[{"abstract":[{"text":"Continuous-time Markov chains are commonly used in practice for modeling biochemical reaction networks in which the inherent randomness of themolecular interactions cannot be ignored. This has motivated recent research effort into methods for parameter inference and experiment design for such models. The major difficulty is that such methods usually require one to iteratively solve the chemical master equation that governs the time evolution of the probability distribution of the system. This, however, is rarely possible, and even approximation techniques remain limited to relatively small and simple systems. An alternative explored in this article is to base methods on only some low-order moments of the entire probability distribution. We summarize the theory behind such moment-based methods for parameter inference and experiment design and provide new case studies where we investigate their performance.","lang":"eng"}],"acknowledgement":"HYCON2; EC; European Commission\r\n","oa_version":"None","publisher":"ACM","scopus_import":1,"quality_controlled":"1","intvolume":" 25","month":"02","publication_status":"published","year":"2015","language":[{"iso":"eng"}],"publication":"ACM Transactions on Modeling and Computer Simulation","day":"01","date_created":"2018-12-11T11:54:25Z","date_published":"2015-02-01T00:00:00Z","issue":"2","doi":"10.1145/2688906","volume":25,"_id":"1861","article_number":"8","type":"journal_article","status":"public","date_updated":"2021-01-12T06:53:41Z","citation":{"short":"J. Ruess, J. Lygeros, ACM Transactions on Modeling and Computer Simulation 25 (2015).","ieee":"J. Ruess and J. Lygeros, “Moment-based methods for parameter inference and experiment design for stochastic biochemical reaction networks,” ACM Transactions on Modeling and Computer Simulation, vol. 25, no. 2. ACM, 2015.","ama":"Ruess J, Lygeros J. Moment-based methods for parameter inference and experiment design for stochastic biochemical reaction networks. ACM Transactions on Modeling and Computer Simulation. 2015;25(2). doi:10.1145/2688906","apa":"Ruess, J., & Lygeros, J. (2015). Moment-based methods for parameter inference and experiment design for stochastic biochemical reaction networks. ACM Transactions on Modeling and Computer Simulation. ACM. https://doi.org/10.1145/2688906","mla":"Ruess, Jakob, and John Lygeros. “Moment-Based Methods for Parameter Inference and Experiment Design for Stochastic Biochemical Reaction Networks.” ACM Transactions on Modeling and Computer Simulation, vol. 25, no. 2, 8, ACM, 2015, doi:10.1145/2688906.","ista":"Ruess J, Lygeros J. 2015. Moment-based methods for parameter inference and experiment design for stochastic biochemical reaction networks. ACM Transactions on Modeling and Computer Simulation. 25(2), 8.","chicago":"Ruess, Jakob, and John Lygeros. “Moment-Based Methods for Parameter Inference and Experiment Design for Stochastic Biochemical Reaction Networks.” ACM Transactions on Modeling and Computer Simulation. ACM, 2015. https://doi.org/10.1145/2688906."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"5238","author":[{"first_name":"Jakob","id":"4A245D00-F248-11E8-B48F-1D18A9856A87","full_name":"Ruess, Jakob","orcid":"0000-0003-1615-3282","last_name":"Ruess"},{"first_name":"John","last_name":"Lygeros","full_name":"Lygeros, John"}],"title":"Moment-based methods for parameter inference and experiment design for stochastic biochemical reaction networks","department":[{"_id":"ToHe"},{"_id":"GaTk"}]},{"oa_version":"None","intvolume":" 58","month":"01","publisher":"ACM","scopus_import":1,"language":[{"iso":"eng"}],"publication":"Communications of the ACM","day":"28","year":"2015","publication_status":"published","date_created":"2018-12-11T11:54:26Z","doi":"10.1145/2701001","date_published":"2015-01-28T00:00:00Z","volume":58,"issue":"2","page":"86-86","_id":"1866","status":"public","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Henzinger, Thomas A., and Jean Raskin. “The Equivalence Problem for Finite Automata: Technical Perspective.” Communications of the ACM, vol. 58, no. 2, ACM, 2015, pp. 86–86, doi:10.1145/2701001.","ama":"Henzinger TA, Raskin J. The equivalence problem for finite automata: Technical perspective. Communications of the ACM. 2015;58(2):86-86. doi:10.1145/2701001","apa":"Henzinger, T. A., & Raskin, J. (2015). The equivalence problem for finite automata: Technical perspective. Communications of the ACM. ACM. https://doi.org/10.1145/2701001","ieee":"T. A. Henzinger and J. Raskin, “The equivalence problem for finite automata: Technical perspective,” Communications of the ACM, vol. 58, no. 2. ACM, pp. 86–86, 2015.","short":"T.A. Henzinger, J. Raskin, Communications of the ACM 58 (2015) 86–86.","chicago":"Henzinger, Thomas A, and Jean Raskin. “The Equivalence Problem for Finite Automata: Technical Perspective.” Communications of the ACM. ACM, 2015. https://doi.org/10.1145/2701001.","ista":"Henzinger TA, Raskin J. 2015. The equivalence problem for finite automata: Technical perspective. Communications of the ACM. 58(2), 86–86."},"date_updated":"2021-01-12T06:53:43Z","title":"The equivalence problem for finite automata: Technical perspective","department":[{"_id":"ToHe"}],"publist_id":"5232","author":[{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger"},{"first_name":"Jean","full_name":"Raskin, Jean","last_name":"Raskin"}]},{"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"The plant hormone auxin is a key regulator of plant growth and development. Differences in auxin distribution within tissues are mediated by the polar auxin transport machinery, and cellular auxin responses occur depending on changes in cellular auxin levels. Multiple receptor systems at the cell surface and in the interior operate to sense and interpret fluctuations in auxin distribution that occur during plant development. Until now, three proteins or protein complexes that can bind auxin have been identified. SCFTIR1 [a SKP1-cullin-1-F-box complex that contains transport inhibitor response 1 (TIR1) as the F-box protein] and S-phase-kinaseassociated protein 2 (SKP2) localize to the nucleus, whereas auxinbinding protein 1 (ABP1), predominantly associates with the endoplasmic reticulum and cell surface. In this Cell Science at a Glance article, we summarize recent discoveries in the field of auxin transport and signaling that have led to the identification of new components of these pathways, as well as their mutual interaction."}],"month":"01","intvolume":" 128","scopus_import":1,"file":[{"checksum":"24c779f4cd9d549ca6833e26f486be27","file_id":"4852","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2018-12-12T10:11:00Z","file_name":"IST-2016-563-v1+1_1.full.pdf","creator":"system","date_updated":"2020-07-14T12:45:19Z","file_size":1688844}],"language":[{"iso":"eng"}],"publication_status":"published","issue":"1","volume":128,"_id":"1871","status":"public","pubrep_id":"563","type":"journal_article","ddc":["570"],"date_updated":"2021-01-12T06:53:45Z","file_date_updated":"2020-07-14T12:45:19Z","department":[{"_id":"JiFr"}],"acknowledgement":"This work was supported by the European Research Council [project ERC-2011-StG-20101109-PSDP]; European Social Fund [grant number CZ.1.07/2.3.00/20.0043] and the Czech Science Foundation GAČR [grant number GA13-40637S]","publisher":"Company of Biologists","quality_controlled":"1","oa":1,"day":"01","publication":"Journal of Cell Science","has_accepted_license":"1","year":"2015","doi":"10.1242/jcs.159418","date_published":"2015-01-01T00:00:00Z","date_created":"2018-12-11T11:54:28Z","page":"1 - 7","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Grones P, Friml J. 2015. Auxin transporters and binding proteins at a glance. Journal of Cell Science. 128(1), 1–7.","chicago":"Grones, Peter, and Jiří Friml. “Auxin Transporters and Binding Proteins at a Glance.” Journal of Cell Science. Company of Biologists, 2015. https://doi.org/10.1242/jcs.159418.","short":"P. Grones, J. Friml, Journal of Cell Science 128 (2015) 1–7.","ieee":"P. Grones and J. Friml, “Auxin transporters and binding proteins at a glance,” Journal of Cell Science, vol. 128, no. 1. Company of Biologists, pp. 1–7, 2015.","ama":"Grones P, Friml J. Auxin transporters and binding proteins at a glance. Journal of Cell Science. 2015;128(1):1-7. doi:10.1242/jcs.159418","apa":"Grones, P., & Friml, J. (2015). Auxin transporters and binding proteins at a glance. Journal of Cell Science. Company of Biologists. https://doi.org/10.1242/jcs.159418","mla":"Grones, Peter, and Jiří Friml. “Auxin Transporters and Binding Proteins at a Glance.” Journal of Cell Science, vol. 128, no. 1, Company of Biologists, 2015, pp. 1–7, doi:10.1242/jcs.159418."},"title":"Auxin transporters and binding proteins at a glance","author":[{"last_name":"Grones","full_name":"Grones, Peter","first_name":"Peter","id":"399876EC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Friml","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí"}],"publist_id":"5225"},{"year":"2015","publication_status":"published","publication":"Hippocampus","language":[{"iso":"eng"}],"day":"01","page":"838 - 857","date_created":"2018-12-11T11:54:29Z","doi":"10.1002/hipo.22407","volume":25,"issue":"7","date_published":"2015-07-01T00:00:00Z","abstract":[{"text":"The hippocampal region, comprising the hippocampal formation and the parahippocampal region, has been one of the most intensively studied parts of the brain for decades. Better understanding of its functional diversity and complexity has led to an increased demand for specificity in experimental procedures and manipulations. In view of the complex 3D structure of the hippocampal region, precisely positioned experimental approaches require a fine-grained architectural description that is available and readable to experimentalists lacking detailed anatomical experience. In this paper, we provide the first cyto- and chemoarchitectural description of the hippocampal formation and parahippocampal region in the rat at high resolution and in the three standard sectional planes: coronal, horizontal and sagittal. The atlas uses a series of adjacent sections stained for neurons and for a number of chemical marker substances, particularly parvalbumin and calbindin. All the borders defined in one plane have been cross-checked against their counterparts in the other two planes. The entire dataset will be made available as a web-based interactive application through the Rodent Brain WorkBench (http://www.rbwb.org) which, together with this paper, provides a unique atlas resource.","lang":"eng"}],"oa_version":"None","scopus_import":1,"publisher":"Wiley","quality_controlled":"1","intvolume":" 25","month":"07","date_updated":"2021-01-12T06:53:46Z","citation":{"ieee":"C. N. Boccara, L. Kjønigsen, I. Hammer, J. Bjaalie, T. Leergaard, and M. Witter, “A three-plane architectonic atlas of the rat hippocampal region,” Hippocampus, vol. 25, no. 7. Wiley, pp. 838–857, 2015.","short":"C.N. Boccara, L. Kjønigsen, I. Hammer, J. Bjaalie, T. Leergaard, M. Witter, Hippocampus 25 (2015) 838–857.","apa":"Boccara, C. N., Kjønigsen, L., Hammer, I., Bjaalie, J., Leergaard, T., & Witter, M. (2015). A three-plane architectonic atlas of the rat hippocampal region. Hippocampus. Wiley. https://doi.org/10.1002/hipo.22407","ama":"Boccara CN, Kjønigsen L, Hammer I, Bjaalie J, Leergaard T, Witter M. A three-plane architectonic atlas of the rat hippocampal region. Hippocampus. 2015;25(7):838-857. doi:10.1002/hipo.22407","mla":"Boccara, Charlotte N., et al. “A Three-Plane Architectonic Atlas of the Rat Hippocampal Region.” Hippocampus, vol. 25, no. 7, Wiley, 2015, pp. 838–57, doi:10.1002/hipo.22407.","ista":"Boccara CN, Kjønigsen L, Hammer I, Bjaalie J, Leergaard T, Witter M. 2015. A three-plane architectonic atlas of the rat hippocampal region. Hippocampus. 25(7), 838–857.","chicago":"Boccara, Charlotte N., Lisa Kjønigsen, Ingvild Hammer, Jan Bjaalie, Trygve Leergaard, and Menno Witter. “A Three-Plane Architectonic Atlas of the Rat Hippocampal Region.” Hippocampus. Wiley, 2015. https://doi.org/10.1002/hipo.22407."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"5222","author":[{"orcid":"0000-0001-7237-5109","full_name":"Boccara, Charlotte","last_name":"Boccara","first_name":"Charlotte","id":"3FC06552-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kjønigsen, Lisa","last_name":"Kjønigsen","first_name":"Lisa"},{"first_name":"Ingvild","last_name":"Hammer","full_name":"Hammer, Ingvild"},{"last_name":"Bjaalie","full_name":"Bjaalie, Jan","first_name":"Jan"},{"first_name":"Trygve","last_name":"Leergaard","full_name":"Leergaard, Trygve"},{"first_name":"Menno","full_name":"Witter, Menno","last_name":"Witter"}],"department":[{"_id":"JoCs"}],"title":"A three-plane architectonic atlas of the rat hippocampal region","_id":"1874","type":"journal_article","status":"public"},{"date_created":"2018-12-11T11:54:28Z","doi":"10.1016/j.artint.2014.12.009","volume":221,"date_published":"2015-04-01T00:00:00Z","page":"46 - 72","language":[{"iso":"eng"}],"publication":"Artificial Intelligence","day":"01","publication_status":"published","year":"2015","intvolume":" 221","month":"04","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1408.2058"}],"publisher":"Elsevier","scopus_import":1,"quality_controlled":"1","oa_version":"Preprint","abstract":[{"text":"We consider partially observable Markov decision processes (POMDPs) with limit-average payoff, where a reward value in the interval [0,1] is associated with every transition, and the payoff of an infinite path is the long-run average of the rewards. We consider two types of path constraints: (i) a quantitative constraint defines the set of paths where the payoff is at least a given threshold λ1ε(0,1]; and (ii) a qualitative constraint which is a special case of the quantitative constraint with λ1=1. We consider the computation of the almost-sure winning set, where the controller needs to ensure that the path constraint is satisfied with probability 1. Our main results for qualitative path constraints are as follows: (i) the problem of deciding the existence of a finite-memory controller is EXPTIME-complete; and (ii) the problem of deciding the existence of an infinite-memory controller is undecidable. For quantitative path constraints we show that the problem of deciding the existence of a finite-memory controller is undecidable. We also present a prototype implementation of our EXPTIME algorithm and experimental results on several examples.","lang":"eng"}],"title":"POMDPs under probabilistic semantics","department":[{"_id":"KrCh"}],"external_id":{"arxiv":["1408.2058"]},"author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"first_name":"Martin","id":"3624234E-F248-11E8-B48F-1D18A9856A87","last_name":"Chmelik","full_name":"Chmelik, Martin"}],"publist_id":"5224","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Chatterjee K, Chmelik M. 2015. POMDPs under probabilistic semantics. Artificial Intelligence. 221, 46–72.","chicago":"Chatterjee, Krishnendu, and Martin Chmelik. “POMDPs under Probabilistic Semantics.” Artificial Intelligence. Elsevier, 2015. https://doi.org/10.1016/j.artint.2014.12.009.","short":"K. Chatterjee, M. Chmelik, Artificial Intelligence 221 (2015) 46–72.","ieee":"K. Chatterjee and M. Chmelik, “POMDPs under probabilistic semantics,” Artificial Intelligence, vol. 221. Elsevier, pp. 46–72, 2015.","apa":"Chatterjee, K., & Chmelik, M. (2015). POMDPs under probabilistic semantics. Artificial Intelligence. Elsevier. https://doi.org/10.1016/j.artint.2014.12.009","ama":"Chatterjee K, Chmelik M. POMDPs under probabilistic semantics. Artificial Intelligence. 2015;221:46-72. doi:10.1016/j.artint.2014.12.009","mla":"Chatterjee, Krishnendu, and Martin Chmelik. “POMDPs under Probabilistic Semantics.” Artificial Intelligence, vol. 221, Elsevier, 2015, pp. 46–72, doi:10.1016/j.artint.2014.12.009."},"date_updated":"2021-01-12T06:53:46Z","status":"public","type":"journal_article","_id":"1873"}]