[{"pubrep_id":"493","oa_version":"Published Version","file":[{"file_name":"IST-2016-493-v1+1_1-s2.0-S1369527415000594-main.pdf","access_level":"open_access","creator":"system","file_size":1047255,"content_type":"application/pdf","file_id":"5277","relation":"main_file","date_updated":"2020-07-14T12:45:17Z","date_created":"2018-12-12T10:17:23Z","checksum":"1683bb0f42ef892a5b3b71a050d65d25"}],"_id":"1810","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 27","title":"Antimicrobial interactions: Mechanisms and implications for drug discovery and resistance evolution","status":"public","ddc":["570"],"abstract":[{"lang":"eng","text":"Combining antibiotics is a promising strategy for increasing treatment efficacy and for controlling resistance evolution. When drugs are combined, their effects on cells may be amplified or weakened, that is the drugs may show synergistic or antagonistic interactions. Recent work revealed the underlying mechanisms of such drug interactions by elucidating the drugs'; joint effects on cell physiology. Moreover, new treatment strategies that use drug combinations to exploit evolutionary tradeoffs were shown to affect the rate of resistance evolution in predictable ways. High throughput studies have further identified drug candidates based on their interactions with established antibiotics and general principles that enable the prediction of drug interactions were suggested. Overall, the conceptual and technical foundation for the rational design of potent drug combinations is rapidly developing."}],"type":"journal_article","date_published":"2015-06-01T00:00:00Z","citation":{"ieee":"M. T. Bollenbach, “Antimicrobial interactions: Mechanisms and implications for drug discovery and resistance evolution,” Current Opinion in Microbiology, vol. 27. Elsevier, pp. 1–9, 2015.","apa":"Bollenbach, M. T. (2015). Antimicrobial interactions: Mechanisms and implications for drug discovery and resistance evolution. Current Opinion in Microbiology. Elsevier. https://doi.org/10.1016/j.mib.2015.05.008","ista":"Bollenbach MT. 2015. Antimicrobial interactions: Mechanisms and implications for drug discovery and resistance evolution. Current Opinion in Microbiology. 27, 1–9.","ama":"Bollenbach MT. Antimicrobial interactions: Mechanisms and implications for drug discovery and resistance evolution. Current Opinion in Microbiology. 2015;27:1-9. doi:10.1016/j.mib.2015.05.008","chicago":"Bollenbach, Mark Tobias. “Antimicrobial Interactions: Mechanisms and Implications for Drug Discovery and Resistance Evolution.” Current Opinion in Microbiology. Elsevier, 2015. https://doi.org/10.1016/j.mib.2015.05.008.","short":"M.T. Bollenbach, Current Opinion in Microbiology 27 (2015) 1–9.","mla":"Bollenbach, Mark Tobias. “Antimicrobial Interactions: Mechanisms and Implications for Drug Discovery and Resistance Evolution.” Current Opinion in Microbiology, vol. 27, Elsevier, 2015, pp. 1–9, doi:10.1016/j.mib.2015.05.008."},"publication":"Current Opinion in Microbiology","page":"1 - 9","has_accepted_license":"1","day":"01","scopus_import":1,"author":[{"full_name":"Bollenbach, Mark Tobias","last_name":"Bollenbach","first_name":"Mark Tobias","orcid":"0000-0003-4398-476X","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87"}],"volume":27,"date_updated":"2021-01-12T06:53:21Z","date_created":"2018-12-11T11:54:08Z","year":"2015","department":[{"_id":"ToBo"}],"publisher":"Elsevier","publication_status":"published","ec_funded":1,"publist_id":"5298","file_date_updated":"2020-07-14T12:45:17Z","doi":"10.1016/j.mib.2015.05.008","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"project":[{"_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","grant_number":"P27201-B22","call_identifier":"FWF","name":"Revealing the mechanisms underlying drug interactions"},{"grant_number":"303507","_id":"25E83C2C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Optimality principles in responses to antibiotics"},{"_id":"25EB3A80-B435-11E9-9278-68D0E5697425","grant_number":"RGP0042/2013","name":"Revealing the fundamental limits of cell growth"}],"quality_controlled":"1","month":"06"},{"_id":"1812","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Exotic roton excitations in quadrupolar Bose–Einstein condensates ","ddc":["530"],"status":"public","intvolume":" 17","pubrep_id":"446","file":[{"checksum":"551f751a75b39b89a1db2f7f498f9a49","date_created":"2018-12-12T10:15:59Z","date_updated":"2020-07-14T12:45:17Z","file_id":"5184","relation":"main_file","creator":"system","file_size":1900925,"content_type":"application/pdf","access_level":"open_access","file_name":"IST-2016-446-v1+1_document.pdf"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"We investigate the occurrence of rotons in a quadrupolar Bose–Einstein condensate confined to two dimensions. Depending on the particle density, the ratio of the contact and quadrupole–quadrupole interactions, and the alignment of the quadrupole moments with respect to the confinement plane, the dispersion relation features two or four point-like roton minima or one ring-shaped minimum. We map out the entire parameter space of the roton behavior and identify the instability regions. We propose to observe the exotic rotons by monitoring the characteristic density wave dynamics resulting from a short local perturbation, and discuss the possibilities to detect the predicted effects in state-of-the-art experiments with ultracold homonuclear molecules.\r\n","lang":"eng"}],"issue":"4","publication":"New Journal of Physics","citation":{"short":"M. Lahrz, M. Lemeshko, L. Mathey, New Journal of Physics 17 (2015).","mla":"Lahrz, Martin, et al. “Exotic Roton Excitations in Quadrupolar Bose–Einstein Condensates .” New Journal of Physics, vol. 17, no. 4, 045005, IOP Publishing Ltd., 2015, doi:10.1088/1367-2630/17/4/045005.","chicago":"Lahrz, Martin, Mikhail Lemeshko, and Ludwig Mathey. “Exotic Roton Excitations in Quadrupolar Bose–Einstein Condensates .” New Journal of Physics. IOP Publishing Ltd., 2015. https://doi.org/10.1088/1367-2630/17/4/045005.","ama":"Lahrz M, Lemeshko M, Mathey L. Exotic roton excitations in quadrupolar Bose–Einstein condensates . New Journal of Physics. 2015;17(4). doi:10.1088/1367-2630/17/4/045005","apa":"Lahrz, M., Lemeshko, M., & Mathey, L. (2015). Exotic roton excitations in quadrupolar Bose–Einstein condensates . New Journal of Physics. IOP Publishing Ltd. https://doi.org/10.1088/1367-2630/17/4/045005","ieee":"M. Lahrz, M. Lemeshko, and L. Mathey, “Exotic roton excitations in quadrupolar Bose–Einstein condensates ,” New Journal of Physics, vol. 17, no. 4. IOP Publishing Ltd., 2015.","ista":"Lahrz M, Lemeshko M, Mathey L. 2015. Exotic roton excitations in quadrupolar Bose–Einstein condensates . New Journal of Physics. 17(4), 045005."},"date_published":"2015-04-01T00:00:00Z","scopus_import":1,"day":"01","has_accepted_license":"1","article_processing_charge":"No","year":"2015","publication_status":"published","publisher":"IOP Publishing Ltd.","department":[{"_id":"MiLe"}],"author":[{"first_name":"Martin","last_name":"Lahrz","full_name":"Lahrz, Martin"},{"full_name":"Lemeshko, Mikhail","last_name":"Lemeshko","first_name":"Mikhail","orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Mathey, Ludwig","first_name":"Ludwig","last_name":"Mathey"}],"date_created":"2018-12-11T11:54:09Z","date_updated":"2021-01-12T06:53:22Z","volume":17,"article_number":"045005","file_date_updated":"2020-07-14T12:45:17Z","publist_id":"5294","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","doi":"10.1088/1367-2630/17/4/045005","language":[{"iso":"eng"}],"month":"04"},{"type":"journal_article","abstract":[{"text":"Atomic form factors are widely used for the characterization of targets and specimens, from crystallography to biology. By using recent mathematical results, here we derive an analytical expression for the atomic form factor within the independent particle model constructed from nonrelativistic screened hydrogenic wave functions. The range of validity of this analytical expression is checked by comparing the analytically obtained form factors with the ones obtained within the Hartee-Fock method. As an example, we apply our analytical expression for the atomic form factor to evaluate the differential cross section for Rayleigh scattering off neutral atoms.","lang":"eng"}],"issue":"5","status":"public","title":"Analytical evaluation of atomic form factors: Application to Rayleigh scattering","intvolume":" 56","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1811","oa_version":"Preprint","scopus_import":1,"day":"20","publication":"Journal of Mathematical Physics","citation":{"ieee":"L. Safari, J. Santos, P. Amaro, K. Jänkälä, and F. Fratini, “Analytical evaluation of atomic form factors: Application to Rayleigh scattering,” Journal of Mathematical Physics, vol. 56, no. 5. American Institute of Physics, 2015.","apa":"Safari, L., Santos, J., Amaro, P., Jänkälä, K., & Fratini, F. (2015). Analytical evaluation of atomic form factors: Application to Rayleigh scattering. Journal of Mathematical Physics. American Institute of Physics. https://doi.org/10.1063/1.4921227","ista":"Safari L, Santos J, Amaro P, Jänkälä K, Fratini F. 2015. Analytical evaluation of atomic form factors: Application to Rayleigh scattering. Journal of Mathematical Physics. 56(5), 052105.","ama":"Safari L, Santos J, Amaro P, Jänkälä K, Fratini F. Analytical evaluation of atomic form factors: Application to Rayleigh scattering. Journal of Mathematical Physics. 2015;56(5). doi:10.1063/1.4921227","chicago":"Safari, Laleh, José Santos, Pedro Amaro, Kari Jänkälä, and Filippo Fratini. “Analytical Evaluation of Atomic Form Factors: Application to Rayleigh Scattering.” Journal of Mathematical Physics. American Institute of Physics, 2015. https://doi.org/10.1063/1.4921227.","short":"L. Safari, J. Santos, P. Amaro, K. Jänkälä, F. Fratini, Journal of Mathematical Physics 56 (2015).","mla":"Safari, Laleh, et al. “Analytical Evaluation of Atomic Form Factors: Application to Rayleigh Scattering.” Journal of Mathematical Physics, vol. 56, no. 5, 052105, American Institute of Physics, 2015, doi:10.1063/1.4921227."},"date_published":"2015-05-20T00:00:00Z","article_number":"052105","publist_id":"5295","ec_funded":1,"publication_status":"published","publisher":"American Institute of Physics","department":[{"_id":"MiLe"}],"year":"2015","acknowledgement":"The research leading to these results has received funding from the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement n◦ [291734]. F.F. acknowledges support by Fundação de Amparo à Pesquisa do estado de Minas Gerais (FAPEMIG), by Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), and by the Austrian Science Fund (FWF) through the START Grant No. Y 591-N16.","date_created":"2018-12-11T11:54:08Z","date_updated":"2021-01-12T06:53:21Z","volume":56,"author":[{"full_name":"Safari, Laleh","first_name":"Laleh","last_name":"Safari","id":"3C325E5E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Santos, José","first_name":"José","last_name":"Santos"},{"full_name":"Amaro, Pedro","last_name":"Amaro","first_name":"Pedro"},{"full_name":"Jänkälä, Kari","first_name":"Kari","last_name":"Jänkälä"},{"full_name":"Fratini, Filippo","last_name":"Fratini","first_name":"Filippo"}],"month":"05","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"main_file_link":[{"url":"http://arxiv.org/abs/1409.0110","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1063/1.4921227"},{"day":"18","month":"05","scopus_import":1,"language":[{"iso":"eng"}],"doi":"10.1103/PhysRevLett.114.203001","date_published":"2015-05-18T00:00:00Z","quality_controlled":"1","main_file_link":[{"url":"http://arxiv.org/abs/1502.03447","open_access":"1"}],"oa":1,"citation":{"chicago":"Schmidt, Richard, and Mikhail Lemeshko. “Rotation of Quantum Impurities in the Presence of a Many-Body Environment.” Physical Review Letters. American Physical Society, 2015. https://doi.org/10.1103/PhysRevLett.114.203001.","short":"R. Schmidt, M. Lemeshko, Physical Review Letters 114 (2015).","mla":"Schmidt, Richard, and Mikhail Lemeshko. “Rotation of Quantum Impurities in the Presence of a Many-Body Environment.” Physical Review Letters, vol. 114, no. 20, 203001, American Physical Society, 2015, doi:10.1103/PhysRevLett.114.203001.","apa":"Schmidt, R., & Lemeshko, M. (2015). Rotation of quantum impurities in the presence of a many-body environment. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.114.203001","ieee":"R. Schmidt and M. Lemeshko, “Rotation of quantum impurities in the presence of a many-body environment,” Physical Review Letters, vol. 114, no. 20. American Physical Society, 2015.","ista":"Schmidt R, Lemeshko M. 2015. Rotation of quantum impurities in the presence of a many-body environment. Physical Review Letters. 114(20), 203001.","ama":"Schmidt R, Lemeshko M. Rotation of quantum impurities in the presence of a many-body environment. Physical Review Letters. 2015;114(20). doi:10.1103/PhysRevLett.114.203001"},"publication":"Physical Review Letters","issue":"20","publist_id":"5293","abstract":[{"text":"We develop a microscopic theory describing a quantum impurity whose rotational degree of freedom is coupled to a many-particle bath. We approach the problem by introducing the concept of an “angulon”—a quantum rotor dressed by a quantum field—and reveal its quasiparticle properties using a combination of variational and diagrammatic techniques. Our theory predicts renormalization of the impurity rotational structure, such as that observed in experiments with molecules in superfluid helium droplets, in terms of a rotational Lamb shift induced by the many-particle environment. Furthermore, we discover a rich many-body-induced fine structure, emerging in rotational spectra due to a redistribution of angular momentum within the quantum many-body system.","lang":"eng"}],"type":"journal_article","article_number":"203001","oa_version":"Preprint","volume":114,"date_created":"2018-12-11T11:54:09Z","date_updated":"2021-01-12T06:53:22Z","author":[{"full_name":"Schmidt, Richard","last_name":"Schmidt","first_name":"Richard"},{"orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","last_name":"Lemeshko","first_name":"Mikhail","full_name":"Lemeshko, Mikhail"}],"publisher":"American Physical Society","department":[{"_id":"MiLe"}],"intvolume":" 114","status":"public","title":"Rotation of quantum impurities in the presence of a many-body environment","publication_status":"published","_id":"1813","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2015"},{"department":[{"_id":"ToHe"}],"publisher":"ACM","intvolume":" 25","title":"Guest editors' introduction to special issue on computational methods in systems biology","publication_status":"published","status":"public","_id":"1808","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2015","volume":25,"oa_version":"None","date_created":"2018-12-11T11:54:07Z","date_updated":"2021-01-12T06:53:20Z","author":[{"full_name":"Gupta, Ashutosh","first_name":"Ashutosh","last_name":"Gupta","id":"335E5684-F248-11E8-B48F-1D18A9856A87"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","first_name":"Thomas A","last_name":"Henzinger","full_name":"Henzinger, Thomas A"}],"type":"journal_article","article_number":"7","issue":"2","publist_id":"5302","quality_controlled":"1","citation":{"mla":"Gupta, Ashutosh, and Thomas A. Henzinger. “Guest Editors’ Introduction to Special Issue on Computational Methods in Systems Biology.” ACM Transactions on Modeling and Computer Simulation, vol. 25, no. 2, 7, ACM, 2015, doi:10.1145/2745799.","short":"A. Gupta, T.A. Henzinger, ACM Transactions on Modeling and Computer Simulation 25 (2015).","chicago":"Gupta, Ashutosh, and Thomas A Henzinger. “Guest Editors’ Introduction to Special Issue on Computational Methods in Systems Biology.” ACM Transactions on Modeling and Computer Simulation. ACM, 2015. https://doi.org/10.1145/2745799.","ama":"Gupta A, Henzinger TA. Guest editors’ introduction to special issue on computational methods in systems biology. ACM Transactions on Modeling and Computer Simulation. 2015;25(2). doi:10.1145/2745799","ista":"Gupta A, Henzinger TA. 2015. Guest editors’ introduction to special issue on computational methods in systems biology. ACM Transactions on Modeling and Computer Simulation. 25(2), 7.","apa":"Gupta, A., & Henzinger, T. A. (2015). Guest editors’ introduction to special issue on computational methods in systems biology. ACM Transactions on Modeling and Computer Simulation. ACM. https://doi.org/10.1145/2745799","ieee":"A. Gupta and T. A. Henzinger, “Guest editors’ introduction to special issue on computational methods in systems biology,” ACM Transactions on Modeling and Computer Simulation, vol. 25, no. 2. ACM, 2015."},"publication":"ACM Transactions on Modeling and Computer Simulation","language":[{"iso":"eng"}],"doi":"10.1145/2745799","date_published":"2015-05-01T00:00:00Z","day":"01","month":"05"},{"month":"03","external_id":{"pmid":["25778702"]},"oa":1,"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4720436/"}],"quality_controlled":"1","doi":"10.1038/nature14215","language":[{"iso":"eng"}],"publist_id":"5289","pmid":1,"year":"2015","department":[{"_id":"CaHe"}],"publisher":"Nature Publishing Group","publication_status":"published","author":[{"full_name":"Porazinski, Sean","last_name":"Porazinski","first_name":"Sean"},{"first_name":"Huijia","last_name":"Wang","full_name":"Wang, Huijia"},{"last_name":"Asaoka","first_name":"Yoichi","full_name":"Asaoka, Yoichi"},{"id":"3ECECA3A-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","last_name":"Behrndt","full_name":"Behrndt, Martin"},{"first_name":"Tatsuo","last_name":"Miyamoto","full_name":"Miyamoto, Tatsuo"},{"full_name":"Morita, Hitoshi","id":"4C6E54C6-F248-11E8-B48F-1D18A9856A87","first_name":"Hitoshi","last_name":"Morita"},{"full_name":"Hata, Shoji","first_name":"Shoji","last_name":"Hata"},{"last_name":"Sasaki","first_name":"Takashi","full_name":"Sasaki, Takashi"},{"full_name":"Krens, Gabriel","id":"2B819732-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4761-5996","first_name":"Gabriel","last_name":"Krens"},{"last_name":"Osada","first_name":"Yumi","full_name":"Osada, Yumi"},{"first_name":"Satoshi","last_name":"Asaka","full_name":"Asaka, Satoshi"},{"full_name":"Momoi, Akihiro","last_name":"Momoi","first_name":"Akihiro"},{"full_name":"Linton, Sarah","first_name":"Sarah","last_name":"Linton"},{"last_name":"Miesfeld","first_name":"Joel","full_name":"Miesfeld, Joel"},{"full_name":"Link, Brian","last_name":"Link","first_name":"Brian"},{"full_name":"Senga, Takeshi","last_name":"Senga","first_name":"Takeshi"},{"last_name":"Castillo Morales","first_name":"Atahualpa","full_name":"Castillo Morales, Atahualpa"},{"full_name":"Urrutia, Araxi","last_name":"Urrutia","first_name":"Araxi"},{"first_name":"Nobuyoshi","last_name":"Shimizu","full_name":"Shimizu, Nobuyoshi"},{"full_name":"Nagase, Hideaki","last_name":"Nagase","first_name":"Hideaki"},{"first_name":"Shinya","last_name":"Matsuura","full_name":"Matsuura, Shinya"},{"last_name":"Bagby","first_name":"Stefan","full_name":"Bagby, Stefan"},{"last_name":"Kondoh","first_name":"Hisato","full_name":"Kondoh, Hisato"},{"full_name":"Nishina, Hiroshi","last_name":"Nishina","first_name":"Hiroshi"},{"last_name":"Heisenberg","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J"},{"full_name":"Furutani Seiki, Makoto","last_name":"Furutani Seiki","first_name":"Makoto"}],"volume":521,"date_created":"2018-12-11T11:54:10Z","date_updated":"2021-01-12T06:53:23Z","scopus_import":1,"day":"16","citation":{"short":"S. Porazinski, H. Wang, Y. Asaoka, M. Behrndt, T. Miyamoto, H. Morita, S. Hata, T. Sasaki, G. Krens, Y. Osada, S. Asaka, A. Momoi, S. Linton, J. Miesfeld, B. Link, T. Senga, A. Castillo Morales, A. Urrutia, N. Shimizu, H. Nagase, S. Matsuura, S. Bagby, H. Kondoh, H. Nishina, C.-P.J. Heisenberg, M. Furutani Seiki, Nature 521 (2015) 217–221.","mla":"Porazinski, Sean, et al. “YAP Is Essential for Tissue Tension to Ensure Vertebrate 3D Body Shape.” Nature, vol. 521, no. 7551, Nature Publishing Group, 2015, pp. 217–21, doi:10.1038/nature14215.","chicago":"Porazinski, Sean, Huijia Wang, Yoichi Asaoka, Martin Behrndt, Tatsuo Miyamoto, Hitoshi Morita, Shoji Hata, et al. “YAP Is Essential for Tissue Tension to Ensure Vertebrate 3D Body Shape.” Nature. Nature Publishing Group, 2015. https://doi.org/10.1038/nature14215.","ama":"Porazinski S, Wang H, Asaoka Y, et al. YAP is essential for tissue tension to ensure vertebrate 3D body shape. Nature. 2015;521(7551):217-221. doi:10.1038/nature14215","ieee":"S. Porazinski et al., “YAP is essential for tissue tension to ensure vertebrate 3D body shape,” Nature, vol. 521, no. 7551. Nature Publishing Group, pp. 217–221, 2015.","apa":"Porazinski, S., Wang, H., Asaoka, Y., Behrndt, M., Miyamoto, T., Morita, H., … Furutani Seiki, M. (2015). YAP is essential for tissue tension to ensure vertebrate 3D body shape. Nature. Nature Publishing Group. https://doi.org/10.1038/nature14215","ista":"Porazinski S, Wang H, Asaoka Y, Behrndt M, Miyamoto T, Morita H, Hata S, Sasaki T, Krens G, Osada Y, Asaka S, Momoi A, Linton S, Miesfeld J, Link B, Senga T, Castillo Morales A, Urrutia A, Shimizu N, Nagase H, Matsuura S, Bagby S, Kondoh H, Nishina H, Heisenberg C-PJ, Furutani Seiki M. 2015. YAP is essential for tissue tension to ensure vertebrate 3D body shape. Nature. 521(7551), 217–221."},"publication":"Nature","page":"217 - 221","date_published":"2015-03-16T00:00:00Z","type":"journal_article","issue":"7551","abstract":[{"lang":"eng","text":"Vertebrates have a unique 3D body shape in which correct tissue and organ shape and alignment are essential for function. For example, vision requires the lens to be centred in the eye cup which must in turn be correctly positioned in the head. Tissue morphogenesis depends on force generation, force transmission through the tissue, and response of tissues and extracellular matrix to force. Although a century ago D'Arcy Thompson postulated that terrestrial animal body shapes are conditioned by gravity, there has been no animal model directly demonstrating how the aforementioned mechano-morphogenetic processes are coordinated to generate a body shape that withstands gravity. Here we report a unique medaka fish (Oryzias latipes) mutant, hirame (hir), which is sensitive to deformation by gravity. hir embryos display a markedly flattened body caused by mutation of YAP, a nuclear executor of Hippo signalling that regulates organ size. We show that actomyosin-mediated tissue tension is reduced in hir embryos, leading to tissue flattening and tissue misalignment, both of which contribute to body flattening. By analysing YAP function in 3D spheroids of human cells, we identify the Rho GTPase activating protein ARHGAP18 as an effector of YAP in controlling tissue tension. Together, these findings reveal a previously unrecognised function of YAP in regulating tissue shape and alignment required for proper 3D body shape. Understanding this morphogenetic function of YAP could facilitate the use of embryonic stem cells to generate complex organs requiring correct alignment of multiple tissues. "}],"_id":"1817","user_id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","intvolume":" 521","title":"YAP is essential for tissue tension to ensure vertebrate 3D body shape","status":"public","oa_version":"Submitted Version"},{"month":"06","external_id":{"arxiv":["1411.3880"]},"oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1411.3880"}],"project":[{"grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"}],"quality_controlled":"1","conference":{"name":"IAAI: Innovative Applications of Artificial Intelligence","end_date":"2015-01-30","start_date":"2015-01-25","location":"Austin, TX, USA"},"language":[{"iso":"eng"}],"publist_id":"5286","ec_funded":1,"acknowledgement":" The research was partly supported by Austrian Science Fund (FWF) Grant No P23499-N23, FWF NFN Grant No S11407-N23 (RiSE), ERC Start grant (279307: Graph Games), and Microsoft faculty fellows award.","year":"2015","department":[{"_id":"KrCh"}],"publisher":"AAAI Press","publication_status":"published","related_material":{"record":[{"id":"1529","status":"public","relation":"later_version"}]},"author":[{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"full_name":"Chmelik, Martin","id":"3624234E-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","last_name":"Chmelik"},{"full_name":"Gupta, Raghav","first_name":"Raghav","last_name":"Gupta"},{"last_name":"Kanodia","first_name":"Ayush","full_name":"Kanodia, Ayush"}],"volume":5,"date_updated":"2023-02-23T10:02:57Z","date_created":"2018-12-11T11:54:11Z","scopus_import":1,"day":"01","citation":{"mla":"Chatterjee, Krishnendu, et al. “Optimal Cost Almost-Sure Reachability in POMDPs.” Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence , vol. 5, AAAI Press, 2015, pp. 3496–502.","short":"K. Chatterjee, M. Chmelik, R. Gupta, A. Kanodia, in:, Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence , AAAI Press, 2015, pp. 3496–3502.","chicago":"Chatterjee, Krishnendu, Martin Chmelik, Raghav Gupta, and Ayush Kanodia. “Optimal Cost Almost-Sure Reachability in POMDPs.” In Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence , 5:3496–3502. AAAI Press, 2015.","ama":"Chatterjee K, Chmelik M, Gupta R, Kanodia A. Optimal cost almost-sure reachability in POMDPs. In: Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence . Vol 5. AAAI Press; 2015:3496-3502.","ista":"Chatterjee K, Chmelik M, Gupta R, Kanodia A. 2015. Optimal cost almost-sure reachability in POMDPs. Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence . IAAI: Innovative Applications of Artificial Intelligence, Artifical Intelligence, vol. 5, 3496–3502.","apa":"Chatterjee, K., Chmelik, M., Gupta, R., & Kanodia, A. (2015). Optimal cost almost-sure reachability in POMDPs. In Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence (Vol. 5, pp. 3496–3502). Austin, TX, USA: AAAI Press.","ieee":"K. Chatterjee, M. Chmelik, R. Gupta, and A. Kanodia, “Optimal cost almost-sure reachability in POMDPs,” in Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence , Austin, TX, USA, 2015, vol. 5, pp. 3496–3502."},"publication":"Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence ","page":"3496-3502","date_published":"2015-06-01T00:00:00Z","type":"conference","alternative_title":["Artifical Intelligence"],"abstract":[{"lang":"eng","text":"We consider partially observable Markov decision processes (POMDPs) with a set of target states and every transition is associated with an integer cost. The optimization objec- tive we study asks to minimize the expected total cost till the target set is reached, while ensuring that the target set is reached almost-surely (with probability 1). We show that for integer costs approximating the optimal cost is undecidable. For positive costs, our results are as follows: (i) we establish matching lower and upper bounds for the optimal cost and the bound is double exponential; (ii) we show that the problem of approximating the optimal cost is decidable and present ap- proximation algorithms developing on the existing algorithms for POMDPs with finite-horizon objectives. While the worst- case running time of our algorithm is double exponential, we present efficient stopping criteria for the algorithm and show experimentally that it performs well in many examples."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1820","intvolume":" 5","title":"Optimal cost almost-sure reachability in POMDPs","status":"public","oa_version":"Preprint"},{"doi":"10.1145/2714572","language":[{"iso":"eng"}],"oa":1,"quality_controlled":"1","project":[{"_id":"25357BD2-B435-11E9-9278-68D0E5697425","grant_number":"P 24352-N23","call_identifier":"FWF","name":"Deep Pictures: Creating Visual and Haptic Vector Images"},{"grant_number":"638176","_id":"2533E772-B435-11E9-9278-68D0E5697425","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","call_identifier":"H2020"}],"month":"04","author":[{"first_name":"Stefan","last_name":"Jeschke","id":"44D6411A-F248-11E8-B48F-1D18A9856A87","full_name":"Jeschke, Stefan"},{"orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","last_name":"Wojtan","first_name":"Christopher J","full_name":"Wojtan, Christopher J"}],"date_created":"2018-12-11T11:54:09Z","date_updated":"2023-02-23T10:15:40Z","volume":34,"year":"2015","publication_status":"published","publisher":"ACM","department":[{"_id":"ChWo"}],"file_date_updated":"2020-07-14T12:45:17Z","publist_id":"5292","ec_funded":1,"article_number":"27","date_published":"2015-04-01T00:00:00Z","publication":"ACM Transactions on Graphics","citation":{"mla":"Jeschke, Stefan, and Chris Wojtan. “Water Wave Animation via Wavefront Parameter Interpolation.” ACM Transactions on Graphics, vol. 34, no. 3, 27, ACM, 2015, doi:10.1145/2714572.","short":"S. Jeschke, C. Wojtan, ACM Transactions on Graphics 34 (2015).","chicago":"Jeschke, Stefan, and Chris Wojtan. “Water Wave Animation via Wavefront Parameter Interpolation.” ACM Transactions on Graphics. ACM, 2015. https://doi.org/10.1145/2714572.","ama":"Jeschke S, Wojtan C. Water wave animation via wavefront parameter interpolation. ACM Transactions on Graphics. 2015;34(3). doi:10.1145/2714572","ista":"Jeschke S, Wojtan C. 2015. Water wave animation via wavefront parameter interpolation. ACM Transactions on Graphics. 34(3), 27.","ieee":"S. Jeschke and C. Wojtan, “Water wave animation via wavefront parameter interpolation,” ACM Transactions on Graphics, vol. 34, no. 3. ACM, 2015.","apa":"Jeschke, S., & Wojtan, C. (2015). Water wave animation via wavefront parameter interpolation. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/2714572"},"day":"01","has_accepted_license":"1","scopus_import":1,"pubrep_id":"575","oa_version":"Submitted Version","file":[{"file_name":"IST-2016-575-v1+1_wavefront_preprint.pdf","access_level":"open_access","file_size":23712153,"content_type":"application/pdf","creator":"system","relation":"main_file","file_id":"4933","date_created":"2018-12-12T10:12:15Z","date_updated":"2020-07-14T12:45:17Z","checksum":"67c9f4fa370def68cdf31299e48bc91f"}],"_id":"1814","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["000"],"status":"public","title":"Water wave animation via wavefront parameter interpolation","intvolume":" 34","abstract":[{"lang":"eng","text":"We present an efficient wavefront tracking algorithm for animating bodies of water that interact with their environment. Our contributions include: a novel wavefront tracking technique that enables dispersion, refraction, reflection, and diffraction in the same simulation; a unique multivalued function interpolation method that enables our simulations to elegantly sidestep the Nyquist limit; a dispersion approximation for efficiently amplifying the number of simulated waves by several orders of magnitude; and additional extensions that allow for time-dependent effects and interactive artistic editing of the resulting animation. Our contributions combine to give us multitudes more wave details than similar algorithms, while maintaining high frame rates and allowing close camera zooms."}],"issue":"3","type":"journal_article"},{"oa_version":"Submitted Version","_id":"1818","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 112","status":"public","title":"Limits to adaptation along environmental gradients","issue":"20","abstract":[{"lang":"eng","text":"Why do species not adapt to ever-wider ranges of conditions, gradually expanding their ecological niche and geographic range? Gene flow across environments has two conflicting effects: although it increases genetic variation, which is a prerequisite for adaptation, gene flow may swamp adaptation to local conditions. In 1956, Haldane proposed that, when the environment varies across space, "swamping" by gene flow creates a positive feedback between low population size and maladaptation, leading to a sharp range margin. However, current deterministic theory shows that, when variance can evolve, there is no such limit. Using simple analytical tools and simulations, we show that genetic drift can generate a sharp margin to a species' range, by reducing genetic variance below the level needed for adaptation to spatially variable conditions. Aided by separation of ecological and evolutionary timescales, the identified effective dimensionless parameters reveal a simple threshold that predicts when adaptation at the range margin fails. Two observable parameters determine the threshold: (i) the effective environmental gradient, which can be measured by the loss of fitness due to dispersal to a different environment; and (ii) the efficacy of selection relative to genetic drift. The theory predicts sharp range margins even in the absence of abrupt changes in the environment. Furthermore, it implies that gradual worsening of conditions across a species' habitat may lead to a sudden range fragmentation, when adaptation to a wide span of conditions within a single species becomes impossible."}],"type":"journal_article","date_published":"2015-05-19T00:00:00Z","citation":{"ieee":"J. Polechova and N. H. Barton, “Limits to adaptation along environmental gradients,” PNAS, vol. 112, no. 20. National Academy of Sciences, pp. 6401–6406, 2015.","apa":"Polechova, J., & Barton, N. H. (2015). Limits to adaptation along environmental gradients. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1421515112","ista":"Polechova J, Barton NH. 2015. Limits to adaptation along environmental gradients. PNAS. 112(20), 6401–6406.","ama":"Polechova J, Barton NH. Limits to adaptation along environmental gradients. PNAS. 2015;112(20):6401-6406. doi:10.1073/pnas.1421515112","chicago":"Polechova, Jitka, and Nicholas H Barton. “Limits to Adaptation along Environmental Gradients.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1421515112.","short":"J. Polechova, N.H. Barton, PNAS 112 (2015) 6401–6406.","mla":"Polechova, Jitka, and Nicholas H. Barton. “Limits to Adaptation along Environmental Gradients.” PNAS, vol. 112, no. 20, National Academy of Sciences, 2015, pp. 6401–06, doi:10.1073/pnas.1421515112."},"publication":"PNAS","page":"6401 - 6406","day":"19","scopus_import":1,"author":[{"full_name":"Polechova, Jitka","id":"3BBFB084-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0951-3112","first_name":"Jitka","last_name":"Polechova"},{"first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"}],"volume":112,"date_created":"2018-12-11T11:54:11Z","date_updated":"2021-01-12T06:53:24Z","pmid":1,"year":"2015","department":[{"_id":"NiBa"}],"publisher":"National Academy of Sciences","publication_status":"published","publist_id":"5288","ec_funded":1,"doi":"10.1073/pnas.1421515112","language":[{"iso":"eng"}],"external_id":{"pmid":["25941385"]},"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4443383/","open_access":"1"}],"oa":1,"project":[{"call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","month":"05"},{"page":"1175 - 1187","publication":"Molecular Plant","citation":{"ista":"Zwiewka M, Nodzyński T, Robert S, Vanneste S, Friml J. 2015. Osmotic stress modulates the balance between exocytosis and clathrin mediated endocytosis in Arabidopsis thaliana. Molecular Plant. 8(8), 1175–1187.","ieee":"M. Zwiewka, T. Nodzyński, S. Robert, S. Vanneste, and J. Friml, “Osmotic stress modulates the balance between exocytosis and clathrin mediated endocytosis in Arabidopsis thaliana,” Molecular Plant, vol. 8, no. 8. Elsevier, pp. 1175–1187, 2015.","apa":"Zwiewka, M., Nodzyński, T., Robert, S., Vanneste, S., & Friml, J. (2015). Osmotic stress modulates the balance between exocytosis and clathrin mediated endocytosis in Arabidopsis thaliana. Molecular Plant. Elsevier. https://doi.org/10.1016/j.molp.2015.03.007","ama":"Zwiewka M, Nodzyński T, Robert S, Vanneste S, Friml J. Osmotic stress modulates the balance between exocytosis and clathrin mediated endocytosis in Arabidopsis thaliana. Molecular Plant. 2015;8(8):1175-1187. doi:10.1016/j.molp.2015.03.007","chicago":"Zwiewka, Marta, Tomasz Nodzyński, Stéphanie Robert, Steffen Vanneste, and Jiří Friml. “Osmotic Stress Modulates the Balance between Exocytosis and Clathrin Mediated Endocytosis in Arabidopsis Thaliana.” Molecular Plant. Elsevier, 2015. https://doi.org/10.1016/j.molp.2015.03.007.","mla":"Zwiewka, Marta, et al. “Osmotic Stress Modulates the Balance between Exocytosis and Clathrin Mediated Endocytosis in Arabidopsis Thaliana.” Molecular Plant, vol. 8, no. 8, Elsevier, 2015, pp. 1175–87, doi:10.1016/j.molp.2015.03.007.","short":"M. Zwiewka, T. Nodzyński, S. Robert, S. Vanneste, J. Friml, Molecular Plant 8 (2015) 1175–1187."},"date_published":"2015-08-03T00:00:00Z","scopus_import":1,"day":"03","status":"public","title":"Osmotic stress modulates the balance between exocytosis and clathrin mediated endocytosis in Arabidopsis thaliana","intvolume":" 8","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1819","oa_version":"None","type":"journal_article","abstract":[{"lang":"eng","text":"The sessile life style of plants creates the need to deal with an often adverse environment, in which water availability can change on a daily basis, challenging the cellular physiology and integrity. Changes in osmotic conditions disrupt the equilibrium of the plasma membrane: hypoosmotic conditions increase and hyperosmotic environment decrease the cell volume. Here, we show that short-term extracellular osmotic treatments are closely followed by a shift in the balance between endocytosis and exocytosis in root meristem cells. Acute hyperosmotic treatments (ionic and nonionic) enhance clathrin-mediated endocytosis simultaneously attenuating exocytosis, whereas hypoosmotic treatments have the opposite effects. In addition to clathrin recruitment to the plasma membrane, components of early endocytic trafficking are essential during hyperosmotic stress responses. Consequently, growth of seedlings defective in elements of clathrin or early endocytic machinery is more sensitive to hyperosmotic treatments. We also found that the endocytotic response to a change of osmotic status in the environment is dominant over the presumably evolutionary more recent regulatory effect of plant hormones, such as auxin. These results imply that osmotic perturbation influences the balance between endocytosis and exocytosis acting through clathrin-mediated endocytosis. We propose that tension on the plasma membrane determines the addition or removal of membranes at the cell surface, thus preserving cell integrity."}],"issue":"8","quality_controlled":"1","project":[{"name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7","grant_number":"282300","_id":"25716A02-B435-11E9-9278-68D0E5697425"}],"language":[{"iso":"eng"}],"doi":"10.1016/j.molp.2015.03.007","month":"08","publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"Elsevier","acknowledgement":"This work was supported by the European Research Council (project ERC-2011-StG-20101109-PSDP); European Social Fund (CZ.1.07/2.3.00/20.0043) and the Czech Science Foundation GAČR (GA13-40637S) to J.F.; project Postdoc I. (CZ.1.07/2.3.00/30.0009) co-financed by the European Social Fund and the state budget of the Czech Republic to M.Z. and T.N..","year":"2015","date_created":"2018-12-11T11:54:11Z","date_updated":"2021-01-12T06:53:24Z","volume":8,"author":[{"first_name":"Marta","last_name":"Zwiewka","full_name":"Zwiewka, Marta"},{"full_name":"Nodzyński, Tomasz","last_name":"Nodzyński","first_name":"Tomasz"},{"full_name":"Robert, Stéphanie","last_name":"Robert","first_name":"Stéphanie"},{"full_name":"Vanneste, Steffen","first_name":"Steffen","last_name":"Vanneste"},{"full_name":"Friml, Jiřĺ","first_name":"Jiřĺ","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"}],"ec_funded":1,"publist_id":"5287"},{"type":"journal_article","abstract":[{"lang":"eng","text":"Abstract Drug combinations are increasingly important in disease treatments, for combating drug resistance, and for elucidating fundamental relationships in cell physiology. When drugs are combined, their individual effects on cells may be amplified or weakened. Such drug interactions are crucial for treatment efficacy, but their underlying mechanisms remain largely unknown. To uncover the causes of drug interactions, we developed a systematic approach based on precise quantification of the individual and joint effects of antibiotics on growth of genome-wide Escherichia coli gene deletion strains. We found that drug interactions between antibiotics representing the main modes of action are highly robust to genetic perturbation. This robustness is encapsulated in a general principle of bacterial growth, which enables the quantitative prediction of mutant growth rates under drug combinations. Rare violations of this principle exposed recurring cellular functions controlling drug interactions. In particular, we found that polysaccharide and ATP synthesis control multiple drug interactions with previously unexplained mechanisms, and small molecule adjuvants targeting these functions synthetically reshape drug interactions in predictable ways. These results provide a new conceptual framework for the design of multidrug combinations and suggest that there are universal mechanisms at the heart of most drug interactions. Synopsis A general principle of bacterial growth enables the prediction of mutant growth rates under drug combinations. Rare violations of this principle expose cellular functions that control drug interactions and can be targeted by small molecules to alter drug interactions in predictable ways. Drug interactions between antibiotics are highly robust to genetic perturbations. A general principle of bacterial growth enables the prediction of mutant growth rates under drug combinations. Rare violations of this principle expose cellular functions that control drug interactions. Diverse drug interactions are controlled by recurring cellular functions, including LPS synthesis and ATP synthesis. A general principle of bacterial growth enables the prediction of mutant growth rates under drug combinations. Rare violations of this principle expose cellular functions that control drug interactions and can be targeted by small molecules to alter drug interactions in predictable ways."}],"issue":"4","ddc":["570"],"title":"Systematic discovery of drug interaction mechanisms","status":"public","intvolume":" 11","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1823","oa_version":"Published Version","file":[{"date_created":"2018-12-12T10:14:34Z","date_updated":"2020-07-14T12:45:17Z","checksum":"4289b518fbe2166682fb1a1ef9b405f3","file_id":"5087","relation":"main_file","creator":"system","content_type":"application/pdf","file_size":1273573,"file_name":"IST-2015-395-v1+1_807.full.pdf","access_level":"open_access"}],"pubrep_id":"395","scopus_import":1,"day":"01","has_accepted_license":"1","publication":"Molecular Systems Biology","citation":{"ama":"Chevereau G, Bollenbach MT. Systematic discovery of drug interaction mechanisms. Molecular Systems Biology. 2015;11(4). doi:10.15252/msb.20156098","apa":"Chevereau, G., & Bollenbach, M. T. (2015). Systematic discovery of drug interaction mechanisms. Molecular Systems Biology. Nature Publishing Group. https://doi.org/10.15252/msb.20156098","ieee":"G. Chevereau and M. T. Bollenbach, “Systematic discovery of drug interaction mechanisms,” Molecular Systems Biology, vol. 11, no. 4. Nature Publishing Group, 2015.","ista":"Chevereau G, Bollenbach MT. 2015. Systematic discovery of drug interaction mechanisms. Molecular Systems Biology. 11(4), 807.","short":"G. Chevereau, M.T. Bollenbach, Molecular Systems Biology 11 (2015).","mla":"Chevereau, Guillaume, and Mark Tobias Bollenbach. “Systematic Discovery of Drug Interaction Mechanisms.” Molecular Systems Biology, vol. 11, no. 4, 807, Nature Publishing Group, 2015, doi:10.15252/msb.20156098.","chicago":"Chevereau, Guillaume, and Mark Tobias Bollenbach. “Systematic Discovery of Drug Interaction Mechanisms.” Molecular Systems Biology. Nature Publishing Group, 2015. https://doi.org/10.15252/msb.20156098."},"date_published":"2015-04-01T00:00:00Z","article_number":"807","file_date_updated":"2020-07-14T12:45:17Z","publist_id":"5283","ec_funded":1,"publication_status":"published","publisher":"Nature Publishing Group","department":[{"_id":"ToBo"}],"year":"2015","date_created":"2018-12-11T11:54:12Z","date_updated":"2021-01-12T06:53:26Z","volume":11,"author":[{"full_name":"Chevereau, Guillaume","id":"424D78A0-F248-11E8-B48F-1D18A9856A87","first_name":"Guillaume","last_name":"Chevereau"},{"full_name":"Bollenbach, Mark Tobias","orcid":"0000-0003-4398-476X","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","last_name":"Bollenbach","first_name":"Mark Tobias"}],"month":"04","quality_controlled":"1","project":[{"call_identifier":"FWF","name":"Revealing the mechanisms underlying drug interactions","grant_number":"P27201-B22","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425"},{"_id":"25EB3A80-B435-11E9-9278-68D0E5697425","grant_number":"RGP0042/2013","name":"Revealing the fundamental limits of cell growth"},{"grant_number":"303507","_id":"25E83C2C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Optimality principles in responses to antibiotics"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.15252/msb.20156098"},{"month":"04","doi":"10.1038/ncomms7977","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","publist_id":"5282","file_date_updated":"2020-07-14T12:45:17Z","article_number":"6977","author":[{"full_name":"Knebel, Johannes","last_name":"Knebel","first_name":"Johannes"},{"last_name":"Weber","first_name":"Markus","full_name":"Weber, Markus"},{"full_name":"Krüger, Torben H","first_name":"Torben H","last_name":"Krüger","id":"3020C786-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4821-3297"},{"full_name":"Frey, Erwin","first_name":"Erwin","last_name":"Frey"}],"volume":6,"date_created":"2018-12-11T11:54:13Z","date_updated":"2021-01-12T06:53:26Z","year":"2015","publisher":"Nature Publishing Group","department":[{"_id":"LaEr"}],"publication_status":"published","has_accepted_license":"1","day":"24","scopus_import":1,"date_published":"2015-04-24T00:00:00Z","citation":{"chicago":"Knebel, Johannes, Markus Weber, Torben H Krüger, and Erwin Frey. “Evolutionary Games of Condensates in Coupled Birth-Death Processes.” Nature Communications. Nature Publishing Group, 2015. https://doi.org/10.1038/ncomms7977.","mla":"Knebel, Johannes, et al. “Evolutionary Games of Condensates in Coupled Birth-Death Processes.” Nature Communications, vol. 6, 6977, Nature Publishing Group, 2015, doi:10.1038/ncomms7977.","short":"J. Knebel, M. Weber, T.H. Krüger, E. Frey, Nature Communications 6 (2015).","ista":"Knebel J, Weber M, Krüger TH, Frey E. 2015. Evolutionary games of condensates in coupled birth-death processes. Nature Communications. 6, 6977.","apa":"Knebel, J., Weber, M., Krüger, T. H., & Frey, E. (2015). Evolutionary games of condensates in coupled birth-death processes. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms7977","ieee":"J. Knebel, M. Weber, T. H. Krüger, and E. Frey, “Evolutionary games of condensates in coupled birth-death processes,” Nature Communications, vol. 6. Nature Publishing Group, 2015.","ama":"Knebel J, Weber M, Krüger TH, Frey E. Evolutionary games of condensates in coupled birth-death processes. Nature Communications. 2015;6. doi:10.1038/ncomms7977"},"publication":"Nature Communications","abstract":[{"lang":"eng","text":"Condensation phenomena arise through a collective behaviour of particles. They are observed in both classical and quantum systems, ranging from the formation of traffic jams in mass transport models to the macroscopic occupation of the energetic ground state in ultra-cold bosonic gases (Bose-Einstein condensation). Recently, it has been shown that a driven and dissipative system of bosons may form multiple condensates. Which states become the condensates has, however, remained elusive thus far. The dynamics of this condensation are described by coupled birth-death processes, which also occur in evolutionary game theory. Here we apply concepts from evolutionary game theory to explain the formation of multiple condensates in such driven-dissipative bosonic systems. We show that the vanishing of relative entropy production determines their selection. The condensation proceeds exponentially fast, but the system never comes to rest. Instead, the occupation numbers of condensates may oscillate, as we demonstrate for a rock-paper-scissors game of condensates."}],"type":"journal_article","pubrep_id":"451","file":[{"checksum":"c4cffb5c8b245e658a34eac71a03e7cc","date_created":"2018-12-12T10:16:54Z","date_updated":"2020-07-14T12:45:17Z","relation":"main_file","file_id":"5245","file_size":1151501,"content_type":"application/pdf","creator":"system","access_level":"open_access","file_name":"IST-2016-451-v1+1_ncomms7977.pdf"}],"oa_version":"Published Version","_id":"1824","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 6","status":"public","ddc":["530"],"title":"Evolutionary games of condensates in coupled birth-death processes"},{"day":"01","scopus_import":1,"date_published":"2015-05-01T00:00:00Z","citation":{"short":"P. Kappeler, S. Cremer, C. Nunn, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 370 (2015).","mla":"Kappeler, Peter, et al. “Sociality and Health: Impacts of Sociality on Disease Susceptibility and Transmission in Animal and Human Societies.” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, vol. 370, no. 1669, 20140116, Royal Society, 2015, doi:10.1098/rstb.2014.0116.","chicago":"Kappeler, Peter, Sylvia Cremer, and Charles Nunn. “Sociality and Health: Impacts of Sociality on Disease Susceptibility and Transmission in Animal and Human Societies.” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. Royal Society, 2015. https://doi.org/10.1098/rstb.2014.0116.","ama":"Kappeler P, Cremer S, Nunn C. Sociality and health: Impacts of sociality on disease susceptibility and transmission in animal and human societies. Philosophical Transactions of the Royal Society of London Series B, Biological Sciences. 2015;370(1669). doi:10.1098/rstb.2014.0116","ieee":"P. Kappeler, S. Cremer, and C. Nunn, “Sociality and health: Impacts of sociality on disease susceptibility and transmission in animal and human societies,” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, vol. 370, no. 1669. Royal Society, 2015.","apa":"Kappeler, P., Cremer, S., & Nunn, C. (2015). Sociality and health: Impacts of sociality on disease susceptibility and transmission in animal and human societies. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. Royal Society. https://doi.org/10.1098/rstb.2014.0116","ista":"Kappeler P, Cremer S, Nunn C. 2015. Sociality and health: Impacts of sociality on disease susceptibility and transmission in animal and human societies. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 370(1669), 20140116."},"publication":"Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences","issue":"1669","abstract":[{"text":"This paper introduces a theme issue presenting the latest developments in research on the impacts of sociality on health and fitness. The articles that follow cover research on societies ranging from insects to humans. Variation in measures of fitness (i.e. survival and reproduction) has been linked to various aspects of sociality in humans and animals alike, and variability in individual health and condition has been recognized as a key mediator of these relationships. Viewed from a broad evolutionary perspective, the evolutionary transitions from a solitary lifestyle to group living have resulted in several new health-related costs and benefits of sociality. Social transmission of parasites within groups represents a major cost of group living, but some behavioural mechanisms, such as grooming, have evolved repeatedly to reduce this cost. Group living also has created novel costs in terms of altered susceptibility to infectious and non-infectious disease as a result of the unavoidable physiological consequences of social competition and integration, which are partly alleviated by social buffering in some vertebrates. Here, we define the relevant aspects of sociality, summarize their health-related costs and benefits, and discuss possible fitness measures in different study systems. Given the pervasive effects of social factors on health and fitness, we propose a synthesis of existing conceptual approaches in disease ecology, ecological immunology and behavioural neurosciences by adding sociality as a key factor, with the goal to generate a broader framework for organismal integration of health-related research.","lang":"eng"}],"type":"journal_article","oa_version":"Submitted Version","_id":"1831","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 370","status":"public","title":"Sociality and health: Impacts of sociality on disease susceptibility and transmission in animal and human societies","month":"05","doi":"10.1098/rstb.2014.0116","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4410382/"}],"external_id":{"pmid":["25870402"]},"quality_controlled":"1","publist_id":"5272","article_number":"20140116","author":[{"first_name":"Peter","last_name":"Kappeler","full_name":"Kappeler, Peter"},{"full_name":"Cremer, Sylvia","first_name":"Sylvia","last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868"},{"full_name":"Nunn, Charles","first_name":"Charles","last_name":"Nunn"}],"volume":370,"date_created":"2018-12-11T11:54:15Z","date_updated":"2021-01-12T06:53:29Z","pmid":1,"acknowledgement":"We thank the German Research Foundation (DFG), the Ministry of Science and Culture of Lower-Saxony (MWK Hannover) and the German Primate Centre (DPZ) for their support of the 9. Göttinger Freilandtage in 2013, a conference at which most contributions to this issue were first presented, the referees of the contributions to this issue for their constructive comments, Meggan Craft for comments, and Helen Eaton for her support in producing this theme issue.","year":"2015","publisher":"Royal Society","department":[{"_id":"SyCr"}],"publication_status":"published"},{"day":"01","article_processing_charge":"No","scopus_import":1,"date_published":"2015-07-01T00:00:00Z","page":"163 - 167","publication":"Journal of Statistical Physics","citation":{"mla":"Akopyan, Arseniy, et al. “Invariant Measures of Genetic Recombination Process.” Journal of Statistical Physics, vol. 160, no. 1, Springer, 2015, pp. 163–67, doi:10.1007/s10955-015-1238-5.","short":"A. Akopyan, S. Pirogov, A. Rybko, Journal of Statistical Physics 160 (2015) 163–167.","chicago":"Akopyan, Arseniy, Sergey Pirogov, and Aleksandr Rybko. “Invariant Measures of Genetic Recombination Process.” Journal of Statistical Physics. Springer, 2015. https://doi.org/10.1007/s10955-015-1238-5.","ama":"Akopyan A, Pirogov S, Rybko A. Invariant measures of genetic recombination process. Journal of Statistical Physics. 2015;160(1):163-167. doi:10.1007/s10955-015-1238-5","ista":"Akopyan A, Pirogov S, Rybko A. 2015. Invariant measures of genetic recombination process. Journal of Statistical Physics. 160(1), 163–167.","apa":"Akopyan, A., Pirogov, S., & Rybko, A. (2015). Invariant measures of genetic recombination process. Journal of Statistical Physics. Springer. https://doi.org/10.1007/s10955-015-1238-5","ieee":"A. Akopyan, S. Pirogov, and A. Rybko, “Invariant measures of genetic recombination process,” Journal of Statistical Physics, vol. 160, no. 1. Springer, pp. 163–167, 2015."},"abstract":[{"lang":"eng","text":"We construct a non-linear Markov process connected with a biological model of a bacterial genome recombination. The description of invariant measures of this process gives us the solution of one problem in elementary probability theory."}],"issue":"1","type":"journal_article","oa_version":"Preprint","title":"Invariant measures of genetic recombination process","status":"public","intvolume":" 160","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1828","month":"07","language":[{"iso":"eng"}],"doi":"10.1007/s10955-015-1238-5","quality_controlled":"1","project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"main_file_link":[{"open_access":"1","url":"arxiv.org/abs/1406.5313"}],"oa":1,"publist_id":"5276","ec_funded":1,"date_updated":"2021-01-12T06:53:28Z","date_created":"2018-12-11T11:54:14Z","volume":160,"author":[{"last_name":"Akopyan","first_name":"Arseniy","orcid":"0000-0002-2548-617X","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","full_name":"Akopyan, Arseniy"},{"last_name":"Pirogov","first_name":"Sergey","full_name":"Pirogov, Sergey"},{"first_name":"Aleksandr","last_name":"Rybko","full_name":"Rybko, Aleksandr"}],"publication_status":"published","publisher":"Springer","department":[{"_id":"HeEd"}],"year":"2015"},{"series_title":"Lecture Notes in Computer Science","scopus_import":1,"day":"01","page":"105 - 131","citation":{"ista":"Cerny P, Henzinger TA, Kovács L, Radhakrishna A, Zwirchmayr J. 2015. Segment abstraction for worst-case execution time analysis. 9032, 105–131.","ieee":"P. Cerny, T. A. Henzinger, L. Kovács, A. Radhakrishna, and J. Zwirchmayr, “Segment abstraction for worst-case execution time analysis,” vol. 9032. Springer, pp. 105–131, 2015.","apa":"Cerny, P., Henzinger, T. A., Kovács, L., Radhakrishna, A., & Zwirchmayr, J. (2015). Segment abstraction for worst-case execution time analysis. Presented at the ESOP: European Symposium on Programming, London, United Kingdom: Springer. https://doi.org/10.1007/978-3-662-46669-8_5","ama":"Cerny P, Henzinger TA, Kovács L, Radhakrishna A, Zwirchmayr J. Segment abstraction for worst-case execution time analysis. 2015;9032:105-131. doi:10.1007/978-3-662-46669-8_5","chicago":"Cerny, Pavol, Thomas A Henzinger, Laura Kovács, Arjun Radhakrishna, and Jakob Zwirchmayr. “Segment Abstraction for Worst-Case Execution Time Analysis.” Lecture Notes in Computer Science. Springer, 2015. https://doi.org/10.1007/978-3-662-46669-8_5.","mla":"Cerny, Pavol, et al. Segment Abstraction for Worst-Case Execution Time Analysis. Vol. 9032, Springer, 2015, pp. 105–31, doi:10.1007/978-3-662-46669-8_5.","short":"P. Cerny, T.A. Henzinger, L. Kovács, A. Radhakrishna, J. Zwirchmayr, 9032 (2015) 105–131."},"date_published":"2015-04-01T00:00:00Z","alternative_title":["LNCS"],"type":"conference","abstract":[{"text":"In the standard framework for worst-case execution time (WCET) analysis of programs, the main data structure is a single instance of integer linear programming (ILP) that represents the whole program. The instance of this NP-hard problem must be solved to find an estimate forWCET, and it must be refined if the estimate is not tight.We propose a new framework for WCET analysis, based on abstract segment trees (ASTs) as the main data structure. The ASTs have two advantages. First, they allow computing WCET by solving a number of independent small ILP instances. Second, ASTs store more expressive constraints, thus enabling a more efficient and precise refinement procedure. In order to realize our framework algorithmically, we develop an algorithm for WCET estimation on ASTs, and we develop an interpolation-based counterexample-guided refinement scheme for ASTs. Furthermore, we extend our framework to obtain parametric estimates of WCET. We experimentally evaluate our approach on a set of examples from WCET benchmark suites and linear-algebra packages. We show that our analysis, with comparable effort, provides WCET estimates that in many cases significantly improve those computed by existing tools.","lang":"eng"}],"title":"Segment abstraction for worst-case execution time analysis","status":"public","intvolume":" 9032","_id":"1836","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","month":"04","quality_controlled":"1","project":[{"grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Reactive Modeling"},{"name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"language":[{"iso":"eng"}],"conference":{"name":"ESOP: European Symposium on Programming","end_date":"2015-04-18","location":"London, United Kingdom","start_date":"2015-04-11"},"doi":"10.1007/978-3-662-46669-8_5","publist_id":"5266","ec_funded":1,"publication_status":"published","publisher":"Springer","department":[{"_id":"ToHe"}],"year":"2015","date_created":"2018-12-11T11:54:16Z","date_updated":"2020-08-11T10:09:32Z","volume":9032,"author":[{"id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87","first_name":"Pavol","last_name":"Cerny","full_name":"Cerny, Pavol"},{"orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A","full_name":"Henzinger, Thomas A"},{"last_name":"Kovács","first_name":"Laura","full_name":"Kovács, Laura"},{"id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87","last_name":"Radhakrishna","first_name":"Arjun","full_name":"Radhakrishna, Arjun"},{"first_name":"Jakob","last_name":"Zwirchmayr","full_name":"Zwirchmayr, Jakob"}]},{"language":[{"iso":"eng"}],"conference":{"start_date":"2015-04-11","location":"London, United Kingdom","end_date":"2015-04-18","name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems"},"doi":"10.1007/978-3-662-46681-0_50","project":[{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"}],"oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/1411.4604","open_access":"1"}],"month":"01","date_updated":"2021-01-12T06:53:32Z","date_created":"2018-12-11T11:54:17Z","volume":9035,"author":[{"first_name":"Roderick","last_name":"Bloem","full_name":"Bloem, Roderick"},{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"},{"first_name":"Swen","last_name":"Jacobs","full_name":"Jacobs, Swen"},{"full_name":"Könighofer, Robert","last_name":"Könighofer","first_name":"Robert"}],"publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"Springer","year":"2015","acknowledgement":"This work was supported by the Austrian Science Fund (FWF) through the research network RiSE (S11406-N23, S11407-N23) and grant nr. P23499-N23, by the European Commission through an ERC Start grant (279307: Graph Games) and project STANCE (317753), as well as by the German Research Foundation (DFG) through SFB/TR 14 AVACS and project ASDPS(JA 2357/2-1).","publist_id":"5264","ec_funded":1,"date_published":"2015-01-01T00:00:00Z","page":"517 - 532","citation":{"ista":"Bloem R, Chatterjee K, Jacobs S, Könighofer R. 2015. Assume-guarantee synthesis for concurrent reactive programs with partial information. TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 9035, 517–532.","apa":"Bloem, R., Chatterjee, K., Jacobs, S., & Könighofer, R. (2015). Assume-guarantee synthesis for concurrent reactive programs with partial information (Vol. 9035, pp. 517–532). Presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, London, United Kingdom: Springer. https://doi.org/10.1007/978-3-662-46681-0_50","ieee":"R. Bloem, K. Chatterjee, S. Jacobs, and R. Könighofer, “Assume-guarantee synthesis for concurrent reactive programs with partial information,” presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, London, United Kingdom, 2015, vol. 9035, pp. 517–532.","ama":"Bloem R, Chatterjee K, Jacobs S, Könighofer R. Assume-guarantee synthesis for concurrent reactive programs with partial information. In: Vol 9035. Springer; 2015:517-532. doi:10.1007/978-3-662-46681-0_50","chicago":"Bloem, Roderick, Krishnendu Chatterjee, Swen Jacobs, and Robert Könighofer. “Assume-Guarantee Synthesis for Concurrent Reactive Programs with Partial Information,” 9035:517–32. Springer, 2015. https://doi.org/10.1007/978-3-662-46681-0_50.","mla":"Bloem, Roderick, et al. Assume-Guarantee Synthesis for Concurrent Reactive Programs with Partial Information. Vol. 9035, Springer, 2015, pp. 517–32, doi:10.1007/978-3-662-46681-0_50.","short":"R. Bloem, K. Chatterjee, S. Jacobs, R. Könighofer, in:, Springer, 2015, pp. 517–532."},"day":"01","scopus_import":1,"oa_version":"Preprint","title":"Assume-guarantee synthesis for concurrent reactive programs with partial information","status":"public","intvolume":" 9035","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1838","abstract":[{"text":"Synthesis of program parts is particularly useful for concurrent systems. However, most approaches do not support common design tasks, like modifying a single process without having to re-synthesize or verify the whole system. Assume-guarantee synthesis (AGS) provides robustness against modifications of system parts, but thus far has been limited to the perfect information setting. This means that local variables cannot be hidden from other processes, which renders synthesis results cumbersome or even impossible to realize.We resolve this shortcoming by defining AGS under partial information. We analyze the complexity and decidability in different settings, showing that the problem has a high worstcase complexity and is undecidable in many interesting cases. Based on these observations, we present a pragmatic algorithm based on bounded synthesis, and demonstrate its practical applicability on several examples.","lang":"eng"}],"alternative_title":["LNCS"],"type":"conference"},{"abstract":[{"lang":"eng","text":"We present MultiGain, a tool to synthesize strategies for Markov decision processes (MDPs) with multiple mean-payoff objectives. Our models are described in PRISM, and our tool uses the existing interface and simulator of PRISM. Our tool extends PRISM by adding novel algorithms for multiple mean-payoff objectives, and also provides features such as (i) generating strategies and exploring them for simulation, and checking them with respect to other properties; and (ii) generating an approximate Pareto curve for two mean-payoff objectives. In addition, we present a new practical algorithm for the analysis of MDPs with multiple mean-payoff objectives under memoryless strategies."}],"type":"conference","alternative_title":["LNCS"],"oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1839","title":"Multigain: A controller synthesis tool for MDPs with multiple mean-payoff objectives","status":"public","intvolume":" 9035","day":"01","series_title":"Lecture Notes in Computer Science","date_published":"2015-01-01T00:00:00Z","citation":{"ama":"Brázdil T, Chatterjee K, Forejt V, Kučera A. Multigain: A controller synthesis tool for MDPs with multiple mean-payoff objectives. 2015;9035:181-187. doi:10.1007/978-3-662-46681-0_12","apa":"Brázdil, T., Chatterjee, K., Forejt, V., & Kučera, A. (2015). Multigain: A controller synthesis tool for MDPs with multiple mean-payoff objectives. Presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, London, United Kingdom: Springer. https://doi.org/10.1007/978-3-662-46681-0_12","ieee":"T. Brázdil, K. Chatterjee, V. Forejt, and A. Kučera, “Multigain: A controller synthesis tool for MDPs with multiple mean-payoff objectives,” vol. 9035. Springer, pp. 181–187, 2015.","ista":"Brázdil T, Chatterjee K, Forejt V, Kučera A. 2015. Multigain: A controller synthesis tool for MDPs with multiple mean-payoff objectives. 9035, 181–187.","short":"T. Brázdil, K. Chatterjee, V. Forejt, A. Kučera, 9035 (2015) 181–187.","mla":"Brázdil, Tomáš, et al. Multigain: A Controller Synthesis Tool for MDPs with Multiple Mean-Payoff Objectives. Vol. 9035, Springer, 2015, pp. 181–87, doi:10.1007/978-3-662-46681-0_12.","chicago":"Brázdil, Tomáš, Krishnendu Chatterjee, Vojtěch Forejt, and Antonín Kučera. “Multigain: A Controller Synthesis Tool for MDPs with Multiple Mean-Payoff Objectives.” Lecture Notes in Computer Science. Springer, 2015. https://doi.org/10.1007/978-3-662-46681-0_12."},"page":"181 - 187","publist_id":"5263","ec_funded":1,"author":[{"first_name":"Tomáš","last_name":"Brázdil","full_name":"Brázdil, Tomáš"},{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"},{"full_name":"Forejt, Vojtěch","last_name":"Forejt","first_name":"Vojtěch"},{"full_name":"Kučera, Antonín","last_name":"Kučera","first_name":"Antonín"}],"date_created":"2018-12-11T11:54:18Z","date_updated":"2020-01-21T13:18:52Z","volume":9035,"year":"2015","publication_status":"published","publisher":"Springer","department":[{"_id":"KrCh"}],"month":"01","conference":{"name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems","location":"London, United Kingdom","start_date":"2015-04-11","end_date":"2015-04-18"},"doi":"10.1007/978-3-662-46681-0_12","language":[{"iso":"eng"}],"main_file_link":[{"url":"http://arxiv.org/abs/1501.03093","open_access":"1"}],"oa":1,"quality_controlled":"1","project":[{"grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF"},{"name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"}]},{"doi":"10.1017/jfm.2015.184","language":[{"iso":"eng"}],"oa":1,"external_id":{"arxiv":["1508.06559"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1508.06559"}],"project":[{"grant_number":"306589","_id":"25152F3A-B435-11E9-9278-68D0E5697425","name":"Decoding the complexity of turbulence at its origin","call_identifier":"FP7"}],"quality_controlled":"1","month":"04","author":[{"orcid":"0000-0003-4312-0179","id":"3A47AE32-F248-11E8-B48F-1D18A9856A87","last_name":"Kühnen","first_name":"Jakob","full_name":"Kühnen, Jakob"},{"last_name":"Braunshier","first_name":"P","full_name":"Braunshier, P"},{"full_name":"Schwegel, M","first_name":"M","last_name":"Schwegel"},{"full_name":"Kuhlmann, Hendrik","first_name":"Hendrik","last_name":"Kuhlmann"},{"full_name":"Hof, Björn","orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof","first_name":"Björn"}],"volume":770,"date_updated":"2021-01-12T06:53:31Z","date_created":"2018-12-11T11:54:17Z","year":"2015","publisher":"Cambridge University Press","department":[{"_id":"BjHo"}],"publication_status":"published","publist_id":"5265","ec_funded":1,"article_number":"R3","date_published":"2015-04-08T00:00:00Z","citation":{"apa":"Kühnen, J., Braunshier, P., Schwegel, M., Kuhlmann, H., & Hof, B. (2015). Subcritical versus supercritical transition to turbulence in curved pipes. Journal of Fluid Mechanics. Cambridge University Press. https://doi.org/10.1017/jfm.2015.184","ieee":"J. Kühnen, P. Braunshier, M. Schwegel, H. Kuhlmann, and B. Hof, “Subcritical versus supercritical transition to turbulence in curved pipes,” Journal of Fluid Mechanics, vol. 770, no. 5. Cambridge University Press, 2015.","ista":"Kühnen J, Braunshier P, Schwegel M, Kuhlmann H, Hof B. 2015. Subcritical versus supercritical transition to turbulence in curved pipes. Journal of Fluid Mechanics. 770(5), R3.","ama":"Kühnen J, Braunshier P, Schwegel M, Kuhlmann H, Hof B. Subcritical versus supercritical transition to turbulence in curved pipes. Journal of Fluid Mechanics. 2015;770(5). doi:10.1017/jfm.2015.184","chicago":"Kühnen, Jakob, P Braunshier, M Schwegel, Hendrik Kuhlmann, and Björn Hof. “Subcritical versus Supercritical Transition to Turbulence in Curved Pipes.” Journal of Fluid Mechanics. Cambridge University Press, 2015. https://doi.org/10.1017/jfm.2015.184.","short":"J. Kühnen, P. Braunshier, M. Schwegel, H. Kuhlmann, B. Hof, Journal of Fluid Mechanics 770 (2015).","mla":"Kühnen, Jakob, et al. “Subcritical versus Supercritical Transition to Turbulence in Curved Pipes.” Journal of Fluid Mechanics, vol. 770, no. 5, R3, Cambridge University Press, 2015, doi:10.1017/jfm.2015.184."},"publication":"Journal of Fluid Mechanics","article_type":"original","article_processing_charge":"No","day":"08","scopus_import":1,"oa_version":"Preprint","_id":"1837","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 770","title":"Subcritical versus supercritical transition to turbulence in curved pipes","status":"public","issue":"5","abstract":[{"lang":"eng","text":"Transition to turbulence in straight pipes occurs in spite of the linear stability of the laminar Hagen-Poiseuille flow if both the amplitude of flow perturbations and the Reynolds number Re exceed a minimum threshold (subcritical transition). As the pipe curvature increases, centrifugal effects become important, modifying the basic flow as well as the most unstable linear modes. If the curvature (tube-to-coiling diameter d/D) is sufficiently large, a Hopf bifurcation (supercritical instability) is encountered before turbulence can be excited (subcritical instability). We trace the instability thresholds in the Re - d/D parameter space in the range 0.01 ≤ d/D\\ ≤ 0.1 by means of laser-Doppler velocimetry and determine the point where the subcritical and supercritical instabilities meet. Two different experimental set-ups are used: a closed system where the pipe forms an axisymmetric torus and an open system employing a helical pipe. Implications for the measurement of friction factors in curved pipes are discussed."}],"type":"journal_article"},{"month":"09","oa":1,"external_id":{"pmid":["25716227"]},"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4497860/","open_access":"1"}],"quality_controlled":"1","doi":"10.1002/ijc.29498","language":[{"iso":"eng"}],"publist_id":"5253","year":"2015","pmid":1,"publication_status":"published","department":[{"_id":"LifeSc"}],"publisher":"Wiley","author":[{"first_name":"Bettina","last_name":"Schwamb","full_name":"Schwamb, Bettina"},{"full_name":"Pick, Robert","last_name":"Pick","first_name":"Robert"},{"full_name":"Fernández, Sara","last_name":"Fernández","first_name":"Sara"},{"last_name":"Völp","first_name":"Kirsten","full_name":"Völp, Kirsten"},{"full_name":"Heering, Jan","last_name":"Heering","first_name":"Jan"},{"first_name":"Volker","last_name":"Dötsch","full_name":"Dötsch, Volker"},{"full_name":"Bösser, Susanne","last_name":"Bösser","first_name":"Susanne"},{"first_name":"Jennifer","last_name":"Jung","full_name":"Jung, Jennifer"},{"first_name":"Rasa","last_name":"Beinoravičiute Kellner","full_name":"Beinoravičiute Kellner, Rasa"},{"first_name":"Josephine","last_name":"Wesely","full_name":"Wesely, Josephine"},{"last_name":"Zörnig","first_name":"Inka","full_name":"Zörnig, Inka"},{"first_name":"Matthias","last_name":"Hammerschmidt","full_name":"Hammerschmidt, Matthias"},{"id":"30845DAA-F248-11E8-B48F-1D18A9856A87","first_name":"Matthias","last_name":"Nowak","full_name":"Nowak, Matthias"},{"last_name":"Penzel","first_name":"Roland","full_name":"Penzel, Roland"},{"full_name":"Zatloukal, Kurt","first_name":"Kurt","last_name":"Zatloukal"},{"full_name":"Joos, Stefan","first_name":"Stefan","last_name":"Joos"},{"first_name":"Ralf","last_name":"Rieker","full_name":"Rieker, Ralf"},{"full_name":"Agaimy, Abbas","first_name":"Abbas","last_name":"Agaimy"},{"last_name":"Söder","first_name":"Stephan","full_name":"Söder, Stephan"},{"first_name":"Kmarie","last_name":"Reid Lombardo","full_name":"Reid Lombardo, Kmarie"},{"full_name":"Kendrick, Michael","first_name":"Michael","last_name":"Kendrick"},{"first_name":"Michael","last_name":"Bardsley","full_name":"Bardsley, Michael"},{"full_name":"Hayashi, Yujiro","first_name":"Yujiro","last_name":"Hayashi"},{"first_name":"David","last_name":"Asuzu","full_name":"Asuzu, David"},{"full_name":"Syed, Sabriya","last_name":"Syed","first_name":"Sabriya"},{"first_name":"Tamás","last_name":"Ördög","full_name":"Ördög, Tamás"},{"last_name":"Zörnig","first_name":"Martin","full_name":"Zörnig, Martin"}],"date_updated":"2021-01-12T06:53:36Z","date_created":"2018-12-11T11:54:20Z","volume":137,"scopus_import":1,"day":"01","article_processing_charge":"No","publication":"International Journal of Cancer","citation":{"ama":"Schwamb B, Pick R, Fernández S, et al. FAM96A is a novel pro-apoptotic tumor suppressor in gastrointestinal stromal tumors. International Journal of Cancer. 2015;137(6):1318-1329. doi:10.1002/ijc.29498","ista":"Schwamb B, Pick R, Fernández S, Völp K, Heering J, Dötsch V, Bösser S, Jung J, Beinoravičiute Kellner R, Wesely J, Zörnig I, Hammerschmidt M, Nowak M, Penzel R, Zatloukal K, Joos S, Rieker R, Agaimy A, Söder S, Reid Lombardo K, Kendrick M, Bardsley M, Hayashi Y, Asuzu D, Syed S, Ördög T, Zörnig M. 2015. FAM96A is a novel pro-apoptotic tumor suppressor in gastrointestinal stromal tumors. International Journal of Cancer. 137(6), 1318–1329.","ieee":"B. Schwamb et al., “FAM96A is a novel pro-apoptotic tumor suppressor in gastrointestinal stromal tumors,” International Journal of Cancer, vol. 137, no. 6. Wiley, pp. 1318–1329, 2015.","apa":"Schwamb, B., Pick, R., Fernández, S., Völp, K., Heering, J., Dötsch, V., … Zörnig, M. (2015). FAM96A is a novel pro-apoptotic tumor suppressor in gastrointestinal stromal tumors. International Journal of Cancer. Wiley. https://doi.org/10.1002/ijc.29498","mla":"Schwamb, Bettina, et al. “FAM96A Is a Novel Pro-Apoptotic Tumor Suppressor in Gastrointestinal Stromal Tumors.” International Journal of Cancer, vol. 137, no. 6, Wiley, 2015, pp. 1318–29, doi:10.1002/ijc.29498.","short":"B. Schwamb, R. Pick, S. Fernández, K. Völp, J. Heering, V. Dötsch, S. Bösser, J. Jung, R. Beinoravičiute Kellner, J. Wesely, I. Zörnig, M. Hammerschmidt, M. Nowak, R. Penzel, K. Zatloukal, S. Joos, R. Rieker, A. Agaimy, S. Söder, K. Reid Lombardo, M. Kendrick, M. Bardsley, Y. Hayashi, D. Asuzu, S. Syed, T. Ördög, M. Zörnig, International Journal of Cancer 137 (2015) 1318–1329.","chicago":"Schwamb, Bettina, Robert Pick, Sara Fernández, Kirsten Völp, Jan Heering, Volker Dötsch, Susanne Bösser, et al. “FAM96A Is a Novel Pro-Apoptotic Tumor Suppressor in Gastrointestinal Stromal Tumors.” International Journal of Cancer. Wiley, 2015. https://doi.org/10.1002/ijc.29498."},"article_type":"original","page":"1318 - 1329","date_published":"2015-09-01T00:00:00Z","type":"journal_article","abstract":[{"text":"The ability to escape apoptosis is a hallmark of cancer-initiating cells and a key factor of resistance to oncolytic therapy. Here, we identify FAM96A as a ubiquitous, evolutionarily conserved apoptosome-activating protein and investigate its potential pro-apoptotic tumor suppressor function in gastrointestinal stromal tumors (GISTs). Interaction between FAM96A and apoptotic peptidase activating factor 1 (APAF1) was identified in yeast two-hybrid screen and further studied by deletion mutants, glutathione-S-transferase pull-down, co-immunoprecipitation and immunofluorescence. Effects of FAM96A overexpression and knock-down on apoptosis sensitivity were examined in cancer cells and zebrafish embryos. Expression of FAM96A in GISTs and histogenetically related cells including interstitial cells of Cajal (ICCs), “fibroblast-like cells” (FLCs) and ICC stem cells (ICC-SCs) was investigated by Northern blotting, reverse transcription—polymerase chain reaction, immunohistochemistry and Western immunoblotting. Tumorigenicity of GIST cells and transformed murine ICC-SCs stably transduced to re-express FAM96A was studied by xeno- and allografting into immunocompromised mice. FAM96A was found to bind APAF1 and to enhance the induction of mitochondrial apoptosis. FAM96A protein or mRNA was dramatically reduced or lost in 106 of 108 GIST samples representing three independent patient cohorts. Whereas ICCs, ICC-SCs and FLCs, the presumed normal counterparts of GIST, were found to robustly express FAM96A protein and mRNA, FAM96A expression was much reduced in tumorigenic ICC-SCs. Re-expression of FAM96A in GIST cells and transformed ICC-SCs increased apoptosis sensitivity and diminished tumorigenicity. Our data suggest FAM96A is a novel pro-apoptotic tumor suppressor that is lost during GIST tumorigenesis.","lang":"eng"}],"issue":"6","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1848","status":"public","title":"FAM96A is a novel pro-apoptotic tumor suppressor in gastrointestinal stromal tumors","intvolume":" 137","oa_version":"Submitted Version"},{"doi":"10.1007/s00236-015-0215-4","language":[{"iso":"eng"}],"oa":1,"project":[{"name":"Quantitative Reactive Modeling","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering"}],"quality_controlled":"1","month":"04","author":[{"full_name":"Beneš, Nikola","first_name":"Nikola","last_name":"Beneš"},{"first_name":"Jan","last_name":"Kretinsky","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8122-2881","full_name":"Kretinsky, Jan"},{"full_name":"Larsen, Kim","first_name":"Kim","last_name":"Larsen"},{"last_name":"Möller","first_name":"Mikael","full_name":"Möller, Mikael"},{"last_name":"Sickert","first_name":"Salomon","full_name":"Sickert, Salomon"},{"full_name":"Srba, Jiří","first_name":"Jiří","last_name":"Srba"}],"volume":52,"date_created":"2018-12-11T11:54:20Z","date_updated":"2021-01-12T06:53:35Z","year":"2015","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"publisher":"Springer","publication_status":"published","publist_id":"5255","ec_funded":1,"file_date_updated":"2020-07-14T12:45:19Z","date_published":"2015-04-01T00:00:00Z","citation":{"chicago":"Beneš, Nikola, Jan Kretinsky, Kim Larsen, Mikael Möller, Salomon Sickert, and Jiří Srba. “Refinement Checking on Parametric Modal Transition Systems.” Acta Informatica. Springer, 2015. https://doi.org/10.1007/s00236-015-0215-4.","short":"N. Beneš, J. Kretinsky, K. Larsen, M. Möller, S. Sickert, J. Srba, Acta Informatica 52 (2015) 269–297.","mla":"Beneš, Nikola, et al. “Refinement Checking on Parametric Modal Transition Systems.” Acta Informatica, vol. 52, no. 2–3, Springer, 2015, pp. 269–97, doi:10.1007/s00236-015-0215-4.","apa":"Beneš, N., Kretinsky, J., Larsen, K., Möller, M., Sickert, S., & Srba, J. (2015). Refinement checking on parametric modal transition systems. Acta Informatica. Springer. https://doi.org/10.1007/s00236-015-0215-4","ieee":"N. Beneš, J. Kretinsky, K. Larsen, M. Möller, S. Sickert, and J. Srba, “Refinement checking on parametric modal transition systems,” Acta Informatica, vol. 52, no. 2–3. Springer, pp. 269–297, 2015.","ista":"Beneš N, Kretinsky J, Larsen K, Möller M, Sickert S, Srba J. 2015. Refinement checking on parametric modal transition systems. Acta Informatica. 52(2–3), 269–297.","ama":"Beneš N, Kretinsky J, Larsen K, Möller M, Sickert S, Srba J. Refinement checking on parametric modal transition systems. Acta Informatica. 2015;52(2-3):269-297. doi:10.1007/s00236-015-0215-4"},"publication":"Acta Informatica","page":"269 - 297","article_type":"original","article_processing_charge":"No","has_accepted_license":"1","day":"01","scopus_import":1,"file":[{"creator":"dernst","file_size":488482,"content_type":"application/pdf","file_name":"2015_ActaInfo_Benes.pdf","access_level":"open_access","date_created":"2020-05-15T08:57:44Z","date_updated":"2020-07-14T12:45:19Z","checksum":"fb4037ddc4fc05f33080dd3547ede350","file_id":"7854","relation":"main_file"}],"oa_version":"Submitted Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1846","intvolume":" 52","ddc":["000"],"title":"Refinement checking on parametric modal transition systems","status":"public","issue":"2-3","abstract":[{"text":"Modal transition systems (MTS) is a well-studied specification formalism of reactive systems supporting a step-wise refinement methodology. Despite its many advantages, the formalism as well as its currently known extensions are incapable of expressing some practically needed aspects in the refinement process like exclusive, conditional and persistent choices. We introduce a new model called parametric modal transition systems (PMTS) together with a general modal refinement notion that overcomes many of the limitations. We investigate the computational complexity of modal and thorough refinement checking on PMTS and its subclasses and provide a direct encoding of the modal refinement problem into quantified Boolean formulae, allowing us to employ state-of-the-art QBF solvers for modal refinement checking. The experiments we report on show that the feasibility of refinement checking is more influenced by the degree of nondeterminism rather than by the syntactic restrictions on the types of formulae allowed in the description of the PMTS.","lang":"eng"}],"type":"journal_article"},{"scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"18","citation":{"mla":"Vandael, David H., et al. “Excitement about Inhibitory Presynaptic Terminals.” Neuron, vol. 85, no. 6, Elsevier, 2015, pp. 1149–51, doi:10.1016/j.neuron.2015.03.006.","short":"D.H. Vandael, C. Espinoza Martinez, P.M. Jonas, Neuron 85 (2015) 1149–1151.","chicago":"Vandael, David H, Claudia Espinoza Martinez, and Peter M Jonas. “Excitement about Inhibitory Presynaptic Terminals.” Neuron. Elsevier, 2015. https://doi.org/10.1016/j.neuron.2015.03.006.","ama":"Vandael DH, Espinoza Martinez C, Jonas PM. Excitement about inhibitory presynaptic terminals. Neuron. 2015;85(6):1149-1151. doi:10.1016/j.neuron.2015.03.006","ista":"Vandael DH, Espinoza Martinez C, Jonas PM. 2015. Excitement about inhibitory presynaptic terminals. Neuron. 85(6), 1149–1151.","ieee":"D. H. Vandael, C. Espinoza Martinez, and P. M. Jonas, “Excitement about inhibitory presynaptic terminals,” Neuron, vol. 85, no. 6. Elsevier, pp. 1149–1151, 2015.","apa":"Vandael, D. H., Espinoza Martinez, C., & Jonas, P. M. (2015). Excitement about inhibitory presynaptic terminals. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2015.03.006"},"publication":"Neuron","page":"1149 - 1151","date_published":"2015-03-18T00:00:00Z","type":"journal_article","issue":"6","abstract":[{"lang":"eng","text":"Based on extrapolation from excitatory synapses, it is often assumed that depletion of the releasable pool of synaptic vesicles is the main factor underlying depression at inhibitory synapses. In this issue of Neuron, using subcellular patch-clamp recording from inhibitory presynaptic terminals, Kawaguchi and Sakaba (2015) show that at Purkinje cell-deep cerebellar nuclei neuron synapses, changes in presynaptic action potential waveform substantially contribute to synaptic depression. Based on extrapolation from excitatory synapses, it is often assumed that depletion of the releasable pool of synaptic vesicles is the main factor underlying depression at inhibitory synapses. In this issue of Neuron, using subcellular patch-clamp recording from inhibitory presynaptic terminals, Kawaguchi and Sakaba (2015) show that at Purkinje cell-deep cerebellar nuclei neuron synapses, changes in presynaptic action potential waveform substantially contribute to synaptic depression."}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"1845","intvolume":" 85","status":"public","ddc":["570"],"title":"Excitement about inhibitory presynaptic terminals","pubrep_id":"822","file":[{"relation":"main_file","file_id":"5192","checksum":"d1808550e376a0eca2a950fda017cfa6","date_created":"2018-12-12T10:16:07Z","date_updated":"2020-07-14T12:45:19Z","access_level":"open_access","file_name":"IST-2017-822-v1+1_Perspective_Fig__Final.pdf","file_size":411832,"content_type":"application/pdf","creator":"system"},{"file_size":100769,"content_type":"application/pdf","creator":"system","file_name":"IST-2017-822-v1+2_Perspective_Final2.pdf","access_level":"open_access","date_created":"2018-12-12T10:16:07Z","date_updated":"2020-07-14T12:45:19Z","checksum":"a279f4ae61e6c8f33d68f69a0d02097d","relation":"main_file","file_id":"5193"}],"oa_version":"Published Version","month":"03","oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"quality_controlled":"1","doi":"10.1016/j.neuron.2015.03.006","language":[{"iso":"eng"}],"publist_id":"5256","file_date_updated":"2020-07-14T12:45:19Z","license":"https://creativecommons.org/licenses/by-nc/4.0/","year":"2015","department":[{"_id":"PeJo"}],"publisher":"Elsevier","publication_status":"published","author":[{"full_name":"Vandael, David H","last_name":"Vandael","first_name":"David H","orcid":"0000-0001-7577-1676","id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-4710-2082","id":"31FFEE2E-F248-11E8-B48F-1D18A9856A87","last_name":"Espinoza Martinez","first_name":"Claudia ","full_name":"Espinoza Martinez, Claudia "},{"last_name":"Jonas","first_name":"Peter M","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","full_name":"Jonas, Peter M"}],"volume":85,"date_created":"2018-12-11T11:54:19Z","date_updated":"2021-10-08T09:07:34Z"},{"oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1840","intvolume":" 60","status":"public","title":"Optimal Kullback-Leibler aggregation via information bottleneck","issue":"4","abstract":[{"text":"In this paper, we present a method for reducing a regular, discrete-time Markov chain (DTMC) to another DTMC with a given, typically much smaller number of states. The cost of reduction is defined as the Kullback-Leibler divergence rate between a projection of the original process through a partition function and a DTMC on the correspondingly partitioned state space. Finding the reduced model with minimal cost is computationally expensive, as it requires an exhaustive search among all state space partitions, and an exact evaluation of the reduction cost for each candidate partition. Our approach deals with the latter problem by minimizing an upper bound on the reduction cost instead of minimizing the exact cost. The proposed upper bound is easy to compute and it is tight if the original chain is lumpable with respect to the partition. Then, we express the problem in the form of information bottleneck optimization, and propose using the agglomerative information bottleneck algorithm for searching a suboptimal partition greedily, rather than exhaustively. The theory is illustrated with examples and one application scenario in the context of modeling bio-molecular interactions.","lang":"eng"}],"type":"journal_article","date_published":"2015-04-01T00:00:00Z","citation":{"mla":"Geiger, Bernhard, et al. “Optimal Kullback-Leibler Aggregation via Information Bottleneck.” IEEE Transactions on Automatic Control, vol. 60, no. 4, IEEE, 2015, pp. 1010–22, doi:10.1109/TAC.2014.2364971.","short":"B. Geiger, T. Petrov, G. Kubin, H. Koeppl, IEEE Transactions on Automatic Control 60 (2015) 1010–1022.","chicago":"Geiger, Bernhard, Tatjana Petrov, Gernot Kubin, and Heinz Koeppl. “Optimal Kullback-Leibler Aggregation via Information Bottleneck.” IEEE Transactions on Automatic Control. IEEE, 2015. https://doi.org/10.1109/TAC.2014.2364971.","ama":"Geiger B, Petrov T, Kubin G, Koeppl H. Optimal Kullback-Leibler aggregation via information bottleneck. IEEE Transactions on Automatic Control. 2015;60(4):1010-1022. doi:10.1109/TAC.2014.2364971","ista":"Geiger B, Petrov T, Kubin G, Koeppl H. 2015. Optimal Kullback-Leibler aggregation via information bottleneck. IEEE Transactions on Automatic Control. 60(4), 1010–1022.","ieee":"B. Geiger, T. Petrov, G. Kubin, and H. Koeppl, “Optimal Kullback-Leibler aggregation via information bottleneck,” IEEE Transactions on Automatic Control, vol. 60, no. 4. IEEE, pp. 1010–1022, 2015.","apa":"Geiger, B., Petrov, T., Kubin, G., & Koeppl, H. (2015). Optimal Kullback-Leibler aggregation via information bottleneck. IEEE Transactions on Automatic Control. IEEE. https://doi.org/10.1109/TAC.2014.2364971"},"publication":"IEEE Transactions on Automatic Control","page":"1010 - 1022","day":"01","scopus_import":1,"author":[{"full_name":"Geiger, Bernhard","first_name":"Bernhard","last_name":"Geiger"},{"last_name":"Petrov","first_name":"Tatjana","orcid":"0000-0002-9041-0905","id":"3D5811FC-F248-11E8-B48F-1D18A9856A87","full_name":"Petrov, Tatjana"},{"full_name":"Kubin, Gernot","first_name":"Gernot","last_name":"Kubin"},{"last_name":"Koeppl","first_name":"Heinz","full_name":"Koeppl, Heinz"}],"volume":60,"date_created":"2018-12-11T11:54:18Z","date_updated":"2021-01-12T06:53:33Z","acknowledgement":"This work was supported by the Austrian Research Association under Project 06/12684, by the Swiss National Science Foundation (SNSF) under Grant PP00P2 128503/1, by the SystemsX.ch (the Swiss Inititative for Systems Biology), and by a SNSF Early Postdoc.Mobility Fellowship grant P2EZP2_148797.\r\n","year":"2015","department":[{"_id":"CaGu"},{"_id":"ToHe"}],"publisher":"IEEE","publication_status":"published","publist_id":"5262","doi":"10.1109/TAC.2014.2364971","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/1304.6603","open_access":"1"}],"quality_controlled":"1","publication_identifier":{"issn":["0018-9286"]},"month":"04"},{"ec_funded":1,"publist_id":"5261","author":[{"full_name":"Kolmogorov, Vladimir","last_name":"Kolmogorov","first_name":"Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"}],"volume":37,"date_updated":"2021-01-12T06:53:33Z","date_created":"2018-12-11T11:54:18Z","year":"2015","publisher":"IEEE","department":[{"_id":"VlKo"}],"publication_status":"published","month":"05","doi":"10.1109/TPAMI.2014.2363465","language":[{"iso":"eng"}],"main_file_link":[{"url":"http://arxiv.org/abs/1309.5655","open_access":"1"}],"oa":1,"project":[{"call_identifier":"FP7","name":"Discrete Optimization in Computer Vision: Theory and Practice","grant_number":"616160","_id":"25FBA906-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","issue":"5","abstract":[{"text":"We propose a new family of message passing techniques for MAP estimation in graphical models which we call Sequential Reweighted Message Passing (SRMP). Special cases include well-known techniques such as Min-Sum Diffusion (MSD) and a faster Sequential Tree-Reweighted Message Passing (TRW-S). Importantly, our derivation is simpler than the original derivation of TRW-S, and does not involve a decomposition into trees. This allows easy generalizations. The new family of algorithms can be viewed as a generalization of TRW-S from pairwise to higher-order graphical models. We test SRMP on several real-world problems with promising results.","lang":"eng"}],"type":"journal_article","oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1841","intvolume":" 37","title":"A new look at reweighted message passing","status":"public","day":"01","scopus_import":1,"date_published":"2015-05-01T00:00:00Z","citation":{"ama":"Kolmogorov V. A new look at reweighted message passing. IEEE Transactions on Pattern Analysis and Machine Intelligence. 2015;37(5):919-930. doi:10.1109/TPAMI.2014.2363465","apa":"Kolmogorov, V. (2015). A new look at reweighted message passing. IEEE Transactions on Pattern Analysis and Machine Intelligence. IEEE. https://doi.org/10.1109/TPAMI.2014.2363465","ieee":"V. Kolmogorov, “A new look at reweighted message passing,” IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 37, no. 5. IEEE, pp. 919–930, 2015.","ista":"Kolmogorov V. 2015. A new look at reweighted message passing. IEEE Transactions on Pattern Analysis and Machine Intelligence. 37(5), 919–930.","short":"V. Kolmogorov, IEEE Transactions on Pattern Analysis and Machine Intelligence 37 (2015) 919–930.","mla":"Kolmogorov, Vladimir. “A New Look at Reweighted Message Passing.” IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 37, no. 5, IEEE, 2015, pp. 919–30, doi:10.1109/TPAMI.2014.2363465.","chicago":"Kolmogorov, Vladimir. “A New Look at Reweighted Message Passing.” IEEE Transactions on Pattern Analysis and Machine Intelligence. IEEE, 2015. https://doi.org/10.1109/TPAMI.2014.2363465."},"publication":"IEEE Transactions on Pattern Analysis and Machine Intelligence","page":"919 - 930"},{"language":[{"iso":"eng"}],"date_published":"2015-09-01T00:00:00Z","doi":"10.1016/j.bbamcr.2015.02.017","page":"2168 - 2172","quality_controlled":"1","citation":{"mla":"Himschoot, Ellie, et al. “Calcium Is an Organizer of Cell Polarity in Plants.” Biochimica et Biophysica Acta - Molecular Cell Research, vol. 1853, no. 9, Elsevier, 2015, pp. 2168–72, doi:10.1016/j.bbamcr.2015.02.017.","short":"E. Himschoot, T. Beeckman, J. Friml, S. Vanneste, Biochimica et Biophysica Acta - Molecular Cell Research 1853 (2015) 2168–2172.","chicago":"Himschoot, Ellie, Tom Beeckman, Jiří Friml, and Steffen Vanneste. “Calcium Is an Organizer of Cell Polarity in Plants.” Biochimica et Biophysica Acta - Molecular Cell Research. Elsevier, 2015. https://doi.org/10.1016/j.bbamcr.2015.02.017.","ama":"Himschoot E, Beeckman T, Friml J, Vanneste S. Calcium is an organizer of cell polarity in plants. Biochimica et Biophysica Acta - Molecular Cell Research. 2015;1853(9):2168-2172. doi:10.1016/j.bbamcr.2015.02.017","ista":"Himschoot E, Beeckman T, Friml J, Vanneste S. 2015. Calcium is an organizer of cell polarity in plants. Biochimica et Biophysica Acta - Molecular Cell Research. 1853(9), 2168–2172.","ieee":"E. Himschoot, T. Beeckman, J. Friml, and S. Vanneste, “Calcium is an organizer of cell polarity in plants,” Biochimica et Biophysica Acta - Molecular Cell Research, vol. 1853, no. 9. Elsevier, pp. 2168–2172, 2015.","apa":"Himschoot, E., Beeckman, T., Friml, J., & Vanneste, S. (2015). Calcium is an organizer of cell polarity in plants. Biochimica et Biophysica Acta - Molecular Cell Research. Elsevier. https://doi.org/10.1016/j.bbamcr.2015.02.017"},"publication":"Biochimica et Biophysica Acta - Molecular Cell Research","month":"09","day":"01","scopus_import":1,"volume":1853,"oa_version":"None","date_created":"2018-12-11T11:54:21Z","date_updated":"2021-01-12T06:53:36Z","author":[{"full_name":"Himschoot, Ellie","first_name":"Ellie","last_name":"Himschoot"},{"last_name":"Beeckman","first_name":"Tom","full_name":"Beeckman, Tom"},{"full_name":"Friml, Jiřĺ","first_name":"Jiřĺ","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"},{"first_name":"Steffen","last_name":"Vanneste","full_name":"Vanneste, Steffen"}],"department":[{"_id":"JiFr"}],"publisher":"Elsevier","intvolume":" 1853","title":"Calcium is an organizer of cell polarity in plants","publication_status":"published","status":"public","acknowledgement":"The contributing authors were supported by the Ghent University Special Research Fund (to E.H.), the Interuniversity Attraction Poles Programme (IAP VI/33 and IUAP P7/29 ‘MARS’), the European Research Council (project ERC-2011-StG-20101109-PSDP, to J.F.), and the Research Foundation Flanders (to S.V.).","_id":"1849","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2015","issue":"9","publist_id":"5252","abstract":[{"lang":"eng","text":"Cell polarity is a fundamental property of pro- and eukaryotic cells. It is necessary for coordination of cell division, cell morphogenesis and signaling processes. How polarity is generated and maintained is a complex issue governed by interconnected feed-back regulations between small GTPase signaling and membrane tension-based signaling that controls membrane trafficking, and cytoskeleton organization and dynamics. Here, we will review the potential role for calcium as a crucial signal that connects and coordinates the respective processes during polarization processes in plants. This article is part of a Special Issue entitled: 13th European Symposium on Calcium."}],"type":"journal_article"},{"month":"03","day":"02","scopus_import":1,"language":[{"iso":"eng"}],"doi":"10.1016/j.molp.2014.12.013","date_published":"2015-03-02T00:00:00Z","page":"356 - 358","quality_controlled":"1","citation":{"ista":"Grones P, Friml J. 2015. ABP1: Finally docking. Molecular Plant. 8(3), 356–358.","ieee":"P. Grones and J. Friml, “ABP1: Finally docking,” Molecular Plant, vol. 8, no. 3. Elsevier, pp. 356–358, 2015.","apa":"Grones, P., & Friml, J. (2015). ABP1: Finally docking. Molecular Plant. Elsevier. https://doi.org/10.1016/j.molp.2014.12.013","ama":"Grones P, Friml J. ABP1: Finally docking. Molecular Plant. 2015;8(3):356-358. doi:10.1016/j.molp.2014.12.013","chicago":"Grones, Peter, and Jiří Friml. “ABP1: Finally Docking.” Molecular Plant. Elsevier, 2015. https://doi.org/10.1016/j.molp.2014.12.013.","mla":"Grones, Peter, and Jiří Friml. “ABP1: Finally Docking.” Molecular Plant, vol. 8, no. 3, Elsevier, 2015, pp. 356–58, doi:10.1016/j.molp.2014.12.013.","short":"P. Grones, J. Friml, Molecular Plant 8 (2015) 356–358."},"publication":"Molecular Plant","publist_id":"5254","issue":"3","type":"journal_article","volume":8,"oa_version":"None","date_created":"2018-12-11T11:54:20Z","date_updated":"2021-01-12T06:53:35Z","author":[{"full_name":"Grones, Peter","first_name":"Peter","last_name":"Grones","id":"399876EC-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiřĺ","full_name":"Friml, Jiřĺ"}],"publisher":"Elsevier","intvolume":" 8","department":[{"_id":"JiFr"}],"publication_status":"published","status":"public","title":"ABP1: Finally docking","acknowledgement":"This work was supported by the European Research Council (project ERC-2011-StG-20101109-PSDP), European Social Fund (CZ.1.07/2.3.00/20.0043), and the Czech Science Foundation GAČR (GA13-40637S).","_id":"1847","year":"2015","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"type":"journal_article","issue":"5","abstract":[{"text":"Entomopathogenic fungi are potent biocontrol agents that are widely used against insect pests, many of which are social insects. Nevertheless, theoretical investigations of their particular life history are scarce. We develop a model that takes into account the main distinguishing features between traditionally studied diseases and obligate killing pathogens, like the (biocontrol-relevant) insect-pathogenic fungi Metarhizium and Beauveria. First, obligate killing entomopathogenic fungi produce new infectious particles (conidiospores) only after host death and not yet on the living host. Second, the killing rates of entomopathogenic fungi depend strongly on the initial exposure dosage, thus we explicitly consider the pathogen load of individual hosts. Further, we make the model applicable not only to solitary host species, but also to group living species by incorporating social interactions between hosts, like the collective disease defences of insect societies. Our results identify the optimal killing rate for the pathogen that minimises its invasion threshold. Furthermore, we find that the rate of contact between hosts has an ambivalent effect: dense interaction networks between individuals are considered to facilitate disease outbreaks because of increased pathogen transmission. In social insects, this is compensated by their collective disease defences, i.e., social immunity. For the type of pathogens considered here, we show that even without social immunity, high contact rates between live individuals dilute the pathogen in the host colony and hence can reduce individual pathogen loads below disease-causing levels.","lang":"eng"}],"_id":"1850","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 372","title":"Fungal disease dynamics in insect societies: Optimal killing rates and the ambivalent effect of high social interaction rates","ddc":["576"],"status":"public","pubrep_id":"329","file":[{"file_name":"IST-2015-329-v1+1_manuscript.pdf","access_level":"open_access","content_type":"application/pdf","file_size":1546914,"creator":"system","relation":"main_file","file_id":"5326","date_created":"2018-12-12T10:18:07Z","date_updated":"2020-07-14T12:45:19Z","checksum":"3c0dcacc900bc45cc65a453dfda4ca43"}],"oa_version":"Submitted Version","scopus_import":1,"has_accepted_license":"1","day":"07","citation":{"ama":"Novak S, Cremer S. Fungal disease dynamics in insect societies: Optimal killing rates and the ambivalent effect of high social interaction rates. Journal of Theoretical Biology. 2015;372(5):54-64. doi:10.1016/j.jtbi.2015.02.018","ista":"Novak S, Cremer S. 2015. Fungal disease dynamics in insect societies: Optimal killing rates and the ambivalent effect of high social interaction rates. Journal of Theoretical Biology. 372(5), 54–64.","ieee":"S. Novak and S. Cremer, “Fungal disease dynamics in insect societies: Optimal killing rates and the ambivalent effect of high social interaction rates,” Journal of Theoretical Biology, vol. 372, no. 5. Elsevier, pp. 54–64, 2015.","apa":"Novak, S., & Cremer, S. (2015). Fungal disease dynamics in insect societies: Optimal killing rates and the ambivalent effect of high social interaction rates. Journal of Theoretical Biology. Elsevier. https://doi.org/10.1016/j.jtbi.2015.02.018","mla":"Novak, Sebastian, and Sylvia Cremer. “Fungal Disease Dynamics in Insect Societies: Optimal Killing Rates and the Ambivalent Effect of High Social Interaction Rates.” Journal of Theoretical Biology, vol. 372, no. 5, Elsevier, 2015, pp. 54–64, doi:10.1016/j.jtbi.2015.02.018.","short":"S. Novak, S. Cremer, Journal of Theoretical Biology 372 (2015) 54–64.","chicago":"Novak, Sebastian, and Sylvia Cremer. “Fungal Disease Dynamics in Insect Societies: Optimal Killing Rates and the Ambivalent Effect of High Social Interaction Rates.” Journal of Theoretical Biology. Elsevier, 2015. https://doi.org/10.1016/j.jtbi.2015.02.018."},"publication":"Journal of Theoretical Biology","page":"54 - 64","date_published":"2015-05-07T00:00:00Z","ec_funded":1,"publist_id":"5251","file_date_updated":"2020-07-14T12:45:19Z","year":"2015","publisher":"Elsevier","department":[{"_id":"NiBa"},{"_id":"SyCr"}],"publication_status":"published","author":[{"full_name":"Novak, Sebastian","last_name":"Novak","first_name":"Sebastian","id":"461468AE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Sylvia","last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia"}],"volume":372,"date_created":"2018-12-11T11:54:21Z","date_updated":"2021-01-12T06:53:37Z","month":"05","oa":1,"project":[{"name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","name":"Social Vaccination in Ant Colonies: from Individual Mechanisms to Society Effects","grant_number":"243071","_id":"25DC711C-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","doi":"10.1016/j.jtbi.2015.02.018","language":[{"iso":"eng"}]},{"month":"02","publication_identifier":{"issn":["0014-3820"],"eissn":["1558-5646"]},"external_id":{"pmid":["25662095"]},"oa":1,"quality_controlled":"1","project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"doi":"10.1111/evo.12618","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:45:19Z","publist_id":"5249","ec_funded":1,"year":"2015","pmid":1,"publication_status":"published","department":[{"_id":"NiBa"},{"_id":"KrCh"}],"publisher":"Wiley","author":[{"full_name":"Priklopil, Tadeas","id":"3C869AA0-F248-11E8-B48F-1D18A9856A87","last_name":"Priklopil","first_name":"Tadeas"},{"full_name":"Kisdi, Eva","first_name":"Eva","last_name":"Kisdi"},{"full_name":"Gyllenberg, Mats","first_name":"Mats","last_name":"Gyllenberg"}],"date_created":"2018-12-11T11:54:21Z","date_updated":"2022-06-07T10:52:37Z","volume":69,"scopus_import":"1","day":"09","article_processing_charge":"No","has_accepted_license":"1","publication":"Evolution","citation":{"ama":"Priklopil T, Kisdi E, Gyllenberg M. Evolutionarily stable mating decisions for sequentially searching females and the stability of reproductive isolation by assortative mating. Evolution. 2015;69(4):1015-1026. doi:10.1111/evo.12618","apa":"Priklopil, T., Kisdi, E., & Gyllenberg, M. (2015). Evolutionarily stable mating decisions for sequentially searching females and the stability of reproductive isolation by assortative mating. Evolution. Wiley. https://doi.org/10.1111/evo.12618","ieee":"T. Priklopil, E. Kisdi, and M. Gyllenberg, “Evolutionarily stable mating decisions for sequentially searching females and the stability of reproductive isolation by assortative mating,” Evolution, vol. 69, no. 4. Wiley, pp. 1015–1026, 2015.","ista":"Priklopil T, Kisdi E, Gyllenberg M. 2015. Evolutionarily stable mating decisions for sequentially searching females and the stability of reproductive isolation by assortative mating. Evolution. 69(4), 1015–1026.","short":"T. Priklopil, E. Kisdi, M. Gyllenberg, Evolution 69 (2015) 1015–1026.","mla":"Priklopil, Tadeas, et al. “Evolutionarily Stable Mating Decisions for Sequentially Searching Females and the Stability of Reproductive Isolation by Assortative Mating.” Evolution, vol. 69, no. 4, Wiley, 2015, pp. 1015–26, doi:10.1111/evo.12618.","chicago":"Priklopil, Tadeas, Eva Kisdi, and Mats Gyllenberg. “Evolutionarily Stable Mating Decisions for Sequentially Searching Females and the Stability of Reproductive Isolation by Assortative Mating.” Evolution. Wiley, 2015. https://doi.org/10.1111/evo.12618."},"article_type":"original","page":"1015 - 1026","date_published":"2015-02-09T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"We consider mating strategies for females who search for males sequentially during a season of limited length. We show that the best strategy rejects a given male type if encountered before a time-threshold but accepts him after. For frequency-independent benefits, we obtain the optimal time-thresholds explicitly for both discrete and continuous distributions of males, and allow for mistakes being made in assessing the correct male type. When the benefits are indirect (genes for the offspring) and the population is under frequency-dependent ecological selection, the benefits depend on the mating strategy of other females as well. This case is particularly relevant to speciation models that seek to explore the stability of reproductive isolation by assortative mating under frequency-dependent ecological selection. We show that the indirect benefits are to be quantified by the reproductive values of couples, and describe how the evolutionarily stable time-thresholds can be found. We conclude with an example based on the Levene model, in which we analyze the evolutionarily stable assortative mating strategies and the strength of reproductive isolation provided by them."}],"issue":"4","_id":"1851","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","ddc":["570"],"title":"Evolutionarily stable mating decisions for sequentially searching females and the stability of reproductive isolation by assortative mating","intvolume":" 69","oa_version":"Submitted Version","file":[{"creator":"dernst","content_type":"application/pdf","file_size":967214,"file_name":"2015_Evolution_Priklopil.pdf","access_level":"open_access","date_created":"2020-05-15T09:05:34Z","date_updated":"2020-07-14T12:45:19Z","checksum":"1e8be0b1d7598a78cd2623d8ee8e7798","file_id":"7855","relation":"main_file"}]},{"language":[{"iso":"eng"}],"date_published":"2015-06-01T00:00:00Z","doi":"10.1109/CVPR.2015.7298890","conference":{"location":"Boston, MA, USA","start_date":"2015-06-07","end_date":"2015-06-12","name":"CVPR: Computer Vision and Pattern Recognition"},"page":"2737 - 2745","project":[{"name":"Lifelong Learning of Visual Scene Understanding","call_identifier":"FP7","grant_number":"308036","_id":"2532554C-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","name":"Discrete Optimization in Computer Vision: Theory and Practice","grant_number":"616160","_id":"25FBA906-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","oa":1,"citation":{"chicago":"Shah, Neel, Vladimir Kolmogorov, and Christoph Lampert. “A Multi-Plane Block-Coordinate Frank-Wolfe Algorithm for Training Structural SVMs with a Costly Max-Oracle,” 2737–45. IEEE, 2015. https://doi.org/10.1109/CVPR.2015.7298890.","mla":"Shah, Neel, et al. A Multi-Plane Block-Coordinate Frank-Wolfe Algorithm for Training Structural SVMs with a Costly Max-Oracle. IEEE, 2015, pp. 2737–45, doi:10.1109/CVPR.2015.7298890.","short":"N. Shah, V. Kolmogorov, C. Lampert, in:, IEEE, 2015, pp. 2737–2745.","ista":"Shah N, Kolmogorov V, Lampert C. 2015. A multi-plane block-coordinate Frank-Wolfe algorithm for training structural SVMs with a costly max-oracle. CVPR: Computer Vision and Pattern Recognition, 2737–2745.","ieee":"N. Shah, V. Kolmogorov, and C. Lampert, “A multi-plane block-coordinate Frank-Wolfe algorithm for training structural SVMs with a costly max-oracle,” presented at the CVPR: Computer Vision and Pattern Recognition, Boston, MA, USA, 2015, pp. 2737–2745.","apa":"Shah, N., Kolmogorov, V., & Lampert, C. (2015). A multi-plane block-coordinate Frank-Wolfe algorithm for training structural SVMs with a costly max-oracle (pp. 2737–2745). Presented at the CVPR: Computer Vision and Pattern Recognition, Boston, MA, USA: IEEE. https://doi.org/10.1109/CVPR.2015.7298890","ama":"Shah N, Kolmogorov V, Lampert C. A multi-plane block-coordinate Frank-Wolfe algorithm for training structural SVMs with a costly max-oracle. In: IEEE; 2015:2737-2745. doi:10.1109/CVPR.2015.7298890"},"main_file_link":[{"url":"http://arxiv.org/abs/1408.6804","open_access":"1"}],"month":"06","day":"01","scopus_import":1,"oa_version":"Preprint","date_created":"2018-12-11T11:54:24Z","date_updated":"2021-01-12T06:53:40Z","author":[{"full_name":"Shah, Neel","id":"31ABAF80-F248-11E8-B48F-1D18A9856A87","last_name":"Shah","first_name":"Neel"},{"full_name":"Kolmogorov, Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","first_name":"Vladimir","last_name":"Kolmogorov"},{"last_name":"Lampert","first_name":"Christoph","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Lampert, Christoph"}],"department":[{"_id":"VlKo"},{"_id":"ChLa"}],"publisher":"IEEE","status":"public","title":"A multi-plane block-coordinate Frank-Wolfe algorithm for training structural SVMs with a costly max-oracle","publication_status":"published","year":"2015","_id":"1859","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"5240","ec_funded":1,"abstract":[{"lang":"eng","text":"Structural support vector machines (SSVMs) are amongst the best performing models for structured computer vision tasks, such as semantic image segmentation or human pose estimation. Training SSVMs, however, is computationally costly, because it requires repeated calls to a structured prediction subroutine (called \\emph{max-oracle}), which has to solve an optimization problem itself, e.g. a graph cut.\r\nIn this work, we introduce a new algorithm for SSVM training that is more efficient than earlier techniques when the max-oracle is computationally expensive, as it is frequently the case in computer vision tasks. The main idea is to (i) combine the recent stochastic Block-Coordinate Frank-Wolfe algorithm with efficient hyperplane caching, and (ii) use an automatic selection rule for deciding whether to call the exact max-oracle or to rely on an approximate one based on the cached hyperplanes.\r\nWe show experimentally that this strategy leads to faster convergence to the optimum with respect to the number of requires oracle calls, and that this translates into faster convergence with respect to the total runtime when the max-oracle is slow compared to the other steps of the algorithm. "}],"type":"conference"},{"scopus_import":1,"day":"01","month":"06","quality_controlled":"1","project":[{"name":"Lifelong Learning of Visual Scene Understanding","call_identifier":"FP7","grant_number":"308036","_id":"2532554C-B435-11E9-9278-68D0E5697425"}],"page":"1401 - 1409","main_file_link":[{"open_access":"1","url":"http://www.cv-foundation.org/openaccess/content_cvpr_2015/papers/Royer_Classifier_Adaptation_at_2015_CVPR_paper.pdf"}],"citation":{"ama":"Royer A, Lampert C. Classifier adaptation at prediction time. In: IEEE; 2015:1401-1409. doi:10.1109/CVPR.2015.7298746","ista":"Royer A, Lampert C. 2015. Classifier adaptation at prediction time. CVPR: Computer Vision and Pattern Recognition, 1401–1409.","apa":"Royer, A., & Lampert, C. (2015). Classifier adaptation at prediction time (pp. 1401–1409). Presented at the CVPR: Computer Vision and Pattern Recognition, Boston, MA, United States: IEEE. https://doi.org/10.1109/CVPR.2015.7298746","ieee":"A. Royer and C. Lampert, “Classifier adaptation at prediction time,” presented at the CVPR: Computer Vision and Pattern Recognition, Boston, MA, United States, 2015, pp. 1401–1409.","mla":"Royer, Amélie, and Christoph Lampert. Classifier Adaptation at Prediction Time. IEEE, 2015, pp. 1401–09, doi:10.1109/CVPR.2015.7298746.","short":"A. Royer, C. Lampert, in:, IEEE, 2015, pp. 1401–1409.","chicago":"Royer, Amélie, and Christoph Lampert. “Classifier Adaptation at Prediction Time,” 1401–9. IEEE, 2015. https://doi.org/10.1109/CVPR.2015.7298746."},"oa":1,"language":[{"iso":"eng"}],"conference":{"location":"Boston, MA, United States","start_date":"2015-06-07","end_date":"2015-06-12","name":"CVPR: Computer Vision and Pattern Recognition"},"doi":"10.1109/CVPR.2015.7298746","date_published":"2015-06-01T00:00:00Z","type":"conference","abstract":[{"lang":"eng","text":"Classifiers for object categorization are usually evaluated by their accuracy on a set of i.i.d. test examples. This provides us with an estimate of the expected error when applying the classifiers to a single new image. In real application, however, classifiers are rarely only used for a single image and then discarded. Instead, they are applied sequentially to many images, and these are typically not i.i.d. samples from a fixed data distribution, but they carry dependencies and their class distribution varies over time. In this work, we argue that the phenomenon of correlated data at prediction time is not a nuisance, but a blessing in disguise. We describe a probabilistic method for adapting classifiers at prediction time without having to retrain them. We also introduce a framework for creating realistically distributed image sequences, which offers a way to benchmark classifier adaptation methods, such as the one we propose. Experiments on the ILSVRC2010 and ILSVRC2012 datasets show that adapting object classification systems at prediction time can significantly reduce their error rate, even with no additional human feedback."}],"publist_id":"5239","ec_funded":1,"title":"Classifier adaptation at prediction time","status":"public","publication_status":"published","department":[{"_id":"ChLa"}],"publisher":"IEEE","_id":"1860","year":"2015","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:54:24Z","date_updated":"2021-01-12T06:53:41Z","oa_version":"Submitted Version","author":[{"full_name":"Royer, Amélie","last_name":"Royer","first_name":"Amélie"},{"last_name":"Lampert","first_name":"Christoph","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Lampert, Christoph"}]},{"scopus_import":1,"month":"10","day":"15","page":"942 - 950","quality_controlled":"1","citation":{"chicago":"Lampert, Christoph. “Predicting the Future Behavior of a Time-Varying Probability Distribution,” 942–50. IEEE, 2015. https://doi.org/10.1109/CVPR.2015.7298696.","mla":"Lampert, Christoph. Predicting the Future Behavior of a Time-Varying Probability Distribution. IEEE, 2015, pp. 942–50, doi:10.1109/CVPR.2015.7298696.","short":"C. Lampert, in:, IEEE, 2015, pp. 942–950.","ista":"Lampert C. 2015. Predicting the future behavior of a time-varying probability distribution. CVPR: Computer Vision and Pattern Recognition, 942–950.","ieee":"C. Lampert, “Predicting the future behavior of a time-varying probability distribution,” presented at the CVPR: Computer Vision and Pattern Recognition, Boston, MA, United States, 2015, pp. 942–950.","apa":"Lampert, C. (2015). Predicting the future behavior of a time-varying probability distribution (pp. 942–950). Presented at the CVPR: Computer Vision and Pattern Recognition, Boston, MA, United States: IEEE. https://doi.org/10.1109/CVPR.2015.7298696","ama":"Lampert C. Predicting the future behavior of a time-varying probability distribution. In: IEEE; 2015:942-950. doi:10.1109/CVPR.2015.7298696"},"external_id":{"arxiv":["1406.5362"]},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1406.5362","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1109/CVPR.2015.7298696","date_published":"2015-10-15T00:00:00Z","conference":{"start_date":"2015-06-07","location":"Boston, MA, United States","end_date":"2015-06-12","name":"CVPR: Computer Vision and Pattern Recognition"},"type":"conference","publist_id":"5241","abstract":[{"lang":"eng","text":"We study the problem of predicting the future, though only in the probabilistic sense of estimating a future state of a time-varying probability distribution. This is not only an interesting academic problem, but solving this extrapolation problem also has many practical application, e.g. for training classifiers that have to operate under time-varying conditions. Our main contribution is a method for predicting the next step of the time-varying distribution from a given sequence of sample sets from earlier time steps. For this we rely on two recent machine learning techniques: embedding probability distributions into a reproducing kernel Hilbert space, and learning operators by vector-valued regression. We illustrate the working principles and the practical usefulness of our method by experiments on synthetic and real data. We also highlight an exemplary application: training a classifier in a domain adaptation setting without having access to examples from the test time distribution at training time."}],"department":[{"_id":"ChLa"}],"publisher":"IEEE","status":"public","title":"Predicting the future behavior of a time-varying probability distribution","publication_status":"published","year":"2015","_id":"1858","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","date_created":"2018-12-11T11:54:24Z","date_updated":"2021-01-12T06:53:40Z","author":[{"full_name":"Lampert, Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","first_name":"Christoph","last_name":"Lampert"}]},{"type":"conference","abstract":[{"text":"Sharing information between multiple tasks enables algorithms to achieve good generalization performance even from small amounts of training data. However, in a realistic scenario of multi-task learning not all tasks are equally related to each other, hence it could be advantageous to transfer information only between the most related tasks. In this work we propose an approach that processes multiple tasks in a sequence with sharing between subsequent tasks instead of solving all tasks jointly. Subsequently, we address the question of curriculum learning of tasks, i.e. finding the best order of tasks to be learned. Our approach is based on a generalization bound criterion for choosing the task order that optimizes the average expected classification performance over all tasks. Our experimental results show that learning multiple related tasks sequentially can be more effective than learning them jointly, the order in which tasks are being solved affects the overall performance, and that our model is able to automatically discover the favourable order of tasks. ","lang":"eng"}],"publist_id":"5243","publication_status":"published","status":"public","title":"Curriculum learning of multiple tasks","department":[{"_id":"ChLa"}],"publisher":"IEEE","_id":"1857","year":"2015","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-02-23T10:17:31Z","date_created":"2018-12-11T11:54:23Z","oa_version":"Preprint","author":[{"full_name":"Pentina, Anastasia","last_name":"Pentina","first_name":"Anastasia","id":"42E87FC6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Sharmanska, Viktoriia","first_name":"Viktoriia","last_name":"Sharmanska","id":"2EA6D09E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0192-9308"},{"full_name":"Lampert, Christoph","first_name":"Christoph","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887"}],"scopus_import":1,"month":"06","day":"01","quality_controlled":"1","page":"5492 - 5500","oa":1,"citation":{"mla":"Pentina, Anastasia, et al. Curriculum Learning of Multiple Tasks. IEEE, 2015, pp. 5492–500, doi:10.1109/CVPR.2015.7299188.","short":"A. Pentina, V. Sharmanska, C. Lampert, in:, IEEE, 2015, pp. 5492–5500.","chicago":"Pentina, Anastasia, Viktoriia Sharmanska, and Christoph Lampert. “Curriculum Learning of Multiple Tasks,” 5492–5500. IEEE, 2015. https://doi.org/10.1109/CVPR.2015.7299188.","ama":"Pentina A, Sharmanska V, Lampert C. Curriculum learning of multiple tasks. In: IEEE; 2015:5492-5500. doi:10.1109/CVPR.2015.7299188","ista":"Pentina A, Sharmanska V, Lampert C. 2015. Curriculum learning of multiple tasks. CVPR: Computer Vision and Pattern Recognition, 5492–5500.","ieee":"A. Pentina, V. Sharmanska, and C. Lampert, “Curriculum learning of multiple tasks,” presented at the CVPR: Computer Vision and Pattern Recognition, Boston, MA, United States, 2015, pp. 5492–5500.","apa":"Pentina, A., Sharmanska, V., & Lampert, C. (2015). Curriculum learning of multiple tasks (pp. 5492–5500). Presented at the CVPR: Computer Vision and Pattern Recognition, Boston, MA, United States: IEEE. https://doi.org/10.1109/CVPR.2015.7299188"},"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1412.1353"}],"language":[{"iso":"eng"}],"conference":{"name":"CVPR: Computer Vision and Pattern Recognition","end_date":"2015-06-12","start_date":"2015-06-07","location":"Boston, MA, United States"},"doi":"10.1109/CVPR.2015.7299188","date_published":"2015-06-01T00:00:00Z"},{"scopus_import":1,"day":"01","citation":{"ama":"Hühner J, Inglés Prieto Á, Neusüß C, Lämmerhofer M, Janovjak HL. Quantification of riboflavin, flavin mononucleotide, and flavin adenine dinucleotide in mammalian model cells by CE with LED-induced fluorescence detection. Electrophoresis. 2015;36(4):518-525. doi:10.1002/elps.201400451","ieee":"J. Hühner, Á. Inglés Prieto, C. Neusüß, M. Lämmerhofer, and H. L. Janovjak, “Quantification of riboflavin, flavin mononucleotide, and flavin adenine dinucleotide in mammalian model cells by CE with LED-induced fluorescence detection,” Electrophoresis, vol. 36, no. 4. Wiley, pp. 518–525, 2015.","apa":"Hühner, J., Inglés Prieto, Á., Neusüß, C., Lämmerhofer, M., & Janovjak, H. L. (2015). Quantification of riboflavin, flavin mononucleotide, and flavin adenine dinucleotide in mammalian model cells by CE with LED-induced fluorescence detection. Electrophoresis. Wiley. https://doi.org/10.1002/elps.201400451","ista":"Hühner J, Inglés Prieto Á, Neusüß C, Lämmerhofer M, Janovjak HL. 2015. Quantification of riboflavin, flavin mononucleotide, and flavin adenine dinucleotide in mammalian model cells by CE with LED-induced fluorescence detection. Electrophoresis. 36(4), 518–525.","short":"J. Hühner, Á. Inglés Prieto, C. Neusüß, M. Lämmerhofer, H.L. Janovjak, Electrophoresis 36 (2015) 518–525.","mla":"Hühner, Jens, et al. “Quantification of Riboflavin, Flavin Mononucleotide, and Flavin Adenine Dinucleotide in Mammalian Model Cells by CE with LED-Induced Fluorescence Detection.” Electrophoresis, vol. 36, no. 4, Wiley, 2015, pp. 518–25, doi:10.1002/elps.201400451.","chicago":"Hühner, Jens, Álvaro Inglés Prieto, Christian Neusüß, Michael Lämmerhofer, and Harald L Janovjak. “Quantification of Riboflavin, Flavin Mononucleotide, and Flavin Adenine Dinucleotide in Mammalian Model Cells by CE with LED-Induced Fluorescence Detection.” Electrophoresis. Wiley, 2015. https://doi.org/10.1002/elps.201400451."},"publication":"Electrophoresis","page":"518 - 525","date_published":"2015-02-01T00:00:00Z","type":"journal_article","issue":"4","abstract":[{"text":"Cultured mammalian cells essential are model systems in basic biology research, production platforms of proteins for medical use, and testbeds in synthetic biology. Flavin cofactors, in particular flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD), are critical for cellular redox reactions and sense light in naturally occurring photoreceptors and optogenetic tools. Here, we quantified flavin contents of commonly used mammalian cell lines. We first compared three procedures for extraction of free and noncovalently protein-bound flavins and verified extraction using fluorescence spectroscopy. For separation, two CE methods with different BGEs were established, and detection was performed by LED-induced fluorescence with limit of detections (LODs 0.5-3.8 nM). We found that riboflavin (RF), FMN, and FAD contents varied significantly between cell lines. RF (3.1-14 amol/cell) and FAD (2.2-17.0 amol/cell) were the predominant flavins, while FMN (0.46-3.4 amol/cell) was found at markedly lower levels. Observed flavin contents agree with those previously extracted from mammalian tissues, yet reduced forms of RF were detected that were not described previously. Quantification of flavins in mammalian cell lines will allow a better understanding of cellular redox reactions and optogenetic tools.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1867","intvolume":" 36","status":"public","title":"Quantification of riboflavin, flavin mononucleotide, and flavin adenine dinucleotide in mammalian model cells by CE with LED-induced fluorescence detection","pubrep_id":"836","oa_version":"None","month":"02","project":[{"name":"Microbial Ion Channels for Synthetic Neurobiology","call_identifier":"FP7","_id":"25548C20-B435-11E9-9278-68D0E5697425","grant_number":"303564"},{"_id":"255BFFFA-B435-11E9-9278-68D0E5697425","grant_number":"RGY0084/2012","name":"In situ real-time imaging of neurotransmitter signaling using designer optical sensors (HFSP Young Investigator)"}],"quality_controlled":"1","doi":"10.1002/elps.201400451","language":[{"iso":"eng"}],"publist_id":"5230","ec_funded":1,"year":"2015","publisher":"Wiley","department":[{"_id":"HaJa"}],"publication_status":"published","author":[{"last_name":"Hühner","first_name":"Jens","full_name":"Hühner, Jens"},{"orcid":"0000-0002-5409-8571","id":"2A9DB292-F248-11E8-B48F-1D18A9856A87","last_name":"Inglés Prieto","first_name":"Álvaro","full_name":"Inglés Prieto, Álvaro"},{"full_name":"Neusüß, Christian","last_name":"Neusüß","first_name":"Christian"},{"last_name":"Lämmerhofer","first_name":"Michael","full_name":"Lämmerhofer, Michael"},{"first_name":"Harald L","last_name":"Janovjak","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8023-9315","full_name":"Janovjak, Harald L"}],"volume":36,"date_updated":"2021-01-12T06:53:43Z","date_created":"2018-12-11T11:54:26Z"},{"month":"02","quality_controlled":"1","project":[{"_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300","name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7"}],"language":[{"iso":"eng"}],"doi":"10.1242/dev.115832","ec_funded":1,"publist_id":"5231","publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"Company of Biologists","acknowledgement":"W.G. is a post-doctoral fellow of the Research Foundation Flanders. H.S.R. is supported by Employment of Best Young Scientists for International Cooperation Empowerment [CZ.1.07/2.3.00/30.0037], co-financed by the European Social Fund and the state budget of the Czech Republic. Mi.S. was funded by the Ramón y Cajal program. This work was supported by the European Research Council [project ERC-2011-StG-20101109-PSDP], project ‘CEITEC – Central European Institute of Technology’ [CZ.1.05/1.1.00/02.0068], the European Social Fund [CZ.1.07/2.3.00/20.0043] and the Czech Science Foundation GACR [GA13-40637S] to J.F. We acknowledge funding from the Biological and Biotechnological Science Research Council (BBSRC) and Engineering Physics Science Research Council (EPSRC) to R.S. and M.B","year":"2015","date_updated":"2021-01-12T06:53:43Z","date_created":"2018-12-11T11:54:26Z","volume":142,"author":[{"first_name":"Hélène","last_name":"Robert","full_name":"Robert, Hélène"},{"full_name":"Grunewald, Wim","first_name":"Wim","last_name":"Grunewald"},{"first_name":"Michael","last_name":"Sauer","full_name":"Sauer, Michael"},{"full_name":"Cannoot, Bernard","last_name":"Cannoot","first_name":"Bernard"},{"full_name":"Soriano, Mercedes","last_name":"Soriano","first_name":"Mercedes"},{"full_name":"Swarup, Ranjan","last_name":"Swarup","first_name":"Ranjan"},{"full_name":"Weijers, Dolf","last_name":"Weijers","first_name":"Dolf"},{"last_name":"Bennett","first_name":"Malcolm","full_name":"Bennett, Malcolm"},{"full_name":"Boutilier, Kim","first_name":"Kim","last_name":"Boutilier"},{"first_name":"Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí"}],"scopus_import":1,"day":"15","page":"702 - 711","publication":"Development","citation":{"apa":"Robert, H., Grunewald, W., Sauer, M., Cannoot, B., Soriano, M., Swarup, R., … Friml, J. (2015). Plant embryogenesis requires AUX/LAX-mediated auxin influx. Development. Company of Biologists. https://doi.org/10.1242/dev.115832","ieee":"H. Robert et al., “Plant embryogenesis requires AUX/LAX-mediated auxin influx,” Development, vol. 142, no. 4. Company of Biologists, pp. 702–711, 2015.","ista":"Robert H, Grunewald W, Sauer M, Cannoot B, Soriano M, Swarup R, Weijers D, Bennett M, Boutilier K, Friml J. 2015. Plant embryogenesis requires AUX/LAX-mediated auxin influx. Development. 142(4), 702–711.","ama":"Robert H, Grunewald W, Sauer M, et al. Plant embryogenesis requires AUX/LAX-mediated auxin influx. Development. 2015;142(4):702-711. doi:10.1242/dev.115832","chicago":"Robert, Hélène, Wim Grunewald, Michael Sauer, Bernard Cannoot, Mercedes Soriano, Ranjan Swarup, Dolf Weijers, Malcolm Bennett, Kim Boutilier, and Jiří Friml. “Plant Embryogenesis Requires AUX/LAX-Mediated Auxin Influx.” Development. Company of Biologists, 2015. https://doi.org/10.1242/dev.115832.","short":"H. Robert, W. Grunewald, M. Sauer, B. Cannoot, M. Soriano, R. Swarup, D. Weijers, M. Bennett, K. Boutilier, J. Friml, Development 142 (2015) 702–711.","mla":"Robert, Hélène, et al. “Plant Embryogenesis Requires AUX/LAX-Mediated Auxin Influx.” Development, vol. 142, no. 4, Company of Biologists, 2015, pp. 702–11, doi:10.1242/dev.115832."},"date_published":"2015-02-15T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"The plant hormone auxin and its directional transport are known to play a crucial role in defining the embryonic axis and subsequent development of the body plan. Although the role of PIN auxin efflux transporters has been clearly assigned during embryonic shoot and root specification, the role of the auxin influx carriers AUX1 and LIKE-AUX1 (LAX) proteins is not well established. Here, we used chemical and genetic tools on Brassica napus microspore-derived embryos and Arabidopsis thaliana zygotic embryos, and demonstrate that AUX1, LAX1 and LAX2 are required for both shoot and root pole formation, in concert with PIN efflux carriers. Furthermore, we uncovered a positive-feedback loop betweenMONOPTEROS(ARF5)-dependent auxin signalling and auxin transport. ThisMONOPTEROSdependent transcriptional regulation of auxin influx (AUX1, LAX1 and LAX2) and auxin efflux (PIN1 and PIN4) carriers by MONOPTEROS helps to maintain proper auxin transport to the root tip. These results indicate that auxin-dependent cell specification during embryo development requires balanced auxin transport involving both influx and efflux mechanisms, and that this transport is maintained by a positive transcriptional feedback on auxin signalling."}],"issue":"4","status":"public","title":"Plant embryogenesis requires AUX/LAX-mediated auxin influx","intvolume":" 142","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1865","oa_version":"None"},{"department":[{"_id":"BjHo"}],"intvolume":" 91","publisher":"American Physical Society","status":"public","publication_status":"published","title":"Early effect in time-dependent, high-dimensional nonlinear dynamical systems with multiple resonances","_id":"1868","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2015","oa_version":"None","volume":91,"date_updated":"2021-01-12T06:53:44Z","date_created":"2018-12-11T11:54:27Z","author":[{"full_name":"Park, Youngyong","first_name":"Youngyong","last_name":"Park"},{"first_name":"Younghae","last_name":"Do","full_name":"Do, Younghae"},{"full_name":"Altmeyer, Sebastian","first_name":"Sebastian","last_name":"Altmeyer","id":"2EE67FDC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5964-0203"},{"full_name":"Lai, Yingcheng","first_name":"Yingcheng","last_name":"Lai"},{"first_name":"Gyuwon","last_name":"Lee","full_name":"Lee, Gyuwon"}],"type":"journal_article","article_number":"022906","issue":"2","publist_id":"5229","abstract":[{"lang":"eng","text":"We investigate high-dimensional nonlinear dynamical systems exhibiting multiple resonances under adiabatic parameter variations. Our motivations come from experimental considerations where time-dependent sweeping of parameters is a practical approach to probing and characterizing the bifurcations of the system. The question is whether bifurcations so detected are faithful representations of the bifurcations intrinsic to the original stationary system. Utilizing a harmonically forced, closed fluid flow system that possesses multiple resonances and solving the Navier-Stokes equation under proper boundary conditions, we uncover the phenomenon of the early effect. Specifically, as a control parameter, e.g., the driving frequency, is adiabatically increased from an initial value, resonances emerge at frequency values that are lower than those in the corresponding stationary system. The phenomenon is established by numerical characterization of physical quantities through the resonances, which include the kinetic energy and the vorticity field, and a heuristic analysis based on the concept of instantaneous frequency. A simple formula is obtained which relates the resonance points in the time-dependent and time-independent systems. Our findings suggest that, in general, any true bifurcation of a nonlinear dynamical system can be unequivocally uncovered through adiabatic parameter sweeping, in spite of a shift in the bifurcation point, which is of value to experimental studies of nonlinear dynamical systems."}],"quality_controlled":"1","citation":{"ama":"Park Y, Do Y, Altmeyer S, Lai Y, Lee G. Early effect in time-dependent, high-dimensional nonlinear dynamical systems with multiple resonances. Physical Review E. 2015;91(2). doi:10.1103/PhysRevE.91.022906","ista":"Park Y, Do Y, Altmeyer S, Lai Y, Lee G. 2015. Early effect in time-dependent, high-dimensional nonlinear dynamical systems with multiple resonances. Physical Review E. 91(2), 022906.","ieee":"Y. Park, Y. Do, S. Altmeyer, Y. Lai, and G. Lee, “Early effect in time-dependent, high-dimensional nonlinear dynamical systems with multiple resonances,” Physical Review E, vol. 91, no. 2. American Physical Society, 2015.","apa":"Park, Y., Do, Y., Altmeyer, S., Lai, Y., & Lee, G. (2015). Early effect in time-dependent, high-dimensional nonlinear dynamical systems with multiple resonances. Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.91.022906","mla":"Park, Youngyong, et al. “Early Effect in Time-Dependent, High-Dimensional Nonlinear Dynamical Systems with Multiple Resonances.” Physical Review E, vol. 91, no. 2, 022906, American Physical Society, 2015, doi:10.1103/PhysRevE.91.022906.","short":"Y. Park, Y. Do, S. Altmeyer, Y. Lai, G. Lee, Physical Review E 91 (2015).","chicago":"Park, Youngyong, Younghae Do, Sebastian Altmeyer, Yingcheng Lai, and Gyuwon Lee. “Early Effect in Time-Dependent, High-Dimensional Nonlinear Dynamical Systems with Multiple Resonances.” Physical Review E. American Physical Society, 2015. https://doi.org/10.1103/PhysRevE.91.022906."},"publication":"Physical Review E","language":[{"iso":"eng"}],"date_published":"2015-02-09T00:00:00Z","doi":"10.1103/PhysRevE.91.022906","scopus_import":1,"publication_identifier":{"issn":["1539-3755"]},"day":"09","month":"02"},{"month":"03","main_file_link":[{"url":"http://arxiv.org/abs/1309.5107","open_access":"1"}],"oa":1,"project":[{"grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7"}],"doi":"10.1007/s00023-014-0333-5","language":[{"iso":"eng"}],"publist_id":"5233","ec_funded":1,"year":"2015","publication_status":"published","publisher":"Springer","department":[{"_id":"LaEr"}],"author":[{"last_name":"Erdös","first_name":"László","orcid":"0000-0001-5366-9603","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","full_name":"Erdös, László"},{"full_name":"Knowles, Antti","first_name":"Antti","last_name":"Knowles"}],"date_updated":"2021-01-12T06:53:42Z","date_created":"2018-12-11T11:54:26Z","volume":16,"scopus_import":1,"day":"01","publication":"Annales Henri Poincare","citation":{"mla":"Erdös, László, and Antti Knowles. “The Altshuler–Shklovskii Formulas for Random Band Matrices II: The General Case.” Annales Henri Poincare, vol. 16, no. 3, Springer, 2015, pp. 709–99, doi:10.1007/s00023-014-0333-5.","short":"L. Erdös, A. Knowles, Annales Henri Poincare 16 (2015) 709–799.","chicago":"Erdös, László, and Antti Knowles. “The Altshuler–Shklovskii Formulas for Random Band Matrices II: The General Case.” Annales Henri Poincare. Springer, 2015. https://doi.org/10.1007/s00023-014-0333-5.","ama":"Erdös L, Knowles A. The Altshuler–Shklovskii formulas for random band matrices II: The general case. Annales Henri Poincare. 2015;16(3):709-799. doi:10.1007/s00023-014-0333-5","ista":"Erdös L, Knowles A. 2015. The Altshuler–Shklovskii formulas for random band matrices II: The general case. Annales Henri Poincare. 16(3), 709–799.","apa":"Erdös, L., & Knowles, A. (2015). The Altshuler–Shklovskii formulas for random band matrices II: The general case. Annales Henri Poincare. Springer. https://doi.org/10.1007/s00023-014-0333-5","ieee":"L. Erdös and A. Knowles, “The Altshuler–Shklovskii formulas for random band matrices II: The general case,” Annales Henri Poincare, vol. 16, no. 3. Springer, pp. 709–799, 2015."},"page":"709 - 799","date_published":"2015-03-01T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"The Altshuler–Shklovskii formulas (Altshuler and Shklovskii, BZh Eksp Teor Fiz 91:200, 1986) predict, for any disordered quantum system in the diffusive regime, a universal power law behaviour for the correlation functions of the mesoscopic eigenvalue density. In this paper and its companion (Erdős and Knowles, The Altshuler–Shklovskii formulas for random band matrices I: the unimodular case, 2013), we prove these formulas for random band matrices. In (Erdős and Knowles, The Altshuler–Shklovskii formulas for random band matrices I: the unimodular case, 2013) we introduced a diagrammatic approach and presented robust estimates on general diagrams under certain simplifying assumptions. In this paper, we remove these assumptions by giving a general estimate of the subleading diagrams. We also give a precise analysis of the leading diagrams which give rise to the Altschuler–Shklovskii power laws. Moreover, we introduce a family of general random band matrices which interpolates between real symmetric (β = 1) and complex Hermitian (β = 2) models, and track the transition for the mesoscopic density–density correlation. Finally, we address the higher-order correlation functions by proving that they behave asymptotically according to a Gaussian process whose covariance is given by the Altshuler–Shklovskii formulas.\r\n"}],"issue":"3","_id":"1864","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"The Altshuler–Shklovskii formulas for random band matrices II: The general case","intvolume":" 16","oa_version":"Preprint"},{"scopus_import":1,"day":"01","month":"02","quality_controlled":"1","citation":{"short":"J. Ruess, J. Lygeros, ACM Transactions on Modeling and Computer Simulation 25 (2015).","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.","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.","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","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.","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."},"publication":"ACM Transactions on Modeling and Computer Simulation","language":[{"iso":"eng"}],"date_published":"2015-02-01T00:00:00Z","doi":"10.1145/2688906","type":"journal_article","article_number":"8","publist_id":"5238","issue":"2","abstract":[{"lang":"eng","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."}],"department":[{"_id":"ToHe"},{"_id":"GaTk"}],"publisher":"ACM","intvolume":" 25","status":"public","publication_status":"published","title":"Moment-based methods for parameter inference and experiment design for stochastic biochemical reaction networks","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1861","year":"2015","acknowledgement":"HYCON2; EC; European Commission\r\n","volume":25,"oa_version":"None","date_updated":"2021-01-12T06:53:41Z","date_created":"2018-12-11T11:54:25Z","author":[{"first_name":"Jakob","last_name":"Ruess","id":"4A245D00-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1615-3282","full_name":"Ruess, Jakob"},{"full_name":"Lygeros, John","last_name":"Lygeros","first_name":"John"}]},{"day":"28","month":"01","scopus_import":1,"date_published":"2015-01-28T00:00:00Z","doi":"10.1145/2701001","language":[{"iso":"eng"}],"citation":{"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.","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","ista":"Henzinger TA, Raskin J. 2015. The equivalence problem for finite automata: Technical perspective. Communications of the ACM. 58(2), 86–86.","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","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.","short":"T.A. Henzinger, J. Raskin, Communications of the ACM 58 (2015) 86–86.","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."},"publication":"Communications of the ACM","page":"86-86","publist_id":"5232","issue":"2","type":"journal_article","author":[{"orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A","full_name":"Henzinger, Thomas A"},{"first_name":"Jean","last_name":"Raskin","full_name":"Raskin, Jean"}],"volume":58,"oa_version":"None","date_updated":"2021-01-12T06:53:43Z","date_created":"2018-12-11T11:54:26Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1866","year":"2015","intvolume":" 58","department":[{"_id":"ToHe"}],"publisher":"ACM","publication_status":"published","title":"The equivalence problem for finite automata: Technical perspective","status":"public"},{"file_date_updated":"2020-07-14T12:45:19Z","publist_id":"5225","publication_status":"published","publisher":"Company of Biologists","department":[{"_id":"JiFr"}],"year":"2015","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]","date_updated":"2021-01-12T06:53:45Z","date_created":"2018-12-11T11:54:28Z","volume":128,"author":[{"full_name":"Grones, Peter","first_name":"Peter","last_name":"Grones","id":"399876EC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí"}],"month":"01","quality_controlled":"1","oa":1,"language":[{"iso":"eng"}],"doi":"10.1242/jcs.159418","type":"journal_article","abstract":[{"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.","lang":"eng"}],"issue":"1","title":"Auxin transporters and binding proteins at a glance","status":"public","ddc":["570"],"intvolume":" 128","_id":"1871","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"file_name":"IST-2016-563-v1+1_1.full.pdf","access_level":"open_access","creator":"system","file_size":1688844,"content_type":"application/pdf","file_id":"4852","relation":"main_file","date_updated":"2020-07-14T12:45:19Z","date_created":"2018-12-12T10:11:00Z","checksum":"24c779f4cd9d549ca6833e26f486be27"}],"oa_version":"Submitted Version","pubrep_id":"563","scopus_import":1,"day":"01","has_accepted_license":"1","page":"1 - 7","publication":"Journal of Cell Science","citation":{"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","ista":"Grones P, Friml J. 2015. Auxin transporters and binding proteins at a glance. Journal of Cell Science. 128(1), 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.","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.","short":"P. Grones, J. Friml, Journal of Cell Science 128 (2015) 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."},"date_published":"2015-01-01T00:00:00Z"},{"author":[{"full_name":"Boccara, Charlotte","orcid":"0000-0001-7237-5109","id":"3FC06552-F248-11E8-B48F-1D18A9856A87","last_name":"Boccara","first_name":"Charlotte"},{"full_name":"Kjønigsen, Lisa","first_name":"Lisa","last_name":"Kjønigsen"},{"first_name":"Ingvild","last_name":"Hammer","full_name":"Hammer, Ingvild"},{"full_name":"Bjaalie, Jan","last_name":"Bjaalie","first_name":"Jan"},{"full_name":"Leergaard, Trygve","first_name":"Trygve","last_name":"Leergaard"},{"full_name":"Witter, Menno","first_name":"Menno","last_name":"Witter"}],"date_created":"2018-12-11T11:54:29Z","date_updated":"2021-01-12T06:53:46Z","volume":25,"oa_version":"None","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1874","year":"2015","status":"public","title":"A three-plane architectonic atlas of the rat hippocampal region","publication_status":"published","publisher":"Wiley","department":[{"_id":"JoCs"}],"intvolume":" 25","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"}],"publist_id":"5222","issue":"7","type":"journal_article","date_published":"2015-07-01T00:00:00Z","doi":"10.1002/hipo.22407","language":[{"iso":"eng"}],"publication":"Hippocampus","citation":{"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.","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.","short":"C.N. Boccara, L. Kjønigsen, I. Hammer, J. Bjaalie, T. Leergaard, M. Witter, Hippocampus 25 (2015) 838–857.","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.","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.","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"},"quality_controlled":"1","page":"838 - 857","month":"07","day":"01","scopus_import":1},{"type":"journal_article","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"}],"publist_id":"5224","_id":"1873","year":"2015","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","status":"public","publication_status":"published","title":"POMDPs under probabilistic semantics","intvolume":" 221","publisher":"Elsevier","department":[{"_id":"KrCh"}],"author":[{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"full_name":"Chmelik, Martin","id":"3624234E-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","last_name":"Chmelik"}],"date_updated":"2021-01-12T06:53:46Z","date_created":"2018-12-11T11:54:28Z","oa_version":"Preprint","volume":221,"scopus_import":1,"day":"01","month":"04","publication":"Artificial Intelligence","external_id":{"arxiv":["1408.2058"]},"citation":{"short":"K. Chatterjee, M. Chmelik, Artificial Intelligence 221 (2015) 46–72.","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.","chicago":"Chatterjee, Krishnendu, and Martin Chmelik. “POMDPs under Probabilistic Semantics.” Artificial Intelligence. Elsevier, 2015. 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","apa":"Chatterjee, K., & Chmelik, M. (2015). POMDPs under probabilistic semantics. Artificial Intelligence. Elsevier. https://doi.org/10.1016/j.artint.2014.12.009","ieee":"K. Chatterjee and M. Chmelik, “POMDPs under probabilistic semantics,” Artificial Intelligence, vol. 221. Elsevier, pp. 46–72, 2015.","ista":"Chatterjee K, Chmelik M. 2015. POMDPs under probabilistic semantics. Artificial Intelligence. 221, 46–72."},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1408.2058","open_access":"1"}],"quality_controlled":"1","page":"46 - 72","date_published":"2015-04-01T00:00:00Z","doi":"10.1016/j.artint.2014.12.009","language":[{"iso":"eng"}]},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","doi":"10.1111/jmi.12211","language":[{"iso":"eng"}],"month":"08","acknowledgement":"The Zeiss Merlin with Gatan 3View2XP and Zeiss Auriga were acquired through a CLEM grant from Minister Ingrid Lieten to the VIB Bio-Imaging-Core. Michiel Krols and Saskia Lippens are the recipients of a fellowship from the FWO (Fonds Wetenschappelijk Onderzoek) of Flanders.","year":"2015","publication_status":"published","publisher":"Wiley-Blackwell","department":[{"_id":"JiFr"}],"author":[{"first_name":"A","last_name":"Kremer","full_name":"Kremer, A"},{"full_name":"Lippens, Stefaan","first_name":"Stefaan","last_name":"Lippens"},{"last_name":"Bartunkova","first_name":"Sonia","full_name":"Bartunkova, Sonia"},{"last_name":"Asselbergh","first_name":"Bob","full_name":"Asselbergh, Bob"},{"full_name":"Blanpain, Cendric","last_name":"Blanpain","first_name":"Cendric"},{"full_name":"Fendrych, Matyas","orcid":"0000-0002-9767-8699","id":"43905548-F248-11E8-B48F-1D18A9856A87","last_name":"Fendrych","first_name":"Matyas"},{"full_name":"Goossens, A","first_name":"A","last_name":"Goossens"},{"last_name":"Holt","first_name":"Matthew","full_name":"Holt, Matthew"},{"first_name":"Sophie","last_name":"Janssens","full_name":"Janssens, Sophie"},{"full_name":"Krols, Michiel","last_name":"Krols","first_name":"Michiel"},{"last_name":"Larsimont","first_name":"Jean","full_name":"Larsimont, Jean"},{"full_name":"Mc Guire, Conor","last_name":"Mc Guire","first_name":"Conor"},{"full_name":"Nowack, Moritz","first_name":"Moritz","last_name":"Nowack"},{"full_name":"Saelens, Xavier","last_name":"Saelens","first_name":"Xavier"},{"first_name":"Andreas","last_name":"Schertel","full_name":"Schertel, Andreas"},{"last_name":"Schepens","first_name":"B","full_name":"Schepens, B"},{"full_name":"Slezak, M","first_name":"M","last_name":"Slezak"},{"last_name":"Timmerman","first_name":"Vincent","full_name":"Timmerman, Vincent"},{"last_name":"Theunis","first_name":"Clara","full_name":"Theunis, Clara"},{"last_name":"Van Brempt","first_name":"Ronald","full_name":"Van Brempt, Ronald"},{"full_name":"Visser, Y","first_name":"Y","last_name":"Visser"},{"first_name":"Christophe","last_name":"Guérin","full_name":"Guérin, Christophe"}],"date_created":"2018-12-11T11:54:30Z","date_updated":"2021-01-12T06:53:48Z","volume":259,"file_date_updated":"2020-07-14T12:45:19Z","publist_id":"5218","publication":"Journal of Microscopy","citation":{"ama":"Kremer A, Lippens S, Bartunkova S, et al. Developing 3D SEM in a broad biological context. Journal of Microscopy. 2015;259(2):80-96. doi:10.1111/jmi.12211","ista":"Kremer A, Lippens S, Bartunkova S, Asselbergh B, Blanpain C, Fendrych M, Goossens A, Holt M, Janssens S, Krols M, Larsimont J, Mc Guire C, Nowack M, Saelens X, Schertel A, Schepens B, Slezak M, Timmerman V, Theunis C, Van Brempt R, Visser Y, Guérin C. 2015. Developing 3D SEM in a broad biological context. Journal of Microscopy. 259(2), 80–96.","ieee":"A. Kremer et al., “Developing 3D SEM in a broad biological context,” Journal of Microscopy, vol. 259, no. 2. Wiley-Blackwell, pp. 80–96, 2015.","apa":"Kremer, A., Lippens, S., Bartunkova, S., Asselbergh, B., Blanpain, C., Fendrych, M., … Guérin, C. (2015). Developing 3D SEM in a broad biological context. Journal of Microscopy. Wiley-Blackwell. https://doi.org/10.1111/jmi.12211","mla":"Kremer, A., et al. “Developing 3D SEM in a Broad Biological Context.” Journal of Microscopy, vol. 259, no. 2, Wiley-Blackwell, 2015, pp. 80–96, doi:10.1111/jmi.12211.","short":"A. Kremer, S. Lippens, S. Bartunkova, B. Asselbergh, C. Blanpain, M. Fendrych, A. Goossens, M. Holt, S. Janssens, M. Krols, J. Larsimont, C. Mc Guire, M. Nowack, X. Saelens, A. Schertel, B. Schepens, M. Slezak, V. Timmerman, C. Theunis, R. Van Brempt, Y. Visser, C. Guérin, Journal of Microscopy 259 (2015) 80–96.","chicago":"Kremer, A, Stefaan Lippens, Sonia Bartunkova, Bob Asselbergh, Cendric Blanpain, Matyas Fendrych, A Goossens, et al. “Developing 3D SEM in a Broad Biological Context.” Journal of Microscopy. Wiley-Blackwell, 2015. https://doi.org/10.1111/jmi.12211."},"page":"80 - 96","date_published":"2015-08-01T00:00:00Z","scopus_import":1,"day":"01","has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1879","title":"Developing 3D SEM in a broad biological context","ddc":["570"],"status":"public","intvolume":" 259","pubrep_id":"459","file":[{"date_updated":"2020-07-14T12:45:19Z","date_created":"2018-12-12T10:11:19Z","checksum":"3649c5372d1644062d728ea9287e367f","file_id":"4872","relation":"main_file","creator":"system","content_type":"application/pdf","file_size":2899898,"file_name":"IST-2016-459-v1+1_KREMER_et_al-2015-Journal_of_Microscopy.pdf","access_level":"open_access"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"When electron microscopy (EM) was introduced in the 1930s it gave scientists their first look into the nanoworld of cells. Over the last 80 years EM has vastly increased our understanding of the complex cellular structures that underlie the diverse functions that cells need to maintain life. One drawback that has been difficult to overcome was the inherent lack of volume information, mainly due to the limit on the thickness of sections that could be viewed in a transmission electron microscope (TEM). For many years scientists struggled to achieve three-dimensional (3D) EM using serial section reconstructions, TEM tomography, and scanning EM (SEM) techniques such as freeze-fracture. Although each technique yielded some special information, they required a significant amount of time and specialist expertise to obtain even a very small 3D EM dataset. Almost 20 years ago scientists began to exploit SEMs to image blocks of embedded tissues and perform serial sectioning of these tissues inside the SEM chamber. Using first focused ion beams (FIB) and subsequently robotic ultramicrotomes (serial block-face, SBF-SEM) microscopists were able to collect large volumes of 3D EM information at resolutions that could address many important biological questions, and do so in an efficient manner. We present here some examples of 3D EM taken from the many diverse specimens that have been imaged in our core facility. We propose that the next major step forward will be to efficiently correlate functional information obtained using light microscopy (LM) with 3D EM datasets to more completely investigate the important links between cell structures and their functions."}],"issue":"2"},{"month":"01","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"project":[{"name":"NSERC Postdoctoral fellowship","_id":"26450934-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","doi":"10.1088/1367-2630/17/1/013022","language":[{"iso":"eng"}],"article_number":"013022","publist_id":"5214","file_date_updated":"2020-07-14T12:45:20Z","year":"2015","acknowledgement":"Support from the Natural Sciences and Engineering Research Council of Canada NSERC (MK and RS) and from the Austrian Science Fund FWF (JY, under project P 22929-N16) is gratefully acknowledged","publisher":"IOP Publishing Ltd.","department":[{"_id":"RoSe"}],"publication_status":"published","author":[{"last_name":"Könenberg","first_name":"Martin","full_name":"Könenberg, Martin"},{"id":"2B5FC9A4-F248-11E8-B48F-1D18A9856A87","last_name":"Moser","first_name":"Thomas","full_name":"Moser, Thomas"},{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","first_name":"Robert","last_name":"Seiringer","full_name":"Seiringer, Robert"},{"full_name":"Yngvason, Jakob","first_name":"Jakob","last_name":"Yngvason"}],"volume":17,"date_updated":"2021-01-12T06:53:48Z","date_created":"2018-12-11T11:54:30Z","scopus_import":1,"has_accepted_license":"1","day":"15","citation":{"apa":"Könenberg, M., Moser, T., Seiringer, R., & Yngvason, J. (2015). Superfluid behavior of a Bose-Einstein condensate in a random potential. New Journal of Physics. IOP Publishing Ltd. https://doi.org/10.1088/1367-2630/17/1/013022","ieee":"M. Könenberg, T. Moser, R. Seiringer, and J. Yngvason, “Superfluid behavior of a Bose-Einstein condensate in a random potential,” New Journal of Physics, vol. 17. IOP Publishing Ltd., 2015.","ista":"Könenberg M, Moser T, Seiringer R, Yngvason J. 2015. Superfluid behavior of a Bose-Einstein condensate in a random potential. New Journal of Physics. 17, 013022.","ama":"Könenberg M, Moser T, Seiringer R, Yngvason J. Superfluid behavior of a Bose-Einstein condensate in a random potential. New Journal of Physics. 2015;17. doi:10.1088/1367-2630/17/1/013022","chicago":"Könenberg, Martin, Thomas Moser, Robert Seiringer, and Jakob Yngvason. “Superfluid Behavior of a Bose-Einstein Condensate in a Random Potential.” New Journal of Physics. IOP Publishing Ltd., 2015. https://doi.org/10.1088/1367-2630/17/1/013022.","short":"M. Könenberg, T. Moser, R. Seiringer, J. Yngvason, New Journal of Physics 17 (2015).","mla":"Könenberg, Martin, et al. “Superfluid Behavior of a Bose-Einstein Condensate in a Random Potential.” New Journal of Physics, vol. 17, 013022, IOP Publishing Ltd., 2015, doi:10.1088/1367-2630/17/1/013022."},"publication":"New Journal of Physics","date_published":"2015-01-15T00:00:00Z","type":"journal_article","abstract":[{"text":"We investigate the relation between Bose-Einstein condensation (BEC) and superfluidity in the ground state of a one-dimensional model of interacting bosons in a strong random potential. We prove rigorously that in a certain parameter regime the superfluid fraction can be arbitrarily small while complete BEC prevails. In another regime there is both complete BEC and complete superfluidity, despite the strong disorder","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1880","intvolume":" 17","title":"Superfluid behavior of a Bose-Einstein condensate in a random potential","ddc":["530"],"status":"public","pubrep_id":"447","file":[{"checksum":"38fdf2b5ac30445e26a5d613abd84b16","date_created":"2018-12-12T10:12:44Z","date_updated":"2020-07-14T12:45:20Z","file_id":"4963","relation":"main_file","creator":"system","file_size":768108,"content_type":"application/pdf","access_level":"open_access","file_name":"IST-2016-447-v1+1_document_1_.pdf"}],"oa_version":"Published Version"},{"scopus_import":1,"day":"30","page":"306 - 324","citation":{"mla":"Fahrenberg, Uli, et al. Compositionality for Quantitative Specifications. Vol. 8997, Springer, 2015, pp. 306–24, doi:10.1007/978-3-319-15317-9_19.","short":"U. Fahrenberg, J. Kretinsky, A. Legay, L. Traonouez, in:, Springer, 2015, pp. 306–324.","chicago":"Fahrenberg, Uli, Jan Kretinsky, Axel Legay, and Louis Traonouez. “Compositionality for Quantitative Specifications,” 8997:306–24. Springer, 2015. https://doi.org/10.1007/978-3-319-15317-9_19.","ama":"Fahrenberg U, Kretinsky J, Legay A, Traonouez L. Compositionality for quantitative specifications. In: Vol 8997. Springer; 2015:306-324. doi:10.1007/978-3-319-15317-9_19","ista":"Fahrenberg U, Kretinsky J, Legay A, Traonouez L. 2015. Compositionality for quantitative specifications. FACS: Formal Aspects of Component Software, LNCS, vol. 8997, 306–324.","ieee":"U. Fahrenberg, J. Kretinsky, A. Legay, and L. Traonouez, “Compositionality for quantitative specifications,” presented at the FACS: Formal Aspects of Component Software, Bertinoro, Italy, 2015, vol. 8997, pp. 306–324.","apa":"Fahrenberg, U., Kretinsky, J., Legay, A., & Traonouez, L. (2015). Compositionality for quantitative specifications (Vol. 8997, pp. 306–324). Presented at the FACS: Formal Aspects of Component Software, Bertinoro, Italy: Springer. https://doi.org/10.1007/978-3-319-15317-9_19"},"date_published":"2015-01-30T00:00:00Z","alternative_title":["LNCS"],"type":"conference","abstract":[{"lang":"eng","text":"We provide a framework for compositional and iterative design and verification of systems with quantitative information, such as rewards, time or energy. It is based on disjunctive modal transition systems where we allow actions to bear various types of quantitative information. Throughout the design process the actions can be further refined and the information made more precise. We show how to compute the results of standard operations on the systems, including the quotient (residual), which has not been previously considered for quantitative non-deterministic systems. Our quantitative framework has close connections to the modal nu-calculus and is compositional with respect to general notions of distances between systems and the standard operations."}],"intvolume":" 8997","title":"Compositionality for quantitative specifications","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1882","oa_version":"Preprint","month":"01","project":[{"call_identifier":"FP7","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/1408.1256","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1007/978-3-319-15317-9_19","conference":{"end_date":"2014-09-12","start_date":"2014-09-10","location":"Bertinoro, Italy","name":"FACS: Formal Aspects of Component Software"},"ec_funded":1,"publist_id":"5216","publisher":"Springer","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"publication_status":"published","acknowledgement":"This research was funded in part by the European Research Council (ERC) under grant agreement 267989 (QUAREM), by the Austrian Science Fund (FWF) project S11402-N23 (RiSE), and by the Czech Science Foundation, grant No. P202/12/G061.","year":"2015","volume":8997,"date_updated":"2021-01-12T06:53:49Z","date_created":"2018-12-11T11:54:31Z","author":[{"full_name":"Fahrenberg, Uli","first_name":"Uli","last_name":"Fahrenberg"},{"full_name":"Kretinsky, Jan","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8122-2881","first_name":"Jan","last_name":"Kretinsky"},{"last_name":"Legay","first_name":"Axel","full_name":"Legay, Axel"},{"full_name":"Traonouez, Louis","first_name":"Louis","last_name":"Traonouez"}]},{"intvolume":" 91","title":"Anomalous scaling in an age-dependent branching model","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1883","oa_version":"Preprint","type":"journal_article","issue":"2","abstract":[{"text":"We introduce a one-parametric family of tree growth models, in which branching probabilities decrease with branch age τ as τ-α. Depending on the exponent α, the scaling of tree depth with tree size n displays a transition between the logarithmic scaling of random trees and an algebraic growth. At the transition (α=1) tree depth grows as (logn)2. This anomalous scaling is in good agreement with the trend observed in evolution of biological species, thus providing a theoretical support for age-dependent speciation and associating it to the occurrence of a critical point.\r\n","lang":"eng"}],"article_type":"original","citation":{"chicago":"Keller-Schmidt, Stephanie, Murat Tugrul, Víctor Eguíluz, Emilio Hernandez Garcia, and Konstantin Klemm. “Anomalous Scaling in an Age-Dependent Branching Model.” Physical Review E Statistical Nonlinear and Soft Matter Physics. American Institute of Physics, 2015. https://doi.org/10.1103/PhysRevE.91.022803.","short":"S. Keller-Schmidt, M. Tugrul, V. Eguíluz, E. Hernandez Garcia, K. Klemm, Physical Review E Statistical Nonlinear and Soft Matter Physics 91 (2015).","mla":"Keller-Schmidt, Stephanie, et al. “Anomalous Scaling in an Age-Dependent Branching Model.” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 91, no. 2, 022803, American Institute of Physics, 2015, doi:10.1103/PhysRevE.91.022803.","ieee":"S. Keller-Schmidt, M. Tugrul, V. Eguíluz, E. Hernandez Garcia, and K. Klemm, “Anomalous scaling in an age-dependent branching model,” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 91, no. 2. American Institute of Physics, 2015.","apa":"Keller-Schmidt, S., Tugrul, M., Eguíluz, V., Hernandez Garcia, E., & Klemm, K. (2015). Anomalous scaling in an age-dependent branching model. Physical Review E Statistical Nonlinear and Soft Matter Physics. American Institute of Physics. https://doi.org/10.1103/PhysRevE.91.022803","ista":"Keller-Schmidt S, Tugrul M, Eguíluz V, Hernandez Garcia E, Klemm K. 2015. Anomalous scaling in an age-dependent branching model. Physical Review E Statistical Nonlinear and Soft Matter Physics. 91(2), 022803.","ama":"Keller-Schmidt S, Tugrul M, Eguíluz V, Hernandez Garcia E, Klemm K. Anomalous scaling in an age-dependent branching model. Physical Review E Statistical Nonlinear and Soft Matter Physics. 2015;91(2). doi:10.1103/PhysRevE.91.022803"},"publication":"Physical Review E Statistical Nonlinear and Soft Matter Physics","date_published":"2015-02-02T00:00:00Z","scopus_import":1,"article_processing_charge":"No","day":"02","publisher":"American Institute of Physics","department":[{"_id":"NiBa"}],"publication_status":"published","year":"2015","volume":91,"date_updated":"2021-01-12T06:53:49Z","date_created":"2018-12-11T11:54:31Z","author":[{"first_name":"Stephanie","last_name":"Keller-Schmidt","full_name":"Keller-Schmidt, Stephanie"},{"last_name":"Tugrul","first_name":"Murat","orcid":"0000-0002-8523-0758","id":"37C323C6-F248-11E8-B48F-1D18A9856A87","full_name":"Tugrul, Murat"},{"full_name":"Eguíluz, Víctor","last_name":"Eguíluz","first_name":"Víctor"},{"full_name":"Hernandez Garcia, Emilio","first_name":"Emilio","last_name":"Hernandez Garcia"},{"first_name":"Konstantin","last_name":"Klemm","full_name":"Klemm, Konstantin"}],"article_number":"022803","publist_id":"5213","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1012.3298"}],"external_id":{"arxiv":["1012.3298"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1103/PhysRevE.91.022803","month":"02"},{"abstract":[{"text":"Petrocoptis is a small genus of chasmophytic plants endemic to the Iberian Peninsula, with some localized populations in the French Pyrenees. Within the genus, a dozen species have been recognized based on morphological diversity, most of them with limited distribution area, in small populations and frequently with potential threats to their survival. To date, however, a molecular evaluation of the current systematic treatments has not been carried out. The aim of the present study is to infer phylogenetic relationships among its subordinate taxa by using plastidial rps16 intron and nuclear internal transcribed spacer (ITS) DNA sequences; and evaluate the phylogenetic placement of the genus Petrocoptis within the family Caryophyllaceae. The monophyly of Petrocoptis is supported by both ITS and rps16 intron sequence analyses. Furthermore, time estimates using BEAST analyses indicate a Middle to Late Miocene diversification (10.59 Myr, 6.44–15.26 Myr highest posterior densities [HPD], for ITS; 14.30 Myr, 8.61–21.00 Myr HPD, for rps16 intron).","lang":"eng"}],"publist_id":"5217","issue":"2","type":"journal_article","date_updated":"2021-01-12T06:53:47Z","date_created":"2018-12-11T11:54:30Z","volume":128,"oa_version":"None","author":[{"id":"2AD56A7A-F248-11E8-B48F-1D18A9856A87","last_name":"Cires Rodriguez","first_name":"Eduardo","full_name":"Cires Rodriguez, Eduardo"},{"first_name":"José","last_name":"Prieto","full_name":"Prieto, José"}],"status":"public","publication_status":"published","title":"Phylogenetic relationships of Petrocoptis A. Braun ex Endl. (Caryophyllaceae), a discussed genus from the Iberian Peninsula","department":[{"_id":"JiFr"}],"publisher":"Springer","intvolume":" 128","year":"2015","_id":"1878","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","day":"24","month":"01","scopus_import":1,"language":[{"iso":"eng"}],"doi":"10.1007/s10265-014-0691-6","date_published":"2015-01-24T00:00:00Z","quality_controlled":"1","page":"223 - 238","publication":"Journal of Plant Research","citation":{"mla":"Cires Rodriguez, Eduardo, and José Prieto. “Phylogenetic Relationships of Petrocoptis A. Braun Ex Endl. (Caryophyllaceae), a Discussed Genus from the Iberian Peninsula.” Journal of Plant Research, vol. 128, no. 2, Springer, 2015, pp. 223–38, doi:10.1007/s10265-014-0691-6.","short":"E. Cires Rodriguez, J. Prieto, Journal of Plant Research 128 (2015) 223–238.","chicago":"Cires Rodriguez, Eduardo, and José Prieto. “Phylogenetic Relationships of Petrocoptis A. Braun Ex Endl. (Caryophyllaceae), a Discussed Genus from the Iberian Peninsula.” Journal of Plant Research. Springer, 2015. https://doi.org/10.1007/s10265-014-0691-6.","ama":"Cires Rodriguez E, Prieto J. Phylogenetic relationships of Petrocoptis A. Braun ex Endl. (Caryophyllaceae), a discussed genus from the Iberian Peninsula. Journal of Plant Research. 2015;128(2):223-238. doi:10.1007/s10265-014-0691-6","ista":"Cires Rodriguez E, Prieto J. 2015. Phylogenetic relationships of Petrocoptis A. Braun ex Endl. (Caryophyllaceae), a discussed genus from the Iberian Peninsula. Journal of Plant Research. 128(2), 223–238.","apa":"Cires Rodriguez, E., & Prieto, J. (2015). Phylogenetic relationships of Petrocoptis A. Braun ex Endl. (Caryophyllaceae), a discussed genus from the Iberian Peninsula. Journal of Plant Research. Springer. https://doi.org/10.1007/s10265-014-0691-6","ieee":"E. Cires Rodriguez and J. Prieto, “Phylogenetic relationships of Petrocoptis A. Braun ex Endl. (Caryophyllaceae), a discussed genus from the Iberian Peninsula,” Journal of Plant Research, vol. 128, no. 2. Springer, pp. 223–238, 2015."}},{"publist_id":"5210","issue":"1","abstract":[{"text":"The concept of positional information is central to our understanding of how cells determine their location in a multicellular structure and thereby their developmental fates. Nevertheless, positional information has neither been defined mathematically nor quantified in a principled way. Here we provide an information-theoretic definition in the context of developmental gene expression patterns and examine the features of expression patterns that affect positional information quantitatively. We connect positional information with the concept of positional error and develop tools to directly measure information and error from experimental data. We illustrate our framework for the case of gap gene expression patterns in the early Drosophila embryo and show how information that is distributed among only four genes is sufficient to determine developmental fates with nearly single-cell resolution. Our approach can be generalized to a variety of different model systems; procedures and examples are discussed in detail. ","lang":"eng"}],"type":"journal_article","volume":199,"oa_version":"Preprint","date_updated":"2021-01-12T06:53:50Z","date_created":"2018-12-11T11:54:32Z","author":[{"full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkacik","first_name":"Gasper"},{"full_name":"Dubuis, Julien","last_name":"Dubuis","first_name":"Julien"},{"last_name":"Petkova","first_name":"Mariela","full_name":"Petkova, Mariela"},{"full_name":"Gregor, Thomas","last_name":"Gregor","first_name":"Thomas"}],"department":[{"_id":"GaTk"}],"intvolume":" 199","publisher":"Genetics Society of America","title":"Positional information, positional error, and readout precision in morphogenesis: A mathematical framework","status":"public","publication_status":"published","_id":"1885","year":"2015","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"01","day":"01","scopus_import":1,"language":[{"iso":"eng"}],"date_published":"2015-01-01T00:00:00Z","doi":"10.1534/genetics.114.171850","page":"39 - 59","quality_controlled":"1","citation":{"ama":"Tkačik G, Dubuis J, Petkova M, Gregor T. Positional information, positional error, and readout precision in morphogenesis: A mathematical framework. Genetics. 2015;199(1):39-59. doi:10.1534/genetics.114.171850","apa":"Tkačik, G., Dubuis, J., Petkova, M., & Gregor, T. (2015). Positional information, positional error, and readout precision in morphogenesis: A mathematical framework. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.114.171850","ieee":"G. Tkačik, J. Dubuis, M. Petkova, and T. Gregor, “Positional information, positional error, and readout precision in morphogenesis: A mathematical framework,” Genetics, vol. 199, no. 1. Genetics Society of America, pp. 39–59, 2015.","ista":"Tkačik G, Dubuis J, Petkova M, Gregor T. 2015. Positional information, positional error, and readout precision in morphogenesis: A mathematical framework. Genetics. 199(1), 39–59.","short":"G. Tkačik, J. Dubuis, M. Petkova, T. Gregor, Genetics 199 (2015) 39–59.","mla":"Tkačik, Gašper, et al. “Positional Information, Positional Error, and Readout Precision in Morphogenesis: A Mathematical Framework.” Genetics, vol. 199, no. 1, Genetics Society of America, 2015, pp. 39–59, doi:10.1534/genetics.114.171850.","chicago":"Tkačik, Gašper, Julien Dubuis, Mariela Petkova, and Thomas Gregor. “Positional Information, Positional Error, and Readout Precision in Morphogenesis: A Mathematical Framework.” Genetics. Genetics Society of America, 2015. https://doi.org/10.1534/genetics.114.171850."},"main_file_link":[{"url":"http://arxiv.org/abs/1404.5599","open_access":"1"}],"oa":1,"publication":"Genetics"},{"abstract":[{"lang":"eng","text":"We typically think of cells as responding to external signals independently by regulating their gene expression levels, yet they often locally exchange information and coordinate. Can such spatial coupling be of benefit for conveying signals subject to gene regulatory noise? Here we extend our information-theoretic framework for gene regulation to spatially extended systems. As an example, we consider a lattice of nuclei responding to a concentration field of a transcriptional regulator (the "input") by expressing a single diffusible target gene. When input concentrations are low, diffusive coupling markedly improves information transmission; optimal gene activation functions also systematically change. A qualitatively new regulatory strategy emerges where individual cells respond to the input in a nearly step-like fashion that is subsequently averaged out by strong diffusion. While motivated by early patterning events in the Drosophila embryo, our framework is generically applicable to spatially coupled stochastic gene expression models."}],"issue":"6","publist_id":"5145","article_number":"062710","type":"journal_article","date_created":"2018-12-11T11:54:49Z","date_updated":"2021-01-12T06:54:13Z","volume":91,"oa_version":"Preprint","author":[{"id":"3E999752-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1287-3779","first_name":"Thomas R","last_name":"Sokolowski","full_name":"Sokolowski, Thomas R"},{"full_name":"Tkacik, Gasper","last_name":"Tkacik","first_name":"Gasper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","status":"public","title":"Optimizing information flow in small genetic networks. IV. Spatial coupling","publisher":"American Institute of Physics","department":[{"_id":"GaTk"}],"intvolume":" 91","_id":"1940","year":"2015","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"15","month":"06","scopus_import":1,"language":[{"iso":"eng"}],"doi":"10.1103/PhysRevE.91.062710","date_published":"2015-06-15T00:00:00Z","quality_controlled":"1","publication":"Physical Review E Statistical Nonlinear and Soft Matter Physics","oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/1501.04015","open_access":"1"}],"citation":{"ama":"Sokolowski TR, Tkačik G. Optimizing information flow in small genetic networks. IV. Spatial coupling. Physical Review E Statistical Nonlinear and Soft Matter Physics. 2015;91(6). doi:10.1103/PhysRevE.91.062710","ieee":"T. R. Sokolowski and G. Tkačik, “Optimizing information flow in small genetic networks. IV. Spatial coupling,” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 91, no. 6. American Institute of Physics, 2015.","apa":"Sokolowski, T. R., & Tkačik, G. (2015). Optimizing information flow in small genetic networks. IV. Spatial coupling. Physical Review E Statistical Nonlinear and Soft Matter Physics. American Institute of Physics. https://doi.org/10.1103/PhysRevE.91.062710","ista":"Sokolowski TR, Tkačik G. 2015. Optimizing information flow in small genetic networks. IV. Spatial coupling. Physical Review E Statistical Nonlinear and Soft Matter Physics. 91(6), 062710.","short":"T.R. Sokolowski, G. Tkačik, Physical Review E Statistical Nonlinear and Soft Matter Physics 91 (2015).","mla":"Sokolowski, Thomas R., and Gašper Tkačik. “Optimizing Information Flow in Small Genetic Networks. IV. Spatial Coupling.” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 91, no. 6, 062710, American Institute of Physics, 2015, doi:10.1103/PhysRevE.91.062710.","chicago":"Sokolowski, Thomas R, and Gašper Tkačik. “Optimizing Information Flow in Small Genetic Networks. IV. Spatial Coupling.” Physical Review E Statistical Nonlinear and Soft Matter Physics. American Institute of Physics, 2015. https://doi.org/10.1103/PhysRevE.91.062710."}},{"_id":"1938","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2015","acknowledgement":"F.P. was supported by the Graduate School of IST Austria. S.S. was partially supported by CRC1060 of the DFG\r\nThe authors thank Olga Symonova and Michael Kerber for sharing their implementation of the persistence algorithm. ","publication_status":"published","status":"public","title":"On the distribution of local extrema in quantum chaos","publisher":"Elsevier","intvolume":" 379","department":[{"_id":"HeEd"}],"author":[{"full_name":"Pausinger, Florian","last_name":"Pausinger","first_name":"Florian","orcid":"0000-0002-8379-3768","id":"2A77D7A2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Steinerberger, Stefan","first_name":"Stefan","last_name":"Steinerberger"}],"date_updated":"2021-01-12T06:54:12Z","date_created":"2018-12-11T11:54:49Z","volume":379,"oa_version":"None","type":"journal_article","abstract":[{"lang":"eng","text":"We numerically investigate the distribution of extrema of 'chaotic' Laplacian eigenfunctions on two-dimensional manifolds. Our contribution is two-fold: (a) we count extrema on grid graphs with a small number of randomly added edges and show the behavior to coincide with the 1957 prediction of Longuet-Higgins for the continuous case and (b) we compute the regularity of their spatial distribution using discrepancy, which is a classical measure from the theory of Monte Carlo integration. The first part suggests that grid graphs with randomly added edges should behave like two-dimensional surfaces with ergodic geodesic flow; in the second part we show that the extrema are more regularly distributed in space than the grid Z2."}],"issue":"6","publist_id":"5152","publication":"Physics Letters, Section A","citation":{"mla":"Pausinger, Florian, and Stefan Steinerberger. “On the Distribution of Local Extrema in Quantum Chaos.” Physics Letters, Section A, vol. 379, no. 6, Elsevier, 2015, pp. 535–41, doi:10.1016/j.physleta.2014.12.010.","short":"F. Pausinger, S. Steinerberger, Physics Letters, Section A 379 (2015) 535–541.","chicago":"Pausinger, Florian, and Stefan Steinerberger. “On the Distribution of Local Extrema in Quantum Chaos.” Physics Letters, Section A. Elsevier, 2015. https://doi.org/10.1016/j.physleta.2014.12.010.","ama":"Pausinger F, Steinerberger S. On the distribution of local extrema in quantum chaos. Physics Letters, Section A. 2015;379(6):535-541. doi:10.1016/j.physleta.2014.12.010","ista":"Pausinger F, Steinerberger S. 2015. On the distribution of local extrema in quantum chaos. Physics Letters, Section A. 379(6), 535–541.","ieee":"F. Pausinger and S. Steinerberger, “On the distribution of local extrema in quantum chaos,” Physics Letters, Section A, vol. 379, no. 6. Elsevier, pp. 535–541, 2015.","apa":"Pausinger, F., & Steinerberger, S. (2015). On the distribution of local extrema in quantum chaos. Physics Letters, Section A. Elsevier. https://doi.org/10.1016/j.physleta.2014.12.010"},"quality_controlled":"1","page":"535 - 541","doi":"10.1016/j.physleta.2014.12.010","date_published":"2015-03-06T00:00:00Z","language":[{"iso":"eng"}],"scopus_import":1,"day":"06","month":"03"},{"type":"journal_article","issue":"2","ec_funded":1,"publist_id":"5140","intvolume":" 23","department":[{"_id":"JiFr"}],"publisher":"Elsevier","title":"Intracellular trafficking and PIN-mediated cell polarity during tropic responses in plants","publication_status":"published","status":"public","_id":"1944","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","year":"2015","acknowledgement":"This work was supported by the European Research Council (project ERC-2011-StG-20101109-PSDP); the Agency for Innovation by Science and Technology (IWT) (predoctoral fellowship to H.R.); and the People Programme (Marie Curie Actions) of the European Union","oa_version":"None","volume":23,"date_updated":"2021-01-12T06:54:15Z","date_created":"2018-12-11T11:54:51Z","author":[{"last_name":"Rakusová","first_name":"Hana","full_name":"Rakusová, Hana"},{"orcid":"0000-0002-9767-8699","id":"43905548-F248-11E8-B48F-1D18A9856A87","last_name":"Fendrych","first_name":"Matyas","full_name":"Fendrych, Matyas"},{"full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jirí","last_name":"Friml"}],"scopus_import":1,"day":"01","month":"02","page":"116 - 123","project":[{"_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300","name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7"},{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"quality_controlled":"1","citation":{"short":"H. Rakusová, M. Fendrych, J. Friml, Current Opinion in Plant Biology 23 (2015) 116–123.","mla":"Rakusová, Hana, et al. “Intracellular Trafficking and PIN-Mediated Cell Polarity during Tropic Responses in Plants.” Current Opinion in Plant Biology, vol. 23, no. 2, Elsevier, 2015, pp. 116–23, doi:10.1016/j.pbi.2014.12.002.","chicago":"Rakusová, Hana, Matyas Fendrych, and Jiří Friml. “Intracellular Trafficking and PIN-Mediated Cell Polarity during Tropic Responses in Plants.” Current Opinion in Plant Biology. Elsevier, 2015. https://doi.org/10.1016/j.pbi.2014.12.002.","ama":"Rakusová H, Fendrych M, Friml J. Intracellular trafficking and PIN-mediated cell polarity during tropic responses in plants. Current Opinion in Plant Biology. 2015;23(2):116-123. doi:10.1016/j.pbi.2014.12.002","apa":"Rakusová, H., Fendrych, M., & Friml, J. (2015). Intracellular trafficking and PIN-mediated cell polarity during tropic responses in plants. Current Opinion in Plant Biology. Elsevier. https://doi.org/10.1016/j.pbi.2014.12.002","ieee":"H. Rakusová, M. Fendrych, and J. Friml, “Intracellular trafficking and PIN-mediated cell polarity during tropic responses in plants,” Current Opinion in Plant Biology, vol. 23, no. 2. Elsevier, pp. 116–123, 2015.","ista":"Rakusová H, Fendrych M, Friml J. 2015. Intracellular trafficking and PIN-mediated cell polarity during tropic responses in plants. Current Opinion in Plant Biology. 23(2), 116–123."},"publication":"Current Opinion in Plant Biology","language":[{"iso":"eng"}],"date_published":"2015-02-01T00:00:00Z","doi":"10.1016/j.pbi.2014.12.002"},{"pubrep_id":"317","oa_version":"Submitted Version","file":[{"relation":"main_file","file_id":"5314","checksum":"f0d4395b600f410a191256ac0b73af32","date_created":"2018-12-12T10:17:56Z","date_updated":"2020-07-14T12:45:22Z","access_level":"open_access","file_name":"IST-2015-317-v1+1_author_version.pdf","content_type":"application/pdf","file_size":399462,"creator":"system"}],"_id":"1992","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Succinct representation of concurrent trace sets","ddc":["005"],"status":"public","abstract":[{"lang":"eng","text":"We present a method and a tool for generating succinct representations of sets of concurrent traces. We focus on trace sets that contain all correct or all incorrect permutations of events from a given trace. We represent trace sets as HB-Formulas that are Boolean combinations of happens-before constraints between events. To generate a representation of incorrect interleavings, our method iteratively explores interleavings that violate the specification and gathers generalizations of the discovered interleavings into an HB-Formula; its complement yields a representation of correct interleavings.\r\n\r\nWe claim that our trace set representations can drive diverse verification, fault localization, repair, and synthesis techniques for concurrent programs. We demonstrate this by using our tool in three case studies involving synchronization synthesis, bug summarization, and abstraction refinement based verification. In each case study, our initial experimental results have been promising.\r\n\r\nIn the first case study, we present an algorithm for inferring missing synchronization from an HB-Formula representing correct interleavings of a given trace. The algorithm applies rules to rewrite specific patterns in the HB-Formula into locks, barriers, and wait-notify constructs. In the second case study, we use an HB-Formula representing incorrect interleavings for bug summarization. While the HB-Formula itself is a concise counterexample summary, we present additional inference rules to help identify specific concurrency bugs such as data races, define-use order violations, and two-stage access bugs. In the final case study, we present a novel predicate learning procedure that uses HB-Formulas representing abstract counterexamples to accelerate counterexample-guided abstraction refinement (CEGAR). In each iteration of the CEGAR loop, the procedure refines the abstraction to eliminate multiple spurious abstract counterexamples drawn from the HB-Formula."}],"type":"conference","date_published":"2015-01-15T00:00:00Z","citation":{"mla":"Gupta, Ashutosh, et al. Succinct Representation of Concurrent Trace Sets. ACM, 2015, pp. 433–44, doi:10.1145/2676726.2677008.","short":"A. Gupta, T.A. Henzinger, A. Radhakrishna, R. Samanta, T. Tarrach, in:, ACM, 2015, pp. 433–444.","chicago":"Gupta, Ashutosh, Thomas A Henzinger, Arjun Radhakrishna, Roopsha Samanta, and Thorsten Tarrach. “Succinct Representation of Concurrent Trace Sets,” 433–44. ACM, 2015. https://doi.org/10.1145/2676726.2677008.","ama":"Gupta A, Henzinger TA, Radhakrishna A, Samanta R, Tarrach T. Succinct representation of concurrent trace sets. In: ACM; 2015:433-444. doi:10.1145/2676726.2677008","ista":"Gupta A, Henzinger TA, Radhakrishna A, Samanta R, Tarrach T. 2015. Succinct representation of concurrent trace sets. POPL: Principles of Programming Languages, 433–444.","ieee":"A. Gupta, T. A. Henzinger, A. Radhakrishna, R. Samanta, and T. Tarrach, “Succinct representation of concurrent trace sets,” presented at the POPL: Principles of Programming Languages, Mumbai, India, 2015, pp. 433–444.","apa":"Gupta, A., Henzinger, T. A., Radhakrishna, A., Samanta, R., & Tarrach, T. (2015). Succinct representation of concurrent trace sets (pp. 433–444). Presented at the POPL: Principles of Programming Languages, Mumbai, India: ACM. https://doi.org/10.1145/2676726.2677008"},"page":"433 - 444","has_accepted_license":"1","day":"15","scopus_import":1,"author":[{"full_name":"Gupta, Ashutosh","last_name":"Gupta","first_name":"Ashutosh","id":"335E5684-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Henzinger, Thomas A","last_name":"Henzinger","first_name":"Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Radhakrishna, Arjun","first_name":"Arjun","last_name":"Radhakrishna","id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87"},{"id":"3D2AAC08-F248-11E8-B48F-1D18A9856A87","first_name":"Roopsha","last_name":"Samanta","full_name":"Samanta, Roopsha"},{"full_name":"Tarrach, Thorsten","last_name":"Tarrach","first_name":"Thorsten","orcid":"0000-0003-4409-8487","id":"3D6E8F2C-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2018-12-11T11:55:05Z","date_updated":"2021-01-12T06:54:33Z","year":"2015","publisher":"ACM","department":[{"_id":"ToHe"}],"publication_status":"published","publist_id":"5091","file_date_updated":"2020-07-14T12:45:22Z","doi":"10.1145/2676726.2677008","conference":{"name":"POPL: Principles of Programming Languages","end_date":"2015-01-17","start_date":"2015-01-15","location":"Mumbai, India"},"language":[{"iso":"eng"}],"oa":1,"quality_controlled":"1","publication_identifier":{"isbn":["978-1-4503-3300-9"]},"month":"01"},{"scopus_import":1,"day":"01","month":"05","oa":1,"citation":{"chicago":"Noren, Patrik. “The Three-State Toric Homogeneous Markov Chain Model Has Markov Degree Two.” Journal of Symbolic Computation. Elsevier, 2015. https://doi.org/10.1016/j.jsc.2014.09.014.","short":"P. Noren, Journal of Symbolic Computation 68/Part 2 (2015) 285–296.","mla":"Noren, Patrik. “The Three-State Toric Homogeneous Markov Chain Model Has Markov Degree Two.” Journal of Symbolic Computation, vol. 68/Part 2, no. May-June, Elsevier, 2015, pp. 285–96, doi:10.1016/j.jsc.2014.09.014.","ieee":"P. Noren, “The three-state toric homogeneous Markov chain model has Markov degree two,” Journal of Symbolic Computation, vol. 68/Part 2, no. May-June. Elsevier, pp. 285–296, 2015.","apa":"Noren, P. (2015). The three-state toric homogeneous Markov chain model has Markov degree two. Journal of Symbolic Computation. Elsevier. https://doi.org/10.1016/j.jsc.2014.09.014","ista":"Noren P. 2015. The three-state toric homogeneous Markov chain model has Markov degree two. Journal of Symbolic Computation. 68/Part 2(May-June), 285–296.","ama":"Noren P. The three-state toric homogeneous Markov chain model has Markov degree two. Journal of Symbolic Computation. 2015;68/Part 2(May-June):285-296. doi:10.1016/j.jsc.2014.09.014"},"main_file_link":[{"url":"http://arxiv.org/abs/1207.0077","open_access":"1"}],"publication":"Journal of Symbolic Computation","page":"285 - 296","quality_controlled":"1","date_published":"2015-05-01T00:00:00Z","doi":"10.1016/j.jsc.2014.09.014","language":[{"iso":"eng"}],"type":"journal_article","publist_id":"5082","issue":"May-June","abstract":[{"lang":"eng","text":"We prove that the three-state toric homogeneous Markov chain model has Markov degree two. In algebraic terminology this means, that a certain class of toric ideals is generated by quadratic binomials. This was conjectured by Haws, Martin del Campo, Takemura and Yoshida, who proved that they are generated by degree six binomials."}],"_id":"1997","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2015","department":[{"_id":"CaUh"}],"publisher":"Elsevier","title":"The three-state toric homogeneous Markov chain model has Markov degree two","publication_status":"published","status":"public","author":[{"full_name":"Noren, Patrik","id":"46870C74-F248-11E8-B48F-1D18A9856A87","first_name":"Patrik","last_name":"Noren"}],"volume":"68/Part 2","oa_version":"Preprint","date_created":"2018-12-11T11:55:07Z","date_updated":"2021-01-12T06:54:35Z"},{"publist_id":"5068","year":"2015","acknowledgement":"Part of the material presented here was contained in the PhD thesis of the first author to which the second author and Thomas Richardson were advisers. The authors wish to thank him for several comments and suggestions. We also thank the reviewers and the Associate Editor for helpful comments. The proof of Proposition 1 uses the idea of Olga Klimova, to whom the authors are also indebted. The second author was supported in part by Grant K-106154 from the Hungarian National Scientific Research Fund (OTKA).","publisher":"Wiley","department":[{"_id":"CaUh"}],"publication_status":"published","author":[{"id":"31934120-F248-11E8-B48F-1D18A9856A87","first_name":"Anna","last_name":"Klimova","full_name":"Klimova, Anna"},{"first_name":"Tamás","last_name":"Rudas","full_name":"Rudas, Tamás"}],"volume":42,"date_updated":"2021-01-12T06:54:41Z","date_created":"2018-12-11T11:55:11Z","month":"09","oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1307.3282"}],"quality_controlled":"1","doi":"10.1111/sjos.12139","language":[{"iso":"eng"}],"type":"journal_article","issue":"3","abstract":[{"text":"The paper describes a generalized iterative proportional fitting procedure that can be used for maximum likelihood estimation in a special class of the general log-linear model. The models in this class, called relational, apply to multivariate discrete sample spaces that do not necessarily have a Cartesian product structure and may not contain an overall effect. When applied to the cell probabilities, the models without the overall effect are curved exponential families and the values of the sufficient statistics are reproduced by the MLE only up to a constant of proportionality. The paper shows that Iterative Proportional Fitting, Generalized Iterative Scaling, and Improved Iterative Scaling fail to work for such models. The algorithm proposed here is based on iterated Bregman projections. As a by-product, estimates of the multiplicative parameters are also obtained. An implementation of the algorithm is available as an R-package.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2008","intvolume":" 42","status":"public","title":"Iterative scaling in curved exponential families","oa_version":"Preprint","scopus_import":1,"day":"01","citation":{"ama":"Klimova A, Rudas T. Iterative scaling in curved exponential families. Scandinavian Journal of Statistics. 2015;42(3):832-847. doi:10.1111/sjos.12139","ista":"Klimova A, Rudas T. 2015. Iterative scaling in curved exponential families. Scandinavian Journal of Statistics. 42(3), 832–847.","ieee":"A. Klimova and T. Rudas, “Iterative scaling in curved exponential families,” Scandinavian Journal of Statistics, vol. 42, no. 3. Wiley, pp. 832–847, 2015.","apa":"Klimova, A., & Rudas, T. (2015). Iterative scaling in curved exponential families. Scandinavian Journal of Statistics. Wiley. https://doi.org/10.1111/sjos.12139","mla":"Klimova, Anna, and Tamás Rudas. “Iterative Scaling in Curved Exponential Families.” Scandinavian Journal of Statistics, vol. 42, no. 3, Wiley, 2015, pp. 832–47, doi:10.1111/sjos.12139.","short":"A. Klimova, T. Rudas, Scandinavian Journal of Statistics 42 (2015) 832–847.","chicago":"Klimova, Anna, and Tamás Rudas. “Iterative Scaling in Curved Exponential Families.” Scandinavian Journal of Statistics. Wiley, 2015. https://doi.org/10.1111/sjos.12139."},"publication":"Scandinavian Journal of Statistics","page":"832 - 847","date_published":"2015-09-01T00:00:00Z"},{"quality_controlled":"1","main_file_link":[{"url":"http://arxiv.org/abs/1109.3436","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1080/10586458.2014.980044","month":"06","publication_status":"published","department":[{"_id":"CaUh"}],"publisher":"Taylor & Francis","year":"2015","date_updated":"2021-01-12T06:54:40Z","date_created":"2018-12-11T11:55:10Z","volume":24,"author":[{"full_name":"Hein, Nicolas","first_name":"Nicolas","last_name":"Hein"},{"full_name":"Hillar, Christopher","last_name":"Hillar","first_name":"Christopher"},{"full_name":"Martin Del Campo Sanchez, Abraham","id":"4CF47F6A-F248-11E8-B48F-1D18A9856A87","last_name":"Martin Del Campo Sanchez","first_name":"Abraham"},{"full_name":"Sottile, Frank","first_name":"Frank","last_name":"Sottile"},{"last_name":"Teitler","first_name":"Zach","full_name":"Teitler, Zach"}],"publist_id":"5070","page":"261 - 269","publication":"Experimental Mathematics","citation":{"chicago":"Hein, Nicolas, Christopher Hillar, Abraham Martin del Campo Sanchez, Frank Sottile, and Zach Teitler. “The Monotone Secant Conjecture in the Real Schubert Calculus.” Experimental Mathematics. Taylor & Francis, 2015. https://doi.org/10.1080/10586458.2014.980044.","short":"N. Hein, C. Hillar, A. Martin del Campo Sanchez, F. Sottile, Z. Teitler, Experimental Mathematics 24 (2015) 261–269.","mla":"Hein, Nicolas, et al. “The Monotone Secant Conjecture in the Real Schubert Calculus.” Experimental Mathematics, vol. 24, no. 3, Taylor & Francis, 2015, pp. 261–69, doi:10.1080/10586458.2014.980044.","apa":"Hein, N., Hillar, C., Martin del Campo Sanchez, A., Sottile, F., & Teitler, Z. (2015). The monotone secant conjecture in the real Schubert calculus. Experimental Mathematics. Taylor & Francis. https://doi.org/10.1080/10586458.2014.980044","ieee":"N. Hein, C. Hillar, A. Martin del Campo Sanchez, F. Sottile, and Z. Teitler, “The monotone secant conjecture in the real Schubert calculus,” Experimental Mathematics, vol. 24, no. 3. Taylor & Francis, pp. 261–269, 2015.","ista":"Hein N, Hillar C, Martin del Campo Sanchez A, Sottile F, Teitler Z. 2015. The monotone secant conjecture in the real Schubert calculus. Experimental Mathematics. 24(3), 261–269.","ama":"Hein N, Hillar C, Martin del Campo Sanchez A, Sottile F, Teitler Z. The monotone secant conjecture in the real Schubert calculus. Experimental Mathematics. 2015;24(3):261-269. doi:10.1080/10586458.2014.980044"},"date_published":"2015-06-23T00:00:00Z","scopus_import":1,"day":"23","article_processing_charge":"No","title":"The monotone secant conjecture in the real Schubert calculus","status":"public","intvolume":" 24","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2006","oa_version":"Preprint","type":"journal_article","abstract":[{"text":"The monotone secant conjecture posits a rich class of polynomial systems, all of whose solutions are real. These systems come from the Schubert calculus on flag manifolds, and the monotone secant conjecture is a compelling generalization of the Shapiro conjecture for Grassmannians (Theorem of Mukhin, Tarasov, and Varchenko). We present some theoretical evidence for this conjecture, as well as computational evidence obtained by 1.9 teraHertz-years of computing, and we discuss some of the phenomena we observed in our data. ","lang":"eng"}],"issue":"3"},{"scopus_import":1,"day":"01","month":"07","publication":"Computational Statistics & Data Analysis","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1404.6617"}],"citation":{"chicago":"Klimova, Anna, Caroline Uhler, and Tamás Rudas. “Faithfulness and Learning Hypergraphs from Discrete Distributions.” Computational Statistics & Data Analysis. Elsevier, 2015. https://doi.org/10.1016/j.csda.2015.01.017.","short":"A. Klimova, C. Uhler, T. Rudas, Computational Statistics & Data Analysis 87 (2015) 57–72.","mla":"Klimova, Anna, et al. “Faithfulness and Learning Hypergraphs from Discrete Distributions.” Computational Statistics & Data Analysis, vol. 87, no. 7, Elsevier, 2015, pp. 57–72, doi:10.1016/j.csda.2015.01.017.","ieee":"A. Klimova, C. Uhler, and T. Rudas, “Faithfulness and learning hypergraphs from discrete distributions,” Computational Statistics & Data Analysis, vol. 87, no. 7. Elsevier, pp. 57–72, 2015.","apa":"Klimova, A., Uhler, C., & Rudas, T. (2015). Faithfulness and learning hypergraphs from discrete distributions. Computational Statistics & Data Analysis. Elsevier. https://doi.org/10.1016/j.csda.2015.01.017","ista":"Klimova A, Uhler C, Rudas T. 2015. Faithfulness and learning hypergraphs from discrete distributions. Computational Statistics & Data Analysis. 87(7), 57–72.","ama":"Klimova A, Uhler C, Rudas T. Faithfulness and learning hypergraphs from discrete distributions. Computational Statistics & Data Analysis. 2015;87(7):57-72. doi:10.1016/j.csda.2015.01.017"},"oa":1,"quality_controlled":"1","page":"57 - 72","doi":"10.1016/j.csda.2015.01.017","date_published":"2015-07-01T00:00:00Z","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"lang":"eng","text":"The concepts of faithfulness and strong-faithfulness are important for statistical learning of graphical models. Graphs are not sufficient for describing the association structure of a discrete distribution. Hypergraphs representing hierarchical log-linear models are considered instead, and the concept of parametric (strong-) faithfulness with respect to a hypergraph is introduced. Strong-faithfulness ensures the existence of uniformly consistent parameter estimators and enables building uniformly consistent procedures for a hypergraph search. The strength of association in a discrete distribution can be quantified with various measures, leading to different concepts of strong-faithfulness. Lower and upper bounds for the proportions of distributions that do not satisfy strong-faithfulness are computed for different parameterizations and measures of association."}],"publist_id":"5062","issue":"7","_id":"2014","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2015","title":"Faithfulness and learning hypergraphs from discrete distributions","publication_status":"published","status":"public","publisher":"Elsevier","department":[{"_id":"CaUh"}],"intvolume":" 87","author":[{"full_name":"Klimova, Anna","id":"31934120-F248-11E8-B48F-1D18A9856A87","last_name":"Klimova","first_name":"Anna"},{"full_name":"Uhler, Caroline","last_name":"Uhler","first_name":"Caroline","orcid":"0000-0002-7008-0216","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Rudas, Tamás","first_name":"Tamás","last_name":"Rudas"}],"date_updated":"2021-01-12T06:54:43Z","date_created":"2018-12-11T11:55:13Z","volume":87,"oa_version":"Preprint"},{"publication":"Biochimica et Biophysica Acta - Molecular Cell Research","citation":{"chicago":"Kawada, Daiki, Hiromu Kobayashi, Tsuyoshi Tomita, Eisuke Nakata, Makoto Nagano, Daria E Siekhaus, Junko Toshima, and Jiro Toshimaa. “The Yeast Arf-GAP Glo3p Is Required for the Endocytic Recycling of Cell Surface Proteins.” Biochimica et Biophysica Acta - Molecular Cell Research. Elsevier, 2015. https://doi.org/10.1016/j.bbamcr.2014.10.009.","short":"D. Kawada, H. Kobayashi, T. Tomita, E. Nakata, M. Nagano, D.E. Siekhaus, J. Toshima, J. Toshimaa, Biochimica et Biophysica Acta - Molecular Cell Research 1853 (2015) 144–156.","mla":"Kawada, Daiki, et al. “The Yeast Arf-GAP Glo3p Is Required for the Endocytic Recycling of Cell Surface Proteins.” Biochimica et Biophysica Acta - Molecular Cell Research, vol. 1853, no. 1, Elsevier, 2015, pp. 144–56, doi:10.1016/j.bbamcr.2014.10.009.","apa":"Kawada, D., Kobayashi, H., Tomita, T., Nakata, E., Nagano, M., Siekhaus, D. E., … Toshimaa, J. (2015). The yeast Arf-GAP Glo3p is required for the endocytic recycling of cell surface proteins. Biochimica et Biophysica Acta - Molecular Cell Research. Elsevier. https://doi.org/10.1016/j.bbamcr.2014.10.009","ieee":"D. Kawada et al., “The yeast Arf-GAP Glo3p is required for the endocytic recycling of cell surface proteins,” Biochimica et Biophysica Acta - Molecular Cell Research, vol. 1853, no. 1. Elsevier, pp. 144–156, 2015.","ista":"Kawada D, Kobayashi H, Tomita T, Nakata E, Nagano M, Siekhaus DE, Toshima J, Toshimaa J. 2015. The yeast Arf-GAP Glo3p is required for the endocytic recycling of cell surface proteins. Biochimica et Biophysica Acta - Molecular Cell Research. 1853(1), 144–156.","ama":"Kawada D, Kobayashi H, Tomita T, et al. The yeast Arf-GAP Glo3p is required for the endocytic recycling of cell surface proteins. Biochimica et Biophysica Acta - Molecular Cell Research. 2015;1853(1):144-156. doi:10.1016/j.bbamcr.2014.10.009"},"page":"144 - 156","date_published":"2015-01-01T00:00:00Z","scopus_import":1,"day":"01","has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2025","title":"The yeast Arf-GAP Glo3p is required for the endocytic recycling of cell surface proteins","ddc":["570"],"status":"public","intvolume":" 1853","pubrep_id":"615","file":[{"access_level":"open_access","file_name":"IST-2016-615-v1+1_BBAMCR.pdf","creator":"system","file_size":926685,"content_type":"application/pdf","file_id":"4936","relation":"main_file","checksum":"5bb328edebb6a91337cadd7d63f961b7","date_created":"2018-12-12T10:12:18Z","date_updated":"2020-07-14T12:45:25Z"}],"oa_version":"Submitted Version","type":"journal_article","abstract":[{"text":"Small GTP-binding proteins of the Ras superfamily play diverse roles in intracellular trafficking. Among them, the Rab, Arf, and Rho families function in successive steps of vesicle transport, in forming vesicles from donor membranes, directing vesicle trafficking toward target membranes and docking vesicles onto target membranes. These proteins act as molecular switches that are controlled by a cycle of GTP binding and hydrolysis regulated by guanine nucleotide exchange factors (GEFs) and GTPase-activating proteins (GAPs). In this study we explored the role of GAPs in the regulation of the endocytic pathway using fluorescently labeled yeast mating pheromone α-factor. Among 25 non-essential GAP mutants, we found that deletion of the GLO3 gene, encoding Arf-GAP protein, caused defective internalization of fluorescently labeled α-factor. Quantitative analysis revealed that glo3Δ cells show defective α-factor binding to the cell surface. Interestingly, Ste2p, the α-factor receptor, was mis-localized from the plasma membrane to the vacuole in glo3Δ cells. Domain deletion mutants of Glo3p revealed that a GAP-independent function, as well as the GAP activity, of Glo3p is important for both α-factor binding and Ste2p localization at the cell surface. Additionally, we found that deletion of the GLO3 gene affects the size and number of Arf1p-residing Golgi compartments and causes a defect in transport from the TGN to the plasma membrane. Furthermore, we demonstrated that glo3Δ cells were defective in the late endosome-to-TGN transport pathway, but not in the early endosome-to-TGN transport pathway. These findings suggest novel roles for Arf-GAP Glo3p in endocytic recycling of cell surface proteins.","lang":"eng"}],"issue":"1","oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"quality_controlled":"1","doi":"10.1016/j.bbamcr.2014.10.009","language":[{"iso":"eng"}],"month":"01","year":"2015","publication_status":"published","department":[{"_id":"DaSi"}],"publisher":"Elsevier","author":[{"last_name":"Kawada","first_name":"Daiki","full_name":"Kawada, Daiki"},{"full_name":"Kobayashi, Hiromu","first_name":"Hiromu","last_name":"Kobayashi"},{"full_name":"Tomita, Tsuyoshi","first_name":"Tsuyoshi","last_name":"Tomita"},{"full_name":"Nakata, Eisuke","last_name":"Nakata","first_name":"Eisuke"},{"first_name":"Makoto","last_name":"Nagano","full_name":"Nagano, Makoto"},{"full_name":"Siekhaus, Daria E","orcid":"0000-0001-8323-8353","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","last_name":"Siekhaus","first_name":"Daria E"},{"last_name":"Toshima","first_name":"Junko","full_name":"Toshima, Junko"},{"full_name":"Toshimaa, Jiro","last_name":"Toshimaa","first_name":"Jiro"}],"date_updated":"2021-01-12T06:54:48Z","date_created":"2018-12-11T11:55:17Z","volume":1853,"file_date_updated":"2020-07-14T12:45:25Z","publist_id":"5047","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/"},{"date_created":"2018-12-11T11:55:18Z","date_updated":"2021-01-12T06:54:51Z","volume":106,"oa_version":"Preprint","author":[{"id":"374A3F1A-F248-11E8-B48F-1D18A9856A87","first_name":"Liang","last_name":"Shi","full_name":"Shi, Liang"},{"full_name":"Rampp, Markus","first_name":"Markus","last_name":"Rampp"},{"first_name":"Björn","last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754","full_name":"Hof, Björn"},{"full_name":"Avila, Marc","first_name":"Marc","last_name":"Avila"}],"publication_status":"published","title":"A hybrid MPI-OpenMP parallel implementation for pseudospectral simulations with application to Taylor-Couette flow","status":"public","intvolume":" 106","publisher":"Elsevier","department":[{"_id":"BjHo"}],"_id":"2030","year":"2015","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"A hybrid-parallel direct-numerical-simulation method with application to turbulent Taylor-Couette flow is presented. The Navier-Stokes equations are discretized in cylindrical coordinates with the spectral Fourier-Galerkin method in the axial and azimuthal directions, and high-order finite differences in the radial direction. Time is advanced by a second-order, semi-implicit projection scheme, which requires the solution of five Helmholtz/Poisson equations, avoids staggered grids and renders very small slip velocities. Nonlinear terms are evaluated with the pseudospectral method. The code is parallelized using a hybrid MPI-OpenMP strategy, which, compared with a flat MPI parallelization, is simpler to implement, allows to reduce inter-node communications and MPI overhead that become relevant at high processor-core counts, and helps to contain the memory footprint. A strong scaling study shows that the hybrid code maintains scalability up to more than 20,000 processor cores and thus allows to perform simulations at higher resolutions than previously feasible. In particular, it opens up the possibility to simulate turbulent Taylor-Couette flows at Reynolds numbers up to O(105). This enables to probe hydrodynamic turbulence in Keplerian flows in experimentally relevant regimes.","lang":"eng"}],"publist_id":"5042","issue":"1","type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1016/j.compfluid.2014.09.021","date_published":"2015-01-01T00:00:00Z","quality_controlled":"1","page":"1 - 11","publication":"Computers and Fluids","oa":1,"citation":{"ista":"Shi L, Rampp M, Hof B, Avila M. 2015. A hybrid MPI-OpenMP parallel implementation for pseudospectral simulations with application to Taylor-Couette flow. Computers and Fluids. 106(1), 1–11.","apa":"Shi, L., Rampp, M., Hof, B., & Avila, M. (2015). A hybrid MPI-OpenMP parallel implementation for pseudospectral simulations with application to Taylor-Couette flow. Computers and Fluids. Elsevier. https://doi.org/10.1016/j.compfluid.2014.09.021","ieee":"L. Shi, M. Rampp, B. Hof, and M. Avila, “A hybrid MPI-OpenMP parallel implementation for pseudospectral simulations with application to Taylor-Couette flow,” Computers and Fluids, vol. 106, no. 1. Elsevier, pp. 1–11, 2015.","ama":"Shi L, Rampp M, Hof B, Avila M. A hybrid MPI-OpenMP parallel implementation for pseudospectral simulations with application to Taylor-Couette flow. Computers and Fluids. 2015;106(1):1-11. doi:10.1016/j.compfluid.2014.09.021","chicago":"Shi, Liang, Markus Rampp, Björn Hof, and Marc Avila. “A Hybrid MPI-OpenMP Parallel Implementation for Pseudospectral Simulations with Application to Taylor-Couette Flow.” Computers and Fluids. Elsevier, 2015. https://doi.org/10.1016/j.compfluid.2014.09.021.","mla":"Shi, Liang, et al. “A Hybrid MPI-OpenMP Parallel Implementation for Pseudospectral Simulations with Application to Taylor-Couette Flow.” Computers and Fluids, vol. 106, no. 1, Elsevier, 2015, pp. 1–11, doi:10.1016/j.compfluid.2014.09.021.","short":"L. Shi, M. Rampp, B. Hof, M. Avila, Computers and Fluids 106 (2015) 1–11."},"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1311.2481"}],"month":"01","day":"01","scopus_import":1},{"volume":15,"date_updated":"2021-01-12T06:54:53Z","date_created":"2018-12-11T11:55:20Z","author":[{"full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","first_name":"Herbert","last_name":"Edelsbrunner"},{"first_name":"Grzegorz","last_name":"Jablonski","id":"4483EF78-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3536-9866","full_name":"Jablonski, Grzegorz"},{"first_name":"Marian","last_name":"Mrozek","full_name":"Mrozek, Marian"}],"publisher":"Springer","department":[{"_id":"HeEd"}],"publication_status":"published","acknowledgement":"This research is partially supported by the Toposys project FP7-ICT-318493-STREP, by ESF under the ACAT Research Network Programme, by the Russian Government under mega project 11.G34.31.0053, and by the Polish National Science Center under Grant No. N201 419639.","year":"2015","publist_id":"5022","ec_funded":1,"file_date_updated":"2020-07-14T12:45:26Z","language":[{"iso":"eng"}],"doi":"10.1007/s10208-014-9223-y","project":[{"grant_number":"318493","_id":"255D761E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Topological Complex Systems"}],"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"month":"10","oa_version":"Published Version","file":[{"checksum":"3566f3a8b0c1bc550e62914a88c584ff","date_created":"2018-12-12T10:08:10Z","date_updated":"2020-07-14T12:45:26Z","relation":"main_file","file_id":"4670","content_type":"application/pdf","file_size":1317546,"creator":"system","access_level":"open_access","file_name":"IST-2016-486-v1+1_s10208-014-9223-y.pdf"}],"pubrep_id":"486","intvolume":" 15","title":"The persistent homology of a self-map","status":"public","ddc":["000"],"_id":"2035","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"5","abstract":[{"lang":"eng","text":"Considering a continuous self-map and the induced endomorphism on homology, we study the eigenvalues and eigenspaces of the latter. Taking a filtration of representations, we define the persistence of the eigenspaces, effectively introducing a hierarchical organization of the map. The algorithm that computes this information for a finite sample is proved to be stable, and to give the correct answer for a sufficiently dense sample. Results computed with an implementation of the algorithm provide evidence of its practical utility.\r\n"}],"type":"journal_article","date_published":"2015-10-01T00:00:00Z","page":"1213 - 1244","citation":{"ama":"Edelsbrunner H, Jablonski G, Mrozek M. The persistent homology of a self-map. Foundations of Computational Mathematics. 2015;15(5):1213-1244. doi:10.1007/s10208-014-9223-y","ista":"Edelsbrunner H, Jablonski G, Mrozek M. 2015. The persistent homology of a self-map. Foundations of Computational Mathematics. 15(5), 1213–1244.","apa":"Edelsbrunner, H., Jablonski, G., & Mrozek, M. (2015). The persistent homology of a self-map. Foundations of Computational Mathematics. Springer. https://doi.org/10.1007/s10208-014-9223-y","ieee":"H. Edelsbrunner, G. Jablonski, and M. Mrozek, “The persistent homology of a self-map,” Foundations of Computational Mathematics, vol. 15, no. 5. Springer, pp. 1213–1244, 2015.","mla":"Edelsbrunner, Herbert, et al. “The Persistent Homology of a Self-Map.” Foundations of Computational Mathematics, vol. 15, no. 5, Springer, 2015, pp. 1213–44, doi:10.1007/s10208-014-9223-y.","short":"H. Edelsbrunner, G. Jablonski, M. Mrozek, Foundations of Computational Mathematics 15 (2015) 1213–1244.","chicago":"Edelsbrunner, Herbert, Grzegorz Jablonski, and Marian Mrozek. “The Persistent Homology of a Self-Map.” Foundations of Computational Mathematics. Springer, 2015. https://doi.org/10.1007/s10208-014-9223-y."},"publication":"Foundations of Computational Mathematics","has_accepted_license":"1","day":"01","scopus_import":1},{"oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2034","intvolume":" 115","status":"public","title":"Probabilistic opacity for Markov decision processes","issue":"1","abstract":[{"lang":"eng","text":"Opacity is a generic security property, that has been defined on (non-probabilistic) transition systems and later on Markov chains with labels. For a secret predicate, given as a subset of runs, and a function describing the view of an external observer, the value of interest for opacity is a measure of the set of runs disclosing the secret. We extend this definition to the richer framework of Markov decision processes, where non-deterministicchoice is combined with probabilistic transitions, and we study related decidability problems with partial or complete observation hypotheses for the schedulers. We prove that all questions are decidable with complete observation and ω-regular secrets. With partial observation, we prove that all quantitative questions are undecidable but the question whether a system is almost surely non-opaquebecomes decidable for a restricted class of ω-regular secrets, as well as for all ω-regular secrets under finite-memory schedulers."}],"type":"journal_article","date_published":"2015-01-01T00:00:00Z","citation":{"mla":"Bérard, Béatrice, et al. “Probabilistic Opacity for Markov Decision Processes.” Information Processing Letters, vol. 115, no. 1, Elsevier, 2015, pp. 52–59, doi:10.1016/j.ipl.2014.09.001.","short":"B. Bérard, K. Chatterjee, N. Sznajder, Information Processing Letters 115 (2015) 52–59.","chicago":"Bérard, Béatrice, Krishnendu Chatterjee, and Nathalie Sznajder. “Probabilistic Opacity for Markov Decision Processes.” Information Processing Letters. Elsevier, 2015. https://doi.org/10.1016/j.ipl.2014.09.001.","ama":"Bérard B, Chatterjee K, Sznajder N. Probabilistic opacity for Markov decision processes. Information Processing Letters. 2015;115(1):52-59. doi:10.1016/j.ipl.2014.09.001","ista":"Bérard B, Chatterjee K, Sznajder N. 2015. Probabilistic opacity for Markov decision processes. Information Processing Letters. 115(1), 52–59.","ieee":"B. Bérard, K. Chatterjee, and N. Sznajder, “Probabilistic opacity for Markov decision processes,” Information Processing Letters, vol. 115, no. 1. Elsevier, pp. 52–59, 2015.","apa":"Bérard, B., Chatterjee, K., & Sznajder, N. (2015). Probabilistic opacity for Markov decision processes. Information Processing Letters. Elsevier. https://doi.org/10.1016/j.ipl.2014.09.001"},"publication":" Information Processing Letters","page":"52 - 59","day":"01","scopus_import":1,"author":[{"last_name":"Bérard","first_name":"Béatrice","full_name":"Bérard, Béatrice"},{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Nathalie","last_name":"Sznajder","full_name":"Sznajder, Nathalie"}],"volume":115,"date_updated":"2021-01-12T06:54:52Z","date_created":"2018-12-11T11:55:20Z","year":"2015","department":[{"_id":"KrCh"}],"publisher":"Elsevier","publication_status":"published","publist_id":"5025","ec_funded":1,"doi":"10.1016/j.ipl.2014.09.001","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1407.4225"}],"project":[{"call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","call_identifier":"FWF","name":"Game Theory"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","month":"01"},{"date_created":"2018-12-11T11:55:37Z","date_updated":"2021-01-12T06:55:13Z","volume":215,"oa_version":"Preprint","author":[{"full_name":"Nam, Phan","last_name":"Nam","first_name":"Phan","id":"404092F4-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","last_name":"Seiringer","first_name":"Robert"}],"status":"public","title":"Collective excitations of Bose gases in the mean-field regime","publication_status":"published","publisher":"Springer","department":[{"_id":"RoSe"}],"intvolume":" 215","_id":"2085","year":"2015","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"We study the spectrum of a large system of N identical bosons interacting via a two-body potential with strength 1/N. In this mean-field regime, Bogoliubov's theory predicts that the spectrum of the N-particle Hamiltonian can be approximated by that of an effective quadratic Hamiltonian acting on Fock space, which describes the fluctuations around a condensed state. Recently, Bogoliubov's theory has been justified rigorously in the case that the low-energy eigenvectors of the N-particle Hamiltonian display complete condensation in the unique minimizer of the corresponding Hartree functional. In this paper, we shall justify Bogoliubov's theory for the high-energy part of the spectrum of the N-particle Hamiltonian corresponding to (non-linear) excited states of the Hartree functional. Moreover, we shall extend the existing results on the excitation spectrum to the case of non-uniqueness and/or degeneracy of the Hartree minimizer. In particular, the latter covers the case of rotating Bose gases, when the rotation speed is large enough to break the symmetry and to produce multiple quantized vortices in the Hartree minimizer. ","lang":"eng"}],"issue":"2","publist_id":"4951","type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1007/s00205-014-0781-6","date_published":"2015-02-01T00:00:00Z","quality_controlled":"1","page":"381 - 417","publication":"Archive for Rational Mechanics and Analysis","main_file_link":[{"url":"http://arxiv.org/abs/1402.1153","open_access":"1"}],"citation":{"mla":"Nam, Phan, and Robert Seiringer. “Collective Excitations of Bose Gases in the Mean-Field Regime.” Archive for Rational Mechanics and Analysis, vol. 215, no. 2, Springer, 2015, pp. 381–417, doi:10.1007/s00205-014-0781-6.","short":"P. Nam, R. Seiringer, Archive for Rational Mechanics and Analysis 215 (2015) 381–417.","chicago":"Nam, Phan, and Robert Seiringer. “Collective Excitations of Bose Gases in the Mean-Field Regime.” Archive for Rational Mechanics and Analysis. Springer, 2015. https://doi.org/10.1007/s00205-014-0781-6.","ama":"Nam P, Seiringer R. Collective excitations of Bose gases in the mean-field regime. Archive for Rational Mechanics and Analysis. 2015;215(2):381-417. doi:10.1007/s00205-014-0781-6","ista":"Nam P, Seiringer R. 2015. Collective excitations of Bose gases in the mean-field regime. Archive for Rational Mechanics and Analysis. 215(2), 381–417.","apa":"Nam, P., & Seiringer, R. (2015). Collective excitations of Bose gases in the mean-field regime. Archive for Rational Mechanics and Analysis. Springer. https://doi.org/10.1007/s00205-014-0781-6","ieee":"P. Nam and R. Seiringer, “Collective excitations of Bose gases in the mean-field regime,” Archive for Rational Mechanics and Analysis, vol. 215, no. 2. Springer, pp. 381–417, 2015."},"oa":1,"day":"01","month":"02","scopus_import":1},{"_id":"2166","year":"2015","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","status":"public","title":"The Altshuler-Shklovskii formulas for random band matrices I: the unimodular case","intvolume":" 333","publisher":"Springer","department":[{"_id":"LaEr"}],"author":[{"full_name":"Erdös, László","first_name":"László","last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603"},{"last_name":"Knowles","first_name":"Antti","full_name":"Knowles, Antti"}],"date_created":"2018-12-11T11:56:05Z","date_updated":"2021-01-12T06:55:43Z","volume":333,"oa_version":"Preprint","type":"journal_article","abstract":[{"text":"We consider the spectral statistics of large random band matrices on mesoscopic energy scales. We show that the correlation function of the local eigenvalue density exhibits a universal power law behaviour that differs from the Wigner-Dyson- Mehta statistics. This law had been predicted in the physics literature by Altshuler and Shklovskii in (Zh Eksp Teor Fiz (Sov Phys JETP) 91(64):220(127), 1986); it describes the correlations of the eigenvalue density in general metallic sampleswith weak disorder. Our result rigorously establishes the Altshuler-Shklovskii formulas for band matrices. In two dimensions, where the leading term vanishes owing to an algebraic cancellation, we identify the first non-vanishing term and show that it differs substantially from the prediction of Kravtsov and Lerner in (Phys Rev Lett 74:2563-2566, 1995). The proof is given in the current paper and its companion (Ann. H. Poincaré. arXiv:1309.5107, 2014). ","lang":"eng"}],"issue":"3","publist_id":"4818","publication":"Communications in Mathematical Physics","oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/1309.5106","open_access":"1"}],"citation":{"chicago":"Erdös, László, and Antti Knowles. “The Altshuler-Shklovskii Formulas for Random Band Matrices I: The Unimodular Case.” Communications in Mathematical Physics. Springer, 2015. https://doi.org/10.1007/s00220-014-2119-5.","short":"L. Erdös, A. Knowles, Communications in Mathematical Physics 333 (2015) 1365–1416.","mla":"Erdös, László, and Antti Knowles. “The Altshuler-Shklovskii Formulas for Random Band Matrices I: The Unimodular Case.” Communications in Mathematical Physics, vol. 333, no. 3, Springer, 2015, pp. 1365–416, doi:10.1007/s00220-014-2119-5.","ieee":"L. Erdös and A. Knowles, “The Altshuler-Shklovskii formulas for random band matrices I: the unimodular case,” Communications in Mathematical Physics, vol. 333, no. 3. Springer, pp. 1365–1416, 2015.","apa":"Erdös, L., & Knowles, A. (2015). The Altshuler-Shklovskii formulas for random band matrices I: the unimodular case. Communications in Mathematical Physics. Springer. https://doi.org/10.1007/s00220-014-2119-5","ista":"Erdös L, Knowles A. 2015. The Altshuler-Shklovskii formulas for random band matrices I: the unimodular case. Communications in Mathematical Physics. 333(3), 1365–1416.","ama":"Erdös L, Knowles A. The Altshuler-Shklovskii formulas for random band matrices I: the unimodular case. Communications in Mathematical Physics. 2015;333(3):1365-1416. doi:10.1007/s00220-014-2119-5"},"quality_controlled":"1","page":"1365 - 1416","date_published":"2015-02-01T00:00:00Z","doi":"10.1007/s00220-014-2119-5","language":[{"iso":"eng"}],"scopus_import":1,"day":"01","month":"02"},{"oa":1,"tmp":{"short":"CC BY-ND (4.0)","image":"/image/cc_by_nd.png","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode"},"project":[{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"name":"Quantitative Reactive Modeling","call_identifier":"FP7","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","doi":"10.2168/LMCS-11(1:20)2015","language":[{"iso":"eng"}],"month":"04","year":"2015","department":[{"_id":"ToHe"}],"publisher":"International Federation of Computational Logic","publication_status":"published","related_material":{"record":[{"status":"public","relation":"earlier_version","id":"2328"}]},"author":[{"full_name":"Chakraborty, Soham","first_name":"Soham","last_name":"Chakraborty"},{"full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A"},{"full_name":"Sezgin, Ali","last_name":"Sezgin","first_name":"Ali"},{"first_name":"Viktor","last_name":"Vafeiadis","full_name":"Vafeiadis, Viktor"}],"volume":11,"date_created":"2018-12-11T11:54:15Z","date_updated":"2023-02-23T10:38:13Z","article_number":"20","publist_id":"5271","ec_funded":1,"file_date_updated":"2020-07-14T12:45:17Z","license":"https://creativecommons.org/licenses/by-nd/4.0/","citation":{"short":"S. Chakraborty, T.A. Henzinger, A. Sezgin, V. Vafeiadis, Logical Methods in Computer Science 11 (2015).","mla":"Chakraborty, Soham, et al. “Aspect-Oriented Linearizability Proofs.” Logical Methods in Computer Science, vol. 11, no. 1, 20, International Federation of Computational Logic, 2015, doi:10.2168/LMCS-11(1:20)2015.","chicago":"Chakraborty, Soham, Thomas A Henzinger, Ali Sezgin, and Viktor Vafeiadis. “Aspect-Oriented Linearizability Proofs.” Logical Methods in Computer Science. International Federation of Computational Logic, 2015. https://doi.org/10.2168/LMCS-11(1:20)2015.","ama":"Chakraborty S, Henzinger TA, Sezgin A, Vafeiadis V. Aspect-oriented linearizability proofs. Logical Methods in Computer Science. 2015;11(1). doi:10.2168/LMCS-11(1:20)2015","ieee":"S. Chakraborty, T. A. Henzinger, A. Sezgin, and V. Vafeiadis, “Aspect-oriented linearizability proofs,” Logical Methods in Computer Science, vol. 11, no. 1. International Federation of Computational Logic, 2015.","apa":"Chakraborty, S., Henzinger, T. A., Sezgin, A., & Vafeiadis, V. (2015). Aspect-oriented linearizability proofs. Logical Methods in Computer Science. International Federation of Computational Logic. https://doi.org/10.2168/LMCS-11(1:20)2015","ista":"Chakraborty S, Henzinger TA, Sezgin A, Vafeiadis V. 2015. Aspect-oriented linearizability proofs. Logical Methods in Computer Science. 11(1), 20."},"publication":"Logical Methods in Computer Science","article_type":"original","date_published":"2015-04-01T00:00:00Z","scopus_import":1,"article_processing_charge":"No","has_accepted_license":"1","day":"01","_id":"1832","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 11","ddc":["000"],"status":"public","title":"Aspect-oriented linearizability proofs","pubrep_id":"390","file":[{"creator":"system","content_type":"application/pdf","file_size":380203,"file_name":"IST-2015-390-v1+1_1502.07639.pdf","access_level":"open_access","date_updated":"2020-07-14T12:45:17Z","date_created":"2018-12-12T10:11:27Z","checksum":"7370e164d0a731f442424a92669efc34","file_id":"4881","relation":"main_file"}],"oa_version":"Published Version","type":"journal_article","issue":"1","abstract":[{"text":"Linearizability of concurrent data structures is usually proved by monolithic simulation arguments relying on the identification of the so-called linearization points. Regrettably, such proofs, whether manual or automatic, are often complicated and scale poorly to advanced non-blocking concurrency patterns, such as helping and optimistic updates. In response, we propose a more modular way of checking linearizability of concurrent queue algorithms that does not involve identifying linearization points. We reduce the task of proving linearizability with respect to the queue specification to establishing four basic properties, each of which can be proved independently by simpler arguments. As a demonstration of our approach, we verify the Herlihy and Wing queue, an algorithm that is challenging to verify by a simulation proof. ","lang":"eng"}]},{"month":"02","language":[{"iso":"eng"}],"doi":"10.1137/130945648","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1311.4219"}],"oa":1,"external_id":{"arxiv":["1311.4219"]},"publist_id":"4673","date_updated":"2023-02-23T10:46:30Z","date_created":"2018-12-11T11:56:41Z","volume":44,"author":[{"full_name":"Kolmogorov, Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","first_name":"Vladimir","last_name":"Kolmogorov"},{"last_name":"Thapper","first_name":"Johan","full_name":"Thapper, Johan"},{"full_name":"Živný, Stanislav","last_name":"Živný","first_name":"Stanislav"}],"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"2518"}]},"publication_status":"published","department":[{"_id":"VlKo"}],"publisher":"SIAM","year":"2015","day":"01","scopus_import":1,"date_published":"2015-02-01T00:00:00Z","page":"1 - 36","publication":"SIAM Journal on Computing","citation":{"chicago":"Kolmogorov, Vladimir, Johan Thapper, and Stanislav Živný. “The Power of Linear Programming for General-Valued CSPs.” SIAM Journal on Computing. SIAM, 2015. https://doi.org/10.1137/130945648.","short":"V. Kolmogorov, J. Thapper, S. Živný, SIAM Journal on Computing 44 (2015) 1–36.","mla":"Kolmogorov, Vladimir, et al. “The Power of Linear Programming for General-Valued CSPs.” SIAM Journal on Computing, vol. 44, no. 1, SIAM, 2015, pp. 1–36, doi:10.1137/130945648.","ieee":"V. Kolmogorov, J. Thapper, and S. Živný, “The power of linear programming for general-valued CSPs,” SIAM Journal on Computing, vol. 44, no. 1. SIAM, pp. 1–36, 2015.","apa":"Kolmogorov, V., Thapper, J., & Živný, S. (2015). The power of linear programming for general-valued CSPs. SIAM Journal on Computing. SIAM. https://doi.org/10.1137/130945648","ista":"Kolmogorov V, Thapper J, Živný S. 2015. The power of linear programming for general-valued CSPs. SIAM Journal on Computing. 44(1), 1–36.","ama":"Kolmogorov V, Thapper J, Živný S. The power of linear programming for general-valued CSPs. SIAM Journal on Computing. 2015;44(1):1-36. doi:10.1137/130945648"},"abstract":[{"lang":"eng","text":"A class of valued constraint satisfaction problems (VCSPs) is characterised by a valued constraint language, a fixed set of cost functions on a finite domain. Finite-valued constraint languages contain functions that take on rational costs and general-valued constraint languages contain functions that take on rational or infinite costs. An instance of the problem is specified by a sum of functions from the language with the goal to minimise the sum. This framework includes and generalises well-studied constraint satisfaction problems (CSPs) and maximum constraint satisfaction problems (Max-CSPs).\r\nOur main result is a precise algebraic characterisation of valued constraint languages whose instances can be solved exactly by the basic linear programming relaxation (BLP). For a general-valued constraint language Γ, BLP is a decision procedure for Γ if and only if Γ admits a symmetric fractional polymorphism of every arity. For a finite-valued constraint language Γ, BLP is a decision procedure if and only if Γ admits a symmetric fractional polymorphism of some arity, or equivalently, if Γ admits a symmetric fractional polymorphism of arity 2.\r\nUsing these results, we obtain tractability of several novel and previously widely-open classes of VCSPs, including problems over valued constraint languages that are: (1) submodular on arbitrary lattices; (2) bisubmodular (also known as k-submodular) on arbitrary finite domains; (3) weakly (and hence strongly) tree-submodular on arbitrary trees. "}],"issue":"1","type":"journal_article","oa_version":"Preprint","title":"The power of linear programming for general-valued CSPs","status":"public","intvolume":" 44","_id":"2271","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87"},{"type":"journal_article","issue":"4","publist_id":"7645","abstract":[{"text":"For suitable pairs of diagonal quadratic forms in eight variables we use the circle method to investigate the density of simultaneous integer solutions and relate this to the problem of estimating linear correlations among sums of two squares.","lang":"eng"}],"extern":1,"_id":"257","acknowledgement":"While working on this paper the first author was supported by ERC grant 306457 and the second author was supported by SwarnaJayanti Fellowship 2011–12, DST, Government of India.","year":"2015","publisher":"Walter de Gruyter GmbH","intvolume":" 27","status":"public","title":"Pairs of diagonal quadratic forms and linear correlations among sums of two squares","publication_status":"published","author":[{"orcid":"0000-0002-8314-0177","id":"35827D50-F248-11E8-B48F-1D18A9856A87","last_name":"Browning","first_name":"Timothy D","full_name":"Timothy Browning"},{"first_name":"Ritabrata","last_name":"Munshi","full_name":"Munshi, Ritabrata"}],"volume":27,"date_created":"2018-12-11T11:45:28Z","date_updated":"2021-01-12T06:58:18Z","day":"10","month":"07","oa":1,"citation":{"mla":"Browning, Timothy D., and Ritabrata Munshi. “Pairs of Diagonal Quadratic Forms and Linear Correlations among Sums of Two Squares.” Forum Mathematicum, vol. 27, no. 4, Walter de Gruyter GmbH, 2015, pp. 2025–50, doi:10.1515/forum-2013-6024.","short":"T.D. Browning, R. Munshi, Forum Mathematicum 27 (2015) 2025–2050.","chicago":"Browning, Timothy D, and Ritabrata Munshi. “Pairs of Diagonal Quadratic Forms and Linear Correlations among Sums of Two Squares.” Forum Mathematicum. Walter de Gruyter GmbH, 2015. https://doi.org/10.1515/forum-2013-6024.","ama":"Browning TD, Munshi R. Pairs of diagonal quadratic forms and linear correlations among sums of two squares. Forum Mathematicum. 2015;27(4):2025-2050. doi:10.1515/forum-2013-6024","ista":"Browning TD, Munshi R. 2015. Pairs of diagonal quadratic forms and linear correlations among sums of two squares. Forum Mathematicum. 27(4), 2025–2050.","ieee":"T. D. Browning and R. Munshi, “Pairs of diagonal quadratic forms and linear correlations among sums of two squares,” Forum Mathematicum, vol. 27, no. 4. Walter de Gruyter GmbH, pp. 2025–2050, 2015.","apa":"Browning, T. D., & Munshi, R. (2015). Pairs of diagonal quadratic forms and linear correlations among sums of two squares. Forum Mathematicum. Walter de Gruyter GmbH. https://doi.org/10.1515/forum-2013-6024"},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1302.2434"}],"publication":"Forum Mathematicum","page":"2025 - 2050","quality_controlled":0,"doi":"10.1515/forum-2013-6024","date_published":"2015-07-10T00:00:00Z"},{"publist_id":"7644","abstract":[{"text":"Given a number field k and a projective algebraic variety X defined over k, the question of whether X contains a k-rational point is both very natural and very difficult. In the event that the set X(k) of k-rational points is not empty, one can also ask how the points of X(k) are distributed. Are they dense in X under the Zariski topology? Are they dense in the set.","lang":"eng"}],"extern":"1","type":"book_chapter","author":[{"full_name":"Browning, Timothy D","orcid":"0000-0002-8314-0177","id":"35827D50-F248-11E8-B48F-1D18A9856A87","last_name":"Browning","first_name":"Timothy D"}],"oa_version":"None","date_updated":"2021-01-12T06:58:22Z","date_created":"2018-12-11T11:45:28Z","year":"2015","_id":"258","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Cambridge University Press","title":"A survey of applications of the circle method to rational points","status":"public","publication_status":"published","day":"01","month":"08","doi":"10.1017/CBO9781316106877.009","date_published":"2015-08-01T00:00:00Z","language":[{"iso":"eng"}],"citation":{"chicago":"Browning, Timothy D. “A Survey of Applications of the Circle Method to Rational Points.” In Arithmetic and Geometry, 89–113. Cambridge University Press, 2015. https://doi.org/10.1017/CBO9781316106877.009.","mla":"Browning, Timothy D. “A Survey of Applications of the Circle Method to Rational Points.” Arithmetic and Geometry, Cambridge University Press, 2015, pp. 89–113, doi:10.1017/CBO9781316106877.009.","short":"T.D. Browning, in:, Arithmetic and Geometry, Cambridge University Press, 2015, pp. 89–113.","ista":"Browning TD. 2015.A survey of applications of the circle method to rational points. In: Arithmetic and Geometry. , 89–113.","ieee":"T. D. Browning, “A survey of applications of the circle method to rational points,” in Arithmetic and Geometry, Cambridge University Press, 2015, pp. 89–113.","apa":"Browning, T. D. (2015). A survey of applications of the circle method to rational points. In Arithmetic and Geometry (pp. 89–113). Cambridge University Press. https://doi.org/10.1017/CBO9781316106877.009","ama":"Browning TD. A survey of applications of the circle method to rational points. In: Arithmetic and Geometry. Cambridge University Press; 2015:89-113. doi:10.1017/CBO9781316106877.009"},"publication":"Arithmetic and Geometry","page":"89 - 113","quality_controlled":"1"},{"abstract":[{"lang":"eng","text":"The Hasse principle and weak approximation is established for non-singular cubic hypersurfaces X over the function field "}],"publist_id":"7643","issue":"3","extern":1,"type":"journal_article","author":[{"last_name":"Browning","first_name":"Timothy D","orcid":"0000-0002-8314-0177","id":"35827D50-F248-11E8-B48F-1D18A9856A87","full_name":"Timothy Browning"},{"first_name":"Pankaj","last_name":"Vishe","full_name":"Vishe, Pankaj"}],"date_created":"2018-12-11T11:45:29Z","date_updated":"2021-01-12T06:58:25Z","volume":25,"_id":"259","year":"2015","acknowledgement":"EP/J018260/1\tEngineering and Physical Sciences Research Council EPSRC","title":"Rational points on cubic hypersurfaces over F_q(t) ","publication_status":"published","status":"public","publisher":"Birkhäuser","intvolume":" 25","month":"06","day":"11","doi":"10.1007/s00039-015-0328-5","date_published":"2015-06-11T00:00:00Z","publication":"Geometric and Functional Analysis","citation":{"mla":"Browning, Timothy D., and Pankaj Vishe. “Rational Points on Cubic Hypersurfaces over F_q(T) .” Geometric and Functional Analysis, vol. 25, no. 3, Birkhäuser, 2015, pp. 671–732, doi:10.1007/s00039-015-0328-5.","short":"T.D. Browning, P. Vishe, Geometric and Functional Analysis 25 (2015) 671–732.","chicago":"Browning, Timothy D, and Pankaj Vishe. “Rational Points on Cubic Hypersurfaces over F_q(T) .” Geometric and Functional Analysis. Birkhäuser, 2015. https://doi.org/10.1007/s00039-015-0328-5.","ama":"Browning TD, Vishe P. Rational points on cubic hypersurfaces over F_q(t) . Geometric and Functional Analysis. 2015;25(3):671-732. doi:10.1007/s00039-015-0328-5","ista":"Browning TD, Vishe P. 2015. Rational points on cubic hypersurfaces over F_q(t) . Geometric and Functional Analysis. 25(3), 671–732.","apa":"Browning, T. D., & Vishe, P. (2015). Rational points on cubic hypersurfaces over F_q(t) . Geometric and Functional Analysis. Birkhäuser. https://doi.org/10.1007/s00039-015-0328-5","ieee":"T. D. Browning and P. Vishe, “Rational points on cubic hypersurfaces over F_q(t) ,” Geometric and Functional Analysis, vol. 25, no. 3. Birkhäuser, pp. 671–732, 2015."},"quality_controlled":0,"page":"671 - 732"},{"status":"public","title":"Average case analysis of the classical algorithm for Markov decision processes with Büchi objectives","intvolume":" 573","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1598","oa_version":"Preprint","type":"journal_article","abstract":[{"text":"We consider Markov decision processes (MDPs) with specifications given as Büchi (liveness) objectives, and examine the problem of computing the set of almost-sure winning vertices such that the objective can be ensured with probability 1 from these vertices. We study for the first time the average-case complexity of the classical algorithm for computing the set of almost-sure winning vertices for MDPs with Büchi objectives. Our contributions are as follows: First, we show that for MDPs with constant out-degree the expected number of iterations is at most logarithmic and the average-case running time is linear (as compared to the worst-case linear number of iterations and quadratic time complexity). Second, for the average-case analysis over all MDPs we show that the expected number of iterations is constant and the average-case running time is linear (again as compared to the worst-case linear number of iterations and quadratic time complexity). Finally we also show that when all MDPs are equally likely, the probability that the classical algorithm requires more than a constant number of iterations is exponentially small.","lang":"eng"}],"issue":"3","page":"71 - 89","publication":"Theoretical Computer Science","citation":{"ista":"Chatterjee K, Joglekar M, Shah N. 2015. Average case analysis of the classical algorithm for Markov decision processes with Büchi objectives. Theoretical Computer Science. 573(3), 71–89.","ieee":"K. Chatterjee, M. Joglekar, and N. Shah, “Average case analysis of the classical algorithm for Markov decision processes with Büchi objectives,” Theoretical Computer Science, vol. 573, no. 3. Elsevier, pp. 71–89, 2015.","apa":"Chatterjee, K., Joglekar, M., & Shah, N. (2015). Average case analysis of the classical algorithm for Markov decision processes with Büchi objectives. Theoretical Computer Science. Elsevier. https://doi.org/10.1016/j.tcs.2015.01.050","ama":"Chatterjee K, Joglekar M, Shah N. Average case analysis of the classical algorithm for Markov decision processes with Büchi objectives. Theoretical Computer Science. 2015;573(3):71-89. doi:10.1016/j.tcs.2015.01.050","chicago":"Chatterjee, Krishnendu, Manas Joglekar, and Nisarg Shah. “Average Case Analysis of the Classical Algorithm for Markov Decision Processes with Büchi Objectives.” Theoretical Computer Science. Elsevier, 2015. https://doi.org/10.1016/j.tcs.2015.01.050.","mla":"Chatterjee, Krishnendu, et al. “Average Case Analysis of the Classical Algorithm for Markov Decision Processes with Büchi Objectives.” Theoretical Computer Science, vol. 573, no. 3, Elsevier, 2015, pp. 71–89, doi:10.1016/j.tcs.2015.01.050.","short":"K. Chatterjee, M. Joglekar, N. Shah, Theoretical Computer Science 573 (2015) 71–89."},"date_published":"2015-03-30T00:00:00Z","scopus_import":1,"day":"30","article_processing_charge":"No","publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"Elsevier","acknowledgement":"The research was supported by FWF Grant No. P 23499-N23, FWF NFN Grant No. S11407-N23 (RiSE), ERC Start Grant (279307: Graph Games), and the Microsoft Faculty Fellows Award. Nisarg Shah is also supported by NSF Grant CCF-1215883.\r\n","year":"2015","date_updated":"2023-02-23T10:55:03Z","date_created":"2018-12-11T11:52:56Z","volume":573,"author":[{"first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"last_name":"Joglekar","first_name":"Manas","full_name":"Joglekar, Manas"},{"full_name":"Shah, Nisarg","last_name":"Shah","first_name":"Nisarg"}],"related_material":{"record":[{"status":"public","relation":"earlier_version","id":"2715"}]},"ec_funded":1,"publist_id":"5571","quality_controlled":"1","project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","call_identifier":"FWF"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"main_file_link":[{"url":"http://arxiv.org/abs/1202.4175","open_access":"1"}],"external_id":{"arxiv":["1202.4175"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1016/j.tcs.2015.01.050","month":"03"},{"oa_version":"None","status":"public","title":"Homological reconstruction and simplification in R3","intvolume":" 48","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1805","abstract":[{"text":"We consider the problem of deciding whether the persistent homology group of a simplicial pair (K,L) can be realized as the homology H∗(X) of some complex X with L ⊂ X ⊂ K. We show that this problem is NP-complete even if K is embedded in double-struck R3. As a consequence, we show that it is NP-hard to simplify level and sublevel sets of scalar functions on double-struck S3 within a given tolerance constraint. This problem has relevance to the visualization of medical images by isosurfaces. We also show an implication to the theory of well groups of scalar functions: not every well group can be realized by some level set, and deciding whether a well group can be realized is NP-hard.","lang":"eng"}],"issue":"8","type":"journal_article","date_published":"2015-06-03T00:00:00Z","page":"606 - 621","publication":"Computational Geometry: Theory and Applications","citation":{"ama":"Attali D, Bauer U, Devillers O, Glisse M, Lieutier A. Homological reconstruction and simplification in R3. Computational Geometry: Theory and Applications. 2015;48(8):606-621. doi:10.1016/j.comgeo.2014.08.010","ista":"Attali D, Bauer U, Devillers O, Glisse M, Lieutier A. 2015. Homological reconstruction and simplification in R3. Computational Geometry: Theory and Applications. 48(8), 606–621.","ieee":"D. Attali, U. Bauer, O. Devillers, M. Glisse, and A. Lieutier, “Homological reconstruction and simplification in R3,” Computational Geometry: Theory and Applications, vol. 48, no. 8. Elsevier, pp. 606–621, 2015.","apa":"Attali, D., Bauer, U., Devillers, O., Glisse, M., & Lieutier, A. (2015). Homological reconstruction and simplification in R3. Computational Geometry: Theory and Applications. Elsevier. https://doi.org/10.1016/j.comgeo.2014.08.010","mla":"Attali, Dominique, et al. “Homological Reconstruction and Simplification in R3.” Computational Geometry: Theory and Applications, vol. 48, no. 8, Elsevier, 2015, pp. 606–21, doi:10.1016/j.comgeo.2014.08.010.","short":"D. Attali, U. Bauer, O. Devillers, M. Glisse, A. Lieutier, Computational Geometry: Theory and Applications 48 (2015) 606–621.","chicago":"Attali, Dominique, Ulrich Bauer, Olivier Devillers, Marc Glisse, and André Lieutier. “Homological Reconstruction and Simplification in R3.” Computational Geometry: Theory and Applications. Elsevier, 2015. https://doi.org/10.1016/j.comgeo.2014.08.010."},"day":"03","scopus_import":1,"date_created":"2018-12-11T11:54:06Z","date_updated":"2023-02-23T10:59:19Z","volume":48,"author":[{"last_name":"Attali","first_name":"Dominique","full_name":"Attali, Dominique"},{"first_name":"Ulrich","last_name":"Bauer","id":"2ADD483A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9683-0724","full_name":"Bauer, Ulrich"},{"full_name":"Devillers, Olivier","last_name":"Devillers","first_name":"Olivier"},{"last_name":"Glisse","first_name":"Marc","full_name":"Glisse, Marc"},{"full_name":"Lieutier, André","last_name":"Lieutier","first_name":"André"}],"related_material":{"record":[{"id":"2812","status":"public","relation":"earlier_version"}]},"publication_status":"published","department":[{"_id":"HeEd"}],"publisher":"Elsevier","year":"2015","ec_funded":1,"publist_id":"5305","language":[{"iso":"eng"}],"doi":"10.1016/j.comgeo.2014.08.010","quality_controlled":"1","project":[{"name":"Topological Complex Systems","call_identifier":"FP7","grant_number":"318493","_id":"255D761E-B435-11E9-9278-68D0E5697425"}],"month":"06"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"333","year":"2015","status":"public","publication_status":"published","title":"Efficient and inexpensive sodium magnesium hybrid battery","intvolume":" 27","publisher":"ACS","author":[{"first_name":"Marc","last_name":"Walter","full_name":"Walter, Marc"},{"last_name":"Kravchyk","first_name":"Kostiantyn","full_name":"Kravchyk, Kostiantyn"},{"full_name":"Ibáñez, Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5013-2843","first_name":"Maria","last_name":"Ibáñez"},{"full_name":"Kovalenko, Maksym","last_name":"Kovalenko","first_name":"Maksym"}],"date_created":"2018-12-11T11:45:52Z","date_updated":"2021-01-12T07:42:42Z","volume":27,"oa_version":"None","type":"journal_article","abstract":[{"text":"We present a hybrid intercalation battery based on a sodium/magnesium (Na/Mg) dual salt electrolyte, metallic magnesium anode, and a cathode based on FeS2 nanocrystals (NCs). Compared to lithium or sodium, metallic magnesium anode is safer due to dendrite-free electroplating and offers extremely high volumetric (3833 mAh cm-3) and gravimetric capacities (2205 mAh g-1). Na-ion cathodes, FeS2 NCs in the present study, may serve as attractive alternatives to Mg-ion cathodes due to the higher voltage of operation and fast, highly reversible insertion of Na-ions. In this proof-of-concept study, electrochemical cycling of the Na/Mg hybrid battery was characterized by high rate capability, high Coulombic efficiency of 99.8%, and high energy density. In particular, with an average discharge voltage of ∼1.1 V and a cathodic capacity of 189 mAh g-1 at a current of 200 mA g-1, the presented Mg/FeS2 hybrid battery delivers energy densities of up to 210 Wh kg-1, comparable to commercial Li-ion batteries and approximately twice as high as state-of-the-art Mg-ion batteries based on Mo6S8 cathodes. Further significant gains in the energy density are expected from the development of Na/Mg electrolytes with a broader electrochemical stability window. Fully based on Earth-abundant elements, hybrid Na-Mg batteries are highly promising for large-scale stationary energy storage. ","lang":"eng"}],"publist_id":"7507","issue":"21","extern":"1","publication":"Chemistry of Materials","citation":{"ama":"Walter M, Kravchyk K, Ibáñez M, Kovalenko M. Efficient and inexpensive sodium magnesium hybrid battery. Chemistry of Materials. 2015;27(21):7452-7458. doi:10.1021/acs.chemmater.5b03531","ista":"Walter M, Kravchyk K, Ibáñez M, Kovalenko M. 2015. Efficient and inexpensive sodium magnesium hybrid battery. Chemistry of Materials. 27(21), 7452–7458.","ieee":"M. Walter, K. Kravchyk, M. Ibáñez, and M. Kovalenko, “Efficient and inexpensive sodium magnesium hybrid battery,” Chemistry of Materials, vol. 27, no. 21. ACS, pp. 7452–7458, 2015.","apa":"Walter, M., Kravchyk, K., Ibáñez, M., & Kovalenko, M. (2015). Efficient and inexpensive sodium magnesium hybrid battery. Chemistry of Materials. ACS. https://doi.org/10.1021/acs.chemmater.5b03531","mla":"Walter, Marc, et al. “Efficient and Inexpensive Sodium Magnesium Hybrid Battery.” Chemistry of Materials, vol. 27, no. 21, ACS, 2015, pp. 7452–58, doi:10.1021/acs.chemmater.5b03531.","short":"M. Walter, K. Kravchyk, M. Ibáñez, M. Kovalenko, Chemistry of Materials 27 (2015) 7452–7458.","chicago":"Walter, Marc, Kostiantyn Kravchyk, Maria Ibáñez, and Maksym Kovalenko. “Efficient and Inexpensive Sodium Magnesium Hybrid Battery.” Chemistry of Materials. ACS, 2015. https://doi.org/10.1021/acs.chemmater.5b03531."},"quality_controlled":"1","article_type":"original","page":"7452 - 7458","date_published":"2015-10-16T00:00:00Z","doi":"10.1021/acs.chemmater.5b03531","language":[{"iso":"eng"}],"month":"10","day":"16","article_processing_charge":"No"},{"article_processing_charge":"No","month":"03","day":"11","page":"4046 - 4049","article_type":"original","quality_controlled":"1","citation":{"ama":"Ibáñez M, Korkosz R, Luo Z, et al. Electron doping in bottom up engineered thermoelectric nanomaterials through HCl mediated ligand displacement. Journal of the American Chemical Society. 2015;137(12):4046-4049. doi:10.1021/jacs.5b00091","ieee":"M. Ibáñez et al., “Electron doping in bottom up engineered thermoelectric nanomaterials through HCl mediated ligand displacement,” Journal of the American Chemical Society, vol. 137, no. 12. American Chemical Society, pp. 4046–4049, 2015.","apa":"Ibáñez, M., Korkosz, R., Luo, Z., Riba, P., Cadavid, D., Ortega, S., … Kanatzidis, M. (2015). Electron doping in bottom up engineered thermoelectric nanomaterials through HCl mediated ligand displacement. Journal of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/jacs.5b00091","ista":"Ibáñez M, Korkosz R, Luo Z, Riba P, Cadavid D, Ortega S, Cabot A, Kanatzidis M. 2015. Electron doping in bottom up engineered thermoelectric nanomaterials through HCl mediated ligand displacement. Journal of the American Chemical Society. 137(12), 4046–4049.","short":"M. Ibáñez, R. Korkosz, Z. Luo, P. Riba, D. Cadavid, S. Ortega, A. Cabot, M. Kanatzidis, Journal of the American Chemical Society 137 (2015) 4046–4049.","mla":"Ibáñez, Maria, et al. “Electron Doping in Bottom up Engineered Thermoelectric Nanomaterials through HCl Mediated Ligand Displacement.” Journal of the American Chemical Society, vol. 137, no. 12, American Chemical Society, 2015, pp. 4046–49, doi:10.1021/jacs.5b00091.","chicago":"Ibáñez, Maria, Rachel Korkosz, Zhishan Luo, Pau Riba, Doris Cadavid, Silvia Ortega, Andreu Cabot, and Mercouri Kanatzidis. “Electron Doping in Bottom up Engineered Thermoelectric Nanomaterials through HCl Mediated Ligand Displacement.” Journal of the American Chemical Society. American Chemical Society, 2015. https://doi.org/10.1021/jacs.5b00091."},"publication":"Journal of the American Chemical Society","language":[{"iso":"eng"}],"date_published":"2015-03-11T00:00:00Z","doi":"10.1021/jacs.5b00091","type":"journal_article","extern":"1","publist_id":"7470","issue":"12","abstract":[{"text":"A simple and effective method to introduce precise amounts of doping in nanomaterials produced from the bottom-up assembly of colloidal nanoparticles (NPs) is described. The procedure takes advantage of a ligand displacement step to incorporate controlled concentrations of halide ions while removing carboxylic acids from the NP surface. Upon consolidation of the NPs into dense pellets, halide ions diffuse within the crystal structure, doping the anion sublattice and achieving n-type electrical doping. Through the characterization of the thermoelectric properties of nanocrystalline PbS, we demonstrate this strategy to be effective to control charge transport properties on thermoelectric nanomaterials assembled from NP building blocks. This approach is subsequently extended to PbTexSe1-x@PbS core-shell NPs, where a significant enhancement of the thermoelectric figure of merit is achieved. ","lang":"eng"}],"publisher":"American Chemical Society","intvolume":" 137","title":"Electron doping in bottom up engineered thermoelectric nanomaterials through HCl mediated ligand displacement","publication_status":"published","status":"public","year":"2015","_id":"354","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"At IREC, work was supported by European Regional Development Funds and the Framework 7 program under project UNION (FP7-NMP 310250). M.I. and S.O. thank AGAUR for their Beatriu i Pinós postdoctoral grant and the PhD grant, respectively. At Northwestern, work was supported by the Revolutionary Materials for Solid State Energy Conversion, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, and Office of Basic Energy Sciences under Award Number DE-SC0001054.","oa_version":"None","volume":137,"date_updated":"2021-01-12T07:44:10Z","date_created":"2018-12-11T11:45:59Z","author":[{"full_name":"Ibáñez, Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5013-2843","first_name":"Maria","last_name":"Ibáñez"},{"full_name":"Korkosz, Rachel","first_name":"Rachel","last_name":"Korkosz"},{"first_name":"Zhishan","last_name":"Luo","full_name":"Luo, Zhishan"},{"full_name":"Riba, Pau","last_name":"Riba","first_name":"Pau"},{"full_name":"Cadavid, Doris","first_name":"Doris","last_name":"Cadavid"},{"full_name":"Ortega, Silvia","first_name":"Silvia","last_name":"Ortega"},{"first_name":"Andreu","last_name":"Cabot","full_name":"Cabot, Andreu"},{"last_name":"Kanatzidis","first_name":"Mercouri","full_name":"Kanatzidis, Mercouri"}]},{"volume":31,"oa_version":"None","date_created":"2018-12-11T11:46:01Z","date_updated":"2021-01-12T07:44:34Z","author":[{"first_name":"Xuelian","last_name":"Yu","full_name":"Yu, Xuelian"},{"full_name":"Liu, Jingjing","first_name":"Jingjing","last_name":"Liu"},{"first_name":"Aziz","last_name":"Genç","full_name":"Genç, Aziz"},{"id":"43C61214-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5013-2843","first_name":"Maria","last_name":"Ibáñez","full_name":"Ibáñez, Maria"},{"full_name":"Luo, Zhishan","first_name":"Zhishan","last_name":"Luo"},{"full_name":"Shavel, Alexey","last_name":"Shavel","first_name":"Alexey"},{"last_name":"Arbiol","first_name":"Jordi","full_name":"Arbiol, Jordi"},{"first_name":"Guangjin","last_name":"Zhang","full_name":"Zhang, Guangjin"},{"full_name":"Zhang, Yihe","first_name":"Yihe","last_name":"Zhang"},{"full_name":"Cabot, Andreu","last_name":"Cabot","first_name":"Andreu"}],"intvolume":" 31","publisher":"American Chemical Society","title":"Cu2ZnSnS4-Ag2S nanoscale p-n heterostructures as sensitizers for photoelectrochemical water splitting","status":"public","publication_status":"published","_id":"360","year":"2015","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","publist_id":"7467","issue":"38","abstract":[{"lang":"eng","text":"A cation exchange-based route was used to produce Cu2ZnSnS4 (CZTS)-Ag2S nanoparticles with controlled composition. We report a detailed study of the formation of such CZTS-Ag2S nanoheterostructures and of their photocatalytic properties. When compared to pure CZTS, the use of nanoscale p-n heterostructures as light absorbers for photocatalytic water splitting provides superior photocurrents. We associate this experimental fact to a higher separation efficiency of the photogenerated electron-hole pairs. We believe this and other type-II nanoheterostructures will open the door to the use of CZTS, with excellent light absorption properties and made of abundant and environmental friendly elements, to the field of photocatalysis. "}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1021/acs.langmuir.5b02490","date_published":"2015-09-29T00:00:00Z","page":"10555 - 10561","citation":{"chicago":"Yu, Xuelian, Jingjing Liu, Aziz Genç, Maria Ibáñez, Zhishan Luo, Alexey Shavel, Jordi Arbiol, Guangjin Zhang, Yihe Zhang, and Andreu Cabot. “Cu2ZnSnS4-Ag2S Nanoscale p-n Heterostructures as Sensitizers for Photoelectrochemical Water Splitting.” Langmuir. American Chemical Society, 2015. https://doi.org/10.1021/acs.langmuir.5b02490.","short":"X. Yu, J. Liu, A. Genç, M. Ibáñez, Z. Luo, A. Shavel, J. Arbiol, G. Zhang, Y. Zhang, A. Cabot, Langmuir 31 (2015) 10555–10561.","mla":"Yu, Xuelian, et al. “Cu2ZnSnS4-Ag2S Nanoscale p-n Heterostructures as Sensitizers for Photoelectrochemical Water Splitting.” Langmuir, vol. 31, no. 38, American Chemical Society, 2015, pp. 10555–61, doi:10.1021/acs.langmuir.5b02490.","ieee":"X. Yu et al., “Cu2ZnSnS4-Ag2S nanoscale p-n heterostructures as sensitizers for photoelectrochemical water splitting,” Langmuir, vol. 31, no. 38. American Chemical Society, pp. 10555–10561, 2015.","apa":"Yu, X., Liu, J., Genç, A., Ibáñez, M., Luo, Z., Shavel, A., … Cabot, A. (2015). Cu2ZnSnS4-Ag2S nanoscale p-n heterostructures as sensitizers for photoelectrochemical water splitting. Langmuir. American Chemical Society. https://doi.org/10.1021/acs.langmuir.5b02490","ista":"Yu X, Liu J, Genç A, Ibáñez M, Luo Z, Shavel A, Arbiol J, Zhang G, Zhang Y, Cabot A. 2015. Cu2ZnSnS4-Ag2S nanoscale p-n heterostructures as sensitizers for photoelectrochemical water splitting. Langmuir. 31(38), 10555–10561.","ama":"Yu X, Liu J, Genç A, et al. Cu2ZnSnS4-Ag2S nanoscale p-n heterostructures as sensitizers for photoelectrochemical water splitting. Langmuir. 2015;31(38):10555-10561. doi:10.1021/acs.langmuir.5b02490"},"publication":"Langmuir","article_processing_charge":"No","month":"09","day":"29"},{"date_published":"2015-04-07T00:00:00Z","doi":"10.1021/la504906q","language":[{"iso":"eng"}],"citation":{"mla":"Lu, Zhishan, et al. “Size and Aspect Ratio Control of Pd Inf 2 Inf Sn Nanorods and Their Water Denitration Properties.” Langmuir, vol. 31, no. 13, American Chemical Society, 2015, pp. 3952–57, doi:10.1021/la504906q.","short":"Z. Lu, M. Ibáñez, A. Antolín, A. Genç, A. Shavel, S. Contreras, F. Medina, J. Arbiol, A. Cabot, Langmuir 31 (2015) 3952–3957.","chicago":"Lu, Zhishan, Maria Ibáñez, Ana Antolín, Aziz Genç, Alexey Shavel, Sandra Contreras, Francesc Medina, Jordi Arbiol, and Andreu Cabot. “Size and Aspect Ratio Control of Pd Inf 2 Inf Sn Nanorods and Their Water Denitration Properties.” Langmuir. American Chemical Society, 2015. https://doi.org/10.1021/la504906q.","ama":"Lu Z, Ibáñez M, Antolín A, et al. Size and aspect ratio control of Pd inf 2 inf Sn nanorods and their water denitration properties. Langmuir. 2015;31(13):3952-3957. doi:10.1021/la504906q","ista":"Lu Z, Ibáñez M, Antolín A, Genç A, Shavel A, Contreras S, Medina F, Arbiol J, Cabot A. 2015. Size and aspect ratio control of Pd inf 2 inf Sn nanorods and their water denitration properties. Langmuir. 31(13), 3952–3957.","apa":"Lu, Z., Ibáñez, M., Antolín, A., Genç, A., Shavel, A., Contreras, S., … Cabot, A. (2015). Size and aspect ratio control of Pd inf 2 inf Sn nanorods and their water denitration properties. Langmuir. American Chemical Society. https://doi.org/10.1021/la504906q","ieee":"Z. Lu et al., “Size and aspect ratio control of Pd inf 2 inf Sn nanorods and their water denitration properties,” Langmuir, vol. 31, no. 13. American Chemical Society, pp. 3952–3957, 2015."},"publication":"Langmuir","page":"3952 - 3957","article_processing_charge":"No","day":"07","month":"04","author":[{"full_name":"Lu, Zhishan","first_name":"Zhishan","last_name":"Lu"},{"last_name":"Ibáñez","first_name":"Maria","orcid":"0000-0001-5013-2843","id":"43C61214-F248-11E8-B48F-1D18A9856A87","full_name":"Ibáñez, Maria"},{"last_name":"Antolín","first_name":"Ana","full_name":"Antolín, Ana"},{"first_name":"Aziz","last_name":"Genç","full_name":"Genç, Aziz"},{"full_name":"Shavel, Alexey","first_name":"Alexey","last_name":"Shavel"},{"last_name":"Contreras","first_name":"Sandra","full_name":"Contreras, Sandra"},{"full_name":"Medina, Francesc","first_name":"Francesc","last_name":"Medina"},{"full_name":"Arbiol, Jordi","last_name":"Arbiol","first_name":"Jordi"},{"last_name":"Cabot","first_name":"Andreu","full_name":"Cabot, Andreu"}],"oa_version":"None","volume":31,"date_created":"2018-12-11T11:46:02Z","date_updated":"2021-01-12T07:44:42Z","year":"2015","_id":"362","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 31","publisher":"American Chemical Society","publication_status":"published","status":"public","title":"Size and aspect ratio control of Pd inf 2 inf Sn nanorods and their water denitration properties","issue":"13","publist_id":"7469","abstract":[{"text":"Monodisperse Pd2Sn nanorods with tuned size and aspect ratio were prepared by co-reduction of metal salts in the presence of trioctylphosphine, amine, and chloride ions. Asymmetric Pd2Sn nanostructures were achieved by the selective desorption of a surfactant mediated by chlorine ions. A preliminary evaluation of the geometry influence on catalytic properties evidenced Pd2Sn nanorods to have improved catalytic performance. In view of these results, Pd2Sn nanorods were also evaluated for water denitration. ","lang":"eng"}],"extern":"1","type":"journal_article"},{"date_published":"2015-12-01T00:00:00Z","publication":"Information and Computation","citation":{"ieee":"K. Chatterjee, L. Doyen, H. Gimbert, and T. A. Henzinger, “Randomness for free,” Information and Computation, vol. 245, no. 12. Elsevier, pp. 3–16, 2015.","apa":"Chatterjee, K., Doyen, L., Gimbert, H., & Henzinger, T. A. (2015). Randomness for free. Information and Computation. Elsevier. https://doi.org/10.1016/j.ic.2015.06.003","ista":"Chatterjee K, Doyen L, Gimbert H, Henzinger TA. 2015. Randomness for free. Information and Computation. 245(12), 3–16.","ama":"Chatterjee K, Doyen L, Gimbert H, Henzinger TA. Randomness for free. Information and Computation. 2015;245(12):3-16. doi:10.1016/j.ic.2015.06.003","chicago":"Chatterjee, Krishnendu, Laurent Doyen, Hugo Gimbert, and Thomas A Henzinger. “Randomness for Free.” Information and Computation. Elsevier, 2015. https://doi.org/10.1016/j.ic.2015.06.003.","short":"K. Chatterjee, L. Doyen, H. Gimbert, T.A. Henzinger, Information and Computation 245 (2015) 3–16.","mla":"Chatterjee, Krishnendu, et al. “Randomness for Free.” Information and Computation, vol. 245, no. 12, Elsevier, 2015, pp. 3–16, doi:10.1016/j.ic.2015.06.003."},"page":"3 - 16","day":"01","scopus_import":1,"oa_version":"Preprint","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1731","title":"Randomness for free","status":"public","intvolume":" 245","abstract":[{"text":"We consider two-player zero-sum games on graphs. These games can be classified on the basis of the information of the players and on the mode of interaction between them. On the basis of information the classification is as follows: (a) partial-observation (both players have partial view of the game); (b) one-sided complete-observation (one player has complete observation); and (c) complete-observation (both players have complete view of the game). On the basis of mode of interaction we have the following classification: (a) concurrent (both players interact simultaneously); and (b) turn-based (both players interact in turn). The two sources of randomness in these games are randomness in transition function and randomness in strategies. In general, randomized strategies are more powerful than deterministic strategies, and randomness in transitions gives more general classes of games. In this work we present a complete characterization for the classes of games where randomness is not helpful in: (a) the transition function probabilistic transition can be simulated by deterministic transition); and (b) strategies (pure strategies are as powerful as randomized strategies). As consequence of our characterization we obtain new undecidability results for these games. ","lang":"eng"}],"issue":"12","type":"journal_article","doi":"10.1016/j.ic.2015.06.003","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/1006.0673","open_access":"1"}],"quality_controlled":"1","project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23"},{"call_identifier":"FWF","name":"Game Theory","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"},{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","call_identifier":"FP7","name":"Quantitative Reactive Modeling"},{"name":"COMponent-Based Embedded Systems design Techniques","call_identifier":"FP7","_id":"25EFB36C-B435-11E9-9278-68D0E5697425","grant_number":"215543"},{"grant_number":"214373","_id":"25F1337C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Design for Embedded Systems"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"month":"12","author":[{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Laurent","last_name":"Doyen","full_name":"Doyen, Laurent"},{"full_name":"Gimbert, Hugo","first_name":"Hugo","last_name":"Gimbert"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","first_name":"Thomas A","last_name":"Henzinger","full_name":"Henzinger, Thomas A"}],"related_material":{"record":[{"status":"public","relation":"earlier_version","id":"3856"}]},"date_updated":"2023-02-23T11:45:42Z","date_created":"2018-12-11T11:53:42Z","volume":245,"year":"2015","publication_status":"published","publisher":"Elsevier","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"publist_id":"5395","ec_funded":1},{"date_created":"2018-12-11T11:45:52Z","date_updated":"2021-01-12T07:42:46Z","oa_version":"None","volume":31,"author":[{"last_name":"Yu","first_name":"Xuelian","full_name":"Yu, Xuelian"},{"full_name":"Liu, Jingjing","first_name":"Jingjing","last_name":"Liu"},{"full_name":"Genç, Aziz","first_name":"Aziz","last_name":"Genç"},{"orcid":"0000-0001-5013-2843","id":"43C61214-F248-11E8-B48F-1D18A9856A87","last_name":"Ibáñez","first_name":"Maria","full_name":"Ibáñez, Maria"},{"full_name":"Luo, Zhishan","first_name":"Zhishan","last_name":"Luo"},{"full_name":"Shavel, Alexey","first_name":"Alexey","last_name":"Shavel"},{"last_name":"Arbiol","first_name":"Jordi","full_name":"Arbiol, Jordi"},{"full_name":"Zhang, Guangjin","last_name":"Zhang","first_name":"Guangjin"},{"full_name":"Zhang, Yihe","last_name":"Zhang","first_name":"Yihe"},{"first_name":"Andreu","last_name":"Cabot","full_name":"Cabot, Andreu"}],"publication_status":"published","status":"public","title":"Cu2ZnSnS4–Ag2S Nanoscale p–n heterostructures as sensitizers for photoelectrochemical water splitting","intvolume":" 31","publisher":"American Chemical Society","year":"2015","_id":"334","acknowledgement":"This work was supported by the European Regional Development Funds, the Framework 7 program under project SCALENANO (FP7-NMP-ENERGY-2011-284486), the Spanish MINECO under Contract ENE2013-46624-C4-3-R and Fundamental Research Funds for the Central Universities (2652015086). Authors acknowledge the funding from Generalitat de Catalunya 2014 SGR 1638.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","abstract":[{"lang":"eng","text":"A cation exchange-based route was used to produce Cu2ZnSnS4 (CZTS)-Ag2S nanoparticles with controlled composition. We report a detailed study of the formation of such CZTS-Ag2S nanoheterostructures and of their photocatalytic properties. When compared to pure CZTS, the use of nanoscale p-n heterostructures as light absorbers for photocatalytic water splitting provides superior photocurrents. We associate this experimental fact to a higher separation efficiency of the photogenerated electron-hole pairs. We believe this and other type-II nanoheterostructures will open the door to the use of CZTS, with excellent light absorption properties and made of abundant and environmental friendly elements, to the field of photocatalysis."}],"issue":"38","publist_id":"7508","type":"journal_article","language":[{"iso":"eng"}],"date_published":"2015-09-07T00:00:00Z","doi":"10.1021/acs.langmuir.5b02490","article_type":"original","quality_controlled":"1","page":"10555 - 10561","publication":"Langmuir","citation":{"ama":"Yu X, Liu J, Genç A, et al. Cu2ZnSnS4–Ag2S Nanoscale p–n heterostructures as sensitizers for photoelectrochemical water splitting. Langmuir. 2015;31(38):10555-10561. doi:10.1021/acs.langmuir.5b02490","apa":"Yu, X., Liu, J., Genç, A., Ibáñez, M., Luo, Z., Shavel, A., … Cabot, A. (2015). Cu2ZnSnS4–Ag2S Nanoscale p–n heterostructures as sensitizers for photoelectrochemical water splitting. Langmuir. American Chemical Society. https://doi.org/10.1021/acs.langmuir.5b02490","ieee":"X. Yu et al., “Cu2ZnSnS4–Ag2S Nanoscale p–n heterostructures as sensitizers for photoelectrochemical water splitting,” Langmuir, vol. 31, no. 38. American Chemical Society, pp. 10555–10561, 2015.","ista":"Yu X, Liu J, Genç A, Ibáñez M, Luo Z, Shavel A, Arbiol J, Zhang G, Zhang Y, Cabot A. 2015. Cu2ZnSnS4–Ag2S Nanoscale p–n heterostructures as sensitizers for photoelectrochemical water splitting. Langmuir. 31(38), 10555–10561.","short":"X. Yu, J. Liu, A. Genç, M. Ibáñez, Z. Luo, A. Shavel, J. Arbiol, G. Zhang, Y. Zhang, A. Cabot, Langmuir 31 (2015) 10555–10561.","mla":"Yu, Xuelian, et al. “Cu2ZnSnS4–Ag2S Nanoscale p–n Heterostructures as Sensitizers for Photoelectrochemical Water Splitting.” Langmuir, vol. 31, no. 38, American Chemical Society, 2015, pp. 10555–61, doi:10.1021/acs.langmuir.5b02490.","chicago":"Yu, Xuelian, Jingjing Liu, Aziz Genç, Maria Ibáñez, Zhishan Luo, Alexey Shavel, Jordi Arbiol, Guangjin Zhang, Yihe Zhang, and Andreu Cabot. “Cu2ZnSnS4–Ag2S Nanoscale p–n Heterostructures as Sensitizers for Photoelectrochemical Water Splitting.” Langmuir. American Chemical Society, 2015. https://doi.org/10.1021/acs.langmuir.5b02490."},"month":"09","day":"07","article_processing_charge":"No"},{"article_processing_charge":"No","day":"26","month":"08","citation":{"ama":"Yu X, An X, Genç A, et al. Cu2ZnSnS4–PtM (M = Co, Ni) nanoheterostructures for photocatalytic hydrogen evolution. Journal of Physical Chemistry C. 2015;119(38):21882-21888. doi:10.1021/acs.jpcc.5b06199","ista":"Yu X, An X, Genç A, Ibáñez M, Arbiol J, Zhang Y, Cabot A. 2015. Cu2ZnSnS4–PtM (M = Co, Ni) nanoheterostructures for photocatalytic hydrogen evolution. Journal of Physical Chemistry C. 119(38), 21882–21888.","apa":"Yu, X., An, X., Genç, A., Ibáñez, M., Arbiol, J., Zhang, Y., & Cabot, A. (2015). Cu2ZnSnS4–PtM (M = Co, Ni) nanoheterostructures for photocatalytic hydrogen evolution. Journal of Physical Chemistry C. American Chemical Society. https://doi.org/10.1021/acs.jpcc.5b06199","ieee":"X. Yu et al., “Cu2ZnSnS4–PtM (M = Co, Ni) nanoheterostructures for photocatalytic hydrogen evolution,” Journal of Physical Chemistry C, vol. 119, no. 38. American Chemical Society, pp. 21882–21888, 2015.","mla":"Yu, Xuelian, et al. “Cu2ZnSnS4–PtM (M = Co, Ni) Nanoheterostructures for Photocatalytic Hydrogen Evolution.” Journal of Physical Chemistry C, vol. 119, no. 38, American Chemical Society, 2015, pp. 21882–88, doi:10.1021/acs.jpcc.5b06199.","short":"X. Yu, X. An, A. Genç, M. Ibáñez, J. Arbiol, Y. Zhang, A. Cabot, Journal of Physical Chemistry C 119 (2015) 21882–21888.","chicago":"Yu, Xuelian, Xiaoqiang An, Aziz Genç, Maria Ibáñez, Jordi Arbiol, Yihe Zhang, and Andreu Cabot. “Cu2ZnSnS4–PtM (M = Co, Ni) Nanoheterostructures for Photocatalytic Hydrogen Evolution.” Journal of Physical Chemistry C. American Chemical Society, 2015. https://doi.org/10.1021/acs.jpcc.5b06199."},"publication":"Journal of Physical Chemistry C","page":"21882 - 21888","doi":"10.1021/acs.jpcc.5b06199","date_published":"2015-08-26T00:00:00Z","language":[{"iso":"eng"}],"type":"journal_article","issue":"38","publist_id":"7468","abstract":[{"lang":"eng","text":"We report the synthesis and photocatalytic and magnetic characterization of colloidal nanoheterostructures formed by combining a Pt-based magnetic metal alloy (PtCo, PtNi) with Cu2ZnSnS4 (CZTS). While CZTS is one of the main candidate materials for solar energy conversion, the introduction of a Pt-based alloy on its surface strongly influences its chemical and electronic properties, ultimately determining its functionality. In this regard, up to a 15-fold increase of the photocatalytic hydrogen evolution activity was obtained with CZTS–PtCo when compared with CZTS. Furthermore, two times higher hydrogen evolution rates were obtained for CZTS–PtCo when compared with CZTS–Pt, in spite of the lower precious metal loading of the former. Besides, the magnetic properties of the PtCo nanoparticles attached to the CZTS nanocrystals were retained in the heterostructures, which could facilitate catalyst purification and recovery for its posterior recycling and/or reutilization."}],"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"361","year":"2015","acknowledgement":"This work was supported by the National Natural Science Foundation of China (Grant 21401212), Fundamental Research Funds for the Central Universities (2652015086), the Framework 7 program under project SCALENANO (FP7-NMP-ENERGY-2011-284486), and the MICINN project ENE2013-46624-C4-3-R. Authors acknowledge the funding from Generalitat de Catalunya 2014 SGR 1638.","intvolume":" 119","publisher":"American Chemical Society","status":"public","publication_status":"published","title":"Cu2ZnSnS4–PtM (M = Co, Ni) nanoheterostructures for photocatalytic hydrogen evolution","author":[{"full_name":"Yu, Xuelian","last_name":"Yu","first_name":"Xuelian"},{"full_name":"An, Xiaoqiang","first_name":"Xiaoqiang","last_name":"An"},{"first_name":"Aziz","last_name":"Genç","full_name":"Genç, Aziz"},{"id":"43C61214-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5013-2843","first_name":"Maria","last_name":"Ibáñez","full_name":"Ibáñez, Maria"},{"full_name":"Arbiol, Jordi","first_name":"Jordi","last_name":"Arbiol"},{"full_name":"Zhang, Yihe","first_name":"Yihe","last_name":"Zhang"},{"last_name":"Cabot","first_name":"Andreu","full_name":"Cabot, Andreu"}],"oa_version":"None","volume":119,"date_created":"2018-12-11T11:46:01Z","date_updated":"2021-01-12T07:44:38Z"},{"date_published":"2015-02-01T00:00:00Z","publication":"Journal of the ACM","citation":{"ista":"Chatterjee K, Henzinger TA, Jobstmann B, Singh R. 2015. Measuring and synthesizing systems in probabilistic environments. Journal of the ACM. 62(1), 9.","apa":"Chatterjee, K., Henzinger, T. A., Jobstmann, B., & Singh, R. (2015). Measuring and synthesizing systems in probabilistic environments. Journal of the ACM. ACM. https://doi.org/10.1145/2699430","ieee":"K. Chatterjee, T. A. Henzinger, B. Jobstmann, and R. Singh, “Measuring and synthesizing systems in probabilistic environments,” Journal of the ACM, vol. 62, no. 1. ACM, 2015.","ama":"Chatterjee K, Henzinger TA, Jobstmann B, Singh R. Measuring and synthesizing systems in probabilistic environments. Journal of the ACM. 2015;62(1). doi:10.1145/2699430","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, Barbara Jobstmann, and Rohit Singh. “Measuring and Synthesizing Systems in Probabilistic Environments.” Journal of the ACM. ACM, 2015. https://doi.org/10.1145/2699430.","mla":"Chatterjee, Krishnendu, et al. “Measuring and Synthesizing Systems in Probabilistic Environments.” Journal of the ACM, vol. 62, no. 1, 9, ACM, 2015, doi:10.1145/2699430.","short":"K. Chatterjee, T.A. Henzinger, B. Jobstmann, R. Singh, Journal of the ACM 62 (2015)."},"day":"01","scopus_import":1,"oa_version":"Preprint","status":"public","title":"Measuring and synthesizing systems in probabilistic environments","intvolume":" 62","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1856","abstract":[{"lang":"eng","text":"The traditional synthesis question given a specification asks for the automatic construction of a system that satisfies the specification, whereas often there exists a preference order among the different systems that satisfy the given specification. Under a probabilistic assumption about the possible inputs, such a preference order is naturally expressed by a weighted automaton, which assigns to each word a value, such that a system is preferred if it generates a higher expected value. We solve the following optimal synthesis problem: given an omega-regular specification, a Markov chain that describes the distribution of inputs, and a weighted automaton that measures how well a system satisfies the given specification under the input assumption, synthesize a system that optimizes the measured value. For safety specifications and quantitative measures that are defined by mean-payoff automata, the optimal synthesis problem reduces to finding a strategy in a Markov decision process (MDP) that is optimal for a long-run average reward objective, which can be achieved in polynomial time. For general omega-regular specifications along with mean-payoff automata, the solution rests on a new, polynomial-time algorithm for computing optimal strategies in MDPs with mean-payoff parity objectives. Our algorithm constructs optimal strategies that consist of two memoryless strategies and a counter. The counter is in general not bounded. To obtain a finite-state system, we show how to construct an ε-optimal strategy with a bounded counter, for all ε > 0. Furthermore, we show how to decide in polynomial time if it is possible to construct an optimal finite-state system (i.e., a system without a counter) for a given specification. We have implemented our approach and the underlying algorithms in a tool that takes qualitative and quantitative specifications and automatically constructs a system that satisfies the qualitative specification and optimizes the quantitative specification, if such a system exists. We present some experimental results showing optimal systems that were automatically generated in this way."}],"issue":"1","type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1145/2699430","quality_controlled":"1","project":[{"name":"Quantitative Reactive Modeling","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23"},{"name":"Game Theory","call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407"},{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1004.0739"}],"oa":1,"month":"02","date_updated":"2023-02-23T11:46:04Z","date_created":"2018-12-11T11:54:23Z","volume":62,"author":[{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee"},{"full_name":"Henzinger, Thomas A","last_name":"Henzinger","first_name":"Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Jobstmann, Barbara","last_name":"Jobstmann","first_name":"Barbara"},{"last_name":"Singh","first_name":"Rohit","full_name":"Singh, Rohit"}],"related_material":{"record":[{"id":"3864","relation":"earlier_version","status":"public"}]},"publication_status":"published","publisher":"ACM","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"year":"2015","publist_id":"5244","ec_funded":1,"article_number":"9"},{"article_processing_charge":"No","day":"07","month":"07","oa":1,"citation":{"ieee":"Z. Alpichshev, F. Mahmood, G. Cao, and N. Gedik, “Confinement deconfinement transition as an indication of spin liquid type behavior in Na2IrO3,” Physical Review Letters, vol. 114, no. 1. American Physical Society, 2015.","apa":"Alpichshev, Z., Mahmood, F., Cao, G., & Gedik, N. (2015). Confinement deconfinement transition as an indication of spin liquid type behavior in Na2IrO3. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.114.017203","ista":"Alpichshev Z, Mahmood F, Cao G, Gedik N. 2015. Confinement deconfinement transition as an indication of spin liquid type behavior in Na2IrO3. Physical Review Letters. 114(1).","ama":"Alpichshev Z, Mahmood F, Cao G, Gedik N. Confinement deconfinement transition as an indication of spin liquid type behavior in Na2IrO3. Physical Review Letters. 2015;114(1). doi:10.1103/PhysRevLett.114.017203","chicago":"Alpichshev, Zhanybek, Fahad Mahmood, Gang Cao, and Nuh Gedik. “Confinement Deconfinement Transition as an Indication of Spin Liquid Type Behavior in Na2IrO3.” Physical Review Letters. American Physical Society, 2015. https://doi.org/10.1103/PhysRevLett.114.017203.","short":"Z. Alpichshev, F. Mahmood, G. Cao, N. Gedik, Physical Review Letters 114 (2015).","mla":"Alpichshev, Zhanybek, et al. “Confinement Deconfinement Transition as an Indication of Spin Liquid Type Behavior in Na2IrO3.” Physical Review Letters, vol. 114, no. 1, American Physical Society, 2015, doi:10.1103/PhysRevLett.114.017203."},"main_file_link":[{"open_access":"1","url":"https://dspace.mit.edu/handle/1721.1/92979"}],"publication":"Physical Review Letters","quality_controlled":"1","article_type":"original","date_published":"2015-07-07T00:00:00Z","doi":"10.1103/PhysRevLett.114.017203","language":[{"iso":"eng"}],"type":"journal_article","publist_id":"7441","issue":"1","abstract":[{"lang":"eng","text":"We use ultrafast optical spectroscopy to observe binding of charged single-particle excitations (SE) in the magnetically frustrated Mott insulator Na2IrO3. Above the antiferromagnetic ordering temperature (TN) the system response is due to both Hubbard excitons (HE) and their constituent unpaired SE. The SE response becomes strongly suppressed immediately below TN. We argue that this increase in binding energy is due to a unique interplay between the frustrated Kitaev and the weak Heisenberg-type ordering term in the Hamiltonian, mediating an effective interaction between the spin-singlet SE. This interaction grows with distance causing the SE to become trapped in the HE, similar to quark confinement inside hadrons. This binding of charged particles, induced by magnetic ordering, is a result of a confinement-deconfinement transition of spin excitations. This observation provides evidence for spin liquid type behavior which is expected in Na2IrO3."}],"extern":"1","year":"2015","_id":"388","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"American Physical Society","intvolume":" 114","title":"Confinement deconfinement transition as an indication of spin liquid type behavior in Na2IrO3","publication_status":"published","status":"public","author":[{"first_name":"Zhanybek","last_name":"Alpichshev","id":"45E67A2A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7183-5203","full_name":"Alpichshev, Zhanybek"},{"first_name":"Fahad","last_name":"Mahmood","full_name":"Mahmood, Fahad"},{"first_name":"Gang","last_name":"Cao","full_name":"Cao, Gang"},{"first_name":"Nuh","last_name":"Gedik","full_name":"Gedik, Nuh"}],"oa_version":"Published Version","volume":114,"date_created":"2018-12-11T11:46:11Z","date_updated":"2021-01-12T07:52:54Z"},{"article_number":"7174888","ec_funded":1,"publist_id":"5489","year":"2015","acknowledgement":"K. C. is supported by the Austrian Science Fund (FWF): P23499-N23 and S11407-N23 (RiSE), an ERC Start Grant (279307: Graph Games), and a Microsoft Faculty Fellows Award. M. H. is supported by the Austrian Science Fund (FWF): P23499-N23 and the Vienna Science and Technology Fund (WWTF) grant ICT10-002. V. L. is supported by the Vienna Science and Technology Fund (WWTF) grant ICT10-002. The research leading to these results has received funding from the European Research Council under the European Union’s Seventh Framework Programme (FP/2007-2013) / ERC Grant Agreement no. 340506.","publisher":"IEEE","department":[{"_id":"KrCh"}],"publication_status":"published","related_material":{"record":[{"id":"464","status":"public","relation":"later_version"}]},"author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"full_name":"Henzinger, Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","orcid":"0000-0002-5008-6530","first_name":"Monika H","last_name":"Henzinger"},{"full_name":"Loitzenbauer, Veronika","first_name":"Veronika","last_name":"Loitzenbauer"}],"volume":"2015-July","date_created":"2018-12-11T11:53:19Z","date_updated":"2023-02-23T12:20:05Z","month":"07","main_file_link":[{"open_access":"1","url":"https://eprints.cs.univie.ac.at/4368/"}],"oa":1,"project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"}],"quality_controlled":"1","doi":"10.1109/LICS.2015.34","conference":{"name":"LICS: Logic in Computer Science","end_date":"2015-07-10","start_date":"2015-07-06","location":"Kyoto, Japan"},"language":[{"iso":"eng"}],"type":"conference","abstract":[{"text":"The computation of the winning set for one-pair Streett objectives and for k-pair Streett objectives in (standard) graphs as well as in game graphs are central problems in computer-aided verification, with application to the verification of closed systems with strong fairness conditions, the verification of open systems, checking interface compatibility, well-formed ness of specifications, and the synthesis of reactive systems. We give faster algorithms for the computation of the winning set for (1) one-pair Streett objectives (aka parity-3 problem) in game graphs and (2) for k-pair Streett objectives in graphs. For both problems this represents the first improvement in asymptotic running time in 15 years.","lang":"eng"}],"_id":"1661","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","title":"Improved algorithms for one-pair and k-pair Streett objectives","status":"public","oa_version":"Submitted Version","scopus_import":"1","article_processing_charge":"No","day":"01","citation":{"short":"K. Chatterjee, M.H. Henzinger, V. Loitzenbauer, in:, Proceedings - Symposium on Logic in Computer Science, IEEE, 2015.","mla":"Chatterjee, Krishnendu, et al. “Improved Algorithms for One-Pair and k-Pair Streett Objectives.” Proceedings - Symposium on Logic in Computer Science, vol. 2015–July, 7174888, IEEE, 2015, doi:10.1109/LICS.2015.34.","chicago":"Chatterjee, Krishnendu, Monika H Henzinger, and Veronika Loitzenbauer. “Improved Algorithms for One-Pair and k-Pair Streett Objectives.” In Proceedings - Symposium on Logic in Computer Science, Vol. 2015–July. IEEE, 2015. https://doi.org/10.1109/LICS.2015.34.","ama":"Chatterjee K, Henzinger MH, Loitzenbauer V. Improved algorithms for one-pair and k-pair Streett objectives. In: Proceedings - Symposium on Logic in Computer Science. Vol 2015-July. IEEE; 2015. doi:10.1109/LICS.2015.34","ieee":"K. Chatterjee, M. H. Henzinger, and V. Loitzenbauer, “Improved algorithms for one-pair and k-pair Streett objectives,” in Proceedings - Symposium on Logic in Computer Science, Kyoto, Japan, 2015, vol. 2015–July.","apa":"Chatterjee, K., Henzinger, M. H., & Loitzenbauer, V. (2015). Improved algorithms for one-pair and k-pair Streett objectives. In Proceedings - Symposium on Logic in Computer Science (Vol. 2015–July). Kyoto, Japan: IEEE. https://doi.org/10.1109/LICS.2015.34","ista":"Chatterjee K, Henzinger MH, Loitzenbauer V. 2015. Improved algorithms for one-pair and k-pair Streett objectives. Proceedings - Symposium on Logic in Computer Science. LICS: Logic in Computer Science vol. 2015–July, 7174888."},"publication":"Proceedings - Symposium on Logic in Computer Science","date_published":"2015-07-01T00:00:00Z"},{"month":"01","tmp":{"short":"CC BY-ND (4.0)","image":"/image/cc_by_nd.png","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode"},"oa":1,"quality_controlled":"1","project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"doi":"10.5802/jep.18","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:46:35Z","ec_funded":1,"publist_id":"7344","year":"2015","publication_status":"published","department":[{"_id":"RoSe"}],"publisher":"Ecole Polytechnique","author":[{"full_name":"Lewin, Mathieu","last_name":"Lewin","first_name":"Mathieu"},{"first_name":"Nam","last_name":"Phan Thanh","id":"404092F4-F248-11E8-B48F-1D18A9856A87","full_name":"Phan Thanh, Nam"},{"full_name":"Rougerie, Nicolas","last_name":"Rougerie","first_name":"Nicolas"}],"date_updated":"2021-01-12T08:00:52Z","date_created":"2018-12-11T11:46:40Z","volume":2,"scopus_import":1,"day":"01","has_accepted_license":"1","publication":"Journal de l'Ecole Polytechnique - Mathematiques","citation":{"mla":"Lewin, Mathieu, et al. “Derivation of Nonlinear Gibbs Measures from Many-Body Quantum Mechanics.” Journal de l’Ecole Polytechnique - Mathematiques, vol. 2, Ecole Polytechnique, 2015, pp. 65–115, doi:10.5802/jep.18.","short":"M. Lewin, P. Nam, N. Rougerie, Journal de l’Ecole Polytechnique - Mathematiques 2 (2015) 65–115.","chicago":"Lewin, Mathieu, Phan Nam, and Nicolas Rougerie. “Derivation of Nonlinear Gibbs Measures from Many-Body Quantum Mechanics.” Journal de l’Ecole Polytechnique - Mathematiques. Ecole Polytechnique, 2015. https://doi.org/10.5802/jep.18.","ama":"Lewin M, Nam P, Rougerie N. Derivation of nonlinear gibbs measures from many-body quantum mechanics. Journal de l’Ecole Polytechnique - Mathematiques. 2015;2:65-115. doi:10.5802/jep.18","ista":"Lewin M, Nam P, Rougerie N. 2015. Derivation of nonlinear gibbs measures from many-body quantum mechanics. Journal de l’Ecole Polytechnique - Mathematiques. 2, 65–115.","ieee":"M. Lewin, P. Nam, and N. Rougerie, “Derivation of nonlinear gibbs measures from many-body quantum mechanics,” Journal de l’Ecole Polytechnique - Mathematiques, vol. 2. Ecole Polytechnique, pp. 65–115, 2015.","apa":"Lewin, M., Nam, P., & Rougerie, N. (2015). Derivation of nonlinear gibbs measures from many-body quantum mechanics. Journal de l’Ecole Polytechnique - Mathematiques. Ecole Polytechnique. https://doi.org/10.5802/jep.18"},"page":"65 - 115","date_published":"2015-01-01T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"We prove that nonlinear Gibbs measures can be obtained from the corresponding many-body, grand-canonical, quantum Gibbs states, in a mean-field limit where the temperature T diverges and the interaction strength behaves as 1/T. We proceed by characterizing the interacting Gibbs state as minimizing a functional counting the free-energy relatively to the non-interacting case. We then perform an infinite-dimensional analogue of phase-space semiclassical analysis, using fine properties of the quantum relative entropy, the link between quantum de Finetti measures and upper/lower symbols in a coherent state basis, as well as Berezin-Lieb type inequalities. Our results cover the measure built on the defocusing nonlinear Schrödinger functional on a finite interval, as well as smoother interactions in dimensions d 2."}],"_id":"473","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Derivation of nonlinear gibbs measures from many-body quantum mechanics","ddc":["539"],"intvolume":" 2","pubrep_id":"951","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"IST-2018-951-v1+1_2015_Thanh-Nam_Derivation_of.pdf","file_size":1084254,"content_type":"application/pdf","creator":"system","relation":"main_file","file_id":"4974","checksum":"a40eb4016717ddc9927154798a4c164a","date_created":"2018-12-12T10:12:53Z","date_updated":"2020-07-14T12:46:35Z"}]},{"scopus_import":1,"day":"15","month":"06","quality_controlled":"1","page":"2866 - 2880","publication":"Journal of Cell Science","citation":{"ama":"Holst K, Guseva D, Schindler S, et al. The serotonin receptor 5-HT7R regulates the morphology and migratory properties of dendritic cells. Journal of Cell Science. 2015;128(15):2866-2880. doi:10.1242/jcs.167999","ista":"Holst K, Guseva D, Schindler S, Sixt MK, Braun A, Chopra H, Pabst O, Ponimaskin E. 2015. The serotonin receptor 5-HT7R regulates the morphology and migratory properties of dendritic cells. Journal of Cell Science. 128(15), 2866–2880.","apa":"Holst, K., Guseva, D., Schindler, S., Sixt, M. K., Braun, A., Chopra, H., … Ponimaskin, E. (2015). The serotonin receptor 5-HT7R regulates the morphology and migratory properties of dendritic cells. Journal of Cell Science. Company of Biologists. https://doi.org/10.1242/jcs.167999","ieee":"K. Holst et al., “The serotonin receptor 5-HT7R regulates the morphology and migratory properties of dendritic cells,” Journal of Cell Science, vol. 128, no. 15. Company of Biologists, pp. 2866–2880, 2015.","mla":"Holst, Katrin, et al. “The Serotonin Receptor 5-HT7R Regulates the Morphology and Migratory Properties of Dendritic Cells.” Journal of Cell Science, vol. 128, no. 15, Company of Biologists, 2015, pp. 2866–80, doi:10.1242/jcs.167999.","short":"K. Holst, D. Guseva, S. Schindler, M.K. Sixt, A. Braun, H. Chopra, O. Pabst, E. Ponimaskin, Journal of Cell Science 128 (2015) 2866–2880.","chicago":"Holst, Katrin, Daria Guseva, Susann Schindler, Michael K Sixt, Armin Braun, Himpriya Chopra, Oliver Pabst, and Evgeni Ponimaskin. “The Serotonin Receptor 5-HT7R Regulates the Morphology and Migratory Properties of Dendritic Cells.” Journal of Cell Science. Company of Biologists, 2015. https://doi.org/10.1242/jcs.167999."},"language":[{"iso":"eng"}],"date_published":"2015-06-15T00:00:00Z","doi":"10.1242/jcs.167999","type":"journal_article","abstract":[{"lang":"eng","text":"Dendritic cells are potent antigen-presenting cells endowed with the unique ability to initiate adaptive immune responses upon inflammation. Inflammatory processes are often associated with an increased production of serotonin, which operates by activating specific receptors. However, the functional role of serotonin receptors in regulation of dendritic cell functions is poorly understood. Here, we demonstrate that expression of serotonin receptor 5-HT7 (5-HT7TR) as well as its downstream effector Cdc42 is upregulated in dendritic cells upon maturation. Although dendritic cell maturation was independent of 5-HT7TR, receptor stimulation affected dendritic cell morphology through Cdc42-mediated signaling. In addition, basal activity of 5-HT7TR was required for the proper expression of the chemokine receptor CCR7, which is a key factor that controls dendritic cell migration. Consistent with this, we observed that 5-HT7TR enhances chemotactic motility of dendritic cells in vitro by modulating their directionality and migration velocity. Accordingly, migration of dendritic cells in murine colon explants was abolished after pharmacological receptor inhibition. Our results indicate that there is a crucial role for 5-HT7TR-Cdc42-mediated signaling in the regulation of dendritic cell morphology and motility, suggesting that 5-HT7TR could be a new target for treatment of a variety of inflammatory and immune disorders."}],"issue":"15","publist_id":"7343","publication_status":"published","title":"The serotonin receptor 5-HT7R regulates the morphology and migratory properties of dendritic cells","status":"public","publisher":"Company of Biologists","intvolume":" 128","department":[{"_id":"MiSi"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"477","year":"2015","date_updated":"2021-01-12T08:00:54Z","date_created":"2018-12-11T11:46:41Z","volume":128,"oa_version":"None","author":[{"last_name":"Holst","first_name":"Katrin","full_name":"Holst, Katrin"},{"last_name":"Guseva","first_name":"Daria","full_name":"Guseva, Daria"},{"full_name":"Schindler, Susann","last_name":"Schindler","first_name":"Susann"},{"orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","first_name":"Michael K","full_name":"Sixt, Michael K"},{"full_name":"Braun, Armin","last_name":"Braun","first_name":"Armin"},{"first_name":"Himpriya","last_name":"Chopra","full_name":"Chopra, Himpriya"},{"last_name":"Pabst","first_name":"Oliver","full_name":"Pabst, Oliver"},{"full_name":"Ponimaskin, Evgeni","last_name":"Ponimaskin","first_name":"Evgeni"}]},{"oa_version":"Preprint","intvolume":" 242","title":"Looking at mean-payoff and total-payoff through windows","status":"public","_id":"523","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"6","abstract":[{"lang":"eng","text":"We consider two-player games played on weighted directed graphs with mean-payoff and total-payoff objectives, two classical quantitative objectives. While for single-dimensional games the complexity and memory bounds for both objectives coincide, we show that in contrast to multi-dimensional mean-payoff games that are known to be coNP-complete, multi-dimensional total-payoff games are undecidable. We introduce conservative approximations of these objectives, where the payoff is considered over a local finite window sliding along a play, instead of the whole play. For single dimension, we show that (i) if the window size is polynomial, deciding the winner takes polynomial time, and (ii) the existence of a bounded window can be decided in NP ∩ coNP, and is at least as hard as solving mean-payoff games. For multiple dimensions, we show that (i) the problem with fixed window size is EXPTIME-complete, and (ii) there is no primitive-recursive algorithm to decide the existence of a bounded window."}],"type":"journal_article","date_published":"2015-03-24T00:00:00Z","page":"25 - 52","citation":{"chicago":"Chatterjee, Krishnendu, Laurent Doyen, Mickael Randour, and Jean Raskin. “Looking at Mean-Payoff and Total-Payoff through Windows.” Information and Computation. Elsevier, 2015. https://doi.org/10.1016/j.ic.2015.03.010.","short":"K. Chatterjee, L. Doyen, M. Randour, J. Raskin, Information and Computation 242 (2015) 25–52.","mla":"Chatterjee, Krishnendu, et al. “Looking at Mean-Payoff and Total-Payoff through Windows.” Information and Computation, vol. 242, no. 6, Elsevier, 2015, pp. 25–52, doi:10.1016/j.ic.2015.03.010.","ieee":"K. Chatterjee, L. Doyen, M. Randour, and J. Raskin, “Looking at mean-payoff and total-payoff through windows,” Information and Computation, vol. 242, no. 6. Elsevier, pp. 25–52, 2015.","apa":"Chatterjee, K., Doyen, L., Randour, M., & Raskin, J. (2015). Looking at mean-payoff and total-payoff through windows. Information and Computation. Elsevier. https://doi.org/10.1016/j.ic.2015.03.010","ista":"Chatterjee K, Doyen L, Randour M, Raskin J. 2015. Looking at mean-payoff and total-payoff through windows. Information and Computation. 242(6), 25–52.","ama":"Chatterjee K, Doyen L, Randour M, Raskin J. Looking at mean-payoff and total-payoff through windows. Information and Computation. 2015;242(6):25-52. doi:10.1016/j.ic.2015.03.010"},"publication":"Information and Computation","day":"24","scopus_import":1,"volume":242,"date_updated":"2023-02-23T10:36:02Z","date_created":"2018-12-11T11:46:57Z","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"2279"}]},"author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"full_name":"Doyen, Laurent","last_name":"Doyen","first_name":"Laurent"},{"last_name":"Randour","first_name":"Mickael","full_name":"Randour, Mickael"},{"last_name":"Raskin","first_name":"Jean","full_name":"Raskin, Jean"}],"publisher":"Elsevier","department":[{"_id":"KrCh"}],"publication_status":"published","year":"2015","ec_funded":1,"publist_id":"7296","language":[{"iso":"eng"}],"doi":"10.1016/j.ic.2015.03.010","project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Game Theory","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1302.4248","open_access":"1"}],"oa":1,"month":"03"},{"scopus_import":1,"month":"10","day":"22","quality_controlled":"1","page":"670 - 683","publication":"Cell","citation":{"ama":"Li W, Ma M, Feng Y, et al. EIN2-directed translational regulation of ethylene signaling in arabidopsis. Cell. 2015;163(3):670-683. doi:10.1016/j.cell.2015.09.037","ista":"Li W, Ma M, Feng Y, Li H, Wang Y, Ma Y, Li M, An F, Guo H. 2015. EIN2-directed translational regulation of ethylene signaling in arabidopsis. Cell. 163(3), 670–683.","ieee":"W. Li et al., “EIN2-directed translational regulation of ethylene signaling in arabidopsis,” Cell, vol. 163, no. 3. Cell Press, pp. 670–683, 2015.","apa":"Li, W., Ma, M., Feng, Y., Li, H., Wang, Y., Ma, Y., … Guo, H. (2015). EIN2-directed translational regulation of ethylene signaling in arabidopsis. Cell. Cell Press. https://doi.org/10.1016/j.cell.2015.09.037","mla":"Li, Wenyang, et al. “EIN2-Directed Translational Regulation of Ethylene Signaling in Arabidopsis.” Cell, vol. 163, no. 3, Cell Press, 2015, pp. 670–83, doi:10.1016/j.cell.2015.09.037.","short":"W. Li, M. Ma, Y. Feng, H. Li, Y. Wang, Y. Ma, M. Li, F. An, H. Guo, Cell 163 (2015) 670–683.","chicago":"Li, Wenyang, Mengdi Ma, Ying Feng, Hongjiang Li, Yichuan Wang, Yutong Ma, Mingzhe Li, Fengying An, and Hongwei Guo. “EIN2-Directed Translational Regulation of Ethylene Signaling in Arabidopsis.” Cell. Cell Press, 2015. https://doi.org/10.1016/j.cell.2015.09.037."},"language":[{"iso":"eng"}],"date_published":"2015-10-22T00:00:00Z","doi":"10.1016/j.cell.2015.09.037","type":"journal_article","abstract":[{"text":"Ethylene is a gaseous phytohormone that plays vital roles in plant growth and development. Previous studies uncovered EIN2 as an essential signal transducer linking ethylene perception on ER to transcriptional regulation in the nucleus through a “cleave and shuttle” model. In this study, we report another mechanism of EIN2-mediated ethylene signaling, whereby EIN2 imposes the translational repression of EBF1 and EBF2 mRNA. We find that the EBF1/2 3′ UTRs mediate EIN2-directed translational repression and identify multiple poly-uridylates (PolyU) motifs as functional cis elements of 3′ UTRs. Furthermore, we demonstrate that ethylene induces EIN2 to associate with 3′ UTRs and target EBF1/2 mRNA to cytoplasmic processing-body (P-body) through interacting with multiple P-body factors, including EIN5 and PABs. Our study illustrates translational regulation as a key step in ethylene signaling and presents mRNA 3′ UTR functioning as a “signal transducer” to sense and relay cellular signaling in plants.","lang":"eng"}],"issue":"3","publist_id":"7285","status":"public","title":"EIN2-directed translational regulation of ethylene signaling in arabidopsis","publication_status":"published","intvolume":" 163","department":[{"_id":"JiFr"}],"publisher":"Cell Press","_id":"532","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2015","date_created":"2018-12-11T11:47:00Z","date_updated":"2021-01-12T08:01:27Z","volume":163,"oa_version":"None","author":[{"full_name":"Li, Wenyang","last_name":"Li","first_name":"Wenyang"},{"last_name":"Ma","first_name":"Mengdi","full_name":"Ma, Mengdi"},{"full_name":"Feng, Ying","first_name":"Ying","last_name":"Feng"},{"full_name":"Li, Hongjiang","id":"33CA54A6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5039-9660","first_name":"Hongjiang","last_name":"Li"},{"full_name":"Wang, Yichuan","first_name":"Yichuan","last_name":"Wang"},{"first_name":"Yutong","last_name":"Ma","full_name":"Ma, Yutong"},{"full_name":"Li, Mingzhe","first_name":"Mingzhe","last_name":"Li"},{"first_name":"Fengying","last_name":"An","full_name":"An, Fengying"},{"last_name":"Guo","first_name":"Hongwei","full_name":"Guo, Hongwei"}]},{"oa_version":"Preprint","status":"public","title":"Qualitative analysis of concurrent mean payoff games","intvolume":" 242","_id":"524","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"We consider concurrent games played by two players on a finite-state graph, where in every round the players simultaneously choose a move, and the current state along with the joint moves determine the successor state. We study the most fundamental objective for concurrent games, namely, mean-payoff or limit-average objective, where a reward is associated to each transition, and the goal of player 1 is to maximize the long-run average of the rewards, and the objective of player 2 is strictly the opposite (i.e., the games are zero-sum). The path constraint for player 1 could be qualitative, i.e., the mean-payoff is the maximal reward, or arbitrarily close to it; or quantitative, i.e., a given threshold between the minimal and maximal reward. We consider the computation of the almost-sure (resp. positive) winning sets, where player 1 can ensure that the path constraint is satisfied with probability 1 (resp. positive probability). Almost-sure winning with qualitative constraint exactly corresponds to the question of whether there exists a strategy to ensure that the payoff is the maximal reward of the game. Our main results for qualitative path constraints are as follows: (1) we establish qualitative determinacy results that show that for every state either player 1 has a strategy to ensure almost-sure (resp. positive) winning against all player-2 strategies, or player 2 has a spoiling strategy to falsify almost-sure (resp. positive) winning against all player-1 strategies; (2) we present optimal strategy complexity results that precisely characterize the classes of strategies required for almost-sure and positive winning for both players; and (3) we present quadratic time algorithms to compute the almost-sure and the positive winning sets, matching the best known bound of the algorithms for much simpler problems (such as reachability objectives). For quantitative constraints we show that a polynomial time solution for the almost-sure or the positive winning set would imply a solution to a long-standing open problem (of solving the value problem of turn-based deterministic mean-payoff games) that is not known to be solvable in polynomial time."}],"issue":"6","type":"journal_article","date_published":"2015-10-11T00:00:00Z","page":"2 - 24","publication":"Information and Computation","citation":{"short":"K. Chatterjee, R. Ibsen-Jensen, Information and Computation 242 (2015) 2–24.","mla":"Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. “Qualitative Analysis of Concurrent Mean Payoff Games.” Information and Computation, vol. 242, no. 6, Elsevier, 2015, pp. 2–24, doi:10.1016/j.ic.2015.03.009.","chicago":"Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. “Qualitative Analysis of Concurrent Mean Payoff Games.” Information and Computation. Elsevier, 2015. https://doi.org/10.1016/j.ic.2015.03.009.","ama":"Chatterjee K, Ibsen-Jensen R. Qualitative analysis of concurrent mean payoff games. Information and Computation. 2015;242(6):2-24. doi:10.1016/j.ic.2015.03.009","ieee":"K. Chatterjee and R. Ibsen-Jensen, “Qualitative analysis of concurrent mean payoff games,” Information and Computation, vol. 242, no. 6. Elsevier, pp. 2–24, 2015.","apa":"Chatterjee, K., & Ibsen-Jensen, R. (2015). Qualitative analysis of concurrent mean payoff games. Information and Computation. Elsevier. https://doi.org/10.1016/j.ic.2015.03.009","ista":"Chatterjee K, Ibsen-Jensen R. 2015. Qualitative analysis of concurrent mean payoff games. Information and Computation. 242(6), 2–24."},"day":"11","scopus_import":1,"date_created":"2018-12-11T11:46:57Z","date_updated":"2023-02-23T12:24:45Z","volume":242,"author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"orcid":"0000-0003-4783-0389","id":"3B699956-F248-11E8-B48F-1D18A9856A87","last_name":"Ibsen-Jensen","first_name":"Rasmus","full_name":"Ibsen-Jensen, Rasmus"}],"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"5403"}]},"publication_status":"published","publisher":"Elsevier","department":[{"_id":"KrCh"}],"year":"2015","publist_id":"7295","language":[{"iso":"eng"}],"doi":"10.1016/j.ic.2015.03.009","quality_controlled":"1","external_id":{"arxiv":["1409.5306"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1409.5306"}],"month":"10"},{"publication":"Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence","citation":{"chicago":"Ahmed, Umair, Krishnendu Chatterjee, and Sumit Gulwani. “Automatic Generation of Alternative Starting Positions for Simple Traditional Board Games.” In Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence, 2:745–52. AAAI Press, 2015.","short":"U. Ahmed, K. Chatterjee, S. Gulwani, in:, Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence, AAAI Press, 2015, pp. 745–752.","mla":"Ahmed, Umair, et al. “Automatic Generation of Alternative Starting Positions for Simple Traditional Board Games.” Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence, vol. 2, AAAI Press, 2015, pp. 745–52.","ieee":"U. Ahmed, K. Chatterjee, and S. Gulwani, “Automatic generation of alternative starting positions for simple traditional board games,” in Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence, Austin, TX, USA, 2015, vol. 2, pp. 745–752.","apa":"Ahmed, U., Chatterjee, K., & Gulwani, S. (2015). Automatic generation of alternative starting positions for simple traditional board games. In Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence (Vol. 2, pp. 745–752). Austin, TX, USA: AAAI Press.","ista":"Ahmed U, Chatterjee K, Gulwani S. 2015. Automatic generation of alternative starting positions for simple traditional board games. Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence. AAAI: Conference on Artificial Intelligence vol. 2, 745–752.","ama":"Ahmed U, Chatterjee K, Gulwani S. Automatic generation of alternative starting positions for simple traditional board games. In: Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence. Vol 2. AAAI Press; 2015:745-752."},"page":"745 - 752","date_published":"2015-01-01T00:00:00Z","scopus_import":1,"day":"01","article_processing_charge":"No","_id":"1481","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Automatic generation of alternative starting positions for simple traditional board games","status":"public","intvolume":" 2","oa_version":"None","type":"conference","abstract":[{"text":"Simple board games, like Tic-Tac-Toe and CONNECT-4, play an important role not only in the development of mathematical and logical skills, but also in the emotional and social development. In this paper, we address the problem of generating targeted starting positions for such games. This can facilitate new approaches for bringing novice players to mastery, and also leads to discovery of interesting game variants. We present an approach that generates starting states of varying hardness levels for player 1 in a two-player board game, given rules of the board game, the desired number of steps required for player 1 to win, and the expertise levels of the two players. Our approach leverages symbolic methods and iterative simulation to efficiently search the extremely large state space. We present experimental results that include discovery of states of varying hardness levels for several simple grid-based board games. The presence of such states for standard game variants like 4×4 Tic-Tac-Toe opens up new games to be played that have never been played as the default start state is heavily biased. ","lang":"eng"}],"oa":1,"main_file_link":[{"url":"https://www.aaai.org/ocs/index.php/AAAI/AAAI15/paper/download/9523/9300","open_access":"1"}],"quality_controlled":"1","project":[{"grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"conference":{"name":"AAAI: Conference on Artificial Intelligence","start_date":"2015-01-25","location":"Austin, TX, USA","end_date":"2015-01-30"},"language":[{"iso":"eng"}],"month":"01","acknowledgement":"A Technical Report of this paper is available at: \r\nhttps://repository.ist.ac.at/id/eprint/146.\r\n","year":"2015","publication_status":"published","publisher":"AAAI Press","department":[{"_id":"KrCh"}],"author":[{"first_name":"Umair","last_name":"Ahmed","full_name":"Ahmed, Umair"},{"first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"last_name":"Gulwani","first_name":"Sumit","full_name":"Gulwani, Sumit"}],"related_material":{"record":[{"id":"5410","status":"public","relation":"earlier_version"}]},"date_created":"2018-12-11T11:52:16Z","date_updated":"2023-02-23T12:25:07Z","volume":2,"publist_id":"5713","ec_funded":1},{"citation":{"chicago":"Chatterjee, Krishnendu, Martin Chmelik, Raghav Gupta, and Ayush Kanodia. “Qualitative Analysis of POMDPs with Temporal Logic Specifications for Robotics Applications,” 325–30. IEEE, 2015. https://doi.org/10.1109/ICRA.2015.7139019.","mla":"Chatterjee, Krishnendu, et al. Qualitative Analysis of POMDPs with Temporal Logic Specifications for Robotics Applications. IEEE, 2015, pp. 325–30, doi:10.1109/ICRA.2015.7139019.","short":"K. Chatterjee, M. Chmelik, R. Gupta, A. Kanodia, in:, IEEE, 2015, pp. 325–330.","ista":"Chatterjee K, Chmelik M, Gupta R, Kanodia A. 2015. Qualitative analysis of POMDPs with temporal logic specifications for robotics applications. ICRA: International Conference on Robotics and Automation, 325–330.","ieee":"K. Chatterjee, M. Chmelik, R. Gupta, and A. Kanodia, “Qualitative analysis of POMDPs with temporal logic specifications for robotics applications,” presented at the ICRA: International Conference on Robotics and Automation, Seattle, WA, United States, 2015, pp. 325–330.","apa":"Chatterjee, K., Chmelik, M., Gupta, R., & Kanodia, A. (2015). Qualitative analysis of POMDPs with temporal logic specifications for robotics applications (pp. 325–330). Presented at the ICRA: International Conference on Robotics and Automation, Seattle, WA, United States: IEEE. https://doi.org/10.1109/ICRA.2015.7139019","ama":"Chatterjee K, Chmelik M, Gupta R, Kanodia A. Qualitative analysis of POMDPs with temporal logic specifications for robotics applications. In: IEEE; 2015:325-330. doi:10.1109/ICRA.2015.7139019"},"page":"325 - 330","date_published":"2015-01-01T00:00:00Z","scopus_import":1,"day":"01","_id":"1732","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Qualitative analysis of POMDPs with temporal logic specifications for robotics applications","oa_version":"Preprint","type":"conference","abstract":[{"lang":"eng","text":"We consider partially observable Markov decision processes (POMDPs), that are a standard framework for robotics applications to model uncertainties present in the real world, with temporal logic specifications. All temporal logic specifications in linear-time temporal logic (LTL) can be expressed as parity objectives. We study the qualitative analysis problem for POMDPs with parity objectives that asks whether there is a controller (policy) to ensure that the objective holds with probability 1 (almost-surely). While the qualitative analysis of POMDPs with parity objectives is undecidable, recent results show that when restricted to finite-memory policies the problem is EXPTIME-complete. While the problem is intractable in theory, we present a practical approach to solve the qualitative analysis problem. We designed several heuristics to deal with the exponential complexity, and have used our implementation on a number of well-known POMDP examples for robotics applications. Our results provide the first practical approach to solve the qualitative analysis of robot motion planning with LTL properties in the presence of uncertainty."}],"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1409.3360"}],"external_id":{"arxiv":["1409.3360"]},"oa":1,"quality_controlled":"1","project":[{"call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"name":"Game Theory","call_identifier":"FWF","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"}],"conference":{"name":"ICRA: International Conference on Robotics and Automation","location":"Seattle, WA, United States","start_date":"2015-05-26","end_date":"2015-05-30"},"doi":"10.1109/ICRA.2015.7139019","language":[{"iso":"eng"}],"month":"01","year":"2015","publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"IEEE","author":[{"first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"id":"3624234E-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","last_name":"Chmelik","full_name":"Chmelik, Martin"},{"last_name":"Gupta","first_name":"Raghav","full_name":"Gupta, Raghav"},{"first_name":"Ayush","last_name":"Kanodia","full_name":"Kanodia, Ayush"}],"related_material":{"record":[{"id":"5424","relation":"earlier_version","status":"public"},{"status":"public","relation":"earlier_version","id":"5426"}]},"date_created":"2018-12-11T11:53:43Z","date_updated":"2023-02-23T12:25:52Z","publist_id":"5394","ec_funded":1},{"has_accepted_license":"1","publication_identifier":{"issn":["2664-1690"]},"month":"02","day":"19","doi":"10.15479/AT:IST-2015-322-v1-1","date_published":"2015-02-19T00:00:00Z","language":[{"iso":"eng"}],"citation":{"ama":"Chatterjee K, Ibsen-Jensen R, Hansen K. The Patience of Concurrent Stochastic Games with Safety and Reachability Objectives. IST Austria; 2015. doi:10.15479/AT:IST-2015-322-v1-1","ista":"Chatterjee K, Ibsen-Jensen R, Hansen K. 2015. The patience of concurrent stochastic games with safety and reachability objectives, IST Austria, 25p.","ieee":"K. Chatterjee, R. Ibsen-Jensen, and K. Hansen, The patience of concurrent stochastic games with safety and reachability objectives. IST Austria, 2015.","apa":"Chatterjee, K., Ibsen-Jensen, R., & Hansen, K. (2015). The patience of concurrent stochastic games with safety and reachability objectives. IST Austria. https://doi.org/10.15479/AT:IST-2015-322-v1-1","mla":"Chatterjee, Krishnendu, et al. The Patience of Concurrent Stochastic Games with Safety and Reachability Objectives. IST Austria, 2015, doi:10.15479/AT:IST-2015-322-v1-1.","short":"K. Chatterjee, R. Ibsen-Jensen, K. Hansen, The Patience of Concurrent Stochastic Games with Safety and Reachability Objectives, IST Austria, 2015.","chicago":"Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Kristoffer Hansen. The Patience of Concurrent Stochastic Games with Safety and Reachability Objectives. IST Austria, 2015. https://doi.org/10.15479/AT:IST-2015-322-v1-1."},"oa":1,"page":"25","abstract":[{"lang":"eng","text":"We consider finite-state concurrent stochastic games, played by k>=2 players for an infinite number of rounds, where in every round, each player simultaneously and independently of the other players chooses an action, whereafter the successor state is determined by a probability distribution given by the current state and the chosen actions. We consider reachability objectives that given a target set of states require that some state in the target set is visited, and the dual safety objectives that given a target set require that only states in the target set are visited. We are interested in the complexity of stationary strategies measured by their patience, which is defined as the inverse of the smallest non-zero probability employed.\r\n\r\n Our main results are as follows: We show that in two-player zero-sum concurrent stochastic games (with reachability objective for one player and the complementary safety objective for the other player): (i) the optimal bound on the patience of optimal and epsilon-optimal strategies, for both players is doubly exponential; and (ii) even in games with a single non-absorbing state exponential (in the number of actions) patience is necessary. In general we study the class of non-zero-sum games admitting epsilon-Nash equilibria. We show that if there is at least one player with reachability objective, then doubly-exponential patience is needed in general for epsilon-Nash equilibrium strategies, whereas in contrast if all players have safety objectives, then the optimal bound on patience for epsilon-Nash equilibrium strategies is only exponential."}],"file_date_updated":"2020-07-14T12:46:53Z","type":"technical_report","alternative_title":["IST Austria Technical Report"],"pubrep_id":"322","author":[{"last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"orcid":"0000-0003-4783-0389","id":"3B699956-F248-11E8-B48F-1D18A9856A87","last_name":"Ibsen-Jensen","first_name":"Rasmus","full_name":"Ibsen-Jensen, Rasmus"},{"last_name":"Hansen","first_name":"Kristoffer","full_name":"Hansen, Kristoffer"}],"oa_version":"Published Version","file":[{"file_id":"5491","relation":"main_file","checksum":"bfb858262c30445b8e472c40069178a2","date_created":"2018-12-12T11:53:31Z","date_updated":"2020-07-14T12:46:53Z","access_level":"open_access","file_name":"IST-2015-322-v1+1_safetygames.pdf","creator":"system","content_type":"application/pdf","file_size":661015}],"date_updated":"2021-01-12T08:02:13Z","date_created":"2018-12-12T11:39:17Z","_id":"5431","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2015","department":[{"_id":"KrCh"}],"publisher":"IST Austria","status":"public","title":"The patience of concurrent stochastic games with safety and reachability objectives","publication_status":"published","ddc":["005","519"]},{"file_date_updated":"2020-07-14T12:46:53Z","abstract":[{"lang":"eng","text":"DEC-POMDPs extend POMDPs to a multi-agent setting, where several agents operate in an uncertain environment independently to achieve a joint objective. DEC-POMDPs have been studied with finite-horizon and infinite-horizon discounted-sum objectives, and there exist solvers both for exact and approximate solutions. In this work we consider Goal-DEC-POMDPs, where given a set of target states, the objective is to ensure that the target set is reached with minimal cost. We consider the indefinite-horizon (infinite-horizon with either discounted-sum, or undiscounted-sum, where absorbing goal states have zero-cost) problem. We present a new method to solve the problem that extends methods for finite-horizon DEC- POMDPs and the RTDP-Bel approach for POMDPs. We present experimental results on several examples, and show our approach presents promising results."}],"alternative_title":["IST Austria Technical Report"],"type":"technical_report","file":[{"file_size":378162,"content_type":"application/pdf","creator":"system","file_name":"IST-2015-326-v1+1_main.pdf","access_level":"open_access","date_updated":"2020-07-14T12:46:53Z","date_created":"2018-12-12T11:53:14Z","checksum":"8542fd0b10aed7811cd41077b8ccb632","relation":"main_file","file_id":"5475"},{"file_id":"6317","relation":"main_file","checksum":"84c31c537bdaf7a91909f18d25d640ab","date_created":"2019-04-16T13:00:33Z","date_updated":"2020-07-14T12:46:53Z","access_level":"closed","file_name":"IST-2015-326-v1+2_authors.txt","creator":"dernst","content_type":"text/plain","file_size":64}],"oa_version":"Published Version","date_updated":"2020-07-14T23:04:59Z","date_created":"2018-12-12T11:39:18Z","pubrep_id":"326","author":[{"full_name":"Anonymous, 1","last_name":"Anonymous","first_name":"1"},{"full_name":"Anonymous, 2","last_name":"Anonymous","first_name":"2"}],"publisher":"IST Austria","ddc":["000"],"title":"Optimal cost indefinite-horizon reachability in goal DEC-POMDPs","status":"public","publication_status":"published","year":"2015","_id":"5434","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","publication_identifier":{"issn":["2664-1690"]},"day":"19","month":"02","language":[{"iso":"eng"}],"date_published":"2015-02-19T00:00:00Z","page":"16","oa":1,"citation":{"ista":"Anonymous 1, Anonymous 2. 2015. Optimal cost indefinite-horizon reachability in goal DEC-POMDPs, IST Austria, 16p.","ieee":"1 Anonymous and 2 Anonymous, Optimal cost indefinite-horizon reachability in goal DEC-POMDPs. IST Austria, 2015.","apa":"Anonymous, 1, & Anonymous, 2. (2015). Optimal cost indefinite-horizon reachability in goal DEC-POMDPs. IST Austria.","ama":"Anonymous 1, Anonymous 2. Optimal Cost Indefinite-Horizon Reachability in Goal DEC-POMDPs. IST Austria; 2015.","chicago":"Anonymous, 1, and 2 Anonymous. Optimal Cost Indefinite-Horizon Reachability in Goal DEC-POMDPs. IST Austria, 2015.","mla":"Anonymous, 1, and 2 Anonymous. Optimal Cost Indefinite-Horizon Reachability in Goal DEC-POMDPs. IST Austria, 2015.","short":"1 Anonymous, 2 Anonymous, Optimal Cost Indefinite-Horizon Reachability in Goal DEC-POMDPs, IST Austria, 2015."}},{"oa_version":"None","_id":"1657","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Unifying two views on multiple mean-payoff objectives in Markov decision processes","abstract":[{"text":"We consider Markov decision processes (MDPs) with multiple limit-average (or mean-payoff) objectives. There exist two different views: (i) ~the expectation semantics, where the goal is to optimize the expected mean-payoff objective, and (ii) ~the satisfaction semantics, where the goal is to maximize the probability of runs such that the mean-payoff value stays above a given vector. We consider optimization with respect to both objectives at once, thus unifying the existing semantics. Precisely, the goal is to optimize the expectation while ensuring the satisfaction constraint. Our problem captures the notion of optimization with respect to strategies that are risk-averse (i.e., Ensure certain probabilistic guarantee). Our main results are as follows: First, we present algorithms for the decision problems, which are always polynomial in the size of the MDP. We also show that an approximation of the Pareto curve can be computed in time polynomial in the size of the MDP, and the approximation factor, but exponential in the number of dimensions. Second, we present a complete characterization of the strategy complexity (in terms of memory bounds and randomization) required to solve our problem. ","lang":"eng"}],"type":"conference","alternative_title":["LICS"],"date_published":"2015-07-01T00:00:00Z","citation":{"ama":"Chatterjee K, Komárková Z, Kretinsky J. Unifying two views on multiple mean-payoff objectives in Markov decision processes. 2015:244-256. doi:10.1109/LICS.2015.32","ista":"Chatterjee K, Komárková Z, Kretinsky J. 2015. Unifying two views on multiple mean-payoff objectives in Markov decision processes. , 244–256.","apa":"Chatterjee, K., Komárková, Z., & Kretinsky, J. (2015). Unifying two views on multiple mean-payoff objectives in Markov decision processes. Presented at the LICS: Logic in Computer Science, Kyoto, Japan: IEEE. https://doi.org/10.1109/LICS.2015.32","ieee":"K. Chatterjee, Z. Komárková, and J. Kretinsky, “Unifying two views on multiple mean-payoff objectives in Markov decision processes.” IEEE, pp. 244–256, 2015.","mla":"Chatterjee, Krishnendu, et al. Unifying Two Views on Multiple Mean-Payoff Objectives in Markov Decision Processes. IEEE, 2015, pp. 244–56, doi:10.1109/LICS.2015.32.","short":"K. Chatterjee, Z. Komárková, J. Kretinsky, (2015) 244–256.","chicago":"Chatterjee, Krishnendu, Zuzana Komárková, and Jan Kretinsky. “Unifying Two Views on Multiple Mean-Payoff Objectives in Markov Decision Processes.” LICS. IEEE, 2015. https://doi.org/10.1109/LICS.2015.32."},"page":"244 - 256","day":"01","scopus_import":1,"series_title":"LICS","related_material":{"record":[{"relation":"later_version","status":"public","id":"466"},{"status":"public","relation":"earlier_version","id":"5429"},{"relation":"earlier_version","status":"public","id":"5435"}]},"author":[{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"last_name":"Komárková","first_name":"Zuzana","full_name":"Komárková, Zuzana"},{"full_name":"Kretinsky, Jan","orcid":"0000-0002-8122-2881","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","last_name":"Kretinsky","first_name":"Jan"}],"date_updated":"2023-02-23T12:26:16Z","date_created":"2018-12-11T11:53:18Z","year":"2015","acknowledgement":"A Technical Report of this paper is available at: https://repository.ist.ac.at/327\r\n","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"publisher":"IEEE","publication_status":"published","publist_id":"5493","ec_funded":1,"doi":"10.1109/LICS.2015.32","conference":{"end_date":"2015-07-10","start_date":"2015-07-06","location":"Kyoto, Japan","name":"LICS: Logic in Computer Science"},"language":[{"iso":"eng"}],"project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"name":"The Wittgenstein Prize","call_identifier":"FWF","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","name":"Quantitative Reactive Modeling","call_identifier":"FP7"},{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"quality_controlled":"1","month":"07"},{"scopus_import":1,"day":"31","citation":{"ama":"Chatterjee K, Henzinger TA, Otop J. Nested weighted automata. In: Proceedings - Symposium on Logic in Computer Science. Vol 2015-July. IEEE; 2015. doi:10.1109/LICS.2015.72","ista":"Chatterjee K, Henzinger TA, Otop J. 2015. Nested weighted automata. Proceedings - Symposium on Logic in Computer Science. LICS: Logic in Computer Science vol. 2015–July, 7174926.","ieee":"K. Chatterjee, T. A. Henzinger, and J. Otop, “Nested weighted automata,” in Proceedings - Symposium on Logic in Computer Science, Kyoto, Japan, 2015, vol. 2015–July.","apa":"Chatterjee, K., Henzinger, T. A., & Otop, J. (2015). Nested weighted automata. In Proceedings - Symposium on Logic in Computer Science (Vol. 2015–July). Kyoto, Japan: IEEE. https://doi.org/10.1109/LICS.2015.72","mla":"Chatterjee, Krishnendu, et al. “Nested Weighted Automata.” Proceedings - Symposium on Logic in Computer Science, vol. 2015–July, 7174926, IEEE, 2015, doi:10.1109/LICS.2015.72.","short":"K. Chatterjee, T.A. Henzinger, J. Otop, in:, Proceedings - Symposium on Logic in Computer Science, IEEE, 2015.","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. “Nested Weighted Automata.” In Proceedings - Symposium on Logic in Computer Science, Vol. 2015–July. IEEE, 2015. https://doi.org/10.1109/LICS.2015.72."},"publication":"Proceedings - Symposium on Logic in Computer Science","date_published":"2015-07-31T00:00:00Z","type":"conference","abstract":[{"text":"Recently there has been a significant effort to handle quantitative properties in formal verification and synthesis. While weighted automata over finite and infinite words provide a natural and flexible framework to express quantitative properties, perhaps surprisingly, some basic system properties such as average response time cannot be expressed using weighted automata, nor in any other know decidable formalism. In this work, we introduce nested weighted automata as a natural extension of weighted automata which makes it possible to express important quantitative properties such as average response time. In nested weighted automata, a master automaton spins off and collects results from weighted slave automata, each of which computes a quantity along a finite portion of an infinite word. Nested weighted automata can be viewed as the quantitative analogue of monitor automata, which are used in run-time verification. We establish an almost complete decidability picture for the basic decision problems about nested weighted automata, and illustrate their applicability in several domains. In particular, nested weighted automata can be used to decide average response time properties.","lang":"eng"}],"status":"public","title":"Nested weighted automata","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1656","oa_version":"None","month":"07","project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","name":"Quantitative Reactive Modeling","call_identifier":"FP7"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"name":"The Wittgenstein Prize","call_identifier":"FWF","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"quality_controlled":"1","external_id":{"arxiv":["1606.03598"]},"language":[{"iso":"eng"}],"doi":"10.1109/LICS.2015.72","conference":{"end_date":"2015-07-10","location":"Kyoto, Japan","start_date":"2015-07-06","name":"LICS: Logic in Computer Science"},"article_number":"7174926","ec_funded":1,"publist_id":"5494","publisher":"IEEE","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"publication_status":"published","year":"2015","acknowledgement":"This research was funded in part by the European Research Council (ERC) under grant agreement 267989 (QUAREM), by the Austrian Science Fund (FWF) projects S11402-N23 (RiSE), Z211-N23 (Wittgenstein Award), FWF Grant No P23499- N23, FWF NFN Grant No S11407-N23 (RiSE), ERC Start grant (279307: Graph Games), and Microsoft faculty fellows award.\r\nA Technical Report of the paper is available at: \r\nhttps://repository.ist.ac.at/331/\r\n","volume":"2015-July","date_updated":"2023-02-23T12:26:19Z","date_created":"2018-12-11T11:53:17Z","related_material":{"record":[{"relation":"later_version","status":"public","id":"467"},{"id":"5415","status":"public","relation":"earlier_version"},{"relation":"earlier_version","status":"public","id":"5436"}]},"author":[{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"},{"full_name":"Otop, Jan","first_name":"Jan","last_name":"Otop","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87"}]},{"publication_identifier":{"issn":["2664-1690"]},"has_accepted_license":"1","day":"12","month":"01","citation":{"ama":"Chatterjee K, Komarkova Z, Kretinsky J. Unifying Two Views on Multiple Mean-Payoff Objectives in Markov Decision Processes. IST Austria; 2015. doi:10.15479/AT:IST-2015-318-v1-1","ista":"Chatterjee K, Komarkova Z, Kretinsky J. 2015. Unifying two views on multiple mean-payoff objectives in Markov decision processes, IST Austria, 41p.","apa":"Chatterjee, K., Komarkova, Z., & Kretinsky, J. (2015). Unifying two views on multiple mean-payoff objectives in Markov decision processes. IST Austria. https://doi.org/10.15479/AT:IST-2015-318-v1-1","ieee":"K. Chatterjee, Z. Komarkova, and J. Kretinsky, Unifying two views on multiple mean-payoff objectives in Markov decision processes. IST Austria, 2015.","mla":"Chatterjee, Krishnendu, et al. Unifying Two Views on Multiple Mean-Payoff Objectives in Markov Decision Processes. IST Austria, 2015, doi:10.15479/AT:IST-2015-318-v1-1.","short":"K. Chatterjee, Z. Komarkova, J. Kretinsky, Unifying Two Views on Multiple Mean-Payoff Objectives in Markov Decision Processes, IST Austria, 2015.","chicago":"Chatterjee, Krishnendu, Zuzana Komarkova, and Jan Kretinsky. Unifying Two Views on Multiple Mean-Payoff Objectives in Markov Decision Processes. IST Austria, 2015. https://doi.org/10.15479/AT:IST-2015-318-v1-1."},"oa":1,"page":"41","doi":"10.15479/AT:IST-2015-318-v1-1","date_published":"2015-01-12T00:00:00Z","language":[{"iso":"eng"}],"type":"technical_report","alternative_title":["IST Austria Technical Report"],"file_date_updated":"2020-07-14T12:46:52Z","abstract":[{"lang":"eng","text":"We consider Markov decision processes (MDPs) with multiple limit-average (or mean-payoff) objectives. \r\nThere have been two different views: (i) the expectation semantics, where the goal is to optimize the expected mean-payoff objective, and (ii) the satisfaction semantics, where the goal is to maximize the probability of runs such that the mean-payoff value stays above a given vector. \r\nWe consider the problem where the goal is to optimize the expectation under the constraint that the satisfaction semantics is ensured, and thus consider a generalization that unifies the existing semantics.\r\nOur problem captures the notion of optimization with respect to strategies that are risk-averse (i.e., ensures certain probabilistic guarantee).\r\nOur main results are algorithms for the decision problem which are always polynomial in the size of the MDP. We also show that an approximation of the Pareto-curve can be computed in time polynomial in the size of the MDP, and the approximation factor, but exponential in the number of dimensions.\r\nFinally, we present a complete characterization of the strategy complexity (in terms of memory bounds and randomization) required to solve our problem."}],"year":"2015","_id":"5429","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"KrCh"}],"publisher":"IST Austria","ddc":["004"],"title":"Unifying two views on multiple mean-payoff objectives in Markov decision processes","status":"public","publication_status":"published","related_material":{"record":[{"id":"1657","status":"public","relation":"later_version"},{"status":"public","relation":"later_version","id":"466"},{"relation":"later_version","status":"public","id":"5435"}]},"pubrep_id":"318","author":[{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"full_name":"Komarkova, Zuzana","first_name":"Zuzana","last_name":"Komarkova"},{"orcid":"0000-0002-8122-2881","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","last_name":"Kretinsky","first_name":"Jan","full_name":"Kretinsky, Jan"}],"file":[{"file_id":"5533","relation":"main_file","date_created":"2018-12-12T11:54:11Z","date_updated":"2020-07-14T12:46:52Z","checksum":"e4869a584567c506349abda9c8ec7db3","file_name":"IST-2015-318-v1+1_main.pdf","access_level":"open_access","creator":"system","file_size":689863,"content_type":"application/pdf"}],"oa_version":"Published Version","date_updated":"2023-02-23T12:26:16Z","date_created":"2018-12-12T11:39:17Z"},{"doi":"10.15479/AT:IST-2015-318-v2-1","date_published":"2015-02-23T00:00:00Z","language":[{"iso":"eng"}],"oa":1,"citation":{"chicago":"Chatterjee, Krishnendu, Zuzana Komarkova, and Jan Kretinsky. Unifying Two Views on Multiple Mean-Payoff Objectives in Markov Decision Processes. IST Austria, 2015. https://doi.org/10.15479/AT:IST-2015-318-v2-1.","short":"K. Chatterjee, Z. Komarkova, J. Kretinsky, Unifying Two Views on Multiple Mean-Payoff Objectives in Markov Decision Processes, IST Austria, 2015.","mla":"Chatterjee, Krishnendu, et al. Unifying Two Views on Multiple Mean-Payoff Objectives in Markov Decision Processes. IST Austria, 2015, doi:10.15479/AT:IST-2015-318-v2-1.","ieee":"K. Chatterjee, Z. Komarkova, and J. Kretinsky, Unifying two views on multiple mean-payoff objectives in Markov decision processes. IST Austria, 2015.","apa":"Chatterjee, K., Komarkova, Z., & Kretinsky, J. (2015). Unifying two views on multiple mean-payoff objectives in Markov decision processes. IST Austria. https://doi.org/10.15479/AT:IST-2015-318-v2-1","ista":"Chatterjee K, Komarkova Z, Kretinsky J. 2015. Unifying two views on multiple mean-payoff objectives in Markov decision processes, IST Austria, 51p.","ama":"Chatterjee K, Komarkova Z, Kretinsky J. Unifying Two Views on Multiple Mean-Payoff Objectives in Markov Decision Processes. IST Austria; 2015. doi:10.15479/AT:IST-2015-318-v2-1"},"page":"51","day":"23","month":"02","publication_identifier":{"issn":["2664-1690"]},"has_accepted_license":"1","author":[{"last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"first_name":"Zuzana","last_name":"Komarkova","full_name":"Komarkova, Zuzana"},{"id":"44CEF464-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8122-2881","first_name":"Jan","last_name":"Kretinsky","full_name":"Kretinsky, Jan"}],"related_material":{"record":[{"relation":"later_version","status":"public","id":"1657"},{"id":"466","status":"public","relation":"later_version"},{"id":"5429","relation":"earlier_version","status":"public"}]},"pubrep_id":"327","date_created":"2018-12-12T11:39:19Z","date_updated":"2023-02-23T12:26:00Z","file":[{"checksum":"75284adec80baabdfe71ff9ebbc27445","date_updated":"2020-07-14T12:46:53Z","date_created":"2018-12-12T11:54:03Z","file_id":"5525","relation":"main_file","creator":"system","file_size":717630,"content_type":"application/pdf","access_level":"open_access","file_name":"IST-2015-318-v2+1_main.pdf"}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"5435","year":"2015","ddc":["004"],"title":"Unifying two views on multiple mean-payoff objectives in Markov decision processes","status":"public","publication_status":"published","publisher":"IST Austria","department":[{"_id":"KrCh"}],"abstract":[{"text":"We consider Markov decision processes (MDPs) with multiple limit-average (or mean-payoff) objectives. \r\nThere have been two different views: (i) the expectation semantics, where the goal is to optimize the expected mean-payoff objective, and (ii) the satisfaction semantics, where the goal is to maximize the probability of runs such that the mean-payoff value stays above a given vector. \r\nWe consider the problem where the goal is to optimize the expectation under the constraint that the satisfaction semantics is ensured, and thus consider a generalization that unifies the existing semantics. Our problem captures the notion of optimization with respect to strategies that are risk-averse (i.e., ensures certain probabilistic guarantee).\r\nOur main results are algorithms for the decision problem which are always polynomial in the size of the MDP.\r\nWe also show that an approximation of the Pareto-curve can be computed in time polynomial in the size of the MDP, and the approximation factor, but exponential in the number of dimensions. Finally, we present a complete characterization of the strategy complexity (in terms of memory bounds and randomization) required to solve our problem.","lang":"eng"}],"file_date_updated":"2020-07-14T12:46:53Z","type":"technical_report","alternative_title":["IST Austria Technical Report"]},{"alternative_title":["IST Austria Technical Report"],"type":"technical_report","abstract":[{"text":"Recently there has been a significant effort to handle quantitative properties in formal verification and synthesis. While weighted automata over finite and infinite words provide a natural and flexible framework to express quantitative properties, perhaps surprisingly, some basic system properties such as average response time cannot be expressed using weighted automata, nor in any other know decidable formalism. In this work, we introduce nested weighted automata as a natural extension of weighted automata which makes it possible to express important quantitative properties such as average response time.\r\nIn nested weighted automata, a master automaton spins off and collects results from weighted slave automata, each of which computes a quantity along a finite portion of an infinite word. Nested weighted automata can be viewed as the quantitative analogue of monitor automata, which are used in run-time verification. We establish an almost complete decidability picture for the basic decision problems about nested weighted automata, and illustrate their applicability in several domains. In particular, nested weighted automata can be used to decide average response time properties.","lang":"eng"}],"file_date_updated":"2020-07-14T12:46:54Z","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"publisher":"IST Austria","publication_status":"published","title":"Nested weighted automata","status":"public","ddc":["000"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"5436","year":"2015","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"IST-2015-170-v2+2_report.pdf","file_size":569991,"content_type":"application/pdf","creator":"system","relation":"main_file","file_id":"5541","checksum":"3c402f47d3669c28d04d1af405a08e3f","date_updated":"2020-07-14T12:46:54Z","date_created":"2018-12-12T11:54:19Z"}],"date_updated":"2023-02-23T12:25:21Z","date_created":"2018-12-12T11:39:19Z","related_material":{"record":[{"relation":"later_version","status":"public","id":"1656"},{"id":"467","status":"public","relation":"later_version"},{"id":"5415","relation":"earlier_version","status":"public"}]},"pubrep_id":"331","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"last_name":"Henzinger","first_name":"Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A"},{"full_name":"Otop, Jan","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","last_name":"Otop"}],"has_accepted_license":"1","publication_identifier":{"issn":["2664-1690"]},"day":"24","month":"04","page":"29","oa":1,"citation":{"short":"K. Chatterjee, T.A. Henzinger, J. Otop, Nested Weighted Automata, IST Austria, 2015.","mla":"Chatterjee, Krishnendu, et al. Nested Weighted Automata. IST Austria, 2015, doi:10.15479/AT:IST-2015-170-v2-2.","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. Nested Weighted Automata. IST Austria, 2015. https://doi.org/10.15479/AT:IST-2015-170-v2-2.","ama":"Chatterjee K, Henzinger TA, Otop J. Nested Weighted Automata. IST Austria; 2015. doi:10.15479/AT:IST-2015-170-v2-2","ieee":"K. Chatterjee, T. A. Henzinger, and J. Otop, Nested weighted automata. IST Austria, 2015.","apa":"Chatterjee, K., Henzinger, T. A., & Otop, J. (2015). Nested weighted automata. IST Austria. https://doi.org/10.15479/AT:IST-2015-170-v2-2","ista":"Chatterjee K, Henzinger TA, Otop J. 2015. Nested weighted automata, IST Austria, 29p."},"language":[{"iso":"eng"}],"doi":"10.15479/AT:IST-2015-170-v2-2","date_published":"2015-04-24T00:00:00Z"},{"page":"750 - 761","citation":{"short":"U. Boker, T.A. Henzinger, J. Otop, in:, LICS, IEEE, 2015, pp. 750–761.","mla":"Boker, Udi, et al. “The Target Discounted-Sum Problem.” LICS, IEEE, 2015, pp. 750–61, doi:10.1109/LICS.2015.74.","chicago":"Boker, Udi, Thomas A Henzinger, and Jan Otop. “The Target Discounted-Sum Problem.” In LICS, 750–61. Logic in Computer Science. IEEE, 2015. https://doi.org/10.1109/LICS.2015.74.","ama":"Boker U, Henzinger TA, Otop J. The target discounted-sum problem. In: LICS. Logic in Computer Science. IEEE; 2015:750-761. doi:10.1109/LICS.2015.74","ieee":"U. Boker, T. A. Henzinger, and J. Otop, “The target discounted-sum problem,” in LICS, Kyoto, Japan, 2015, pp. 750–761.","apa":"Boker, U., Henzinger, T. A., & Otop, J. (2015). The target discounted-sum problem. In LICS (pp. 750–761). Kyoto, Japan: IEEE. https://doi.org/10.1109/LICS.2015.74","ista":"Boker U, Henzinger TA, Otop J. 2015. The target discounted-sum problem. LICS. LICS: Logic in Computer ScienceLogic in Computer Science, 750–761."},"publication":"LICS","date_published":"2015-07-01T00:00:00Z","series_title":"Logic in Computer Science","scopus_import":1,"has_accepted_license":"1","article_processing_charge":"No","day":"01","status":"public","title":"The target discounted-sum problem","ddc":["000"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1659","oa_version":"Submitted Version","file":[{"file_size":340215,"content_type":"application/pdf","creator":"dernst","file_name":"2015_LICS_Boker.pdf","access_level":"open_access","date_updated":"2020-07-14T12:45:10Z","date_created":"2020-05-15T08:53:29Z","checksum":"6abebca9c1a620e9e103a8f9222befac","relation":"main_file","file_id":"7852"}],"type":"conference","abstract":[{"text":"The target discounted-sum problem is the following: Given a rational discount factor 0 < λ < 1 and three rational values a, b, and t, does there exist a finite or an infinite sequence w ε(a, b)∗ or w ε(a, b)w, such that Σ|w| i=0 w(i)λi equals t? The problem turns out to relate to many fields of mathematics and computer science, and its decidability question is surprisingly hard to solve. We solve the finite version of the problem, and show the hardness of the infinite version, linking it to various areas and open problems in mathematics and computer science: β-expansions, discounted-sum automata, piecewise affine maps, and generalizations of the Cantor set. We provide some partial results to the infinite version, among which are solutions to its restriction to eventually-periodic sequences and to the cases that λ λ 1/2 or λ = 1/n, for every n ε N. We use our results for solving some open problems on discounted-sum automata, among which are the exact-value problem for nondeterministic automata over finite words and the universality and inclusion problems for functional automata.","lang":"eng"}],"project":[{"name":"Quantitative Reactive Modeling","call_identifier":"FP7","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"name":"The Wittgenstein Prize","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211"}],"quality_controlled":"1","oa":1,"language":[{"iso":"eng"}],"doi":"10.1109/LICS.2015.74","conference":{"name":"LICS: Logic in Computer Science","start_date":"2015-007-06","location":"Kyoto, Japan","end_date":"2015-07-10"},"publication_identifier":{"eisbn":["978-1-4799-8875-4 "],"issn":["1043-6871 "]},"month":"07","department":[{"_id":"ToHe"}],"publisher":"IEEE","publication_status":"published","year":"2015","acknowledgement":"A technical report of the article is available at: https://research-explorer.app.ist.ac.at/record/5439","date_updated":"2023-02-23T12:26:27Z","date_created":"2018-12-11T11:53:19Z","related_material":{"record":[{"id":"5439","status":"public","relation":"earlier_version"}]},"author":[{"id":"31E297B6-F248-11E8-B48F-1D18A9856A87","first_name":"Udi","last_name":"Boker","full_name":"Boker, Udi"},{"first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"},{"first_name":"Jan","last_name":"Otop","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","full_name":"Otop, Jan"}],"ec_funded":1,"publist_id":"5491","file_date_updated":"2020-07-14T12:45:10Z"},{"quality_controlled":"1","project":[{"grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","call_identifier":"FP7"},{"call_identifier":"FWF","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211"},{"call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23"},{"name":"Game Theory","call_identifier":"FWF","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1504.08259"}],"oa":1,"external_id":{"arxiv":["1504.08259"]},"language":[{"iso":"eng"}],"conference":{"end_date":"2015-07-10","location":"Kyoto, Japan","start_date":"2015-07-06","name":"ICALP: Automata, Languages and Programming"},"doi":"10.1007/978-3-662-47666-6_10","month":"07","publication_identifier":{"isbn":["978-3-662-47665-9"]},"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"year":"2015","date_created":"2018-12-11T11:53:01Z","date_updated":"2023-02-23T12:26:24Z","volume":9135,"author":[{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","first_name":"Thomas A","last_name":"Henzinger"},{"full_name":"Ibsen-Jensen, Rasmus","first_name":"Rasmus","last_name":"Ibsen-Jensen","id":"3B699956-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4783-0389"},{"id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","last_name":"Otop","full_name":"Otop, Jan"}],"related_material":{"record":[{"id":"465","status":"public","relation":"later_version"},{"relation":"earlier_version","status":"public","id":"5438"}]},"ec_funded":1,"publist_id":"5556","page":"121 - 133","publication":"42nd International Colloquium","citation":{"mla":"Chatterjee, Krishnendu, et al. “Edit Distance for Pushdown Automata.” 42nd International Colloquium, vol. 9135, no. Part II, Springer Nature, 2015, pp. 121–33, doi:10.1007/978-3-662-47666-6_10.","short":"K. Chatterjee, T.A. Henzinger, R. Ibsen-Jensen, J. Otop, in:, 42nd International Colloquium, Springer Nature, 2015, pp. 121–133.","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, Rasmus Ibsen-Jensen, and Jan Otop. “Edit Distance for Pushdown Automata.” In 42nd International Colloquium, 9135:121–33. Springer Nature, 2015. https://doi.org/10.1007/978-3-662-47666-6_10.","ama":"Chatterjee K, Henzinger TA, Ibsen-Jensen R, Otop J. Edit distance for pushdown automata. In: 42nd International Colloquium. Vol 9135. Springer Nature; 2015:121-133. doi:10.1007/978-3-662-47666-6_10","ista":"Chatterjee K, Henzinger TA, Ibsen-Jensen R, Otop J. 2015. Edit distance for pushdown automata. 42nd International Colloquium. ICALP: Automata, Languages and Programming, LNCS, vol. 9135, 121–133.","apa":"Chatterjee, K., Henzinger, T. A., Ibsen-Jensen, R., & Otop, J. (2015). Edit distance for pushdown automata. In 42nd International Colloquium (Vol. 9135, pp. 121–133). Kyoto, Japan: Springer Nature. https://doi.org/10.1007/978-3-662-47666-6_10","ieee":"K. Chatterjee, T. A. Henzinger, R. Ibsen-Jensen, and J. Otop, “Edit distance for pushdown automata,” in 42nd International Colloquium, Kyoto, Japan, 2015, vol. 9135, no. Part II, pp. 121–133."},"date_published":"2015-07-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","status":"public","title":"Edit distance for pushdown automata","intvolume":" 9135","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"1610","oa_version":"None","pubrep_id":"321","alternative_title":["LNCS"],"type":"conference","abstract":[{"lang":"eng","text":"The edit distance between two words w1, w2 is the minimal number of word operations (letter insertions, deletions, and substitutions) necessary to transform w1 to w2. The edit distance generalizes to languages L1,L2, where the edit distance is the minimal number k such that for every word from L1 there exists a word in L2 with edit distance at most k. We study the edit distance computation problem between pushdown automata and their subclasses. The problem of computing edit distance to pushdown automata is undecidable, and in practice, the interesting question is to compute the edit distance from a pushdown automaton (the implementation, a standard model for programs with recursion) to a regular language (the specification). In this work, we present a complete picture of decidability and complexity for deciding whether, for a given threshold k, the edit distance from a pushdown automaton to a finite automaton is at most k."}],"issue":"Part II"},{"alternative_title":["IST Austria Technical Report"],"type":"technical_report","file_date_updated":"2020-07-14T12:46:54Z","abstract":[{"text":"We consider the core algorithmic problems related to verification of systems with respect to three classical quantitative properties, namely, the mean-payoff property, the ratio property, and the minimum initial credit for energy property. \r\nThe algorithmic problem given a graph and a quantitative property asks to compute the optimal value (the infimum value over all traces) from every node of the graph. We consider graphs with constant treewidth, and it is well-known that the control-flow graphs of most programs have constant treewidth. Let $n$ denote the number of nodes of a graph, $m$ the number of edges (for constant treewidth graphs $m=O(n)$) and $W$ the largest absolute value of the weights.\r\nOur main theoretical results are as follows.\r\nFirst, for constant treewidth graphs we present an algorithm that approximates the mean-payoff value within a multiplicative factor of $\\epsilon$ in time $O(n \\cdot \\log (n/\\epsilon))$ and linear space, as compared to the classical algorithms that require quadratic time. Second, for the ratio property we present an algorithm that for constant treewidth graphs works in time $O(n \\cdot \\log (|a\\cdot b|))=O(n\\cdot\\log (n\\cdot W))$, when the output is $\\frac{a}{b}$, as compared to the previously best known algorithm with running time $O(n^2 \\cdot \\log (n\\cdot W))$. Third, for the minimum initial credit problem we show that (i)~for general graphs the problem can be solved in $O(n^2\\cdot m)$ time and the associated decision problem can be solved in $O(n\\cdot m)$ time, improving the previous known $O(n^3\\cdot m\\cdot \\log (n\\cdot W))$ and $O(n^2 \\cdot m)$ bounds, respectively; and (ii)~for constant treewidth graphs we present an algorithm that requires $O(n\\cdot \\log n)$ time, improving the previous known $O(n^4 \\cdot \\log (n \\cdot W))$ bound.\r\nWe have implemented some of our algorithms and show that they present a significant speedup on standard benchmarks. ","lang":"eng"}],"publisher":"IST Austria","department":[{"_id":"KrCh"}],"ddc":["000"],"title":"Faster algorithms for quantitative verification in constant treewidth graphs","status":"public","publication_status":"published","_id":"5437","year":"2015","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"access_level":"open_access","file_name":"IST-2015-330-v2+1_main.pdf","creator":"system","content_type":"application/pdf","file_size":1072137,"file_id":"5473","relation":"main_file","checksum":"f5917c20f84018b362d385c000a2e123","date_updated":"2020-07-14T12:46:54Z","date_created":"2018-12-12T11:53:12Z"}],"oa_version":"Published Version","date_created":"2018-12-12T11:39:19Z","date_updated":"2023-02-23T12:26:05Z","pubrep_id":"333","related_material":{"record":[{"id":"1607","relation":"later_version","status":"public"},{"relation":"earlier_version","status":"public","id":"5430"}]},"author":[{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"id":"3B699956-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4783-0389","first_name":"Rasmus","last_name":"Ibsen-Jensen","full_name":"Ibsen-Jensen, Rasmus"},{"last_name":"Pavlogiannis","first_name":"Andreas","orcid":"0000-0002-8943-0722","id":"49704004-F248-11E8-B48F-1D18A9856A87","full_name":"Pavlogiannis, Andreas"}],"has_accepted_license":"1","publication_identifier":{"issn":["2664-1690"]},"day":"27","month":"04","page":"27","citation":{"apa":"Chatterjee, K., Ibsen-Jensen, R., & Pavlogiannis, A. (2015). Faster algorithms for quantitative verification in constant treewidth graphs. IST Austria. https://doi.org/10.15479/AT:IST-2015-330-v2-1","ieee":"K. Chatterjee, R. Ibsen-Jensen, and A. Pavlogiannis, Faster algorithms for quantitative verification in constant treewidth graphs. IST Austria, 2015.","ista":"Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. 2015. Faster algorithms for quantitative verification in constant treewidth graphs, IST Austria, 27p.","ama":"Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. Faster Algorithms for Quantitative Verification in Constant Treewidth Graphs. IST Austria; 2015. doi:10.15479/AT:IST-2015-330-v2-1","chicago":"Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Andreas Pavlogiannis. Faster Algorithms for Quantitative Verification in Constant Treewidth Graphs. IST Austria, 2015. https://doi.org/10.15479/AT:IST-2015-330-v2-1.","short":"K. Chatterjee, R. Ibsen-Jensen, A. Pavlogiannis, Faster Algorithms for Quantitative Verification in Constant Treewidth Graphs, IST Austria, 2015.","mla":"Chatterjee, Krishnendu, et al. Faster Algorithms for Quantitative Verification in Constant Treewidth Graphs. IST Austria, 2015, doi:10.15479/AT:IST-2015-330-v2-1."},"oa":1,"language":[{"iso":"eng"}],"doi":"10.15479/AT:IST-2015-330-v2-1","date_published":"2015-04-27T00:00:00Z"},{"_id":"5430","year":"2015","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","ddc":["000"],"status":"public","title":"Faster algorithms for quantitative verification in constant treewidth graphs","department":[{"_id":"KrCh"}],"publisher":"IST Austria","author":[{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee"},{"full_name":"Ibsen-Jensen, Rasmus","id":"3B699956-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4783-0389","first_name":"Rasmus","last_name":"Ibsen-Jensen"},{"full_name":"Pavlogiannis, Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8943-0722","first_name":"Andreas","last_name":"Pavlogiannis"}],"pubrep_id":"319","related_material":{"record":[{"id":"1607","relation":"later_version","status":"public"},{"id":"5437","relation":"later_version","status":"public"}]},"date_created":"2018-12-12T11:39:17Z","date_updated":"2023-02-23T12:26:22Z","file":[{"content_type":"application/pdf","file_size":1089651,"creator":"system","file_name":"IST-2015-319-v1+1_long.pdf","access_level":"open_access","date_updated":"2020-07-14T12:46:52Z","date_created":"2018-12-12T11:53:21Z","checksum":"62c6ea01e342553dcafb88a070fb1ad5","relation":"main_file","file_id":"5482"}],"oa_version":"Published Version","type":"technical_report","alternative_title":["IST Austria Technical Report"],"file_date_updated":"2020-07-14T12:46:52Z","abstract":[{"text":"We consider the core algorithmic problems related to verification of systems with respect to three classical quantitative properties, namely, the mean- payoff property, the ratio property, and the minimum initial credit for energy property. The algorithmic problem given a graph and a quantitative property asks to compute the optimal value (the infimum value over all traces) from every node of the graph. We consider graphs with constant treewidth, and it is well-known that the control-flow graphs of most programs have constant treewidth. Let n denote the number of nodes of a graph, m the number of edges (for constant treewidth graphs m = O ( n ) ) and W the largest absolute value of the weights. Our main theoretical results are as follows. First, for constant treewidth graphs we present an algorithm that approximates the mean-payoff value within a mul- tiplicative factor of ∊ in time O ( n · log( n/∊ )) and linear space, as compared to the classical algorithms that require quadratic time. Second, for the ratio property we present an algorithm that for constant treewidth graphs works in time O ( n · log( | a · b · n | )) = O ( n · log( n · W )) , when the output is a b , as compared to the previously best known algorithm with running time O ( n 2 · log( n · W )) . Third, for the minimum initial credit problem we show that (i) for general graphs the problem can be solved in O ( n 2 · m ) time and the associated decision problem can be solved in O ( n · m ) time, improving the previous known O ( n 3 · m · log( n · W )) and O ( n 2 · m ) bounds, respectively; and (ii) for constant treewidth graphs we present an algorithm that requires O ( n · log n ) time, improving the previous known O ( n 4 · log( n · W )) bound. We have implemented some of our algorithms and show that they present a significant speedup on standard benchmarks.","lang":"eng"}],"citation":{"ama":"Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. Faster Algorithms for Quantitative Verification in Constant Treewidth Graphs. IST Austria; 2015. doi:10.15479/AT:IST-2015-319-v1-1","apa":"Chatterjee, K., Ibsen-Jensen, R., & Pavlogiannis, A. (2015). Faster algorithms for quantitative verification in constant treewidth graphs. IST Austria. https://doi.org/10.15479/AT:IST-2015-319-v1-1","ieee":"K. Chatterjee, R. Ibsen-Jensen, and A. Pavlogiannis, Faster algorithms for quantitative verification in constant treewidth graphs. IST Austria, 2015.","ista":"Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. 2015. Faster algorithms for quantitative verification in constant treewidth graphs, IST Austria, 31p.","short":"K. Chatterjee, R. Ibsen-Jensen, A. Pavlogiannis, Faster Algorithms for Quantitative Verification in Constant Treewidth Graphs, IST Austria, 2015.","mla":"Chatterjee, Krishnendu, et al. Faster Algorithms for Quantitative Verification in Constant Treewidth Graphs. IST Austria, 2015, doi:10.15479/AT:IST-2015-319-v1-1.","chicago":"Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Andreas Pavlogiannis. Faster Algorithms for Quantitative Verification in Constant Treewidth Graphs. IST Austria, 2015. https://doi.org/10.15479/AT:IST-2015-319-v1-1."},"oa":1,"page":"31","doi":"10.15479/AT:IST-2015-319-v1-1","date_published":"2015-02-10T00:00:00Z","language":[{"iso":"eng"}],"month":"02","day":"10","has_accepted_license":"1","publication_identifier":{"issn":["2664-1690"]}},{"publication_status":"published","status":"public","ddc":["004","512","513"],"title":"The target discounted-sum problem","department":[{"_id":"ToHe"}],"publisher":"IST Austria","year":"2015","_id":"5439","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-12T11:39:20Z","date_updated":"2023-02-23T10:08:48Z","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"5517","date_updated":"2020-07-14T12:46:55Z","date_created":"2018-12-12T11:53:55Z","checksum":"40405907aa012acece1bc26cf0be554d","file_name":"IST-2015-335-v1+1_report.pdf","access_level":"open_access","content_type":"application/pdf","file_size":589619,"creator":"system"}],"author":[{"first_name":"Udi","last_name":"Boker","id":"31E297B6-F248-11E8-B48F-1D18A9856A87","full_name":"Boker, Udi"},{"full_name":"Henzinger, Thomas A","first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724"},{"full_name":"Otop, Jan","last_name":"Otop","first_name":"Jan","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"id":"1659","status":"public","relation":"later_version"}]},"pubrep_id":"335","alternative_title":["IST Austria Technical Report"],"type":"technical_report","abstract":[{"lang":"eng","text":"The target discounted-sum problem is the following: Given a rational discount factor 0 < λ < 1 and three rational values a, b, and t, does there exist a finite or an infinite sequence w ε(a, b)∗ or w ε(a, b)w, such that Σ|w| i=0 w(i)λi equals t? The problem turns out to relate to many fields of mathematics and computer science, and its decidability question is surprisingly hard to solve. We solve the finite version of the problem, and show the hardness of the infinite version, linking it to various areas and open problems in mathematics and computer science: β-expansions, discounted-sum automata, piecewise affine maps, and generalizations of the Cantor set. We provide some partial results to the infinite version, among which are solutions to its restriction to eventually-periodic sequences and to the cases that λ λ 1/2 or λ = 1/n, for every n ε N. We use our results for solving some open problems on discounted-sum automata, among which are the exact-value problem for nondeterministic automata over finite words and the universality and inclusion problems for functional automata. "}],"file_date_updated":"2020-07-14T12:46:55Z","page":"20","oa":1,"citation":{"ama":"Boker U, Henzinger TA, Otop J. The Target Discounted-Sum Problem. IST Austria; 2015. doi:10.15479/AT:IST-2015-335-v1-1","apa":"Boker, U., Henzinger, T. A., & Otop, J. (2015). The target discounted-sum problem. IST Austria. https://doi.org/10.15479/AT:IST-2015-335-v1-1","ieee":"U. Boker, T. A. Henzinger, and J. Otop, The target discounted-sum problem. IST Austria, 2015.","ista":"Boker U, Henzinger TA, Otop J. 2015. The target discounted-sum problem, IST Austria, 20p.","short":"U. Boker, T.A. Henzinger, J. Otop, The Target Discounted-Sum Problem, IST Austria, 2015.","mla":"Boker, Udi, et al. The Target Discounted-Sum Problem. IST Austria, 2015, doi:10.15479/AT:IST-2015-335-v1-1.","chicago":"Boker, Udi, Thomas A Henzinger, and Jan Otop. The Target Discounted-Sum Problem. IST Austria, 2015. https://doi.org/10.15479/AT:IST-2015-335-v1-1."},"language":[{"iso":"eng"}],"doi":"10.15479/AT:IST-2015-335-v1-1","date_published":"2015-05-18T00:00:00Z","month":"05","day":"18","publication_identifier":{"issn":["2664-1690"]},"has_accepted_license":"1"},{"day":"05","month":"05","has_accepted_license":"1","publication_identifier":{"issn":["2664-1690"]},"language":[{"iso":"eng"}],"date_published":"2015-05-05T00:00:00Z","doi":"10.15479/AT:IST-2015-334-v1-1","page":"15","citation":{"chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, Rasmus Ibsen-Jensen, and Jan Otop. Edit Distance for Pushdown Automata. IST Austria, 2015. https://doi.org/10.15479/AT:IST-2015-334-v1-1.","mla":"Chatterjee, Krishnendu, et al. Edit Distance for Pushdown Automata. IST Austria, 2015, doi:10.15479/AT:IST-2015-334-v1-1.","short":"K. Chatterjee, T.A. Henzinger, R. Ibsen-Jensen, J. Otop, Edit Distance for Pushdown Automata, IST Austria, 2015.","ista":"Chatterjee K, Henzinger TA, Ibsen-Jensen R, Otop J. 2015. Edit distance for pushdown automata, IST Austria, 15p.","apa":"Chatterjee, K., Henzinger, T. A., Ibsen-Jensen, R., & Otop, J. (2015). Edit distance for pushdown automata. IST Austria. https://doi.org/10.15479/AT:IST-2015-334-v1-1","ieee":"K. Chatterjee, T. A. Henzinger, R. Ibsen-Jensen, and J. Otop, Edit distance for pushdown automata. IST Austria, 2015.","ama":"Chatterjee K, Henzinger TA, Ibsen-Jensen R, Otop J. Edit Distance for Pushdown Automata. IST Austria; 2015. doi:10.15479/AT:IST-2015-334-v1-1"},"oa":1,"abstract":[{"lang":"eng","text":"The edit distance between two words w1, w2 is the minimal number of word operations (letter insertions, deletions, and substitutions) necessary to transform w1 to w2. The edit distance generalizes to languages L1, L2, where the edit distance is the minimal number k such that for every word from L1 there exists a word in L2 with edit distance at most k. We study the edit distance computation problem between pushdown automata and their subclasses.\r\nThe problem of computing edit distance to a pushdown automaton is undecidable, and in practice, the interesting question is to compute the edit distance from a pushdown automaton (the implementation, a standard model for programs with recursion) to a regular language (the specification). In this work, we present a complete picture of decidability and complexity for deciding whether, for a given threshold k, the edit distance from a pushdown automaton to a finite automaton is at most k. "}],"file_date_updated":"2020-07-14T12:46:55Z","alternative_title":["IST Austria Technical Report"],"type":"technical_report","date_created":"2018-12-12T11:39:20Z","date_updated":"2023-02-23T12:20:08Z","oa_version":"Published Version","file":[{"file_id":"5518","relation":"main_file","checksum":"8a5f2d77560e552af87eb1982437a43b","date_updated":"2020-07-14T12:46:55Z","date_created":"2018-12-12T11:53:56Z","access_level":"open_access","file_name":"IST-2015-334-v1+1_report.pdf","creator":"system","content_type":"application/pdf","file_size":422573}],"author":[{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A"},{"full_name":"Ibsen-Jensen, Rasmus","last_name":"Ibsen-Jensen","first_name":"Rasmus","orcid":"0000-0003-4783-0389","id":"3B699956-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Otop, Jan","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","last_name":"Otop","first_name":"Jan"}],"related_material":{"record":[{"id":"1610","relation":"later_version","status":"public"},{"relation":"later_version","status":"public","id":"465"}]},"pubrep_id":"334","status":"public","title":"Edit distance for pushdown automata","publication_status":"published","ddc":["004"],"publisher":"IST Austria","department":[{"_id":"KrCh"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"5438","year":"2015"},{"type":"technical_report","alternative_title":["IST Austria Technical Report"],"abstract":[{"text":"Evolution occurs in populations of reproducing individuals. The structure of the population affects the outcome of the evolutionary process. Evolutionary graph theory is a powerful approach to study this phenomenon. There are two graphs. The interaction graph specifies who interacts with whom for payoff in the context of evolution. The replacement graph specifies who competes with whom for reproduction. The vertices of the two graphs are the same, and each vertex corresponds to an individual of the population. The fitness (or the reproductive rate) is a non-negative number, and depends on the payoff. A key quantity is the fixation probability of a new mutant. It is defined as the probability that a newly introduced mutant (on a single vertex) generates a lineage of offspring which eventually takes over the entire population of resident individuals. The basic computational questions are as follows: (i) the qualitative question asks whether the fixation probability is positive; and (ii) the quantitative approximation question asks for an approximation of the fixation probability. Our main results are as follows: First, we consider a special case of the general problem, where the residents do not reproduce. We show that the qualitative question is NP-complete, and the quantitative approximation question is #P-complete, and the hardness results hold even in the special case where the interaction and the replacement graphs coincide. Second, we show that in general both the qualitative and the quantitative approximation questions are PSPACE-complete. The PSPACE-hardness result for quantitative approximation holds even when the fitness is always positive.","lang":"eng"}],"file_date_updated":"2020-07-14T12:46:56Z","_id":"5440","year":"2015","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"KrCh"}],"publisher":"IST Austria","publication_status":"published","ddc":["005","576"],"status":"public","title":"The complexity of evolutionary games on graphs","pubrep_id":"338","related_material":{"record":[{"id":"5421","status":"public","relation":"earlier_version"},{"id":"5432","status":"public","relation":"earlier_version"}]},"author":[{"first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"full_name":"Ibsen-Jensen, Rasmus","last_name":"Ibsen-Jensen","first_name":"Rasmus","orcid":"0000-0003-4783-0389","id":"3B699956-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Nowak, Martin","last_name":"Nowak","first_name":"Martin"}],"oa_version":"Published Version","file":[{"file_name":"IST-2015-323-v2+2_main.pdf","access_level":"open_access","file_size":466161,"content_type":"application/pdf","creator":"system","relation":"main_file","file_id":"5484","date_created":"2018-12-12T11:53:23Z","date_updated":"2020-07-14T12:46:56Z","checksum":"66aace7d367032af97c15e35c9be9636"}],"date_created":"2018-12-12T11:39:21Z","date_updated":"2023-02-23T12:26:10Z","publication_identifier":{"issn":["2664-1690"]},"has_accepted_license":"1","day":"16","month":"06","citation":{"chicago":"Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Martin Nowak. The Complexity of Evolutionary Games on Graphs. IST Austria, 2015. https://doi.org/10.15479/AT:IST-2015-323-v2-2.","short":"K. Chatterjee, R. Ibsen-Jensen, M. Nowak, The Complexity of Evolutionary Games on Graphs, IST Austria, 2015.","mla":"Chatterjee, Krishnendu, et al. The Complexity of Evolutionary Games on Graphs. IST Austria, 2015, doi:10.15479/AT:IST-2015-323-v2-2.","ieee":"K. Chatterjee, R. Ibsen-Jensen, and M. Nowak, The complexity of evolutionary games on graphs. IST Austria, 2015.","apa":"Chatterjee, K., Ibsen-Jensen, R., & Nowak, M. (2015). The complexity of evolutionary games on graphs. IST Austria. https://doi.org/10.15479/AT:IST-2015-323-v2-2","ista":"Chatterjee K, Ibsen-Jensen R, Nowak M. 2015. The complexity of evolutionary games on graphs, IST Austria, 18p.","ama":"Chatterjee K, Ibsen-Jensen R, Nowak M. The Complexity of Evolutionary Games on Graphs. IST Austria; 2015. doi:10.15479/AT:IST-2015-323-v2-2"},"oa":1,"page":"18","date_published":"2015-06-16T00:00:00Z","doi":"10.15479/AT:IST-2015-323-v2-2","language":[{"iso":"eng"}]},{"page":"29","citation":{"ama":"Chatterjee K, Ibsen-Jensen R, Nowak M. The Complexity of Evolutionary Games on Graphs. IST Austria; 2015. doi:10.15479/AT:IST-2015-323-v1-1","ista":"Chatterjee K, Ibsen-Jensen R, Nowak M. 2015. The complexity of evolutionary games on graphs, IST Austria, 29p.","apa":"Chatterjee, K., Ibsen-Jensen, R., & Nowak, M. (2015). The complexity of evolutionary games on graphs. IST Austria. https://doi.org/10.15479/AT:IST-2015-323-v1-1","ieee":"K. Chatterjee, R. Ibsen-Jensen, and M. Nowak, The complexity of evolutionary games on graphs. IST Austria, 2015.","mla":"Chatterjee, Krishnendu, et al. The Complexity of Evolutionary Games on Graphs. IST Austria, 2015, doi:10.15479/AT:IST-2015-323-v1-1.","short":"K. Chatterjee, R. Ibsen-Jensen, M. Nowak, The Complexity of Evolutionary Games on Graphs, IST Austria, 2015.","chicago":"Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Martin Nowak. The Complexity of Evolutionary Games on Graphs. IST Austria, 2015. https://doi.org/10.15479/AT:IST-2015-323-v1-1."},"oa":1,"language":[{"iso":"eng"}],"doi":"10.15479/AT:IST-2015-323-v1-1","date_published":"2015-02-19T00:00:00Z","has_accepted_license":"1","publication_identifier":{"issn":["2664-1690"]},"day":"19","month":"02","department":[{"_id":"KrCh"}],"publisher":"IST Austria","title":"The complexity of evolutionary games on graphs","status":"public","ddc":["005","576"],"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"5432","year":"2015","oa_version":"Published Version","file":[{"file_name":"IST-2015-323-v1+1_main.pdf","access_level":"open_access","creator":"system","content_type":"application/pdf","file_size":576347,"file_id":"5519","relation":"main_file","date_created":"2018-12-12T11:53:57Z","date_updated":"2020-07-14T12:46:53Z","checksum":"546c1b291d545e7b24aaaf4199dac671"}],"date_updated":"2023-02-23T12:26:33Z","date_created":"2018-12-12T11:39:18Z","pubrep_id":"323","related_material":{"record":[{"status":"public","relation":"earlier_version","id":"5421"},{"id":"5440","relation":"later_version","status":"public"}]},"author":[{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-4783-0389","id":"3B699956-F248-11E8-B48F-1D18A9856A87","last_name":"Ibsen-Jensen","first_name":"Rasmus","full_name":"Ibsen-Jensen, Rasmus"},{"last_name":"Nowak","first_name":"Martin","full_name":"Nowak, Martin"}],"alternative_title":["IST Austria Technical Report"],"type":"technical_report","abstract":[{"text":"Evolution occurs in populations of reproducing individuals. The structure of the population affects the outcome of the evolutionary process. Evolutionary graph theory is a powerful approach to study this phenomenon. There are two graphs. The interaction graph specifies who interacts with whom in the context of evolution.The replacement graph specifies who competes with whom for reproduction. \r\nThe vertices of the two graphs are the same, and each vertex corresponds to an individual of the population. A key quantity is the fixation probability of a new mutant. It is defined as the probability that a newly introduced mutant (on a single vertex) generates a lineage of offspring which eventually takes over the entire population of resident individuals. The basic computational questions are as follows: (i) the qualitative question asks whether the fixation probability is positive; and (ii) the quantitative approximation question asks for an approximation of the fixation probability. \r\nOur main results are:\r\n(1) We show that the qualitative question is NP-complete and the quantitative approximation question is #P-hard in the special case when the interaction and the replacement graphs coincide and even with the restriction that the resident individuals do not reproduce (which corresponds to an invading population taking over an empty structure).\r\n(2) We show that in general the qualitative question is PSPACE-complete and the quantitative approximation question is PSPACE-hard and can be solved in exponential time.\r\n","lang":"eng"}],"file_date_updated":"2020-07-14T12:46:53Z"},{"date_published":"2015-12-30T00:00:00Z","doi":"10.15479/AT:IST-2015-399-v1-1","language":[{"iso":"eng"}],"citation":{"ama":"Reiter J, Makohon-Moore A, Gerold J, et al. Reconstructing Robust Phylogenies of Metastatic Cancers. IST Austria; 2015. doi:10.15479/AT:IST-2015-399-v1-1","ieee":"J. Reiter et al., Reconstructing robust phylogenies of metastatic cancers. IST Austria, 2015.","apa":"Reiter, J., Makohon-Moore, A., Gerold, J., Bozic, I., Chatterjee, K., Iacobuzio-Donahue, C., … Nowak, M. (2015). Reconstructing robust phylogenies of metastatic cancers. IST Austria. https://doi.org/10.15479/AT:IST-2015-399-v1-1","ista":"Reiter J, Makohon-Moore A, Gerold J, Bozic I, Chatterjee K, Iacobuzio-Donahue C, Vogelstein B, Nowak M. 2015. Reconstructing robust phylogenies of metastatic cancers, IST Austria, 25p.","short":"J. Reiter, A. Makohon-Moore, J. Gerold, I. Bozic, K. Chatterjee, C. Iacobuzio-Donahue, B. Vogelstein, M. Nowak, Reconstructing Robust Phylogenies of Metastatic Cancers, IST Austria, 2015.","mla":"Reiter, Johannes, et al. Reconstructing Robust Phylogenies of Metastatic Cancers. IST Austria, 2015, doi:10.15479/AT:IST-2015-399-v1-1.","chicago":"Reiter, Johannes, Alvin Makohon-Moore, Jeffrey Gerold, Ivana Bozic, Krishnendu Chatterjee, Christine Iacobuzio-Donahue, Bert Vogelstein, and Martin Nowak. Reconstructing Robust Phylogenies of Metastatic Cancers. IST Austria, 2015. https://doi.org/10.15479/AT:IST-2015-399-v1-1."},"oa":1,"page":"25","month":"12","day":"30","publication_identifier":{"issn":["2664-1690"]},"has_accepted_license":"1","author":[{"full_name":"Reiter, Johannes","first_name":"Johannes","last_name":"Reiter","id":"4A918E98-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0170-7353"},{"full_name":"Makohon-Moore, Alvin","last_name":"Makohon-Moore","first_name":"Alvin"},{"full_name":"Gerold, Jeffrey","last_name":"Gerold","first_name":"Jeffrey"},{"full_name":"Bozic, Ivana","first_name":"Ivana","last_name":"Bozic"},{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"},{"full_name":"Iacobuzio-Donahue, Christine","last_name":"Iacobuzio-Donahue","first_name":"Christine"},{"full_name":"Vogelstein, Bert","last_name":"Vogelstein","first_name":"Bert"},{"first_name":"Martin","last_name":"Nowak","full_name":"Nowak, Martin"}],"pubrep_id":"399","date_updated":"2020-07-14T23:05:07Z","date_created":"2018-12-12T11:39:22Z","file":[{"file_id":"5485","relation":"main_file","checksum":"c47d33bdda06181753c0af36f16e7b5d","date_created":"2018-12-12T11:53:24Z","date_updated":"2020-07-14T12:46:58Z","access_level":"open_access","file_name":"IST-2015-399-v1+1_treeomics.pdf","creator":"system","file_size":3533200,"content_type":"application/pdf"}],"oa_version":"Published Version","_id":"5444","year":"2015","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","publication_status":"published","title":"Reconstructing robust phylogenies of metastatic cancers","ddc":["000","576"],"publisher":"IST Austria","department":[{"_id":"KrCh"}],"abstract":[{"lang":"eng","text":"A comprehensive understanding of the clonal evolution of cancer is critical for understanding neoplasia. Genome-wide sequencing data enables evolutionary studies at unprecedented depth. However, classical phylogenetic methods often struggle with noisy sequencing data of impure DNA samples and fail to detect subclones that have different evolutionary trajectories. We have developed a tool, called Treeomics, that allows us to reconstruct the phylogeny of a cancer with commonly available sequencing technologies. Using Bayesian inference and Integer Linear Programming, robust phylogenies consistent with the biological processes underlying cancer evolution were obtained for pancreatic, ovarian, and prostate cancers. Furthermore, Treeomics correctly identified sequencing artifacts such as those resulting from low statistical power; nearly 7% of variants were misclassified by conventional statistical methods. These artifacts can skew phylogenies by creating illusory tumor heterogeneity among distinct samples. Importantly, we show that the evolutionary trees generated with Treeomics are mathematically optimal."}],"file_date_updated":"2020-07-14T12:46:58Z","type":"technical_report","alternative_title":["IST Austria Technical Report"]}]