ieee":"R. Der and G. S. Martius, “Self organized behavior generation for musculoskeletal robots,” <i>Frontiers in Neurorobotics</i>, vol. 11, no. MAR. Frontiers Research Foundation, 2017.","ista":"Der R, Martius GS. 2017. Self organized behavior generation for musculoskeletal robots. Frontiers in Neurorobotics. 11(MAR), 00008.","short":"R. Der, G.S. Martius, Frontiers in Neurorobotics 11 (2017).","ama":"Der R, Martius GS. Self organized behavior generation for musculoskeletal robots. <i>Frontiers in Neurorobotics</i>. 2017;11(MAR). doi:<a href=\"https://doi.org/10.3389/fnbot.2017.00008\">10.3389/fnbot.2017.00008</a>","chicago":"Der, Ralf, and Georg S Martius. “Self Organized Behavior Generation for Musculoskeletal Robots.” <i>Frontiers in Neurorobotics</i>. Frontiers Research Foundation, 2017. <a href=\"https://doi.org/10.3389/fnbot.2017.00008\">https://doi.org/10.3389/fnbot.2017.00008</a>.","apa":"Der, R., &#38; Martius, G. S. (2017). Self organized behavior generation for musculoskeletal robots. <i>Frontiers in Neurorobotics</i>. Frontiers Research Foundation. <a href=\"https://doi.org/10.3389/fnbot.2017.00008\">https://doi.org/10.3389/fnbot.2017.00008</a>","mla":"Der, Ralf, and Georg S. Martius. “Self Organized Behavior Generation for Musculoskeletal Robots.” <i>Frontiers in Neurorobotics</i>, vol. 11, no. MAR, 00008, Frontiers Research Foundation, 2017, doi:<a href=\"https://doi.org/10.3389/fnbot.2017.00008\">10.3389/fnbot.2017.00008</a>."},"publication_identifier":{"issn":["16625218"]},"pubrep_id":"903","language":[{"iso":"eng"}],"department":[{"_id":"ChLa"},{"_id":"GaTk"}],"publist_id":"7078","article_processing_charge":"Yes","file":[{"date_created":"2018-12-12T10:18:49Z","date_updated":"2020-07-14T12:47:33Z","file_name":"IST-2017-903-v1+1_fnbot-11-00008.pdf","relation":"main_file","access_level":"open_access","checksum":"b1bc43f96d1df3313c03032c2a46388d","creator":"system","file_size":8439566,"content_type":"application/pdf","file_id":"5371"}],"title":"Self organized behavior generation for musculoskeletal robots","author":[{"full_name":"Der, Ralf","last_name":"Der","first_name":"Ralf"},{"id":"3A276B68-F248-11E8-B48F-1D18A9856A87","first_name":"Georg S","last_name":"Martius","full_name":"Martius, Georg S"}],"user_id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","publisher":"Frontiers Research Foundation","has_accepted_license":"1","ec_funded":1,"oa_version":"Published Version","doi":"10.3389/fnbot.2017.00008","publication":"Frontiers in Neurorobotics","status":"public","day":"16","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2018-12-11T11:47:45Z","ddc":["006"],"volume":11,"year":"2017","issue":"MAR","oa":1,"date_updated":"2021-01-12T08:08:04Z","article_number":"00008","month":"03","intvolume":"        11","date_published":"2017-03-16T00:00:00Z"},{"citation":{"short":"F. Kage, M. Winterhoff, V. Dimchev, J. Müller, T. Thalheim, A. Freise, S. Brühmann, J. Kollasser, J. Block, G.A. Dimchev, M. Geyer, H. Schnittler, C. Brakebusch, T. Stradal, M. Carlier, M.K. Sixt, J. Käs, J. Faix, K. Rottner, Nature Communications 8 (2017).","ieee":"F. Kage <i>et al.</i>, “FMNL formins boost lamellipodial force generation,” <i>Nature Communications</i>, vol. 8. Nature Publishing Group, 2017.","ista":"Kage F, Winterhoff M, Dimchev V, Müller J, Thalheim T, Freise A, Brühmann S, Kollasser J, Block J, Dimchev GA, Geyer M, Schnittler H, Brakebusch C, Stradal T, Carlier M, Sixt MK, Käs J, Faix J, Rottner K. 2017. FMNL formins boost lamellipodial force generation. Nature Communications. 8, 14832.","ama":"Kage F, Winterhoff M, Dimchev V, et al. FMNL formins boost lamellipodial force generation. <i>Nature Communications</i>. 2017;8. doi:<a href=\"https://doi.org/10.1038/ncomms14832\">10.1038/ncomms14832</a>","chicago":"Kage, Frieda, Moritz Winterhoff, Vanessa Dimchev, Jan Müller, Tobias Thalheim, Anika Freise, Stefan Brühmann, et al. “FMNL Formins Boost Lamellipodial Force Generation.” <i>Nature Communications</i>. Nature Publishing Group, 2017. <a href=\"https://doi.org/10.1038/ncomms14832\">https://doi.org/10.1038/ncomms14832</a>.","apa":"Kage, F., Winterhoff, M., Dimchev, V., Müller, J., Thalheim, T., Freise, A., … Rottner, K. (2017). FMNL formins boost lamellipodial force generation. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncomms14832\">https://doi.org/10.1038/ncomms14832</a>","mla":"Kage, Frieda, et al. “FMNL Formins Boost Lamellipodial Force Generation.” <i>Nature Communications</i>, vol. 8, 14832, Nature Publishing Group, 2017, doi:<a href=\"https://doi.org/10.1038/ncomms14832\">10.1038/ncomms14832</a>."},"publication_identifier":{"issn":["20411723"]},"file_date_updated":"2020-07-14T12:47:34Z","type":"journal_article","abstract":[{"lang":"eng","text":"Migration frequently involves Rac-mediated protrusion of lamellipodia, formed by Arp2/3 complex-dependent branching thought to be crucial for force generation and stability of these networks. The formins FMNL2 and FMNL3 are Cdc42 effectors targeting to the lamellipodium tip and shown here to nucleate and elongate actin filaments with complementary activities in vitro. In migrating B16-F1 melanoma cells, both formins contribute to the velocity of lamellipodium protrusion. Loss of FMNL2/3 function in melanoma cells and fibroblasts reduces lamellipodial width, actin filament density and -bundling, without changing patterns of Arp2/3 complex incorporation. Strikingly, in melanoma cells, FMNL2/3 gene inactivation almost completely abolishes protrusion forces exerted by lamellipodia and modifies their ultrastructural organization. Consistently, CRISPR/Cas-mediated depletion of FMNL2/3 in fibroblasts reduces both migration and capability of cells to move against viscous media. Together, we conclude that force generation in lamellipodia strongly depends on FMNL formin activity, operating in addition to Arp2/3 complex-dependent filament branching."}],"scopus_import":1,"_id":"659","quality_controlled":"1","publication_status":"published","has_accepted_license":"1","publisher":"Nature Publishing Group","file":[{"file_size":9523746,"creator":"system","file_id":"5072","content_type":"application/pdf","relation":"main_file","checksum":"dae30190291c3630e8102d8714a8d23e","access_level":"open_access","file_name":"IST-2017-902-v1+1_Kage_et_al-2017-Nature_Communications.pdf","date_updated":"2020-07-14T12:47:34Z","date_created":"2018-12-12T10:14:21Z"}],"author":[{"last_name":"Kage","first_name":"Frieda","full_name":"Kage, Frieda"},{"full_name":"Winterhoff, Moritz","first_name":"Moritz","last_name":"Winterhoff"},{"full_name":"Dimchev, Vanessa","first_name":"Vanessa","last_name":"Dimchev"},{"full_name":"Müller, Jan","id":"AD07FDB4-0F61-11EA-8158-C4CC64CEAA8D","first_name":"Jan","last_name":"Müller"},{"first_name":"Tobias","last_name":"Thalheim","full_name":"Thalheim, Tobias"},{"full_name":"Freise, Anika","last_name":"Freise","first_name":"Anika"},{"full_name":"Brühmann, Stefan","first_name":"Stefan","last_name":"Brühmann"},{"full_name":"Kollasser, Jana","last_name":"Kollasser","first_name":"Jana"},{"full_name":"Block, Jennifer","first_name":"Jennifer","last_name":"Block"},{"first_name":"Georgi A","last_name":"Dimchev","full_name":"Dimchev, Georgi A"},{"full_name":"Geyer, Matthias","last_name":"Geyer","first_name":"Matthias"},{"first_name":"Hams","last_name":"Schnittler","full_name":"Schnittler, Hams"},{"full_name":"Brakebusch, Cord","first_name":"Cord","last_name":"Brakebusch"},{"full_name":"Stradal, Theresia","last_name":"Stradal","first_name":"Theresia"},{"full_name":"Carlier, Marie","first_name":"Marie","last_name":"Carlier"},{"full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","orcid":"0000-0002-6620-9179","last_name":"Sixt"},{"full_name":"Käs, Josef","last_name":"Käs","first_name":"Josef"},{"last_name":"Faix","first_name":"Jan","full_name":"Faix, Jan"},{"last_name":"Rottner","first_name":"Klemens","full_name":"Rottner, Klemens"}],"title":"FMNL formins boost lamellipodial force generation","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","department":[{"_id":"MiSi"}],"publist_id":"7075","language":[{"iso":"eng"}],"pubrep_id":"902","volume":8,"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2018-12-11T11:47:46Z","ddc":["570"],"day":"22","status":"public","doi":"10.1038/ncomms14832","publication":"Nature Communications","oa_version":"Published Version","month":"03","intvolume":"         8","date_published":"2017-03-22T00:00:00Z","article_number":"14832","date_updated":"2021-01-12T08:08:06Z","oa":1,"year":"2017"},{"oa_version":"Submitted Version","doi":"10.1073/pnas.1620274114","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5380103/"}],"publication":"PNAS","date_created":"2018-12-11T11:47:46Z","day":"28","status":"public","pmid":1,"volume":114,"year":"2017","external_id":{"pmid":["28280102"]},"page":"3427 - 3432","date_updated":"2021-01-12T08:08:09Z","issue":"13","oa":1,"month":"03","intvolume":"       114","date_published":"2017-03-28T00:00:00Z","acknowledgement":"We thank Philippe Cluzel for helpful discussions and Gunnar Pruessner for data analysis advice. This work was supported by the Francis Crick Institute, which receives its core funding from Cancer Research UK Grant FC001163, Medical Research Council Grant FC001163, and Wellcome Trust Grant FC001163. This work was also supported by European Research Council Advanced Grant Project 323042 (to C.D. and T.S.).","publication_status":"published","_id":"660","quality_controlled":"1","citation":{"ista":"Rickman J, Düllberg CF, Cade N, Griffin L, Surrey T. 2017. Steady state EB cap size fluctuations are determined by stochastic microtubule growth and maturation. PNAS. 114(13), 3427–3432.","ieee":"J. Rickman, C. F. Düllberg, N. Cade, L. Griffin, and T. Surrey, “Steady state EB cap size fluctuations are determined by stochastic microtubule growth and maturation,” <i>PNAS</i>, vol. 114, no. 13. National Academy of Sciences, pp. 3427–3432, 2017.","short":"J. Rickman, C.F. Düllberg, N. Cade, L. Griffin, T. Surrey, PNAS 114 (2017) 3427–3432.","ama":"Rickman J, Düllberg CF, Cade N, Griffin L, Surrey T. Steady state EB cap size fluctuations are determined by stochastic microtubule growth and maturation. <i>PNAS</i>. 2017;114(13):3427-3432. doi:<a href=\"https://doi.org/10.1073/pnas.1620274114\">10.1073/pnas.1620274114</a>","chicago":"Rickman, Jamie, Christian F Düllberg, Nicholas Cade, Lewis Griffin, and Thomas Surrey. “Steady State EB Cap Size Fluctuations Are Determined by Stochastic Microtubule Growth and Maturation.” <i>PNAS</i>. National Academy of Sciences, 2017. <a href=\"https://doi.org/10.1073/pnas.1620274114\">https://doi.org/10.1073/pnas.1620274114</a>.","apa":"Rickman, J., Düllberg, C. F., Cade, N., Griffin, L., &#38; Surrey, T. (2017). Steady state EB cap size fluctuations are determined by stochastic microtubule growth and maturation. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1620274114\">https://doi.org/10.1073/pnas.1620274114</a>","mla":"Rickman, Jamie, et al. “Steady State EB Cap Size Fluctuations Are Determined by Stochastic Microtubule Growth and Maturation.” <i>PNAS</i>, vol. 114, no. 13, National Academy of Sciences, 2017, pp. 3427–32, doi:<a href=\"https://doi.org/10.1073/pnas.1620274114\">10.1073/pnas.1620274114</a>."},"publication_identifier":{"issn":["00278424"]},"type":"journal_article","scopus_import":1,"abstract":[{"lang":"eng","text":"Growing microtubules are protected from depolymerization by the presence of a GTP or GDP/Pi cap. End-binding proteins of the EB1 family bind to the stabilizing cap, allowing monitoring of its size in real time. The cap size has been shown to correlate with instantaneous microtubule stability. Here we have quantitatively characterized the properties of cap size fluctuations during steadystate growth and have developed a theory predicting their timescale and amplitude from the kinetics of microtubule growth and cap maturation. In contrast to growth speed fluctuations, cap size fluctuations show a characteristic timescale, which is defined by the lifetime of the cap sites. Growth fluctuations affect the amplitude of cap size fluctuations; however, cap size does not affect growth speed, indicating that microtubules are far from instability during most of their time of growth. Our theory provides the basis for a quantitative understanding of microtubule stability fluctuations during steady-state growth."}],"language":[{"iso":"eng"}],"department":[{"_id":"MaLo"}],"publist_id":"7073","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Rickman, Jamie","first_name":"Jamie","last_name":"Rickman"},{"id":"459064DC-F248-11E8-B48F-1D18A9856A87","first_name":"Christian F","last_name":"Düllberg","orcid":"0000-0001-6335-9748","full_name":"Düllberg, Christian F"},{"first_name":"Nicholas","last_name":"Cade","full_name":"Cade, Nicholas"},{"full_name":"Griffin, Lewis","first_name":"Lewis","last_name":"Griffin"},{"first_name":"Thomas","last_name":"Surrey","full_name":"Surrey, Thomas"}],"title":"Steady state EB cap size fluctuations are determined by stochastic microtubule growth and maturation","publisher":"National Academy of Sciences"},{"day":"27","status":"public","date_created":"2018-12-11T11:47:46Z","volume":19,"pmid":1,"ec_funded":1,"oa_version":"Submitted Version","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"50"},{"id":"8350","relation":"dissertation_contains","status":"public"}]},"publication":"Nature Cell Biology","main_file_link":[{"url":"https://europepmc.org/articles/pmc5635970","open_access":"1"}],"doi":"10.1038/ncb3492","oa":1,"acknowledged_ssus":[{"_id":"SSU"}],"date_updated":"2024-03-25T23:30:21Z","date_published":"2017-03-27T00:00:00Z","month":"03","intvolume":"        19","year":"2017","external_id":{"pmid":["28346437"]},"page":"306 - 317","quality_controlled":"1","_id":"661","abstract":[{"text":"During embryonic development, mechanical forces are essential for cellular rearrangements driving tissue morphogenesis. Here, we show that in the early zebrafish embryo, friction forces are generated at the interface between anterior axial mesoderm (prechordal plate, ppl) progenitors migrating towards the animal pole and neurectoderm progenitors moving in the opposite direction towards the vegetal pole of the embryo. These friction forces lead to global rearrangement of cells within the neurectoderm and determine the position of the neural anlage. Using a combination of experiments and simulations, we show that this process depends on hydrodynamic coupling between neurectoderm and ppl as a result of E-cadherin-mediated adhesion between those tissues. Our data thus establish the emergence of friction forces at the interface between moving tissues as a critical force-generating process shaping the embryo.","lang":"eng"}],"scopus_import":1,"type":"journal_article","citation":{"apa":"Smutny, M., Ákos, Z., Grigolon, S., Shamipour, S., Ruprecht, V., Capek, D., … Heisenberg, C.-P. J. (2017). Friction forces position the neural anlage. <i>Nature Cell Biology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncb3492\">https://doi.org/10.1038/ncb3492</a>","mla":"Smutny, Michael, et al. “Friction Forces Position the Neural Anlage.” <i>Nature Cell Biology</i>, vol. 19, Nature Publishing Group, 2017, pp. 306–17, doi:<a href=\"https://doi.org/10.1038/ncb3492\">10.1038/ncb3492</a>.","ama":"Smutny M, Ákos Z, Grigolon S, et al. Friction forces position the neural anlage. <i>Nature Cell Biology</i>. 2017;19:306-317. doi:<a href=\"https://doi.org/10.1038/ncb3492\">10.1038/ncb3492</a>","short":"M. Smutny, Z. Ákos, S. Grigolon, S. Shamipour, V. Ruprecht, D. Capek, M. Behrndt, E. Papusheva, M. Tada, B. Hof, T. Vicsek, G. Salbreux, C.-P.J. Heisenberg, Nature Cell Biology 19 (2017) 306–317.","ista":"Smutny M, Ákos Z, Grigolon S, Shamipour S, Ruprecht V, Capek D, Behrndt M, Papusheva E, Tada M, Hof B, Vicsek T, Salbreux G, Heisenberg C-PJ. 2017. Friction forces position the neural anlage. Nature Cell Biology. 19, 306–317.","ieee":"M. Smutny <i>et al.</i>, “Friction forces position the neural anlage,” <i>Nature Cell Biology</i>, vol. 19. Nature Publishing Group, pp. 306–317, 2017.","chicago":"Smutny, Michael, Zsuzsa Ákos, Silvia Grigolon, Shayan Shamipour, Verena Ruprecht, Daniel Capek, Martin Behrndt, et al. “Friction Forces Position the Neural Anlage.” <i>Nature Cell Biology</i>. Nature Publishing Group, 2017. <a href=\"https://doi.org/10.1038/ncb3492\">https://doi.org/10.1038/ncb3492</a>."},"publication_identifier":{"issn":["14657392"]},"publication_status":"published","project":[{"call_identifier":"FP7","grant_number":"306589","name":"Decoding the complexity of turbulence at its origin","_id":"25152F3A-B435-11E9-9278-68D0E5697425"},{"name":"Control of Epithelial Cell Layer Spreading in Zebrafish","_id":"252ABD0A-B435-11E9-9278-68D0E5697425","grant_number":"I 930-B20","call_identifier":"FWF"}],"author":[{"full_name":"Smutny, Michael","id":"3FE6E4E8-F248-11E8-B48F-1D18A9856A87","first_name":"Michael","orcid":"0000-0002-5920-9090","last_name":"Smutny"},{"last_name":"Ákos","first_name":"Zsuzsa","full_name":"Ákos, Zsuzsa"},{"full_name":"Grigolon, Silvia","last_name":"Grigolon","first_name":"Silvia"},{"last_name":"Shamipour","first_name":"Shayan","id":"40B34FE2-F248-11E8-B48F-1D18A9856A87","full_name":"Shamipour, Shayan"},{"last_name":"Ruprecht","first_name":"Verena","full_name":"Ruprecht, Verena"},{"full_name":"Capek, Daniel","id":"31C42484-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel","orcid":"0000-0001-5199-9940","last_name":"Capek"},{"full_name":"Behrndt, Martin","last_name":"Behrndt","id":"3ECECA3A-F248-11E8-B48F-1D18A9856A87","first_name":"Martin"},{"full_name":"Papusheva, Ekaterina","first_name":"Ekaterina","id":"41DB591E-F248-11E8-B48F-1D18A9856A87","last_name":"Papusheva"},{"last_name":"Tada","first_name":"Masazumi","full_name":"Tada, Masazumi"},{"full_name":"Hof, Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn","last_name":"Hof","orcid":"0000-0003-2057-2754"},{"last_name":"Vicsek","first_name":"Tamás","full_name":"Vicsek, Tamás"},{"first_name":"Guillaume","last_name":"Salbreux","full_name":"Salbreux, Guillaume"},{"last_name":"Heisenberg","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Friction forces position the neural anlage","publisher":"Nature Publishing Group","language":[{"iso":"eng"}],"publist_id":"7074","department":[{"_id":"CaHe"},{"_id":"BjHo"},{"_id":"Bio"}]},{"publication":"Journal of Symbolic Computation","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.jsc.2016.03.008"}],"doi":"10.1016/j.jsc.2016.03.008","ec_funded":1,"oa_version":"Published Version","isi":1,"related_material":{"record":[{"status":"public","relation":"earlier_version","id":"10894"}]},"volume":78,"day":"01","status":"public","date_created":"2018-12-11T11:51:59Z","page":"76 - 90","external_id":{"isi":["000384396000005"]},"year":"2017","date_published":"2017-01-01T00:00:00Z","intvolume":"        78","month":"01","oa":1,"date_updated":"2023-09-20T09:42:40Z","publication_status":"published","project":[{"grant_number":"318493","call_identifier":"FP7","_id":"255D761E-B435-11E9-9278-68D0E5697425","name":"Topological Complex Systems"}],"abstract":[{"lang":"eng","text":"Phat is an open-source C. ++ library for the computation of persistent homology by matrix reduction, targeted towards developers of software for topological data analysis. We aim for a simple generic design that decouples algorithms from data structures without sacrificing efficiency or user-friendliness. We provide numerous different reduction strategies as well as data types to store and manipulate the boundary matrix. We compare the different combinations through extensive experimental evaluation and identify optimization techniques that work well in practical situations. We also compare our software with various other publicly available libraries for persistent homology."}],"scopus_import":"1","type":"journal_article","publication_identifier":{"issn":[" 07477171"]},"citation":{"mla":"Bauer, Ulrich, et al. “Phat - Persistent Homology Algorithms Toolbox.” <i>Journal of Symbolic Computation</i>, vol. 78, Academic Press, 2017, pp. 76–90, doi:<a href=\"https://doi.org/10.1016/j.jsc.2016.03.008\">10.1016/j.jsc.2016.03.008</a>.","apa":"Bauer, U., Kerber, M., Reininghaus, J., &#38; Wagner, H. (2017). Phat - Persistent homology algorithms toolbox. <i>Journal of Symbolic Computation</i>. Academic Press. <a href=\"https://doi.org/10.1016/j.jsc.2016.03.008\">https://doi.org/10.1016/j.jsc.2016.03.008</a>","chicago":"Bauer, Ulrich, Michael Kerber, Jan Reininghaus, and Hubert Wagner. “Phat - Persistent Homology Algorithms Toolbox.” <i>Journal of Symbolic Computation</i>. Academic Press, 2017. <a href=\"https://doi.org/10.1016/j.jsc.2016.03.008\">https://doi.org/10.1016/j.jsc.2016.03.008</a>.","ieee":"U. Bauer, M. Kerber, J. Reininghaus, and H. Wagner, “Phat - Persistent homology algorithms toolbox,” <i>Journal of Symbolic Computation</i>, vol. 78. Academic Press, pp. 76–90, 2017.","short":"U. Bauer, M. Kerber, J. Reininghaus, H. Wagner, Journal of Symbolic Computation 78 (2017) 76–90.","ista":"Bauer U, Kerber M, Reininghaus J, Wagner H. 2017. Phat - Persistent homology algorithms toolbox. Journal of Symbolic Computation. 78, 76–90.","ama":"Bauer U, Kerber M, Reininghaus J, Wagner H. Phat - Persistent homology algorithms toolbox. <i>Journal of Symbolic Computation</i>. 2017;78:76-90. doi:<a href=\"https://doi.org/10.1016/j.jsc.2016.03.008\">10.1016/j.jsc.2016.03.008</a>"},"quality_controlled":"1","_id":"1433","publist_id":"5765","department":[{"_id":"HeEd"}],"article_processing_charge":"No","article_type":"original","language":[{"iso":"eng"}],"publisher":"Academic Press","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"full_name":"Bauer, Ulrich","first_name":"Ulrich","last_name":"Bauer"},{"full_name":"Kerber, Michael","first_name":"Michael","last_name":"Kerber"},{"first_name":"Jan","last_name":"Reininghaus","full_name":"Reininghaus, Jan"},{"full_name":"Wagner, Hubert","first_name":"Hubert","id":"379CA8B8-F248-11E8-B48F-1D18A9856A87","last_name":"Wagner"}],"title":"Phat - Persistent homology algorithms toolbox"},{"volume":167,"day":"01","status":"public","date_created":"2018-12-11T11:52:32Z","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["530"],"doi":"10.1007/s00440-015-0692-y","publication":"Probability Theory and Related Fields","isi":1,"oa_version":"Published Version","ec_funded":1,"acknowledgement":"Z. Bao was supported by ERC Advanced Grant RANMAT No. 338804; L. Erdős was partially supported by ERC Advanced Grant RANMAT No. 338804.\r\nOpen access funding provided by Institute of Science and Technology (IST Austria). The authors are very grateful to the anonymous referees for careful reading and valuable comments, which helped to improve the organization.","intvolume":"       167","month":"04","date_published":"2017-04-01T00:00:00Z","issue":"3-4","oa":1,"date_updated":"2023-09-20T09:42:12Z","page":"673 - 776","external_id":{"isi":["000398842700004"]},"year":"2017","type":"journal_article","file_date_updated":"2020-07-14T12:45:00Z","abstract":[{"lang":"eng","text":"We consider N×N Hermitian random matrices H consisting of blocks of size M≥N6/7. The matrix elements are i.i.d. within the blocks, close to a Gaussian in the four moment matching sense, but their distribution varies from block to block to form a block-band structure, with an essential band width M. We show that the entries of the Green’s function G(z)=(H−z)−1 satisfy the local semicircle law with spectral parameter z=E+iη down to the real axis for any η≫N−1, using a combination of the supersymmetry method inspired by Shcherbina (J Stat Phys 155(3): 466–499, 2014) and the Green’s function comparison strategy. Previous estimates were valid only for η≫M−1. The new estimate also implies that the eigenvectors in the middle of the spectrum are fully delocalized."}],"scopus_import":"1","citation":{"apa":"Bao, Z., &#38; Erdös, L. (2017). Delocalization for a class of random block band matrices. <i>Probability Theory and Related Fields</i>. Springer. <a href=\"https://doi.org/10.1007/s00440-015-0692-y\">https://doi.org/10.1007/s00440-015-0692-y</a>","mla":"Bao, Zhigang, and László Erdös. “Delocalization for a Class of Random Block Band Matrices.” <i>Probability Theory and Related Fields</i>, vol. 167, no. 3–4, Springer, 2017, pp. 673–776, doi:<a href=\"https://doi.org/10.1007/s00440-015-0692-y\">10.1007/s00440-015-0692-y</a>.","ama":"Bao Z, Erdös L. Delocalization for a class of random block band matrices. <i>Probability Theory and Related Fields</i>. 2017;167(3-4):673-776. doi:<a href=\"https://doi.org/10.1007/s00440-015-0692-y\">10.1007/s00440-015-0692-y</a>","ieee":"Z. Bao and L. Erdös, “Delocalization for a class of random block band matrices,” <i>Probability Theory and Related Fields</i>, vol. 167, no. 3–4. Springer, pp. 673–776, 2017.","short":"Z. Bao, L. Erdös, Probability Theory and Related Fields 167 (2017) 673–776.","ista":"Bao Z, Erdös L. 2017. Delocalization for a class of random block band matrices. Probability Theory and Related Fields. 167(3–4), 673–776.","chicago":"Bao, Zhigang, and László Erdös. “Delocalization for a Class of Random Block Band Matrices.” <i>Probability Theory and Related Fields</i>. Springer, 2017. <a href=\"https://doi.org/10.1007/s00440-015-0692-y\">https://doi.org/10.1007/s00440-015-0692-y</a>."},"publication_identifier":{"issn":["01788051"]},"quality_controlled":"1","_id":"1528","publication_status":"published","project":[{"call_identifier":"FP7","grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","name":"Random matrices, universality and disordered quantum systems"}],"publisher":"Springer","has_accepted_license":"1","file":[{"content_type":"application/pdf","file_id":"4665","creator":"system","file_size":1615755,"access_level":"open_access","relation":"main_file","checksum":"67afa85ff1e220cbc1f9f477a828513c","file_name":"IST-2016-489-v1+1_s00440-015-0692-y.pdf","date_created":"2018-12-12T10:08:05Z","date_updated":"2020-07-14T12:45:00Z"}],"title":"Delocalization for a class of random block band matrices","author":[{"id":"442E6A6C-F248-11E8-B48F-1D18A9856A87","first_name":"Zhigang","last_name":"Bao","orcid":"0000-0003-3036-1475","full_name":"Bao, Zhigang"},{"orcid":"0000-0001-5366-9603","last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László","full_name":"Erdös, László"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"5644","department":[{"_id":"LaEr"}],"article_processing_charge":"Yes (via OA deal)","pubrep_id":"489","article_type":"original","language":[{"iso":"eng"}]},{"author":[{"last_name":"Kretinsky","orcid":"0000-0002-8122-2881","first_name":"Jan","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","full_name":"Kretinsky, Jan"},{"first_name":"Tobias","id":"b21b0c15-30a2-11eb-80dc-f13ca25802e1","last_name":"Meggendorfer","orcid":"0000-0002-1712-2165","full_name":"Meggendorfer, Tobias"},{"full_name":"Waldmann, Clara","first_name":"Clara","last_name":"Waldmann"},{"last_name":"Weininger","first_name":"Maximilian","full_name":"Weininger, Maximilian"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Index appearance record for transforming Rabin automata into parity automata","publisher":"Springer","language":[{"iso":"eng"}],"article_processing_charge":"No","department":[{"_id":"KrCh"}],"_id":"13160","quality_controlled":"1","publication_identifier":{"isbn":["9783662545768"],"eissn":["1611-3349"],"eisbn":["9783662545775"],"issn":["0302-9743"]},"citation":{"ama":"Kretinsky J, Meggendorfer T, Waldmann C, Weininger M. Index appearance record for transforming Rabin automata into parity automata. In: <i>Tools and Algorithms for the Construction and Analysis of Systems</i>. Vol 10205. Springer; 2017:443-460. doi:<a href=\"https://doi.org/10.1007/978-3-662-54577-5_26\">10.1007/978-3-662-54577-5_26</a>","ista":"Kretinsky J, Meggendorfer T, Waldmann C, Weininger M. 2017. Index appearance record for transforming Rabin automata into parity automata. Tools and Algorithms for the Construction and Analysis of Systems. TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 10205, 443–460.","ieee":"J. Kretinsky, T. Meggendorfer, C. Waldmann, and M. Weininger, “Index appearance record for transforming Rabin automata into parity automata,” in <i>Tools and Algorithms for the Construction and Analysis of Systems</i>, Uppsala, Sweden, 2017, vol. 10205, pp. 443–460.","short":"J. Kretinsky, T. Meggendorfer, C. Waldmann, M. Weininger, in:, Tools and Algorithms for the Construction and Analysis of Systems, Springer, 2017, pp. 443–460.","chicago":"Kretinsky, Jan, Tobias Meggendorfer, Clara Waldmann, and Maximilian Weininger. “Index Appearance Record for Transforming Rabin Automata into Parity Automata.” In <i>Tools and Algorithms for the Construction and Analysis of Systems</i>, 10205:443–60. Springer, 2017. <a href=\"https://doi.org/10.1007/978-3-662-54577-5_26\">https://doi.org/10.1007/978-3-662-54577-5_26</a>.","apa":"Kretinsky, J., Meggendorfer, T., Waldmann, C., &#38; Weininger, M. (2017). Index appearance record for transforming Rabin automata into parity automata. In <i>Tools and Algorithms for the Construction and Analysis of Systems</i> (Vol. 10205, pp. 443–460). Uppsala, Sweden: Springer. <a href=\"https://doi.org/10.1007/978-3-662-54577-5_26\">https://doi.org/10.1007/978-3-662-54577-5_26</a>","mla":"Kretinsky, Jan, et al. “Index Appearance Record for Transforming Rabin Automata into Parity Automata.” <i>Tools and Algorithms for the Construction and Analysis of Systems</i>, vol. 10205, Springer, 2017, pp. 443–60, doi:<a href=\"https://doi.org/10.1007/978-3-662-54577-5_26\">10.1007/978-3-662-54577-5_26</a>."},"type":"conference","abstract":[{"lang":"eng","text":"Transforming deterministic ω\r\n-automata into deterministic parity automata is traditionally done using variants of appearance records. We present a more efficient variant of this approach, tailored to Rabin automata, and several optimizations applicable to all appearance records. We compare the methods experimentally and find out that our method produces smaller automata than previous approaches. Moreover, the experiments demonstrate the potential of our method for LTL synthesis, using LTL-to-Rabin translators. It leads to significantly smaller parity automata when compared to state-of-the-art approaches on complex formulae."}],"arxiv":1,"publication_status":"published","date_updated":"2023-06-21T13:29:46Z","oa":1,"month":"03","intvolume":"     10205","date_published":"2017-03-31T00:00:00Z","alternative_title":["LNCS"],"acknowledgement":"This work is partially funded by the DFG project “Verified Model Checkers” and by the Czech Science Foundation, grant No. P202/12/G061.","year":"2017","external_id":{"arxiv":["1701.05738"]},"page":"443-460","conference":{"name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems","start_date":"2017-04-22","end_date":"2017-04-29","location":"Uppsala, Sweden"},"date_created":"2023-06-21T13:21:14Z","day":"31","status":"public","volume":10205,"oa_version":"Preprint","doi":"10.1007/978-3-662-54577-5_26","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.1701.05738"}],"publication":"Tools and Algorithms for the Construction and Analysis of Systems"},{"oa":1,"issue":"2","date_updated":"2023-09-20T11:14:42Z","date_published":"2017-06-01T00:00:00Z","intvolume":"        78","month":"06","year":"2017","page":"681 - 713","external_id":{"isi":["000400379500013"]},"day":"01","status":"public","date_created":"2018-12-11T11:51:27Z","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["576"],"volume":78,"oa_version":"Published Version","ec_funded":1,"isi":1,"publication":"Algorithmica","doi":"10.1007/s00453-016-0212-1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Towards a runtime comparison of natural and artificial evolution","author":[{"orcid":"0000-0003-2361-3953","last_name":"Paixao","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","first_name":"Tiago","full_name":"Paixao, Tiago"},{"first_name":"Jorge","last_name":"Pérez Heredia","full_name":"Pérez Heredia, Jorge"},{"full_name":"Sudholt, Dirk","last_name":"Sudholt","first_name":"Dirk"},{"full_name":"Trubenova, Barbora","orcid":"0000-0002-6873-2967","last_name":"Trubenova","id":"42302D54-F248-11E8-B48F-1D18A9856A87","first_name":"Barbora"}],"file":[{"relation":"main_file","checksum":"7873f665a0c598ac747c908f34cb14b9","access_level":"open_access","file_size":710206,"creator":"system","file_id":"4805","content_type":"application/pdf","date_created":"2018-12-12T10:10:19Z","date_updated":"2020-07-14T12:44:44Z","file_name":"IST-2016-658-v1+1_s00453-016-0212-1.pdf"}],"publisher":"Springer","has_accepted_license":"1","pubrep_id":"658","language":[{"iso":"eng"}],"publist_id":"5931","department":[{"_id":"NiBa"},{"_id":"CaGu"}],"article_processing_charge":"No","quality_controlled":"1","_id":"1336","scopus_import":"1","abstract":[{"lang":"eng","text":"Evolutionary algorithms (EAs) form a popular optimisation paradigm inspired by natural evolution. In recent years the field of evolutionary computation has developed a rigorous analytical theory to analyse the runtimes of EAs on many illustrative problems. Here we apply this theory to a simple model of natural evolution. In the Strong Selection Weak Mutation (SSWM) evolutionary regime the time between occurrences of new mutations is much longer than the time it takes for a mutated genotype to take over the population. In this situation, the population only contains copies of one genotype and evolution can be modelled as a stochastic process evolving one genotype by means of mutation and selection between the resident and the mutated genotype. The probability of accepting the mutated genotype then depends on the change in fitness. We study this process, SSWM, from an algorithmic perspective, quantifying its expected optimisation time for various parameters and investigating differences to a similar evolutionary algorithm, the well-known (1+1) EA. We show that SSWM can have a moderate advantage over the (1+1) EA at crossing fitness valleys and study an example where SSWM outperforms the (1+1) EA by taking advantage of information on the fitness gradient."}],"file_date_updated":"2020-07-14T12:44:44Z","type":"journal_article","citation":{"chicago":"Paixao, Tiago, Jorge Pérez Heredia, Dirk Sudholt, and Barbora Trubenova. “Towards a Runtime Comparison of Natural and Artificial Evolution.” <i>Algorithmica</i>. Springer, 2017. <a href=\"https://doi.org/10.1007/s00453-016-0212-1\">https://doi.org/10.1007/s00453-016-0212-1</a>.","ama":"Paixao T, Pérez Heredia J, Sudholt D, Trubenova B. Towards a runtime comparison of natural and artificial evolution. <i>Algorithmica</i>. 2017;78(2):681-713. doi:<a href=\"https://doi.org/10.1007/s00453-016-0212-1\">10.1007/s00453-016-0212-1</a>","ista":"Paixao T, Pérez Heredia J, Sudholt D, Trubenova B. 2017. Towards a runtime comparison of natural and artificial evolution. Algorithmica. 78(2), 681–713.","ieee":"T. Paixao, J. Pérez Heredia, D. Sudholt, and B. Trubenova, “Towards a runtime comparison of natural and artificial evolution,” <i>Algorithmica</i>, vol. 78, no. 2. Springer, pp. 681–713, 2017.","short":"T. Paixao, J. Pérez Heredia, D. Sudholt, B. Trubenova, Algorithmica 78 (2017) 681–713.","mla":"Paixao, Tiago, et al. “Towards a Runtime Comparison of Natural and Artificial Evolution.” <i>Algorithmica</i>, vol. 78, no. 2, Springer, 2017, pp. 681–713, doi:<a href=\"https://doi.org/10.1007/s00453-016-0212-1\">10.1007/s00453-016-0212-1</a>.","apa":"Paixao, T., Pérez Heredia, J., Sudholt, D., &#38; Trubenova, B. (2017). Towards a runtime comparison of natural and artificial evolution. <i>Algorithmica</i>. Springer. <a href=\"https://doi.org/10.1007/s00453-016-0212-1\">https://doi.org/10.1007/s00453-016-0212-1</a>"},"publication_identifier":{"issn":["01784617"]},"publication_status":"published","project":[{"grant_number":"618091","call_identifier":"FP7","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation"}]},{"project":[{"_id":"258DCDE6-B435-11E9-9278-68D0E5697425","name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7","grant_number":"338804"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"publication_status":"published","_id":"1337","quality_controlled":"1","citation":{"ama":"Ajanki OH, Erdös L, Krüger TH. Universality for general Wigner-type matrices. <i>Probability Theory and Related Fields</i>. 2017;169(3-4):667-727. doi:<a href=\"https://doi.org/10.1007/s00440-016-0740-2\">10.1007/s00440-016-0740-2</a>","ieee":"O. H. Ajanki, L. Erdös, and T. H. Krüger, “Universality for general Wigner-type matrices,” <i>Probability Theory and Related Fields</i>, vol. 169, no. 3–4. Springer, pp. 667–727, 2017.","short":"O.H. Ajanki, L. Erdös, T.H. Krüger, Probability Theory and Related Fields 169 (2017) 667–727.","ista":"Ajanki OH, Erdös L, Krüger TH. 2017. Universality for general Wigner-type matrices. Probability Theory and Related Fields. 169(3–4), 667–727.","chicago":"Ajanki, Oskari H, László Erdös, and Torben H Krüger. “Universality for General Wigner-Type Matrices.” <i>Probability Theory and Related Fields</i>. Springer, 2017. <a href=\"https://doi.org/10.1007/s00440-016-0740-2\">https://doi.org/10.1007/s00440-016-0740-2</a>.","apa":"Ajanki, O. H., Erdös, L., &#38; Krüger, T. H. (2017). Universality for general Wigner-type matrices. <i>Probability Theory and Related Fields</i>. Springer. <a href=\"https://doi.org/10.1007/s00440-016-0740-2\">https://doi.org/10.1007/s00440-016-0740-2</a>","mla":"Ajanki, Oskari H., et al. “Universality for General Wigner-Type Matrices.” <i>Probability Theory and Related Fields</i>, vol. 169, no. 3–4, Springer, 2017, pp. 667–727, doi:<a href=\"https://doi.org/10.1007/s00440-016-0740-2\">10.1007/s00440-016-0740-2</a>."},"publication_identifier":{"issn":["01788051"]},"file_date_updated":"2020-07-14T12:44:44Z","type":"journal_article","scopus_import":"1","abstract":[{"text":"We consider the local eigenvalue distribution of large self-adjoint N×N random matrices H=H∗ with centered independent entries. In contrast to previous works the matrix of variances sij=\\mathbbmE|hij|2 is not assumed to be stochastic. Hence the density of states is not the Wigner semicircle law. Its possible shapes are described in the companion paper (Ajanki et al. in Quadratic Vector Equations on the Complex Upper Half Plane. arXiv:1506.05095). We show that as N grows, the resolvent, G(z)=(H−z)−1, converges to a diagonal matrix, diag(m(z)), where m(z)=(m1(z),…,mN(z)) solves the vector equation −1/mi(z)=z+∑jsijmj(z) that has been analyzed in Ajanki et al. (Quadratic Vector Equations on the Complex Upper Half Plane. arXiv:1506.05095). We prove a local law down to the smallest spectral resolution scale, and bulk universality for both real symmetric and complex hermitian symmetry classes.","lang":"eng"}],"language":[{"iso":"eng"}],"pubrep_id":"657","article_processing_charge":"Yes (via OA deal)","publist_id":"5930","department":[{"_id":"LaEr"}],"file":[{"date_created":"2018-12-12T10:08:25Z","date_updated":"2020-07-14T12:44:44Z","file_name":"IST-2017-657-v1+2_s00440-016-0740-2.pdf","access_level":"open_access","checksum":"29f5a72c3f91e408aeb9e78344973803","relation":"main_file","creator":"system","file_size":988843,"content_type":"application/pdf","file_id":"4686"}],"author":[{"last_name":"Ajanki","first_name":"Oskari H","id":"36F2FB7E-F248-11E8-B48F-1D18A9856A87","full_name":"Ajanki, Oskari H"},{"full_name":"Erdös, László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László","last_name":"Erdös","orcid":"0000-0001-5366-9603"},{"first_name":"Torben H","id":"3020C786-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4821-3297","last_name":"Krüger","full_name":"Krüger, Torben H"}],"title":"Universality for general Wigner-type matrices","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","has_accepted_license":"1","publisher":"Springer","isi":1,"ec_funded":1,"oa_version":"Published Version","doi":"10.1007/s00440-016-0740-2","publication":"Probability Theory and Related Fields","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["510","530"],"date_created":"2018-12-11T11:51:27Z","day":"01","status":"public","volume":169,"year":"2017","page":"667 - 727","external_id":{"isi":["000414358400002"]},"date_updated":"2023-09-20T11:14:17Z","issue":"3-4","oa":1,"intvolume":"       169","month":"12","date_published":"2017-12-01T00:00:00Z","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria).  "},{"_id":"1338","quality_controlled":"1","citation":{"apa":"Cerny, P., Clarke, E., Henzinger, T. A., Radhakrishna, A., Ryzhyk, L., Samanta, R., &#38; Tarrach, T. (2017). From non-preemptive to preemptive scheduling using synchronization synthesis. <i>Formal Methods in System Design</i>. Springer. <a href=\"https://doi.org/10.1007/s10703-016-0256-5\">https://doi.org/10.1007/s10703-016-0256-5</a>","mla":"Cerny, Pavol, et al. “From Non-Preemptive to Preemptive Scheduling Using Synchronization Synthesis.” <i>Formal Methods in System Design</i>, vol. 50, no. 2–3, Springer, 2017, pp. 97–139, doi:<a href=\"https://doi.org/10.1007/s10703-016-0256-5\">10.1007/s10703-016-0256-5</a>.","ista":"Cerny P, Clarke E, Henzinger TA, Radhakrishna A, Ryzhyk L, Samanta R, Tarrach T. 2017. From non-preemptive to preemptive scheduling using synchronization synthesis. Formal Methods in System Design. 50(2–3), 97–139.","ieee":"P. Cerny <i>et al.</i>, “From non-preemptive to preemptive scheduling using synchronization synthesis,” <i>Formal Methods in System Design</i>, vol. 50, no. 2–3. Springer, pp. 97–139, 2017.","short":"P. Cerny, E. Clarke, T.A. Henzinger, A. Radhakrishna, L. Ryzhyk, R. Samanta, T. Tarrach, Formal Methods in System Design 50 (2017) 97–139.","ama":"Cerny P, Clarke E, Henzinger TA, et al. From non-preemptive to preemptive scheduling using synchronization synthesis. <i>Formal Methods in System Design</i>. 2017;50(2-3):97-139. doi:<a href=\"https://doi.org/10.1007/s10703-016-0256-5\">10.1007/s10703-016-0256-5</a>","chicago":"Cerny, Pavol, Edmund Clarke, Thomas A Henzinger, Arjun Radhakrishna, Leonid Ryzhyk, Roopsha Samanta, and Thorsten Tarrach. “From Non-Preemptive to Preemptive Scheduling Using Synchronization Synthesis.” <i>Formal Methods in System Design</i>. Springer, 2017. <a href=\"https://doi.org/10.1007/s10703-016-0256-5\">https://doi.org/10.1007/s10703-016-0256-5</a>."},"scopus_import":"1","abstract":[{"lang":"eng","text":"We present a computer-aided programming approach to concurrency. The approach allows programmers to program assuming a friendly, non-preemptive scheduler, and our synthesis procedure inserts synchronization to ensure that the final program works even with a preemptive scheduler. The correctness specification is implicit, inferred from the non-preemptive behavior. Let us consider sequences of calls that the program makes to an external interface. The specification requires that any such sequence produced under a preemptive scheduler should be included in the set of sequences produced under a non-preemptive scheduler. We guarantee that our synthesis does not introduce deadlocks and that the synchronization inserted is optimal w.r.t. a given objective function. The solution is based on a finitary abstraction, an algorithm for bounded language inclusion modulo an independence relation, and generation of a set of global constraints over synchronization placements. Each model of the global constraints set corresponds to a correctness-ensuring synchronization placement. The placement that is optimal w.r.t. the given objective function is chosen as the synchronization solution. We apply the approach to device-driver programming, where the driver threads call the software interface of the device and the API provided by the operating system. Our experiments demonstrate that our synthesis method is precise and efficient. The implicit specification helped us find one concurrency bug previously missed when model-checking using an explicit, user-provided specification. We implemented objective functions for coarse-grained and fine-grained locking and observed that different synchronization placements are produced for our experiments, favoring a minimal number of synchronization operations or maximum concurrency, respectively."}],"type":"journal_article","file_date_updated":"2020-07-14T12:44:44Z","project":[{"name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","call_identifier":"FP7"},{"name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","grant_number":"Z211","call_identifier":"FWF"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"publication_status":"published","title":"From non-preemptive to preemptive scheduling using synchronization synthesis","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"last_name":"Cerny","id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87","first_name":"Pavol","full_name":"Cerny, Pavol"},{"last_name":"Clarke","first_name":"Edmund","full_name":"Clarke, Edmund"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","last_name":"Henzinger","full_name":"Henzinger, Thomas A"},{"full_name":"Radhakrishna, Arjun","first_name":"Arjun","id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87","last_name":"Radhakrishna"},{"first_name":"Leonid","last_name":"Ryzhyk","full_name":"Ryzhyk, Leonid"},{"id":"3D2AAC08-F248-11E8-B48F-1D18A9856A87","first_name":"Roopsha","last_name":"Samanta","full_name":"Samanta, Roopsha"},{"id":"3D6E8F2C-F248-11E8-B48F-1D18A9856A87","first_name":"Thorsten","last_name":"Tarrach","orcid":"0000-0003-4409-8487","full_name":"Tarrach, Thorsten"}],"file":[{"access_level":"open_access","relation":"main_file","checksum":"1163dfd997e8212c789525d4178b1653","file_id":"4985","content_type":"application/pdf","file_size":1416170,"creator":"system","date_created":"2018-12-12T10:13:05Z","date_updated":"2020-07-14T12:44:44Z","file_name":"IST-2016-656-v1+1_s10703-016-0256-5.pdf"}],"has_accepted_license":"1","publisher":"Springer","language":[{"iso":"eng"}],"pubrep_id":"656","article_processing_charge":"No","department":[{"_id":"ToHe"}],"publist_id":"5929","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["000"],"date_created":"2018-12-11T11:51:27Z","status":"public","day":"01","volume":50,"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"1729"}]},"ec_funded":1,"oa_version":"Published Version","isi":1,"publication":"Formal Methods in System Design","doi":"10.1007/s10703-016-0256-5","date_updated":"2023-09-20T11:13:51Z","oa":1,"issue":"2-3","date_published":"2017-06-01T00:00:00Z","intvolume":"        50","month":"06","year":"2017","page":"97 - 139","external_id":{"isi":["000399888900001"]}},{"oa_version":"Published Version","ec_funded":1,"isi":1,"related_material":{"record":[{"id":"1835","relation":"earlier_version","status":"public"}]},"publication":"Acta Informatica","doi":"10.1007/s00236-016-0278-x","status":"public","day":"01","date_created":"2018-12-11T11:51:32Z","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["006","576"],"volume":54,"year":"2017","external_id":{"isi":["000414343200003"]},"page":"765 - 787","oa":1,"issue":"8","date_updated":"2025-05-28T11:57:04Z","date_published":"2017-12-01T00:00:00Z","intvolume":"        54","month":"12","publication_status":"published","project":[{"call_identifier":"FP7","grant_number":"267989","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23"},{"name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z211"},{"_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","call_identifier":"FP7","grant_number":"618091"},{"grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme"},{"_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7","grant_number":"250152"}],"quality_controlled":"1","_id":"1351","scopus_import":"1","abstract":[{"lang":"eng","text":"The behaviour of gene regulatory networks (GRNs) is typically analysed using simulation-based statistical testing-like methods. In this paper, we demonstrate that we can replace this approach by a formal verification-like method that gives higher assurance and scalability. We focus on Wagner’s weighted GRN model with varying weights, which is used in evolutionary biology. In the model, weight parameters represent the gene interaction strength that may change due to genetic mutations. For a property of interest, we synthesise the constraints over the parameter space that represent the set of GRNs satisfying the property. We experimentally show that our parameter synthesis procedure computes the mutational robustness of GRNs—an important problem of interest in evolutionary biology—more efficiently than the classical simulation method. We specify the property in linear temporal logic. We employ symbolic bounded model checking and SMT solving to compute the space of GRNs that satisfy the property, which amounts to synthesizing a set of linear constraints on the weights."}],"type":"journal_article","file_date_updated":"2020-07-14T12:44:46Z","citation":{"ama":"Giacobbe M, Guet CC, Gupta A, Henzinger TA, Paixao T, Petrov T. Model checking the evolution of gene regulatory networks. <i>Acta Informatica</i>. 2017;54(8):765-787. doi:<a href=\"https://doi.org/10.1007/s00236-016-0278-x\">10.1007/s00236-016-0278-x</a>","ista":"Giacobbe M, Guet CC, Gupta A, Henzinger TA, Paixao T, Petrov T. 2017. Model checking the evolution of gene regulatory networks. Acta Informatica. 54(8), 765–787.","short":"M. Giacobbe, C.C. Guet, A. Gupta, T.A. Henzinger, T. Paixao, T. Petrov, Acta Informatica 54 (2017) 765–787.","ieee":"M. Giacobbe, C. C. Guet, A. Gupta, T. A. Henzinger, T. Paixao, and T. Petrov, “Model checking the evolution of gene regulatory networks,” <i>Acta Informatica</i>, vol. 54, no. 8. Springer, pp. 765–787, 2017.","chicago":"Giacobbe, Mirco, Calin C Guet, Ashutosh Gupta, Thomas A Henzinger, Tiago Paixao, and Tatjana Petrov. “Model Checking the Evolution of Gene Regulatory Networks.” <i>Acta Informatica</i>. Springer, 2017. <a href=\"https://doi.org/10.1007/s00236-016-0278-x\">https://doi.org/10.1007/s00236-016-0278-x</a>.","apa":"Giacobbe, M., Guet, C. C., Gupta, A., Henzinger, T. A., Paixao, T., &#38; Petrov, T. (2017). Model checking the evolution of gene regulatory networks. <i>Acta Informatica</i>. Springer. <a href=\"https://doi.org/10.1007/s00236-016-0278-x\">https://doi.org/10.1007/s00236-016-0278-x</a>","mla":"Giacobbe, Mirco, et al. “Model Checking the Evolution of Gene Regulatory Networks.” <i>Acta Informatica</i>, vol. 54, no. 8, Springer, 2017, pp. 765–87, doi:<a href=\"https://doi.org/10.1007/s00236-016-0278-x\">10.1007/s00236-016-0278-x</a>."},"publication_identifier":{"issn":["00015903"]},"pubrep_id":"649","language":[{"iso":"eng"}],"department":[{"_id":"ToHe"},{"_id":"CaGu"},{"_id":"NiBa"}],"publist_id":"5898","article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Model checking the evolution of gene regulatory networks","author":[{"id":"3444EA5E-F248-11E8-B48F-1D18A9856A87","first_name":"Mirco","orcid":"0000-0001-8180-0904","last_name":"Giacobbe","full_name":"Giacobbe, Mirco"},{"first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C"},{"full_name":"Gupta, Ashutosh","last_name":"Gupta","id":"335E5684-F248-11E8-B48F-1D18A9856A87","first_name":"Ashutosh"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger","full_name":"Henzinger, Thomas A"},{"full_name":"Paixao, Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","first_name":"Tiago","last_name":"Paixao","orcid":"0000-0003-2361-3953"},{"last_name":"Petrov","orcid":"0000-0002-9041-0905","id":"3D5811FC-F248-11E8-B48F-1D18A9856A87","first_name":"Tatjana","full_name":"Petrov, Tatjana"}],"file":[{"content_type":"application/pdf","file_id":"5841","file_size":755241,"creator":"dernst","access_level":"open_access","checksum":"4e661d9135d7f8c342e8e258dee76f3e","relation":"main_file","file_name":"2017_ActaInformatica_Giacobbe.pdf","date_created":"2019-01-17T15:57:29Z","date_updated":"2020-07-14T12:44:46Z"}],"publisher":"Springer","has_accepted_license":"1"}]