[{"title":"Modular parameter identification of biomolecular networks","status":"public","author":[{"last_name":"Lang","first_name":"Moritz","id":"29E0800A-F248-11E8-B48F-1D18A9856A87","full_name":"Lang, Moritz"},{"last_name":"Stelling","first_name":"Jörg","full_name":"Stelling, Jörg"}],"issue":"6","quality_controlled":"1","page":"B988 - B1008","publisher":"Society for Industrial and Applied Mathematics ","publication":"SIAM Journal on Scientific Computing","intvolume":"        38","has_accepted_license":"1","volume":38,"date_published":"2016-11-15T00:00:00Z","date_created":"2018-12-11T11:50:31Z","month":"11","day":"15","citation":{"ieee":"M. Lang and J. Stelling, “Modular parameter identification of biomolecular networks,” <i>SIAM Journal on Scientific Computing</i>, vol. 38, no. 6. Society for Industrial and Applied Mathematics , pp. B988–B1008, 2016.","apa":"Lang, M., &#38; Stelling, J. (2016). Modular parameter identification of biomolecular networks. <i>SIAM Journal on Scientific Computing</i>. Society for Industrial and Applied Mathematics . <a href=\"https://doi.org/10.1137/15M103306X\">https://doi.org/10.1137/15M103306X</a>","short":"M. Lang, J. Stelling, SIAM Journal on Scientific Computing 38 (2016) B988–B1008.","mla":"Lang, Moritz, and Jörg Stelling. “Modular Parameter Identification of Biomolecular Networks.” <i>SIAM Journal on Scientific Computing</i>, vol. 38, no. 6, Society for Industrial and Applied Mathematics , 2016, pp. B988–1008, doi:<a href=\"https://doi.org/10.1137/15M103306X\">10.1137/15M103306X</a>.","ama":"Lang M, Stelling J. Modular parameter identification of biomolecular networks. <i>SIAM Journal on Scientific Computing</i>. 2016;38(6):B988-B1008. doi:<a href=\"https://doi.org/10.1137/15M103306X\">10.1137/15M103306X</a>","ista":"Lang M, Stelling J. 2016. Modular parameter identification of biomolecular networks. SIAM Journal on Scientific Computing. 38(6), B988–B1008.","chicago":"Lang, Moritz, and Jörg Stelling. “Modular Parameter Identification of Biomolecular Networks.” <i>SIAM Journal on Scientific Computing</i>. Society for Industrial and Applied Mathematics , 2016. <a href=\"https://doi.org/10.1137/15M103306X\">https://doi.org/10.1137/15M103306X</a>."},"file":[{"date_created":"2018-12-12T10:14:41Z","creator":"system","file_id":"5095","relation":"main_file","file_size":871964,"access_level":"local","content_type":"application/pdf","file_name":"IST-2017-811-v1+1_modular_parameter_identification.pdf","date_updated":"2020-07-14T12:44:37Z","checksum":"781bc3ffd30b2dd65b7727c5a285fc78"}],"date_updated":"2021-01-12T06:48:49Z","abstract":[{"lang":"eng","text":"The increasing complexity of dynamic models in systems and synthetic biology poses computational challenges especially for the identification of model parameters. While modularization of the corresponding optimization problems could help reduce the “curse of dimensionality,” abundant feedback and crosstalk mechanisms prohibit a simple decomposition of most biomolecular networks into subnetworks, or modules. Drawing on ideas from network modularization and multiple-shooting optimization, we present here a modular parameter identification approach that explicitly allows for such interdependencies. Interfaces between our modules are given by the experimentally measured molecular species. This definition allows deriving good (initial) estimates for the inter-module communication directly from the experimental data. Given these estimates, the states and parameter sensitivities of different modules can be integrated independently. To achieve consistency between modules, we iteratively adjust the estimates for inter-module communication while optimizing the parameters. After convergence to an optimal parameter set---but not during earlier iterations---the intermodule communication as well as the individual modules\\' state dynamics agree with the dynamics of the nonmodularized network. Our modular parameter identification approach allows for easy parallelization; it can reduce the computational complexity for larger networks and decrease the probability to converge to suboptimal local minima. We demonstrate the algorithm\\'s performance in parameter estimation for two biomolecular networks, a synthetic genetic oscillator and a mammalian signaling pathway."}],"file_date_updated":"2020-07-14T12:44:37Z","_id":"1170","language":[{"iso":"eng"}],"ddc":["003","518","570","621"],"publication_status":"published","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"publist_id":"6186","doi":"10.1137/15M103306X","oa_version":"Submitted Version","type":"journal_article","year":"2016","scopus_import":1,"pubrep_id":"811"},{"citation":{"ieee":"G. Tkačik, “Understanding regulatory networks requires more than computing a multitude of graph statistics: Comment on &#38;quot;Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function&#38;quot; by O. C. Martin et al.,” <i>Physics of Life Reviews</i>, vol. 17. Elsevier, pp. 166–167, 2016.","short":"G. Tkačik, Physics of Life Reviews 17 (2016) 166–167.","apa":"Tkačik, G. (2016). Understanding regulatory networks requires more than computing a multitude of graph statistics: Comment on &#38;quot;Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function&#38;quot; by O. C. Martin et al. <i>Physics of Life Reviews</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.plrev.2016.06.005\">https://doi.org/10.1016/j.plrev.2016.06.005</a>","chicago":"Tkačik, Gašper. “Understanding Regulatory Networks Requires More than Computing a Multitude of Graph Statistics: Comment on &#38;quot;Drivers of Structural Features in Gene Regulatory Networks: From Biophysical Constraints to Biological Function&#38;quot; by O. C. Martin et Al.” <i>Physics of Life Reviews</i>. Elsevier, 2016. <a href=\"https://doi.org/10.1016/j.plrev.2016.06.005\">https://doi.org/10.1016/j.plrev.2016.06.005</a>.","mla":"Tkačik, Gašper. “Understanding Regulatory Networks Requires More than Computing a Multitude of Graph Statistics: Comment on &#38;quot;Drivers of Structural Features in Gene Regulatory Networks: From Biophysical Constraints to Biological Function&#38;quot; by O. C. Martin et Al.” <i>Physics of Life Reviews</i>, vol. 17, Elsevier, 2016, pp. 166–67, doi:<a href=\"https://doi.org/10.1016/j.plrev.2016.06.005\">10.1016/j.plrev.2016.06.005</a>.","ista":"Tkačik G. 2016. Understanding regulatory networks requires more than computing a multitude of graph statistics: Comment on &#38;quot;Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function&#38;quot; by O. C. Martin et al. Physics of Life Reviews. 17, 166–167.","ama":"Tkačik G. Understanding regulatory networks requires more than computing a multitude of graph statistics: Comment on &#38;quot;Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function&#38;quot; by O. C. Martin et al. <i>Physics of Life Reviews</i>. 2016;17:166-167. doi:<a href=\"https://doi.org/10.1016/j.plrev.2016.06.005\">10.1016/j.plrev.2016.06.005</a>"},"day":"01","date_updated":"2021-01-12T06:48:50Z","scopus_import":1,"year":"2016","type":"journal_article","oa_version":"None","date_published":"2016-07-01T00:00:00Z","date_created":"2018-12-11T11:50:32Z","month":"07","volume":17,"doi":"10.1016/j.plrev.2016.06.005","publist_id":"6185","publisher":"Elsevier","page":"166 - 167","quality_controlled":"1","intvolume":"        17","department":[{"_id":"GaTk"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publication":"Physics of Life Reviews","publication_status":"published","_id":"1171","language":[{"iso":"eng"}],"author":[{"first_name":"Gasper","last_name":"Tkacik","orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"title":"Understanding regulatory networks requires more than computing a multitude of graph statistics: Comment on &quot;Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function&quot; by O. C. Martin et al.","status":"public"},{"file_date_updated":"2020-07-14T12:44:37Z","acknowledgement":"H.S. thanks NCBS for hospitality. We thank Vivek Malhotra and Mukund Thattai for critical discussions and suggestions.","abstract":[{"text":"A central issue in cell biology is the physico-chemical basis of organelle biogenesis in intracellular trafficking pathways, its most impressive manifestation being the biogenesis of Golgi cisternae. At a basic level, such morphologically and chemically distinct compartments should arise from an interplay between the molecular transport and chemical maturation. Here, we formulate analytically tractable, minimalist models, that incorporate this interplay between transport and chemical progression in physical space, and explore the conditions for de novo biogenesis of distinct cisternae. We propose new quantitative measures that can discriminate between the various models of transport in a qualitative manner-this includes measures of the dynamics in steady state and the dynamical response to perturbations of the kind amenable to live-cell imaging.","lang":"eng"}],"department":[{"_id":"NiBa"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","ddc":["576"],"publication_status":"published","language":[{"iso":"eng"}],"_id":"1172","oa_version":"Published Version","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1038/srep38840","publist_id":"6183","pubrep_id":"737","scopus_import":1,"year":"2016","type":"journal_article","oa":1,"author":[{"first_name":"Himani","last_name":"Sachdeva","full_name":"Sachdeva, Himani","id":"42377A0A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Barma, Mustansir","first_name":"Mustansir","last_name":"Barma"},{"full_name":"Rao, Madan","first_name":"Madan","last_name":"Rao"}],"article_number":"38840","title":"Nonequilibrium description of de novo biogenesis and transport through Golgi-like cisternae","status":"public","publisher":"Nature Publishing Group","quality_controlled":"1","intvolume":"         6","publication":"Scientific Reports","date_published":"2016-12-19T00:00:00Z","date_created":"2018-12-11T11:50:32Z","month":"12","has_accepted_license":"1","volume":6,"file":[{"checksum":"cb378732da885ea4959ec5b845fb6e52","date_updated":"2020-07-14T12:44:37Z","file_name":"IST-2017-737-v1+1_srep38840.pdf","content_type":"application/pdf","access_level":"open_access","file_size":760967,"file_id":"4977","creator":"system","relation":"main_file","date_created":"2018-12-12T10:12:56Z"}],"citation":{"apa":"Sachdeva, H., Barma, M., &#38; Rao, M. (2016). Nonequilibrium description of de novo biogenesis and transport through Golgi-like cisternae. <i>Scientific Reports</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/srep38840\">https://doi.org/10.1038/srep38840</a>","short":"H. Sachdeva, M. Barma, M. Rao, Scientific Reports 6 (2016).","ieee":"H. Sachdeva, M. Barma, and M. Rao, “Nonequilibrium description of de novo biogenesis and transport through Golgi-like cisternae,” <i>Scientific Reports</i>, vol. 6. Nature Publishing Group, 2016.","chicago":"Sachdeva, Himani, Mustansir Barma, and Madan Rao. “Nonequilibrium Description of de Novo Biogenesis and Transport through Golgi-like Cisternae.” <i>Scientific Reports</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/srep38840\">https://doi.org/10.1038/srep38840</a>.","ista":"Sachdeva H, Barma M, Rao M. 2016. Nonequilibrium description of de novo biogenesis and transport through Golgi-like cisternae. Scientific Reports. 6, 38840.","ama":"Sachdeva H, Barma M, Rao M. Nonequilibrium description of de novo biogenesis and transport through Golgi-like cisternae. <i>Scientific Reports</i>. 2016;6. doi:<a href=\"https://doi.org/10.1038/srep38840\">10.1038/srep38840</a>","mla":"Sachdeva, Himani, et al. “Nonequilibrium Description of de Novo Biogenesis and Transport through Golgi-like Cisternae.” <i>Scientific Reports</i>, vol. 6, 38840, Nature Publishing Group, 2016, doi:<a href=\"https://doi.org/10.1038/srep38840\">10.1038/srep38840</a>."},"day":"19","date_updated":"2021-01-12T06:48:50Z"},{"status":"public","abstract":[{"lang":"eng","text":"Boldyreva, Palacio and Warinschi introduced a multiple forking game as an extension of general forking. The notion of (multiple) forking is a useful abstraction from the actual simulation of cryptographic scheme to the adversary in a security reduction, and is achieved through the intermediary of a so-called wrapper algorithm. Multiple forking has turned out to be a useful tool in the security argument of several cryptographic protocols. However, a reduction employing multiple forking incurs a significant degradation of (Formula presented.) , where (Formula presented.) denotes the upper bound on the underlying random oracle calls and (Formula presented.) , the number of forkings. In this work we take a closer look at the reasons for the degradation with a tighter security bound in mind. We nail down the exact set of conditions for success in the multiple forking game. A careful analysis of the cryptographic schemes and corresponding security reduction employing multiple forking leads to the formulation of ‘dependence’ and ‘independence’ conditions pertaining to the output of the wrapper in different rounds. Based on the (in)dependence conditions we propose a general framework of multiple forking and a General Multiple Forking Lemma. Leveraging (in)dependence to the full allows us to improve the degradation factor in the multiple forking game by a factor of (Formula presented.). By implication, the cost of a single forking involving two random oracles (augmented forking) matches that involving a single random oracle (elementary forking). Finally, we study the effect of these observations on the concrete security of existing schemes employing multiple forking. We conclude that by careful design of the protocol (and the wrapper in the security reduction) it is possible to harness our observations to the full extent."}],"title":"A closer look at multiple-forking: Leveraging (in)dependence for a tighter bound","acknowledgement":"We are grateful to the anonymous reviewers for their insightful comments. The\r\ndetailed reports helped us a lot to address the technical mistakes as well as to improve the overall presentation of the paper.","author":[{"first_name":"Chethan","last_name":"Kamath Hosdurg","id":"4BD3F30E-F248-11E8-B48F-1D18A9856A87","full_name":"Kamath Hosdurg, Chethan"},{"full_name":"Chatterjee, Sanjit","last_name":"Chatterjee","first_name":"Sanjit"}],"oa":1,"_id":"1177","language":[{"iso":"eng"}],"publication_status":"published","issue":"4","publication":"Algorithmica","intvolume":"        74","department":[{"_id":"KrPi"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"http://eprint.iacr.org/2013/651"}],"page":"1321 - 1362","publisher":"Springer","publist_id":"6177","doi":"10.1007/s00453-015-9997-6","volume":74,"month":"04","date_created":"2018-12-11T11:50:33Z","date_published":"2016-04-01T00:00:00Z","oa_version":"Submitted Version","type":"journal_article","year":"2016","date_updated":"2021-01-12T06:48:52Z","day":"01","citation":{"short":"C. Kamath Hosdurg, S. Chatterjee, Algorithmica 74 (2016) 1321–1362.","apa":"Kamath Hosdurg, C., &#38; Chatterjee, S. (2016). A closer look at multiple-forking: Leveraging (in)dependence for a tighter bound. <i>Algorithmica</i>. Springer. <a href=\"https://doi.org/10.1007/s00453-015-9997-6\">https://doi.org/10.1007/s00453-015-9997-6</a>","ieee":"C. Kamath Hosdurg and S. Chatterjee, “A closer look at multiple-forking: Leveraging (in)dependence for a tighter bound,” <i>Algorithmica</i>, vol. 74, no. 4. Springer, pp. 1321–1362, 2016.","ama":"Kamath Hosdurg C, Chatterjee S. A closer look at multiple-forking: Leveraging (in)dependence for a tighter bound. <i>Algorithmica</i>. 2016;74(4):1321-1362. doi:<a href=\"https://doi.org/10.1007/s00453-015-9997-6\">10.1007/s00453-015-9997-6</a>","ista":"Kamath Hosdurg C, Chatterjee S. 2016. A closer look at multiple-forking: Leveraging (in)dependence for a tighter bound. Algorithmica. 74(4), 1321–1362.","mla":"Kamath Hosdurg, Chethan, and Sanjit Chatterjee. “A Closer Look at Multiple-Forking: Leveraging (in)Dependence for a Tighter Bound.” <i>Algorithmica</i>, vol. 74, no. 4, Springer, 2016, pp. 1321–62, doi:<a href=\"https://doi.org/10.1007/s00453-015-9997-6\">10.1007/s00453-015-9997-6</a>.","chicago":"Kamath Hosdurg, Chethan, and Sanjit Chatterjee. “A Closer Look at Multiple-Forking: Leveraging (in)Dependence for a Tighter Bound.” <i>Algorithmica</i>. Springer, 2016. <a href=\"https://doi.org/10.1007/s00453-015-9997-6\">https://doi.org/10.1007/s00453-015-9997-6</a>."}},{"scopus_import":1,"type":"conference","year":"2016","publist_id":"6175","doi":"10.1007/978-3-662-53641-4_8","oa_version":"Preprint","publication_status":"published","language":[{"iso":"eng"}],"_id":"1179","department":[{"_id":"KrPi"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","project":[{"name":"Teaching Old Crypto New Tricks","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"682815"}],"ec_funded":1,"abstract":[{"text":"Computational notions of entropy have recently found many applications, including leakage-resilient cryptography, deterministic encryption or memory delegation. The two main types of results which make computational notions so useful are (1) Chain rules, which quantify by how much the computational entropy of a variable decreases if conditioned on some other variable (2) Transformations, which quantify to which extend one type of entropy implies another.\r\n\r\nSuch chain rules and transformations typically lose a significant amount in quality of the entropy, and are the reason why applying these results one gets rather weak quantitative security bounds. In this paper we for the first time prove lower bounds in this context, showing that existing results for transformations are, unfortunately, basically optimal for non-adaptive black-box reductions (and it’s hard to imagine how non black-box reductions or adaptivity could be useful here.)\r\n\r\nA variable X has k bits of HILL entropy of quality (ϵ,s)\r\nif there exists a variable Y with k bits min-entropy which cannot be distinguished from X with advantage ϵ\r\n\r\nby distinguishing circuits of size s. A weaker notion is Metric entropy, where we switch quantifiers, and only require that for every distinguisher of size s, such a Y exists.\r\n\r\nWe first describe our result concerning transformations. By definition, HILL implies Metric without any loss in quality. Metric entropy often comes up in applications, but must be transformed to HILL for meaningful security guarantees. The best known result states that if a variable X has k bits of Metric entropy of quality (ϵ,s)\r\n, then it has k bits of HILL with quality (2ϵ,s⋅ϵ2). We show that this loss of a factor Ω(ϵ−2)\r\n\r\nin circuit size is necessary. In fact, we show the stronger result that this loss is already necessary when transforming so called deterministic real valued Metric entropy to randomised boolean Metric (both these variants of Metric entropy are implied by HILL without loss in quality).\r\n\r\nThe chain rule for HILL entropy states that if X has k bits of HILL entropy of quality (ϵ,s)\r\n, then for any variable Z of length m, X conditioned on Z has k−m bits of HILL entropy with quality (ϵ,s⋅ϵ2/2m). We show that a loss of Ω(2m/ϵ) in circuit size necessary here. Note that this still leaves a gap of ϵ between the known bound and our lower bound.","lang":"eng"}],"acknowledgement":"K. Pietrzak—Supported by the European Research Council consolidator grant (682815-TOCNeT).\r\nM. Skórski—Supported by the National Science Center, Poland (2015/17/N/ST6/03564).","alternative_title":["LNCS"],"conference":{"start_date":"2016-10-31","location":"Beijing, China","end_date":"2016-11-03","name":"TCC: Theory of Cryptography Conference"},"date_updated":"2021-01-12T06:48:53Z","day":"22","citation":{"apa":"Pietrzak, K. Z., &#38; Maciej, S. (2016). Pseudoentropy: Lower-bounds for chain rules and transformations (Vol. 9985, pp. 183–203). Presented at the TCC: Theory of Cryptography Conference, Beijing, China: Springer. <a href=\"https://doi.org/10.1007/978-3-662-53641-4_8\">https://doi.org/10.1007/978-3-662-53641-4_8</a>","short":"K.Z. Pietrzak, S. Maciej, in:, Springer, 2016, pp. 183–203.","ieee":"K. Z. Pietrzak and S. Maciej, “Pseudoentropy: Lower-bounds for chain rules and transformations,” presented at the TCC: Theory of Cryptography Conference, Beijing, China, 2016, vol. 9985, pp. 183–203.","chicago":"Pietrzak, Krzysztof Z, and Skorski Maciej. “Pseudoentropy: Lower-Bounds for Chain Rules and Transformations,” 9985:183–203. Springer, 2016. <a href=\"https://doi.org/10.1007/978-3-662-53641-4_8\">https://doi.org/10.1007/978-3-662-53641-4_8</a>.","ista":"Pietrzak KZ, Maciej S. 2016. Pseudoentropy: Lower-bounds for chain rules and transformations. TCC: Theory of Cryptography Conference, LNCS, vol. 9985, 183–203.","ama":"Pietrzak KZ, Maciej S. Pseudoentropy: Lower-bounds for chain rules and transformations. In: Vol 9985. Springer; 2016:183-203. doi:<a href=\"https://doi.org/10.1007/978-3-662-53641-4_8\">10.1007/978-3-662-53641-4_8</a>","mla":"Pietrzak, Krzysztof Z., and Skorski Maciej. <i>Pseudoentropy: Lower-Bounds for Chain Rules and Transformations</i>. Vol. 9985, Springer, 2016, pp. 183–203, doi:<a href=\"https://doi.org/10.1007/978-3-662-53641-4_8\">10.1007/978-3-662-53641-4_8</a>."},"volume":9985,"month":"10","date_created":"2018-12-11T11:50:34Z","date_published":"2016-10-22T00:00:00Z","intvolume":"      9985","publisher":"Springer","quality_controlled":"1","main_file_link":[{"url":"https://eprint.iacr.org/2016/159","open_access":"1"}],"page":"183 - 203","status":"public","title":"Pseudoentropy: Lower-bounds for chain rules and transformations","author":[{"orcid":"0000-0002-9139-1654","last_name":"Pietrzak","first_name":"Krzysztof Z","full_name":"Pietrzak, Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Maciej, Skorski","last_name":"Maciej","first_name":"Skorski"}],"oa":1},{"article_processing_charge":"No","file_date_updated":"2020-07-14T12:48:09Z","publication_identifier":{"isbn":["9780262339360"]},"ec_funded":1,"abstract":[{"text":"With the accelerated development of robot technologies, optimal control becomes one of the central themes of research. In traditional approaches, the controller, by its internal functionality, finds appropriate actions on the basis of the history of sensor values, guided by the goals, intentions, objectives, learning schemes, and so forth. The idea is that the controller controls the world---the body plus its environment---as reliably as possible. This paper focuses on new lines of self-organization for developmental robotics. We apply the recently developed differential extrinsic synaptic plasticity to a muscle-tendon driven arm-shoulder system from the Myorobotics toolkit. In the experiments, we observe a vast variety of self-organized behavior patterns: when left alone, the arm realizes pseudo-random sequences of different poses. By applying physical forces, the system can be entrained into definite motion patterns like wiping a table. Most interestingly, after attaching an object, the controller gets in a functional resonance with the object's internal dynamics, starting to shake spontaneously bottles half-filled with water or sensitively driving an attached pendulum into a circular mode. When attached to the crank of a wheel the neural system independently discovers how to rotate it. In this way, the robot discovers affordances of objects its body is interacting with.","lang":"eng"}],"user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","department":[{"_id":"ChLa"},{"_id":"GaTk"}],"project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"language":[{"iso":"eng"}],"_id":"8094","publication_status":"published","ddc":["610"],"oa_version":"Published Version","doi":"10.7551/978-0-262-33936-0-ch029","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"type":"conference","year":"2016","scopus_import":1,"author":[{"id":"3A276B68-F248-11E8-B48F-1D18A9856A87","full_name":"Martius, Georg S","last_name":"Martius","first_name":"Georg S"},{"full_name":"Hostettler, Rafael","last_name":"Hostettler","first_name":"Rafael"},{"last_name":"Knoll","first_name":"Alois","full_name":"Knoll, Alois"},{"last_name":"Der","first_name":"Ralf","full_name":"Der, Ralf"}],"oa":1,"status":"public","title":"Self-organized control of an tendon driven arm by differential extrinsic plasticity","publication":"Proceedings of the Artificial Life Conference 2016","intvolume":"        28","quality_controlled":"1","page":"142-143","publisher":"MIT Press","month":"09","date_created":"2020-07-05T22:00:47Z","date_published":"2016-09-01T00:00:00Z","volume":28,"has_accepted_license":"1","date_updated":"2021-01-12T08:16:53Z","citation":{"short":"G.S. Martius, R. Hostettler, A. Knoll, R. Der, in:, Proceedings of the Artificial Life Conference 2016, MIT Press, 2016, pp. 142–143.","apa":"Martius, G. S., Hostettler, R., Knoll, A., &#38; Der, R. (2016). Self-organized control of an tendon driven arm by differential extrinsic plasticity. In <i>Proceedings of the Artificial Life Conference 2016</i> (Vol. 28, pp. 142–143). Cancun, Mexico: MIT Press. <a href=\"https://doi.org/10.7551/978-0-262-33936-0-ch029\">https://doi.org/10.7551/978-0-262-33936-0-ch029</a>","ieee":"G. S. Martius, R. Hostettler, A. Knoll, and R. Der, “Self-organized control of an tendon driven arm by differential extrinsic plasticity,” in <i>Proceedings of the Artificial Life Conference 2016</i>, Cancun, Mexico, 2016, vol. 28, pp. 142–143.","chicago":"Martius, Georg S, Rafael Hostettler, Alois Knoll, and Ralf Der. “Self-Organized Control of an Tendon Driven Arm by Differential Extrinsic Plasticity.” In <i>Proceedings of the Artificial Life Conference 2016</i>, 28:142–43. MIT Press, 2016. <a href=\"https://doi.org/10.7551/978-0-262-33936-0-ch029\">https://doi.org/10.7551/978-0-262-33936-0-ch029</a>.","ista":"Martius GS, Hostettler R, Knoll A, Der R. 2016. Self-organized control of an tendon driven arm by differential extrinsic plasticity. Proceedings of the Artificial Life Conference 2016. ALIFE 2016: 15th International Conference on the Synthesis and Simulation of Living Systems vol. 28, 142–143.","ama":"Martius GS, Hostettler R, Knoll A, Der R. Self-organized control of an tendon driven arm by differential extrinsic plasticity. In: <i>Proceedings of the Artificial Life Conference 2016</i>. Vol 28. MIT Press; 2016:142-143. doi:<a href=\"https://doi.org/10.7551/978-0-262-33936-0-ch029\">10.7551/978-0-262-33936-0-ch029</a>","mla":"Martius, Georg S., et al. “Self-Organized Control of an Tendon Driven Arm by Differential Extrinsic Plasticity.” <i>Proceedings of the Artificial Life Conference 2016</i>, vol. 28, MIT Press, 2016, pp. 142–43, doi:<a href=\"https://doi.org/10.7551/978-0-262-33936-0-ch029\">10.7551/978-0-262-33936-0-ch029</a>."},"day":"01","file":[{"file_name":"2016_ProcALIFE_Martius.pdf","date_updated":"2020-07-14T12:48:09Z","checksum":"cff63e7a4b8ac466ba51a9c84153a940","date_created":"2020-07-06T12:59:09Z","relation":"main_file","creator":"cziletti","file_id":"8096","file_size":678670,"access_level":"open_access","content_type":"application/pdf"}],"conference":{"name":"ALIFE 2016: 15th International Conference on the Synthesis and Simulation of Living Systems","start_date":"2016-07-04","location":"Cancun, Mexico","end_date":"2016-07-08"}},{"pubrep_id":"469","year":"2016","type":"journal_article","scopus_import":"1","oa_version":"Published Version","publist_id":"5550","doi":"10.1002/hipo.22550","tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"PeJo"}],"language":[{"iso":"eng"}],"_id":"1616","publication_status":"published","ddc":["570"],"article_processing_charge":"No","acknowledgement":"The authors thank Jose Guzman for critically reading prior versions of the manuscript. They also thank T. Asenov for\r\nengineering mechanical devices, A. Schlögl for efficient pro-gramming, F. Marr for technical assistance, and E. Kramberger for manuscript editing.","file_date_updated":"2020-07-14T12:45:07Z","publication_identifier":{"eissn":["1098-1063"],"issn":["1050-9631"]},"abstract":[{"lang":"eng","text":"The hippocampus plays a key role in learning and memory. Previous studies suggested that the main types of principal neurons, dentate gyrus granule cells (GCs), CA3 pyramidal neurons, and CA1 pyramidal neurons, differ in their activity pattern, with sparse firing in GCs and more frequent firing in CA3 and CA1 pyramidal neurons. It has been assumed but never shown that such different activity may be caused by differential synaptic excitation. To test this hypothesis, we performed high-resolution whole-cell patch-clamp recordings in anesthetized rats in vivo. In contrast to previous in vitro data, both CA3 and CA1 pyramidal neurons fired action potentials spontaneously, with a frequency of ∼3–6 Hz, whereas GCs were silent. Furthermore, both CA3 and CA1 cells primarily fired in bursts. To determine the underlying mechanisms, we quantitatively assessed the frequency of spontaneous excitatory synaptic input, the passive membrane properties, and the active membrane characteristics. Surprisingly, GCs showed comparable synaptic excitation to CA3 and CA1 cells and the highest ratio of excitation versus hyperpolarizing inhibition. Thus, differential synaptic excitation is not responsible for differences in firing. Moreover, the three types of hippocampal neurons markedly differed in their passive properties. While GCs showed the most negative membrane potential, CA3 pyramidal neurons had the highest input resistance and the slowest membrane time constant. The three types of neurons also differed in the active membrane characteristics. GCs showed the highest action potential threshold, but displayed the largest gain of the input-output curves. In conclusion, our results reveal that differential firing of the three main types of hippocampal principal neurons in vivo is not primarily caused by differences in the characteristics of the synaptic input, but by the distinct properties of synaptic integration and input-output transformation."}],"date_updated":"2023-10-17T10:02:02Z","citation":{"chicago":"Kowalski, Janina, Jian Gan, Peter M Jonas, and Alejandro Pernia-Andrade. “Intrinsic Membrane Properties Determine Hippocampal Differential Firing Pattern in Vivo in Anesthetized Rats.” <i>Hippocampus</i>. Wiley, 2016. <a href=\"https://doi.org/10.1002/hipo.22550\">https://doi.org/10.1002/hipo.22550</a>.","mla":"Kowalski, Janina, et al. “Intrinsic Membrane Properties Determine Hippocampal Differential Firing Pattern in Vivo in Anesthetized Rats.” <i>Hippocampus</i>, vol. 26, no. 5, Wiley, 2016, pp. 668–82, doi:<a href=\"https://doi.org/10.1002/hipo.22550\">10.1002/hipo.22550</a>.","ista":"Kowalski J, Gan J, Jonas PM, Pernia-Andrade A. 2016. Intrinsic membrane properties determine hippocampal differential firing pattern in vivo in anesthetized rats. Hippocampus. 26(5), 668–682.","ama":"Kowalski J, Gan J, Jonas PM, Pernia-Andrade A. Intrinsic membrane properties determine hippocampal differential firing pattern in vivo in anesthetized rats. <i>Hippocampus</i>. 2016;26(5):668-682. doi:<a href=\"https://doi.org/10.1002/hipo.22550\">10.1002/hipo.22550</a>","ieee":"J. Kowalski, J. Gan, P. M. Jonas, and A. Pernia-Andrade, “Intrinsic membrane properties determine hippocampal differential firing pattern in vivo in anesthetized rats,” <i>Hippocampus</i>, vol. 26, no. 5. Wiley, pp. 668–682, 2016.","apa":"Kowalski, J., Gan, J., Jonas, P. M., &#38; Pernia-Andrade, A. (2016). Intrinsic membrane properties determine hippocampal differential firing pattern in vivo in anesthetized rats. <i>Hippocampus</i>. Wiley. <a href=\"https://doi.org/10.1002/hipo.22550\">https://doi.org/10.1002/hipo.22550</a>","short":"J. Kowalski, J. Gan, P.M. Jonas, A. Pernia-Andrade, Hippocampus 26 (2016) 668–682."},"day":"01","file":[{"file_size":905348,"relation":"main_file","creator":"system","file_id":"5033","date_created":"2018-12-12T10:13:47Z","content_type":"application/pdf","access_level":"open_access","date_updated":"2020-07-14T12:45:07Z","file_name":"IST-2016-469-v1+1_Kowalski_et_al-Hippocampus.pdf","checksum":"284b72b12fbe15474833ed3d4549f86b"}],"month":"05","date_published":"2016-05-01T00:00:00Z","date_created":"2018-12-11T11:53:03Z","volume":26,"has_accepted_license":"1","publication":"Hippocampus","intvolume":"        26","quality_controlled":"1","page":"668 - 682","publisher":"Wiley","issue":"5","author":[{"first_name":"Janina","last_name":"Kowalski","id":"3F3CA136-F248-11E8-B48F-1D18A9856A87","full_name":"Kowalski, Janina"},{"last_name":"Gan","first_name":"Jian","id":"3614E438-F248-11E8-B48F-1D18A9856A87","full_name":"Gan, Jian"},{"full_name":"Jonas, Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804","last_name":"Jonas","first_name":"Peter M"},{"last_name":"Pernia-Andrade","first_name":"Alejandro","full_name":"Pernia-Andrade, Alejandro","id":"36963E98-F248-11E8-B48F-1D18A9856A87"}],"oa":1,"status":"public","title":"Intrinsic membrane properties determine hippocampal differential firing pattern in vivo in anesthetized rats"},{"department":[{"_id":"HeEd"}],"intvolume":"        33","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publication":"Journal of Complexity","publisher":"Academic Press","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1510.00251"}],"page":"199 - 216","quality_controlled":"1","publication_status":"published","_id":"1617","language":[{"iso":"eng"}],"author":[{"full_name":"Pausinger, Florian","id":"2A77D7A2-F248-11E8-B48F-1D18A9856A87","first_name":"Florian","last_name":"Pausinger","orcid":"0000-0002-8379-3768"},{"full_name":"Steinerberger, Stefan","first_name":"Stefan","last_name":"Steinerberger"}],"acknowledgement":"We are grateful to the referee whose suggestions greatly improved the quality and clarity of the exposition.","oa":1,"status":"public","title":"On the discrepancy of jittered sampling","abstract":[{"lang":"eng","text":"We study the discrepancy of jittered sampling sets: such a set P⊂ [0,1]d is generated for fixed m∈ℕ by partitioning [0,1]d into md axis aligned cubes of equal measure and placing a random point inside each of the N=md cubes. We prove that, for N sufficiently large, 1/10 d/N1/2+1/2d ≤EDN∗(P)≤ √d(log N) 1/2/N1/2+1/2d, where the upper bound with an unspecified constant Cd was proven earlier by Beck. Our proof makes crucial use of the sharp Dvoretzky-Kiefer-Wolfowitz inequality and a suitably taylored Bernstein inequality; we have reasons to believe that the upper bound has the sharp scaling in N. Additional heuristics suggest that jittered sampling should be able to improve known bounds on the inverse of the star-discrepancy in the regime N≳dd. We also prove a partition principle showing that every partition of [0,1]d combined with a jittered sampling construction gives rise to a set whose expected squared L2-discrepancy is smaller than that of purely random points."}],"date_updated":"2021-01-12T06:52:02Z","citation":{"ista":"Pausinger F, Steinerberger S. 2016. On the discrepancy of jittered sampling. Journal of Complexity. 33, 199–216.","ama":"Pausinger F, Steinerberger S. On the discrepancy of jittered sampling. <i>Journal of Complexity</i>. 2016;33:199-216. doi:<a href=\"https://doi.org/10.1016/j.jco.2015.11.003\">10.1016/j.jco.2015.11.003</a>","mla":"Pausinger, Florian, and Stefan Steinerberger. “On the Discrepancy of Jittered Sampling.” <i>Journal of Complexity</i>, vol. 33, Academic Press, 2016, pp. 199–216, doi:<a href=\"https://doi.org/10.1016/j.jco.2015.11.003\">10.1016/j.jco.2015.11.003</a>.","chicago":"Pausinger, Florian, and Stefan Steinerberger. “On the Discrepancy of Jittered Sampling.” <i>Journal of Complexity</i>. Academic Press, 2016. <a href=\"https://doi.org/10.1016/j.jco.2015.11.003\">https://doi.org/10.1016/j.jco.2015.11.003</a>.","short":"F. Pausinger, S. Steinerberger, Journal of Complexity 33 (2016) 199–216.","apa":"Pausinger, F., &#38; Steinerberger, S. (2016). On the discrepancy of jittered sampling. <i>Journal of Complexity</i>. Academic Press. <a href=\"https://doi.org/10.1016/j.jco.2015.11.003\">https://doi.org/10.1016/j.jco.2015.11.003</a>","ieee":"F. Pausinger and S. Steinerberger, “On the discrepancy of jittered sampling,” <i>Journal of Complexity</i>, vol. 33. Academic Press, pp. 199–216, 2016."},"day":"01","scopus_import":1,"type":"journal_article","year":"2016","month":"04","oa_version":"Submitted Version","date_created":"2018-12-11T11:53:03Z","date_published":"2016-04-01T00:00:00Z","volume":33,"doi":"10.1016/j.jco.2015.11.003","publist_id":"5549"},{"volume":342,"month":"02","date_created":"2018-12-11T11:53:04Z","date_published":"2016-02-01T00:00:00Z","date_updated":"2021-01-12T06:52:03Z","day":"01","citation":{"short":"R. Frank, C. Hainzl, R. Seiringer, J. Solovej, Communications in Mathematical Physics 342 (2016) 189–216.","apa":"Frank, R., Hainzl, C., Seiringer, R., &#38; Solovej, J. (2016). The external field dependence of the BCS critical temperature. <i>Communications in Mathematical Physics</i>. Springer. <a href=\"https://doi.org/10.1007/s00220-015-2526-2\">https://doi.org/10.1007/s00220-015-2526-2</a>","ieee":"R. Frank, C. Hainzl, R. Seiringer, and J. Solovej, “The external field dependence of the BCS critical temperature,” <i>Communications in Mathematical Physics</i>, vol. 342, no. 1. Springer, pp. 189–216, 2016.","ista":"Frank R, Hainzl C, Seiringer R, Solovej J. 2016. The external field dependence of the BCS critical temperature. Communications in Mathematical Physics. 342(1), 189–216.","ama":"Frank R, Hainzl C, Seiringer R, Solovej J. The external field dependence of the BCS critical temperature. <i>Communications in Mathematical Physics</i>. 2016;342(1):189-216. doi:<a href=\"https://doi.org/10.1007/s00220-015-2526-2\">10.1007/s00220-015-2526-2</a>","mla":"Frank, Rupert, et al. “The External Field Dependence of the BCS Critical Temperature.” <i>Communications in Mathematical Physics</i>, vol. 342, no. 1, Springer, 2016, pp. 189–216, doi:<a href=\"https://doi.org/10.1007/s00220-015-2526-2\">10.1007/s00220-015-2526-2</a>.","chicago":"Frank, Rupert, Christian Hainzl, Robert Seiringer, and Jan Solovej. “The External Field Dependence of the BCS Critical Temperature.” <i>Communications in Mathematical Physics</i>. Springer, 2016. <a href=\"https://doi.org/10.1007/s00220-015-2526-2\">https://doi.org/10.1007/s00220-015-2526-2</a>."},"status":"public","title":"The external field dependence of the BCS critical temperature","author":[{"full_name":"Frank, Rupert","last_name":"Frank","first_name":"Rupert"},{"full_name":"Hainzl, Christian","first_name":"Christian","last_name":"Hainzl"},{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","full_name":"Seiringer, Robert","last_name":"Seiringer","orcid":"0000-0002-6781-0521","first_name":"Robert"},{"full_name":"Solovej, Jan","last_name":"Solovej","first_name":"Jan"}],"oa":1,"issue":"1","intvolume":"       342","publication":"Communications in Mathematical Physics","publisher":"Springer","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1410.2352"}],"quality_controlled":"1","page":"189 - 216","publist_id":"5546","doi":"10.1007/s00220-015-2526-2","oa_version":"Submitted Version","scopus_import":1,"year":"2016","type":"journal_article","abstract":[{"lang":"eng","text":"We consider the Bardeen–Cooper–Schrieffer free energy functional for particles interacting via a two-body potential on a microscopic scale and in the presence of weak external fields varying on a macroscopic scale. We study the influence of the external fields on the critical temperature. We show that in the limit where the ratio between the microscopic and macroscopic scale tends to zero, the next to leading order of the critical temperature is determined by the lowest eigenvalue of the linearization of the Ginzburg–Landau equation."}],"acknowledgement":"The authors are grateful to I. M. Sigal for useful discussions. Financial support from the US National Science Foundation through Grants PHY-1347399 and DMS-1363432 (R.L.F.), from the Danish council for independent research and from ERC Advanced Grant 321029 (J.P.S.) is acknowledged.","publication_status":"published","language":[{"iso":"eng"}],"_id":"1620","department":[{"_id":"RoSe"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87"},{"abstract":[{"lang":"eng","text":"We prove analogues of the Lieb–Thirring and Hardy–Lieb–Thirring inequalities for many-body quantum systems with fractional kinetic operators and homogeneous interaction potentials, where no anti-symmetry on the wave functions is assumed. These many-body inequalities imply interesting one-body interpolation inequalities, and we show that the corresponding one- and many-body inequalities are actually equivalent in certain cases."}],"ec_funded":1,"acknowledgement":"We thank Jan  Philip  Solovej, Robert Seiringer and Vladimir Maz’ya for helpful discussions, as well as Rupert Frank\r\nand the anonymous referee for useful comments. Part of this work has been carried out during a visit at the Institut Mittag-Leffler (Stockholm). D.L. acknowledges financial support by the grant KAW 2010.0063 from the Knut and Alice Wallenberg Foundation and the Swedish Research Council grant no. 2013-4734. P.T.N. is 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. F.P. acknowledges support from the ERC project no. 321029 “The\r\nmathematics of the structure of matter”.","language":[{"iso":"eng"}],"_id":"1622","publication_status":"published","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"RoSe"}],"doi":"10.1007/s00205-015-0923-5","publist_id":"5542","oa_version":"Submitted Version","year":"2016","type":"journal_article","scopus_import":1,"title":"Fractional Hardy–Lieb–Thirring and related Inequalities for interacting systems","status":"public","oa":1,"author":[{"last_name":"Lundholm","first_name":"Douglas","full_name":"Lundholm, Douglas"},{"first_name":"Phan","last_name":"Nam","id":"404092F4-F248-11E8-B48F-1D18A9856A87","full_name":"Nam, Phan"},{"first_name":"Fabian","last_name":"Portmann","full_name":"Portmann, Fabian"}],"issue":"3","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1501.04570"}],"quality_controlled":"1","page":"1343 - 1382","publisher":"Springer","publication":"Archive for Rational Mechanics and Analysis","intvolume":"       219","volume":219,"date_published":"2016-03-01T00:00:00Z","date_created":"2018-12-11T11:53:05Z","month":"03","citation":{"ama":"Lundholm D, Nam P, Portmann F. Fractional Hardy–Lieb–Thirring and related Inequalities for interacting systems. <i>Archive for Rational Mechanics and Analysis</i>. 2016;219(3):1343-1382. doi:<a href=\"https://doi.org/10.1007/s00205-015-0923-5\">10.1007/s00205-015-0923-5</a>","ista":"Lundholm D, Nam P, Portmann F. 2016. Fractional Hardy–Lieb–Thirring and related Inequalities for interacting systems. Archive for Rational Mechanics and Analysis. 219(3), 1343–1382.","mla":"Lundholm, Douglas, et al. “Fractional Hardy–Lieb–Thirring and Related Inequalities for Interacting Systems.” <i>Archive for Rational Mechanics and Analysis</i>, vol. 219, no. 3, Springer, 2016, pp. 1343–82, doi:<a href=\"https://doi.org/10.1007/s00205-015-0923-5\">10.1007/s00205-015-0923-5</a>.","chicago":"Lundholm, Douglas, Phan Nam, and Fabian Portmann. “Fractional Hardy–Lieb–Thirring and Related Inequalities for Interacting Systems.” <i>Archive for Rational Mechanics and Analysis</i>. Springer, 2016. <a href=\"https://doi.org/10.1007/s00205-015-0923-5\">https://doi.org/10.1007/s00205-015-0923-5</a>.","short":"D. Lundholm, P. Nam, F. Portmann, Archive for Rational Mechanics and Analysis 219 (2016) 1343–1382.","apa":"Lundholm, D., Nam, P., &#38; Portmann, F. (2016). Fractional Hardy–Lieb–Thirring and related Inequalities for interacting systems. <i>Archive for Rational Mechanics and Analysis</i>. Springer. <a href=\"https://doi.org/10.1007/s00205-015-0923-5\">https://doi.org/10.1007/s00205-015-0923-5</a>","ieee":"D. Lundholm, P. Nam, and F. Portmann, “Fractional Hardy–Lieb–Thirring and related Inequalities for interacting systems,” <i>Archive for Rational Mechanics and Analysis</i>, vol. 219, no. 3. Springer, pp. 1343–1382, 2016."},"day":"01","date_updated":"2021-01-12T06:52:04Z"},{"month":"04","date_created":"2018-12-11T11:53:08Z","date_published":"2016-04-01T00:00:00Z","volume":108,"has_accepted_license":"1","date_updated":"2021-01-12T06:52:07Z","file":[{"date_created":"2018-12-12T10:11:12Z","file_size":1684043,"file_id":"4865","creator":"system","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"IST-2016-465-v1+1_1-s2.0-S0040580915001094-main.pdf","date_updated":"2020-07-14T12:45:07Z","checksum":"6a65ba187994d4ad86c1c509e0ff482a"}],"day":"01","citation":{"ieee":"J. Kelleher, A. Etheridge, A. Véber, and N. H. Barton, “Spread of pedigree versus genetic ancestry in spatially distributed populations,” <i>Theoretical Population Biology</i>, vol. 108. Academic Press, pp. 1–12, 2016.","short":"J. Kelleher, A. Etheridge, A. Véber, N.H. Barton, Theoretical Population Biology 108 (2016) 1–12.","apa":"Kelleher, J., Etheridge, A., Véber, A., &#38; Barton, N. H. (2016). Spread of pedigree versus genetic ancestry in spatially distributed populations. <i>Theoretical Population Biology</i>. Academic Press. <a href=\"https://doi.org/10.1016/j.tpb.2015.10.008\">https://doi.org/10.1016/j.tpb.2015.10.008</a>","mla":"Kelleher, Jerome, et al. “Spread of Pedigree versus Genetic Ancestry in Spatially Distributed Populations.” <i>Theoretical Population Biology</i>, vol. 108, Academic Press, 2016, pp. 1–12, doi:<a href=\"https://doi.org/10.1016/j.tpb.2015.10.008\">10.1016/j.tpb.2015.10.008</a>.","ista":"Kelleher J, Etheridge A, Véber A, Barton NH. 2016. Spread of pedigree versus genetic ancestry in spatially distributed populations. Theoretical Population Biology. 108, 1–12.","ama":"Kelleher J, Etheridge A, Véber A, Barton NH. Spread of pedigree versus genetic ancestry in spatially distributed populations. <i>Theoretical Population Biology</i>. 2016;108:1-12. doi:<a href=\"https://doi.org/10.1016/j.tpb.2015.10.008\">10.1016/j.tpb.2015.10.008</a>","chicago":"Kelleher, Jerome, Alison Etheridge, Amandine Véber, and Nicholas H Barton. “Spread of Pedigree versus Genetic Ancestry in Spatially Distributed Populations.” <i>Theoretical Population Biology</i>. Academic Press, 2016. <a href=\"https://doi.org/10.1016/j.tpb.2015.10.008\">https://doi.org/10.1016/j.tpb.2015.10.008</a>."},"author":[{"last_name":"Kelleher","first_name":"Jerome","full_name":"Kelleher, Jerome"},{"full_name":"Etheridge, Alison","last_name":"Etheridge","first_name":"Alison"},{"full_name":"Véber, Amandine","first_name":"Amandine","last_name":"Véber"},{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240"}],"oa":1,"status":"public","title":"Spread of pedigree versus genetic ancestry in spatially distributed populations","intvolume":"       108","publication":"Theoretical Population Biology","publisher":"Academic Press","quality_controlled":"1","page":"1 - 12","oa_version":"Published Version","publist_id":"5524","doi":"10.1016/j.tpb.2015.10.008","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"pubrep_id":"465","scopus_import":1,"type":"journal_article","year":"2016","file_date_updated":"2020-07-14T12:45:07Z","ec_funded":1,"abstract":[{"text":"Ancestral processes are fundamental to modern population genetics and spatial structure has been the subject of intense interest for many years. Despite this interest, almost nothing is known about the distribution of the locations of pedigree or genetic ancestors. Using both spatially continuous and stepping-stone models, we show that the distribution of pedigree ancestors approaches a travelling wave, for which we develop two alternative approximations. The speed and width of the wave are sensitive to the local details of the model. After a short time, genetic ancestors spread far more slowly than pedigree ancestors, ultimately diffusing out with radius ## rather than spreading at constant speed. In contrast to the wave of pedigree ancestors, the spread of genetic ancestry is insensitive to the local details of the models.","lang":"eng"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"NiBa"}],"project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation"}],"ddc":["576"],"publication_status":"published","_id":"1631","language":[{"iso":"eng"}]},{"year":"2016","type":"journal_article","scopus_import":1,"pubrep_id":"1001","doi":"10.1007/s00344-015-9553-2","publist_id":"5512","oa_version":"Preprint","language":[{"iso":"eng"}],"_id":"1641","publication_status":"published","ddc":["581"],"department":[{"_id":"JiFr"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"The plant hormone auxin (indole-3-acetic acid) is a major regulator of plant growth and development including embryo and root patterning, lateral organ formation and growth responses to environmental stimuli. Auxin is directionally transported from cell to cell by the action of specific auxin influx [AUXIN-RESISTANT1 (AUX1)] and efflux [PIN-FORMED (PIN)] transport regulators, whose polar, subcellular localizations are aligned with the direction of the auxin flow. Auxin itself regulates its own transport by modulation of the expression and subcellular localization of the auxin transporters. Increased auxin levels promote the transcription of PIN2 and AUX1 genes as well as stabilize PIN proteins at the plasma membrane, whereas prolonged auxin exposure increases the turnover of PIN proteins and their degradation in the vacuole. In this study, we applied a forward genetic approach, to identify molecular components playing a role in the auxin-mediated degradation. We generated EMS-mutagenized Arabidopsis PIN2::PIN2:GFP, AUX1::AUX1:YFP eir1aux1 populations and designed a screen for mutants with persistently strong fluorescent signals of the tagged PIN2 and AUX1 after prolonged treatment with the synthetic auxin 2,4-dichlorophenoxyacetic acid (2,4-D). This approach yielded novel auxin degradation mutants defective in trafficking and degradation of PIN2 and AUX1 proteins and established a role for auxin-mediated degradation in plant development.","lang":"eng"}],"file_date_updated":"2020-07-14T12:45:08Z","acknowledgement":"European Social Fund (CZ.1.07/2.3.00/20.0043) and the Czech Science Foundation GAČR (GA13-40637S) to JF. ","citation":{"short":"R. Zemová, M. Zwiewka, A. Bielach, H. Robert, J. Friml, Journal of Plant Growth Regulation 35 (2016) 465–476.","apa":"Zemová, R., Zwiewka, M., Bielach, A., Robert, H., &#38; Friml, J. (2016). A forward genetic screen for new regulators of auxin mediated degradation of auxin transport proteins in Arabidopsis thaliana. <i>Journal of Plant Growth Regulation</i>. Springer. <a href=\"https://doi.org/10.1007/s00344-015-9553-2\">https://doi.org/10.1007/s00344-015-9553-2</a>","ieee":"R. Zemová, M. Zwiewka, A. Bielach, H. Robert, and J. Friml, “A forward genetic screen for new regulators of auxin mediated degradation of auxin transport proteins in Arabidopsis thaliana,” <i>Journal of Plant Growth Regulation</i>, vol. 35, no. 2. Springer, pp. 465–476, 2016.","chicago":"Zemová, Radka, Marta Zwiewka, Agnieszka Bielach, Hélène Robert, and Jiří Friml. “A Forward Genetic Screen for New Regulators of Auxin Mediated Degradation of Auxin Transport Proteins in Arabidopsis Thaliana.” <i>Journal of Plant Growth Regulation</i>. Springer, 2016. <a href=\"https://doi.org/10.1007/s00344-015-9553-2\">https://doi.org/10.1007/s00344-015-9553-2</a>.","ista":"Zemová R, Zwiewka M, Bielach A, Robert H, Friml J. 2016. A forward genetic screen for new regulators of auxin mediated degradation of auxin transport proteins in Arabidopsis thaliana. Journal of Plant Growth Regulation. 35(2), 465–476.","ama":"Zemová R, Zwiewka M, Bielach A, Robert H, Friml J. A forward genetic screen for new regulators of auxin mediated degradation of auxin transport proteins in Arabidopsis thaliana. <i>Journal of Plant Growth Regulation</i>. 2016;35(2):465-476. doi:<a href=\"https://doi.org/10.1007/s00344-015-9553-2\">10.1007/s00344-015-9553-2</a>","mla":"Zemová, Radka, et al. “A Forward Genetic Screen for New Regulators of Auxin Mediated Degradation of Auxin Transport Proteins in Arabidopsis Thaliana.” <i>Journal of Plant Growth Regulation</i>, vol. 35, no. 2, Springer, 2016, pp. 465–76, doi:<a href=\"https://doi.org/10.1007/s00344-015-9553-2\">10.1007/s00344-015-9553-2</a>."},"day":"01","file":[{"file_name":"IST-2018-1001-v1+1_Zemova_JPlantGrowthRegul_2016_proofs.pdf","date_updated":"2020-07-14T12:45:08Z","checksum":"0dc6a300cde6536ceedd2bcdd2060efb","date_created":"2018-12-12T10:08:34Z","creator":"system","file_id":"4695","relation":"main_file","file_size":5637591,"access_level":"open_access","content_type":"application/pdf"}],"date_updated":"2021-01-12T06:52:11Z","has_accepted_license":"1","volume":35,"date_published":"2016-06-01T00:00:00Z","date_created":"2018-12-11T11:53:12Z","month":"06","issue":"2","page":"465 - 476","quality_controlled":"1","publisher":"Springer","publication":"Journal of Plant Growth Regulation","intvolume":"        35","title":"A forward genetic screen for new regulators of auxin mediated degradation of auxin transport proteins in Arabidopsis thaliana","status":"public","oa":1,"author":[{"first_name":"Radka","last_name":"Zemová","full_name":"Zemová, Radka"},{"full_name":"Zwiewka, Marta","last_name":"Zwiewka","first_name":"Marta"},{"last_name":"Bielach","first_name":"Agnieszka","full_name":"Bielach, Agnieszka"},{"full_name":"Robert, Hélène","first_name":"Hélène","last_name":"Robert"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí","last_name":"Friml","orcid":"0000-0002-8302-7596","first_name":"Jirí"}]},{"month":"01","date_published":"2016-01-08T00:00:00Z","date_created":"2018-12-11T11:53:16Z","volume":9452,"has_accepted_license":"1","date_updated":"2021-01-12T06:52:16Z","day":"08","citation":{"ama":"Okamoto T, Pietrzak KZ, Waters B, Wichs D. New realizations of somewhere statistically binding hashing and positional accumulators. In: Vol 9452. Springer; 2016:121-145. doi:<a href=\"https://doi.org/10.1007/978-3-662-48797-6_6\">10.1007/978-3-662-48797-6_6</a>","ista":"Okamoto T, Pietrzak KZ, Waters B, Wichs D. 2016. New realizations of somewhere statistically binding hashing and positional accumulators. ASIACRYPT: Theory and Application of Cryptology and Information Security, LNCS, vol. 9452, 121–145.","mla":"Okamoto, Tatsuaki, et al. <i>New Realizations of Somewhere Statistically Binding Hashing and Positional Accumulators</i>. Vol. 9452, Springer, 2016, pp. 121–45, doi:<a href=\"https://doi.org/10.1007/978-3-662-48797-6_6\">10.1007/978-3-662-48797-6_6</a>.","chicago":"Okamoto, Tatsuaki, Krzysztof Z Pietrzak, Brent Waters, and Daniel Wichs. “New Realizations of Somewhere Statistically Binding Hashing and Positional Accumulators,” 9452:121–45. Springer, 2016. <a href=\"https://doi.org/10.1007/978-3-662-48797-6_6\">https://doi.org/10.1007/978-3-662-48797-6_6</a>.","short":"T. Okamoto, K.Z. Pietrzak, B. Waters, D. Wichs, in:, Springer, 2016, pp. 121–145.","apa":"Okamoto, T., Pietrzak, K. Z., Waters, B., &#38; Wichs, D. (2016). New realizations of somewhere statistically binding hashing and positional accumulators (Vol. 9452, pp. 121–145). Presented at the ASIACRYPT: Theory and Application of Cryptology and Information Security, Auckland, New Zealand: Springer. <a href=\"https://doi.org/10.1007/978-3-662-48797-6_6\">https://doi.org/10.1007/978-3-662-48797-6_6</a>","ieee":"T. Okamoto, K. Z. Pietrzak, B. Waters, and D. Wichs, “New realizations of somewhere statistically binding hashing and positional accumulators,” presented at the ASIACRYPT: Theory and Application of Cryptology and Information Security, Auckland, New Zealand, 2016, vol. 9452, pp. 121–145."},"file":[{"checksum":"a57711cb660c5b17b42bb47275a00180","date_updated":"2020-07-14T12:45:08Z","file_name":"IST-2016-677-v1+1_869.pdf","content_type":"application/pdf","access_level":"open_access","file_size":580088,"creator":"system","file_id":"4923","relation":"main_file","date_created":"2018-12-12T10:12:05Z"}],"conference":{"location":"Auckland, New Zealand","start_date":"2015-11-29","end_date":"2015-12-03","name":"ASIACRYPT: Theory and Application of Cryptology and Information Security"},"author":[{"last_name":"Okamoto","first_name":"Tatsuaki","full_name":"Okamoto, Tatsuaki"},{"first_name":"Krzysztof Z","last_name":"Pietrzak","orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","full_name":"Pietrzak, Krzysztof Z"},{"last_name":"Waters","first_name":"Brent","full_name":"Waters, Brent"},{"full_name":"Wichs, Daniel","first_name":"Daniel","last_name":"Wichs"}],"oa":1,"status":"public","title":"New realizations of somewhere statistically binding hashing and positional accumulators","intvolume":"      9452","quality_controlled":"1","page":"121 - 145","publisher":"Springer","oa_version":"Submitted Version","doi":"10.1007/978-3-662-48797-6_6","publist_id":"5497","pubrep_id":"677","year":"2016","type":"conference","scopus_import":1,"alternative_title":["LNCS"],"file_date_updated":"2020-07-14T12:45:08Z","ec_funded":1,"abstract":[{"lang":"eng","text":"A somewhere statistically binding (SSB) hash, introduced by Hubáček and Wichs (ITCS ’15), can be used to hash a long string x to a short digest y = H hk (x) using a public hashing-key hk. Furthermore, there is a way to set up the hash key hk to make it statistically binding on some arbitrary hidden position i, meaning that: (1) the digest y completely determines the i’th bit (or symbol) of x so that all pre-images of y have the same value in the i’th position, (2) it is computationally infeasible to distinguish the position i on which hk is statistically binding from any other position i’. Lastly, the hash should have a local opening property analogous to Merkle-Tree hashing, meaning that given x and y = H hk (x) it should be possible to create a short proof π that certifies the value of the i’th bit (or symbol) of x without having to provide the entire input x. A similar primitive called a positional accumulator, introduced by Koppula, Lewko and Waters (STOC ’15) further supports dynamic updates of the hashed value. These tools, which are interesting in their own right, also serve as one of the main technical components in several recent works building advanced applications from indistinguishability obfuscation (iO).\r\n\r\nThe prior constructions of SSB hashing and positional accumulators required fully homomorphic encryption (FHE) and iO respectively. In this work, we give new constructions of these tools based on well studied number-theoretic assumptions such as DDH, Phi-Hiding and DCR, as well as a general construction from lossy/injective functions."}],"department":[{"_id":"KrPi"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"_id":"258C570E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"259668","name":"Provable Security for Physical Cryptography"}],"language":[{"iso":"eng"}],"_id":"1653","publication_status":"published","ddc":["000"]},{"volume":287,"has_accepted_license":"1","month":"01","date_created":"2018-12-11T11:53:20Z","date_published":"2016-01-10T00:00:00Z","related_material":{"record":[{"status":"public","id":"1399","relation":"dissertation_contains"}]},"date_updated":"2023-09-07T11:41:25Z","day":"10","citation":{"ieee":"H. Edelsbrunner and F. Pausinger, “Approximation and convergence of the intrinsic volume,” <i>Advances in Mathematics</i>, vol. 287. Academic Press, pp. 674–703, 2016.","apa":"Edelsbrunner, H., &#38; Pausinger, F. (2016). Approximation and convergence of the intrinsic volume. <i>Advances in Mathematics</i>. Academic Press. <a href=\"https://doi.org/10.1016/j.aim.2015.10.004\">https://doi.org/10.1016/j.aim.2015.10.004</a>","short":"H. Edelsbrunner, F. Pausinger, Advances in Mathematics 287 (2016) 674–703.","chicago":"Edelsbrunner, Herbert, and Florian Pausinger. “Approximation and Convergence of the Intrinsic Volume.” <i>Advances in Mathematics</i>. Academic Press, 2016. <a href=\"https://doi.org/10.1016/j.aim.2015.10.004\">https://doi.org/10.1016/j.aim.2015.10.004</a>.","mla":"Edelsbrunner, Herbert, and Florian Pausinger. “Approximation and Convergence of the Intrinsic Volume.” <i>Advances in Mathematics</i>, vol. 287, Academic Press, 2016, pp. 674–703, doi:<a href=\"https://doi.org/10.1016/j.aim.2015.10.004\">10.1016/j.aim.2015.10.004</a>.","ama":"Edelsbrunner H, Pausinger F. Approximation and convergence of the intrinsic volume. <i>Advances in Mathematics</i>. 2016;287:674-703. doi:<a href=\"https://doi.org/10.1016/j.aim.2015.10.004\">10.1016/j.aim.2015.10.004</a>","ista":"Edelsbrunner H, Pausinger F. 2016. Approximation and convergence of the intrinsic volume. Advances in Mathematics. 287, 674–703."},"file":[{"checksum":"f8869ec110c35c852ef6a37425374af7","date_updated":"2020-07-14T12:45:10Z","file_name":"IST-2017-774-v1+1_2016-J-03-FirstIntVolume.pdf","content_type":"application/pdf","access_level":"open_access","creator":"system","relation":"main_file","file_id":"4928","file_size":248985,"date_created":"2018-12-12T10:12:10Z"}],"status":"public","title":"Approximation and convergence of the intrinsic volume","author":[{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","first_name":"Herbert"},{"id":"2A77D7A2-F248-11E8-B48F-1D18A9856A87","full_name":"Pausinger, Florian","orcid":"0000-0002-8379-3768","last_name":"Pausinger","first_name":"Florian"}],"oa":1,"publication":"Advances in Mathematics","intvolume":"       287","quality_controlled":"1","page":"674 - 703","publisher":"Academic Press","doi":"10.1016/j.aim.2015.10.004","publist_id":"5488","tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"oa_version":"Published Version","year":"2016","type":"journal_article","scopus_import":1,"pubrep_id":"774","ec_funded":1,"abstract":[{"lang":"eng","text":"We introduce a modification of the classic notion of intrinsic volume using persistence moments of height functions. Evaluating the modified first intrinsic volume on digital approximations of a compact body with smoothly embedded boundary in Rn, we prove convergence to the first intrinsic volume of the body as the resolution of the approximation improves. We have weaker results for the other modified intrinsic volumes, proving they converge to the corresponding intrinsic volumes of the n-dimensional unit ball."}],"acknowledgement":"This research is partially supported by the Toposys project FP7-ICT-318493-STREP, and by ESF under the ACAT Research Network Programme.\r\nBoth authors thank Anne Marie Svane for her comments on an early version of this paper. The second author wishes to thank Eva B. Vedel Jensen and Markus Kiderlen from Aarhus University for enlightening discussions and their kind hospitality during a visit of their department in 2014.","file_date_updated":"2020-07-14T12:45:10Z","language":[{"iso":"eng"}],"_id":"1662","publication_status":"published","ddc":["004"],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"HeEd"}],"project":[{"name":"Topological Complex Systems","grant_number":"318493","call_identifier":"FP7","_id":"255D761E-B435-11E9-9278-68D0E5697425"}]},{"publisher":"Springer","quality_controlled":"1","page":"449 - 467","intvolume":"        18","publication":"International Journal on Software Tools for Technology Transfer","issue":"4","oa":1,"author":[{"first_name":"Sergiy","orcid":"0000-0002-0686-0365","last_name":"Bogomolov","full_name":"Bogomolov, Sergiy","id":"369D9A44-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Alexandre","last_name":"Donzé","full_name":"Donzé, Alexandre"},{"full_name":"Frehse, Goran","first_name":"Goran","last_name":"Frehse"},{"first_name":"Radu","last_name":"Grosu","full_name":"Grosu, Radu"},{"last_name":"Johnson","first_name":"Taylor","full_name":"Johnson, Taylor"},{"first_name":"Hamed","last_name":"Ladan","full_name":"Ladan, Hamed"},{"first_name":"Andreas","last_name":"Podelski","full_name":"Podelski, Andreas"},{"full_name":"Wehrle, Martin","first_name":"Martin","last_name":"Wehrle"}],"title":"Guided search for hybrid systems based on coarse-grained space abstractions","status":"public","file":[{"date_updated":"2020-07-14T12:45:13Z","file_name":"IST-2016-457-v1+1_s10009-015-0393-y.pdf","checksum":"31561d7705599a9bd4ea816accc0752e","creator":"system","relation":"main_file","file_id":"5146","file_size":2296522,"date_created":"2018-12-12T10:15:26Z","content_type":"application/pdf","access_level":"open_access"}],"citation":{"ieee":"S. Bogomolov <i>et al.</i>, “Guided search for hybrid systems based on coarse-grained space abstractions,” <i>International Journal on Software Tools for Technology Transfer</i>, vol. 18, no. 4. Springer, pp. 449–467, 2016.","apa":"Bogomolov, S., Donzé, A., Frehse, G., Grosu, R., Johnson, T., Ladan, H., … Wehrle, M. (2016). Guided search for hybrid systems based on coarse-grained space abstractions. <i>International Journal on Software Tools for Technology Transfer</i>. Springer. <a href=\"https://doi.org/10.1007/s10009-015-0393-y\">https://doi.org/10.1007/s10009-015-0393-y</a>","short":"S. Bogomolov, A. Donzé, G. Frehse, R. Grosu, T. Johnson, H. Ladan, A. Podelski, M. Wehrle, International Journal on Software Tools for Technology Transfer 18 (2016) 449–467.","chicago":"Bogomolov, Sergiy, Alexandre Donzé, Goran Frehse, Radu Grosu, Taylor Johnson, Hamed Ladan, Andreas Podelski, and Martin Wehrle. “Guided Search for Hybrid Systems Based on Coarse-Grained Space Abstractions.” <i>International Journal on Software Tools for Technology Transfer</i>. Springer, 2016. <a href=\"https://doi.org/10.1007/s10009-015-0393-y\">https://doi.org/10.1007/s10009-015-0393-y</a>.","mla":"Bogomolov, Sergiy, et al. “Guided Search for Hybrid Systems Based on Coarse-Grained Space Abstractions.” <i>International Journal on Software Tools for Technology Transfer</i>, vol. 18, no. 4, Springer, 2016, pp. 449–67, doi:<a href=\"https://doi.org/10.1007/s10009-015-0393-y\">10.1007/s10009-015-0393-y</a>.","ama":"Bogomolov S, Donzé A, Frehse G, et al. Guided search for hybrid systems based on coarse-grained space abstractions. <i>International Journal on Software Tools for Technology Transfer</i>. 2016;18(4):449-467. doi:<a href=\"https://doi.org/10.1007/s10009-015-0393-y\">10.1007/s10009-015-0393-y</a>","ista":"Bogomolov S, Donzé A, Frehse G, Grosu R, Johnson T, Ladan H, Podelski A, Wehrle M. 2016. Guided search for hybrid systems based on coarse-grained space abstractions. International Journal on Software Tools for Technology Transfer. 18(4), 449–467."},"day":"01","date_updated":"2021-01-12T06:52:38Z","date_published":"2016-08-01T00:00:00Z","date_created":"2018-12-11T11:53:34Z","month":"08","has_accepted_license":"1","volume":18,"project":[{"name":"Quantitative Reactive Modeling","grant_number":"267989","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"name":"The Wittgenstein Prize","grant_number":"Z211","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"ToHe"}],"publication_status":"published","ddc":["000"],"_id":"1705","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:45:13Z","article_processing_charge":"Yes (via OA deal)","abstract":[{"text":"Hybrid systems represent an important and powerful formalism for modeling real-world applications such as embedded systems. A verification tool like SpaceEx is based on the exploration of a symbolic search space (the region space). As a verification tool, it is typically optimized towards proving the absence of errors. In some settings, e.g., when the verification tool is employed in a feedback-directed design cycle, one would like to have the option to call a version that is optimized towards finding an error trajectory in the region space. A recent approach in this direction is based on guided search. Guided search relies on a cost function that indicates which states are promising to be explored, and preferably explores more promising states first. In this paper, we propose an abstraction-based cost function based on coarse-grained space abstractions for guiding the reachability analysis. For this purpose, a suitable abstraction technique that exploits the flexible granularity of modern reachability analysis algorithms is introduced. The new cost function is an effective extension of pattern database approaches that have been successfully applied in other areas. The approach has been implemented in the SpaceEx model checker. The evaluation shows its practical potential.","lang":"eng"}],"ec_funded":1,"pubrep_id":"457","scopus_import":1,"type":"journal_article","year":"2016","oa_version":"Published Version","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publist_id":"5431","doi":"10.1007/s10009-015-0393-y"},{"date_updated":"2021-01-12T06:52:39Z","day":"11","citation":{"ieee":"J. Pielorz and C. Lampert, “Optimal geospatial allocation of volunteers for crisis management,” presented at the ICT-DM: Information and Communication Technologies for Disaster Management, Rennes, France, 2016.","short":"J. Pielorz, C. Lampert, in:, IEEE, 2016.","apa":"Pielorz, J., &#38; Lampert, C. (2016). Optimal geospatial allocation of volunteers for crisis management. Presented at the ICT-DM: Information and Communication Technologies for Disaster Management, Rennes, France: IEEE. <a href=\"https://doi.org/10.1109/ICT-DM.2015.7402041\">https://doi.org/10.1109/ICT-DM.2015.7402041</a>","mla":"Pielorz, Jasmin, and Christoph Lampert. <i>Optimal Geospatial Allocation of Volunteers for Crisis Management</i>. 7402041, IEEE, 2016, doi:<a href=\"https://doi.org/10.1109/ICT-DM.2015.7402041\">10.1109/ICT-DM.2015.7402041</a>.","ama":"Pielorz J, Lampert C. Optimal geospatial allocation of volunteers for crisis management. In: IEEE; 2016. doi:<a href=\"https://doi.org/10.1109/ICT-DM.2015.7402041\">10.1109/ICT-DM.2015.7402041</a>","ista":"Pielorz J, Lampert C. 2016. Optimal geospatial allocation of volunteers for crisis management. ICT-DM: Information and Communication Technologies for Disaster Management, 7402041.","chicago":"Pielorz, Jasmin, and Christoph Lampert. “Optimal Geospatial Allocation of Volunteers for Crisis Management.” IEEE, 2016. <a href=\"https://doi.org/10.1109/ICT-DM.2015.7402041\">https://doi.org/10.1109/ICT-DM.2015.7402041</a>."},"conference":{"name":"ICT-DM: Information and Communication Technologies for Disaster Management","end_date":"2015-12-02","location":"Rennes, France","start_date":"2015-11-30"},"scopus_import":1,"type":"conference","year":"2016","month":"02","oa_version":"None","date_created":"2018-12-11T11:53:35Z","date_published":"2016-02-11T00:00:00Z","publist_id":"5429","doi":"10.1109/ICT-DM.2015.7402041","department":[{"_id":"ChLa"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"IEEE","quality_controlled":"1","publication_status":"published","language":[{"iso":"eng"}],"_id":"1707","author":[{"id":"49BC895A-F248-11E8-B48F-1D18A9856A87","full_name":"Pielorz, Jasmin","last_name":"Pielorz","first_name":"Jasmin"},{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Lampert, Christoph","last_name":"Lampert","orcid":"0000-0001-8622-7887","first_name":"Christoph"}],"acknowledgement":"The DRIVER FP7 project has received funding from the European Unions Seventh Framework Programme for research, technological development and demonstration under grant agreement no 607798. RE-ACTA was funded within the framework of the Austrian Security Research Programme KIRAS by the Federal Ministry for Transport, Innovation and Technology.","status":"public","article_number":"7402041","abstract":[{"text":"Volunteer supporters play an important role in modern crisis and disaster management. In the times of mobile Internet devices, help from thousands of volunteers can be requested within a short time span, thus relieving professional helpers from minor chores or geographically spread-out tasks. However, the simultaneous availability of many volunteers also poses new problems. In particular, the volunteer efforts must be well coordinated, or otherwise situations might emerge in which too many idle volunteers at one location become more of a burden than a relief to the professionals.\r\nIn this work, we study the task of optimally assigning volunteers to selected locations, e.g. in order to perform regular measurements, to report on damage, or to distribute information or resources to the population in a crisis situation. We formulate the assignment tasks as an optimization problem and propose an effective and efficient solution procedure. Experiments on real data of the Team Österreich, consisting of over 36,000 Austrian volunteers, show the effectiveness and efficiency of our approach.","lang":"eng"}],"title":"Optimal geospatial allocation of volunteers for crisis management"},{"publisher":"Springer","quality_controlled":"1","page":"17 - 46","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1210.0508"}],"intvolume":"        76","publication":"Algorithmica","issue":"1","oa":1,"author":[{"last_name":"Kolmogorov","first_name":"Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","full_name":"Kolmogorov, Vladimir"},{"last_name":"Takhanov","first_name":"Rustem","id":"2CCAC26C-F248-11E8-B48F-1D18A9856A87","full_name":"Takhanov, Rustem"}],"title":"Inference algorithms for pattern-based CRFs on sequence data","status":"public","day":"01","citation":{"short":"V. Kolmogorov, R. Takhanov, Algorithmica 76 (2016) 17–46.","apa":"Kolmogorov, V., &#38; Takhanov, R. (2016). Inference algorithms for pattern-based CRFs on sequence data. <i>Algorithmica</i>. Springer. <a href=\"https://doi.org/10.1007/s00453-015-0017-7\">https://doi.org/10.1007/s00453-015-0017-7</a>","ieee":"V. Kolmogorov and R. Takhanov, “Inference algorithms for pattern-based CRFs on sequence data,” <i>Algorithmica</i>, vol. 76, no. 1. Springer, pp. 17–46, 2016.","ama":"Kolmogorov V, Takhanov R. Inference algorithms for pattern-based CRFs on sequence data. <i>Algorithmica</i>. 2016;76(1):17-46. doi:<a href=\"https://doi.org/10.1007/s00453-015-0017-7\">10.1007/s00453-015-0017-7</a>","ista":"Kolmogorov V, Takhanov R. 2016. Inference algorithms for pattern-based CRFs on sequence data. Algorithmica. 76(1), 17–46.","mla":"Kolmogorov, Vladimir, and Rustem Takhanov. “Inference Algorithms for Pattern-Based CRFs on Sequence Data.” <i>Algorithmica</i>, vol. 76, no. 1, Springer, 2016, pp. 17–46, doi:<a href=\"https://doi.org/10.1007/s00453-015-0017-7\">10.1007/s00453-015-0017-7</a>.","chicago":"Kolmogorov, Vladimir, and Rustem Takhanov. “Inference Algorithms for Pattern-Based CRFs on Sequence Data.” <i>Algorithmica</i>. Springer, 2016. <a href=\"https://doi.org/10.1007/s00453-015-0017-7\">https://doi.org/10.1007/s00453-015-0017-7</a>."},"date_updated":"2023-10-17T09:51:31Z","related_material":{"record":[{"id":"2272","relation":"earlier_version","status":"public"}]},"date_created":"2018-12-11T11:54:02Z","date_published":"2016-09-01T00:00:00Z","month":"09","volume":76,"external_id":{"arxiv":["1210.0508"]},"project":[{"name":"Discrete Optimization in Computer Vision: Theory and Practice","_id":"25FBA906-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"616160"}],"department":[{"_id":"VlKo"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","_id":"1794","language":[{"iso":"eng"}],"acknowledgement":"This work has been partially supported by the European Research Council under the European Unions Seventh Framework Programme (FP7/2007-2013)/ERC grant agreement no. 616160.","abstract":[{"lang":"eng","text":"We consider Conditional random fields (CRFs) with pattern-based potentials defined on a chain. In this model the energy of a string (labeling) (Formula presented.) is the sum of terms over intervals [i, j] where each term is non-zero only if the substring (Formula presented.) equals a prespecified pattern w. Such CRFs can be naturally applied to many sequence tagging problems. We present efficient algorithms for the three standard inference tasks in a CRF, namely computing (i) the partition function, (ii) marginals, and (iii) computing the MAP. Their complexities are respectively (Formula presented.), (Formula presented.) and (Formula presented.) where L is the combined length of input patterns, (Formula presented.) is the maximum length of a pattern, and D is the input alphabet. This improves on the previous algorithms of Ye et al. (NIPS, 2009) whose complexities are respectively (Formula presented.), (Formula presented.) and (Formula presented.), where (Formula presented.) is the number of input patterns. In addition, we give an efficient algorithm for sampling, and revisit the case of MAP with non-positive weights."}],"ec_funded":1,"scopus_import":1,"type":"journal_article","arxiv":1,"year":"2016","oa_version":"Preprint","publist_id":"5316","doi":"10.1007/s00453-015-0017-7"},{"volume":143,"publist_id":"5270","doi":"10.1016/j.jmva.2015.10.005","oa_version":"Preprint","date_published":"2016-01-01T00:00:00Z","date_created":"2018-12-11T11:54:15Z","month":"01","scopus_import":1,"year":"2016","type":"journal_article","day":"01","citation":{"chicago":"Klimova, Anna, and Tamás Rudas. “On the Closure of Relational Models.” <i>Journal of Multivariate Analysis</i>. Elsevier, 2016. <a href=\"https://doi.org/10.1016/j.jmva.2015.10.005\">https://doi.org/10.1016/j.jmva.2015.10.005</a>.","ista":"Klimova A, Rudas T. 2016. On the closure of relational models. Journal of Multivariate Analysis. 143, 440–452.","ama":"Klimova A, Rudas T. On the closure of relational models. <i>Journal of Multivariate Analysis</i>. 2016;143:440-452. doi:<a href=\"https://doi.org/10.1016/j.jmva.2015.10.005\">10.1016/j.jmva.2015.10.005</a>","mla":"Klimova, Anna, and Tamás Rudas. “On the Closure of Relational Models.” <i>Journal of Multivariate Analysis</i>, vol. 143, Elsevier, 2016, pp. 440–52, doi:<a href=\"https://doi.org/10.1016/j.jmva.2015.10.005\">10.1016/j.jmva.2015.10.005</a>.","apa":"Klimova, A., &#38; Rudas, T. (2016). On the closure of relational models. <i>Journal of Multivariate Analysis</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jmva.2015.10.005\">https://doi.org/10.1016/j.jmva.2015.10.005</a>","short":"A. Klimova, T. Rudas, Journal of Multivariate Analysis 143 (2016) 440–452.","ieee":"A. Klimova and T. Rudas, “On the closure of relational models,” <i>Journal of Multivariate Analysis</i>, vol. 143. Elsevier, pp. 440–452, 2016."},"date_updated":"2021-01-12T06:53:30Z","abstract":[{"lang":"eng","text":"Relational models for contingency tables are generalizations of log-linear models, allowing effects associated with arbitrary subsets of cells in the table, and not necessarily containing the overall effect, that is, a common parameter in every cell. Similarly to log-linear models, relational models can be extended to non-negative distributions, but the extension requires more complex methods. An extended relational model is defined as an algebraic variety, and it turns out to be the closure of the original model with respect to the Bregman divergence. In the extended relational model, the MLE of the cell parameters always exists and is unique, but some of its properties may be different from those of the MLE under log-linear models. The MLE can be computed using a generalized iterative scaling procedure based on Bregman projections. "}],"title":"On the closure of relational models","status":"public","oa":1,"author":[{"id":"31934120-F248-11E8-B48F-1D18A9856A87","full_name":"Klimova, Anna","last_name":"Klimova","first_name":"Anna"},{"full_name":"Rudas, Tamás","first_name":"Tamás","last_name":"Rudas"}],"publication_status":"published","language":[{"iso":"eng"}],"_id":"1833","publisher":"Elsevier","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1501.00600"}],"page":"440 - 452","intvolume":"       143","department":[{"_id":"CaUh"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publication":"Journal of Multivariate Analysis"},{"publication_status":"published","language":[{"iso":"eng"}],"_id":"1881","project":[{"name":"Random matrices, universality and disordered quantum systems","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"338804"}],"department":[{"_id":"LaEr"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"We consider random matrices of the form H=W+λV, λ∈ℝ+, where W is a real symmetric or complex Hermitian Wigner matrix of size N and V is a real bounded diagonal random matrix of size N with i.i.d.\\ entries that are independent of W. We assume subexponential decay for the matrix entries of W and we choose λ∼1, so that the eigenvalues of W and λV are typically of the same order. Further, we assume that the density of the entries of V is supported on a single interval and is convex near the edges of its support. In this paper we prove that there is λ+∈ℝ+ such that the largest eigenvalues of H are in the limit of large N determined by the order statistics of V for λ&gt;λ+. In particular, the largest eigenvalue of H has a Weibull distribution in the limit N→∞ if λ&gt;λ+. Moreover, for N sufficiently large, we show that the eigenvectors associated to the largest eigenvalues are partially localized for λ&gt;λ+, while they are completely delocalized for λ&lt;λ+. Similar results hold for the lowest eigenvalues. ","lang":"eng"}],"ec_funded":1,"acknowledgement":"Most of the presented work was obtained while Kevin Schnelli was staying at the IAS with the support of\r\nThe Fund For Math.","scopus_import":1,"type":"journal_article","year":"2016","publist_id":"5215","doi":"10.1007/s00440-014-0610-8","oa_version":"Preprint","issue":"1-2","publisher":"Springer","main_file_link":[{"url":"http://arxiv.org/abs/1310.7057","open_access":"1"}],"page":"165 - 241","quality_controlled":"1","intvolume":"       164","publication":"Probability Theory and Related Fields","title":"Extremal eigenvalues and eigenvectors of deformed Wigner matrices","status":"public","oa":1,"author":[{"full_name":"Lee, Jioon","first_name":"Jioon","last_name":"Lee"},{"last_name":"Schnelli","orcid":"0000-0003-0954-3231","first_name":"Kevin","id":"434AD0AE-F248-11E8-B48F-1D18A9856A87","full_name":"Schnelli, Kevin"}],"day":"01","citation":{"ieee":"J. Lee and K. Schnelli, “Extremal eigenvalues and eigenvectors of deformed Wigner matrices,” <i>Probability Theory and Related Fields</i>, vol. 164, no. 1–2. Springer, pp. 165–241, 2016.","apa":"Lee, J., &#38; Schnelli, K. (2016). Extremal eigenvalues and eigenvectors of deformed Wigner matrices. <i>Probability Theory and Related Fields</i>. Springer. <a href=\"https://doi.org/10.1007/s00440-014-0610-8\">https://doi.org/10.1007/s00440-014-0610-8</a>","short":"J. Lee, K. Schnelli, Probability Theory and Related Fields 164 (2016) 165–241.","chicago":"Lee, Jioon, and Kevin Schnelli. “Extremal Eigenvalues and Eigenvectors of Deformed Wigner Matrices.” <i>Probability Theory and Related Fields</i>. Springer, 2016. <a href=\"https://doi.org/10.1007/s00440-014-0610-8\">https://doi.org/10.1007/s00440-014-0610-8</a>.","mla":"Lee, Jioon, and Kevin Schnelli. “Extremal Eigenvalues and Eigenvectors of Deformed Wigner Matrices.” <i>Probability Theory and Related Fields</i>, vol. 164, no. 1–2, Springer, 2016, pp. 165–241, doi:<a href=\"https://doi.org/10.1007/s00440-014-0610-8\">10.1007/s00440-014-0610-8</a>.","ista":"Lee J, Schnelli K. 2016. Extremal eigenvalues and eigenvectors of deformed Wigner matrices. Probability Theory and Related Fields. 164(1–2), 165–241.","ama":"Lee J, Schnelli K. Extremal eigenvalues and eigenvectors of deformed Wigner matrices. <i>Probability Theory and Related Fields</i>. 2016;164(1-2):165-241. doi:<a href=\"https://doi.org/10.1007/s00440-014-0610-8\">10.1007/s00440-014-0610-8</a>"},"date_updated":"2021-01-12T06:53:49Z","volume":164,"date_published":"2016-02-01T00:00:00Z","date_created":"2018-12-11T11:54:31Z","month":"02"},{"status":"public","title":"The complexity of deciding legality of a single step of magic: The gathering","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu"},{"last_name":"Ibsen-Jensen","orcid":"0000-0003-4783-0389","first_name":"Rasmus","full_name":"Ibsen-Jensen, Rasmus","id":"3B699956-F248-11E8-B48F-1D18A9856A87"}],"oa":1,"intvolume":"       285","publisher":"IOS Press","quality_controlled":"1","page":"1432 - 1439","volume":285,"has_accepted_license":"1","month":"01","date_published":"2016-01-01T00:00:00Z","date_created":"2018-12-11T11:46:41Z","conference":{"name":"ECAI: European Conference on Artificial Intelligence","start_date":"2016-08-29","location":"The Hague, Netherlands","end_date":"2016-09-02"},"date_updated":"2021-01-12T08:00:54Z","file":[{"access_level":"open_access","content_type":"application/pdf","date_created":"2018-12-12T10:07:59Z","file_size":2116225,"creator":"system","relation":"main_file","file_id":"4658","checksum":"848043c812ace05e459579c923f3d3cf","file_name":"IST-2018-950-v1+1_2016_Chatterjee_The_complexity.pdf","date_updated":"2020-07-14T12:46:35Z"}],"day":"01","citation":{"chicago":"Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. “The Complexity of Deciding Legality of a Single Step of Magic: The Gathering,” 285:1432–39. IOS Press, 2016. <a href=\"https://doi.org/10.3233/978-1-61499-672-9-1432\">https://doi.org/10.3233/978-1-61499-672-9-1432</a>.","ista":"Chatterjee K, Ibsen-Jensen R. 2016. The complexity of deciding legality of a single step of magic: The gathering. ECAI: European Conference on Artificial Intelligence, Frontiers in Artificial Intelligence and Applications, vol. 285, 1432–1439.","ama":"Chatterjee K, Ibsen-Jensen R. The complexity of deciding legality of a single step of magic: The gathering. In: Vol 285. IOS Press; 2016:1432-1439. doi:<a href=\"https://doi.org/10.3233/978-1-61499-672-9-1432\">10.3233/978-1-61499-672-9-1432</a>","mla":"Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. <i>The Complexity of Deciding Legality of a Single Step of Magic: The Gathering</i>. Vol. 285, IOS Press, 2016, pp. 1432–39, doi:<a href=\"https://doi.org/10.3233/978-1-61499-672-9-1432\">10.3233/978-1-61499-672-9-1432</a>.","short":"K. Chatterjee, R. Ibsen-Jensen, in:, IOS Press, 2016, pp. 1432–1439.","apa":"Chatterjee, K., &#38; Ibsen-Jensen, R. (2016). The complexity of deciding legality of a single step of magic: The gathering (Vol. 285, pp. 1432–1439). Presented at the ECAI: European Conference on Artificial Intelligence, The Hague, Netherlands: IOS Press. <a href=\"https://doi.org/10.3233/978-1-61499-672-9-1432\">https://doi.org/10.3233/978-1-61499-672-9-1432</a>","ieee":"K. Chatterjee and R. Ibsen-Jensen, “The complexity of deciding legality of a single step of magic: The gathering,” presented at the ECAI: European Conference on Artificial Intelligence, The Hague, Netherlands, 2016, vol. 285, pp. 1432–1439."},"abstract":[{"text":"Magic: the Gathering is a game about magical combat for any number of players. Formally it is a zero-sum, imperfect information stochastic game that consists of a potentially unbounded number of steps. We consider the problem of deciding if a move is legal in a given single step of Magic. We show that the problem is (a) coNP-complete in general; and (b) in P if either of two small sets of cards are not used. Our lower bound holds even for single-player Magic games. The significant aspects of our results are as follows: First, in most real-life game problems, the task of deciding whether a given move is legal in a single step is trivial, and the computationally hard task is to find the best sequence of legal moves in the presence of multiple players. In contrast, quite uniquely our hardness result holds for single step and with only one-player. Second, we establish efficient algorithms for important special cases of Magic.","lang":"eng"}],"alternative_title":["Frontiers in Artificial Intelligence and Applications"],"file_date_updated":"2020-07-14T12:46:35Z","publication_status":"published","ddc":["004"],"language":[{"iso":"eng"}],"_id":"478","department":[{"_id":"KrCh"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"7342","doi":"10.3233/978-1-61499-672-9-1432","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png"},"oa_version":"Published Version","scopus_import":1,"type":"conference","year":"2016","pubrep_id":"950"}]