--- _id: '1697' abstract: - lang: eng text: Motion tracking is a challenge the visual system has to solve by reading out the retinal population. It is still unclear how the information from different neurons can be combined together to estimate the position of an object. Here we recorded a large population of ganglion cells in a dense patch of salamander and guinea pig retinas while displaying a bar moving diffusively. We show that the bar’s position can be reconstructed from retinal activity with a precision in the hyperacuity regime using a linear decoder acting on 100+ cells. We then took advantage of this unprecedented precision to explore the spatial structure of the retina’s population code. The classical view would have suggested that the firing rates of the cells form a moving hill of activity tracking the bar’s position. Instead, we found that most ganglion cells in the salamander fired sparsely and idiosyncratically, so that their neural image did not track the bar. Furthermore, ganglion cell activity spanned an area much larger than predicted by their receptive fields, with cells coding for motion far in their surround. As a result, population redundancy was high, and we could find multiple, disjoint subsets of neurons that encoded the trajectory with high precision. This organization allows for diverse collections of ganglion cells to represent high-accuracy motion information in a form easily read out by downstream neural circuits. acknowledgement: 'This work was supported by grants EY 014196 and EY 017934 to MJB, ANR OPTIMA, the French State program Investissements d’Avenir managed by the Agence Nationale de la Recherche [LIFESENSES: ANR-10-LABX-65], and by a EC grant from the Human Brain Project (CLAP) to OM, the Austrian Research Foundation FWF P25651 to VBS and GT. VBS is partially supported by contracts MEC, Spain (Grant No. AYA2010- 22111-C03-02, Grant No. AYA2013-48623-C2-2 and FEDER Funds).' article_number: e1004304 author: - first_name: Olivier full_name: Marre, Olivier last_name: Marre - first_name: Vicente full_name: Botella Soler, Vicente id: 421234E8-F248-11E8-B48F-1D18A9856A87 last_name: Botella Soler orcid: 0000-0002-8790-1914 - first_name: Kristina full_name: Simmons, Kristina last_name: Simmons - first_name: Thierry full_name: Mora, Thierry last_name: Mora - first_name: Gasper full_name: Tkacik, Gasper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkacik orcid: 0000-0002-6699-1455 - first_name: Michael full_name: Berry, Michael last_name: Berry citation: ama: Marre O, Botella Soler V, Simmons K, Mora T, Tkačik G, Berry M. High accuracy decoding of dynamical motion from a large retinal population. PLoS Computational Biology. 2015;11(7). doi:10.1371/journal.pcbi.1004304 apa: Marre, O., Botella Soler, V., Simmons, K., Mora, T., Tkačik, G., & Berry, M. (2015). High accuracy decoding of dynamical motion from a large retinal population. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1004304 chicago: Marre, Olivier, Vicente Botella Soler, Kristina Simmons, Thierry Mora, Gašper Tkačik, and Michael Berry. “High Accuracy Decoding of Dynamical Motion from a Large Retinal Population.” PLoS Computational Biology. Public Library of Science, 2015. https://doi.org/10.1371/journal.pcbi.1004304. ieee: O. Marre, V. Botella Soler, K. Simmons, T. Mora, G. Tkačik, and M. Berry, “High accuracy decoding of dynamical motion from a large retinal population,” PLoS Computational Biology, vol. 11, no. 7. Public Library of Science, 2015. ista: Marre O, Botella Soler V, Simmons K, Mora T, Tkačik G, Berry M. 2015. High accuracy decoding of dynamical motion from a large retinal population. PLoS Computational Biology. 11(7), e1004304. mla: Marre, Olivier, et al. “High Accuracy Decoding of Dynamical Motion from a Large Retinal Population.” PLoS Computational Biology, vol. 11, no. 7, e1004304, Public Library of Science, 2015, doi:10.1371/journal.pcbi.1004304. short: O. Marre, V. Botella Soler, K. Simmons, T. Mora, G. Tkačik, M. Berry, PLoS Computational Biology 11 (2015). date_created: 2018-12-11T11:53:31Z date_published: 2015-07-01T00:00:00Z date_updated: 2021-01-12T06:52:35Z day: '01' ddc: - '570' department: - _id: GaTk doi: 10.1371/journal.pcbi.1004304 file: - access_level: open_access checksum: 472b979f3f1cffb37b3e503f085115ca content_type: application/pdf creator: system date_created: 2018-12-12T10:16:25Z date_updated: 2020-07-14T12:45:12Z file_id: '5212' file_name: IST-2016-455-v1+1_journal.pcbi.1004304.pdf file_size: 4673930 relation: main_file file_date_updated: 2020-07-14T12:45:12Z has_accepted_license: '1' intvolume: ' 11' issue: '7' language: - iso: eng month: '07' oa: 1 oa_version: Published Version project: - _id: 254D1A94-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 25651-N26 name: Sensitivity to higher-order statistics in natural scenes publication: PLoS Computational Biology publication_status: published publisher: Public Library of Science publist_id: '5447' pubrep_id: '455' quality_controlled: '1' scopus_import: 1 status: public title: High accuracy decoding of dynamical motion from a large retinal population tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 11 year: '2015' ... --- _id: '1699' abstract: - lang: eng text: By hybridization and backcrossing, alleles can surmount species boundaries and be incorporated into the genome of a related species. This introgression of genes is of particular evolutionary relevance if it involves the transfer of adaptations between populations. However, any beneficial allele will typically be associated with other alien alleles that are often deleterious and hamper the introgression process. In order to describe the introgression of an adaptive allele, we set up a stochastic model with an explicit genetic makeup of linked and unlinked deleterious alleles. Based on the theory of reducible multitype branching processes, we derive a recursive expression for the establishment probability of the beneficial allele after a single hybridization event. We furthermore study the probability that slightly deleterious alleles hitchhike to fixation. The key to the analysis is a split of the process into a stochastic phase in which the advantageous alleles establishes and a deterministic phase in which it sweeps to fixation. We thereafter apply the theory to a set of biologically relevant scenarios such as introgression in the presence of many unlinked or few closely linked deleterious alleles. A comparison to computer simulations shows that the approximations work well over a large parameter range. acknowledgement: This work was made possible with financial support by the Vienna Science and Technology Fund (WWTF), by the Deutsche Forschungsgemeinschaft (DFG), Research Unit 1078 Natural selection in structured populations, by the Austrian Science Fund (FWF) via funding for the Vienna Graduate School for Population Genetics, and by a “For Women in Science” fellowship (L’Oréal Österreich in cooperation with the Austrian Commission for UNESCO and the Austrian Academy of Sciences with financial support from the Federal Ministry for Science and Research Austria). author: - first_name: Hildegard full_name: Uecker, Hildegard id: 2DB8F68A-F248-11E8-B48F-1D18A9856A87 last_name: Uecker orcid: 0000-0001-9435-2813 - first_name: Derek full_name: Setter, Derek last_name: Setter - first_name: Joachim full_name: Hermisson, Joachim last_name: Hermisson citation: ama: Uecker H, Setter D, Hermisson J. Adaptive gene introgression after secondary contact. Journal of Mathematical Biology. 2015;70(7):1523-1580. doi:10.1007/s00285-014-0802-y apa: Uecker, H., Setter, D., & Hermisson, J. (2015). Adaptive gene introgression after secondary contact. Journal of Mathematical Biology. Springer. https://doi.org/10.1007/s00285-014-0802-y chicago: Uecker, Hildegard, Derek Setter, and Joachim Hermisson. “Adaptive Gene Introgression after Secondary Contact.” Journal of Mathematical Biology. Springer, 2015. https://doi.org/10.1007/s00285-014-0802-y. ieee: H. Uecker, D. Setter, and J. Hermisson, “Adaptive gene introgression after secondary contact,” Journal of Mathematical Biology, vol. 70, no. 7. Springer, pp. 1523–1580, 2015. ista: Uecker H, Setter D, Hermisson J. 2015. Adaptive gene introgression after secondary contact. Journal of Mathematical Biology. 70(7), 1523–1580. mla: Uecker, Hildegard, et al. “Adaptive Gene Introgression after Secondary Contact.” Journal of Mathematical Biology, vol. 70, no. 7, Springer, 2015, pp. 1523–80, doi:10.1007/s00285-014-0802-y. short: H. Uecker, D. Setter, J. Hermisson, Journal of Mathematical Biology 70 (2015) 1523–1580. date_created: 2018-12-11T11:53:32Z date_published: 2015-06-01T00:00:00Z date_updated: 2023-02-23T10:10:36Z day: '01' ddc: - '576' department: - _id: NiBa doi: 10.1007/s00285-014-0802-y file: - access_level: open_access checksum: 00e3a67bda05d4cc165b3a48b41ef9ad content_type: application/pdf creator: system date_created: 2018-12-12T10:14:27Z date_updated: 2020-07-14T12:45:12Z file_id: '5079' file_name: IST-2016-458-v1+1_s00285-014-0802-y.pdf file_size: 1321527 relation: main_file file_date_updated: 2020-07-14T12:45:12Z has_accepted_license: '1' intvolume: ' 70' issue: '7' language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: 1523 - 1580 project: - _id: 25B67606-B435-11E9-9278-68D0E5697425 name: L'OREAL Fellowship publication: Journal of Mathematical Biology publication_status: published publisher: Springer publist_id: '5442' pubrep_id: '458' quality_controlled: '1' scopus_import: 1 status: public title: Adaptive gene introgression after secondary contact tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 70 year: '2015' ... --- _id: '1696' abstract: - lang: eng text: The recently proposed diagrammatic expansion (DE) technique for the full Gutzwiller wave function (GWF) is applied to the Anderson lattice model. This approach allows for a systematic evaluation of the expectation values with full Gutzwiller wave function in finite-dimensional systems. It introduces results extending in an essential manner those obtained by means of the standard Gutzwiller approximation (GA), which is variationally exact only in infinite dimensions. Within the DE-GWF approach we discuss the principal paramagnetic properties and their relevance to heavy-fermion systems. We demonstrate the formation of an effective, narrow f band originating from atomic f-electron states and subsequently interpret this behavior as a direct itineracy of f electrons; it represents a combined effect of both the hybridization and the correlations induced by the Coulomb repulsive interaction. Such a feature is absent on the level of GA, which is equivalent to the zeroth order of our expansion. Formation of the hybridization- and electron-concentration-dependent narrow f band rationalizes the common assumption of such dispersion of f levels in the phenomenological modeling of the band structure of CeCoIn5. Moreover, it is shown that the emerging f-electron direct itineracy leads in a natural manner to three physically distinct regimes within a single model that are frequently discussed for 4f- or 5f-electron compounds as separate model situations. We identify these regimes as (i) the mixed-valence regime, (ii) Kondo/almost-Kondo insulating regime, and (iii) the Kondo-lattice limit when the f-electron occupancy is very close to the f-state half filling, ⟨nˆf⟩→1. The nonstandard features of the emerging correlated quantum liquid state are stressed. acknowledgement: The work was partly supported by the National Science Centre (NCN) under MAESTRO, Grant No. DEC-2012/04/A/ST3/00342. M.W. acknowledges the hospitality of the Institute of Science and Technology Austria during the final stage of development of the present work, as well as partial financial support from the Society-Environment-Technology project of the Jagiellonian University for that stay. J.K. acknowledges support from the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007-2013) under REA Grant Agreement No. [291734 ]. article_number: '125135' author: - first_name: Marcin full_name: Wysokiński, Marcin last_name: Wysokiński - first_name: Jan full_name: Kaczmarczyk, Jan id: 46C405DE-F248-11E8-B48F-1D18A9856A87 last_name: Kaczmarczyk orcid: 0000-0002-1629-3675 - first_name: Jozef full_name: Spałek, Jozef last_name: Spałek citation: ama: 'Wysokiński M, Kaczmarczyk J, Spałek J. Gutzwiller wave function solution for Anderson lattice model: Emerging universal regimes of heavy quasiparticle states. Physical Review B. 2015;92(12). doi:10.1103/PhysRevB.92.125135' apa: 'Wysokiński, M., Kaczmarczyk, J., & Spałek, J. (2015). Gutzwiller wave function solution for Anderson lattice model: Emerging universal regimes of heavy quasiparticle states. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.92.125135' chicago: 'Wysokiński, Marcin, Jan Kaczmarczyk, and Jozef Spałek. “Gutzwiller Wave Function Solution for Anderson Lattice Model: Emerging Universal Regimes of Heavy Quasiparticle States.” Physical Review B. American Physical Society, 2015. https://doi.org/10.1103/PhysRevB.92.125135.' ieee: 'M. Wysokiński, J. Kaczmarczyk, and J. Spałek, “Gutzwiller wave function solution for Anderson lattice model: Emerging universal regimes of heavy quasiparticle states,” Physical Review B, vol. 92, no. 12. American Physical Society, 2015.' ista: 'Wysokiński M, Kaczmarczyk J, Spałek J. 2015. Gutzwiller wave function solution for Anderson lattice model: Emerging universal regimes of heavy quasiparticle states. Physical Review B. 92(12), 125135.' mla: 'Wysokiński, Marcin, et al. “Gutzwiller Wave Function Solution for Anderson Lattice Model: Emerging Universal Regimes of Heavy Quasiparticle States.” Physical Review B, vol. 92, no. 12, 125135, American Physical Society, 2015, doi:10.1103/PhysRevB.92.125135.' short: M. Wysokiński, J. Kaczmarczyk, J. Spałek, Physical Review B 92 (2015). date_created: 2018-12-11T11:53:31Z date_published: 2015-09-18T00:00:00Z date_updated: 2021-01-12T06:52:35Z day: '18' department: - _id: MiLe doi: 10.1103/PhysRevB.92.125135 ec_funded: 1 intvolume: ' 92' issue: '12' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1505.07003 month: '09' oa: 1 oa_version: Preprint project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Physical Review B publication_status: published publisher: American Physical Society publist_id: '5448' quality_controlled: '1' scopus_import: 1 status: public title: 'Gutzwiller wave function solution for Anderson lattice model: Emerging universal regimes of heavy quasiparticle states' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 92 year: '2015' ... --- _id: '1701' abstract: - lang: eng text: 'The activity of a neural network is defined by patterns of spiking and silence from the individual neurons. Because spikes are (relatively) sparse, patterns of activity with increasing numbers of spikes are less probable, but, with more spikes, the number of possible patterns increases. This tradeoff between probability and numerosity is mathematically equivalent to the relationship between entropy and energy in statistical physics. We construct this relationship for populations of up to N = 160 neurons in a small patch of the vertebrate retina, using a combination of direct and model-based analyses of experiments on the response of this network to naturalistic movies. We see signs of a thermodynamic limit, where the entropy per neuron approaches a smooth function of the energy per neuron as N increases. The form of this function corresponds to the distribution of activity being poised near an unusual kind of critical point. We suggest further tests of criticality, and give a brief discussion of its functional significance. ' acknowledgement: "Research was supported in part by National Science Foundation Grants PHY-1305525, PHY-1451171, and CCF-0939370, by National Institutes of Health Grant R01 EY14196, and by Austrian Science Foundation Grant FWF P25651. Additional support was provided by the\r\nFannie and John Hertz Foundation, by the Swartz Foundation, by the W. M. Keck Foundation, and by the Simons Foundation." author: - first_name: Gasper full_name: Tkacik, Gasper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkacik orcid: 0000-0002-6699-1455 - first_name: Thierry full_name: Mora, Thierry last_name: Mora - first_name: Olivier full_name: Marre, Olivier last_name: Marre - first_name: Dario full_name: Amodei, Dario last_name: Amodei - first_name: Stephanie full_name: Palmer, Stephanie last_name: Palmer - first_name: Michael full_name: Berry Ii, Michael last_name: Berry Ii - first_name: William full_name: Bialek, William last_name: Bialek citation: ama: Tkačik G, Mora T, Marre O, et al. Thermodynamics and signatures of criticality in a network of neurons. PNAS. 2015;112(37):11508-11513. doi:10.1073/pnas.1514188112 apa: Tkačik, G., Mora, T., Marre, O., Amodei, D., Palmer, S., Berry Ii, M., & Bialek, W. (2015). Thermodynamics and signatures of criticality in a network of neurons. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1514188112 chicago: Tkačik, Gašper, Thierry Mora, Olivier Marre, Dario Amodei, Stephanie Palmer, Michael Berry Ii, and William Bialek. “Thermodynamics and Signatures of Criticality in a Network of Neurons.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1514188112. ieee: G. Tkačik et al., “Thermodynamics and signatures of criticality in a network of neurons,” PNAS, vol. 112, no. 37. National Academy of Sciences, pp. 11508–11513, 2015. ista: Tkačik G, Mora T, Marre O, Amodei D, Palmer S, Berry Ii M, Bialek W. 2015. Thermodynamics and signatures of criticality in a network of neurons. PNAS. 112(37), 11508–11513. mla: Tkačik, Gašper, et al. “Thermodynamics and Signatures of Criticality in a Network of Neurons.” PNAS, vol. 112, no. 37, National Academy of Sciences, 2015, pp. 11508–13, doi:10.1073/pnas.1514188112. short: G. Tkačik, T. Mora, O. Marre, D. Amodei, S. Palmer, M. Berry Ii, W. Bialek, PNAS 112 (2015) 11508–11513. date_created: 2018-12-11T11:53:33Z date_published: 2015-09-15T00:00:00Z date_updated: 2021-01-12T06:52:37Z day: '15' department: - _id: GaTk doi: 10.1073/pnas.1514188112 external_id: pmid: - '26330611' intvolume: ' 112' issue: '37' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4577210/ month: '09' oa: 1 oa_version: Submitted Version page: 11508 - 11513 pmid: 1 project: - _id: 254D1A94-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 25651-N26 name: Sensitivity to higher-order statistics in natural scenes publication: PNAS publication_status: published publisher: National Academy of Sciences publist_id: '5440' quality_controlled: '1' scopus_import: 1 status: public title: Thermodynamics and signatures of criticality in a network of neurons type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 112 year: '2015' ... --- _id: '1698' abstract: - lang: eng text: 'In mean-payoff games, the objective of the protagonist is to ensure that the limit average of an infinite sequence of numeric weights is nonnegative. In energy games, the objective is to ensure that the running sum of weights is always nonnegative. Multi-mean-payoff and multi-energy games replace individual weights by tuples, and the limit average (resp., running sum) of each coordinate must be (resp., remain) nonnegative. We prove finite-memory determinacy of multi-energy games and show inter-reducibility of multi-mean-payoff and multi-energy games for finite-memory strategies. We improve the computational complexity for solving both classes with finite-memory strategies: we prove coNP-completeness improving the previous known EXPSPACE bound. For memoryless strategies, we show that deciding the existence of a winning strategy for the protagonist is NP-complete. We present the first solution of multi-mean-payoff games with infinite-memory strategies: we show that mean-payoff-sup objectives can be decided in NP∩coNP, whereas mean-payoff-inf objectives are coNP-complete.' acknowledgement: 'The research was partly supported by Austrian Science Fund (FWF) Grant No P23499-N23, FWF NFN Grant No S11407-N23 and S11402-N23 (RiSE), ERC Start grant (279307: Graph Games), Microsoft faculty fellows award, the ERC Advanced Grant QUAREM (267989: Quantitative Reactive Modeling), European project Cassting (FP7-601148), ERC Start grant (279499: inVEST).' author: - first_name: Yaron full_name: Velner, Yaron last_name: Velner - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Laurent full_name: Doyen, Laurent last_name: Doyen - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Alexander full_name: Rabinovich, Alexander last_name: Rabinovich - first_name: Jean full_name: Raskin, Jean last_name: Raskin citation: ama: Velner Y, Chatterjee K, Doyen L, Henzinger TA, Rabinovich A, Raskin J. The complexity of multi-mean-payoff and multi-energy games. Information and Computation. 2015;241(4):177-196. doi:10.1016/j.ic.2015.03.001 apa: Velner, Y., Chatterjee, K., Doyen, L., Henzinger, T. A., Rabinovich, A., & Raskin, J. (2015). The complexity of multi-mean-payoff and multi-energy games. Information and Computation. Elsevier. https://doi.org/10.1016/j.ic.2015.03.001 chicago: Velner, Yaron, Krishnendu Chatterjee, Laurent Doyen, Thomas A Henzinger, Alexander Rabinovich, and Jean Raskin. “The Complexity of Multi-Mean-Payoff and Multi-Energy Games.” Information and Computation. Elsevier, 2015. https://doi.org/10.1016/j.ic.2015.03.001. ieee: Y. Velner, K. Chatterjee, L. Doyen, T. A. Henzinger, A. Rabinovich, and J. Raskin, “The complexity of multi-mean-payoff and multi-energy games,” Information and Computation, vol. 241, no. 4. Elsevier, pp. 177–196, 2015. ista: Velner Y, Chatterjee K, Doyen L, Henzinger TA, Rabinovich A, Raskin J. 2015. The complexity of multi-mean-payoff and multi-energy games. Information and Computation. 241(4), 177–196. mla: Velner, Yaron, et al. “The Complexity of Multi-Mean-Payoff and Multi-Energy Games.” Information and Computation, vol. 241, no. 4, Elsevier, 2015, pp. 177–96, doi:10.1016/j.ic.2015.03.001. short: Y. Velner, K. Chatterjee, L. Doyen, T.A. Henzinger, A. Rabinovich, J. Raskin, Information and Computation 241 (2015) 177–196. date_created: 2018-12-11T11:53:32Z date_published: 2015-04-01T00:00:00Z date_updated: 2021-01-12T06:52:36Z day: '01' department: - _id: KrCh - _id: ToHe doi: 10.1016/j.ic.2015.03.001 ec_funded: 1 intvolume: ' 241' issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1209.3234 month: '04' oa: 1 oa_version: Preprint page: 177 - 196 project: - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling publication: Information and Computation publication_status: published publisher: Elsevier publist_id: '5443' quality_controlled: '1' scopus_import: 1 status: public title: The complexity of multi-mean-payoff and multi-energy games type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 241 year: '2015' ... --- _id: '1700' abstract: - lang: eng text: We use the dual boson approach to reveal the phase diagram of the Fermi-Hubbard model with long-range dipole-dipole interactions. By using a large-scale finite-temperature calculation on a 64×64 square lattice we demonstrate the existence of a novel phase, possessing an "ultralong-range" order. The fingerprint of this phase - the density correlation function - features a nontrivial behavior on a scale of tens of lattice sites. We study the properties and the stability of the ultralong-range-ordered phase, and show that it is accessible in modern experiments with ultracold polar molecules and magnetic atoms. acknowledgement: The work is supported by European Research Council (ERC) Advanced Grant No. 338957 FEMTO/NANO. article_number: '081106' author: - first_name: Erik full_name: Van Loon, Erik last_name: Van Loon - first_name: Mikhail full_name: Katsnelson, Mikhail last_name: Katsnelson - first_name: Mikhail full_name: Lemeshko, Mikhail id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 citation: ama: Van Loon E, Katsnelson M, Lemeshko M. Ultralong-range order in the Fermi-Hubbard model with long-range interactions. Physical Review B. 2015;92(8). doi:10.1103/PhysRevB.92.081106 apa: Van Loon, E., Katsnelson, M., & Lemeshko, M. (2015). Ultralong-range order in the Fermi-Hubbard model with long-range interactions. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.92.081106 chicago: Van Loon, Erik, Mikhail Katsnelson, and Mikhail Lemeshko. “Ultralong-Range Order in the Fermi-Hubbard Model with Long-Range Interactions.” Physical Review B. American Physical Society, 2015. https://doi.org/10.1103/PhysRevB.92.081106. ieee: E. Van Loon, M. Katsnelson, and M. Lemeshko, “Ultralong-range order in the Fermi-Hubbard model with long-range interactions,” Physical Review B, vol. 92, no. 8. American Physical Society, 2015. ista: Van Loon E, Katsnelson M, Lemeshko M. 2015. Ultralong-range order in the Fermi-Hubbard model with long-range interactions. Physical Review B. 92(8), 081106. mla: Van Loon, Erik, et al. “Ultralong-Range Order in the Fermi-Hubbard Model with Long-Range Interactions.” Physical Review B, vol. 92, no. 8, 081106, American Physical Society, 2015, doi:10.1103/PhysRevB.92.081106. short: E. Van Loon, M. Katsnelson, M. Lemeshko, Physical Review B 92 (2015). date_created: 2018-12-11T11:53:32Z date_published: 2015-08-10T00:00:00Z date_updated: 2021-01-12T06:52:37Z day: '10' department: - _id: MiLe doi: 10.1103/PhysRevB.92.081106 intvolume: ' 92' issue: '8' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1506.06007 month: '08' oa: 1 oa_version: Preprint publication: Physical Review B publication_status: published publisher: American Physical Society publist_id: '5441' scopus_import: 1 status: public title: Ultralong-range order in the Fermi-Hubbard model with long-range interactions type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 92 year: '2015' ... --- _id: '1704' abstract: - lang: eng text: Given a convex function (Formula presented.) and two hermitian matrices A and B, Lewin and Sabin study in (Lett Math Phys 104:691–705, 2014) the relative entropy defined by (Formula presented.). Among other things, they prove that the so-defined quantity is monotone if and only if (Formula presented.) is operator monotone. The monotonicity is then used to properly define (Formula presented.) for bounded self-adjoint operators acting on an infinite-dimensional Hilbert space by a limiting procedure. More precisely, for an increasing sequence of finite-dimensional projections (Formula presented.) with (Formula presented.) strongly, the limit (Formula presented.) is shown to exist and to be independent of the sequence of projections (Formula presented.). The question whether this sequence converges to its "obvious" limit, namely (Formula presented.), has been left open. We answer this question in principle affirmatively and show that (Formula presented.). If the operators A and B are regular enough, that is (A − B), (Formula presented.) and (Formula presented.) are trace-class, the identity (Formula presented.) holds. author: - first_name: Andreas full_name: Deuchert, Andreas last_name: Deuchert orcid: 0000-0003-3146-6746 - first_name: Christian full_name: Hainzl, Christian last_name: Hainzl - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: ama: Deuchert A, Hainzl C, Seiringer R. Note on a family of monotone quantum relative entropies. Letters in Mathematical Physics. 2015;105(10):1449-1466. doi:10.1007/s11005-015-0787-5 apa: Deuchert, A., Hainzl, C., & Seiringer, R. (2015). Note on a family of monotone quantum relative entropies. Letters in Mathematical Physics. Springer. https://doi.org/10.1007/s11005-015-0787-5 chicago: Deuchert, Andreas, Christian Hainzl, and Robert Seiringer. “Note on a Family of Monotone Quantum Relative Entropies.” Letters in Mathematical Physics. Springer, 2015. https://doi.org/10.1007/s11005-015-0787-5. ieee: A. Deuchert, C. Hainzl, and R. Seiringer, “Note on a family of monotone quantum relative entropies,” Letters in Mathematical Physics, vol. 105, no. 10. Springer, pp. 1449–1466, 2015. ista: Deuchert A, Hainzl C, Seiringer R. 2015. Note on a family of monotone quantum relative entropies. Letters in Mathematical Physics. 105(10), 1449–1466. mla: Deuchert, Andreas, et al. “Note on a Family of Monotone Quantum Relative Entropies.” Letters in Mathematical Physics, vol. 105, no. 10, Springer, 2015, pp. 1449–66, doi:10.1007/s11005-015-0787-5. short: A. Deuchert, C. Hainzl, R. Seiringer, Letters in Mathematical Physics 105 (2015) 1449–1466. date_created: 2018-12-11T11:53:34Z date_published: 2015-08-05T00:00:00Z date_updated: 2021-01-12T06:52:38Z day: '05' ddc: - '510' department: - _id: RoSe doi: 10.1007/s11005-015-0787-5 file: - access_level: open_access checksum: fd7307282a314cc1fbbaef77b187516b content_type: application/pdf creator: dernst date_created: 2019-01-15T14:42:07Z date_updated: 2020-07-14T12:45:13Z file_id: '5836' file_name: 2015_LettersMathPhys_Deuchert.pdf file_size: 484967 relation: main_file file_date_updated: 2020-07-14T12:45:13Z has_accepted_license: '1' intvolume: ' 105' issue: '10' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1502.07205 month: '08' oa: 1 oa_version: Preprint page: 1449 - 1466 publication: Letters in Mathematical Physics publication_status: published publisher: Springer publist_id: '5432' quality_controlled: '1' scopus_import: 1 status: public title: Note on a family of monotone quantum relative entropies tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 105 year: '2015' ... --- _id: '1703' abstract: - lang: eng text: Vegetation clearing and land-use change have depleted many natural plant communities to the point where restoration is required. A major impediment to the success of rebuilding complex vegetation communities is having regular access to sufficient quantities of high-quality seed. Seed-production areas (SPAs) can help generate this seed, but these must be underpinned by a broad genetic base to maximise the evolutionary potential of restored populations. However, genetic bottlenecks can occur at the collection, establishment and production stages in SPAs, requiring genetic evaluation. This is especially relevant for species that may take many years before a return on SPA investment is realised. Two recently established yellow box (Eucalyptus melliodora A.Cunn. ex Schauer, Myrtaceae) SPAs were evaluated to determine whether genetic bottlenecks had occurred between seed collection and SPA establishment. No evidence was found to suggest that a significant loss of genetic diversity had occurred at this stage, although there was a significant difference in diversity between the two SPAs. Complex population genetic structure was also observed in the seed used to source the SPAs, with up to eight groups identified. Plant survival in the SPAs was influenced by seed collection location but not by SPA location and was not associated with genetic diversity. There were also no associations between genetic diversity and plant growth. These data highlighted the importance of chance events when establishing SPAs and indicated that the two yellow box SPAs are likely to provide genetically diverse seed sources for future restoration projects, especially by pooling seed from both SPAs. author: - first_name: Linda full_name: Broadhurst, Linda last_name: Broadhurst - first_name: Graham full_name: Fifield, Graham last_name: Fifield - first_name: Bindi full_name: Vanzella, Bindi last_name: Vanzella - first_name: Melinda full_name: Pickup, Melinda id: 2C78037E-F248-11E8-B48F-1D18A9856A87 last_name: Pickup orcid: 0000-0001-6118-0541 citation: ama: Broadhurst L, Fifield G, Vanzella B, Pickup M. An evaluation of the genetic structure of seed sources and the maintenance of genetic diversity during establishment of two yellow box (Eucalyptus melliodora) seed-production areas. Australian Journal of Botany. 2015;63(5):455-466. doi:10.1071/BT15023 apa: Broadhurst, L., Fifield, G., Vanzella, B., & Pickup, M. (2015). An evaluation of the genetic structure of seed sources and the maintenance of genetic diversity during establishment of two yellow box (Eucalyptus melliodora) seed-production areas. Australian Journal of Botany. CSIRO. https://doi.org/10.1071/BT15023 chicago: Broadhurst, Linda, Graham Fifield, Bindi Vanzella, and Melinda Pickup. “An Evaluation of the Genetic Structure of Seed Sources and the Maintenance of Genetic Diversity during Establishment of Two Yellow Box (Eucalyptus Melliodora) Seed-Production Areas.” Australian Journal of Botany. CSIRO, 2015. https://doi.org/10.1071/BT15023. ieee: L. Broadhurst, G. Fifield, B. Vanzella, and M. Pickup, “An evaluation of the genetic structure of seed sources and the maintenance of genetic diversity during establishment of two yellow box (Eucalyptus melliodora) seed-production areas,” Australian Journal of Botany, vol. 63, no. 5. CSIRO, pp. 455–466, 2015. ista: Broadhurst L, Fifield G, Vanzella B, Pickup M. 2015. An evaluation of the genetic structure of seed sources and the maintenance of genetic diversity during establishment of two yellow box (Eucalyptus melliodora) seed-production areas. Australian Journal of Botany. 63(5), 455–466. mla: Broadhurst, Linda, et al. “An Evaluation of the Genetic Structure of Seed Sources and the Maintenance of Genetic Diversity during Establishment of Two Yellow Box (Eucalyptus Melliodora) Seed-Production Areas.” Australian Journal of Botany, vol. 63, no. 5, CSIRO, 2015, pp. 455–66, doi:10.1071/BT15023. short: L. Broadhurst, G. Fifield, B. Vanzella, M. Pickup, Australian Journal of Botany 63 (2015) 455–466. date_created: 2018-12-11T11:53:34Z date_published: 2015-05-26T00:00:00Z date_updated: 2021-01-12T06:52:38Z day: '26' department: - _id: NiBa doi: 10.1071/BT15023 intvolume: ' 63' issue: '5' language: - iso: eng month: '05' oa_version: None page: 455 - 466 publication: Australian Journal of Botany publication_status: published publisher: CSIRO publist_id: '5434' quality_controlled: '1' scopus_import: 1 status: public title: An evaluation of the genetic structure of seed sources and the maintenance of genetic diversity during establishment of two yellow box (Eucalyptus melliodora) seed-production areas type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 63 year: '2015' ... --- _id: '1706' abstract: - lang: eng text: We consider a problem of learning kernels for use in SVM classification in the multi-task and lifelong scenarios and provide generalization bounds on the error of a large margin classifier. Our results show that, under mild conditions on the family of kernels used for learning, solving several related tasks simultaneously is beneficial over single task learning. In particular, as the number of observed tasks grows, assuming that in the considered family of kernels there exists one that yields low approximation error on all tasks, the overhead associated with learning such a kernel vanishes and the complexity converges to that of learning when this good kernel is given to the learner. alternative_title: - LNCS author: - first_name: Anastasia full_name: Pentina, Anastasia id: 42E87FC6-F248-11E8-B48F-1D18A9856A87 last_name: Pentina - first_name: Shai full_name: Ben David, Shai last_name: Ben David citation: ama: 'Pentina A, Ben David S. Multi-task and lifelong learning of kernels. In: Vol 9355. Springer; 2015:194-208. doi:10.1007/978-3-319-24486-0_13' apa: 'Pentina, A., & Ben David, S. (2015). Multi-task and lifelong learning of kernels (Vol. 9355, pp. 194–208). Presented at the ALT: Algorithmic Learning Theory, Banff, AB, Canada: Springer. https://doi.org/10.1007/978-3-319-24486-0_13' chicago: Pentina, Anastasia, and Shai Ben David. “Multi-Task and Lifelong Learning of Kernels,” 9355:194–208. Springer, 2015. https://doi.org/10.1007/978-3-319-24486-0_13. ieee: 'A. Pentina and S. Ben David, “Multi-task and lifelong learning of kernels,” presented at the ALT: Algorithmic Learning Theory, Banff, AB, Canada, 2015, vol. 9355, pp. 194–208.' ista: 'Pentina A, Ben David S. 2015. Multi-task and lifelong learning of kernels. ALT: Algorithmic Learning Theory, LNCS, vol. 9355, 194–208.' mla: Pentina, Anastasia, and Shai Ben David. Multi-Task and Lifelong Learning of Kernels. Vol. 9355, Springer, 2015, pp. 194–208, doi:10.1007/978-3-319-24486-0_13. short: A. Pentina, S. Ben David, in:, Springer, 2015, pp. 194–208. conference: end_date: 2015-10-06 location: Banff, AB, Canada name: 'ALT: Algorithmic Learning Theory' start_date: 2015-10-04 date_created: 2018-12-11T11:53:35Z date_published: 2015-01-01T00:00:00Z date_updated: 2021-01-12T06:52:39Z day: '01' department: - _id: ChLa doi: 10.1007/978-3-319-24486-0_13 ec_funded: 1 intvolume: ' 9355' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1602.06531 month: '01' oa: 1 oa_version: Preprint page: 194 - 208 project: - _id: 2532554C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '308036' name: Lifelong Learning of Visual Scene Understanding publication_status: published publisher: Springer publist_id: '5430' quality_controlled: '1' scopus_import: 1 status: public title: Multi-task and lifelong learning of kernels type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9355 year: '2015' ... --- _id: '1712' abstract: - lang: eng text: The majority of immune cells in Drosophila melanogaster are plasmatocytes; they carry out similar functions to vertebrate macrophages, influencing development as well as protecting against infection and cancer. Plasmatocytes, sometimes referred to with the broader term of hemocytes, migrate widely during embryonic development and cycle in the larvae between sessile and circulating positions. Here we discuss the similarities of plasmatocyte developmental migration and its functions to that of vertebrate macrophages, considering the recent controversy regarding the functions of Drosophila PDGF/VEGF related ligands. We also examine recent findings on the significance of adhesion for plasmatocyte migration in the embryo, as well as proliferation, trans-differentiation, and tumor responses in the larva. We spotlight parallels throughout to vertebrate immune responses. author: - first_name: Aparna full_name: Ratheesh, Aparna id: 2F064CFE-F248-11E8-B48F-1D18A9856A87 last_name: Ratheesh - first_name: Vera full_name: Belyaeva, Vera id: 47F080FE-F248-11E8-B48F-1D18A9856A87 last_name: Belyaeva - first_name: Daria E full_name: Siekhaus, Daria E id: 3D224B9E-F248-11E8-B48F-1D18A9856A87 last_name: Siekhaus orcid: 0000-0001-8323-8353 citation: ama: Ratheesh A, Belyaeva V, Siekhaus DE. Drosophila immune cell migration and adhesion during embryonic development and larval immune responses. Current Opinion in Cell Biology. 2015;36(10):71-79. doi:10.1016/j.ceb.2015.07.003 apa: Ratheesh, A., Belyaeva, V., & Siekhaus, D. E. (2015). Drosophila immune cell migration and adhesion during embryonic development and larval immune responses. Current Opinion in Cell Biology. Elsevier. https://doi.org/10.1016/j.ceb.2015.07.003 chicago: Ratheesh, Aparna, Vera Belyaeva, and Daria E Siekhaus. “Drosophila Immune Cell Migration and Adhesion during Embryonic Development and Larval Immune Responses.” Current Opinion in Cell Biology. Elsevier, 2015. https://doi.org/10.1016/j.ceb.2015.07.003. ieee: A. Ratheesh, V. Belyaeva, and D. E. Siekhaus, “Drosophila immune cell migration and adhesion during embryonic development and larval immune responses,” Current Opinion in Cell Biology, vol. 36, no. 10. Elsevier, pp. 71–79, 2015. ista: Ratheesh A, Belyaeva V, Siekhaus DE. 2015. Drosophila immune cell migration and adhesion during embryonic development and larval immune responses. Current Opinion in Cell Biology. 36(10), 71–79. mla: Ratheesh, Aparna, et al. “Drosophila Immune Cell Migration and Adhesion during Embryonic Development and Larval Immune Responses.” Current Opinion in Cell Biology, vol. 36, no. 10, Elsevier, 2015, pp. 71–79, doi:10.1016/j.ceb.2015.07.003. short: A. Ratheesh, V. Belyaeva, D.E. Siekhaus, Current Opinion in Cell Biology 36 (2015) 71–79. date_created: 2018-12-11T11:53:36Z date_published: 2015-10-01T00:00:00Z date_updated: 2021-01-12T06:52:41Z day: '01' ddc: - '573' department: - _id: DaSi doi: 10.1016/j.ceb.2015.07.003 ec_funded: 1 file: - access_level: open_access checksum: bbb1ee39ca52929aefe4f48752b166ee content_type: application/pdf creator: system date_created: 2018-12-12T10:14:44Z date_updated: 2020-07-14T12:45:13Z file_id: '5098' file_name: IST-2015-346-v1+1_Current_Opinion_Review_Ratheesh_et_al_2015.pdf file_size: 1023680 relation: main_file file_date_updated: 2020-07-14T12:45:13Z has_accepted_license: '1' intvolume: ' 36' issue: '10' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-nd/4.0/ month: '10' oa: 1 oa_version: Published Version page: 71 - 79 project: - _id: 2536F660-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '334077' name: Investigating the role of transporters in invasive migration through junctions publication: Current Opinion in Cell Biology publication_status: published publisher: Elsevier publist_id: '5421' pubrep_id: '346' quality_controlled: '1' scopus_import: 1 status: public title: Drosophila immune cell migration and adhesion during embryonic development and larval immune responses tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 36 year: '2015' ... --- _id: '1710' abstract: - lang: eng text: 'We consider the hollow on the half-plane {(x, y) : y ≤ 0} ⊂ ℝ2 defined by a function u : (-1, 1) → ℝ, u(x) < 0, and a vertical flow of point particles incident on the hollow. It is assumed that u satisfies the so-called single impact condition (SIC): each incident particle is elastically reflected by graph(u) and goes away without hitting the graph of u anymore. We solve the problem: find the function u minimizing the force of resistance created by the flow. We show that the graph of the minimizer is formed by two arcs of parabolas symmetric to each other with respect to the y-axis. Assuming that the resistance of u ≡ 0 equals 1, we show that the minimal resistance equals π/2 - 2arctan(1/2) ≈ 0.6435. This result completes the previously obtained result [SIAM J. Math. Anal., 46 (2014), pp. 2730-2742] stating in particular that the minimal resistance of a hollow in higher dimensions equals 0.5. We additionally consider a similar problem of minimal resistance, where the hollow in the half-space {(x1,...,xd,y) : y ≤ 0} ⊂ ℝd+1 is defined by a radial function U satisfying the SIC, U(x) = u(|x|), with x = (x1,...,xd), u(ξ) < 0 for 0 ≤ ξ < 1, and u(ξ) = 0 for ξ ≥ 1, and the flow is parallel to the y-axis. The minimal resistance is greater than 0.5 (and coincides with 0.6435 when d = 1) and converges to 0.5 as d → ∞.' author: - first_name: Arseniy full_name: Akopyan, Arseniy id: 430D2C90-F248-11E8-B48F-1D18A9856A87 last_name: Akopyan orcid: 0000-0002-2548-617X - first_name: Alexander full_name: Plakhov, Alexander last_name: Plakhov citation: ama: Akopyan A, Plakhov A. Minimal resistance of curves under the single impact assumption. Society for Industrial and Applied Mathematics. 2015;47(4):2754-2769. doi:10.1137/140993843 apa: Akopyan, A., & Plakhov, A. (2015). Minimal resistance of curves under the single impact assumption. Society for Industrial and Applied Mathematics. SIAM. https://doi.org/10.1137/140993843 chicago: Akopyan, Arseniy, and Alexander Plakhov. “Minimal Resistance of Curves under the Single Impact Assumption.” Society for Industrial and Applied Mathematics. SIAM, 2015. https://doi.org/10.1137/140993843. ieee: A. Akopyan and A. Plakhov, “Minimal resistance of curves under the single impact assumption,” Society for Industrial and Applied Mathematics, vol. 47, no. 4. SIAM, pp. 2754–2769, 2015. ista: Akopyan A, Plakhov A. 2015. Minimal resistance of curves under the single impact assumption. Society for Industrial and Applied Mathematics. 47(4), 2754–2769. mla: Akopyan, Arseniy, and Alexander Plakhov. “Minimal Resistance of Curves under the Single Impact Assumption.” Society for Industrial and Applied Mathematics, vol. 47, no. 4, SIAM, 2015, pp. 2754–69, doi:10.1137/140993843. short: A. Akopyan, A. Plakhov, Society for Industrial and Applied Mathematics 47 (2015) 2754–2769. date_created: 2018-12-11T11:53:36Z date_published: 2015-07-14T00:00:00Z date_updated: 2021-01-12T06:52:41Z day: '14' department: - _id: HeEd doi: 10.1137/140993843 ec_funded: 1 intvolume: ' 47' issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1410.3736 month: '07' oa: 1 oa_version: Preprint page: 2754 - 2769 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Society for Industrial and Applied Mathematics publication_status: published publisher: SIAM publist_id: '5423' quality_controlled: '1' scopus_import: 1 status: public title: Minimal resistance of curves under the single impact assumption type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 47 year: '2015' ... --- _id: '1730' abstract: - lang: eng text: How much cutting is needed to simplify the topology of a surface? We provide bounds for several instances of this question, for the minimum length of topologically non-trivial closed curves, pants decompositions, and cut graphs with a given combinatorial map in triangulated combinatorial surfaces (or their dual cross-metric counterpart). Our work builds upon Riemannian systolic inequalities, which bound the minimum length of non-trivial closed curves in terms of the genus and the area of the surface. We first describe a systematic way to translate Riemannian systolic inequalities to a discrete setting, and vice-versa. This implies a conjecture by Przytycka and Przytycki (Graph structure theory. Contemporary Mathematics, vol. 147, 1993), a number of new systolic inequalities in the discrete setting, and the fact that a theorem of Hutchinson on the edge-width of triangulated surfaces and Gromov’s systolic inequality for surfaces are essentially equivalent. We also discuss how these proofs generalize to higher dimensions. Then we focus on topological decompositions of surfaces. Relying on ideas of Buser, we prove the existence of pants decompositions of length O(g^(3/2)n^(1/2)) for any triangulated combinatorial surface of genus g with n triangles, and describe an O(gn)-time algorithm to compute such a decomposition. Finally, we consider the problem of embedding a cut graph (or more generally a cellular graph) with a given combinatorial map on a given surface. Using random triangulations, we prove (essentially) that, for any choice of a combinatorial map, there are some surfaces on which any cellular embedding with that combinatorial map has length superlinear in the number of triangles of the triangulated combinatorial surface. There is also a similar result for graphs embedded on polyhedral triangulations. author: - first_name: Éric full_name: Colin De Verdière, Éric last_name: Colin De Verdière - first_name: Alfredo full_name: Hubard, Alfredo last_name: Hubard - first_name: Arnaud N full_name: De Mesmay, Arnaud N id: 3DB2F25C-F248-11E8-B48F-1D18A9856A87 last_name: De Mesmay citation: ama: Colin De Verdière É, Hubard A, de Mesmay AN. Discrete systolic inequalities and decompositions of triangulated surfaces. Discrete & Computational Geometry. 2015;53(3):587-620. doi:10.1007/s00454-015-9679-9 apa: Colin De Verdière, É., Hubard, A., & de Mesmay, A. N. (2015). Discrete systolic inequalities and decompositions of triangulated surfaces. Discrete & Computational Geometry. Springer. https://doi.org/10.1007/s00454-015-9679-9 chicago: Colin De Verdière, Éric, Alfredo Hubard, and Arnaud N de Mesmay. “Discrete Systolic Inequalities and Decompositions of Triangulated Surfaces.” Discrete & Computational Geometry. Springer, 2015. https://doi.org/10.1007/s00454-015-9679-9. ieee: É. Colin De Verdière, A. Hubard, and A. N. de Mesmay, “Discrete systolic inequalities and decompositions of triangulated surfaces,” Discrete & Computational Geometry, vol. 53, no. 3. Springer, pp. 587–620, 2015. ista: Colin De Verdière É, Hubard A, de Mesmay AN. 2015. Discrete systolic inequalities and decompositions of triangulated surfaces. Discrete & Computational Geometry. 53(3), 587–620. mla: Colin De Verdière, Éric, et al. “Discrete Systolic Inequalities and Decompositions of Triangulated Surfaces.” Discrete & Computational Geometry, vol. 53, no. 3, Springer, 2015, pp. 587–620, doi:10.1007/s00454-015-9679-9. short: É. Colin De Verdière, A. Hubard, A.N. de Mesmay, Discrete & Computational Geometry 53 (2015) 587–620. date_created: 2018-12-11T11:53:42Z date_published: 2015-04-02T00:00:00Z date_updated: 2021-01-12T06:52:49Z day: '02' department: - _id: UlWa doi: 10.1007/s00454-015-9679-9 intvolume: ' 53' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1408.4036 month: '04' oa: 1 oa_version: Preprint page: 587 - 620 publication: Discrete & Computational Geometry publication_status: published publisher: Springer publist_id: '5397' quality_controlled: '1' scopus_import: 1 status: public title: Discrete systolic inequalities and decompositions of triangulated surfaces type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 53 year: '2015' ... --- _id: '1735' abstract: - lang: eng text: This work presents a method for efficiently simplifying the pressure projection step in a liquid simulation. We first devise a straightforward dimension reduction technique that dramatically reduces the cost of solving the pressure projection. Next, we introduce a novel change of basis that satisfies free-surface boundary conditions exactly, regardless of the accuracy of the pressure solve. When combined, these ideas greatly reduce the computational complexity of the pressure solve without compromising free surface boundary conditions at the highest level of detail. Our techniques are easy to parallelize, and they effectively eliminate the computational bottleneck for large liquid simulations. acknowledgement: The first author was supported by a JSPS Postdoctoral Fellowship for Research Abroad author: - first_name: Ryoichi full_name: Ando, Ryoichi last_name: Ando - first_name: Nils full_name: Thürey, Nils last_name: Thürey - first_name: Christopher J full_name: Wojtan, Christopher J id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87 last_name: Wojtan orcid: 0000-0001-6646-5546 citation: ama: Ando R, Thürey N, Wojtan C. A dimension-reduced pressure solver for liquid simulations. Computer Graphics Forum. 2015;34(2):473-480. doi:10.1111/cgf.12576 apa: Ando, R., Thürey, N., & Wojtan, C. (2015). A dimension-reduced pressure solver for liquid simulations. Computer Graphics Forum. Wiley. https://doi.org/10.1111/cgf.12576 chicago: Ando, Ryoichi, Nils Thürey, and Chris Wojtan. “A Dimension-Reduced Pressure Solver for Liquid Simulations.” Computer Graphics Forum. Wiley, 2015. https://doi.org/10.1111/cgf.12576. ieee: R. Ando, N. Thürey, and C. Wojtan, “A dimension-reduced pressure solver for liquid simulations,” Computer Graphics Forum, vol. 34, no. 2. Wiley, pp. 473–480, 2015. ista: Ando R, Thürey N, Wojtan C. 2015. A dimension-reduced pressure solver for liquid simulations. Computer Graphics Forum. 34(2), 473–480. mla: Ando, Ryoichi, et al. “A Dimension-Reduced Pressure Solver for Liquid Simulations.” Computer Graphics Forum, vol. 34, no. 2, Wiley, 2015, pp. 473–80, doi:10.1111/cgf.12576. short: R. Ando, N. Thürey, C. Wojtan, Computer Graphics Forum 34 (2015) 473–480. date_created: 2018-12-11T11:53:44Z date_published: 2015-05-01T00:00:00Z date_updated: 2023-02-23T10:12:11Z day: '01' ddc: - '000' department: - _id: ChWo doi: 10.1111/cgf.12576 file: - access_level: open_access checksum: 590752bf977855b337a80f78a9bc2404 content_type: application/pdf creator: system date_created: 2018-12-12T10:16:30Z date_updated: 2020-07-14T12:45:15Z file_id: '5218' file_name: IST-2016-607-v1+1_coarsegrid.pdf file_size: 6312352 relation: main_file file_date_updated: 2020-07-14T12:45:15Z has_accepted_license: '1' intvolume: ' 34' issue: '2' language: - iso: eng month: '05' oa: 1 oa_version: Submitted Version page: 473 - 480 publication: Computer Graphics Forum publication_status: published publisher: Wiley publist_id: '5389' pubrep_id: '607' quality_controlled: '1' scopus_import: 1 status: public title: A dimension-reduced pressure solver for liquid simulations type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 34 year: '2015' ... --- _id: '1734' abstract: - lang: eng text: Facial appearance capture is now firmly established within academic research and used extensively across various application domains, perhaps most prominently in the entertainment industry through the design of virtual characters in video games and films. While significant progress has occurred over the last two decades, no single survey currently exists that discusses the similarities, differences, and practical considerations of the available appearance capture techniques as applied to human faces. A central difficulty of facial appearance capture is the way light interacts with skin-which has a complex multi-layered structure-and the interactions that occur below the skin surface can, by definition, only be observed indirectly. In this report, we distinguish between two broad strategies for dealing with this complexity. "Image-based methods" try to exhaustively capture the exact face appearance under different lighting and viewing conditions, and then render the face through weighted image combinations. "Parametric methods" instead fit the captured reflectance data to some parametric appearance model used during rendering, allowing for a more lightweight and flexible representation but at the cost of potentially increased rendering complexity or inexact reproduction. The goal of this report is to provide an overview that can guide practitioners and researchers in assessing the tradeoffs between current approaches and identifying directions for future advances in facial appearance capture. author: - first_name: Oliver full_name: Klehm, Oliver last_name: Klehm - first_name: Fabrice full_name: Rousselle, Fabrice last_name: Rousselle - first_name: Marios full_name: Papas, Marios last_name: Papas - first_name: Derek full_name: Bradley, Derek last_name: Bradley - first_name: Christophe full_name: Hery, Christophe last_name: Hery - first_name: Bernd full_name: Bickel, Bernd id: 49876194-F248-11E8-B48F-1D18A9856A87 last_name: Bickel orcid: 0000-0001-6511-9385 - first_name: Wojciech full_name: Jarosz, Wojciech last_name: Jarosz - first_name: Thabo full_name: Beeler, Thabo last_name: Beeler citation: ama: Klehm O, Rousselle F, Papas M, et al. Recent advances in facial appearance capture. Computer Graphics Forum. 2015;34(2):709-733. doi:10.1111/cgf.12594 apa: Klehm, O., Rousselle, F., Papas, M., Bradley, D., Hery, C., Bickel, B., … Beeler, T. (2015). Recent advances in facial appearance capture. Computer Graphics Forum. Wiley-Blackwell. https://doi.org/10.1111/cgf.12594 chicago: Klehm, Oliver, Fabrice Rousselle, Marios Papas, Derek Bradley, Christophe Hery, Bernd Bickel, Wojciech Jarosz, and Thabo Beeler. “Recent Advances in Facial Appearance Capture.” Computer Graphics Forum. Wiley-Blackwell, 2015. https://doi.org/10.1111/cgf.12594. ieee: O. Klehm et al., “Recent advances in facial appearance capture,” Computer Graphics Forum, vol. 34, no. 2. Wiley-Blackwell, pp. 709–733, 2015. ista: Klehm O, Rousselle F, Papas M, Bradley D, Hery C, Bickel B, Jarosz W, Beeler T. 2015. Recent advances in facial appearance capture. Computer Graphics Forum. 34(2), 709–733. mla: Klehm, Oliver, et al. “Recent Advances in Facial Appearance Capture.” Computer Graphics Forum, vol. 34, no. 2, Wiley-Blackwell, 2015, pp. 709–33, doi:10.1111/cgf.12594. short: O. Klehm, F. Rousselle, M. Papas, D. Bradley, C. Hery, B. Bickel, W. Jarosz, T. Beeler, Computer Graphics Forum 34 (2015) 709–733. date_created: 2018-12-11T11:53:43Z date_published: 2015-05-01T00:00:00Z date_updated: 2021-01-12T06:52:52Z day: '01' department: - _id: BeBi doi: 10.1111/cgf.12594 intvolume: ' 34' issue: '2' language: - iso: eng main_file_link: - url: https://graphics.ethz.ch/~mpapas/publications/fac_star.pdf month: '05' oa_version: None page: 709 - 733 publication: Computer Graphics Forum publication_status: published publisher: Wiley-Blackwell publist_id: '5391' quality_controlled: '1' scopus_import: 1 status: public title: Recent advances in facial appearance capture type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 34 year: '2015' ... --- _id: '1789' abstract: - lang: eng text: Intellectual disability (ID) has an estimated prevalence of 2-3%. Due to its extreme heterogeneity, the genetic basis of ID remains elusive in many cases. Recently, whole exome sequencing (WES) studies revealed that a large proportion of sporadic cases are caused by de novo gene variants. To identify further genes involved in ID, we performed WES in 250 patients with unexplained ID and their unaffected parents and included exomes of 51 previously sequenced child-parents trios in the analysis. Exome analysis revealed de novo intragenic variants in SET domain-containing 5 (SETD5) in two patients. One patient carried a nonsense variant, and the other an 81 bp deletion located across a splice-donor site. Chromosomal microarray diagnostics further identified four de novo non-recurrent microdeletions encompassing SETD5. CRISPR/Cas9 mutation modelling of the two intragenic variants demonstrated nonsense-mediated decay of the resulting transcripts, pointing to a loss-of-function (LoF) and haploinsufficiency as the common disease-causing mechanism of intragenic SETD5 sequence variants and SETD5-containing microdeletions. In silico domain prediction of SETD5, a predicted SET domain-containing histone methyltransferase (HMT), substantiated the presence of a SET domain and identified a novel putative PHD domain, strengthening a functional link to well-known histone-modifying ID genes. All six patients presented with ID and certain facial dysmorphisms, suggesting that SETD5 sequence variants contribute substantially to the microdeletion 3p25.3 phenotype. The present report of two SETD5 LoF variants in 301 patients demonstrates a prevalence of 0.7% and thus SETD5 variants as a relatively frequent cause of ID. author: - first_name: Alma full_name: Kuechler, Alma last_name: Kuechler - first_name: Alexander full_name: Zink, Alexander last_name: Zink - first_name: Thomas full_name: Wieland, Thomas last_name: Wieland - first_name: Hermann full_name: Lüdecke, Hermann last_name: Lüdecke - first_name: Kirsten full_name: Cremer, Kirsten last_name: Cremer - first_name: Leonardo full_name: Salviati, Leonardo last_name: Salviati - first_name: Pamela full_name: Magini, Pamela last_name: Magini - first_name: Kimia full_name: Najafi, Kimia last_name: Najafi - first_name: Christiane full_name: Zweier, Christiane last_name: Zweier - first_name: Johanna full_name: Czeschik, Johanna last_name: Czeschik - first_name: Stefan full_name: Aretz, Stefan last_name: Aretz - first_name: Sabine full_name: Endele, Sabine last_name: Endele - first_name: Federica full_name: Tamburrino, Federica last_name: Tamburrino - first_name: Claudia full_name: Pinato, Claudia last_name: Pinato - first_name: Maurizio full_name: Clementi, Maurizio last_name: Clementi - first_name: Jasmin full_name: Gundlach, Jasmin last_name: Gundlach - first_name: Carina full_name: Maylahn, Carina last_name: Maylahn - first_name: Laura full_name: Mazzanti, Laura last_name: Mazzanti - first_name: Eva full_name: Wohlleber, Eva last_name: Wohlleber - first_name: Thomas full_name: Schwarzmayr, Thomas last_name: Schwarzmayr - first_name: Roxana full_name: Kariminejad, Roxana last_name: Kariminejad - first_name: Avner full_name: Schlessinger, Avner last_name: Schlessinger - first_name: Dagmar full_name: Wieczorek, Dagmar last_name: Wieczorek - first_name: Tim full_name: Strom, Tim last_name: Strom - first_name: Gaia full_name: Novarino, Gaia id: 3E57A680-F248-11E8-B48F-1D18A9856A87 last_name: Novarino orcid: 0000-0002-7673-7178 - first_name: Hartmut full_name: Engels, Hartmut last_name: Engels citation: ama: Kuechler A, Zink A, Wieland T, et al. Loss-of-function variants of SETD5 cause intellectual disability and the core phenotype of microdeletion 3p25.3 syndrome. European Journal of Human Genetics. 2015;23(6):753-760. doi:10.1038/ejhg.2014.165 apa: Kuechler, A., Zink, A., Wieland, T., Lüdecke, H., Cremer, K., Salviati, L., … Engels, H. (2015). Loss-of-function variants of SETD5 cause intellectual disability and the core phenotype of microdeletion 3p25.3 syndrome. European Journal of Human Genetics. Nature Publishing Group. https://doi.org/10.1038/ejhg.2014.165 chicago: Kuechler, Alma, Alexander Zink, Thomas Wieland, Hermann Lüdecke, Kirsten Cremer, Leonardo Salviati, Pamela Magini, et al. “Loss-of-Function Variants of SETD5 Cause Intellectual Disability and the Core Phenotype of Microdeletion 3p25.3 Syndrome.” European Journal of Human Genetics. Nature Publishing Group, 2015. https://doi.org/10.1038/ejhg.2014.165. ieee: A. Kuechler et al., “Loss-of-function variants of SETD5 cause intellectual disability and the core phenotype of microdeletion 3p25.3 syndrome,” European Journal of Human Genetics, vol. 23, no. 6. Nature Publishing Group, pp. 753–760, 2015. ista: Kuechler A, Zink A, Wieland T, Lüdecke H, Cremer K, Salviati L, Magini P, Najafi K, Zweier C, Czeschik J, Aretz S, Endele S, Tamburrino F, Pinato C, Clementi M, Gundlach J, Maylahn C, Mazzanti L, Wohlleber E, Schwarzmayr T, Kariminejad R, Schlessinger A, Wieczorek D, Strom T, Novarino G, Engels H. 2015. Loss-of-function variants of SETD5 cause intellectual disability and the core phenotype of microdeletion 3p25.3 syndrome. European Journal of Human Genetics. 23(6), 753–760. mla: Kuechler, Alma, et al. “Loss-of-Function Variants of SETD5 Cause Intellectual Disability and the Core Phenotype of Microdeletion 3p25.3 Syndrome.” European Journal of Human Genetics, vol. 23, no. 6, Nature Publishing Group, 2015, pp. 753–60, doi:10.1038/ejhg.2014.165. short: A. Kuechler, A. Zink, T. Wieland, H. Lüdecke, K. Cremer, L. Salviati, P. Magini, K. Najafi, C. Zweier, J. Czeschik, S. Aretz, S. Endele, F. Tamburrino, C. Pinato, M. Clementi, J. Gundlach, C. Maylahn, L. Mazzanti, E. Wohlleber, T. Schwarzmayr, R. Kariminejad, A. Schlessinger, D. Wieczorek, T. Strom, G. Novarino, H. Engels, European Journal of Human Genetics 23 (2015) 753–760. date_created: 2018-12-11T11:54:01Z date_published: 2015-06-15T00:00:00Z date_updated: 2021-01-12T06:53:12Z day: '15' department: - _id: GaNo doi: 10.1038/ejhg.2014.165 external_id: pmid: - '25138099' intvolume: ' 23' issue: '6' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4795044/ month: '06' oa: 1 oa_version: Submitted Version page: 753 - 760 pmid: 1 publication: European Journal of Human Genetics publication_status: published publisher: Nature Publishing Group publist_id: '5324' quality_controlled: '1' status: public title: Loss-of-function variants of SETD5 cause intellectual disability and the core phenotype of microdeletion 3p25.3 syndrome type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 23 year: '2015' ... --- _id: '1804' abstract: - lang: eng text: It is known that in classical fluids turbulence typically occurs at high Reynolds numbers. But can turbulence occur at low Reynolds numbers? Here we investigate the transition to turbulence in the classic Taylor-Couette system in which the rotating fluids are manufactured ferrofluids with magnetized nanoparticles embedded in liquid carriers. We find that, in the presence of a magnetic field transverse to the symmetry axis of the system, turbulence can occur at Reynolds numbers that are at least one order of magnitude smaller than those in conventional fluids. This is established by extensive computational ferrohydrodynamics through a detailed investigation of transitions in the flow structure, and characterization of behaviors of physical quantities such as the energy, the wave number, and the angular momentum through the bifurcations. A finding is that, as the magnetic field is increased, onset of turbulence can be determined accurately and reliably. Our results imply that experimental investigation of turbulence may be feasible by using ferrofluids. Our study of transition to and evolution of turbulence in the Taylor-Couette ferrofluidic flow system provides insights into the challenging problem of turbulence control. article_number: '10781' author: - first_name: Sebastian full_name: Altmeyer, Sebastian id: 2EE67FDC-F248-11E8-B48F-1D18A9856A87 last_name: Altmeyer orcid: 0000-0001-5964-0203 - first_name: Younghae full_name: Do, Younghae last_name: Do - first_name: Ying full_name: Lai, Ying last_name: Lai citation: ama: Altmeyer S, Do Y, Lai Y. Transition to turbulence in Taylor-Couette ferrofluidic flow. Scientific Reports. 2015;5. doi:10.1038/srep10781 apa: Altmeyer, S., Do, Y., & Lai, Y. (2015). Transition to turbulence in Taylor-Couette ferrofluidic flow. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/srep10781 chicago: Altmeyer, Sebastian, Younghae Do, and Ying Lai. “Transition to Turbulence in Taylor-Couette Ferrofluidic Flow.” Scientific Reports. Nature Publishing Group, 2015. https://doi.org/10.1038/srep10781. ieee: S. Altmeyer, Y. Do, and Y. Lai, “Transition to turbulence in Taylor-Couette ferrofluidic flow,” Scientific Reports, vol. 5. Nature Publishing Group, 2015. ista: Altmeyer S, Do Y, Lai Y. 2015. Transition to turbulence in Taylor-Couette ferrofluidic flow. Scientific Reports. 5, 10781. mla: Altmeyer, Sebastian, et al. “Transition to Turbulence in Taylor-Couette Ferrofluidic Flow.” Scientific Reports, vol. 5, 10781, Nature Publishing Group, 2015, doi:10.1038/srep10781. short: S. Altmeyer, Y. Do, Y. Lai, Scientific Reports 5 (2015). date_created: 2018-12-11T11:54:06Z date_published: 2015-06-12T00:00:00Z date_updated: 2021-01-12T06:53:18Z day: '12' ddc: - '530' department: - _id: BjHo doi: 10.1038/srep10781 file: - access_level: open_access checksum: 7716f582f8c9d82d8f2bf80bf896b440 content_type: application/pdf creator: system date_created: 2018-12-12T10:17:26Z date_updated: 2020-07-14T12:45:16Z file_id: '5280' file_name: IST-2016-450-v1+1_srep10781.pdf file_size: 2449723 relation: main_file file_date_updated: 2020-07-14T12:45:16Z has_accepted_license: '1' intvolume: ' 5' language: - iso: eng month: '06' oa: 1 oa_version: Published Version publication: Scientific Reports publication_status: published publisher: Nature Publishing Group publist_id: '5306' pubrep_id: '450' quality_controlled: '1' scopus_import: 1 status: public title: Transition to turbulence in Taylor-Couette ferrofluidic flow tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 5 year: '2015' ... --- _id: '1807' abstract: - lang: eng text: We study a double Cahn-Hilliard type functional related to the Gross-Pitaevskii energy of two-components Bose-Einstein condensates. In the case of large but same order intercomponent and intracomponent coupling strengths, we prove Γ-convergence to a perimeter minimisation functional with an inhomogeneous surface tension. We study the asymptotic behavior of the surface tension as the ratio between the intercomponent and intracomponent coupling strengths becomes very small or very large and obtain good agreement with the physical literature. We obtain as a consequence, symmetry breaking of the minimisers for the harmonic potential. author: - first_name: Michael full_name: Goldman, Michael last_name: Goldman - first_name: Jimena full_name: Royo-Letelier, Jimena id: 4D3BED28-F248-11E8-B48F-1D18A9856A87 last_name: Royo-Letelier citation: ama: Goldman M, Royo-Letelier J. Sharp interface limit for two components Bose-Einstein condensates. ESAIM - Control, Optimisation and Calculus of Variations. 2015;21(3):603-624. doi:10.1051/cocv/2014040 apa: Goldman, M., & Royo-Letelier, J. (2015). Sharp interface limit for two components Bose-Einstein condensates. ESAIM - Control, Optimisation and Calculus of Variations. EDP Sciences. https://doi.org/10.1051/cocv/2014040 chicago: Goldman, Michael, and Jimena Royo-Letelier. “Sharp Interface Limit for Two Components Bose-Einstein Condensates.” ESAIM - Control, Optimisation and Calculus of Variations. EDP Sciences, 2015. https://doi.org/10.1051/cocv/2014040. ieee: M. Goldman and J. Royo-Letelier, “Sharp interface limit for two components Bose-Einstein condensates,” ESAIM - Control, Optimisation and Calculus of Variations, vol. 21, no. 3. EDP Sciences, pp. 603–624, 2015. ista: Goldman M, Royo-Letelier J. 2015. Sharp interface limit for two components Bose-Einstein condensates. ESAIM - Control, Optimisation and Calculus of Variations. 21(3), 603–624. mla: Goldman, Michael, and Jimena Royo-Letelier. “Sharp Interface Limit for Two Components Bose-Einstein Condensates.” ESAIM - Control, Optimisation and Calculus of Variations, vol. 21, no. 3, EDP Sciences, 2015, pp. 603–24, doi:10.1051/cocv/2014040. short: M. Goldman, J. Royo-Letelier, ESAIM - Control, Optimisation and Calculus of Variations 21 (2015) 603–624. date_created: 2018-12-11T11:54:07Z date_published: 2015-05-01T00:00:00Z date_updated: 2021-01-12T06:53:20Z day: '01' department: - _id: RoSe doi: 10.1051/cocv/2014040 intvolume: ' 21' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1401.1727 month: '05' oa: 1 oa_version: Preprint page: 603 - 624 publication: ESAIM - Control, Optimisation and Calculus of Variations publication_status: published publisher: EDP Sciences publist_id: '5303' quality_controlled: '1' scopus_import: 1 status: public title: Sharp interface limit for two components Bose-Einstein condensates type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 21 year: '2015' ... --- _id: '1810' 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. author: - first_name: Mark Tobias full_name: Bollenbach, Mark Tobias id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87 last_name: Bollenbach orcid: 0000-0003-4398-476X citation: 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' 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' 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.' 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.' ista: 'Bollenbach MT. 2015. Antimicrobial interactions: Mechanisms and implications for drug discovery and resistance evolution. Current Opinion in Microbiology. 27, 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.' short: M.T. Bollenbach, Current Opinion in Microbiology 27 (2015) 1–9. date_created: 2018-12-11T11:54:08Z date_published: 2015-06-01T00:00:00Z date_updated: 2021-01-12T06:53:21Z day: '01' ddc: - '570' department: - _id: ToBo doi: 10.1016/j.mib.2015.05.008 ec_funded: 1 file: - access_level: open_access checksum: 1683bb0f42ef892a5b3b71a050d65d25 content_type: application/pdf creator: system date_created: 2018-12-12T10:17:23Z date_updated: 2020-07-14T12:45:17Z file_id: '5277' file_name: IST-2016-493-v1+1_1-s2.0-S1369527415000594-main.pdf file_size: 1047255 relation: main_file file_date_updated: 2020-07-14T12:45:17Z has_accepted_license: '1' intvolume: ' 27' language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: 1 - 9 project: - _id: 25E9AF9E-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P27201-B22 name: Revealing the mechanisms underlying drug interactions - _id: 25E83C2C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '303507' 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 publication: Current Opinion in Microbiology publication_status: published publisher: Elsevier publist_id: '5298' pubrep_id: '493' quality_controlled: '1' scopus_import: 1 status: public title: 'Antimicrobial interactions: Mechanisms and implications for drug discovery and resistance evolution' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 27 year: '2015' ... --- _id: '1812' abstract: - lang: eng 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" article_number: '045005' article_processing_charge: No author: - first_name: Martin full_name: Lahrz, Martin last_name: Lahrz - first_name: Mikhail full_name: Lemeshko, Mikhail id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 - first_name: Ludwig full_name: Mathey, Ludwig last_name: Mathey citation: 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 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. 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. 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. short: M. Lahrz, M. Lemeshko, L. Mathey, New Journal of Physics 17 (2015). date_created: 2018-12-11T11:54:09Z date_published: 2015-04-01T00:00:00Z date_updated: 2021-01-12T06:53:22Z day: '01' ddc: - '530' department: - _id: MiLe doi: 10.1088/1367-2630/17/4/045005 file: - access_level: open_access checksum: 551f751a75b39b89a1db2f7f498f9a49 content_type: application/pdf creator: system date_created: 2018-12-12T10:15:59Z date_updated: 2020-07-14T12:45:17Z file_id: '5184' file_name: IST-2016-446-v1+1_document.pdf file_size: 1900925 relation: main_file file_date_updated: 2020-07-14T12:45:17Z has_accepted_license: '1' intvolume: ' 17' issue: '4' language: - iso: eng month: '04' oa: 1 oa_version: Published Version publication: New Journal of Physics publication_status: published publisher: IOP Publishing Ltd. publist_id: '5294' pubrep_id: '446' quality_controlled: '1' scopus_import: 1 status: public title: 'Exotic roton excitations in quadrupolar Bose–Einstein condensates ' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 17 year: '2015' ... --- _id: '1811' abstract: - lang: eng 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. 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. article_number: '052105' author: - first_name: Laleh full_name: Safari, Laleh id: 3C325E5E-F248-11E8-B48F-1D18A9856A87 last_name: Safari - first_name: José full_name: Santos, José last_name: Santos - first_name: Pedro full_name: Amaro, Pedro last_name: Amaro - first_name: Kari full_name: Jänkälä, Kari last_name: Jänkälä - first_name: Filippo full_name: Fratini, Filippo last_name: Fratini citation: 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' 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' 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.' 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.' 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.' 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.' short: L. Safari, J. Santos, P. Amaro, K. Jänkälä, F. Fratini, Journal of Mathematical Physics 56 (2015). date_created: 2018-12-11T11:54:08Z date_published: 2015-05-20T00:00:00Z date_updated: 2021-01-12T06:53:21Z day: '20' department: - _id: MiLe doi: 10.1063/1.4921227 ec_funded: 1 intvolume: ' 56' issue: '5' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1409.0110 month: '05' oa: 1 oa_version: Preprint project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Journal of Mathematical Physics publication_status: published publisher: American Institute of Physics publist_id: '5295' scopus_import: 1 status: public title: 'Analytical evaluation of atomic form factors: Application to Rayleigh scattering' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 56 year: '2015' ... --- _id: '1813' abstract: - lang: eng 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. article_number: '203001' author: - first_name: Richard full_name: Schmidt, Richard last_name: Schmidt - first_name: Mikhail full_name: Lemeshko, Mikhail id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 citation: 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 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 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. 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. 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. short: R. Schmidt, M. Lemeshko, Physical Review Letters 114 (2015). date_created: 2018-12-11T11:54:09Z date_published: 2015-05-18T00:00:00Z date_updated: 2021-01-12T06:53:22Z day: '18' department: - _id: MiLe doi: 10.1103/PhysRevLett.114.203001 intvolume: ' 114' issue: '20' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1502.03447 month: '05' oa: 1 oa_version: Preprint publication: Physical Review Letters publication_status: published publisher: American Physical Society publist_id: '5293' quality_controlled: '1' scopus_import: 1 status: public title: Rotation of quantum impurities in the presence of a many-body environment type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 114 year: '2015' ... --- _id: '1808' article_number: '7' author: - first_name: Ashutosh full_name: Gupta, Ashutosh id: 335E5684-F248-11E8-B48F-1D18A9856A87 last_name: Gupta - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 citation: 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 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 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. 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. 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. 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). date_created: 2018-12-11T11:54:07Z date_published: 2015-05-01T00:00:00Z date_updated: 2021-01-12T06:53:20Z day: '01' department: - _id: ToHe doi: 10.1145/2745799 intvolume: ' 25' issue: '2' language: - iso: eng month: '05' oa_version: None publication: ACM Transactions on Modeling and Computer Simulation publication_status: published publisher: ACM publist_id: '5302' quality_controlled: '1' status: public title: Guest editors' introduction to special issue on computational methods in systems biology type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 25 year: '2015' ... --- _id: '1817' 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. ' author: - first_name: Sean full_name: Porazinski, Sean last_name: Porazinski - first_name: Huijia full_name: Wang, Huijia last_name: Wang - first_name: Yoichi full_name: Asaoka, Yoichi last_name: Asaoka - first_name: Martin full_name: Behrndt, Martin id: 3ECECA3A-F248-11E8-B48F-1D18A9856A87 last_name: Behrndt - first_name: Tatsuo full_name: Miyamoto, Tatsuo last_name: Miyamoto - first_name: Hitoshi full_name: Morita, Hitoshi id: 4C6E54C6-F248-11E8-B48F-1D18A9856A87 last_name: Morita - first_name: Shoji full_name: Hata, Shoji last_name: Hata - first_name: Takashi full_name: Sasaki, Takashi last_name: Sasaki - first_name: Gabriel full_name: Krens, Gabriel id: 2B819732-F248-11E8-B48F-1D18A9856A87 last_name: Krens orcid: 0000-0003-4761-5996 - first_name: Yumi full_name: Osada, Yumi last_name: Osada - first_name: Satoshi full_name: Asaka, Satoshi last_name: Asaka - first_name: Akihiro full_name: Momoi, Akihiro last_name: Momoi - first_name: Sarah full_name: Linton, Sarah last_name: Linton - first_name: Joel full_name: Miesfeld, Joel last_name: Miesfeld - first_name: Brian full_name: Link, Brian last_name: Link - first_name: Takeshi full_name: Senga, Takeshi last_name: Senga - first_name: Atahualpa full_name: Castillo Morales, Atahualpa last_name: Castillo Morales - first_name: Araxi full_name: Urrutia, Araxi last_name: Urrutia - first_name: Nobuyoshi full_name: Shimizu, Nobuyoshi last_name: Shimizu - first_name: Hideaki full_name: Nagase, Hideaki last_name: Nagase - first_name: Shinya full_name: Matsuura, Shinya last_name: Matsuura - first_name: Stefan full_name: Bagby, Stefan last_name: Bagby - first_name: Hisato full_name: Kondoh, Hisato last_name: Kondoh - first_name: Hiroshi full_name: Nishina, Hiroshi last_name: Nishina - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 - first_name: Makoto full_name: Furutani Seiki, Makoto last_name: Furutani Seiki citation: 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 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 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. 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. 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. 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. 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. date_created: 2018-12-11T11:54:10Z date_published: 2015-03-16T00:00:00Z date_updated: 2021-01-12T06:53:23Z day: '16' department: - _id: CaHe doi: 10.1038/nature14215 external_id: pmid: - '25778702' intvolume: ' 521' issue: '7551' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4720436/ month: '03' oa: 1 oa_version: Submitted Version page: 217 - 221 pmid: 1 publication: Nature publication_status: published publisher: Nature Publishing Group publist_id: '5289' quality_controlled: '1' scopus_import: 1 status: public title: YAP is essential for tissue tension to ensure vertebrate 3D body shape type: journal_article user_id: 2EBD1598-F248-11E8-B48F-1D18A9856A87 volume: 521 year: '2015' ... --- _id: '1820' 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.' 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.' alternative_title: - Artifical Intelligence author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Martin full_name: Chmelik, Martin id: 3624234E-F248-11E8-B48F-1D18A9856A87 last_name: Chmelik - first_name: Raghav full_name: Gupta, Raghav last_name: Gupta - first_name: Ayush full_name: Kanodia, Ayush last_name: Kanodia citation: 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.' 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.' 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. 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. 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.' 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. conference: end_date: 2015-01-30 location: Austin, TX, USA name: 'IAAI: Innovative Applications of Artificial Intelligence' start_date: 2015-01-25 date_created: 2018-12-11T11:54:11Z date_published: 2015-06-01T00:00:00Z date_updated: 2023-02-23T10:02:57Z day: '01' department: - _id: KrCh ec_funded: 1 external_id: arxiv: - '1411.3880' intvolume: ' 5' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1411.3880 month: '06' oa: 1 oa_version: Preprint page: 3496-3502 project: - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' publication: 'Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence ' publication_status: published publisher: AAAI Press publist_id: '5286' quality_controlled: '1' related_material: record: - id: '1529' relation: later_version status: public scopus_import: 1 status: public title: Optimal cost almost-sure reachability in POMDPs type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 5 year: '2015' ... --- _id: '1814' 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.' article_number: '27' author: - first_name: Stefan full_name: Jeschke, Stefan id: 44D6411A-F248-11E8-B48F-1D18A9856A87 last_name: Jeschke - first_name: Christopher J full_name: Wojtan, Christopher J id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87 last_name: Wojtan orcid: 0000-0001-6646-5546 citation: ama: Jeschke S, Wojtan C. Water wave animation via wavefront parameter interpolation. ACM Transactions on Graphics. 2015;34(3). doi:10.1145/2714572 apa: Jeschke, S., & Wojtan, C. (2015). Water wave animation via wavefront parameter interpolation. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/2714572 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. ieee: S. Jeschke and C. Wojtan, “Water wave animation via wavefront parameter interpolation,” ACM Transactions on Graphics, vol. 34, no. 3. ACM, 2015. ista: Jeschke S, Wojtan C. 2015. Water wave animation via wavefront parameter interpolation. ACM Transactions on Graphics. 34(3), 27. 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). date_created: 2018-12-11T11:54:09Z date_published: 2015-04-01T00:00:00Z date_updated: 2023-02-23T10:15:40Z day: '01' ddc: - '000' department: - _id: ChWo doi: 10.1145/2714572 ec_funded: 1 file: - access_level: open_access checksum: 67c9f4fa370def68cdf31299e48bc91f content_type: application/pdf creator: system date_created: 2018-12-12T10:12:15Z date_updated: 2020-07-14T12:45:17Z file_id: '4933' file_name: IST-2016-575-v1+1_wavefront_preprint.pdf file_size: 23712153 relation: main_file file_date_updated: 2020-07-14T12:45:17Z has_accepted_license: '1' intvolume: ' 34' issue: '3' language: - iso: eng month: '04' oa: 1 oa_version: Submitted Version project: - _id: 25357BD2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 24352-N23 name: 'Deep Pictures: Creating Visual and Haptic Vector Images' - _id: 2533E772-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '638176' name: Efficient Simulation of Natural Phenomena at Extremely Large Scales publication: ACM Transactions on Graphics publication_status: published publisher: ACM publist_id: '5292' pubrep_id: '575' quality_controlled: '1' scopus_import: 1 status: public title: Water wave animation via wavefront parameter interpolation type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 34 year: '2015' ... --- _id: '1818' 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.' author: - first_name: Jitka full_name: Polechova, Jitka id: 3BBFB084-F248-11E8-B48F-1D18A9856A87 last_name: Polechova orcid: 0000-0003-0951-3112 - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: Polechova J, Barton NH. Limits to adaptation along environmental gradients. PNAS. 2015;112(20):6401-6406. doi:10.1073/pnas.1421515112 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 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. 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. ista: Polechova J, Barton NH. 2015. Limits to adaptation along environmental gradients. PNAS. 112(20), 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. short: J. Polechova, N.H. Barton, PNAS 112 (2015) 6401–6406. date_created: 2018-12-11T11:54:11Z date_published: 2015-05-19T00:00:00Z date_updated: 2021-01-12T06:53:24Z day: '19' department: - _id: NiBa doi: 10.1073/pnas.1421515112 ec_funded: 1 external_id: pmid: - '25941385' intvolume: ' 112' issue: '20' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4443383/ month: '05' oa: 1 oa_version: Submitted Version page: 6401 - 6406 pmid: 1 project: - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation publication: PNAS publication_status: published publisher: National Academy of Sciences publist_id: '5288' quality_controlled: '1' scopus_import: 1 status: public title: Limits to adaptation along environmental gradients type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 112 year: '2015' ... --- _id: '1819' 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.' 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.. author: - first_name: Marta full_name: Zwiewka, Marta last_name: Zwiewka - first_name: Tomasz full_name: Nodzyński, Tomasz last_name: Nodzyński - first_name: Stéphanie full_name: Robert, Stéphanie last_name: Robert - first_name: Steffen full_name: Vanneste, Steffen last_name: Vanneste - first_name: Jiřĺ full_name: Friml, Jiřĺ id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: 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 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 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. 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. 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. 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_created: 2018-12-11T11:54:11Z date_published: 2015-08-03T00:00:00Z date_updated: 2021-01-12T06:53:24Z day: '03' department: - _id: JiFr doi: 10.1016/j.molp.2015.03.007 ec_funded: 1 intvolume: ' 8' issue: '8' language: - iso: eng month: '08' oa_version: None page: 1175 - 1187 project: - _id: 25716A02-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '282300' name: Polarity and subcellular dynamics in plants publication: Molecular Plant publication_status: published publisher: Elsevier publist_id: '5287' quality_controlled: '1' scopus_import: 1 status: public title: Osmotic stress modulates the balance between exocytosis and clathrin mediated endocytosis in Arabidopsis thaliana type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8 year: '2015' ... --- _id: '1823' 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. article_number: '807' author: - first_name: Guillaume full_name: Chevereau, Guillaume id: 424D78A0-F248-11E8-B48F-1D18A9856A87 last_name: Chevereau - first_name: Mark Tobias full_name: Bollenbach, Mark Tobias id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87 last_name: Bollenbach orcid: 0000-0003-4398-476X 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 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. 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. 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. short: G. Chevereau, M.T. Bollenbach, Molecular Systems Biology 11 (2015). date_created: 2018-12-11T11:54:12Z date_published: 2015-04-01T00:00:00Z date_updated: 2021-01-12T06:53:26Z day: '01' ddc: - '570' department: - _id: ToBo doi: 10.15252/msb.20156098 ec_funded: 1 file: - access_level: open_access checksum: 4289b518fbe2166682fb1a1ef9b405f3 content_type: application/pdf creator: system date_created: 2018-12-12T10:14:34Z date_updated: 2020-07-14T12:45:17Z file_id: '5087' file_name: IST-2015-395-v1+1_807.full.pdf file_size: 1273573 relation: main_file file_date_updated: 2020-07-14T12:45:17Z has_accepted_license: '1' intvolume: ' 11' issue: '4' language: - iso: eng month: '04' oa: 1 oa_version: Published Version project: - _id: 25E9AF9E-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P27201-B22 name: Revealing the mechanisms underlying drug interactions - _id: 25EB3A80-B435-11E9-9278-68D0E5697425 grant_number: RGP0042/2013 name: Revealing the fundamental limits of cell growth - _id: 25E83C2C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '303507' name: Optimality principles in responses to antibiotics publication: Molecular Systems Biology publication_status: published publisher: Nature Publishing Group publist_id: '5283' pubrep_id: '395' quality_controlled: '1' scopus_import: 1 status: public title: Systematic discovery of drug interaction mechanisms tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 11 year: '2015' ... --- _id: '1824' 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. article_number: '6977' author: - first_name: Johannes full_name: Knebel, Johannes last_name: Knebel - first_name: Markus full_name: Weber, Markus last_name: Weber - first_name: Torben H full_name: Krüger, Torben H id: 3020C786-F248-11E8-B48F-1D18A9856A87 last_name: Krüger orcid: 0000-0002-4821-3297 - first_name: Erwin full_name: Frey, Erwin last_name: Frey citation: 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 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 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. 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. ista: Knebel J, Weber M, Krüger TH, Frey E. 2015. Evolutionary games of condensates in coupled birth-death processes. Nature Communications. 6, 6977. 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). date_created: 2018-12-11T11:54:13Z date_published: 2015-04-24T00:00:00Z date_updated: 2021-01-12T06:53:26Z day: '24' ddc: - '530' department: - _id: LaEr doi: 10.1038/ncomms7977 file: - access_level: open_access checksum: c4cffb5c8b245e658a34eac71a03e7cc content_type: application/pdf creator: system date_created: 2018-12-12T10:16:54Z date_updated: 2020-07-14T12:45:17Z file_id: '5245' file_name: IST-2016-451-v1+1_ncomms7977.pdf file_size: 1151501 relation: main_file file_date_updated: 2020-07-14T12:45:17Z has_accepted_license: '1' intvolume: ' 6' language: - iso: eng month: '04' oa: 1 oa_version: Published Version publication: Nature Communications publication_status: published publisher: Nature Publishing Group publist_id: '5282' pubrep_id: '451' quality_controlled: '1' scopus_import: 1 status: public title: Evolutionary games of condensates in coupled birth-death processes tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 6 year: '2015' ... --- _id: '1831' abstract: - lang: eng 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. 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. article_number: '20140116' author: - first_name: Peter full_name: Kappeler, Peter last_name: Kappeler - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 - first_name: Charles full_name: Nunn, Charles last_name: Nunn citation: 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' 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' 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.' 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.' 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.' 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.' short: P. Kappeler, S. Cremer, C. Nunn, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 370 (2015). date_created: 2018-12-11T11:54:15Z date_published: 2015-05-01T00:00:00Z date_updated: 2021-01-12T06:53:29Z day: '01' department: - _id: SyCr doi: 10.1098/rstb.2014.0116 external_id: pmid: - '25870402' intvolume: ' 370' issue: '1669' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4410382/ month: '05' oa: 1 oa_version: Submitted Version pmid: 1 publication: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences publication_status: published publisher: Royal Society publist_id: '5272' quality_controlled: '1' scopus_import: 1 status: public title: 'Sociality and health: Impacts of sociality on disease susceptibility and transmission in animal and human societies' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 370 year: '2015' ... --- _id: '1828' 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. article_processing_charge: No author: - first_name: Arseniy full_name: Akopyan, Arseniy id: 430D2C90-F248-11E8-B48F-1D18A9856A87 last_name: Akopyan orcid: 0000-0002-2548-617X - first_name: Sergey full_name: Pirogov, Sergey last_name: Pirogov - first_name: Aleksandr full_name: Rybko, Aleksandr last_name: Rybko citation: 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 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 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. 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. ista: Akopyan A, Pirogov S, Rybko A. 2015. Invariant measures of genetic recombination process. Journal of Statistical Physics. 160(1), 163–167. 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. date_created: 2018-12-11T11:54:14Z date_published: 2015-07-01T00:00:00Z date_updated: 2021-01-12T06:53:28Z day: '01' department: - _id: HeEd doi: 10.1007/s10955-015-1238-5 ec_funded: 1 intvolume: ' 160' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: arxiv.org/abs/1406.5313 month: '07' oa: 1 oa_version: Preprint page: 163 - 167 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Journal of Statistical Physics publication_status: published publisher: Springer publist_id: '5276' quality_controlled: '1' scopus_import: 1 status: public title: Invariant measures of genetic recombination process type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 160 year: '2015' ... --- _id: '1836' abstract: - lang: eng 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. alternative_title: - LNCS author: - first_name: Pavol full_name: Cerny, Pavol id: 4DCBEFFE-F248-11E8-B48F-1D18A9856A87 last_name: Cerny - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Laura full_name: Kovács, Laura last_name: Kovács - first_name: Arjun full_name: Radhakrishna, Arjun id: 3B51CAC4-F248-11E8-B48F-1D18A9856A87 last_name: Radhakrishna - first_name: Jakob full_name: Zwirchmayr, Jakob last_name: Zwirchmayr citation: 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 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' 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. 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. ista: Cerny P, Henzinger TA, Kovács L, Radhakrishna A, Zwirchmayr J. 2015. Segment abstraction for worst-case execution time analysis. 9032, 105–131. 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. conference: end_date: 2015-04-18 location: London, United Kingdom name: 'ESOP: European Symposium on Programming' start_date: 2015-04-11 date_created: 2018-12-11T11:54:16Z date_published: 2015-04-01T00:00:00Z date_updated: 2020-08-11T10:09:32Z day: '01' department: - _id: ToHe doi: 10.1007/978-3-662-46669-8_5 ec_funded: 1 intvolume: ' 9032' language: - iso: eng month: '04' oa_version: None page: 105 - 131 project: - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering publication_status: published publisher: Springer publist_id: '5266' quality_controlled: '1' scopus_import: 1 series_title: Lecture Notes in Computer Science status: public title: Segment abstraction for worst-case execution time analysis type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9032 year: '2015' ... --- _id: '1838' abstract: - lang: eng 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. 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).' alternative_title: - LNCS author: - first_name: Roderick full_name: Bloem, Roderick last_name: Bloem - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Swen full_name: Jacobs, Swen last_name: Jacobs - first_name: Robert full_name: Könighofer, Robert last_name: Könighofer citation: 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' 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' 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. 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.' 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.' 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. conference: end_date: 2015-04-18 location: London, United Kingdom name: 'TACAS: Tools and Algorithms for the Construction and Analysis of Systems' start_date: 2015-04-11 date_created: 2018-12-11T11:54:17Z date_published: 2015-01-01T00:00:00Z date_updated: 2021-01-12T06:53:32Z day: '01' department: - _id: KrCh doi: 10.1007/978-3-662-46681-0_50 ec_funded: 1 intvolume: ' 9035' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1411.4604 month: '01' oa: 1 oa_version: Preprint page: 517 - 532 project: - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' publication_status: published publisher: Springer publist_id: '5264' scopus_import: 1 status: public title: Assume-guarantee synthesis for concurrent reactive programs with partial information type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9035 year: '2015' ... --- _id: '1839' 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. alternative_title: - LNCS author: - first_name: Tomáš full_name: Brázdil, Tomáš last_name: Brázdil - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Vojtěch full_name: Forejt, Vojtěch last_name: Forejt - first_name: Antonín full_name: Kučera, Antonín last_name: Kučera 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' 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.' 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.' 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.' short: T. Brázdil, K. Chatterjee, V. Forejt, A. Kučera, 9035 (2015) 181–187. conference: end_date: 2015-04-18 location: London, United Kingdom name: 'TACAS: Tools and Algorithms for the Construction and Analysis of Systems' start_date: 2015-04-11 date_created: 2018-12-11T11:54:18Z date_published: 2015-01-01T00:00:00Z date_updated: 2020-01-21T13:18:52Z day: '01' department: - _id: KrCh doi: 10.1007/978-3-662-46681-0_12 ec_funded: 1 intvolume: ' 9035' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1501.03093 month: '01' oa: 1 oa_version: Preprint page: 181 - 187 project: - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' publication_status: published publisher: Springer publist_id: '5263' quality_controlled: '1' series_title: Lecture Notes in Computer Science status: public title: 'Multigain: A controller synthesis tool for MDPs with multiple mean-payoff objectives' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9035 year: '2015' ... --- _id: '1837' 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.' article_number: R3 article_processing_charge: No article_type: original author: - first_name: Jakob full_name: Kühnen, Jakob id: 3A47AE32-F248-11E8-B48F-1D18A9856A87 last_name: Kühnen orcid: 0000-0003-4312-0179 - first_name: P full_name: Braunshier, P last_name: Braunshier - first_name: M full_name: Schwegel, M last_name: Schwegel - first_name: Hendrik full_name: Kuhlmann, Hendrik last_name: Kuhlmann - first_name: Björn full_name: Hof, Björn id: 3A374330-F248-11E8-B48F-1D18A9856A87 last_name: Hof orcid: 0000-0003-2057-2754 citation: 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 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 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. 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. 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. short: J. Kühnen, P. Braunshier, M. Schwegel, H. Kuhlmann, B. Hof, Journal of Fluid Mechanics 770 (2015). date_created: 2018-12-11T11:54:17Z date_published: 2015-04-08T00:00:00Z date_updated: 2021-01-12T06:53:31Z day: '08' department: - _id: BjHo doi: 10.1017/jfm.2015.184 ec_funded: 1 external_id: arxiv: - '1508.06559' intvolume: ' 770' issue: '5' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1508.06559 month: '04' oa: 1 oa_version: Preprint project: - _id: 25152F3A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '306589' name: Decoding the complexity of turbulence at its origin publication: Journal of Fluid Mechanics publication_status: published publisher: Cambridge University Press publist_id: '5265' quality_controlled: '1' scopus_import: 1 status: public title: Subcritical versus supercritical transition to turbulence in curved pipes type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 770 year: '2015' ... --- _id: '1846' abstract: - lang: eng 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. article_processing_charge: No article_type: original author: - first_name: Nikola full_name: Beneš, Nikola last_name: Beneš - first_name: Jan full_name: Kretinsky, Jan id: 44CEF464-F248-11E8-B48F-1D18A9856A87 last_name: Kretinsky orcid: 0000-0002-8122-2881 - first_name: Kim full_name: Larsen, Kim last_name: Larsen - first_name: Mikael full_name: Möller, Mikael last_name: Möller - first_name: Salomon full_name: Sickert, Salomon last_name: Sickert - first_name: Jiří full_name: Srba, Jiří last_name: Srba citation: 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 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 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. 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. 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. short: N. Beneš, J. Kretinsky, K. Larsen, M. Möller, S. Sickert, J. Srba, Acta Informatica 52 (2015) 269–297. date_created: 2018-12-11T11:54:20Z date_published: 2015-04-01T00:00:00Z date_updated: 2021-01-12T06:53:35Z day: '01' ddc: - '000' department: - _id: ToHe - _id: KrCh doi: 10.1007/s00236-015-0215-4 ec_funded: 1 file: - access_level: open_access checksum: fb4037ddc4fc05f33080dd3547ede350 content_type: application/pdf creator: dernst date_created: 2020-05-15T08:57:44Z date_updated: 2020-07-14T12:45:19Z file_id: '7854' file_name: 2015_ActaInfo_Benes.pdf file_size: 488482 relation: main_file file_date_updated: 2020-07-14T12:45:19Z has_accepted_license: '1' intvolume: ' 52' issue: 2-3 language: - iso: eng month: '04' oa: 1 oa_version: Submitted Version page: 269 - 297 project: - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering publication: Acta Informatica publication_status: published publisher: Springer publist_id: '5255' quality_controlled: '1' scopus_import: 1 status: public title: Refinement checking on parametric modal transition systems type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 52 year: '2015' ... --- _id: '1845' 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. article_processing_charge: No author: - first_name: David H full_name: Vandael, David H id: 3AE48E0A-F248-11E8-B48F-1D18A9856A87 last_name: Vandael orcid: 0000-0001-7577-1676 - first_name: 'Claudia ' full_name: 'Espinoza Martinez, Claudia ' id: 31FFEE2E-F248-11E8-B48F-1D18A9856A87 last_name: Espinoza Martinez orcid: 0000-0003-4710-2082 - first_name: Peter M full_name: Jonas, Peter M id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 citation: 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 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 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. 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. ista: Vandael DH, Espinoza Martinez C, Jonas PM. 2015. Excitement about inhibitory presynaptic terminals. Neuron. 85(6), 1149–1151. 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. date_created: 2018-12-11T11:54:19Z date_published: 2015-03-18T00:00:00Z date_updated: 2021-10-08T09:07:34Z day: '18' ddc: - '570' department: - _id: PeJo doi: 10.1016/j.neuron.2015.03.006 file: - access_level: open_access checksum: d1808550e376a0eca2a950fda017cfa6 content_type: application/pdf creator: system date_created: 2018-12-12T10:16:07Z date_updated: 2020-07-14T12:45:19Z file_id: '5192' file_name: IST-2017-822-v1+1_Perspective_Fig__Final.pdf file_size: 411832 relation: main_file - access_level: open_access checksum: a279f4ae61e6c8f33d68f69a0d02097d content_type: application/pdf creator: system date_created: 2018-12-12T10:16:07Z date_updated: 2020-07-14T12:45:19Z file_id: '5193' file_name: IST-2017-822-v1+2_Perspective_Final2.pdf file_size: 100769 relation: main_file file_date_updated: 2020-07-14T12:45:19Z has_accepted_license: '1' intvolume: ' 85' issue: '6' language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: 1149 - 1151 publication: Neuron publication_status: published publisher: Elsevier publist_id: '5256' pubrep_id: '822' quality_controlled: '1' scopus_import: '1' status: public title: Excitement about inhibitory presynaptic terminals tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 85 year: '2015' ... --- _id: '1840' abstract: - lang: eng 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. 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" author: - first_name: Bernhard full_name: Geiger, Bernhard last_name: Geiger - first_name: Tatjana full_name: Petrov, Tatjana id: 3D5811FC-F248-11E8-B48F-1D18A9856A87 last_name: Petrov orcid: 0000-0002-9041-0905 - first_name: Gernot full_name: Kubin, Gernot last_name: Kubin - first_name: Heinz full_name: Koeppl, Heinz last_name: Koeppl citation: 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 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 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. 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. 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. 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. date_created: 2018-12-11T11:54:18Z date_published: 2015-04-01T00:00:00Z date_updated: 2021-01-12T06:53:33Z day: '01' department: - _id: CaGu - _id: ToHe doi: 10.1109/TAC.2014.2364971 intvolume: ' 60' issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1304.6603 month: '04' oa: 1 oa_version: Preprint page: 1010 - 1022 publication: IEEE Transactions on Automatic Control publication_identifier: issn: - 0018-9286 publication_status: published publisher: IEEE publist_id: '5262' quality_controlled: '1' scopus_import: 1 status: public title: Optimal Kullback-Leibler aggregation via information bottleneck type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 60 year: '2015' ... --- _id: '1841' abstract: - lang: eng 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. author: - first_name: Vladimir full_name: Kolmogorov, Vladimir id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov 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 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. 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. 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. short: V. Kolmogorov, IEEE Transactions on Pattern Analysis and Machine Intelligence 37 (2015) 919–930. date_created: 2018-12-11T11:54:18Z date_published: 2015-05-01T00:00:00Z date_updated: 2021-01-12T06:53:33Z day: '01' department: - _id: VlKo doi: 10.1109/TPAMI.2014.2363465 ec_funded: 1 intvolume: ' 37' issue: '5' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1309.5655 month: '05' oa: 1 oa_version: Preprint page: 919 - 930 project: - _id: 25FBA906-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '616160' name: 'Discrete Optimization in Computer Vision: Theory and Practice' publication: IEEE Transactions on Pattern Analysis and Machine Intelligence publication_status: published publisher: IEEE publist_id: '5261' quality_controlled: '1' scopus_import: 1 status: public title: A new look at reweighted message passing type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 37 year: '2015' ... --- _id: '1849' 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.' 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.). author: - first_name: Ellie full_name: Himschoot, Ellie last_name: Himschoot - first_name: Tom full_name: Beeckman, Tom last_name: Beeckman - first_name: Jiřĺ full_name: Friml, Jiřĺ id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Steffen full_name: Vanneste, Steffen last_name: Vanneste citation: 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 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 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. 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. 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. 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. date_created: 2018-12-11T11:54:21Z date_published: 2015-09-01T00:00:00Z date_updated: 2021-01-12T06:53:36Z day: '01' department: - _id: JiFr doi: 10.1016/j.bbamcr.2015.02.017 intvolume: ' 1853' issue: '9' language: - iso: eng month: '09' oa_version: None page: 2168 - 2172 publication: Biochimica et Biophysica Acta - Molecular Cell Research publication_status: published publisher: Elsevier publist_id: '5252' quality_controlled: '1' scopus_import: 1 status: public title: Calcium is an organizer of cell polarity in plants type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 1853 year: '2015' ... --- _id: '1847' 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). author: - first_name: Peter full_name: Grones, Peter id: 399876EC-F248-11E8-B48F-1D18A9856A87 last_name: Grones - first_name: Jiřĺ full_name: Friml, Jiřĺ id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: 'Grones P, Friml J. ABP1: Finally docking. Molecular Plant. 2015;8(3):356-358. doi:10.1016/j.molp.2014.12.013' apa: 'Grones, P., & Friml, J. (2015). ABP1: Finally docking. Molecular Plant. Elsevier. https://doi.org/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.' ieee: 'P. Grones and J. Friml, “ABP1: Finally docking,” Molecular Plant, vol. 8, no. 3. Elsevier, pp. 356–358, 2015.' ista: 'Grones P, Friml J. 2015. ABP1: Finally docking. Molecular Plant. 8(3), 356–358.' 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. date_created: 2018-12-11T11:54:20Z date_published: 2015-03-02T00:00:00Z date_updated: 2021-01-12T06:53:35Z day: '02' department: - _id: JiFr doi: 10.1016/j.molp.2014.12.013 intvolume: ' 8' issue: '3' language: - iso: eng month: '03' oa_version: None page: 356 - 358 publication: Molecular Plant publication_status: published publisher: Elsevier publist_id: '5254' quality_controlled: '1' scopus_import: 1 status: public title: 'ABP1: Finally docking' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8 year: '2015' ... --- _id: '1850' abstract: - lang: eng 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.' author: - first_name: Sebastian full_name: Novak, Sebastian id: 461468AE-F248-11E8-B48F-1D18A9856A87 last_name: Novak - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 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' 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' 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.' 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.' 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.' 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. date_created: 2018-12-11T11:54:21Z date_published: 2015-05-07T00:00:00Z date_updated: 2021-01-12T06:53:37Z day: '07' ddc: - '576' department: - _id: NiBa - _id: SyCr doi: 10.1016/j.jtbi.2015.02.018 ec_funded: 1 file: - access_level: open_access checksum: 3c0dcacc900bc45cc65a453dfda4ca43 content_type: application/pdf creator: system date_created: 2018-12-12T10:18:07Z date_updated: 2020-07-14T12:45:19Z file_id: '5326' file_name: IST-2015-329-v1+1_manuscript.pdf file_size: 1546914 relation: main_file file_date_updated: 2020-07-14T12:45:19Z has_accepted_license: '1' intvolume: ' 372' issue: '5' language: - iso: eng month: '05' oa: 1 oa_version: Submitted Version page: 54 - 64 project: - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation - _id: 25DC711C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '243071' name: 'Social Vaccination in Ant Colonies: from Individual Mechanisms to Society Effects' publication: Journal of Theoretical Biology publication_status: published publisher: Elsevier publist_id: '5251' pubrep_id: '329' quality_controlled: '1' scopus_import: 1 status: public title: 'Fungal disease dynamics in insect societies: Optimal killing rates and the ambivalent effect of high social interaction rates' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 372 year: '2015' ... --- _id: '1851' 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. article_processing_charge: No article_type: original author: - first_name: Tadeas full_name: Priklopil, Tadeas id: 3C869AA0-F248-11E8-B48F-1D18A9856A87 last_name: Priklopil - first_name: Eva full_name: Kisdi, Eva last_name: Kisdi - first_name: Mats full_name: Gyllenberg, Mats last_name: Gyllenberg 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 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. 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. 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. short: T. Priklopil, E. Kisdi, M. Gyllenberg, Evolution 69 (2015) 1015–1026. date_created: 2018-12-11T11:54:21Z date_published: 2015-02-09T00:00:00Z date_updated: 2022-06-07T10:52:37Z day: '09' ddc: - '570' department: - _id: NiBa - _id: KrCh doi: 10.1111/evo.12618 ec_funded: 1 external_id: pmid: - '25662095' file: - access_level: open_access checksum: 1e8be0b1d7598a78cd2623d8ee8e7798 content_type: application/pdf creator: dernst date_created: 2020-05-15T09:05:34Z date_updated: 2020-07-14T12:45:19Z file_id: '7855' file_name: 2015_Evolution_Priklopil.pdf file_size: 967214 relation: main_file file_date_updated: 2020-07-14T12:45:19Z has_accepted_license: '1' intvolume: ' 69' issue: '4' language: - iso: eng month: '02' oa: 1 oa_version: Submitted Version page: 1015 - 1026 pmid: 1 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Evolution publication_identifier: eissn: - 1558-5646 issn: - 0014-3820 publication_status: published publisher: Wiley publist_id: '5249' quality_controlled: '1' scopus_import: '1' status: public title: Evolutionarily stable mating decisions for sequentially searching females and the stability of reproductive isolation by assortative mating type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 69 year: '2015' ... --- _id: '1859' 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. " author: - first_name: Neel full_name: Shah, Neel id: 31ABAF80-F248-11E8-B48F-1D18A9856A87 last_name: Shah - first_name: Vladimir full_name: Kolmogorov, Vladimir id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 citation: 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' 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' 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. 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.' 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.' 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. conference: end_date: 2015-06-12 location: Boston, MA, USA name: 'CVPR: Computer Vision and Pattern Recognition' start_date: 2015-06-07 date_created: 2018-12-11T11:54:24Z date_published: 2015-06-01T00:00:00Z date_updated: 2021-01-12T06:53:40Z day: '01' department: - _id: VlKo - _id: ChLa doi: 10.1109/CVPR.2015.7298890 ec_funded: 1 language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1408.6804 month: '06' oa: 1 oa_version: Preprint page: 2737 - 2745 project: - _id: 2532554C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '308036' name: Lifelong Learning of Visual Scene Understanding - _id: 25FBA906-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '616160' name: 'Discrete Optimization in Computer Vision: Theory and Practice' publication_status: published publisher: IEEE publist_id: '5240' quality_controlled: '1' scopus_import: 1 status: public title: A multi-plane block-coordinate Frank-Wolfe algorithm for training structural SVMs with a costly max-oracle type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2015' ... --- _id: '1860' 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. author: - first_name: Amélie full_name: Royer, Amélie last_name: Royer - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 citation: ama: 'Royer A, Lampert C. Classifier adaptation at prediction time. In: IEEE; 2015:1401-1409. doi:10.1109/CVPR.2015.7298746' 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' chicago: Royer, Amélie, and Christoph Lampert. “Classifier Adaptation at Prediction Time,” 1401–9. IEEE, 2015. 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.' ista: 'Royer A, Lampert C. 2015. Classifier adaptation at prediction time. CVPR: Computer Vision and Pattern Recognition, 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. conference: end_date: 2015-06-12 location: Boston, MA, United States name: 'CVPR: Computer Vision and Pattern Recognition' start_date: 2015-06-07 date_created: 2018-12-11T11:54:24Z date_published: 2015-06-01T00:00:00Z date_updated: 2021-01-12T06:53:41Z day: '01' department: - _id: ChLa doi: 10.1109/CVPR.2015.7298746 ec_funded: 1 language: - iso: eng 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 month: '06' oa: 1 oa_version: Submitted Version page: 1401 - 1409 project: - _id: 2532554C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '308036' name: Lifelong Learning of Visual Scene Understanding publication_status: published publisher: IEEE publist_id: '5239' quality_controlled: '1' scopus_import: 1 status: public title: Classifier adaptation at prediction time type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2015' ... --- _id: '1858' 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.' author: - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 citation: ama: 'Lampert C. Predicting the future behavior of a time-varying probability distribution. In: IEEE; 2015:942-950. doi:10.1109/CVPR.2015.7298696' 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' 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. 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.' ista: 'Lampert C. 2015. Predicting the future behavior of a time-varying probability distribution. CVPR: Computer Vision and Pattern Recognition, 942–950.' 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. conference: end_date: 2015-06-12 location: Boston, MA, United States name: 'CVPR: Computer Vision and Pattern Recognition' start_date: 2015-06-07 date_created: 2018-12-11T11:54:24Z date_published: 2015-10-15T00:00:00Z date_updated: 2021-01-12T06:53:40Z day: '15' department: - _id: ChLa doi: 10.1109/CVPR.2015.7298696 external_id: arxiv: - '1406.5362' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1406.5362 month: '10' oa: 1 oa_version: Preprint page: 942 - 950 publication_status: published publisher: IEEE publist_id: '5241' quality_controlled: '1' scopus_import: 1 status: public title: Predicting the future behavior of a time-varying probability distribution type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2015' ... --- _id: '1857' abstract: - lang: eng 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. ' author: - first_name: Anastasia full_name: Pentina, Anastasia id: 42E87FC6-F248-11E8-B48F-1D18A9856A87 last_name: Pentina - first_name: Viktoriia full_name: Sharmanska, Viktoriia id: 2EA6D09E-F248-11E8-B48F-1D18A9856A87 last_name: Sharmanska orcid: 0000-0003-0192-9308 - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 citation: ama: 'Pentina A, Sharmanska V, Lampert C. Curriculum learning of multiple tasks. In: IEEE; 2015:5492-5500. doi:10.1109/CVPR.2015.7299188' 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' 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. 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.' ista: 'Pentina A, Sharmanska V, Lampert C. 2015. Curriculum learning of multiple tasks. CVPR: Computer Vision and Pattern Recognition, 5492–5500.' 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. conference: end_date: 2015-06-12 location: Boston, MA, United States name: 'CVPR: Computer Vision and Pattern Recognition' start_date: 2015-06-07 date_created: 2018-12-11T11:54:23Z date_published: 2015-06-01T00:00:00Z date_updated: 2023-02-23T10:17:31Z day: '01' department: - _id: ChLa doi: 10.1109/CVPR.2015.7299188 language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1412.1353 month: '06' oa: 1 oa_version: Preprint page: 5492 - 5500 publication_status: published publisher: IEEE publist_id: '5243' quality_controlled: '1' scopus_import: 1 status: public title: Curriculum learning of multiple tasks type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2015' ... --- _id: '1867' abstract: - lang: eng 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. author: - first_name: Jens full_name: Hühner, Jens last_name: Hühner - first_name: Álvaro full_name: Inglés Prieto, Álvaro id: 2A9DB292-F248-11E8-B48F-1D18A9856A87 last_name: Inglés Prieto orcid: 0000-0002-5409-8571 - first_name: Christian full_name: Neusüß, Christian last_name: Neusüß - first_name: Michael full_name: Lämmerhofer, Michael last_name: Lämmerhofer - first_name: Harald L full_name: Janovjak, Harald L id: 33BA6C30-F248-11E8-B48F-1D18A9856A87 last_name: Janovjak orcid: 0000-0002-8023-9315 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 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 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. 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. 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. 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. short: J. Hühner, Á. Inglés Prieto, C. Neusüß, M. Lämmerhofer, H.L. Janovjak, Electrophoresis 36 (2015) 518–525. date_created: 2018-12-11T11:54:26Z date_published: 2015-02-01T00:00:00Z date_updated: 2021-01-12T06:53:43Z day: '01' department: - _id: HaJa doi: 10.1002/elps.201400451 ec_funded: 1 intvolume: ' 36' issue: '4' language: - iso: eng month: '02' oa_version: None page: 518 - 525 project: - _id: 25548C20-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '303564' name: Microbial Ion Channels for Synthetic Neurobiology - _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) publication: Electrophoresis publication_status: published publisher: Wiley publist_id: '5230' pubrep_id: '836' quality_controlled: '1' scopus_import: 1 status: public title: Quantification of riboflavin, flavin mononucleotide, and flavin adenine dinucleotide in mammalian model cells by CE with LED-induced fluorescence detection type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 36 year: '2015' ... --- _id: '1865' 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. 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 author: - first_name: Hélène full_name: Robert, Hélène last_name: Robert - first_name: Wim full_name: Grunewald, Wim last_name: Grunewald - first_name: Michael full_name: Sauer, Michael last_name: Sauer - first_name: Bernard full_name: Cannoot, Bernard last_name: Cannoot - first_name: Mercedes full_name: Soriano, Mercedes last_name: Soriano - first_name: Ranjan full_name: Swarup, Ranjan last_name: Swarup - first_name: Dolf full_name: Weijers, Dolf last_name: Weijers - first_name: Malcolm full_name: Bennett, Malcolm last_name: Bennett - first_name: Kim full_name: Boutilier, Kim last_name: Boutilier - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: 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 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 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. 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. 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. 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. date_created: 2018-12-11T11:54:26Z date_published: 2015-02-15T00:00:00Z date_updated: 2021-01-12T06:53:43Z day: '15' department: - _id: JiFr doi: 10.1242/dev.115832 ec_funded: 1 intvolume: ' 142' issue: '4' language: - iso: eng month: '02' oa_version: None page: 702 - 711 project: - _id: 25716A02-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '282300' name: Polarity and subcellular dynamics in plants publication: Development publication_status: published publisher: Company of Biologists publist_id: '5231' quality_controlled: '1' scopus_import: 1 status: public title: Plant embryogenesis requires AUX/LAX-mediated auxin influx type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 142 year: '2015' ... --- _id: '1868' 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. article_number: '022906' author: - first_name: Youngyong full_name: Park, Youngyong last_name: Park - first_name: Younghae full_name: Do, Younghae last_name: Do - first_name: Sebastian full_name: Altmeyer, Sebastian id: 2EE67FDC-F248-11E8-B48F-1D18A9856A87 last_name: Altmeyer orcid: 0000-0001-5964-0203 - first_name: Yingcheng full_name: Lai, Yingcheng last_name: Lai - first_name: Gyuwon full_name: Lee, Gyuwon last_name: Lee 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 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 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. 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. 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. 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). date_created: 2018-12-11T11:54:27Z date_published: 2015-02-09T00:00:00Z date_updated: 2021-01-12T06:53:44Z day: '09' department: - _id: BjHo doi: 10.1103/PhysRevE.91.022906 intvolume: ' 91' issue: '2' language: - iso: eng month: '02' oa_version: None publication: Physical Review E publication_identifier: issn: - 1539-3755 publication_status: published publisher: American Physical Society publist_id: '5229' quality_controlled: '1' scopus_import: 1 status: public title: Early effect in time-dependent, high-dimensional nonlinear dynamical systems with multiple resonances type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 91 year: '2015' ... --- _id: '1864' 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" author: - first_name: László full_name: Erdös, László id: 4DBD5372-F248-11E8-B48F-1D18A9856A87 last_name: Erdös orcid: 0000-0001-5366-9603 - first_name: Antti full_name: Knowles, Antti last_name: Knowles citation: 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' 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' 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.' 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.' 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.' 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. date_created: 2018-12-11T11:54:26Z date_published: 2015-03-01T00:00:00Z date_updated: 2021-01-12T06:53:42Z day: '01' department: - _id: LaEr doi: 10.1007/s00023-014-0333-5 ec_funded: 1 intvolume: ' 16' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1309.5107 month: '03' oa: 1 oa_version: Preprint page: 709 - 799 project: - _id: 258DCDE6-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '338804' name: Random matrices, universality and disordered quantum systems publication: Annales Henri Poincare publication_status: published publisher: Springer publist_id: '5233' scopus_import: 1 status: public title: 'The Altshuler–Shklovskii formulas for random band matrices II: The general case' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 16 year: '2015' ... --- _id: '1861' 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. acknowledgement: "HYCON2; EC; European Commission\r\n" article_number: '8' author: - first_name: Jakob full_name: Ruess, Jakob id: 4A245D00-F248-11E8-B48F-1D18A9856A87 last_name: Ruess orcid: 0000-0003-1615-3282 - first_name: John full_name: Lygeros, John last_name: Lygeros citation: 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 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. 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. 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. short: J. Ruess, J. Lygeros, ACM Transactions on Modeling and Computer Simulation 25 (2015). date_created: 2018-12-11T11:54:25Z date_published: 2015-02-01T00:00:00Z date_updated: 2021-01-12T06:53:41Z day: '01' department: - _id: ToHe - _id: GaTk doi: 10.1145/2688906 intvolume: ' 25' issue: '2' language: - iso: eng month: '02' oa_version: None publication: ACM Transactions on Modeling and Computer Simulation publication_status: published publisher: ACM publist_id: '5238' quality_controlled: '1' scopus_import: 1 status: public title: Moment-based methods for parameter inference and experiment design for stochastic biochemical reaction networks type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 25 year: '2015' ... --- _id: '1866' author: - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Jean full_name: Raskin, Jean last_name: Raskin citation: ama: 'Henzinger TA, Raskin J. The equivalence problem for finite automata: Technical perspective. Communications of the ACM. 2015;58(2):86-86. doi:10.1145/2701001' apa: 'Henzinger, T. A., & Raskin, J. (2015). The equivalence problem for finite automata: Technical perspective. Communications of the ACM. ACM. https://doi.org/10.1145/2701001' 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.' 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.' ista: 'Henzinger TA, Raskin J. 2015. The equivalence problem for finite automata: Technical perspective. Communications of the ACM. 58(2), 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.' short: T.A. Henzinger, J. Raskin, Communications of the ACM 58 (2015) 86–86. date_created: 2018-12-11T11:54:26Z date_published: 2015-01-28T00:00:00Z date_updated: 2021-01-12T06:53:43Z day: '28' department: - _id: ToHe doi: 10.1145/2701001 intvolume: ' 58' issue: '2' language: - iso: eng month: '01' oa_version: None page: 86-86 publication: Communications of the ACM publication_status: published publisher: ACM publist_id: '5232' scopus_import: 1 status: public title: 'The equivalence problem for finite automata: Technical perspective' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 58 year: '2015' ... --- _id: '1871' abstract: - lang: eng text: The plant hormone auxin is a key regulator of plant growth and development. Differences in auxin distribution within tissues are mediated by the polar auxin transport machinery, and cellular auxin responses occur depending on changes in cellular auxin levels. Multiple receptor systems at the cell surface and in the interior operate to sense and interpret fluctuations in auxin distribution that occur during plant development. Until now, three proteins or protein complexes that can bind auxin have been identified. SCFTIR1 [a SKP1-cullin-1-F-box complex that contains transport inhibitor response 1 (TIR1) as the F-box protein] and S-phase-kinaseassociated protein 2 (SKP2) localize to the nucleus, whereas auxinbinding protein 1 (ABP1), predominantly associates with the endoplasmic reticulum and cell surface. In this Cell Science at a Glance article, we summarize recent discoveries in the field of auxin transport and signaling that have led to the identification of new components of these pathways, as well as their mutual interaction. 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] author: - first_name: Peter full_name: Grones, Peter id: 399876EC-F248-11E8-B48F-1D18A9856A87 last_name: Grones - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 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 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 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. 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. ista: Grones P, Friml J. 2015. Auxin transporters and binding proteins at a glance. Journal of Cell Science. 128(1), 1–7. 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. date_created: 2018-12-11T11:54:28Z date_published: 2015-01-01T00:00:00Z date_updated: 2021-01-12T06:53:45Z day: '01' ddc: - '570' department: - _id: JiFr doi: 10.1242/jcs.159418 file: - access_level: open_access checksum: 24c779f4cd9d549ca6833e26f486be27 content_type: application/pdf creator: system date_created: 2018-12-12T10:11:00Z date_updated: 2020-07-14T12:45:19Z file_id: '4852' file_name: IST-2016-563-v1+1_1.full.pdf file_size: 1688844 relation: main_file file_date_updated: 2020-07-14T12:45:19Z has_accepted_license: '1' intvolume: ' 128' issue: '1' language: - iso: eng month: '01' oa: 1 oa_version: Submitted Version page: 1 - 7 publication: Journal of Cell Science publication_status: published publisher: Company of Biologists publist_id: '5225' pubrep_id: '563' quality_controlled: '1' scopus_import: 1 status: public title: Auxin transporters and binding proteins at a glance type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 128 year: '2015' ... --- _id: '1874' abstract: - lang: eng 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.' author: - first_name: Charlotte full_name: Boccara, Charlotte id: 3FC06552-F248-11E8-B48F-1D18A9856A87 last_name: Boccara orcid: 0000-0001-7237-5109 - first_name: Lisa full_name: Kjønigsen, Lisa last_name: Kjønigsen - first_name: Ingvild full_name: Hammer, Ingvild last_name: Hammer - first_name: Jan full_name: Bjaalie, Jan last_name: Bjaalie - first_name: Trygve full_name: Leergaard, Trygve last_name: Leergaard - first_name: Menno full_name: Witter, Menno last_name: Witter citation: 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 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 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. 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. 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. 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. date_created: 2018-12-11T11:54:29Z date_published: 2015-07-01T00:00:00Z date_updated: 2021-01-12T06:53:46Z day: '01' department: - _id: JoCs doi: 10.1002/hipo.22407 intvolume: ' 25' issue: '7' language: - iso: eng month: '07' oa_version: None page: 838 - 857 publication: Hippocampus publication_status: published publisher: Wiley publist_id: '5222' quality_controlled: '1' scopus_import: 1 status: public title: A three-plane architectonic atlas of the rat hippocampal region type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 25 year: '2015' ... --- _id: '1873' abstract: - lang: eng 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.' author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Martin full_name: Chmelik, Martin id: 3624234E-F248-11E8-B48F-1D18A9856A87 last_name: Chmelik citation: 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 chicago: Chatterjee, Krishnendu, and Martin Chmelik. “POMDPs under Probabilistic Semantics.” Artificial Intelligence. Elsevier, 2015. 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. 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. short: K. Chatterjee, M. Chmelik, Artificial Intelligence 221 (2015) 46–72. date_created: 2018-12-11T11:54:28Z date_published: 2015-04-01T00:00:00Z date_updated: 2021-01-12T06:53:46Z day: '01' department: - _id: KrCh doi: 10.1016/j.artint.2014.12.009 external_id: arxiv: - '1408.2058' intvolume: ' 221' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1408.2058 month: '04' oa: 1 oa_version: Preprint page: 46 - 72 publication: Artificial Intelligence publication_status: published publisher: Elsevier publist_id: '5224' quality_controlled: '1' scopus_import: 1 status: public title: POMDPs under probabilistic semantics type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 221 year: '2015' ... --- _id: '1879' 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. 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. author: - first_name: A full_name: Kremer, A last_name: Kremer - first_name: Stefaan full_name: Lippens, Stefaan last_name: Lippens - first_name: Sonia full_name: Bartunkova, Sonia last_name: Bartunkova - first_name: Bob full_name: Asselbergh, Bob last_name: Asselbergh - first_name: Cendric full_name: Blanpain, Cendric last_name: Blanpain - first_name: Matyas full_name: Fendrych, Matyas id: 43905548-F248-11E8-B48F-1D18A9856A87 last_name: Fendrych orcid: 0000-0002-9767-8699 - first_name: A full_name: Goossens, A last_name: Goossens - first_name: Matthew full_name: Holt, Matthew last_name: Holt - first_name: Sophie full_name: Janssens, Sophie last_name: Janssens - first_name: Michiel full_name: Krols, Michiel last_name: Krols - first_name: Jean full_name: Larsimont, Jean last_name: Larsimont - first_name: Conor full_name: Mc Guire, Conor last_name: Mc Guire - first_name: Moritz full_name: Nowack, Moritz last_name: Nowack - first_name: Xavier full_name: Saelens, Xavier last_name: Saelens - first_name: Andreas full_name: Schertel, Andreas last_name: Schertel - first_name: B full_name: Schepens, B last_name: Schepens - first_name: M full_name: Slezak, M last_name: Slezak - first_name: Vincent full_name: Timmerman, Vincent last_name: Timmerman - first_name: Clara full_name: Theunis, Clara last_name: Theunis - first_name: Ronald full_name: Van Brempt, Ronald last_name: Van Brempt - first_name: Y full_name: Visser, Y last_name: Visser - first_name: Christophe full_name: Guérin, Christophe last_name: Guérin 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 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 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. 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. 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. 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. date_created: 2018-12-11T11:54:30Z date_published: 2015-08-01T00:00:00Z date_updated: 2021-01-12T06:53:48Z day: '01' ddc: - '570' department: - _id: JiFr doi: 10.1111/jmi.12211 file: - access_level: open_access checksum: 3649c5372d1644062d728ea9287e367f content_type: application/pdf creator: system date_created: 2018-12-12T10:11:19Z date_updated: 2020-07-14T12:45:19Z file_id: '4872' file_name: IST-2016-459-v1+1_KREMER_et_al-2015-Journal_of_Microscopy.pdf file_size: 2899898 relation: main_file file_date_updated: 2020-07-14T12:45:19Z has_accepted_license: '1' intvolume: ' 259' issue: '2' language: - iso: eng month: '08' oa: 1 oa_version: Published Version page: 80 - 96 publication: Journal of Microscopy publication_status: published publisher: Wiley-Blackwell publist_id: '5218' pubrep_id: '459' quality_controlled: '1' scopus_import: 1 status: public title: Developing 3D SEM in a broad biological context tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 259 year: '2015' ... --- _id: '1880' abstract: - lang: eng 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 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 article_number: '013022' author: - first_name: Martin full_name: Könenberg, Martin last_name: Könenberg - first_name: Thomas full_name: Moser, Thomas id: 2B5FC9A4-F248-11E8-B48F-1D18A9856A87 last_name: Moser - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 - first_name: Jakob full_name: Yngvason, Jakob last_name: Yngvason citation: 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 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 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. 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. 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. short: M. Könenberg, T. Moser, R. Seiringer, J. Yngvason, New Journal of Physics 17 (2015). date_created: 2018-12-11T11:54:30Z date_published: 2015-01-15T00:00:00Z date_updated: 2021-01-12T06:53:48Z day: '15' ddc: - '530' department: - _id: RoSe doi: 10.1088/1367-2630/17/1/013022 file: - access_level: open_access checksum: 38fdf2b5ac30445e26a5d613abd84b16 content_type: application/pdf creator: system date_created: 2018-12-12T10:12:44Z date_updated: 2020-07-14T12:45:20Z file_id: '4963' file_name: IST-2016-447-v1+1_document_1_.pdf file_size: 768108 relation: main_file file_date_updated: 2020-07-14T12:45:20Z has_accepted_license: '1' intvolume: ' 17' language: - iso: eng month: '01' oa: 1 oa_version: Published Version project: - _id: 26450934-B435-11E9-9278-68D0E5697425 name: NSERC Postdoctoral fellowship publication: New Journal of Physics publication_status: published publisher: IOP Publishing Ltd. publist_id: '5214' pubrep_id: '447' quality_controlled: '1' scopus_import: 1 status: public title: Superfluid behavior of a Bose-Einstein condensate in a random potential tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 17 year: '2015' ... --- _id: '1882' 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. 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. alternative_title: - LNCS author: - first_name: Uli full_name: Fahrenberg, Uli last_name: Fahrenberg - first_name: Jan full_name: Kretinsky, Jan id: 44CEF464-F248-11E8-B48F-1D18A9856A87 last_name: Kretinsky orcid: 0000-0002-8122-2881 - first_name: Axel full_name: Legay, Axel last_name: Legay - first_name: Louis full_name: Traonouez, Louis last_name: Traonouez citation: 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' 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' 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. 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.' 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.' 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. conference: end_date: 2014-09-12 location: Bertinoro, Italy name: 'FACS: Formal Aspects of Component Software' start_date: 2014-09-10 date_created: 2018-12-11T11:54:31Z date_published: 2015-01-30T00:00:00Z date_updated: 2021-01-12T06:53:49Z day: '30' department: - _id: ToHe - _id: KrCh doi: 10.1007/978-3-319-15317-9_19 ec_funded: 1 intvolume: ' 8997' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1408.1256 month: '01' oa: 1 oa_version: Preprint page: 306 - 324 project: - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering publication_status: published publisher: Springer publist_id: '5216' quality_controlled: '1' scopus_import: 1 status: public title: Compositionality for quantitative specifications type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8997 year: '2015' ... --- _id: '1883' abstract: - lang: eng 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" article_number: '022803' article_processing_charge: No article_type: original author: - first_name: Stephanie full_name: Keller-Schmidt, Stephanie last_name: Keller-Schmidt - first_name: Murat full_name: Tugrul, Murat id: 37C323C6-F248-11E8-B48F-1D18A9856A87 last_name: Tugrul orcid: 0000-0002-8523-0758 - first_name: Víctor full_name: Eguíluz, Víctor last_name: Eguíluz - first_name: Emilio full_name: Hernandez Garcia, Emilio last_name: Hernandez Garcia - first_name: Konstantin full_name: Klemm, Konstantin last_name: Klemm citation: 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 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 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. 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. 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. 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. short: S. Keller-Schmidt, M. Tugrul, V. Eguíluz, E. Hernandez Garcia, K. Klemm, Physical Review E Statistical Nonlinear and Soft Matter Physics 91 (2015). date_created: 2018-12-11T11:54:31Z date_published: 2015-02-02T00:00:00Z date_updated: 2021-01-12T06:53:49Z day: '02' department: - _id: NiBa doi: 10.1103/PhysRevE.91.022803 external_id: arxiv: - '1012.3298' intvolume: ' 91' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1012.3298 month: '02' oa: 1 oa_version: Preprint publication: Physical Review E Statistical Nonlinear and Soft Matter Physics publication_status: published publisher: American Institute of Physics publist_id: '5213' quality_controlled: '1' scopus_import: 1 status: public title: Anomalous scaling in an age-dependent branching model type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 91 year: '2015' ... --- _id: '1878' abstract: - lang: eng 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). author: - first_name: Eduardo full_name: Cires Rodriguez, Eduardo id: 2AD56A7A-F248-11E8-B48F-1D18A9856A87 last_name: Cires Rodriguez - first_name: José full_name: Prieto, José last_name: Prieto citation: 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 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 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. 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. 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. 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. date_created: 2018-12-11T11:54:30Z date_published: 2015-01-24T00:00:00Z date_updated: 2021-01-12T06:53:47Z day: '24' department: - _id: JiFr doi: 10.1007/s10265-014-0691-6 intvolume: ' 128' issue: '2' language: - iso: eng month: '01' oa_version: None page: 223 - 238 publication: Journal of Plant Research publication_status: published publisher: Springer publist_id: '5217' quality_controlled: '1' scopus_import: 1 status: public title: Phylogenetic relationships of Petrocoptis A. Braun ex Endl. (Caryophyllaceae), a discussed genus from the Iberian Peninsula type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 128 year: '2015' ... --- _id: '1885' abstract: - lang: eng 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. ' author: - first_name: Gasper full_name: Tkacik, Gasper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkacik orcid: 0000-0002-6699-1455 - first_name: Julien full_name: Dubuis, Julien last_name: Dubuis - first_name: Mariela full_name: Petkova, Mariela last_name: Petkova - first_name: Thomas full_name: Gregor, Thomas last_name: Gregor 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' 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.' 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.' 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.' short: G. Tkačik, J. Dubuis, M. Petkova, T. Gregor, Genetics 199 (2015) 39–59. date_created: 2018-12-11T11:54:32Z date_published: 2015-01-01T00:00:00Z date_updated: 2021-01-12T06:53:50Z day: '01' department: - _id: GaTk doi: 10.1534/genetics.114.171850 intvolume: ' 199' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1404.5599 month: '01' oa: 1 oa_version: Preprint page: 39 - 59 publication: Genetics publication_status: published publisher: Genetics Society of America publist_id: '5210' quality_controlled: '1' scopus_import: 1 status: public title: 'Positional information, positional error, and readout precision in morphogenesis: A mathematical framework' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 199 year: '2015' ... --- _id: '1940' 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. article_number: '062710' author: - first_name: Thomas R full_name: Sokolowski, Thomas R id: 3E999752-F248-11E8-B48F-1D18A9856A87 last_name: Sokolowski orcid: 0000-0002-1287-3779 - first_name: Gasper full_name: Tkacik, Gasper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkacik orcid: 0000-0002-6699-1455 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 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 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. 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. 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. 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. short: T.R. Sokolowski, G. Tkačik, Physical Review E Statistical Nonlinear and Soft Matter Physics 91 (2015). date_created: 2018-12-11T11:54:49Z date_published: 2015-06-15T00:00:00Z date_updated: 2021-01-12T06:54:13Z day: '15' department: - _id: GaTk doi: 10.1103/PhysRevE.91.062710 intvolume: ' 91' issue: '6' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1501.04015 month: '06' oa: 1 oa_version: Preprint publication: Physical Review E Statistical Nonlinear and Soft Matter Physics publication_status: published publisher: American Institute of Physics publist_id: '5145' quality_controlled: '1' scopus_import: 1 status: public title: Optimizing information flow in small genetic networks. IV. Spatial coupling type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 91 year: '2015' ... --- _id: '1938' 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.' 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. " author: - first_name: Florian full_name: Pausinger, Florian id: 2A77D7A2-F248-11E8-B48F-1D18A9856A87 last_name: Pausinger orcid: 0000-0002-8379-3768 - first_name: Stefan full_name: Steinerberger, Stefan last_name: Steinerberger citation: 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 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 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. 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. ista: Pausinger F, Steinerberger S. 2015. On the distribution of local extrema in quantum chaos. Physics Letters, Section A. 379(6), 535–541. 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. date_created: 2018-12-11T11:54:49Z date_published: 2015-03-06T00:00:00Z date_updated: 2021-01-12T06:54:12Z day: '06' department: - _id: HeEd doi: 10.1016/j.physleta.2014.12.010 intvolume: ' 379' issue: '6' language: - iso: eng month: '03' oa_version: None page: 535 - 541 publication: Physics Letters, Section A publication_status: published publisher: Elsevier publist_id: '5152' quality_controlled: '1' scopus_import: 1 status: public title: On the distribution of local extrema in quantum chaos type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 379 year: '2015' ... --- _id: '1944' 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 author: - first_name: Hana full_name: Rakusová, Hana last_name: Rakusová - first_name: Matyas full_name: Fendrych, Matyas id: 43905548-F248-11E8-B48F-1D18A9856A87 last_name: Fendrych orcid: 0000-0002-9767-8699 - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: 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 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. 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. 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. short: H. Rakusová, M. Fendrych, J. Friml, Current Opinion in Plant Biology 23 (2015) 116–123. date_created: 2018-12-11T11:54:51Z date_published: 2015-02-01T00:00:00Z date_updated: 2021-01-12T06:54:15Z day: '01' department: - _id: JiFr doi: 10.1016/j.pbi.2014.12.002 ec_funded: 1 intvolume: ' 23' issue: '2' language: - iso: eng month: '02' oa_version: None page: 116 - 123 project: - _id: 25716A02-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '282300' name: Polarity and subcellular dynamics in plants - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Current Opinion in Plant Biology publication_status: published publisher: Elsevier publist_id: '5140' quality_controlled: '1' scopus_import: 1 status: public title: Intracellular trafficking and PIN-mediated cell polarity during tropic responses in plants type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 23 year: '2015' ... --- _id: '1992' 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." author: - first_name: Ashutosh full_name: Gupta, Ashutosh id: 335E5684-F248-11E8-B48F-1D18A9856A87 last_name: Gupta - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Arjun full_name: Radhakrishna, Arjun id: 3B51CAC4-F248-11E8-B48F-1D18A9856A87 last_name: Radhakrishna - first_name: Roopsha full_name: Samanta, Roopsha id: 3D2AAC08-F248-11E8-B48F-1D18A9856A87 last_name: Samanta - first_name: Thorsten full_name: Tarrach, Thorsten id: 3D6E8F2C-F248-11E8-B48F-1D18A9856A87 last_name: Tarrach orcid: 0000-0003-4409-8487 citation: 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' 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' 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. 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.' 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.' 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. conference: end_date: 2015-01-17 location: Mumbai, India name: 'POPL: Principles of Programming Languages' start_date: 2015-01-15 date_created: 2018-12-11T11:55:05Z date_published: 2015-01-15T00:00:00Z date_updated: 2021-01-12T06:54:33Z day: '15' ddc: - '005' department: - _id: ToHe doi: 10.1145/2676726.2677008 file: - access_level: open_access checksum: f0d4395b600f410a191256ac0b73af32 content_type: application/pdf creator: system date_created: 2018-12-12T10:17:56Z date_updated: 2020-07-14T12:45:22Z file_id: '5314' file_name: IST-2015-317-v1+1_author_version.pdf file_size: 399462 relation: main_file file_date_updated: 2020-07-14T12:45:22Z has_accepted_license: '1' language: - iso: eng month: '01' oa: 1 oa_version: Submitted Version page: 433 - 444 publication_identifier: isbn: - 978-1-4503-3300-9 publication_status: published publisher: ACM publist_id: '5091' pubrep_id: '317' quality_controlled: '1' scopus_import: 1 status: public title: Succinct representation of concurrent trace sets type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2015' ... --- _id: '1997' 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. author: - first_name: Patrik full_name: Noren, Patrik id: 46870C74-F248-11E8-B48F-1D18A9856A87 last_name: Noren citation: 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 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 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. 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. 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. 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. short: P. Noren, Journal of Symbolic Computation 68/Part 2 (2015) 285–296. date_created: 2018-12-11T11:55:07Z date_published: 2015-05-01T00:00:00Z date_updated: 2021-01-12T06:54:35Z day: '01' department: - _id: CaUh doi: 10.1016/j.jsc.2014.09.014 issue: May-June language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1207.0077 month: '05' oa: 1 oa_version: Preprint page: 285 - 296 publication: Journal of Symbolic Computation publication_status: published publisher: Elsevier publist_id: '5082' quality_controlled: '1' scopus_import: 1 status: public title: The three-state toric homogeneous Markov chain model has Markov degree two type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 68/Part 2 year: '2015' ... --- _id: '2008' abstract: - lang: eng 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. 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). author: - first_name: Anna full_name: Klimova, Anna id: 31934120-F248-11E8-B48F-1D18A9856A87 last_name: Klimova - first_name: Tamás full_name: Rudas, Tamás last_name: Rudas 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 apa: Klimova, A., & Rudas, T. (2015). Iterative scaling in curved exponential families. Scandinavian Journal of Statistics. Wiley. https://doi.org/10.1111/sjos.12139 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. 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. ista: Klimova A, Rudas T. 2015. Iterative scaling in curved exponential families. Scandinavian Journal of Statistics. 42(3), 832–847. 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. date_created: 2018-12-11T11:55:11Z date_published: 2015-09-01T00:00:00Z date_updated: 2021-01-12T06:54:41Z day: '01' department: - _id: CaUh doi: 10.1111/sjos.12139 intvolume: ' 42' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1307.3282 month: '09' oa: 1 oa_version: Preprint page: 832 - 847 publication: Scandinavian Journal of Statistics publication_status: published publisher: Wiley publist_id: '5068' quality_controlled: '1' scopus_import: 1 status: public title: Iterative scaling in curved exponential families type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 42 year: '2015' ... --- _id: '2006' abstract: - lang: eng 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. ' article_processing_charge: No author: - first_name: Nicolas full_name: Hein, Nicolas last_name: Hein - first_name: Christopher full_name: Hillar, Christopher last_name: Hillar - first_name: Abraham full_name: Martin Del Campo Sanchez, Abraham id: 4CF47F6A-F248-11E8-B48F-1D18A9856A87 last_name: Martin Del Campo Sanchez - first_name: Frank full_name: Sottile, Frank last_name: Sottile - first_name: Zach full_name: Teitler, Zach last_name: Teitler citation: 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 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 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. 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. 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. short: N. Hein, C. Hillar, A. Martin del Campo Sanchez, F. Sottile, Z. Teitler, Experimental Mathematics 24 (2015) 261–269. date_created: 2018-12-11T11:55:10Z date_published: 2015-06-23T00:00:00Z date_updated: 2021-01-12T06:54:40Z day: '23' department: - _id: CaUh doi: 10.1080/10586458.2014.980044 intvolume: ' 24' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1109.3436 month: '06' oa: 1 oa_version: Preprint page: 261 - 269 publication: Experimental Mathematics publication_status: published publisher: Taylor & Francis publist_id: '5070' quality_controlled: '1' scopus_import: 1 status: public title: The monotone secant conjecture in the real Schubert calculus type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 24 year: '2015' ... --- _id: '2014' 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. author: - first_name: Anna full_name: Klimova, Anna id: 31934120-F248-11E8-B48F-1D18A9856A87 last_name: Klimova - first_name: Caroline full_name: Uhler, Caroline id: 49ADD78E-F248-11E8-B48F-1D18A9856A87 last_name: Uhler orcid: 0000-0002-7008-0216 - first_name: Tamás full_name: Rudas, Tamás last_name: Rudas citation: 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 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 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. 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. ista: Klimova A, Uhler C, Rudas T. 2015. Faithfulness and learning hypergraphs from discrete distributions. Computational Statistics & Data Analysis. 87(7), 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. short: A. Klimova, C. Uhler, T. Rudas, Computational Statistics & Data Analysis 87 (2015) 57–72. date_created: 2018-12-11T11:55:13Z date_published: 2015-07-01T00:00:00Z date_updated: 2021-01-12T06:54:43Z day: '01' department: - _id: CaUh doi: 10.1016/j.csda.2015.01.017 intvolume: ' 87' issue: '7' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1404.6617 month: '07' oa: 1 oa_version: Preprint page: 57 - 72 publication: Computational Statistics & Data Analysis publication_status: published publisher: Elsevier publist_id: '5062' quality_controlled: '1' scopus_import: 1 status: public title: Faithfulness and learning hypergraphs from discrete distributions type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 87 year: '2015' ... --- _id: '2025' abstract: - lang: eng 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. author: - first_name: Daiki full_name: Kawada, Daiki last_name: Kawada - first_name: Hiromu full_name: Kobayashi, Hiromu last_name: Kobayashi - first_name: Tsuyoshi full_name: Tomita, Tsuyoshi last_name: Tomita - first_name: Eisuke full_name: Nakata, Eisuke last_name: Nakata - first_name: Makoto full_name: Nagano, Makoto last_name: Nagano - first_name: Daria E full_name: Siekhaus, Daria E id: 3D224B9E-F248-11E8-B48F-1D18A9856A87 last_name: Siekhaus orcid: 0000-0001-8323-8353 - first_name: Junko full_name: Toshima, Junko last_name: Toshima - first_name: Jiro full_name: Toshimaa, Jiro last_name: Toshimaa citation: 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 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 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. 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. 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. 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. date_created: 2018-12-11T11:55:17Z date_published: 2015-01-01T00:00:00Z date_updated: 2021-01-12T06:54:48Z day: '01' ddc: - '570' department: - _id: DaSi doi: 10.1016/j.bbamcr.2014.10.009 file: - access_level: open_access checksum: 5bb328edebb6a91337cadd7d63f961b7 content_type: application/pdf creator: system date_created: 2018-12-12T10:12:18Z date_updated: 2020-07-14T12:45:25Z file_id: '4936' file_name: IST-2016-615-v1+1_BBAMCR.pdf file_size: 926685 relation: main_file file_date_updated: 2020-07-14T12:45:25Z has_accepted_license: '1' intvolume: ' 1853' issue: '1' language: - iso: eng month: '01' oa: 1 oa_version: Submitted Version page: 144 - 156 publication: Biochimica et Biophysica Acta - Molecular Cell Research publication_status: published publisher: Elsevier publist_id: '5047' pubrep_id: '615' quality_controlled: '1' scopus_import: 1 status: public title: The yeast Arf-GAP Glo3p is required for the endocytic recycling of cell surface proteins tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 1853 year: '2015' ... --- _id: '2030' abstract: - lang: eng 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. author: - first_name: Liang full_name: Shi, Liang id: 374A3F1A-F248-11E8-B48F-1D18A9856A87 last_name: Shi - first_name: Markus full_name: Rampp, Markus last_name: Rampp - first_name: Björn full_name: Hof, Björn id: 3A374330-F248-11E8-B48F-1D18A9856A87 last_name: Hof orcid: 0000-0003-2057-2754 - first_name: Marc full_name: Avila, Marc last_name: Avila citation: 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 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 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. 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. 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. 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. date_created: 2018-12-11T11:55:18Z date_published: 2015-01-01T00:00:00Z date_updated: 2021-01-12T06:54:51Z day: '01' department: - _id: BjHo doi: 10.1016/j.compfluid.2014.09.021 intvolume: ' 106' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1311.2481 month: '01' oa: 1 oa_version: Preprint page: 1 - 11 publication: Computers and Fluids publication_status: published publisher: Elsevier publist_id: '5042' quality_controlled: '1' scopus_import: 1 status: public title: A hybrid MPI-OpenMP parallel implementation for pseudospectral simulations with application to Taylor-Couette flow type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 106 year: '2015' ... --- _id: '2035' 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" 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. author: - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Grzegorz full_name: Jablonski, Grzegorz id: 4483EF78-F248-11E8-B48F-1D18A9856A87 last_name: Jablonski orcid: 0000-0002-3536-9866 - first_name: Marian full_name: Mrozek, Marian last_name: Mrozek 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 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 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. 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. ista: Edelsbrunner H, Jablonski G, Mrozek M. 2015. The persistent homology of a self-map. Foundations of Computational Mathematics. 15(5), 1213–1244. 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. date_created: 2018-12-11T11:55:20Z date_published: 2015-10-01T00:00:00Z date_updated: 2021-01-12T06:54:53Z day: '01' ddc: - '000' department: - _id: HeEd doi: 10.1007/s10208-014-9223-y ec_funded: 1 file: - access_level: open_access checksum: 3566f3a8b0c1bc550e62914a88c584ff content_type: application/pdf creator: system date_created: 2018-12-12T10:08:10Z date_updated: 2020-07-14T12:45:26Z file_id: '4670' file_name: IST-2016-486-v1+1_s10208-014-9223-y.pdf file_size: 1317546 relation: main_file file_date_updated: 2020-07-14T12:45:26Z has_accepted_license: '1' intvolume: ' 15' issue: '5' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: 1213 - 1244 project: - _id: 255D761E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '318493' name: Topological Complex Systems publication: Foundations of Computational Mathematics publication_status: published publisher: Springer publist_id: '5022' pubrep_id: '486' quality_controlled: '1' scopus_import: 1 status: public title: The persistent homology of a self-map tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 15 year: '2015' ... --- _id: '2034' 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. author: - first_name: Béatrice full_name: Bérard, Béatrice last_name: Bérard - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Nathalie full_name: Sznajder, Nathalie last_name: Sznajder citation: 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 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 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. 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. ista: Bérard B, Chatterjee K, Sznajder N. 2015. Probabilistic opacity for Markov decision processes. Information Processing Letters. 115(1), 52–59. 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. date_created: 2018-12-11T11:55:20Z date_published: 2015-01-01T00:00:00Z date_updated: 2021-01-12T06:54:52Z day: '01' department: - _id: KrCh doi: 10.1016/j.ipl.2014.09.001 ec_funded: 1 intvolume: ' 115' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1407.4225 month: '01' oa: 1 oa_version: Preprint page: 52 - 59 project: - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication: ' Information Processing Letters' publication_status: published publisher: Elsevier publist_id: '5025' quality_controlled: '1' scopus_import: 1 status: public title: Probabilistic opacity for Markov decision processes type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 115 year: '2015' ... --- _id: '2085' abstract: - lang: eng 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. ' author: - first_name: Phan full_name: Nam, Phan id: 404092F4-F248-11E8-B48F-1D18A9856A87 last_name: Nam - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: 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 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 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. 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. 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. 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. date_created: 2018-12-11T11:55:37Z date_published: 2015-02-01T00:00:00Z date_updated: 2021-01-12T06:55:13Z day: '01' department: - _id: RoSe doi: 10.1007/s00205-014-0781-6 intvolume: ' 215' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1402.1153 month: '02' oa: 1 oa_version: Preprint page: 381 - 417 publication: Archive for Rational Mechanics and Analysis publication_status: published publisher: Springer publist_id: '4951' quality_controlled: '1' scopus_import: 1 status: public title: Collective excitations of Bose gases in the mean-field regime type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 215 year: '2015' ... --- _id: '2166' abstract: - lang: eng 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). ' author: - first_name: László full_name: Erdös, László id: 4DBD5372-F248-11E8-B48F-1D18A9856A87 last_name: Erdös orcid: 0000-0001-5366-9603 - first_name: Antti full_name: Knowles, Antti last_name: Knowles citation: 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' 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' 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.' 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.' 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.' 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.' short: L. Erdös, A. Knowles, Communications in Mathematical Physics 333 (2015) 1365–1416. date_created: 2018-12-11T11:56:05Z date_published: 2015-02-01T00:00:00Z date_updated: 2021-01-12T06:55:43Z day: '01' department: - _id: LaEr doi: 10.1007/s00220-014-2119-5 intvolume: ' 333' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1309.5106 month: '02' oa: 1 oa_version: Preprint page: 1365 - 1416 publication: Communications in Mathematical Physics publication_status: published publisher: Springer publist_id: '4818' quality_controlled: '1' scopus_import: 1 status: public title: 'The Altshuler-Shklovskii formulas for random band matrices I: the unimodular case' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 333 year: '2015' ... --- _id: '1832' abstract: - lang: eng 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. ' article_number: '20' article_processing_charge: No article_type: original author: - first_name: Soham full_name: Chakraborty, Soham last_name: Chakraborty - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Ali full_name: Sezgin, Ali last_name: Sezgin - first_name: Viktor full_name: Vafeiadis, Viktor last_name: Vafeiadis citation: 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 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 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. 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. ista: Chakraborty S, Henzinger TA, Sezgin A, Vafeiadis V. 2015. Aspect-oriented linearizability proofs. Logical Methods in Computer Science. 11(1), 20. 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. short: S. Chakraborty, T.A. Henzinger, A. Sezgin, V. Vafeiadis, Logical Methods in Computer Science 11 (2015). date_created: 2018-12-11T11:54:15Z date_published: 2015-04-01T00:00:00Z date_updated: 2023-02-23T10:38:13Z day: '01' ddc: - '000' department: - _id: ToHe doi: 10.2168/LMCS-11(1:20)2015 ec_funded: 1 file: - access_level: open_access checksum: 7370e164d0a731f442424a92669efc34 content_type: application/pdf creator: system date_created: 2018-12-12T10:11:27Z date_updated: 2020-07-14T12:45:17Z file_id: '4881' file_name: IST-2015-390-v1+1_1502.07639.pdf file_size: 380203 relation: main_file file_date_updated: 2020-07-14T12:45:17Z has_accepted_license: '1' intvolume: ' 11' issue: '1' language: - iso: eng license: https://creativecommons.org/licenses/by-nd/4.0/ month: '04' oa: 1 oa_version: Published Version project: - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling publication: Logical Methods in Computer Science publication_status: published publisher: International Federation of Computational Logic publist_id: '5271' pubrep_id: '390' quality_controlled: '1' related_material: record: - id: '2328' relation: earlier_version status: public scopus_import: 1 status: public title: Aspect-oriented linearizability proofs tmp: image: /image/cc_by_nd.png legal_code_url: https://creativecommons.org/licenses/by-nd/4.0/legalcode name: Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0) short: CC BY-ND (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 11 year: '2015' ... --- _id: '2271' 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. " author: - first_name: Vladimir full_name: Kolmogorov, Vladimir id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov - first_name: Johan full_name: Thapper, Johan last_name: Thapper - first_name: Stanislav full_name: Živný, Stanislav last_name: Živný citation: 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 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 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. 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. 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. 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. short: V. Kolmogorov, J. Thapper, S. Živný, SIAM Journal on Computing 44 (2015) 1–36. date_created: 2018-12-11T11:56:41Z date_published: 2015-02-01T00:00:00Z date_updated: 2023-02-23T10:46:30Z day: '01' department: - _id: VlKo doi: 10.1137/130945648 external_id: arxiv: - '1311.4219' intvolume: ' 44' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1311.4219 month: '02' oa: 1 oa_version: Preprint page: 1 - 36 publication: SIAM Journal on Computing publication_status: published publisher: SIAM publist_id: '4673' quality_controlled: '1' related_material: record: - id: '2518' relation: earlier_version status: public scopus_import: 1 status: public title: The power of linear programming for general-valued CSPs type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 44 year: '2015' ... --- _id: '1598' abstract: - lang: eng 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.' 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" article_processing_charge: No author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Manas full_name: Joglekar, Manas last_name: Joglekar - first_name: Nisarg full_name: Shah, Nisarg last_name: Shah citation: 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 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 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. 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. 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. 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_created: 2018-12-11T11:52:56Z date_published: 2015-03-30T00:00:00Z date_updated: 2023-02-23T10:55:03Z day: '30' department: - _id: KrCh doi: 10.1016/j.tcs.2015.01.050 ec_funded: 1 external_id: arxiv: - '1202.4175' intvolume: ' 573' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1202.4175 month: '03' oa: 1 oa_version: Preprint page: 71 - 89 project: - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication: Theoretical Computer Science publication_status: published publisher: Elsevier publist_id: '5571' quality_controlled: '1' related_material: record: - id: '2715' relation: earlier_version status: public scopus_import: 1 status: public title: Average case analysis of the classical algorithm for Markov decision processes with Büchi objectives type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 573 year: '2015' ... --- _id: '1805' abstract: - lang: eng 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.' author: - first_name: Dominique full_name: Attali, Dominique last_name: Attali - first_name: Ulrich full_name: Bauer, Ulrich id: 2ADD483A-F248-11E8-B48F-1D18A9856A87 last_name: Bauer orcid: 0000-0002-9683-0724 - first_name: Olivier full_name: Devillers, Olivier last_name: Devillers - first_name: Marc full_name: Glisse, Marc last_name: Glisse - first_name: André full_name: Lieutier, André last_name: Lieutier 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' 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' 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.' 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.' 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.' 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.' date_created: 2018-12-11T11:54:06Z date_published: 2015-06-03T00:00:00Z date_updated: 2023-02-23T10:59:19Z day: '03' department: - _id: HeEd doi: 10.1016/j.comgeo.2014.08.010 ec_funded: 1 intvolume: ' 48' issue: '8' language: - iso: eng month: '06' oa_version: None page: 606 - 621 project: - _id: 255D761E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '318493' name: Topological Complex Systems publication: 'Computational Geometry: Theory and Applications' publication_status: published publisher: Elsevier publist_id: '5305' quality_controlled: '1' related_material: record: - id: '2812' relation: earlier_version status: public scopus_import: 1 status: public title: Homological reconstruction and simplification in R3 type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 48 year: '2015' ... --- _id: '1731' abstract: - lang: eng 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. ' author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Laurent full_name: Doyen, Laurent last_name: Doyen - first_name: Hugo full_name: Gimbert, Hugo last_name: Gimbert - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 citation: 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 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 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. 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. ista: Chatterjee K, Doyen L, Gimbert H, Henzinger TA. 2015. Randomness for free. Information and Computation. 245(12), 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. short: K. Chatterjee, L. Doyen, H. Gimbert, T.A. Henzinger, Information and Computation 245 (2015) 3–16. date_created: 2018-12-11T11:53:42Z date_published: 2015-12-01T00:00:00Z date_updated: 2023-02-23T11:45:42Z day: '01' department: - _id: KrCh - _id: ToHe doi: 10.1016/j.ic.2015.06.003 ec_funded: 1 intvolume: ' 245' issue: '12' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1006.0673 month: '12' oa: 1 oa_version: Preprint page: 3 - 16 project: - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 25EFB36C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '215543' name: COMponent-Based Embedded Systems design Techniques - _id: 25F1337C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '214373' name: Design for Embedded Systems - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering publication: Information and Computation publication_status: published publisher: Elsevier publist_id: '5395' quality_controlled: '1' related_material: record: - id: '3856' relation: earlier_version status: public scopus_import: 1 status: public title: Randomness for free type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 245 year: '2015' ... --- _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.' article_number: '9' author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Barbara full_name: Jobstmann, Barbara last_name: Jobstmann - first_name: Rohit full_name: Singh, Rohit last_name: Singh citation: 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 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 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. 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. ista: Chatterjee K, Henzinger TA, Jobstmann B, Singh R. 2015. Measuring and synthesizing systems in probabilistic environments. Journal of the ACM. 62(1), 9. 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). date_created: 2018-12-11T11:54:23Z date_published: 2015-02-01T00:00:00Z date_updated: 2023-02-23T11:46:04Z day: '01' department: - _id: KrCh - _id: ToHe doi: 10.1145/2699430 ec_funded: 1 intvolume: ' 62' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1004.0739 month: '02' oa: 1 oa_version: Preprint project: - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication: Journal of the ACM publication_status: published publisher: ACM publist_id: '5244' quality_controlled: '1' related_material: record: - id: '3864' relation: earlier_version status: public scopus_import: 1 status: public title: Measuring and synthesizing systems in probabilistic environments type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 62 year: '2015' ... --- _id: '1661' abstract: - lang: eng 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. 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.' article_number: '7174888' article_processing_charge: No author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Veronika full_name: Loitzenbauer, Veronika last_name: Loitzenbauer citation: 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' 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' 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. 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. 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.' 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. short: K. Chatterjee, M.H. Henzinger, V. Loitzenbauer, in:, Proceedings - Symposium on Logic in Computer Science, IEEE, 2015. conference: end_date: 2015-07-10 location: Kyoto, Japan name: 'LICS: Logic in Computer Science' start_date: 2015-07-06 date_created: 2018-12-11T11:53:19Z date_published: 2015-07-01T00:00:00Z date_updated: 2023-02-23T12:20:05Z day: '01' department: - _id: KrCh doi: 10.1109/LICS.2015.34 ec_funded: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://eprints.cs.univie.ac.at/4368/ month: '07' oa: 1 oa_version: Submitted Version project: - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' publication: Proceedings - Symposium on Logic in Computer Science publication_status: published publisher: IEEE publist_id: '5489' quality_controlled: '1' related_material: record: - id: '464' relation: later_version status: public scopus_import: '1' status: public title: Improved algorithms for one-pair and k-pair Streett objectives type: conference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf volume: 2015-July year: '2015' ... --- _id: '473' 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. author: - first_name: Mathieu full_name: Lewin, Mathieu last_name: Lewin - first_name: Nam full_name: Phan Thanh, Nam id: 404092F4-F248-11E8-B48F-1D18A9856A87 last_name: Phan Thanh - first_name: Nicolas full_name: Rougerie, Nicolas last_name: Rougerie citation: 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 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 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. 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. 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. 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. date_created: 2018-12-11T11:46:40Z date_published: 2015-01-01T00:00:00Z date_updated: 2021-01-12T08:00:52Z day: '01' ddc: - '539' department: - _id: RoSe doi: 10.5802/jep.18 ec_funded: 1 file: - access_level: open_access checksum: a40eb4016717ddc9927154798a4c164a content_type: application/pdf creator: system date_created: 2018-12-12T10:12:53Z date_updated: 2020-07-14T12:46:35Z file_id: '4974' file_name: IST-2018-951-v1+1_2015_Thanh-Nam_Derivation_of.pdf file_size: 1084254 relation: main_file file_date_updated: 2020-07-14T12:46:35Z has_accepted_license: '1' intvolume: ' 2' language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: 65 - 115 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Journal de l'Ecole Polytechnique - Mathematiques publication_status: published publisher: Ecole Polytechnique publist_id: '7344' pubrep_id: '951' quality_controlled: '1' scopus_import: 1 status: public title: Derivation of nonlinear gibbs measures from many-body quantum mechanics tmp: image: /image/cc_by_nd.png legal_code_url: https://creativecommons.org/licenses/by-nd/4.0/legalcode name: Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0) short: CC BY-ND (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 2 year: '2015' ... --- _id: '477' 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. author: - first_name: Katrin full_name: Holst, Katrin last_name: Holst - first_name: Daria full_name: Guseva, Daria last_name: Guseva - first_name: Susann full_name: Schindler, Susann last_name: Schindler - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 - first_name: Armin full_name: Braun, Armin last_name: Braun - first_name: Himpriya full_name: Chopra, Himpriya last_name: Chopra - first_name: Oliver full_name: Pabst, Oliver last_name: Pabst - first_name: Evgeni full_name: Ponimaskin, Evgeni last_name: Ponimaskin 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 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 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. 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. 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. 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. date_created: 2018-12-11T11:46:41Z date_published: 2015-06-15T00:00:00Z date_updated: 2021-01-12T08:00:54Z day: '15' department: - _id: MiSi doi: 10.1242/jcs.167999 intvolume: ' 128' issue: '15' language: - iso: eng month: '06' oa_version: None page: 2866 - 2880 publication: Journal of Cell Science publication_status: published publisher: Company of Biologists publist_id: '7343' quality_controlled: '1' scopus_import: 1 status: public title: The serotonin receptor 5-HT7R regulates the morphology and migratory properties of dendritic cells type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 128 year: '2015' ... --- _id: '523' 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. author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Laurent full_name: Doyen, Laurent last_name: Doyen - first_name: Mickael full_name: Randour, Mickael last_name: Randour - first_name: Jean full_name: Raskin, Jean last_name: Raskin citation: 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 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 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. 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. 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. 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. short: K. Chatterjee, L. Doyen, M. Randour, J. Raskin, Information and Computation 242 (2015) 25–52. date_created: 2018-12-11T11:46:57Z date_published: 2015-03-24T00:00:00Z date_updated: 2023-02-23T10:36:02Z day: '24' department: - _id: KrCh doi: 10.1016/j.ic.2015.03.010 ec_funded: 1 intvolume: ' 242' issue: '6' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1302.4248 month: '03' oa: 1 oa_version: Preprint page: 25 - 52 project: - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication: Information and Computation publication_status: published publisher: Elsevier publist_id: '7296' quality_controlled: '1' related_material: record: - id: '2279' relation: earlier_version status: public scopus_import: 1 status: public title: Looking at mean-payoff and total-payoff through windows type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 242 year: '2015' ... --- _id: '532' abstract: - lang: eng 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. author: - first_name: Wenyang full_name: Li, Wenyang last_name: Li - first_name: Mengdi full_name: Ma, Mengdi last_name: Ma - first_name: Ying full_name: Feng, Ying last_name: Feng - first_name: Hongjiang full_name: Li, Hongjiang id: 33CA54A6-F248-11E8-B48F-1D18A9856A87 last_name: Li orcid: 0000-0001-5039-9660 - first_name: Yichuan full_name: Wang, Yichuan last_name: Wang - first_name: Yutong full_name: Ma, Yutong last_name: Ma - first_name: Mingzhe full_name: Li, Mingzhe last_name: Li - first_name: Fengying full_name: An, Fengying last_name: An - first_name: Hongwei full_name: Guo, Hongwei last_name: Guo 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 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 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. 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. 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. 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. date_created: 2018-12-11T11:47:00Z date_published: 2015-10-22T00:00:00Z date_updated: 2021-01-12T08:01:27Z day: '22' department: - _id: JiFr doi: 10.1016/j.cell.2015.09.037 intvolume: ' 163' issue: '3' language: - iso: eng month: '10' oa_version: None page: 670 - 683 publication: Cell publication_status: published publisher: Cell Press publist_id: '7285' quality_controlled: '1' scopus_import: 1 status: public title: EIN2-directed translational regulation of ethylene signaling in arabidopsis type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 163 year: '2015' ... --- _id: '524' 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.' author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Rasmus full_name: Ibsen-Jensen, Rasmus id: 3B699956-F248-11E8-B48F-1D18A9856A87 last_name: Ibsen-Jensen orcid: 0000-0003-4783-0389 citation: 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 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 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. 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. ista: Chatterjee K, Ibsen-Jensen R. 2015. Qualitative analysis of concurrent mean payoff games. Information and Computation. 242(6), 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. short: K. Chatterjee, R. Ibsen-Jensen, Information and Computation 242 (2015) 2–24. date_created: 2018-12-11T11:46:57Z date_published: 2015-10-11T00:00:00Z date_updated: 2023-02-23T12:24:45Z day: '11' department: - _id: KrCh doi: 10.1016/j.ic.2015.03.009 external_id: arxiv: - '1409.5306' intvolume: ' 242' issue: '6' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1409.5306 month: '10' oa: 1 oa_version: Preprint page: 2 - 24 publication: Information and Computation publication_status: published publisher: Elsevier publist_id: '7295' quality_controlled: '1' related_material: record: - id: '5403' relation: earlier_version status: public scopus_import: 1 status: public title: Qualitative analysis of concurrent mean payoff games type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 242 year: '2015' ... --- _id: '1481' abstract: - lang: eng 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. ' acknowledgement: "A Technical Report of this paper is available at: \r\nhttps://repository.ist.ac.at/id/eprint/146.\r\n" article_processing_charge: No author: - first_name: Umair full_name: Ahmed, Umair last_name: Ahmed - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Sumit full_name: Gulwani, Sumit last_name: Gulwani citation: 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.' 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.' 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. 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. 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.' 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. short: U. Ahmed, K. Chatterjee, S. Gulwani, in:, Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence, AAAI Press, 2015, pp. 745–752. conference: end_date: 2015-01-30 location: Austin, TX, USA name: 'AAAI: Conference on Artificial Intelligence' start_date: 2015-01-25 date_created: 2018-12-11T11:52:16Z date_published: 2015-01-01T00:00:00Z date_updated: 2023-02-23T12:25:07Z day: '01' department: - _id: KrCh ec_funded: 1 intvolume: ' 2' language: - iso: eng main_file_link: - open_access: '1' url: https://www.aaai.org/ocs/index.php/AAAI/AAAI15/paper/download/9523/9300 month: '01' oa: 1 oa_version: None page: 745 - 752 project: - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication: Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence publication_status: published publisher: AAAI Press publist_id: '5713' quality_controlled: '1' related_material: record: - id: '5410' relation: earlier_version status: public scopus_import: 1 status: public title: Automatic generation of alternative starting positions for simple traditional board games type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 2 year: '2015' ... --- _id: '1732' 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. author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Martin full_name: Chmelik, Martin id: 3624234E-F248-11E8-B48F-1D18A9856A87 last_name: Chmelik - first_name: Raghav full_name: Gupta, Raghav last_name: Gupta - first_name: Ayush full_name: Kanodia, Ayush last_name: Kanodia citation: 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' 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' 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. 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.' 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.' 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. conference: end_date: 2015-05-30 location: Seattle, WA, United States name: 'ICRA: International Conference on Robotics and Automation' start_date: 2015-05-26 date_created: 2018-12-11T11:53:43Z date_published: 2015-01-01T00:00:00Z date_updated: 2023-02-23T12:25:52Z day: '01' department: - _id: KrCh doi: 10.1109/ICRA.2015.7139019 ec_funded: 1 external_id: arxiv: - '1409.3360' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1409.3360 month: '01' oa: 1 oa_version: Preprint page: 325 - 330 project: - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' publication_status: published publisher: IEEE publist_id: '5394' quality_controlled: '1' related_material: record: - id: '5424' relation: earlier_version status: public - id: '5426' relation: earlier_version status: public scopus_import: 1 status: public title: Qualitative analysis of POMDPs with temporal logic specifications for robotics applications type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2015' ... --- _id: '5431' 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." alternative_title: - IST Austria Technical Report author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Rasmus full_name: Ibsen-Jensen, Rasmus id: 3B699956-F248-11E8-B48F-1D18A9856A87 last_name: Ibsen-Jensen orcid: 0000-0003-4783-0389 - first_name: Kristoffer full_name: Hansen, Kristoffer last_name: Hansen 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 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 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. ieee: K. Chatterjee, R. Ibsen-Jensen, and K. Hansen, The patience of concurrent stochastic games with safety and reachability objectives. IST Austria, 2015. ista: Chatterjee K, Ibsen-Jensen R, Hansen K. 2015. The patience of concurrent stochastic games with safety and reachability objectives, IST Austria, 25p. 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. date_created: 2018-12-12T11:39:17Z date_published: 2015-02-19T00:00:00Z date_updated: 2021-01-12T08:02:13Z day: '19' ddc: - '005' - '519' department: - _id: KrCh doi: 10.15479/AT:IST-2015-322-v1-1 file: - access_level: open_access checksum: bfb858262c30445b8e472c40069178a2 content_type: application/pdf creator: system date_created: 2018-12-12T11:53:31Z date_updated: 2020-07-14T12:46:53Z file_id: '5491' file_name: IST-2015-322-v1+1_safetygames.pdf file_size: 661015 relation: main_file file_date_updated: 2020-07-14T12:46:53Z has_accepted_license: '1' language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: '25' publication_identifier: issn: - 2664-1690 publication_status: published publisher: IST Austria pubrep_id: '322' status: public title: The patience of concurrent stochastic games with safety and reachability objectives type: technical_report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2015' ... --- _id: '1657' abstract: - lang: eng 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. ' acknowledgement: "A Technical Report of this paper is available at: https://repository.ist.ac.at/327\r\n" alternative_title: - LICS author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Zuzana full_name: Komárková, Zuzana last_name: Komárková - first_name: Jan full_name: Kretinsky, Jan id: 44CEF464-F248-11E8-B48F-1D18A9856A87 last_name: Kretinsky orcid: 0000-0002-8122-2881 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 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' 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. 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. ista: Chatterjee K, Komárková Z, Kretinsky J. 2015. Unifying two views on multiple mean-payoff objectives in Markov decision processes. , 244–256. 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. conference: end_date: 2015-07-10 location: Kyoto, Japan name: 'LICS: Logic in Computer Science' start_date: 2015-07-06 date_created: 2018-12-11T11:53:18Z date_published: 2015-07-01T00:00:00Z date_updated: 2023-02-23T12:26:16Z day: '01' department: - _id: KrCh - _id: ToHe doi: 10.1109/LICS.2015.32 ec_funded: 1 language: - iso: eng month: '07' oa_version: None page: 244 - 256 project: - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication_status: published publisher: IEEE publist_id: '5493' quality_controlled: '1' related_material: record: - id: '466' relation: later_version status: public - id: '5429' relation: earlier_version status: public - id: '5435' relation: earlier_version status: public scopus_import: 1 series_title: LICS status: public title: Unifying two views on multiple mean-payoff objectives in Markov decision processes type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2015' ... --- _id: '1656' abstract: - lang: eng 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. 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" article_number: '7174926' author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Jan full_name: Otop, Jan id: 2FC5DA74-F248-11E8-B48F-1D18A9856A87 last_name: Otop 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' 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' 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. 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. 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.' 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. conference: end_date: 2015-07-10 location: Kyoto, Japan name: 'LICS: Logic in Computer Science' start_date: 2015-07-06 date_created: 2018-12-11T11:53:17Z date_published: 2015-07-31T00:00:00Z date_updated: 2023-02-23T12:26:19Z day: '31' department: - _id: KrCh - _id: ToHe doi: 10.1109/LICS.2015.72 ec_funded: 1 external_id: arxiv: - '1606.03598' language: - iso: eng month: '07' oa_version: None project: - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication: Proceedings - Symposium on Logic in Computer Science publication_status: published publisher: IEEE publist_id: '5494' quality_controlled: '1' related_material: record: - id: '467' relation: later_version status: public - id: '5415' relation: earlier_version status: public - id: '5436' relation: earlier_version status: public scopus_import: 1 status: public title: Nested weighted automata type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 2015-July year: '2015' ... --- _id: '5429' 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." alternative_title: - IST Austria Technical Report author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Zuzana full_name: Komarkova, Zuzana last_name: Komarkova - first_name: Jan full_name: Kretinsky, Jan id: 44CEF464-F248-11E8-B48F-1D18A9856A87 last_name: Kretinsky orcid: 0000-0002-8122-2881 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 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 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. ieee: K. Chatterjee, Z. Komarkova, and J. Kretinsky, Unifying two views on multiple mean-payoff objectives in Markov decision processes. IST Austria, 2015. ista: Chatterjee K, Komarkova Z, Kretinsky J. 2015. Unifying two views on multiple mean-payoff objectives in Markov decision processes, IST Austria, 41p. 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. date_created: 2018-12-12T11:39:17Z date_published: 2015-01-12T00:00:00Z date_updated: 2023-02-23T12:26:16Z day: '12' ddc: - '004' department: - _id: KrCh doi: 10.15479/AT:IST-2015-318-v1-1 file: - access_level: open_access checksum: e4869a584567c506349abda9c8ec7db3 content_type: application/pdf creator: system date_created: 2018-12-12T11:54:11Z date_updated: 2020-07-14T12:46:52Z file_id: '5533' file_name: IST-2015-318-v1+1_main.pdf file_size: 689863 relation: main_file file_date_updated: 2020-07-14T12:46:52Z has_accepted_license: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: '41' publication_identifier: issn: - 2664-1690 publication_status: published publisher: IST Austria pubrep_id: '318' related_material: record: - id: '1657' relation: later_version status: public - id: '466' relation: later_version status: public - id: '5435' relation: later_version status: public status: public title: Unifying two views on multiple mean-payoff objectives in Markov decision processes type: technical_report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2015' ... --- _id: '5435' 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. 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." alternative_title: - IST Austria Technical Report author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Zuzana full_name: Komarkova, Zuzana last_name: Komarkova - first_name: Jan full_name: Kretinsky, Jan id: 44CEF464-F248-11E8-B48F-1D18A9856A87 last_name: Kretinsky orcid: 0000-0002-8122-2881 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-v2-1 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 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. ieee: K. Chatterjee, Z. Komarkova, and J. Kretinsky, Unifying two views on multiple mean-payoff objectives in Markov decision processes. IST Austria, 2015. ista: Chatterjee K, Komarkova Z, Kretinsky J. 2015. Unifying two views on multiple mean-payoff objectives in Markov decision processes, IST Austria, 51p. 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. short: K. Chatterjee, Z. Komarkova, J. Kretinsky, Unifying Two Views on Multiple Mean-Payoff Objectives in Markov Decision Processes, IST Austria, 2015. date_created: 2018-12-12T11:39:19Z date_published: 2015-02-23T00:00:00Z date_updated: 2023-02-23T12:26:00Z day: '23' ddc: - '004' department: - _id: KrCh doi: 10.15479/AT:IST-2015-318-v2-1 file: - access_level: open_access checksum: 75284adec80baabdfe71ff9ebbc27445 content_type: application/pdf creator: system date_created: 2018-12-12T11:54:03Z date_updated: 2020-07-14T12:46:53Z file_id: '5525' file_name: IST-2015-318-v2+1_main.pdf file_size: 717630 relation: main_file file_date_updated: 2020-07-14T12:46:53Z has_accepted_license: '1' language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: '51' publication_identifier: issn: - 2664-1690 publication_status: published publisher: IST Austria pubrep_id: '327' related_material: record: - id: '1657' relation: later_version status: public - id: '466' relation: later_version status: public - id: '5429' relation: earlier_version status: public status: public title: Unifying two views on multiple mean-payoff objectives in Markov decision processes type: technical_report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2015' ... --- _id: '5436' abstract: - lang: eng 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." alternative_title: - IST Austria Technical Report author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Jan full_name: Otop, Jan id: 2FC5DA74-F248-11E8-B48F-1D18A9856A87 last_name: Otop citation: ama: Chatterjee K, Henzinger TA, Otop J. Nested Weighted Automata. IST Austria; 2015. doi:10.15479/AT:IST-2015-170-v2-2 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 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. ieee: K. Chatterjee, T. A. Henzinger, and J. Otop, Nested weighted automata. IST Austria, 2015. ista: Chatterjee K, Henzinger TA, Otop J. 2015. Nested weighted automata, IST Austria, 29p. mla: Chatterjee, Krishnendu, et al. Nested Weighted Automata. IST Austria, 2015, doi:10.15479/AT:IST-2015-170-v2-2. short: K. Chatterjee, T.A. Henzinger, J. Otop, Nested Weighted Automata, IST Austria, 2015. date_created: 2018-12-12T11:39:19Z date_published: 2015-04-24T00:00:00Z date_updated: 2023-02-23T12:25:21Z day: '24' ddc: - '000' department: - _id: KrCh - _id: ToHe doi: 10.15479/AT:IST-2015-170-v2-2 file: - access_level: open_access checksum: 3c402f47d3669c28d04d1af405a08e3f content_type: application/pdf creator: system date_created: 2018-12-12T11:54:19Z date_updated: 2020-07-14T12:46:54Z file_id: '5541' file_name: IST-2015-170-v2+2_report.pdf file_size: 569991 relation: main_file file_date_updated: 2020-07-14T12:46:54Z has_accepted_license: '1' language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: '29' publication_identifier: issn: - 2664-1690 publication_status: published publisher: IST Austria pubrep_id: '331' related_material: record: - id: '1656' relation: later_version status: public - id: '467' relation: later_version status: public - id: '5415' relation: earlier_version status: public status: public title: Nested weighted automata type: technical_report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2015' ... --- _id: '1659' 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.' acknowledgement: 'A technical report of the article is available at: https://research-explorer.app.ist.ac.at/record/5439' article_processing_charge: No author: - first_name: Udi full_name: Boker, Udi id: 31E297B6-F248-11E8-B48F-1D18A9856A87 last_name: Boker - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Jan full_name: Otop, Jan id: 2FC5DA74-F248-11E8-B48F-1D18A9856A87 last_name: Otop citation: 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' 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' 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. ieee: U. Boker, T. A. Henzinger, and J. Otop, “The target discounted-sum problem,” in LICS, Kyoto, Japan, 2015, pp. 750–761. ista: 'Boker U, Henzinger TA, Otop J. 2015. The target discounted-sum problem. LICS. LICS: Logic in Computer ScienceLogic in Computer Science, 750–761.' mla: Boker, Udi, et al. “The Target Discounted-Sum Problem.” LICS, IEEE, 2015, pp. 750–61, doi:10.1109/LICS.2015.74. short: U. Boker, T.A. Henzinger, J. Otop, in:, LICS, IEEE, 2015, pp. 750–761. conference: end_date: 2015-07-10 location: Kyoto, Japan name: 'LICS: Logic in Computer Science' start_date: 2015-007-06 date_created: 2018-12-11T11:53:19Z date_published: 2015-07-01T00:00:00Z date_updated: 2023-02-23T12:26:27Z day: '01' ddc: - '000' department: - _id: ToHe doi: 10.1109/LICS.2015.74 ec_funded: 1 file: - access_level: open_access checksum: 6abebca9c1a620e9e103a8f9222befac content_type: application/pdf creator: dernst date_created: 2020-05-15T08:53:29Z date_updated: 2020-07-14T12:45:10Z file_id: '7852' file_name: 2015_LICS_Boker.pdf file_size: 340215 relation: main_file file_date_updated: 2020-07-14T12:45:10Z has_accepted_license: '1' language: - iso: eng month: '07' oa: 1 oa_version: Submitted Version page: 750 - 761 project: - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize publication: LICS publication_identifier: eisbn: - '978-1-4799-8875-4 ' issn: - '1043-6871 ' publication_status: published publisher: IEEE publist_id: '5491' quality_controlled: '1' related_material: record: - id: '5439' relation: earlier_version status: public scopus_import: 1 series_title: Logic in Computer Science status: public title: The target discounted-sum problem type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2015' ... --- _id: '1610' 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. alternative_title: - LNCS article_processing_charge: No author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Rasmus full_name: Ibsen-Jensen, Rasmus id: 3B699956-F248-11E8-B48F-1D18A9856A87 last_name: Ibsen-Jensen orcid: 0000-0003-4783-0389 - first_name: Jan full_name: Otop, Jan id: 2FC5DA74-F248-11E8-B48F-1D18A9856A87 last_name: Otop citation: 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' 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' 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. 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. 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.' 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. conference: end_date: 2015-07-10 location: Kyoto, Japan name: 'ICALP: Automata, Languages and Programming' start_date: 2015-07-06 date_created: 2018-12-11T11:53:01Z date_published: 2015-07-01T00:00:00Z date_updated: 2023-02-23T12:26:24Z day: '01' department: - _id: KrCh - _id: ToHe doi: 10.1007/978-3-662-47666-6_10 ec_funded: 1 external_id: arxiv: - '1504.08259' intvolume: ' 9135' issue: Part II language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1504.08259 month: '07' oa: 1 oa_version: None page: 121 - 133 project: - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering publication: 42nd International Colloquium publication_identifier: isbn: - 978-3-662-47665-9 publication_status: published publisher: Springer Nature publist_id: '5556' pubrep_id: '321' quality_controlled: '1' related_material: record: - id: '465' relation: later_version status: public - id: '5438' relation: earlier_version status: public scopus_import: '1' status: public title: Edit distance for pushdown automata type: conference user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 9135 year: '2015' ... --- _id: '5437' abstract: - lang: eng 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. " alternative_title: - IST Austria Technical Report author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Rasmus full_name: Ibsen-Jensen, Rasmus id: 3B699956-F248-11E8-B48F-1D18A9856A87 last_name: Ibsen-Jensen orcid: 0000-0003-4783-0389 - first_name: Andreas full_name: Pavlogiannis, Andreas id: 49704004-F248-11E8-B48F-1D18A9856A87 last_name: Pavlogiannis orcid: 0000-0002-8943-0722 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-2015-330-v2-1 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-2015-330-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. 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. 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. short: K. Chatterjee, R. Ibsen-Jensen, A. Pavlogiannis, Faster Algorithms for Quantitative Verification in Constant Treewidth Graphs, IST Austria, 2015. date_created: 2018-12-12T11:39:19Z date_published: 2015-04-27T00:00:00Z date_updated: 2023-02-23T12:26:05Z day: '27' ddc: - '000' department: - _id: KrCh doi: 10.15479/AT:IST-2015-330-v2-1 file: - access_level: open_access checksum: f5917c20f84018b362d385c000a2e123 content_type: application/pdf creator: system date_created: 2018-12-12T11:53:12Z date_updated: 2020-07-14T12:46:54Z file_id: '5473' file_name: IST-2015-330-v2+1_main.pdf file_size: 1072137 relation: main_file file_date_updated: 2020-07-14T12:46:54Z has_accepted_license: '1' language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: '27' publication_identifier: issn: - 2664-1690 publication_status: published publisher: IST Austria pubrep_id: '333' related_material: record: - id: '1607' relation: later_version status: public - id: '5430' relation: earlier_version status: public status: public title: Faster algorithms for quantitative verification in constant treewidth graphs type: technical_report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2015' ... --- _id: '5430' abstract: - lang: eng 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. alternative_title: - IST Austria Technical Report author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Rasmus full_name: Ibsen-Jensen, Rasmus id: 3B699956-F248-11E8-B48F-1D18A9856A87 last_name: Ibsen-Jensen orcid: 0000-0003-4783-0389 - first_name: Andreas full_name: Pavlogiannis, Andreas id: 49704004-F248-11E8-B48F-1D18A9856A87 last_name: Pavlogiannis orcid: 0000-0002-8943-0722 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 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. 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. 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. short: K. Chatterjee, R. Ibsen-Jensen, A. Pavlogiannis, Faster Algorithms for Quantitative Verification in Constant Treewidth Graphs, IST Austria, 2015. date_created: 2018-12-12T11:39:17Z date_published: 2015-02-10T00:00:00Z date_updated: 2023-02-23T12:26:22Z day: '10' ddc: - '000' department: - _id: KrCh doi: 10.15479/AT:IST-2015-319-v1-1 file: - access_level: open_access checksum: 62c6ea01e342553dcafb88a070fb1ad5 content_type: application/pdf creator: system date_created: 2018-12-12T11:53:21Z date_updated: 2020-07-14T12:46:52Z file_id: '5482' file_name: IST-2015-319-v1+1_long.pdf file_size: 1089651 relation: main_file file_date_updated: 2020-07-14T12:46:52Z has_accepted_license: '1' language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: '31' publication_identifier: issn: - 2664-1690 publication_status: published publisher: IST Austria pubrep_id: '319' related_material: record: - id: '1607' relation: later_version status: public - id: '5437' relation: later_version status: public status: public title: Faster algorithms for quantitative verification in constant treewidth graphs type: technical_report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2015' ...