[{"oa_version":"Preprint","issue":"4","main_file_link":[{"url":"http://arxiv.org/abs/1404.2106","open_access":"1"}],"author":[{"first_name":"Anna","last_name":"Gundert","full_name":"Gundert, Anna"},{"orcid":"0000-0002-1494-0568","last_name":"Wagner","full_name":"Wagner, Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","first_name":"Uli"}],"day":"01","publication":"Proceedings of the American Mathematical Society","date_published":"2016-04-01T00:00:00Z","external_id":{"isi":["000369298400040"],"arxiv":["1404.2106"]},"abstract":[{"lang":"eng","text":"For random graphs, the containment problem considers the probability that a binomial random graph G(n, p) contains a given graph as a substructure. When asking for the graph as a topological minor, i.e., for a copy of a subdivision of the given graph, it is well known that the (sharp) threshold is at p = 1/n. We consider a natural analogue of this question for higher-dimensional random complexes Xk(n, p), first studied by Cohen, Costa, Farber and Kappeler for k = 2. Improving previous results, we show that p = Θ(1/ √n) is the (coarse) threshold for containing a subdivision of any fixed complete 2-complex. For higher dimensions k &gt; 2, we get that p = O(n−1/k) is an upper bound for the threshold probability of containing a subdivision of a fixed k-dimensional complex."}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2018-12-11T11:52:30Z","acknowledgement":"This research was supported by the Swiss National Science Foundation (SNF Projects 200021-125309 and 200020-138230","doi":"10.1090/proc/12824","year":"2016","publication_status":"published","type":"journal_article","title":"On topological minors in random simplicial complexes","language":[{"iso":"eng"}],"isi":1,"quality_controlled":"1","volume":144,"citation":{"chicago":"Gundert, Anna, and Uli Wagner. “On Topological Minors in Random Simplicial Complexes.” <i>Proceedings of the American Mathematical Society</i>. American Mathematical Society, 2016. <a href=\"https://doi.org/10.1090/proc/12824\">https://doi.org/10.1090/proc/12824</a>.","ama":"Gundert A, Wagner U. On topological minors in random simplicial complexes. <i>Proceedings of the American Mathematical Society</i>. 2016;144(4):1815-1828. doi:<a href=\"https://doi.org/10.1090/proc/12824\">10.1090/proc/12824</a>","ieee":"A. Gundert and U. Wagner, “On topological minors in random simplicial complexes,” <i>Proceedings of the American Mathematical Society</i>, vol. 144, no. 4. American Mathematical Society, pp. 1815–1828, 2016.","mla":"Gundert, Anna, and Uli Wagner. “On Topological Minors in Random Simplicial Complexes.” <i>Proceedings of the American Mathematical Society</i>, vol. 144, no. 4, American Mathematical Society, 2016, pp. 1815–28, doi:<a href=\"https://doi.org/10.1090/proc/12824\">10.1090/proc/12824</a>.","apa":"Gundert, A., &#38; Wagner, U. (2016). On topological minors in random simplicial complexes. <i>Proceedings of the American Mathematical Society</i>. American Mathematical Society. <a href=\"https://doi.org/10.1090/proc/12824\">https://doi.org/10.1090/proc/12824</a>","ista":"Gundert A, Wagner U. 2016. On topological minors in random simplicial complexes. Proceedings of the American Mathematical Society. 144(4), 1815–1828.","short":"A. Gundert, U. Wagner, Proceedings of the American Mathematical Society 144 (2016) 1815–1828."},"page":"1815 - 1828","article_processing_charge":"No","month":"04","intvolume":"       144","publisher":"American Mathematical Society","publist_id":"5650","oa":1,"date_updated":"2025-09-18T11:07:39Z","status":"public","corr_author":"1","_id":"1523","scopus_import":"1","arxiv":1,"department":[{"_id":"UlWa"}]},{"abstract":[{"lang":"eng","text":"When designing genetic circuits, the typical primitives used in major existing modelling formalisms are gene interaction graphs, where edges between genes denote either an activation or inhibition relation. However, when designing experiments, it is important to be precise about the low-level mechanistic details as to how each such relation is implemented. The rule-based modelling language Kappa allows to unambiguously specify mechanistic details such as DNA binding sites, dimerisation of transcription factors, or co-operative interactions. Such a detailed description comes with complexity and computationally costly executions. We propose a general method for automatically transforming a rule-based program, by eliminating intermediate species and adjusting the rate constants accordingly. To the best of our knowledge, we show the first automated reduction of rule-based models based on equilibrium approximations.\r\nOur algorithm is an adaptation of an existing algorithm, which was designed for reducing reaction-based programs; our version of the algorithm scans the rule-based Kappa model in search for those interaction patterns known to be amenable to equilibrium approximations (e.g. Michaelis-Menten scheme). Additional checks are then performed in order to verify if the reduction is meaningful in the context of the full model. The reduced model is efficiently obtained by static inspection over the rule-set. The tool is tested on a detailed rule-based model of a λ-phage switch, which lists 92 rules and 13 agents. The reduced model has 11 rules and 5 agents, and provides a dramatic reduction in simulation time of several orders of magnitude."}],"date_published":"2016-01-10T00:00:00Z","external_id":{"arxiv":["1501.00440"]},"author":[{"last_name":"Beica","full_name":"Beica, Andreea","first_name":"Andreea"},{"orcid":"0000-0001-6220-2052","last_name":"Guet","full_name":"Guet, Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C"},{"id":"3D5811FC-F248-11E8-B48F-1D18A9856A87","first_name":"Tatjana","last_name":"Petrov","full_name":"Petrov, Tatjana","orcid":"0000-0002-9041-0905"}],"day":"10","oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1501.00440"}],"type":"conference","title":"Efficient reduction of kappa models by static inspection of the rule-set","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7"}],"language":[{"iso":"eng"}],"publication_status":"published","doi":"10.1007/978-3-319-26916-0_10","acknowledgement":"This research was supported by the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no. 291734, and the SNSF Early Postdoc.Mobility Fellowship, the grant number P2EZP2_148797.","year":"2016","conference":{"end_date":"2015-09-05","location":"Madrid, Spain","start_date":"2015-09-04","name":"HSB: Hybrid Systems Biology"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","alternative_title":["LNCS"],"date_created":"2018-12-11T11:52:31Z","intvolume":"      9271","publisher":"Springer","month":"01","page":"173 - 191","article_processing_charge":"No","ec_funded":1,"volume":9271,"quality_controlled":"1","citation":{"ama":"Beica A, Guet CC, Petrov T. Efficient reduction of kappa models by static inspection of the rule-set. In: Vol 9271. Springer; 2016:173-191. doi:<a href=\"https://doi.org/10.1007/978-3-319-26916-0_10\">10.1007/978-3-319-26916-0_10</a>","chicago":"Beica, Andreea, Calin C Guet, and Tatjana Petrov. “Efficient Reduction of Kappa Models by Static Inspection of the Rule-Set,” 9271:173–91. Springer, 2016. <a href=\"https://doi.org/10.1007/978-3-319-26916-0_10\">https://doi.org/10.1007/978-3-319-26916-0_10</a>.","ieee":"A. Beica, C. C. Guet, and T. Petrov, “Efficient reduction of kappa models by static inspection of the rule-set,” presented at the HSB: Hybrid Systems Biology, Madrid, Spain, 2016, vol. 9271, pp. 173–191.","apa":"Beica, A., Guet, C. C., &#38; Petrov, T. (2016). Efficient reduction of kappa models by static inspection of the rule-set (Vol. 9271, pp. 173–191). Presented at the HSB: Hybrid Systems Biology, Madrid, Spain: Springer. <a href=\"https://doi.org/10.1007/978-3-319-26916-0_10\">https://doi.org/10.1007/978-3-319-26916-0_10</a>","mla":"Beica, Andreea, et al. <i>Efficient Reduction of Kappa Models by Static Inspection of the Rule-Set</i>. Vol. 9271, Springer, 2016, pp. 173–91, doi:<a href=\"https://doi.org/10.1007/978-3-319-26916-0_10\">10.1007/978-3-319-26916-0_10</a>.","short":"A. Beica, C.C. Guet, T. Petrov, in:, Springer, 2016, pp. 173–191.","ista":"Beica A, Guet CC, Petrov T. 2016. Efficient reduction of kappa models by static inspection of the rule-set. HSB: Hybrid Systems Biology, LNCS, vol. 9271, 173–191."},"arxiv":1,"scopus_import":"1","department":[{"_id":"CaGu"},{"_id":"ToHe"}],"status":"public","corr_author":"1","_id":"1524","date_updated":"2025-06-04T12:06:27Z","publist_id":"5649","oa":1},{"intvolume":"      9583","publisher":"Springer","month":"01","page":"250 - 267","article_processing_charge":"No","ec_funded":1,"volume":9583,"quality_controlled":"1","citation":{"chicago":"Henzinger, Thomas A, Jan Otop, and Roopsha Samanta. “Lipschitz Robustness of Timed I/O Systems,” 9583:250–67. Springer, 2016. <a href=\"https://doi.org/10.1007/978-3-662-49122-5_12\">https://doi.org/10.1007/978-3-662-49122-5_12</a>.","ama":"Henzinger TA, Otop J, Samanta R. Lipschitz robustness of timed I/O systems. In: Vol 9583. Springer; 2016:250-267. doi:<a href=\"https://doi.org/10.1007/978-3-662-49122-5_12\">10.1007/978-3-662-49122-5_12</a>","ieee":"T. A. Henzinger, J. Otop, and R. Samanta, “Lipschitz robustness of timed I/O systems,” presented at the VMCAI: Verification, Model Checking and Abstract Interpretation, St. Petersburg, FL, USA, 2016, vol. 9583, pp. 250–267.","mla":"Henzinger, Thomas A., et al. <i>Lipschitz Robustness of Timed I/O Systems</i>. Vol. 9583, Springer, 2016, pp. 250–67, doi:<a href=\"https://doi.org/10.1007/978-3-662-49122-5_12\">10.1007/978-3-662-49122-5_12</a>.","apa":"Henzinger, T. A., Otop, J., &#38; Samanta, R. (2016). Lipschitz robustness of timed I/O systems (Vol. 9583, pp. 250–267). Presented at the VMCAI: Verification, Model Checking and Abstract Interpretation, St. Petersburg, FL, USA: Springer. <a href=\"https://doi.org/10.1007/978-3-662-49122-5_12\">https://doi.org/10.1007/978-3-662-49122-5_12</a>","short":"T.A. Henzinger, J. Otop, R. Samanta, in:, Springer, 2016, pp. 250–267.","ista":"Henzinger TA, Otop J, Samanta R. 2016. Lipschitz robustness of timed I/O systems. VMCAI: Verification, Model Checking and Abstract Interpretation, LNCS, vol. 9583, 250–267."},"scopus_import":"1","arxiv":1,"department":[{"_id":"ToHe"}],"status":"public","_id":"1526","corr_author":"1","date_updated":"2025-09-18T11:06:25Z","publist_id":"5647","oa":1,"abstract":[{"text":"We present the first study of robustness of systems that are both timed as well as reactive (I/O). We study the behavior of such timed I/O systems in the presence of uncertain inputs and formalize their robustness using the analytic notion of Lipschitz continuity: a timed I/O system is K-(Lipschitz) robust if the perturbation in its output is at most K times the perturbation in its input. We quantify input and output perturbation using similarity functions over timed words such as the timed version of the Manhattan distance and the Skorokhod distance. We consider two models of timed I/O systems — timed transducers and asynchronous sequential circuits. We show that K-robustness of timed transducers can be decided in polynomial space under certain conditions. For asynchronous sequential circuits, we reduce K-robustness w.r.t. timed Manhattan distances to K-robustness of discrete letter-to-letter transducers and show PSpace-completeness of the problem.","lang":"eng"}],"date_published":"2016-01-01T00:00:00Z","external_id":{"isi":["000375148800012"],"arxiv":["1506.01233"]},"author":[{"orcid":"0000−0002−2985−7724","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","last_name":"Henzinger"},{"full_name":"Otop, Jan","last_name":"Otop","first_name":"Jan","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87"},{"id":"3D2AAC08-F248-11E8-B48F-1D18A9856A87","first_name":"Roopsha","last_name":"Samanta","full_name":"Samanta, Roopsha"}],"day":"01","oa_version":"Preprint","main_file_link":[{"url":"http://arxiv.org/abs/1506.01233","open_access":"1"}],"type":"conference","title":"Lipschitz robustness of timed I/O systems","project":[{"grant_number":"267989","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"call_identifier":"FWF","grant_number":"Z211","name":"Formal methods for the design and analysis of complex systems","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","call_identifier":"FWF"}],"isi":1,"language":[{"iso":"eng"}],"publication_status":"published","acknowledgement":"This research was supported in part by the European Research Council (ERC) under grant 267989 (QUAREM), by the Austrian Science Fund (FWF) under grants S11402-N23 (RiSE) and Z211-N23 (Wittgenstein Award), and by the National Science Centre (NCN), Poland under grant 2014/15/D/ST6/04543.","doi":"10.1007/978-3-662-49122-5_12","year":"2016","conference":{"end_date":"2016-01-19","start_date":"2016-01-17","name":"VMCAI: Verification, Model Checking and Abstract Interpretation","location":"St. Petersburg, FL, USA"},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","alternative_title":["LNCS"],"date_created":"2018-12-11T11:52:32Z"},{"abstract":[{"text":"We consider partially observable Markov decision processes (POMDPs) with a set of target states and an integer cost associated with every transition. The optimization objective we study asks to minimize the expected total cost of reaching a state in the target set, while ensuring that the target set is reached almost surely (with probability 1). We show that for integer costs approximating the optimal cost is undecidable. For positive costs, our results are as follows: (i) we establish matching lower and upper bounds for the optimal cost, both double exponential in the POMDP state space size; (ii) we show that the problem of approximating the optimal cost is decidable and present approximation algorithms developing on the existing algorithms for POMDPs with finite-horizon objectives. While the worst-case running time of our algorithm is double exponential, we also present efficient stopping criteria for the algorithm and show experimentally that it performs well in many examples of interest.","lang":"eng"}],"publication":"Artificial Intelligence","date_published":"2016-05-01T00:00:00Z","external_id":{"isi":["000372683700002"],"arxiv":["1411.3880"]},"author":[{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Chmelik, Martin","last_name":"Chmelik","first_name":"Martin","id":"3624234E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Raghav","full_name":"Gupta, Raghav","last_name":"Gupta"},{"last_name":"Kanodia","full_name":"Kanodia, Ayush","first_name":"Ayush"}],"day":"01","oa_version":"Preprint","main_file_link":[{"url":"http://arxiv.org/abs/1411.3880","open_access":"1"}],"type":"journal_article","title":"Optimal cost almost-sure reachability in POMDPs","project":[{"call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"}],"language":[{"iso":"eng"}],"isi":1,"publication_status":"published","doi":"10.1016/j.artint.2016.01.007","acknowledgement":"We thank Blai Bonet for helping us with RTDP-Bel. The research was partly supported by Austrian Science Fund (FWF) Grant No P23499-N23, FWF NFN Grant No S11407-N23 (RiSE), ERC Start grant (279307: Graph Games), and Microsoft faculty fellows award.","year":"2016","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2018-12-11T11:52:33Z","intvolume":"       234","publisher":"Elsevier","month":"05","page":"26 - 48","ec_funded":1,"article_processing_charge":"No","volume":234,"quality_controlled":"1","citation":{"mla":"Chatterjee, Krishnendu, et al. “Optimal Cost Almost-Sure Reachability in POMDPs.” <i>Artificial Intelligence</i>, vol. 234, Elsevier, 2016, pp. 26–48, doi:<a href=\"https://doi.org/10.1016/j.artint.2016.01.007\">10.1016/j.artint.2016.01.007</a>.","apa":"Chatterjee, K., Chmelik, M., Gupta, R., &#38; Kanodia, A. (2016). Optimal cost almost-sure reachability in POMDPs. <i>Artificial Intelligence</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.artint.2016.01.007\">https://doi.org/10.1016/j.artint.2016.01.007</a>","ista":"Chatterjee K, Chmelik M, Gupta R, Kanodia A. 2016. Optimal cost almost-sure reachability in POMDPs. Artificial Intelligence. 234, 26–48.","short":"K. Chatterjee, M. Chmelik, R. Gupta, A. Kanodia, Artificial Intelligence 234 (2016) 26–48.","ama":"Chatterjee K, Chmelik M, Gupta R, Kanodia A. Optimal cost almost-sure reachability in POMDPs. <i>Artificial Intelligence</i>. 2016;234:26-48. doi:<a href=\"https://doi.org/10.1016/j.artint.2016.01.007\">10.1016/j.artint.2016.01.007</a>","chicago":"Chatterjee, Krishnendu, Martin Chmelik, Raghav Gupta, and Ayush Kanodia. “Optimal Cost Almost-Sure Reachability in POMDPs.” <i>Artificial Intelligence</i>. Elsevier, 2016. <a href=\"https://doi.org/10.1016/j.artint.2016.01.007\">https://doi.org/10.1016/j.artint.2016.01.007</a>.","ieee":"K. Chatterjee, M. Chmelik, R. Gupta, and A. Kanodia, “Optimal cost almost-sure reachability in POMDPs,” <i>Artificial Intelligence</i>, vol. 234. Elsevier, pp. 26–48, 2016."},"scopus_import":"1","arxiv":1,"department":[{"_id":"KrCh"}],"status":"public","corr_author":"1","_id":"1529","date_updated":"2025-09-18T11:05:09Z","publist_id":"5642","oa":1,"related_material":{"record":[{"status":"public","relation":"earlier_version","id":"5425"},{"id":"1820","status":"public","relation":"earlier_version"}]}},{"author":[{"first_name":"Phan","id":"404092F4-F248-11E8-B48F-1D18A9856A87","full_name":"Nam, Phan","last_name":"Nam"},{"id":"4197AD04-F248-11E8-B48F-1D18A9856A87","first_name":"Marcin M","last_name":"Napiórkowski","full_name":"Napiórkowski, Marcin M"},{"first_name":"Jan","last_name":"Solovej","full_name":"Solovej, Jan"}],"day":"01","oa_version":"Submitted Version","main_file_link":[{"url":"http://arxiv.org/abs/1508.07321","open_access":"1"}],"issue":"11","abstract":[{"text":"We provide general conditions for which bosonic quadratic Hamiltonians on Fock spaces can be diagonalized by Bogoliubov transformations. Our results cover the case when quantum systems have infinite degrees of freedom and the associated one-body kinetic and paring operators are unbounded. Our sufficient conditions are optimal in the sense that they become necessary when the relevant one-body operators commute.","lang":"eng"}],"publication":"Journal of Functional Analysis","date_published":"2016-06-01T00:00:00Z","external_id":{"arxiv":["1508.07321"],"isi":["000375241700011"]},"acknowledgement":"We thank Jan Dereziński for several inspiring discussions and useful remarks. We thank the referee for helpful comments. J.P.S. thanks the Erwin Schrödinger Institute for the hospitality during the thematic programme “Quantum many-body systems, random matrices, and disorder”. We gratefully acknowledge the financial supports by the European Union's Seventh Framework Programme under the ERC Advanced Grant ERC-2012-AdG 321029 (J.P.S.) and the REA grant agreement No. 291734 (P.T.N.), as well as the support of the National Science Center (NCN) grant No. 2012/07/N/ST1/03185 and the Austrian Science Fund (FWF) project No. P 27533-N27 (M.N.).","doi":"10.1016/j.jfa.2015.12.007","year":"2016","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2018-12-11T11:52:38Z","type":"journal_article","title":"Diagonalization of bosonic quadratic Hamiltonians by Bogoliubov transformations","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7"},{"call_identifier":"FWF","grant_number":"P27533_N27","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","_id":"25C878CE-B435-11E9-9278-68D0E5697425"}],"language":[{"iso":"eng"}],"isi":1,"publication_status":"published","page":"4340 - 4368","article_processing_charge":"No","ec_funded":1,"quality_controlled":"1","volume":270,"citation":{"apa":"Nam, P., Napiórkowski, M. M., &#38; Solovej, J. (2016). Diagonalization of bosonic quadratic Hamiltonians by Bogoliubov transformations. <i>Journal of Functional Analysis</i>. Academic Press. <a href=\"https://doi.org/10.1016/j.jfa.2015.12.007\">https://doi.org/10.1016/j.jfa.2015.12.007</a>","mla":"Nam, Phan, et al. “Diagonalization of Bosonic Quadratic Hamiltonians by Bogoliubov Transformations.” <i>Journal of Functional Analysis</i>, vol. 270, no. 11, Academic Press, 2016, pp. 4340–68, doi:<a href=\"https://doi.org/10.1016/j.jfa.2015.12.007\">10.1016/j.jfa.2015.12.007</a>.","ista":"Nam P, Napiórkowski MM, Solovej J. 2016. Diagonalization of bosonic quadratic Hamiltonians by Bogoliubov transformations. Journal of Functional Analysis. 270(11), 4340–4368.","short":"P. Nam, M.M. Napiórkowski, J. Solovej, Journal of Functional Analysis 270 (2016) 4340–4368.","chicago":"Nam, Phan, Marcin M Napiórkowski, and Jan Solovej. “Diagonalization of Bosonic Quadratic Hamiltonians by Bogoliubov Transformations.” <i>Journal of Functional Analysis</i>. Academic Press, 2016. <a href=\"https://doi.org/10.1016/j.jfa.2015.12.007\">https://doi.org/10.1016/j.jfa.2015.12.007</a>.","ama":"Nam P, Napiórkowski MM, Solovej J. Diagonalization of bosonic quadratic Hamiltonians by Bogoliubov transformations. <i>Journal of Functional Analysis</i>. 2016;270(11):4340-4368. doi:<a href=\"https://doi.org/10.1016/j.jfa.2015.12.007\">10.1016/j.jfa.2015.12.007</a>","ieee":"P. Nam, M. M. Napiórkowski, and J. Solovej, “Diagonalization of bosonic quadratic Hamiltonians by Bogoliubov transformations,” <i>Journal of Functional Analysis</i>, vol. 270, no. 11. Academic Press, pp. 4340–4368, 2016."},"intvolume":"       270","publisher":"Academic Press","month":"06","date_updated":"2025-09-18T11:04:09Z","publist_id":"5626","oa":1,"arxiv":1,"scopus_import":"1","department":[{"_id":"RoSe"}],"status":"public","corr_author":"1","_id":"1545"},{"conference":{"location":"Krakow, Poland","start_date":"2016-08-22","name":"MFCS: Mathematical Foundations of Computer Science","end_date":"2016-08-26"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","alternative_title":["LIPIcs"],"date_created":"2018-12-11T11:49:58Z","doi":"10.4230/LIPIcs.MFCS.2016.25","acknowledgement":"K. C., M. H., and W. D. are partially supported by the Vienna Science and Technology Fund (WWTF) through project ICT15-003. K. C. is partially supported by the Austrian Science Fund (FWF) NFN Grant No S11407-N23 (RiSE/SHiNE) and an ERC Start grant (279307","article_number":"25","year":"2016","publication_status":"published","type":"conference","title":"Conditionally optimal algorithms for generalized Büchi Games","project":[{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"}],"language":[{"iso":"eng"}],"oa_version":"Published Version","author":[{"orcid":"0000-0002-4561-241X","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"},{"first_name":"Wolfgang","last_name":"Dvorák","full_name":"Dvorák, Wolfgang"},{"id":"540c9bbd-f2de-11ec-812d-d04a5be85630","first_name":"Monika H","last_name":"Henzinger","full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530"},{"full_name":"Loitzenbauer, Veronika","last_name":"Loitzenbauer","first_name":"Veronika"}],"day":"01","date_published":"2016-08-01T00:00:00Z","file":[{"date_updated":"2018-12-12T10:16:02Z","creator":"system","file_size":632786,"content_type":"application/pdf","date_created":"2018-12-12T10:16:02Z","access_level":"open_access","relation":"main_file","file_id":"5187","file_name":"IST-2017-779-v1+1_LIPIcs-MFCS-2016-25.pdf"}],"abstract":[{"text":"Games on graphs provide the appropriate framework to study several central problems in computer science, such as verification and synthesis of reactive systems. One of the most basic objectives for games on graphs is the liveness (or Büchi) objective that given a target set of vertices requires that some vertex in the target set is visited infinitely often. We study generalized Büchi objectives (i.e., conjunction of liveness objectives), and implications between two generalized Büchi objectives (known as GR(1) objectives), that arise in numerous applications in computer-aided verification. We present improved algorithms and conditional super-linear lower bounds based on widely believed assumptions about the complexity of (A1) combinatorial Boolean matrix multiplication and (A2) CNF-SAT. We consider graph games with n vertices, m edges, and generalized Büchi objectives with k conjunctions. First, we present an algorithm with running time O(k*n^2), improving the previously known O(k*n*m) and O(k^2*n^2) worst-case bounds. Our algorithm is optimal for dense graphs under (A1). Second, we show that the basic algorithm for the problem is optimal for sparse graphs when the target sets have constant size under (A2). Finally, we consider GR(1) objectives, with k_1 conjunctions in the antecedent and k_2 conjunctions in the consequent, and present an O(k_1 k_2 n^{2.5})-time algorithm, improving the previously known O(k_1*k_2*n*m)-time algorithm for m &gt; n^{1.5}. ","lang":"eng"}],"publist_id":"6317","oa":1,"date_updated":"2025-07-10T11:49:55Z","status":"public","_id":"1068","scopus_import":"1","file_date_updated":"2018-12-12T10:16:02Z","department":[{"_id":"KrCh"}],"ddc":["000","004","006"],"pubrep_id":"779","volume":58,"quality_controlled":"1","citation":{"ama":"Chatterjee K, Dvorák W, Henzinger M, Loitzenbauer V. Conditionally optimal algorithms for generalized Büchi Games. In: Vol 58. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2016. doi:<a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2016.25\">10.4230/LIPIcs.MFCS.2016.25</a>","chicago":"Chatterjee, Krishnendu, Wolfgang Dvorák, Monika Henzinger, and Veronika Loitzenbauer. “Conditionally Optimal Algorithms for Generalized Büchi Games,” Vol. 58. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016. <a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2016.25\">https://doi.org/10.4230/LIPIcs.MFCS.2016.25</a>.","ieee":"K. Chatterjee, W. Dvorák, M. Henzinger, and V. Loitzenbauer, “Conditionally optimal algorithms for generalized Büchi Games,” presented at the MFCS: Mathematical Foundations of Computer Science, Krakow, Poland, 2016, vol. 58.","mla":"Chatterjee, Krishnendu, et al. <i>Conditionally Optimal Algorithms for Generalized Büchi Games</i>. Vol. 58, 25, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016, doi:<a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2016.25\">10.4230/LIPIcs.MFCS.2016.25</a>.","apa":"Chatterjee, K., Dvorák, W., Henzinger, M., &#38; Loitzenbauer, V. (2016). Conditionally optimal algorithms for generalized Büchi Games (Vol. 58). Presented at the MFCS: Mathematical Foundations of Computer Science, Krakow, Poland: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2016.25\">https://doi.org/10.4230/LIPIcs.MFCS.2016.25</a>","ista":"Chatterjee K, Dvorák W, Henzinger M, Loitzenbauer V. 2016. Conditionally optimal algorithms for generalized Büchi Games. MFCS: Mathematical Foundations of Computer Science, LIPIcs, vol. 58, 25.","short":"K. Chatterjee, W. Dvorák, M. Henzinger, V. Loitzenbauer, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016."},"has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","short":"CC BY (3.0)","image":"/images/cc_by.png"},"ec_funded":1,"article_processing_charge":"No","month":"08","intvolume":"        58","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik"},{"date_created":"2018-12-11T11:49:59Z","alternative_title":["LIPIcs"],"conference":{"end_date":"2016-07-15","start_date":"2016-07-12","name":"ICALP: Automata, Languages and Programming","location":"Rome, Italy"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"100","year":"2016","acknowledgement":"Ventsislav Chonev is supported by Austrian Science Fund (FWF) NFN Grant No S11407-N23 (RiSE/SHiNE), ERC Start grant (279307:  Graph Games), and ERC Advanced Grant (267989: QUAREM).","doi":"10.4230/LIPIcs.ICALP.2016.100","publication_status":"published","language":[{"iso":"eng"}],"title":"On the skolem problem for continuous linear dynamical systems","type":"conference","project":[{"call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","call_identifier":"FP7"},{"grant_number":"267989","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"oa_version":"Published Version","day":"01","author":[{"first_name":"Ventsislav K","id":"36CBE2E6-F248-11E8-B48F-1D18A9856A87","full_name":"Chonev, Ventsislav K","last_name":"Chonev"},{"last_name":"Ouaknine","full_name":"Ouaknine, Joël","first_name":"Joël"},{"full_name":"Worrell, James","last_name":"Worrell","first_name":"James"}],"date_published":"2016-08-01T00:00:00Z","file":[{"file_id":"5213","file_name":"IST-2017-778-v1+1_LIPIcs-ICALP-2016-100.pdf","relation":"main_file","access_level":"open_access","creator":"system","date_updated":"2018-12-12T10:16:26Z","content_type":"application/pdf","date_created":"2018-12-12T10:16:26Z","file_size":521415}],"abstract":[{"text":"The Continuous Skolem Problem asks whether a real-valued function satisfying a linear differen-\r\ntial equation has a zero in a given interval of real numbers. This is a fundamental reachability\r\nproblem for continuous linear dynamical systems, such as linear hybrid automata and continuous-\r\ntime Markov chains. Decidability of the problem is currently open – indeed decidability is open\r\neven for the sub-problem in which a zero is sought in a bounded interval. In this paper we show\r\ndecidability of the bounded problem subject to Schanuel’s Conjecture, a unifying conjecture in\r\ntranscendental number theory. We furthermore analyse the unbounded problem in terms of the\r\nfrequencies of the differential equation, that is, the imaginary parts of the characteristic roots.\r\nWe show that the unbounded problem can be reduced to the bounded problem if there is at most\r\none rationally linearly independent frequency, or if there are two rationally linearly independent\r\nfrequencies and all characteristic roots are simple. We complete the picture by showing that de-\r\ncidability of the unbounded problem in the case of two (or more) rationally linearly independent\r\nfrequencies would entail a major new effectiveness result in Diophantine approximation, namely\r\ncomputability of the Diophantine-approximation types of all real algebraic numbers.","lang":"eng"}],"oa":1,"publist_id":"6314","date_updated":"2025-06-03T11:32:08Z","_id":"1069","status":"public","file_date_updated":"2018-12-12T10:16:26Z","department":[{"_id":"KrCh"}],"ddc":["004","006"],"scopus_import":"1","citation":{"mla":"Chonev, Ventsislav K., et al. <i>On the Skolem Problem for Continuous Linear Dynamical Systems</i>. Vol. 55, 100, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016, doi:<a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2016.100\">10.4230/LIPIcs.ICALP.2016.100</a>.","apa":"Chonev, V. K., Ouaknine, J., &#38; Worrell, J. (2016). On the skolem problem for continuous linear dynamical systems (Vol. 55). Presented at the ICALP: Automata, Languages and Programming, Rome, Italy: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2016.100\">https://doi.org/10.4230/LIPIcs.ICALP.2016.100</a>","short":"V.K. Chonev, J. Ouaknine, J. Worrell, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016.","ista":"Chonev VK, Ouaknine J, Worrell J. 2016. On the skolem problem for continuous linear dynamical systems. ICALP: Automata, Languages and Programming, LIPIcs, vol. 55, 100.","ama":"Chonev VK, Ouaknine J, Worrell J. On the skolem problem for continuous linear dynamical systems. In: Vol 55. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2016. doi:<a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2016.100\">10.4230/LIPIcs.ICALP.2016.100</a>","chicago":"Chonev, Ventsislav K, Joël Ouaknine, and James Worrell. “On the Skolem Problem for Continuous Linear Dynamical Systems,” Vol. 55. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016. <a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2016.100\">https://doi.org/10.4230/LIPIcs.ICALP.2016.100</a>.","ieee":"V. K. Chonev, J. Ouaknine, and J. Worrell, “On the skolem problem for continuous linear dynamical systems,” presented at the ICALP: Automata, Languages and Programming, Rome, Italy, 2016, vol. 55."},"has_accepted_license":"1","pubrep_id":"778","volume":55,"quality_controlled":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"ec_funded":1,"article_processing_charge":"No","month":"08","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","intvolume":"        55"},{"year":"2016","article_number":"98","acknowledgement":"This research was partially supported by Austrian Science Fund (FWF) NFN Grant No S11407-N23 (RiSE/SHiNE), ERC Start grant (279307: Graph Games), Vienna Science and Technology Fund (WWTF) through project ICT15-003, and European project Cassting (FP7-601148).\r\n\r\nWe thank Stefan Göller and anonymous reviewers for their insightful\r\ncomments and suggestions.\r\n","doi":"10.4230/LIPIcs.ICALP.2016.98","alternative_title":["LIPIcs"],"date_created":"2018-12-11T11:49:59Z","conference":{"end_date":"2016-07-15","location":"Rome, Italy","name":"ICALP: Automata, Languages and Programming","start_date":"2016-07-12"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"type":"conference","title":"Computation tree logic for synchronization properties","project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","call_identifier":"FWF"},{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003"}],"publication_status":"published","day":"01","author":[{"orcid":"0000-0002-4561-241X","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"},{"last_name":"Doyen","full_name":"Doyen, Laurent","first_name":"Laurent"}],"oa_version":"Published Version","abstract":[{"text":"We present a logic that extends CTL (Computation Tree Logic) with operators that express synchronization properties. A property is synchronized in a system if it holds in all paths of a certain length. The new logic is obtained by using the same path quantifiers and temporal operators as in CTL, but allowing a different order of the quantifiers. This small syntactic variation induces a logic that can express non-regular properties for which known extensions of MSO with equality of path length are undecidable. We show that our variant of CTL is decidable and that the model-checking problem is in Delta_3^P = P^{NP^NP}, and is DP-hard. We analogously consider quantifier exchange in extensions of CTL, and we present operators defined using basic operators of CTL* that express the occurrence of infinitely many synchronization points. We show that the model-checking problem remains in Delta_3^P. The distinguishing power of CTL and of our new logic coincide if the Next operator is allowed in the logics, thus the classical bisimulation quotient can be used for state-space reduction before model checking. ","lang":"eng"}],"file":[{"date_updated":"2018-12-12T10:08:52Z","creator":"system","file_size":546133,"content_type":"application/pdf","date_created":"2018-12-12T10:08:52Z","relation":"main_file","access_level":"open_access","file_id":"4714","file_name":"IST-2017-812-v1+1_LIPIcs-ICALP-2016-98.pdf"}],"date_published":"2016-01-01T00:00:00Z","date_updated":"2025-06-03T11:18:54Z","oa":1,"publist_id":"6313","department":[{"_id":"KrCh"}],"file_date_updated":"2018-12-12T10:08:52Z","ddc":["005"],"scopus_import":"1","_id":"1070","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"ec_funded":1,"article_processing_charge":"No","citation":{"ista":"Chatterjee K, Doyen L. 2016. Computation tree logic for synchronization properties. ICALP: Automata, Languages and Programming, LIPIcs, vol. 55, 98.","short":"K. Chatterjee, L. Doyen, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016.","apa":"Chatterjee, K., &#38; Doyen, L. (2016). Computation tree logic for synchronization properties (Vol. 55). Presented at the ICALP: Automata, Languages and Programming, Rome, Italy: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2016.98\">https://doi.org/10.4230/LIPIcs.ICALP.2016.98</a>","mla":"Chatterjee, Krishnendu, and Laurent Doyen. <i>Computation Tree Logic for Synchronization Properties</i>. Vol. 55, 98, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016, doi:<a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2016.98\">10.4230/LIPIcs.ICALP.2016.98</a>.","ieee":"K. Chatterjee and L. Doyen, “Computation tree logic for synchronization properties,” presented at the ICALP: Automata, Languages and Programming, Rome, Italy, 2016, vol. 55.","ama":"Chatterjee K, Doyen L. Computation tree logic for synchronization properties. In: Vol 55. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2016. doi:<a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2016.98\">10.4230/LIPIcs.ICALP.2016.98</a>","chicago":"Chatterjee, Krishnendu, and Laurent Doyen. “Computation Tree Logic for Synchronization Properties,” Vol. 55. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016. <a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2016.98\">https://doi.org/10.4230/LIPIcs.ICALP.2016.98</a>."},"has_accepted_license":"1","volume":55,"quality_controlled":"1","pubrep_id":"812","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","intvolume":"        55","month":"01"},{"oa_version":"Published Version","author":[{"first_name":"Łukasz","last_name":"Łangowski","full_name":"Łangowski, Łukasz"},{"last_name":"Wabnik","full_name":"Wabnik, Krzysztof T","id":"4DE369A4-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof T","orcid":"0000-0001-7263-0560"},{"orcid":"0000-0001-5039-9660","full_name":"Li, Hongjiang","last_name":"Li","first_name":"Hongjiang","id":"33CA54A6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Vanneste, Steffen","last_name":"Vanneste","first_name":"Steffen"},{"first_name":"Satoshi","full_name":"Naramoto, Satoshi","last_name":"Naramoto"},{"full_name":"Tanaka, Hirokazu","last_name":"Tanaka","first_name":"Hirokazu"},{"orcid":"0000-0002-8302-7596","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí","last_name":"Friml"}],"day":"19","publication":"Cell Discovery","external_id":{"isi":["000414797400001"]},"date_published":"2016-07-19T00:00:00Z","file":[{"file_name":"IST-2017-757-v1+1_celldisc201618.pdf","file_id":"5017","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2018-12-12T10:13:33Z","file_size":5261671,"creator":"system","date_updated":"2018-12-12T10:13:33Z"}],"abstract":[{"text":"The asymmetric localization of proteins in the plasma membrane domains of eukaryotic cells is a fundamental manifestation of cell polarity that is central to multicellular organization and developmental patterning. In plants, the mechanisms underlying the polar localization of cargo proteins are still largely unknown and appear to be fundamentally distinct from those operating in mammals. Here, we present a systematic, quantitative comparative analysis of the polar delivery and subcellular localization of proteins that characterize distinct polar plasma membrane domains in plant cells. The combination of microscopic analyses and computational modeling revealed a mechanistic framework common to diverse polar cargos and underlying the establishment and maintenance of apical, basal, and lateral polar domains in plant cells. This mechanism depends on the polar secretion, constitutive endocytic recycling, and restricted lateral diffusion of cargos within the plasma membrane. Moreover, our observations suggest that polar cargo distribution involves the individual protein potential to form clusters within the plasma membrane and interact with the extracellular matrix. Our observations provide insights into the shared cellular mechanisms of polar cargo delivery and polarity maintenance in plant cells.","lang":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2018-12-11T11:50:02Z","doi":"10.1038/celldisc.2016.18","acknowledgement":"We thank Bonnie Bartel, Jenny Russinova and Niko Geldner\r\nfor sharing published material, Martine de Cock and Annick\r\nBleys for help in preparing the manuscript. This work was\r\nsupported by the European Research Council (project\r\nERC-2011-StG-20101109-PSDP); Czech Science Foundation\r\nGAČR (GA13-40637S); project CEITEC—Central European\r\nInstitute of Technology (CZ.1.05/1.1.00/02.0068). SV is a\r\npostdoctoral fellow of the Research Foundation-Flanders.\r\nSN is a Project Assistant Professor supported by the Japanese\r\nSociety for the Promotion of Science (JSPS; 30612022 to SN),\r\nthe NC-CARP project of the Ministry of Education, Culture,\r\nSports, Science and Technology in Japan to SN.","year":"2016","article_number":"16018","publication_status":"published","project":[{"call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300","name":"Polarity and subcellular dynamics in plants"}],"title":"Cellular mechanisms for cargo delivery and polarity maintenance at different polar domains in plant cells","type":"journal_article","isi":1,"language":[{"iso":"eng"}],"volume":2,"pubrep_id":"757","quality_controlled":"1","has_accepted_license":"1","citation":{"ieee":"Ł. Łangowski <i>et al.</i>, “Cellular mechanisms for cargo delivery and polarity maintenance at different polar domains in plant cells,” <i>Cell Discovery</i>, vol. 2. Nature Publishing Group, 2016.","ama":"Łangowski Ł, Wabnik KT, Li H, et al. Cellular mechanisms for cargo delivery and polarity maintenance at different polar domains in plant cells. <i>Cell Discovery</i>. 2016;2. doi:<a href=\"https://doi.org/10.1038/celldisc.2016.18\">10.1038/celldisc.2016.18</a>","chicago":"Łangowski, Łukasz, Krzysztof T Wabnik, Hongjiang Li, Steffen Vanneste, Satoshi Naramoto, Hirokazu Tanaka, and Jiří Friml. “Cellular Mechanisms for Cargo Delivery and Polarity Maintenance at Different Polar Domains in Plant Cells.” <i>Cell Discovery</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/celldisc.2016.18\">https://doi.org/10.1038/celldisc.2016.18</a>.","ista":"Łangowski Ł, Wabnik KT, Li H, Vanneste S, Naramoto S, Tanaka H, Friml J. 2016. Cellular mechanisms for cargo delivery and polarity maintenance at different polar domains in plant cells. Cell Discovery. 2, 16018.","short":"Ł. Łangowski, K.T. Wabnik, H. Li, S. Vanneste, S. Naramoto, H. Tanaka, J. Friml, Cell Discovery 2 (2016).","mla":"Łangowski, Łukasz, et al. “Cellular Mechanisms for Cargo Delivery and Polarity Maintenance at Different Polar Domains in Plant Cells.” <i>Cell Discovery</i>, vol. 2, 16018, Nature Publishing Group, 2016, doi:<a href=\"https://doi.org/10.1038/celldisc.2016.18\">10.1038/celldisc.2016.18</a>.","apa":"Łangowski, Ł., Wabnik, K. T., Li, H., Vanneste, S., Naramoto, S., Tanaka, H., &#38; Friml, J. (2016). Cellular mechanisms for cargo delivery and polarity maintenance at different polar domains in plant cells. <i>Cell Discovery</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/celldisc.2016.18\">https://doi.org/10.1038/celldisc.2016.18</a>"},"ec_funded":1,"article_processing_charge":"No","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"month":"07","intvolume":"         2","publisher":"Nature Publishing Group","publist_id":"6299","oa":1,"date_updated":"2025-09-22T14:19:46Z","status":"public","_id":"1081","scopus_import":"1","ddc":["580"],"department":[{"_id":"EvBe"},{"_id":"JiFr"}],"file_date_updated":"2018-12-12T10:13:33Z"},{"quality_controlled":"1","volume":29,"citation":{"ieee":"M. J. Chalk, O. Marre, and G. Tkačik, “Relevant sparse codes with variational information bottleneck,” presented at the NIPS: Neural Information Processing Systems, Barcelona, Spain, 2016, vol. 29, pp. 1965–1973.","chicago":"Chalk, Matthew J, Olivier Marre, and Gašper Tkačik. “Relevant Sparse Codes with Variational Information Bottleneck,” 29:1965–73. Neural Information Processing Systems Foundation, 2016.","ama":"Chalk MJ, Marre O, Tkačik G. Relevant sparse codes with variational information bottleneck. In: Vol 29. Neural Information Processing Systems Foundation; 2016:1965-1973.","ista":"Chalk MJ, Marre O, Tkačik G. 2016. Relevant sparse codes with variational information bottleneck. NIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 29, 1965–1973.","short":"M.J. Chalk, O. Marre, G. Tkačik, in:, Neural Information Processing Systems Foundation, 2016, pp. 1965–1973.","apa":"Chalk, M. J., Marre, O., &#38; Tkačik, G. (2016). Relevant sparse codes with variational information bottleneck (Vol. 29, pp. 1965–1973). Presented at the NIPS: Neural Information Processing Systems, Barcelona, Spain: Neural Information Processing Systems Foundation.","mla":"Chalk, Matthew J., et al. <i>Relevant Sparse Codes with Variational Information Bottleneck</i>. Vol. 29, Neural Information Processing Systems Foundation, 2016, pp. 1965–73."},"page":"1965-1973","article_processing_charge":"No","month":"12","intvolume":"        29","publisher":"Neural Information Processing Systems Foundation","publist_id":"6298","oa":1,"related_material":{"link":[{"relation":"other","url":"https://papers.nips.cc/paper/6101-relevant-sparse-codes-with-variational-information-bottleneck"}]},"date_updated":"2025-06-03T11:33:51Z","status":"public","_id":"1082","scopus_import":"1","arxiv":1,"department":[{"_id":"GaTk"}],"oa_version":"Preprint","main_file_link":[{"url":"https://arxiv.org/abs/1605.07332","open_access":"1"}],"author":[{"first_name":"Matthew J","id":"2BAAC544-F248-11E8-B48F-1D18A9856A87","full_name":"Chalk, Matthew J","last_name":"Chalk","orcid":"0000-0001-7782-4436"},{"full_name":"Marre, Olivier","last_name":"Marre","first_name":"Olivier"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper","last_name":"Tkacik","full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455"}],"day":"01","external_id":{"arxiv":["1605.07332"]},"date_published":"2016-12-01T00:00:00Z","abstract":[{"lang":"eng","text":"In many applications, it is desirable to extract only the relevant aspects of data. A principled way to do this is the information bottleneck (IB) method, where one seeks a code that maximises information about a relevance variable, Y, while constraining the information encoded about the original data, X. Unfortunately however, the IB method is computationally demanding when data are high-dimensional and/or non-gaussian. Here we propose an approximate variational scheme for maximising a lower bound on the IB objective, analogous to variational EM. Using this method, we derive an IB algorithm to recover features that are both relevant and sparse. Finally, we demonstrate how kernelised versions of the algorithm can be used to address a broad range of problems with non-linear relation between X and Y."}],"conference":{"location":"Barcelona, Spain","start_date":"2016-12-05","name":"NIPS: Neural Information Processing Systems","end_date":"2016-12-10"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","alternative_title":["Advances in Neural Information Processing Systems"],"date_created":"2018-12-11T11:50:03Z","year":"2016","publication_status":"published","title":"Relevant sparse codes with variational information bottleneck","type":"conference","language":[{"iso":"eng"}]},{"article_processing_charge":"No","page":"2318 - 2334","citation":{"mla":"Booker, Sam, et al. “KCTD12 Auxiliary Proteins Modulate Kinetics of GABAB Receptor-Mediated Inhibition in Cholecystokinin-Containing Interneurons.” <i>Cerebral Cortex</i>, vol. 27, no. 3, Oxford University Press, 2016, pp. 2318–34, doi:<a href=\"https://doi.org/10.1093/cercor/bhw090\">10.1093/cercor/bhw090</a>.","apa":"Booker, S., Althof, D., Gross, A., Loreth, D., Müller, J., Unger, A., … Kulik, Á. (2016). KCTD12 auxiliary proteins modulate kinetics of GABAB receptor-mediated inhibition in Cholecystokinin-containing interneurons. <i>Cerebral Cortex</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/cercor/bhw090\">https://doi.org/10.1093/cercor/bhw090</a>","short":"S. Booker, D. Althof, A. Gross, D. Loreth, J. Müller, A. Unger, B. Fakler, A. Varro, M. Watanabe, M. Gassmann, B. Bettler, R. Shigemoto, I. Vida, Á. Kulik, Cerebral Cortex 27 (2016) 2318–2334.","ista":"Booker S, Althof D, Gross A, Loreth D, Müller J, Unger A, Fakler B, Varro A, Watanabe M, Gassmann M, Bettler B, Shigemoto R, Vida I, Kulik Á. 2016. KCTD12 auxiliary proteins modulate kinetics of GABAB receptor-mediated inhibition in Cholecystokinin-containing interneurons. Cerebral Cortex. 27(3), 2318–2334.","ama":"Booker S, Althof D, Gross A, et al. KCTD12 auxiliary proteins modulate kinetics of GABAB receptor-mediated inhibition in Cholecystokinin-containing interneurons. <i>Cerebral Cortex</i>. 2016;27(3):2318-2334. doi:<a href=\"https://doi.org/10.1093/cercor/bhw090\">10.1093/cercor/bhw090</a>","chicago":"Booker, Sam, Daniel Althof, Anna Gross, Desiree Loreth, Johanna Müller, Andreas Unger, Bernd Fakler, et al. “KCTD12 Auxiliary Proteins Modulate Kinetics of GABAB Receptor-Mediated Inhibition in Cholecystokinin-Containing Interneurons.” <i>Cerebral Cortex</i>. Oxford University Press, 2016. <a href=\"https://doi.org/10.1093/cercor/bhw090\">https://doi.org/10.1093/cercor/bhw090</a>.","ieee":"S. Booker <i>et al.</i>, “KCTD12 auxiliary proteins modulate kinetics of GABAB receptor-mediated inhibition in Cholecystokinin-containing interneurons,” <i>Cerebral Cortex</i>, vol. 27, no. 3. Oxford University Press, pp. 2318–2334, 2016."},"volume":27,"quality_controlled":"1","publisher":"Oxford University Press","intvolume":"        27","month":"04","date_updated":"2025-09-22T14:19:11Z","publist_id":"6297","department":[{"_id":"RySh"}],"scopus_import":"1","_id":"1083","status":"public","day":"12","author":[{"first_name":"Sam","last_name":"Booker","full_name":"Booker, Sam"},{"first_name":"Daniel","full_name":"Althof, Daniel","last_name":"Althof"},{"first_name":"Anna","last_name":"Gross","full_name":"Gross, Anna"},{"last_name":"Loreth","full_name":"Loreth, Desiree","first_name":"Desiree"},{"full_name":"Müller, Johanna","last_name":"Müller","first_name":"Johanna"},{"first_name":"Andreas","last_name":"Unger","full_name":"Unger, Andreas"},{"full_name":"Fakler, Bernd","last_name":"Fakler","first_name":"Bernd"},{"full_name":"Varro, Andrea","last_name":"Varro","first_name":"Andrea"},{"last_name":"Watanabe","full_name":"Watanabe, Masahiko","first_name":"Masahiko"},{"first_name":"Martin","last_name":"Gassmann","full_name":"Gassmann, Martin"},{"first_name":"Bernhard","full_name":"Bettler, Bernhard","last_name":"Bettler"},{"orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi","last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi"},{"first_name":"Imre","full_name":"Vida, Imre","last_name":"Vida"},{"last_name":"Kulik","full_name":"Kulik, Ákos","first_name":"Ákos"}],"issue":"3","oa_version":"None","abstract":[{"text":" Cholecystokinin-expressing interneurons (CCK-INs) mediate behavior state-dependent inhibition in cortical circuits and themselves receive strong GABAergic input. However, it remains unclear to what extent GABABreceptors (GABABRs) contribute to their inhibitory control. Using immunoelectron microscopy, we found that CCK-INs in the rat hippocampus possessed high levels of dendritic GABABRs and KCTD12 auxiliary proteins, whereas postsynaptic effector Kir3 channels were present at lower levels. Consistently, whole-cell recordings revealed slow GABABR-mediated inhibitory postsynaptic currents (IPSCs) in most CCK-INs. In spite of the higher surface density of GABABRs in CCK-INs than in CA1 principal cells, the amplitudes of IPSCs were comparable, suggesting that the expression of Kir3 channels is the limiting factor for the GABABR currents in these INs. Morphological analysis showed that CCK-INs were diverse, comprising perisomatic-targeting basket cells (BCs), as well as dendrite-targeting (DT) interneurons, including a previously undescribed DT type. GABABR-mediated IPSCs in CCK-INs were large in BCs, but small in DT subtypes. In response to prolonged activation, GABABR-mediated currents displayed strong desensitization, which was absent in KCTD12-deficient mice. This study highlights that GABABRs differentially control CCK-IN subtypes, and the kinetics and desensitization of GABABR-mediated currents are modulated by KCTD12 proteins. ","lang":"eng"}],"date_published":"2016-04-12T00:00:00Z","external_id":{"isi":["000397636600048"]},"publication":"Cerebral Cortex","year":"2016","doi":"10.1093/cercor/bhw090","acknowledgement":"This work was supported by the Deutsche Forschungsgemeinschaft (DFG SFB 780 A2, A.K.; SFB TR3 I.V. and EXC 257, I.V.; FOR 2143, A.K. and I.V.), Spemann Graduate School (D.A.), BIOSS-2 (A6, A.K.), the Swiss National Science Foundation (3100A0-117816, B.B.), The McNaught Bequest (S.A.B. and I.V.), and Tenovus Scotland (I.V.).\r\n\r\n\r\nWe thank Cheryl Hutton and Chinmaya Sadangi for their contributions to neuronal reconstruction as well as Natalie Wernet, Sigrun Nestel, Anikó Schneider, Ina Wolter, and Ulrich Noeller for their excellent technical support. VGAT-Venus transgenic rats were generated by Drs Y. Yanagawa, M. Hirabayashi, and Y. Kawaguchi in National Institute for Physiological Sciences, Okazaki, Japan, using pCS2-Venus provided by Dr A. Miyawaki. The monoclonal mouse CCK antibody was generously provided by Dr G.V. Ohning, CURE Center, UCLA, CA. ","date_created":"2018-12-11T11:50:03Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"language":[{"iso":"eng"}],"type":"journal_article","title":"KCTD12 auxiliary proteins modulate kinetics of GABAB receptor-mediated inhibition in Cholecystokinin-containing interneurons","publication_status":"published"},{"year":"2016","article_number":"24","acknowledgement":"This research was supported in part by the Austrian Science Fund (FWF) under grants S11402-N23\r\n(RiSE/SHiNE) and Z211-N23 (Wittgenstein Award), ERC Start grant (279307: Graph Games), Vienna\r\nScience and Technology Fund (WWTF) through project ICT15-003 and by the National Science Centre\r\n(NCN), Poland under grant 2014/15/D/ST6/04543.","doi":"10.4230/LIPIcs.MFCS.2016.24","alternative_title":["LIPIcs"],"date_created":"2018-12-11T11:50:05Z","conference":{"end_date":"2016-08-26","location":"Krakow; Poland","name":"MFCS: Mathematical Foundations of Computer Science","start_date":"2016-08-22"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"title":"Nested weighted limit-average automata of bounded width","type":"conference","project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","call_identifier":"FWF"},{"name":"Formal methods for the design and analysis of complex systems","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"},{"name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425"}],"publication_status":"published","day":"01","author":[{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger","full_name":"Henzinger, Thomas A"},{"first_name":"Jan","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","full_name":"Otop, Jan","last_name":"Otop"}],"oa_version":"Published Version","abstract":[{"text":" While weighted automata provide a natural framework to express quantitative properties, many basic properties like average response time cannot be expressed with weighted automata. Nested weighted automata extend weighted automata and consist of a master automaton and a set of slave automata that are invoked by the master automaton. Nested weighted automata are strictly more expressive than weighted automata (e.g., average response time can be expressed with nested weighted automata), but the basic decision questions have higher complexity (e.g., for deterministic automata, the emptiness question for nested weighted automata is PSPACE-hard, whereas the corresponding complexity for weighted automata is PTIME). We consider a natural subclass of nested weighted automata where at any point at most a bounded number k of slave automata can be active. We focus on automata whose master value function is the limit average. We show that these nested weighted automata with bounded width are strictly more expressive than weighted automata (e.g., average response time with no overlapping requests can be expressed with bound k=1, but not with non-nested weighted automata). We show that the complexity of the basic decision problems (i.e., emptiness and universality) for the subclass with k constant matches the complexity for weighted automata. Moreover, when k is part of the input given in unary we establish PSPACE-completeness.","lang":"eng"}],"date_published":"2016-08-01T00:00:00Z","file":[{"creator":"system","date_updated":"2018-12-12T10:17:31Z","content_type":"application/pdf","date_created":"2018-12-12T10:17:31Z","file_size":564560,"file_id":"5286","file_name":"IST-2017-795-v1+1_LIPIcs-MFCS-2016-24.pdf","access_level":"open_access","relation":"main_file"}],"date_updated":"2025-07-10T11:50:02Z","oa":1,"publist_id":"6286","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"file_date_updated":"2018-12-12T10:17:31Z","ddc":["004"],"scopus_import":"1","_id":"1090","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"article_processing_charge":"No","ec_funded":1,"citation":{"mla":"Chatterjee, Krishnendu, et al. <i>Nested Weighted Limit-Average Automata of Bounded Width</i>. Vol. 58, 24, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016, doi:<a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2016.24\">10.4230/LIPIcs.MFCS.2016.24</a>.","apa":"Chatterjee, K., Henzinger, T. A., &#38; Otop, J. (2016). Nested weighted limit-average automata of bounded width (Vol. 58). Presented at the MFCS: Mathematical Foundations of Computer Science, Krakow; Poland: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2016.24\">https://doi.org/10.4230/LIPIcs.MFCS.2016.24</a>","short":"K. Chatterjee, T.A. Henzinger, J. Otop, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016.","ista":"Chatterjee K, Henzinger TA, Otop J. 2016. Nested weighted limit-average automata of bounded width. MFCS: Mathematical Foundations of Computer Science, LIPIcs, vol. 58, 24.","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. “Nested Weighted Limit-Average Automata of Bounded Width,” Vol. 58. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016. <a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2016.24\">https://doi.org/10.4230/LIPIcs.MFCS.2016.24</a>.","ama":"Chatterjee K, Henzinger TA, Otop J. Nested weighted limit-average automata of bounded width. In: Vol 58. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2016. doi:<a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2016.24\">10.4230/LIPIcs.MFCS.2016.24</a>","ieee":"K. Chatterjee, T. A. Henzinger, and J. Otop, “Nested weighted limit-average automata of bounded width,” presented at the MFCS: Mathematical Foundations of Computer Science, Krakow; Poland, 2016, vol. 58."},"has_accepted_license":"1","quality_controlled":"1","volume":58,"pubrep_id":"795","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","intvolume":"        58","month":"08"},{"intvolume":"      1474","publisher":"Springer","month":"08","page":"203 - 216","ec_funded":1,"acknowledged_ssus":[{"_id":"EM-Fac"}],"article_processing_charge":"No","volume":1474,"quality_controlled":"1","citation":{"short":"H. Harada, R. Shigemoto, in:, High-Resolution Imaging of Cellular Proteins, Springer, 2016, pp. 203–216.","ista":"Harada H, Shigemoto R. 2016.Immunogold protein localization on grid-glued freeze-fracture replicas. In: High-Resolution Imaging of Cellular Proteins. Methods in Molecular Biology, vol. 1474, 203–216.","apa":"Harada, H., &#38; Shigemoto, R. (2016). Immunogold protein localization on grid-glued freeze-fracture replicas. In <i>High-Resolution Imaging of Cellular Proteins</i> (Vol. 1474, pp. 203–216). Springer. <a href=\"https://doi.org/10.1007/978-1-4939-6352-2_12\">https://doi.org/10.1007/978-1-4939-6352-2_12</a>","mla":"Harada, Harumi, and Ryuichi Shigemoto. “Immunogold Protein Localization on Grid-Glued Freeze-Fracture Replicas.” <i>High-Resolution Imaging of Cellular Proteins</i>, vol. 1474, Springer, 2016, pp. 203–16, doi:<a href=\"https://doi.org/10.1007/978-1-4939-6352-2_12\">10.1007/978-1-4939-6352-2_12</a>.","ieee":"H. Harada and R. Shigemoto, “Immunogold protein localization on grid-glued freeze-fracture replicas,” in <i>High-Resolution Imaging of Cellular Proteins</i>, vol. 1474, Springer, 2016, pp. 203–216.","chicago":"Harada, Harumi, and Ryuichi Shigemoto. “Immunogold Protein Localization on Grid-Glued Freeze-Fracture Replicas.” In <i>High-Resolution Imaging of Cellular Proteins</i>, 1474:203–16. Springer, 2016. <a href=\"https://doi.org/10.1007/978-1-4939-6352-2_12\">https://doi.org/10.1007/978-1-4939-6352-2_12</a>.","ama":"Harada H, Shigemoto R. Immunogold protein localization on grid-glued freeze-fracture replicas. In: <i>High-Resolution Imaging of Cellular Proteins</i>. Vol 1474. Springer; 2016:203-216. doi:<a href=\"https://doi.org/10.1007/978-1-4939-6352-2_12\">10.1007/978-1-4939-6352-2_12</a>"},"department":[{"_id":"RySh"}],"status":"public","_id":"1094","date_updated":"2025-04-15T07:12:21Z","publist_id":"6281","abstract":[{"lang":"eng","text":"Immunogold labeling of freeze-fracture replicas has recently been used for high-resolution visualization of protein localization in electron microscopy. This method has higher labeling efficiency than conventional immunogold methods for membrane molecules allowing precise quantitative measurements. However, one of the limitations of freeze-fracture replica immunolabeling is difficulty in keeping structural orientation and identifying labeled profiles in complex tissues like brain. The difficulty is partly due to fragmentation of freeze-fracture replica preparations during labeling procedures and limited morphological clues on the replica surface. To overcome these issues, we introduce here a grid-glued replica method combined with SEM observation. This method allows histological staining before dissolving the tissue and easy handling of replicas during immunogold labeling, and keeps the whole replica surface intact without fragmentation. The procedure described here is also useful for matched double-replica analysis allowing further identification of labeled profiles in corresponding P-face and E-face."}],"publication":"High-Resolution Imaging of Cellular Proteins","date_published":"2016-08-12T00:00:00Z","author":[{"orcid":"0000-0001-7429-7896","full_name":"Harada, Harumi","last_name":"Harada","first_name":"Harumi","id":"2E55CDF2-F248-11E8-B48F-1D18A9856A87"},{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi","last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444"}],"day":"12","oa_version":"None","title":"Immunogold protein localization on grid-glued freeze-fracture replicas","type":"book_chapter","project":[{"call_identifier":"FP7","grant_number":"604102","name":"Localization of ion channels and receptors by two and three-dimensional immunoelectron microscopic approaches","_id":"25CD3DD2-B435-11E9-9278-68D0E5697425"}],"language":[{"iso":"eng"}],"publication_status":"published","acknowledgement":"We thank Prof. Elek Molnár for providing us a pan-AMPAR anti-body used in Fig.2 and Dr. Ludek Lovicar for technical assistance in scanning electron microscope imaging. This work was supported by the European Union (HBP—Project Ref. 604102). ","doi":"10.1007/978-1-4939-6352-2_12","year":"2016","publication_identifier":{"eissn":["1611-3349"],"issn":["0302-9743"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","alternative_title":["Methods in Molecular Biology"],"date_created":"2018-12-11T11:50:06Z"},{"publication_status":"published","language":[{"iso":"eng"}],"project":[{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","name":"Quantitative Reactive Modeling"},{"grant_number":"Z211","name":"Formal methods for the design and analysis of complex systems","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"type":"conference","title":"Local linearizability for concurrent container-type data structures","alternative_title":["LIPIcs"],"date_created":"2018-12-11T11:50:07Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","conference":{"end_date":"2016-08-26","location":"Quebec City; Canada","name":"CONCUR: Concurrency Theory","start_date":"2016-08-23"},"article_number":"6","year":"2016","doi":"10.4230/LIPIcs.CONCUR.2016.6","acknowledgement":"This work has been supported by the National Research Network RiSE on Rigorous Systems Engineering\r\n(Austrian Science Fund (FWF): S11402-N23, S11403-N23, S11404-N23, S11411-N23), a Google\r\nPhD Fellowship, an Erwin Schrödinger Fellowship (Austrian Science Fund (FWF): J3696-N26), EPSRC\r\ngrants EP/H005633/1 and EP/K008528/1, the Vienna Science and Technology Fund (WWTF) trough\r\ngrant PROSEED, the European Research Council (ERC) under grant 267989 (QUAREM) and by the\r\nAustrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award).","file":[{"creator":"system","date_updated":"2018-12-12T10:10:10Z","content_type":"application/pdf","date_created":"2018-12-12T10:10:10Z","file_size":589747,"file_id":"4795","file_name":"IST-2017-793-v1+1_LIPIcs-CONCUR-2016-6.pdf","relation":"main_file","access_level":"open_access"}],"date_published":"2016-08-01T00:00:00Z","publication":"Leibniz International Proceedings in Informatics","abstract":[{"lang":"eng","text":" The semantics of concurrent data structures is usually given by a sequential specification and a consistency condition. Linearizability is the most popular consistency condition due to its simplicity and general applicability. Nevertheless, for applications that do not require all guarantees offered by linearizability, recent research has focused on improving performance and scalability of concurrent data structures by relaxing their semantics. In this paper, we present local linearizability, a relaxed consistency condition that is applicable to container-type concurrent data structures like pools, queues, and stacks. While linearizability requires that the effect of each operation is observed by all threads at the same time, local linearizability only requires that for each thread T, the effects of its local insertion operations and the effects of those removal operations that remove values inserted by T are observed by all threads at the same time. We investigate theoretical and practical properties of local linearizability and its relationship to many existing consistency conditions. We present a generic implementation method for locally linearizable data structures that uses existing linearizable data structures as building blocks. Our implementations show performance and scalability improvements over the original building blocks and outperform the fastest existing container-type implementations. "}],"oa_version":"Published Version","day":"01","author":[{"full_name":"Haas, Andreas","last_name":"Haas","first_name":"Andreas"},{"full_name":"Henzinger, Thomas A","last_name":"Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724"},{"first_name":"Andreas","full_name":"Holzer, Andreas","last_name":"Holzer"},{"first_name":"Christoph","full_name":"Kirsch, Christoph","last_name":"Kirsch"},{"last_name":"Lippautz","full_name":"Lippautz, Michael","first_name":"Michael"},{"first_name":"Hannes","full_name":"Payer, Hannes","last_name":"Payer"},{"full_name":"Sezgin, Ali","last_name":"Sezgin","first_name":"Ali","id":"4C7638DA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ana","full_name":"Sokolova, Ana","last_name":"Sokolova"},{"first_name":"Helmut","full_name":"Veith, Helmut","last_name":"Veith"}],"_id":"1095","status":"public","ddc":["004"],"file_date_updated":"2018-12-12T10:10:10Z","department":[{"_id":"ToHe"}],"scopus_import":1,"oa":1,"publist_id":"6280","date_updated":"2025-04-15T06:25:58Z","month":"08","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","intvolume":"        59","has_accepted_license":"1","citation":{"ieee":"A. Haas <i>et al.</i>, “Local linearizability for concurrent container-type data structures,” in <i>Leibniz International Proceedings in Informatics</i>, Quebec City; Canada, 2016, vol. 59.","chicago":"Haas, Andreas, Thomas A Henzinger, Andreas Holzer, Christoph Kirsch, Michael Lippautz, Hannes Payer, Ali Sezgin, Ana Sokolova, and Helmut Veith. “Local Linearizability for Concurrent Container-Type Data Structures.” In <i>Leibniz International Proceedings in Informatics</i>, Vol. 59. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016. <a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2016.6\">https://doi.org/10.4230/LIPIcs.CONCUR.2016.6</a>.","ama":"Haas A, Henzinger TA, Holzer A, et al. Local linearizability for concurrent container-type data structures. In: <i>Leibniz International Proceedings in Informatics</i>. Vol 59. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2016. doi:<a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2016.6\">10.4230/LIPIcs.CONCUR.2016.6</a>","ista":"Haas A, Henzinger TA, Holzer A, Kirsch C, Lippautz M, Payer H, Sezgin A, Sokolova A, Veith H. 2016. Local linearizability for concurrent container-type data structures. Leibniz International Proceedings in Informatics. CONCUR: Concurrency Theory, LIPIcs, vol. 59, 6.","short":"A. Haas, T.A. Henzinger, A. Holzer, C. Kirsch, M. Lippautz, H. Payer, A. Sezgin, A. Sokolova, H. Veith, in:, Leibniz International Proceedings in Informatics, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016.","apa":"Haas, A., Henzinger, T. A., Holzer, A., Kirsch, C., Lippautz, M., Payer, H., … Veith, H. (2016). Local linearizability for concurrent container-type data structures. In <i>Leibniz International Proceedings in Informatics</i> (Vol. 59). Quebec City; Canada: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2016.6\">https://doi.org/10.4230/LIPIcs.CONCUR.2016.6</a>","mla":"Haas, Andreas, et al. “Local Linearizability for Concurrent Container-Type Data Structures.” <i>Leibniz International Proceedings in Informatics</i>, vol. 59, 6, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016, doi:<a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2016.6\">10.4230/LIPIcs.CONCUR.2016.6</a>."},"volume":59,"quality_controlled":"1","pubrep_id":"793","ec_funded":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"}},{"oa":1,"publist_id":"6278","date_updated":"2025-09-22T14:17:29Z","_id":"1097","status":"public","file_date_updated":"2018-12-12T10:17:42Z","department":[{"_id":"BeBi"}],"ddc":["006"],"scopus_import":"1","citation":{"ista":"Du T, Schulz A, Zhu B, Bickel B, Matusik W. 2016. Computational multicopter design. SIGGRAPH Asia: Conference and Exhibition on Computer Graphics and Interactive Techniques in Asia, ACM Transactions on Graphics, vol. 35, 227.","short":"T. Du, A. Schulz, B. Zhu, B. Bickel, W. Matusik, in:, ACM, 2016.","apa":"Du, T., Schulz, A., Zhu, B., Bickel, B., &#38; Matusik, W. (2016). Computational multicopter design (Vol. 35). Presented at the SIGGRAPH Asia: Conference and Exhibition on Computer Graphics and Interactive Techniques in Asia, Macao, China: ACM. <a href=\"https://doi.org/10.1145/2980179.2982427\">https://doi.org/10.1145/2980179.2982427</a>","mla":"Du, Tao, et al. <i>Computational Multicopter Design</i>. Vol. 35, no. 6, 227, ACM, 2016, doi:<a href=\"https://doi.org/10.1145/2980179.2982427\">10.1145/2980179.2982427</a>.","ieee":"T. Du, A. Schulz, B. Zhu, B. Bickel, and W. Matusik, “Computational multicopter design,” presented at the SIGGRAPH Asia: Conference and Exhibition on Computer Graphics and Interactive Techniques in Asia, Macao, China, 2016, vol. 35, no. 6.","ama":"Du T, Schulz A, Zhu B, Bickel B, Matusik W. Computational multicopter design. In: Vol 35. ACM; 2016. doi:<a href=\"https://doi.org/10.1145/2980179.2982427\">10.1145/2980179.2982427</a>","chicago":"Du, Tao, Adriana Schulz, Bo Zhu, Bernd Bickel, and Wojciech Matusik. “Computational Multicopter Design,” Vol. 35. ACM, 2016. <a href=\"https://doi.org/10.1145/2980179.2982427\">https://doi.org/10.1145/2980179.2982427</a>."},"has_accepted_license":"1","quality_controlled":"1","volume":35,"pubrep_id":"759","ec_funded":1,"article_processing_charge":"No","month":"11","publisher":"ACM","intvolume":"        35","date_created":"2018-12-11T11:50:07Z","alternative_title":["ACM Transactions on Graphics"],"conference":{"end_date":"2016-12-08","start_date":"2016-12-05","name":"SIGGRAPH Asia: Conference and Exhibition on Computer Graphics and Interactive Techniques in Asia","location":"Macao, China"},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2016","article_number":"227","acknowledgement":"We thank Nobuyuki Umetani for his insightful suggestions in our discussions. We thank Alan Schultz and his colleagues at NRL for building the hexacopter and for the valuable discussions. We thank Randall Davis, Boris Katz, and Howard Shrobe at MIT for their advice. We are grateful to Nick Bandiera for preprocessing mechanical parts and providing 3D printing technical support; Charles Blouin from RCBenchmark for dynamometer hardware support; Brian Saavedra for the composition UI; Yingzhe Yuan for data acquisition and video recording in the experiments; Michael Foshey and David Kim for their comments on the draft of the paper. \r\n\r\n\r\nThis work was partially supported by Air Force Research Laboratory’s sponsorship of Julia: A Fresh Approach to Technical Computing and Data Processing (Sponsor Award ID FA8750-15-2- 0272, MIT Award ID 024831-00003), and NSF Expedition project (Sponsor Award ID CCF-1138967, MIT Award ID 020610-00002). The views expressed herein are not endorsed by the sponsors. This project has also received funding from the European Union’s Horizon 2020 research and innovation program under grant agreement No 645599. ","doi":"10.1145/2980179.2982427","publication_status":"published","language":[{"iso":"eng"}],"isi":1,"type":"conference","title":"Computational multicopter design","project":[{"name":"Soft-bodied intelligence for Manipulation","grant_number":"645599","_id":"25082902-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"issue":"6","oa_version":"Submitted Version","day":"01","author":[{"first_name":"Tao","last_name":"Du","full_name":"Du, Tao"},{"full_name":"Schulz, Adriana","last_name":"Schulz","first_name":"Adriana"},{"first_name":"Bo","full_name":"Zhu, Bo","last_name":"Zhu"},{"first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","full_name":"Bickel, Bernd","last_name":"Bickel","orcid":"0000-0001-6511-9385"},{"first_name":"Wojciech","last_name":"Matusik","full_name":"Matusik, Wojciech"}],"date_published":"2016-11-01T00:00:00Z","external_id":{"isi":["000388446200069"]},"file":[{"relation":"main_file","access_level":"open_access","file_id":"5298","file_name":"IST-2017-759-v1+1_copter.pdf","file_size":33114420,"content_type":"application/pdf","date_created":"2018-12-12T10:17:42Z","date_updated":"2018-12-12T10:17:42Z","creator":"system"}],"abstract":[{"lang":"eng","text":"We present an interactive system for computational design, optimization, and fabrication of multicopters. Our computational approach allows non-experts to design, explore, and evaluate a wide range of different multicopters. We provide users with an intuitive interface for assembling a multicopter from a collection of components (e.g., propellers, motors, and carbon fiber rods). Our algorithm interactively optimizes shape and controller parameters of the current design to ensure its proper operation. In addition, we allow incorporating a variety of other metrics (such as payload, battery usage, size, and cost) into the design process and exploring tradeoffs between them. We show the efficacy of our method and system by designing, optimizing, fabricating, and operating multicopters with complex geometries and propeller configurations. We also demonstrate the ability of our optimization algorithm to improve the multicopter performance under different metrics."}]},{"intvolume":"        29","publisher":"Neural Information Processing Systems Foundation","month":"12","page":"3619-3627","article_processing_charge":"No","ec_funded":1,"quality_controlled":"1","pubrep_id":"775","volume":29,"citation":{"ieee":"A. Pentina and R. Urner, “Lifelong learning with weighted majority votes,” presented at the NIPS: Neural Information Processing Systems, Barcelona, Spain, 2016, vol. 29, pp. 3619–3627.","ama":"Pentina A, Urner R. Lifelong learning with weighted majority votes. In: Vol 29. Neural Information Processing Systems Foundation; 2016:3619-3627.","chicago":"Pentina, Anastasia, and Ruth Urner. “Lifelong Learning with Weighted Majority Votes,” 29:3619–27. Neural Information Processing Systems Foundation, 2016.","short":"A. Pentina, R. Urner, in:, Neural Information Processing Systems Foundation, 2016, pp. 3619–3627.","ista":"Pentina A, Urner R. 2016. Lifelong learning with weighted majority votes. NIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 29, 3619–3627.","apa":"Pentina, A., &#38; Urner, R. (2016). Lifelong learning with weighted majority votes (Vol. 29, pp. 3619–3627). Presented at the NIPS: Neural Information Processing Systems, Barcelona, Spain: Neural Information Processing Systems Foundation.","mla":"Pentina, Anastasia, and Ruth Urner. <i>Lifelong Learning with Weighted Majority Votes</i>. Vol. 29, Neural Information Processing Systems Foundation, 2016, pp. 3619–27."},"has_accepted_license":"1","scopus_import":"1","file_date_updated":"2018-12-12T10:12:43Z","department":[{"_id":"ChLa"}],"ddc":["006"],"status":"public","_id":"1098","date_updated":"2025-06-03T11:35:58Z","publist_id":"6277","oa":1,"abstract":[{"text":"Better understanding of the potential benefits of information transfer and representation learning is an important step towards the goal of building intelligent systems that are able to persist in the world and learn over time. In this work, we consider a setting where the learner encounters a stream of tasks but is able to retain only limited information from each encountered task, such as a learned predictor. In contrast to most previous works analyzing this scenario, we do not make any distributional assumptions on the task generating process. Instead, we formulate a complexity measure that captures the diversity of the observed tasks. We provide a lifelong learning algorithm with error guarantees for every observed task (rather than on average). We show sample complexity reductions in comparison to solving every task in isolation in terms of our task complexity measure. Further, our algorithmic framework can naturally be viewed as learning a representation from encountered tasks with a neural network.","lang":"eng"}],"file":[{"file_size":237111,"content_type":"application/pdf","date_created":"2018-12-12T10:12:42Z","date_updated":"2018-12-12T10:12:42Z","creator":"system","relation":"main_file","access_level":"open_access","file_id":"4961","file_name":"IST-2017-775-v1+1_main.pdf"},{"creator":"system","date_updated":"2018-12-12T10:12:43Z","content_type":"application/pdf","date_created":"2018-12-12T10:12:43Z","file_size":185818,"file_name":"IST-2017-775-v1+2_supplementary.pdf","file_id":"4962","access_level":"open_access","relation":"main_file"}],"date_published":"2016-12-01T00:00:00Z","author":[{"first_name":"Anastasia","id":"42E87FC6-F248-11E8-B48F-1D18A9856A87","full_name":"Pentina, Anastasia","last_name":"Pentina"},{"last_name":"Urner","full_name":"Urner, Ruth","first_name":"Ruth"}],"day":"01","oa_version":"Published Version","type":"conference","title":"Lifelong learning with weighted majority votes","project":[{"call_identifier":"FP7","_id":"2532554C-B435-11E9-9278-68D0E5697425","grant_number":"308036","name":"Lifelong Learning of Visual Scene Understanding"}],"language":[{"iso":"eng"}],"publication_status":"published","acknowledgement":"This work was in parts funded by the European Research Council under the European Union’s Seventh Framework Programme (FP7/2007-2013)/ERC grant agreement no 308036.\r\n\r\n","year":"2016","conference":{"end_date":"2016-12-10","name":"NIPS: Neural Information Processing Systems","start_date":"2016-12-05","location":"Barcelona, Spain"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","alternative_title":["Advances in Neural Information Processing Systems"],"date_created":"2018-12-11T11:50:08Z"},{"day":"01","author":[{"first_name":"Luigi","full_name":"Malomo, Luigi","last_name":"Malomo"},{"last_name":"Pietroni","full_name":"Pietroni, Nico","first_name":"Nico"},{"last_name":"Bickel","full_name":"Bickel, Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd","orcid":"0000-0001-6511-9385"},{"first_name":"Paolo","last_name":"Cignoni","full_name":"Cignoni, Paolo"}],"issue":"6","oa_version":"Submitted Version","abstract":[{"text":"We present FlexMolds, a novel computational approach to automatically design flexible, reusable molds that, once 3D printed, allow us to physically fabricate, by means of liquid casting, multiple copies of complex shapes with rich surface details and complex topology. The approach to design such flexible molds is based on a greedy bottom-up search of possible cuts over an object, evaluating for each possible cut the feasibility of the resulting mold. We use a dynamic simulation approach to evaluate candidate molds, providing a heuristic to generate forces that are able to open, detach, and remove a complex mold from the object it surrounds. We have tested the approach with a number of objects with nontrivial shapes and topologies.","lang":"eng"}],"external_id":{"isi":["000388446200065"]},"file":[{"relation":"main_file","access_level":"open_access","file_id":"4918","file_name":"IST-2017-760-v1+1_flexmolds.pdf","date_updated":"2018-12-12T10:12:01Z","creator":"system","file_size":11122029,"content_type":"application/pdf","date_created":"2018-12-12T10:12:01Z"}],"date_published":"2016-11-01T00:00:00Z","year":"2016","article_number":"223","acknowledgement":"The armadillo, bunny and dragon models are courtesy of the Stanford  3D  Scanning  Repository.   The  bimba,  fertility  and  elephant models are courtesy of the AIM@SHAPE Shape Repository.  \r\nThis project has received funding from the European Union’s Horizon 2020  research  and  innovation  programme  under  grant  agreement\r\nNo. 645599.","doi":"10.1145/2980179.2982397","alternative_title":["ACM Transactions on Graphics"],"date_created":"2018-12-11T11:50:08Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","conference":{"end_date":"2016-12-08","location":"Macao, China","start_date":"2016-12-05","name":"SIGGRAPH Asia: Conference and Exhibition on Computer Graphics and Interactive Techniques in Asia"},"language":[{"iso":"eng"}],"isi":1,"project":[{"call_identifier":"H2020","grant_number":"645599","name":"Soft-bodied intelligence for Manipulation","_id":"25082902-B435-11E9-9278-68D0E5697425"}],"type":"conference","title":"FlexMolds: Automatic design of flexible shells for molding","publication_status":"published","ec_funded":1,"article_processing_charge":"No","has_accepted_license":"1","citation":{"ieee":"L. Malomo, N. Pietroni, B. Bickel, and P. Cignoni, “FlexMolds: Automatic design of flexible shells for molding,” presented at the SIGGRAPH Asia: Conference and Exhibition on Computer Graphics and Interactive Techniques in Asia, Macao, China, 2016, vol. 35, no. 6.","ama":"Malomo L, Pietroni N, Bickel B, Cignoni P. FlexMolds: Automatic design of flexible shells for molding. In: Vol 35. ACM; 2016. doi:<a href=\"https://doi.org/10.1145/2980179.2982397\">10.1145/2980179.2982397</a>","chicago":"Malomo, Luigi, Nico Pietroni, Bernd Bickel, and Paolo Cignoni. “FlexMolds: Automatic Design of Flexible Shells for Molding,” Vol. 35. ACM, 2016. <a href=\"https://doi.org/10.1145/2980179.2982397\">https://doi.org/10.1145/2980179.2982397</a>.","short":"L. Malomo, N. Pietroni, B. Bickel, P. Cignoni, in:, ACM, 2016.","ista":"Malomo L, Pietroni N, Bickel B, Cignoni P. 2016. FlexMolds: Automatic design of flexible shells for molding. SIGGRAPH Asia: Conference and Exhibition on Computer Graphics and Interactive Techniques in Asia, ACM Transactions on Graphics, vol. 35, 223.","apa":"Malomo, L., Pietroni, N., Bickel, B., &#38; Cignoni, P. (2016). FlexMolds: Automatic design of flexible shells for molding (Vol. 35). Presented at the SIGGRAPH Asia: Conference and Exhibition on Computer Graphics and Interactive Techniques in Asia, Macao, China: ACM. <a href=\"https://doi.org/10.1145/2980179.2982397\">https://doi.org/10.1145/2980179.2982397</a>","mla":"Malomo, Luigi, et al. <i>FlexMolds: Automatic Design of Flexible Shells for Molding</i>. Vol. 35, no. 6, 223, ACM, 2016, doi:<a href=\"https://doi.org/10.1145/2980179.2982397\">10.1145/2980179.2982397</a>."},"pubrep_id":"760","volume":35,"quality_controlled":"1","publisher":"ACM","intvolume":"        35","month":"11","date_updated":"2025-09-22T14:16:02Z","oa":1,"publist_id":"6276","ddc":["000","005"],"department":[{"_id":"BeBi"}],"file_date_updated":"2018-12-12T10:12:01Z","scopus_import":"1","_id":"1099","status":"public"},{"publication_status":"published","title":"Rangefinder: A semisynthetic FRET sensor design algorithm","type":"journal_article","isi":1,"language":[{"iso":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2018-12-11T11:50:09Z","doi":"10.1021/acssensors.6b00576","acknowledgement":"J.A.M., J.H.W., and W.H.Z. were supported by Australian\r\nPostgraduate Awards (APA), AS Sargeson Supplementary\r\nscholarships, and RSC supplementary scholarships. C.J.J.\r\nacknowledges support from a Human Frontiers in Science\r\nYoung Investigator Award and a Discovery Project and Future\r\nFellowship from the Australian Research Council. M.L.O. is\r\nsupported by an Australian Research Council Discovery Project\r\n(DP130102153) and the Merit Allocation Scheme of the\r\nNational Computational Infrastructure.","year":"2016","publication":"ACS SENSORS","date_published":"2016-11-10T00:00:00Z","external_id":{"isi":["000388914800003"]},"abstract":[{"text":"Optical sensors based on the phenomenon of Förster resonance energy transfer (FRET) are powerful tools that have advanced the study of small molecules in biological systems. However, sensor construction is not trivial and often requires multiple rounds of engineering or an ability to screen large numbers of variants. A method that would allow the accurate rational design of FRET sensors would expedite the production of biologically useful sensors. Here, we present Rangefinder, a computational algorithm that allows rapid in silico screening of dye attachment sites in a ligand-binding protein for the conjugation of a dye molecule to act as a Förster acceptor for a fused fluorescent protein. We present three ratiometric fluorescent sensors designed with Rangefinder, including a maltose sensor with a dynamic range of &gt;300% and the first sensors for the most abundant sialic acid in human cells, N-acetylneuraminic acid. Provided a ligand-binding protein exists, it is our expectation that this model will facilitate the design of an optical sensor for any small molecule of interest.","lang":"eng"}],"oa_version":"None","issue":"11","author":[{"first_name":"Joshua","full_name":"Mitchell, Joshua","last_name":"Mitchell"},{"first_name":"Jason","last_name":"Whitfield","full_name":"Whitfield, Jason"},{"first_name":"William","full_name":"Zhang, William","last_name":"Zhang"},{"last_name":"Henneberger","full_name":"Henneberger, Christian","first_name":"Christian"},{"id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","first_name":"Harald L","last_name":"Janovjak","full_name":"Janovjak, Harald L","orcid":"0000-0002-8023-9315"},{"full_name":"O'Mara, Megan","last_name":"O'Mara","first_name":"Megan"},{"first_name":"Colin","full_name":"Jackson, Colin","last_name":"Jackson"}],"day":"10","status":"public","_id":"1101","scopus_import":"1","department":[{"_id":"HaJa"}],"publist_id":"6274","date_updated":"2025-09-22T14:14:58Z","month":"11","intvolume":"         1","publisher":"American Chemical Society","volume":1,"quality_controlled":"1","citation":{"ama":"Mitchell J, Whitfield J, Zhang W, et al. Rangefinder: A semisynthetic FRET sensor design algorithm. <i>ACS SENSORS</i>. 2016;1(11):1286-1290. doi:<a href=\"https://doi.org/10.1021/acssensors.6b00576\">10.1021/acssensors.6b00576</a>","chicago":"Mitchell, Joshua, Jason Whitfield, William Zhang, Christian Henneberger, Harald L Janovjak, Megan O’Mara, and Colin Jackson. “Rangefinder: A Semisynthetic FRET Sensor Design Algorithm.” <i>ACS SENSORS</i>. American Chemical Society, 2016. <a href=\"https://doi.org/10.1021/acssensors.6b00576\">https://doi.org/10.1021/acssensors.6b00576</a>.","ieee":"J. Mitchell <i>et al.</i>, “Rangefinder: A semisynthetic FRET sensor design algorithm,” <i>ACS SENSORS</i>, vol. 1, no. 11. American Chemical Society, pp. 1286–1290, 2016.","mla":"Mitchell, Joshua, et al. “Rangefinder: A Semisynthetic FRET Sensor Design Algorithm.” <i>ACS SENSORS</i>, vol. 1, no. 11, American Chemical Society, 2016, pp. 1286–90, doi:<a href=\"https://doi.org/10.1021/acssensors.6b00576\">10.1021/acssensors.6b00576</a>.","apa":"Mitchell, J., Whitfield, J., Zhang, W., Henneberger, C., Janovjak, H. L., O’Mara, M., &#38; Jackson, C. (2016). Rangefinder: A semisynthetic FRET sensor design algorithm. <i>ACS SENSORS</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acssensors.6b00576\">https://doi.org/10.1021/acssensors.6b00576</a>","ista":"Mitchell J, Whitfield J, Zhang W, Henneberger C, Janovjak HL, O’Mara M, Jackson C. 2016. Rangefinder: A semisynthetic FRET sensor design algorithm. ACS SENSORS. 1(11), 1286–1290.","short":"J. Mitchell, J. Whitfield, W. Zhang, C. Henneberger, H.L. Janovjak, M. O’Mara, C. Jackson, ACS SENSORS 1 (2016) 1286–1290."},"page":"1286 - 1290","article_processing_charge":"No"},{"author":[{"first_name":"Amit","full_name":"Gurung, Amit","last_name":"Gurung"},{"last_name":"Deka","full_name":"Deka, Arup","first_name":"Arup"},{"full_name":"Bartocci, Ezio","last_name":"Bartocci","first_name":"Ezio"},{"orcid":"0000-0002-0686-0365","last_name":"Bogomolov","full_name":"Bogomolov, Sergiy","id":"369D9A44-F248-11E8-B48F-1D18A9856A87","first_name":"Sergiy"},{"first_name":"Radu","last_name":"Grosu","full_name":"Grosu, Radu"},{"first_name":"Rajarshi","full_name":"Ray, Rajarshi","last_name":"Ray"}],"day":"27","oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1606.05473"}],"abstract":[{"lang":"eng","text":"We propose two parallel state-space-exploration algorithms for hybrid automaton (HA), with the goal of enhancing performance on multi-core shared-memory systems. The first uses the parallel, breadth-first-search algorithm (PBFS) of the SPIN model checker, when traversing the discrete modes of the HA, and enhances it with a parallel exploration of the continuous states within each mode. We show that this simple-minded extension of PBFS does not provide the desired load balancing in many HA benchmarks. The second algorithm is a task-parallel BFS algorithm (TP-BFS), which uses a cheap precomputation of the cost associated with the post operations (both continuous and discrete) in order to improve load balancing. We illustrate the TP-BFS and the cost precomputation of the post operators on a support-function-based algorithm for state-space exploration. The performance comparison of the two algorithms shows that, in general, TP-BFS provides a better utilization/load-balancing of the CPU. Both algorithms are implemented in the model checker XSpeed. Our experiments show a maximum speed-up of more than 2000 χ on a navigation benchmark, with respect to SpaceEx LGG scenario. In order to make the comparison fair, we employed an equal number of post operations in both tools. To the best of our knowledge, this paper represents the first attempt to provide parallel, reachability-analysis algorithms for HA."}],"date_published":"2016-12-27T00:00:00Z","external_id":{"arxiv":["1606.05473"]},"acknowledgement":"This work was supported in part by DST-SERB, GoI under Project No. YSS/2014/000623 and by the European Research Council (ERC) under grant 267989 (QUAREM) and by the Austrian Science Fund (FWF) under grants S11402-N23, S11405-N23 and S11412-N23 (RiSE/SHiNE) and Z211-N23 (Wittgenstein Award).","doi":"10.1109/MEMCOD.2016.7797741","year":"2016","article_number":"7797741","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","conference":{"location":"Kanpur, India ","start_date":"2016-11-18","name":"MEMOCODE: Conference on Formal Methods and Models for System Design","end_date":"2016-11-20"},"date_created":"2018-12-11T11:50:09Z","project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","grant_number":"267989","call_identifier":"FP7"},{"call_identifier":"FWF","grant_number":"Z211","name":"Formal methods for the design and analysis of complex systems","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"type":"conference","title":"Parallel reachability analysis for hybrid systems","language":[{"iso":"eng"}],"publication_status":"published","ec_funded":1,"article_processing_charge":"No","quality_controlled":"1","citation":{"ieee":"A. Gurung, A. Deka, E. Bartocci, S. Bogomolov, R. Grosu, and R. Ray, “Parallel reachability analysis for hybrid systems,” presented at the MEMOCODE: Conference on Formal Methods and Models for System Design, Kanpur, India , 2016.","ama":"Gurung A, Deka A, Bartocci E, Bogomolov S, Grosu R, Ray R. Parallel reachability analysis for hybrid systems. In: IEEE; 2016. doi:<a href=\"https://doi.org/10.1109/MEMCOD.2016.7797741\">10.1109/MEMCOD.2016.7797741</a>","chicago":"Gurung, Amit, Arup Deka, Ezio Bartocci, Sergiy Bogomolov, Radu Grosu, and Rajarshi Ray. “Parallel Reachability Analysis for Hybrid Systems.” IEEE, 2016. <a href=\"https://doi.org/10.1109/MEMCOD.2016.7797741\">https://doi.org/10.1109/MEMCOD.2016.7797741</a>.","ista":"Gurung A, Deka A, Bartocci E, Bogomolov S, Grosu R, Ray R. 2016. Parallel reachability analysis for hybrid systems. MEMOCODE: Conference on Formal Methods and Models for System Design, 7797741.","short":"A. Gurung, A. Deka, E. Bartocci, S. Bogomolov, R. Grosu, R. Ray, in:, IEEE, 2016.","apa":"Gurung, A., Deka, A., Bartocci, E., Bogomolov, S., Grosu, R., &#38; Ray, R. (2016). Parallel reachability analysis for hybrid systems. Presented at the MEMOCODE: Conference on Formal Methods and Models for System Design, Kanpur, India : IEEE. <a href=\"https://doi.org/10.1109/MEMCOD.2016.7797741\">https://doi.org/10.1109/MEMCOD.2016.7797741</a>","mla":"Gurung, Amit, et al. <i>Parallel Reachability Analysis for Hybrid Systems</i>. 7797741, IEEE, 2016, doi:<a href=\"https://doi.org/10.1109/MEMCOD.2016.7797741\">10.1109/MEMCOD.2016.7797741</a>."},"publisher":"IEEE","month":"12","date_updated":"2025-06-04T11:52:29Z","publist_id":"6272","oa":1,"scopus_import":"1","arxiv":1,"department":[{"_id":"ToHe"}],"status":"public","_id":"1103"},{"month":"12","publisher":"Neural Information Processing Systems Foundation","intvolume":"        29","citation":{"chicago":"Savin, Cristina, and Gašper Tkačik. “Estimating Nonlinear Neural Response Functions Using GP Priors and Kronecker Methods,” 29:3610–18. Neural Information Processing Systems Foundation, 2016.","ama":"Savin C, Tkačik G. Estimating nonlinear neural response functions using GP priors and Kronecker methods. In: Vol 29. Neural Information Processing Systems Foundation; 2016:3610-3618.","ieee":"C. Savin and G. Tkačik, “Estimating nonlinear neural response functions using GP priors and Kronecker methods,” presented at the NIPS: Neural Information Processing Systems, Barcelona; Spain, 2016, vol. 29, pp. 3610–3618.","mla":"Savin, Cristina, and Gašper Tkačik. <i>Estimating Nonlinear Neural Response Functions Using GP Priors and Kronecker Methods</i>. Vol. 29, Neural Information Processing Systems Foundation, 2016, pp. 3610–18.","apa":"Savin, C., &#38; Tkačik, G. (2016). Estimating nonlinear neural response functions using GP priors and Kronecker methods (Vol. 29, pp. 3610–3618). Presented at the NIPS: Neural Information Processing Systems, Barcelona; Spain: Neural Information Processing Systems Foundation.","short":"C. Savin, G. Tkačik, in:, Neural Information Processing Systems Foundation, 2016, pp. 3610–3618.","ista":"Savin C, Tkačik G. 2016. Estimating nonlinear neural response functions using GP priors and Kronecker methods. NIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 29, 3610–3618."},"quality_controlled":"1","volume":29,"ec_funded":1,"article_processing_charge":"No","page":"3610-3618","_id":"1105","corr_author":"1","status":"public","department":[{"_id":"GaTk"}],"scopus_import":"1","oa":1,"publist_id":"6265","date_updated":"2025-06-03T11:36:49Z","date_published":"2016-12-01T00:00:00Z","abstract":[{"text":"Jointly characterizing neural responses in terms of several external variables promises novel insights into circuit function, but remains computationally prohibitive in practice. Here we use gaussian process (GP) priors and exploit recent advances in fast GP inference and learning based on Kronecker methods, to efficiently estimate multidimensional nonlinear tuning functions. Our estimator require considerably less data than traditional methods and further provides principled uncertainty estimates. We apply these tools to hippocampal recordings during open field exploration and use them to characterize the joint dependence of CA1 responses on the position of the animal and several other variables, including the animal\\'s speed, direction of motion, and network oscillations.Our results provide an unprecedentedly detailed quantification of the tuning of hippocampal neurons. The model\\'s generality suggests that our approach can be used to estimate neural response properties in other brain regions.","lang":"eng"}],"main_file_link":[{"url":"http://papers.nips.cc/paper/6153-estimating-nonlinear-neural-response-functions-using-gp-priors-and-kronecker-methods","open_access":"1"}],"oa_version":"None","day":"01","author":[{"last_name":"Savin","full_name":"Savin, Cristina","id":"3933349E-F248-11E8-B48F-1D18A9856A87","first_name":"Cristina"},{"orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper","last_name":"Tkacik","first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","language":[{"iso":"eng"}],"project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"type":"conference","title":"Estimating nonlinear neural response functions using GP priors and Kronecker methods","date_created":"2018-12-11T11:50:10Z","alternative_title":["Advances in Neural Information Processing Systems"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","conference":{"start_date":"2016-12-05","name":"NIPS: Neural Information Processing Systems","location":"Barcelona; Spain","end_date":"2016-12-10"},"year":"2016","acknowledgement":"We  thank  Jozsef  Csicsvari  for  kindly  sharing  the  CA1  data.\r\nThis work was supported by the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme(FP7/2007-2013) under REA grant agreement no. 291734."}]