[{"title":"A small number of open Ca(2+) channels trigger transmitter release at a central GABAergic synapse","month":"01","extern":1,"issue":"1","_id":"3829","quality_controlled":0,"publisher":"Nature Publishing Group","author":[{"last_name":"Bucurenciu","first_name":"Iancu","full_name":"Bucurenciu, Iancu"},{"last_name":"Bischofberger","first_name":"Josef","full_name":"Bischofberger, Josef"},{"first_name":"Peter M","full_name":"Peter Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804","last_name":"Jonas"}],"citation":{"apa":"Bucurenciu, I., Bischofberger, J., &#38; Jonas, P. M. (2010). A small number of open Ca(2+) channels trigger transmitter release at a central GABAergic synapse. <i>Nature Neuroscience</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nn.2461 \">https://doi.org/10.1038/nn.2461 </a>","ieee":"I. Bucurenciu, J. Bischofberger, and P. M. Jonas, “A small number of open Ca(2+) channels trigger transmitter release at a central GABAergic synapse,” <i>Nature Neuroscience</i>, vol. 13, no. 1. Nature Publishing Group, pp. 19–21, 2010.","ista":"Bucurenciu I, Bischofberger J, Jonas PM. 2010. A small number of open Ca(2+) channels trigger transmitter release at a central GABAergic synapse. Nature Neuroscience. 13(1), 19–21.","mla":"Bucurenciu, Iancu, et al. “A Small Number of Open Ca(2+) Channels Trigger Transmitter Release at a Central GABAergic Synapse.” <i>Nature Neuroscience</i>, vol. 13, no. 1, Nature Publishing Group, 2010, pp. 19–21, doi:<a href=\"https://doi.org/10.1038/nn.2461 \">10.1038/nn.2461 </a>.","chicago":"Bucurenciu, Iancu, Josef Bischofberger, and Peter M Jonas. “A Small Number of Open Ca(2+) Channels Trigger Transmitter Release at a Central GABAergic Synapse.” <i>Nature Neuroscience</i>. Nature Publishing Group, 2010. <a href=\"https://doi.org/10.1038/nn.2461 \">https://doi.org/10.1038/nn.2461 </a>.","ama":"Bucurenciu I, Bischofberger J, Jonas PM. A small number of open Ca(2+) channels trigger transmitter release at a central GABAergic synapse. <i>Nature Neuroscience</i>. 2010;13(1):19-21. doi:<a href=\"https://doi.org/10.1038/nn.2461 \">10.1038/nn.2461 </a>","short":"I. Bucurenciu, J. Bischofberger, P.M. Jonas, Nature Neuroscience 13 (2010) 19–21."},"abstract":[{"lang":"eng","text":"To determine the number of open Ca(2+) channels necessary for transmitter release at the inhibitory basket cell-granule cell synapse in rat hippocampus, we combined presynaptic Ca(2+) imaging, recording of postsynaptic currents and modeling. We found that that the opening of three or fewer Ca(2+) channels triggered transmitter release. Furthermore, a small number of Ca(2+) channels were able to evoke release with high temporal precision, despite stochastic Ca(2+) channel opening."}],"year":"2010","page":"19 - 21","publication_status":"published","volume":13,"date_updated":"2021-01-12T07:52:29Z","type":"journal_article","status":"public","intvolume":"        13","doi":"10.1038/nn.2461 ","day":"01","publist_id":"2380","date_created":"2018-12-11T12:05:24Z","date_published":"2010-01-01T00:00:00Z","publication":"Nature Neuroscience"},{"year":"2010","page":"52 - 8","publication_status":"published","quality_controlled":0,"publisher":"American Association for the Advancement of Science","citation":{"short":"H. Hu, M. Martina, P.M. Jonas, Science 327 (2010) 52–8.","ama":"Hu H, Martina M, Jonas PM. Dendritic mechanisms underlying rapid synaptic activation of fast-spiking hippocampal interneurons. <i>Science</i>. 2010;327(5961):52-58. doi:<a href=\"https://doi.org/10.1126/science.1177876\">10.1126/science.1177876</a>","mla":"Hu, Hua, et al. “Dendritic Mechanisms Underlying Rapid Synaptic Activation of Fast-Spiking Hippocampal Interneurons.” <i>Science</i>, vol. 327, no. 5961, American Association for the Advancement of Science, 2010, pp. 52–58, doi:<a href=\"https://doi.org/10.1126/science.1177876\">10.1126/science.1177876</a>.","chicago":"Hu, Hua, Marco Martina, and Peter M Jonas. “Dendritic Mechanisms Underlying Rapid Synaptic Activation of Fast-Spiking Hippocampal Interneurons.” <i>Science</i>. American Association for the Advancement of Science, 2010. <a href=\"https://doi.org/10.1126/science.1177876\">https://doi.org/10.1126/science.1177876</a>.","ista":"Hu H, Martina M, Jonas PM. 2010. Dendritic mechanisms underlying rapid synaptic activation of fast-spiking hippocampal interneurons. Science. 327(5961), 52–8.","ieee":"H. Hu, M. Martina, and P. M. Jonas, “Dendritic mechanisms underlying rapid synaptic activation of fast-spiking hippocampal interneurons,” <i>Science</i>, vol. 327, no. 5961. American Association for the Advancement of Science, pp. 52–8, 2010.","apa":"Hu, H., Martina, M., &#38; Jonas, P. M. (2010). Dendritic mechanisms underlying rapid synaptic activation of fast-spiking hippocampal interneurons. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.1177876\">https://doi.org/10.1126/science.1177876</a>"},"abstract":[{"lang":"eng","text":"Fast-spiking, parvalbumin-expressing basket cells (BCs) are important for feedforward and feedback inhibition. During network activity, BCs respond with short latency and high temporal precision. It is thought that the specific properties of input synapses are responsible for rapid recruitment. However, a potential contribution of active dendritic conductances has not been addressed. We combined confocal imaging and patch-clamp techniques to obtain simultaneous somatodendritic recordings from BCs. Action potentials were initiated in the BC axon and backpropagated into the dendrites with reduced amplitude and little activity dependence. These properties were explained by a high K+ to Na+ conductance ratio in BC dendrites. Computational analysis indicated that dendritic K+ channels convey unique integration properties to BCs, leading to the rapid and temporally precise activation by excitatory inputs."}],"author":[{"id":"4AC0145C-F248-11E8-B48F-1D18A9856A87","last_name":"Hu","first_name":"Hua","full_name":"Hua Hu"},{"last_name":"Martina","first_name":"Marco","full_name":"Martina, Marco"},{"last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804","first_name":"Peter M","full_name":"Peter Jonas"}],"extern":1,"_id":"3830","issue":"5961","title":"Dendritic mechanisms underlying rapid synaptic activation of fast-spiking hippocampal interneurons","month":"01","publication":"Science","doi":"10.1126/science.1177876","intvolume":"       327","day":"01","date_published":"2010-01-01T00:00:00Z","publist_id":"2381","date_created":"2018-12-11T12:05:24Z","date_updated":"2021-01-12T07:52:30Z","volume":327,"type":"journal_article","status":"public"},{"publication":"PNAS","date_published":"2010-01-01T00:00:00Z","date_created":"2018-12-11T12:05:24Z","publist_id":"2379","day":"01","intvolume":"       107","doi":"10.1073/pnas.0910716107","status":"public","type":"journal_article","date_updated":"2021-01-12T07:52:31Z","volume":107,"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2818894/#!po=4.16667","open_access":"1"}],"publication_status":"published","year":"2010","page":"894 - 9","citation":{"chicago":"Norenberg, Anja, Hua Hu, Imre Vida, Marlene Bartos, and Peter M Jonas. “Distinct Nonuniform Cable Properties Optimize Rapid and Efficient Activation of Fast-Spiking GABAergic Interneurons.” <i>PNAS</i>. National Academy of Sciences, 2010. <a href=\"https://doi.org/10.1073/pnas.0910716107\">https://doi.org/10.1073/pnas.0910716107</a>.","mla":"Norenberg, Anja, et al. “Distinct Nonuniform Cable Properties Optimize Rapid and Efficient Activation of Fast-Spiking GABAergic Interneurons.” <i>PNAS</i>, vol. 107, no. 2, National Academy of Sciences, 2010, pp. 894–99, doi:<a href=\"https://doi.org/10.1073/pnas.0910716107\">10.1073/pnas.0910716107</a>.","ista":"Norenberg A, Hu H, Vida I, Bartos M, Jonas PM. 2010. Distinct nonuniform cable properties optimize rapid and efficient activation of fast-spiking GABAergic interneurons. PNAS. 107(2), 894–9.","ieee":"A. Norenberg, H. Hu, I. Vida, M. Bartos, and P. M. Jonas, “Distinct nonuniform cable properties optimize rapid and efficient activation of fast-spiking GABAergic interneurons,” <i>PNAS</i>, vol. 107, no. 2. National Academy of Sciences, pp. 894–9, 2010.","apa":"Norenberg, A., Hu, H., Vida, I., Bartos, M., &#38; Jonas, P. M. (2010). Distinct nonuniform cable properties optimize rapid and efficient activation of fast-spiking GABAergic interneurons. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.0910716107\">https://doi.org/10.1073/pnas.0910716107</a>","short":"A. Norenberg, H. Hu, I. Vida, M. Bartos, P.M. Jonas, PNAS 107 (2010) 894–9.","ama":"Norenberg A, Hu H, Vida I, Bartos M, Jonas PM. Distinct nonuniform cable properties optimize rapid and efficient activation of fast-spiking GABAergic interneurons. <i>PNAS</i>. 2010;107(2):894-899. doi:<a href=\"https://doi.org/10.1073/pnas.0910716107\">10.1073/pnas.0910716107</a>"},"abstract":[{"lang":"eng","text":"Fast-spiking, parvalbumin-expressing basket cells (BCs) play a key role in feedforward and feedback inhibition in the hippocampus. However, the dendritic mechanisms underlying rapid interneuron recruitment have remained unclear. To quantitatively address this question, we developed detailed passive cable models of BCs in the dentate gyrus based on dual somatic or somatodendritic recordings and complete morphologic reconstructions. Both specific membrane capacitance and axial resistivity were comparable to those of pyramidal neurons, but the average somatodendritic specific membrane resistance (R(m)) was substantially lower in BCs. Furthermore, R(m) was markedly nonuniform, being lowest in soma and proximal dendrites, intermediate in distal dendrites, and highest in the axon. Thus, the somatodendritic gradient of R(m) was the reverse of that in pyramidal neurons. Further computational analysis revealed that these unique cable properties accelerate the time course of synaptic potentials at the soma in response to fast inputs, while boosting the efficacy of slow distal inputs. These properties will facilitate both rapid phasic and efficient tonic activation of BCs in hippocampal microcircuits."}],"author":[{"full_name":"Norenberg, Anja","first_name":"Anja","last_name":"Norenberg"},{"first_name":"Hua","full_name":"Hua Hu","id":"4AC0145C-F248-11E8-B48F-1D18A9856A87","last_name":"Hu"},{"last_name":"Vida","full_name":"Vida, Imre","first_name":"Imre"},{"last_name":"Bartos","first_name":"Marlene","full_name":"Bartos, Marlene"},{"full_name":"Peter Jonas","first_name":"Peter M","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas"}],"publisher":"National Academy of Sciences","quality_controlled":0,"oa":1,"_id":"3831","issue":"2","extern":1,"month":"01","title":"Distinct nonuniform cable properties optimize rapid and efficient activation of fast-spiking GABAergic interneurons"},{"type":"journal_article","scopus_import":"1","volume":66,"date_created":"2018-12-11T12:05:25Z","doi":"10.1016/j.neuron.2010.04.003","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"language":[{"iso":"eng"}],"title":"Beyond TARPs: The growing list of auxiliary AMPAR subunits","month":"04","oa":1,"oa_version":"Published Version","issue":"1","citation":{"ista":"Guzmán J, Jonas PM. 2010. Beyond TARPs: The growing list of auxiliary AMPAR subunits. Neuron. 66(1), 8–10.","ieee":"J. Guzmán and P. M. Jonas, “Beyond TARPs: The growing list of auxiliary AMPAR subunits,” <i>Neuron</i>, vol. 66, no. 1. Elsevier, pp. 8–10, 2010.","apa":"Guzmán, J., &#38; Jonas, P. M. (2010). Beyond TARPs: The growing list of auxiliary AMPAR subunits. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2010.04.003\">https://doi.org/10.1016/j.neuron.2010.04.003</a>","chicago":"Guzmán, José, and Peter M Jonas. “Beyond TARPs: The Growing List of Auxiliary AMPAR Subunits.” <i>Neuron</i>. Elsevier, 2010. <a href=\"https://doi.org/10.1016/j.neuron.2010.04.003\">https://doi.org/10.1016/j.neuron.2010.04.003</a>.","mla":"Guzmán, José, and Peter M. Jonas. “Beyond TARPs: The Growing List of Auxiliary AMPAR Subunits.” <i>Neuron</i>, vol. 66, no. 1, Elsevier, 2010, pp. 8–10, doi:<a href=\"https://doi.org/10.1016/j.neuron.2010.04.003\">10.1016/j.neuron.2010.04.003</a>.","ama":"Guzmán J, Jonas PM. Beyond TARPs: The growing list of auxiliary AMPAR subunits. <i>Neuron</i>. 2010;66(1):8-10. doi:<a href=\"https://doi.org/10.1016/j.neuron.2010.04.003\">10.1016/j.neuron.2010.04.003</a>","short":"J. Guzmán, P.M. Jonas, Neuron 66 (2010) 8–10."},"isi":1,"article_processing_charge":"No","quality_controlled":"1","publication_status":"published","ddc":["570"],"status":"public","external_id":{"pmid":["20399724"],"isi":["000277016200004"]},"date_updated":"2026-06-18T18:47:22Z","date_published":"2010-04-15T00:00:00Z","publist_id":"2377","intvolume":"        66","day":"15","publication":"Neuron","department":[{"_id":"PeJo"}],"corr_author":"1","_id":"3832","abstract":[{"lang":"eng","text":"A recent paper by von Engelhardt et al. identifies a novel auxiliary subunit of native AMPARs, termedCKAMP44. Unlike other auxiliary subunits, CKAMP44 accelerates desensitization and prolongs recovery from desensitization. CKAMP44 is highly expressed in hippocampal dentate gyrus granule cells and decreases the paired-pulse ratio at perforant path input synapses. Thus, both principal and auxiliary AMPAR subunits control the time course of signaling at glutamatergic synapses."}],"author":[{"full_name":"Guzmán, José","first_name":"José","last_name":"Guzmán","orcid":"0000-0003-2209-5242","id":"30CC5506-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Jonas, Peter M","first_name":"Peter M","last_name":"Jonas","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"}],"publisher":"Elsevier","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/20399724","open_access":"1"}],"year":"2010","page":"8 - 10"},{"date_published":"2010-03-19T00:00:00Z","publist_id":"2378","intvolume":"        31","day":"19","status":"public","external_id":{"isi":["000276245400005"]},"date_updated":"2025-09-30T09:38:44Z","publication":"The European Journal of Neuroscience","department":[{"_id":"PeJo"}],"_id":"3833","corr_author":"1","page":"1194 - 1195","year":"2010","author":[{"first_name":"Peter M","full_name":"Jonas, Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804","last_name":"Jonas"},{"full_name":"Hefft, Stefan","first_name":"Stefan","last_name":"Hefft"}],"publisher":"Wiley-Blackwell","date_created":"2018-12-11T12:05:25Z","doi":"10.1111/j.1460-9568.2010.07189.x","type":"journal_article","scopus_import":"1","volume":31,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa_version":"None","issue":"7","language":[{"iso":"eng"}],"month":"03","title":"GABA release at terminals of CCK-interneurons: Synchrony, asynchrony and modulation by cannabinoid receptors (commentary on Ali &amp; Todorova)","publication_status":"published","isi":1,"citation":{"ama":"Jonas PM, Hefft S. GABA release at terminals of CCK-interneurons: Synchrony, asynchrony and modulation by cannabinoid receptors (commentary on Ali &#38;amp; Todorova). <i>The European Journal of Neuroscience</i>. 2010;31(7):1194-1195. doi:<a href=\"https://doi.org/10.1111/j.1460-9568.2010.07189.x\">10.1111/j.1460-9568.2010.07189.x</a>","short":"P.M. Jonas, S. Hefft, The European Journal of Neuroscience 31 (2010) 1194–1195.","ieee":"P. M. Jonas and S. Hefft, “GABA release at terminals of CCK-interneurons: Synchrony, asynchrony and modulation by cannabinoid receptors (commentary on Ali &#38;amp; Todorova),” <i>The European Journal of Neuroscience</i>, vol. 31, no. 7. Wiley-Blackwell, pp. 1194–1195, 2010.","apa":"Jonas, P. M., &#38; Hefft, S. (2010). GABA release at terminals of CCK-interneurons: Synchrony, asynchrony and modulation by cannabinoid receptors (commentary on Ali &#38;amp; Todorova). <i>The European Journal of Neuroscience</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/j.1460-9568.2010.07189.x\">https://doi.org/10.1111/j.1460-9568.2010.07189.x</a>","ista":"Jonas PM, Hefft S. 2010. GABA release at terminals of CCK-interneurons: Synchrony, asynchrony and modulation by cannabinoid receptors (commentary on Ali &#38;amp; Todorova). The European Journal of Neuroscience. 31(7), 1194–1195.","chicago":"Jonas, Peter M, and Stefan Hefft. “GABA Release at Terminals of CCK-Interneurons: Synchrony, Asynchrony and Modulation by Cannabinoid Receptors (Commentary on Ali &#38;amp; Todorova).” <i>The European Journal of Neuroscience</i>. Wiley-Blackwell, 2010. <a href=\"https://doi.org/10.1111/j.1460-9568.2010.07189.x\">https://doi.org/10.1111/j.1460-9568.2010.07189.x</a>.","mla":"Jonas, Peter M., and Stefan Hefft. “GABA Release at Terminals of CCK-Interneurons: Synchrony, Asynchrony and Modulation by Cannabinoid Receptors (Commentary on Ali &#38;amp; Todorova).” <i>The European Journal of Neuroscience</i>, vol. 31, no. 7, Wiley-Blackwell, 2010, pp. 1194–95, doi:<a href=\"https://doi.org/10.1111/j.1460-9568.2010.07189.x\">10.1111/j.1460-9568.2010.07189.x</a>."},"quality_controlled":"1","article_processing_charge":"No"},{"intvolume":"         4","day":"08","publist_id":"2374","date_published":"2010-04-08T00:00:00Z","date_updated":"2025-09-30T09:37:27Z","external_id":{"isi":["000277612700001"]},"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"status":"public","ddc":["005"],"publication":"BMC Systems Biology","department":[{"_id":"ToHe"}],"_id":"3834","corr_author":"1","pubrep_id":"72","acknowledgement":"This research has been partially funded by the Swiss National Science Foundation under grant 205321-111840 and by the Cluster of Excellence on Multimodal Computing and Interaction at Saarland University.","file":[{"content_type":"application/pdf","access_level":"open_access","file_size":1919130,"date_updated":"2020-07-14T12:46:16Z","creator":"system","date_created":"2018-12-12T10:16:29Z","checksum":"220239fae76f7b03c4d7f05d74ef426f","file_id":"5217","file_name":"IST-2012-72-v1+1_Solving_the_chemical_master_equation_using_sliding_windows.pdf","relation":"main_file"}],"year":"2010","page":"1 - 19","file_date_updated":"2020-07-14T12:46:16Z","publisher":"BioMed Central","author":[{"last_name":"Wolf","first_name":"Verena","full_name":"Wolf, Verena"},{"last_name":"Goel","first_name":"Rushil","full_name":"Goel, Rushil"},{"first_name":"Maria","full_name":"Mateescu, Maria","id":"3B43276C-F248-11E8-B48F-1D18A9856A87","last_name":"Mateescu"},{"full_name":"Henzinger, Thomas A","first_name":"Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger"}],"abstract":[{"text":"Background\r\n\r\nThe chemical master equation (CME) is a system of ordinary differential equations that describes the evolution of a network of chemical reactions as a stochastic process. Its solution yields the probability density vector of the system at each point in time. Solving the CME numerically is in many cases computationally expensive or even infeasible as the number of reachable states can be very large or infinite. We introduce the sliding window method, which computes an approximate solution of the CME by performing a sequence of local analysis steps. In each step, only a manageable subset of states is considered, representing a &quot;window&quot; into the state space. In subsequent steps, the window follows the direction in which the probability mass moves, until the time period of interest has elapsed. We construct the window based on a deterministic approximation of the future behavior of the system by estimating upper and lower bounds on the populations of the chemical species.\r\nResults\r\n\r\nIn order to show the effectiveness of our approach, we apply it to several examples previously described in the literature. The experimental results show that the proposed method speeds up the analysis considerably, compared to a global analysis, while still providing high accuracy.\r\n\r\n\r\nConclusions\r\n\r\nThe sliding window method is a novel approach to address the performance problems of numerical algorithms for the solution of the chemical master equation. The method efficiently approximates the probability distributions at the time points of interest for a variety of chemically reacting systems, including systems for which no upper bound on the population sizes of the chemical species is known a priori.","lang":"eng"}],"doi":"10.1186/1752-0509-4-42","date_created":"2018-12-11T12:05:25Z","volume":4,"scopus_import":"1","type":"journal_article","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","has_accepted_license":"1","issue":"42","oa_version":"Published Version","oa":1,"title":"Solving the chemical master equation using sliding windows","month":"04","language":[{"iso":"eng"}],"publication_status":"published","quality_controlled":"1","article_processing_charge":"No","isi":1,"citation":{"ama":"Wolf V, Goel R, Mateescu M, Henzinger TA. Solving the chemical master equation using sliding windows. <i>BMC Systems Biology</i>. 2010;4(42):1-19. doi:<a href=\"https://doi.org/10.1186/1752-0509-4-42\">10.1186/1752-0509-4-42</a>","short":"V. Wolf, R. Goel, M. Mateescu, T.A. Henzinger, BMC Systems Biology 4 (2010) 1–19.","ista":"Wolf V, Goel R, Mateescu M, Henzinger TA. 2010. Solving the chemical master equation using sliding windows. BMC Systems Biology. 4(42), 1–19.","apa":"Wolf, V., Goel, R., Mateescu, M., &#38; Henzinger, T. A. (2010). Solving the chemical master equation using sliding windows. <i>BMC Systems Biology</i>. BioMed Central. <a href=\"https://doi.org/10.1186/1752-0509-4-42\">https://doi.org/10.1186/1752-0509-4-42</a>","ieee":"V. Wolf, R. Goel, M. Mateescu, and T. A. Henzinger, “Solving the chemical master equation using sliding windows,” <i>BMC Systems Biology</i>, vol. 4, no. 42. BioMed Central, pp. 1–19, 2010.","chicago":"Wolf, Verena, Rushil Goel, Maria Mateescu, and Thomas A Henzinger. “Solving the Chemical Master Equation Using Sliding Windows.” <i>BMC Systems Biology</i>. BioMed Central, 2010. <a href=\"https://doi.org/10.1186/1752-0509-4-42\">https://doi.org/10.1186/1752-0509-4-42</a>.","mla":"Wolf, Verena, et al. “Solving the Chemical Master Equation Using Sliding Windows.” <i>BMC Systems Biology</i>, vol. 4, no. 42, BioMed Central, 2010, pp. 1–19, doi:<a href=\"https://doi.org/10.1186/1752-0509-4-42\">10.1186/1752-0509-4-42</a>."}},{"publication_status":"published","quality_controlled":"1","citation":{"mla":"Henzinger, Thomas A., et al. <i>Hybrid Numerical Solution of the Chemical Master Equation</i>. Springer, 2010, pp. 55–65, doi:<a href=\"https://doi.org/10.1145/1839764.1839772\">10.1145/1839764.1839772</a>.","chicago":"Henzinger, Thomas A, Maria Mateescu, Linar Mikeev, and Verena Wolf. “Hybrid Numerical Solution of the Chemical Master Equation,” 55–65. Springer, 2010. <a href=\"https://doi.org/10.1145/1839764.1839772\">https://doi.org/10.1145/1839764.1839772</a>.","ista":"Henzinger TA, Mateescu M, Mikeev L, Wolf V. 2010. Hybrid numerical solution of the chemical master equation. CMSB: Computational Methods in Systems Biology, 55–65.","ieee":"T. A. Henzinger, M. Mateescu, L. Mikeev, and V. Wolf, “Hybrid numerical solution of the chemical master equation,” presented at the CMSB: Computational Methods in Systems Biology, Trento, Italy, 2010, pp. 55–65.","apa":"Henzinger, T. A., Mateescu, M., Mikeev, L., &#38; Wolf, V. (2010). Hybrid numerical solution of the chemical master equation (pp. 55–65). Presented at the CMSB: Computational Methods in Systems Biology, Trento, Italy: Springer. <a href=\"https://doi.org/10.1145/1839764.1839772\">https://doi.org/10.1145/1839764.1839772</a>","short":"T.A. Henzinger, M. Mateescu, L. Mikeev, V. Wolf, in:, Springer, 2010, pp. 55–65.","ama":"Henzinger TA, Mateescu M, Mikeev L, Wolf V. Hybrid numerical solution of the chemical master equation. In: Springer; 2010:55-65. doi:<a href=\"https://doi.org/10.1145/1839764.1839772\">10.1145/1839764.1839772</a>"},"has_accepted_license":"1","oa":1,"oa_version":"Submitted Version","month":"09","title":"Hybrid numerical solution of the chemical master equation","language":[{"iso":"eng"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","doi":"10.1145/1839764.1839772","date_created":"2018-12-11T12:05:27Z","scopus_import":1,"type":"conference","year":"2010","page":"55 - 65","file_date_updated":"2020-07-14T12:46:16Z","publisher":"Springer","abstract":[{"lang":"eng","text":"We present a numerical approximation technique for the analysis of continuous-time Markov chains that describe net- works of biochemical reactions and play an important role in the stochastic modeling of biological systems. Our approach is based on the construction of a stochastic hybrid model in which certain discrete random variables of the original Markov chain are approximated by continuous deterministic variables. We compute the solution of the stochastic hybrid model using a numerical algorithm that discretizes time and in each step performs a mutual update of the transient prob- ability distribution of the discrete stochastic variables and the values of the continuous deterministic variables. We im- plemented the algorithm and we demonstrate its usefulness and efficiency on several case studies from systems biology."}],"author":[{"first_name":"Thomas A","full_name":"Henzinger, Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724"},{"first_name":"Maria","full_name":"Mateescu, Maria","last_name":"Mateescu"},{"last_name":"Mikeev","first_name":"Linar","full_name":"Mikeev, Linar"},{"last_name":"Wolf","full_name":"Wolf, Verena","first_name":"Verena"}],"_id":"3838","file":[{"access_level":"open_access","content_type":"application/pdf","date_updated":"2020-07-14T12:46:16Z","file_size":671790,"checksum":"81cb6f0babd97151b171d1ce86582831","date_created":"2018-12-12T10:15:55Z","creator":"system","file_id":"5179","file_name":"IST-2012-68-v1+1_Hybrid_Numerical_Solution_of_the_Chemical_Master_Equation.pdf","relation":"main_file"}],"pubrep_id":"68","conference":{"location":"Trento, Italy","end_date":"2010-10-01","start_date":"2010-09-29","name":"CMSB: Computational Methods in Systems Biology"},"department":[{"_id":"ToHe"}],"day":"29","date_published":"2010-09-29T00:00:00Z","publist_id":"2356","date_updated":"2021-01-12T07:52:33Z","ddc":["004"],"status":"public"},{"department":[{"_id":"ToHe"}],"conference":{"location":"Madrid, Spain","end_date":"2010-01-19","start_date":"2010-01-17","name":"VMCAI: Verification, Model Checking and Abstract Interpretation"},"ddc":["005"],"status":"public","date_updated":"2021-01-12T07:52:33Z","date_published":"2010-01-01T00:00:00Z","publist_id":"2357","intvolume":"      5944","day":"01","abstract":[{"lang":"eng","text":"We present a loop property generation method for loops iterating over multi-dimensional arrays. When used on matrices, our method is able to infer their shapes (also called types), such as upper-triangular, diagonal, etc. To gen- erate loop properties, we first transform a nested loop iterating over a multi- dimensional array into an equivalent collection of unnested loops. Then, we in- fer quantified loop invariants for each unnested loop using a generalization of a recurrence-based invariant generation technique. These loop invariants give us conditions on matrices from which we can derive matrix types automatically us- ing theorem provers. Invariant generation is implemented in the software package Aligator and types are derived by theorem provers and SMT solvers, including Vampire and Z3. When run on the Java matrix package JAMA, our tool was able to infer automatically all matrix types describing the matrix shapes guaranteed by JAMA’s API."}],"author":[{"first_name":"Thomas A","full_name":"Henzinger, Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724"},{"last_name":"Hottelier","first_name":"Thibaud","full_name":"Hottelier, Thibaud"},{"last_name":"Kovács","first_name":"Laura","full_name":"Kovács, Laura"},{"last_name":"Voronkov","full_name":"Voronkov, Andrei","first_name":"Andrei"}],"publisher":"Springer","file_date_updated":"2020-07-14T12:46:16Z","page":"163 - 179","year":"2010","file":[{"file_name":"IST-2012-69-v1+1_Invariant_and_type_inference_for_matrices.pdf","relation":"main_file","file_size":251265,"date_updated":"2020-07-14T12:46:16Z","access_level":"open_access","content_type":"application/pdf","file_id":"4989","checksum":"da69b13a2d9a7a316c909e09c1090cef","creator":"system","date_created":"2018-12-12T10:13:09Z"}],"acknowledgement":"The research was supported by the Swiss NSF.","pubrep_id":"69","_id":"3839","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","type":"conference","scopus_import":1,"volume":5944,"date_created":"2018-12-11T12:05:27Z","doi":"10.1007/978-3-642-11319-2_14","citation":{"ama":"Henzinger TA, Hottelier T, Kovács L, Voronkov A. Invariant and type inference for matrices. In: Vol 5944. Springer; 2010:163-179. doi:<a href=\"https://doi.org/10.1007/978-3-642-11319-2_14\">10.1007/978-3-642-11319-2_14</a>","short":"T.A. Henzinger, T. Hottelier, L. Kovács, A. Voronkov, in:, Springer, 2010, pp. 163–179.","ista":"Henzinger TA, Hottelier T, Kovács L, Voronkov A. 2010. Invariant and type inference for matrices. VMCAI: Verification, Model Checking and Abstract Interpretation, LNCS, vol. 5944, 163–179.","ieee":"T. A. Henzinger, T. Hottelier, L. Kovács, and A. Voronkov, “Invariant and type inference for matrices,” presented at the VMCAI: Verification, Model Checking and Abstract Interpretation, Madrid, Spain, 2010, vol. 5944, pp. 163–179.","apa":"Henzinger, T. A., Hottelier, T., Kovács, L., &#38; Voronkov, A. (2010). Invariant and type inference for matrices (Vol. 5944, pp. 163–179). Presented at the VMCAI: Verification, Model Checking and Abstract Interpretation, Madrid, Spain: Springer. <a href=\"https://doi.org/10.1007/978-3-642-11319-2_14\">https://doi.org/10.1007/978-3-642-11319-2_14</a>","chicago":"Henzinger, Thomas A, Thibaud Hottelier, Laura Kovács, and Andrei Voronkov. “Invariant and Type Inference for Matrices,” 5944:163–79. Springer, 2010. <a href=\"https://doi.org/10.1007/978-3-642-11319-2_14\">https://doi.org/10.1007/978-3-642-11319-2_14</a>.","mla":"Henzinger, Thomas A., et al. <i>Invariant and Type Inference for Matrices</i>. Vol. 5944, Springer, 2010, pp. 163–79, doi:<a href=\"https://doi.org/10.1007/978-3-642-11319-2_14\">10.1007/978-3-642-11319-2_14</a>."},"quality_controlled":"1","publication_status":"published","language":[{"iso":"eng"}],"month":"01","title":"Invariant and type inference for matrices","oa":1,"oa_version":"Submitted Version","has_accepted_license":"1","alternative_title":["LNCS"]},{"citation":{"chicago":"Henzinger, Thomas A. “From Boolean to Quantitative Notions of Correctness,” 45:157–58. ACM, 2010. <a href=\"https://doi.org/10.1145/1706299.1706319\">https://doi.org/10.1145/1706299.1706319</a>.","mla":"Henzinger, Thomas A. <i>From Boolean to Quantitative Notions of Correctness</i>. Vol. 45, no. 1, ACM, 2010, pp. 157–58, doi:<a href=\"https://doi.org/10.1145/1706299.1706319\">10.1145/1706299.1706319</a>.","ista":"Henzinger TA. 2010. From boolean to quantitative notions of correctness. POPL: Principles of Programming Languages vol. 45, 157–158.","apa":"Henzinger, T. A. (2010). From boolean to quantitative notions of correctness (Vol. 45, pp. 157–158). Presented at the POPL: Principles of Programming Languages, Madrid, Spain: ACM. <a href=\"https://doi.org/10.1145/1706299.1706319\">https://doi.org/10.1145/1706299.1706319</a>","ieee":"T. A. Henzinger, “From boolean to quantitative notions of correctness,” presented at the POPL: Principles of Programming Languages, Madrid, Spain, 2010, vol. 45, no. 1, pp. 157–158.","short":"T.A. Henzinger, in:, ACM, 2010, pp. 157–158.","ama":"Henzinger TA. From boolean to quantitative notions of correctness. In: Vol 45. ACM; 2010:157-158. doi:<a href=\"https://doi.org/10.1145/1706299.1706319\">10.1145/1706299.1706319</a>"},"isi":1,"quality_controlled":"1","article_processing_charge":"No","publication_status":"published","language":[{"iso":"eng"}],"month":"01","title":"From boolean to quantitative notions of correctness","issue":"1","oa_version":"None","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","type":"conference","scopus_import":"1","volume":45,"date_created":"2018-12-11T12:05:27Z","doi":"10.1145/1706299.1706319","abstract":[{"lang":"eng","text":"Classical formalizations of systems and properties are boolean: given a system and a property, the property is either true or false of the system. Correspondingly, classical methods for system analysis determine the truth value of a property, preferably giving a proof if the property is true, and a counterexample if the property is false; classical methods for system synthesis construct a system for which a property is true; classical methods for system transformation, composition, and abstraction aim to preserve the truth of properties. The boolean view is prevalent even if the system, the property, or both refer to numerical quantities, such as the times or probabilities of events. For example, a timed automaton either satisfies or violates a formula of a real-time logic; a stochastic process either satisfies or violates a formula of a probabilistic logic. The classical black-and-white view partitions the world into \"correct\" and \"incorrect\" systems, offering few nuances. In reality, of several systems that satisfy a property in the boolean sense, often some are more desirable than others, and of the many systems that violate a property, usually some are less objectionable than others. For instance, among the systems that satisfy the response property that every request be granted, we may prefer systems that grant requests quickly (the quicker, the better), or we may prefer systems that issue few unnecessary grants (the fewer, the better); and among the systems that violate the response property, we may prefer systems that serve many initial requests (the more, the better), or we may prefer systems that serve many requests in the long run (the greater the fraction of served to unserved requests, the better). Formally, while a boolean notion of correctness is given by a preorder on systems and properties, a quantitative notion of correctness is defined by a directed metric on systems and properties, where the distance between a system and a property provides a measure of \"fit\" or \"desirability.\" There are many ways how such distances can be defined. In a linear-time framework, one assigns numerical values to individual behaviors before assigning values to systems and properties, which are sets of behaviors. For example, the value of a single behavior may be a discounted value, which is largely determined by a prefix of the behavior, e.g., by the number of requests that are granted before the first request that is not granted; or a limit value, which is independent of any finite prefix. A limit value may be an average, such as the average response time over an infinite sequence of requests and grants, or a supremum, such as the worst-case response time. Similarly, the value of a set of behaviors may be an extremum or an average across the values of all behaviors in the set: in this way one can measure the worst of all possible average-case response times, or the average of all possible worst-case response times, etc. Accordingly, the distance between two sets of behaviors may be defined as the worst or average difference between the values of corresponding behaviors. In summary, we propagate replacing boolean specifications for the correctness of systems with quantitative measures for the desirability of systems. In quantitative analysis, the aim is to compute the distance between a system and a property (or between two systems, or two properties); in quantitative synthesis, the objective is to construct a system that has minimal distance from a given property. Multiple quantitative measures can be prioritized (e.g., combined lexicographically into a single measure) or studied along the Pareto curve. Quantitative transformations, compositions, and abstractions of systems are useful if they allow us to bound the induced change in distance from a property. We present some initial results in some of these directions. We also give some potential applications, which not only generalize tradiditional correctness concerns in the functional, timed, and probabilistic domains, but also capture such system measures as resource use, performance, cost, reliability, and robustness."}],"author":[{"first_name":"Thomas A","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","last_name":"Henzinger"}],"publisher":"ACM","page":"157 - 158","year":"2010","acknowledgement":"This talk surveys joint work with Roderick Bloem, Krishnendu Chatterjee, Laurent Doyen, and Barbara Jobstmann.","corr_author":"1","_id":"3840","department":[{"_id":"ToHe"}],"conference":{"start_date":"2010-01-17","name":"POPL: Principles of Programming Languages","location":"Madrid, Spain","end_date":"2010-01-23"},"status":"public","external_id":{"isi":["000281053800014"]},"date_updated":"2025-09-30T09:36:44Z","date_published":"2010-01-17T00:00:00Z","publist_id":"2354","intvolume":"        45","day":"17"},{"title":"Fast adaptive uniformization of the chemical master equation","month":"11","language":[{"iso":"eng"}],"has_accepted_license":"1","related_material":{"record":[{"relation":"earlier_version","id":"3843","status":"public"}]},"oa":1,"oa_version":"Submitted Version","issue":"6","quality_controlled":"1","article_processing_charge":"No","citation":{"chicago":"Didier, Frédéric, Thomas A Henzinger, Maria Mateescu, and Verena Wolf. “Fast Adaptive Uniformization of the Chemical Master Equation.” <i>IET Systems Biology</i>. Institution of Engineering and Technology, 2010. <a href=\"https://doi.org/10.1049/iet-syb.2010.0005\">https://doi.org/10.1049/iet-syb.2010.0005</a>.","mla":"Didier, Frédéric, et al. “Fast Adaptive Uniformization of the Chemical Master Equation.” <i>IET Systems Biology</i>, vol. 4, no. 6, Institution of Engineering and Technology, 2010, pp. 441–52, doi:<a href=\"https://doi.org/10.1049/iet-syb.2010.0005\">10.1049/iet-syb.2010.0005</a>.","ieee":"F. Didier, T. A. Henzinger, M. Mateescu, and V. Wolf, “Fast adaptive uniformization of the chemical master equation,” <i>IET Systems Biology</i>, vol. 4, no. 6. Institution of Engineering and Technology, pp. 441–452, 2010.","apa":"Didier, F., Henzinger, T. A., Mateescu, M., &#38; Wolf, V. (2010). Fast adaptive uniformization of the chemical master equation. <i>IET Systems Biology</i>. Institution of Engineering and Technology. <a href=\"https://doi.org/10.1049/iet-syb.2010.0005\">https://doi.org/10.1049/iet-syb.2010.0005</a>","ista":"Didier F, Henzinger TA, Mateescu M, Wolf V. 2010. Fast adaptive uniformization of the chemical master equation. IET Systems Biology. 4(6), 441–452.","short":"F. Didier, T.A. Henzinger, M. Mateescu, V. Wolf, IET Systems Biology 4 (2010) 441–452.","ama":"Didier F, Henzinger TA, Mateescu M, Wolf V. Fast adaptive uniformization of the chemical master equation. <i>IET Systems Biology</i>. 2010;4(6):441-452. doi:<a href=\"https://doi.org/10.1049/iet-syb.2010.0005\">10.1049/iet-syb.2010.0005</a>"},"isi":1,"publication_status":"published","scopus_import":"1","volume":4,"type":"journal_article","doi":"10.1049/iet-syb.2010.0005","date_created":"2018-12-11T12:05:28Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","file":[{"relation":"main_file","file_name":"IST-2012-66-v1+1_Fast_adaptive_uniformization_of_the_chemical_master_equation.pdf","checksum":"9a3bde48f43203991a0b3c6a277c2f5b","creator":"system","date_created":"2018-12-12T10:17:02Z","file_id":"5254","access_level":"open_access","content_type":"application/pdf","file_size":222890,"date_updated":"2020-07-14T12:46:16Z"}],"pubrep_id":"66","_id":"3842","publisher":"Institution of Engineering and Technology","abstract":[{"lang":"eng","text":"Within systems biology there is an increasing interest in the stochastic behavior of biochemical reaction networks. An appropriate stochastic description is provided by the chemical master equation, which represents a continuous-time Markov chain (CTMC). The uniformization technique is an efficient method to compute probability distributions of a CTMC if the number of states is manageable. However, the size of a CTMC that represents a biochemical reaction network is usually far beyond what is feasible. In this paper we present an on-the-fly variant of uniformization, where we improve the original algorithm at the cost of a small approximation error. By means of several examples, we show that our approach is particularly well-suited for biochemical reaction networks."}],"author":[{"first_name":"Frédéric","full_name":"Didier, Frédéric","last_name":"Didier"},{"last_name":"Henzinger","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","first_name":"Thomas A"},{"last_name":"Mateescu","first_name":"Maria","full_name":"Mateescu, Maria"},{"full_name":"Wolf, Verena","first_name":"Verena","last_name":"Wolf"}],"page":"441 - 452","year":"2010","file_date_updated":"2020-07-14T12:46:16Z","date_updated":"2025-09-30T09:54:51Z","external_id":{"isi":["000284108800011"]},"ddc":["570"],"status":"public","day":"15","intvolume":"         4","date_published":"2010-11-15T00:00:00Z","publist_id":"2349","publication":"IET Systems Biology","department":[{"_id":"ToHe"}]},{"external_id":{"isi":["000288062700025"]},"date_updated":"2025-09-30T09:35:47Z","ddc":["005"],"status":"public","day":"01","intvolume":"      6397","date_published":"2010-10-01T00:00:00Z","publist_id":"2342","department":[{"_id":"ToHe"}],"conference":{"end_date":"2010-10-15","location":"Yogyakarta, Indonesia","name":"LPAR: Logic for Programming, Artificial Intelligence, and Reasoning","start_date":"2010-10-10"},"corr_author":"1","file":[{"file_name":"IST-2012-64-v1+1_Aligators_for_arrays.pdf","relation":"main_file","date_updated":"2020-07-14T12:46:17Z","file_size":186143,"access_level":"open_access","content_type":"application/pdf","file_id":"4790","checksum":"913af269da6710f2174f470b48ab7a82","creator":"system","date_created":"2018-12-12T10:10:05Z"}],"pubrep_id":"64","_id":"3845","publisher":"Springer","abstract":[{"lang":"eng","text":"This paper presents Aligators, a tool for the generation of universally quantified array invariants. Aligators leverages recurrence solving and algebraic techniques to carry out inductive reasoning over array content. The Aligators’ loop extraction module allows treatment of multi-path loops by exploiting their commutativity and serializability properties. Our experience in applying Aligators on a collection of loops from open source software projects indicates the applicability of recurrence and algebraic solving techniques for reasoning about arrays."}],"author":[{"full_name":"Henzinger, Thomas A","first_name":"Thomas A","last_name":"Henzinger","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hottelier","full_name":"Hottelier, Thibaud","first_name":"Thibaud"},{"full_name":"Kovács, Laura","first_name":"Laura","last_name":"Kovács"},{"last_name":"Rybalchenko","first_name":"Andrey","full_name":"Rybalchenko, Andrey"}],"page":"348 - 356","year":"2010","file_date_updated":"2020-07-14T12:46:17Z","scopus_import":"1","volume":6397,"type":"conference","doi":"10.1007/978-3-642-16242-8_25","date_created":"2018-12-11T12:05:29Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Aligators for arrays","month":"10","language":[{"iso":"eng"}],"alternative_title":["LNCS"],"has_accepted_license":"1","oa":1,"oa_version":"Submitted Version","article_processing_charge":"No","quality_controlled":"1","isi":1,"citation":{"short":"T.A. Henzinger, T. Hottelier, L. Kovács, A. Rybalchenko, in:, Springer, 2010, pp. 348–356.","ama":"Henzinger TA, Hottelier T, Kovács L, Rybalchenko A. Aligators for arrays. In: Vol 6397. Springer; 2010:348-356. doi:<a href=\"https://doi.org/10.1007/978-3-642-16242-8_25\">10.1007/978-3-642-16242-8_25</a>","chicago":"Henzinger, Thomas A, Thibaud Hottelier, Laura Kovács, and Andrey Rybalchenko. “Aligators for Arrays,” 6397:348–56. Springer, 2010. <a href=\"https://doi.org/10.1007/978-3-642-16242-8_25\">https://doi.org/10.1007/978-3-642-16242-8_25</a>.","mla":"Henzinger, Thomas A., et al. <i>Aligators for Arrays</i>. Vol. 6397, Springer, 2010, pp. 348–56, doi:<a href=\"https://doi.org/10.1007/978-3-642-16242-8_25\">10.1007/978-3-642-16242-8_25</a>.","ista":"Henzinger TA, Hottelier T, Kovács L, Rybalchenko A. 2010. Aligators for arrays. LPAR: Logic for Programming, Artificial Intelligence, and Reasoning, LNCS, vol. 6397, 348–356.","ieee":"T. A. Henzinger, T. Hottelier, L. Kovács, and A. Rybalchenko, “Aligators for arrays,” presented at the LPAR: Logic for Programming, Artificial Intelligence, and Reasoning, Yogyakarta, Indonesia, 2010, vol. 6397, pp. 348–356.","apa":"Henzinger, T. A., Hottelier, T., Kovács, L., &#38; Rybalchenko, A. (2010). Aligators for arrays (Vol. 6397, pp. 348–356). Presented at the LPAR: Logic for Programming, Artificial Intelligence, and Reasoning, Yogyakarta, Indonesia: Springer. <a href=\"https://doi.org/10.1007/978-3-642-16242-8_25\">https://doi.org/10.1007/978-3-642-16242-8_25</a>"},"publication_status":"published"},{"date_updated":"2021-01-12T07:52:37Z","ddc":["004"],"status":"public","day":"14","date_published":"2010-10-14T00:00:00Z","publist_id":"2339","department":[{"_id":"ToHe"},{"_id":"CaGu"}],"conference":{"end_date":"2010-09-18","location":"Williamsburg, USA","name":"QEST: Quantitative Evaluation of Systems","start_date":"2010-09-15"},"file":[{"relation":"main_file","file_name":"IST-2012-63-v1+1_SABRE-A_tool_for_the_stochastic_analysis_of_biochemical_reaction_networks.pdf","date_created":"2018-12-12T10:09:03Z","creator":"system","checksum":"38707b149d2174f01be406e794ffa849","file_id":"4726","content_type":"application/pdf","access_level":"open_access","file_size":433824,"date_updated":"2020-07-14T12:46:17Z"}],"pubrep_id":"63","_id":"3847","publisher":"IEEE","abstract":[{"text":"The importance of stochasticity within biological systems has been shown repeatedly during the last years and has raised the need for efficient stochastic tools. We present SABRE, a tool for stochastic analysis of biochemical reaction networks. SABRE implements fast adaptive uniformization (FAU), a direct numerical approximation algorithm for computing transient solutions of biochemical reaction networks. Biochemical reactions networks represent biological systems studied at a molecular level and these reactions can be modeled as transitions of a Markov chain. SABRE accepts as input the formalism of guarded commands, which it interprets either as continuous-time or as discrete-time Markov chains. Besides operating in a stochastic mode, SABRE may also perform a deterministic analysis by directly computing a mean-field approximation of the system under study. We illustrate the different functionalities of SABRE by means of biological case studies.","lang":"eng"}],"author":[{"first_name":"Frédéric","full_name":"Didier, Frédéric","last_name":"Didier"},{"full_name":"Henzinger, Thomas A","first_name":"Thomas A","last_name":"Henzinger","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Mateescu","full_name":"Mateescu, Maria","first_name":"Maria"},{"last_name":"Wolf","full_name":"Wolf, Verena","first_name":"Verena"}],"year":"2010","page":"193 - 194","file_date_updated":"2020-07-14T12:46:17Z","scopus_import":1,"type":"conference","doi":"10.1109/QEST.2010.33","date_created":"2018-12-11T12:05:29Z","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","month":"10","title":"SABRE: A tool for the stochastic analysis of biochemical reaction networks","language":[{"iso":"eng"}],"has_accepted_license":"1","oa":1,"oa_version":"Submitted Version","quality_controlled":"1","citation":{"short":"F. Didier, T.A. Henzinger, M. Mateescu, V. Wolf, in:, IEEE, 2010, pp. 193–194.","ama":"Didier F, Henzinger TA, Mateescu M, Wolf V. SABRE: A tool for the stochastic analysis of biochemical reaction networks. In: IEEE; 2010:193-194. doi:<a href=\"https://doi.org/10.1109/QEST.2010.33\">10.1109/QEST.2010.33</a>","mla":"Didier, Frédéric, et al. <i>SABRE: A Tool for the Stochastic Analysis of Biochemical Reaction Networks</i>. IEEE, 2010, pp. 193–94, doi:<a href=\"https://doi.org/10.1109/QEST.2010.33\">10.1109/QEST.2010.33</a>.","chicago":"Didier, Frédéric, Thomas A Henzinger, Maria Mateescu, and Verena Wolf. “SABRE: A Tool for the Stochastic Analysis of Biochemical Reaction Networks,” 193–94. IEEE, 2010. <a href=\"https://doi.org/10.1109/QEST.2010.33\">https://doi.org/10.1109/QEST.2010.33</a>.","ieee":"F. Didier, T. A. Henzinger, M. Mateescu, and V. Wolf, “SABRE: A tool for the stochastic analysis of biochemical reaction networks,” presented at the QEST: Quantitative Evaluation of Systems, Williamsburg, USA, 2010, pp. 193–194.","apa":"Didier, F., Henzinger, T. A., Mateescu, M., &#38; Wolf, V. (2010). SABRE: A tool for the stochastic analysis of biochemical reaction networks (pp. 193–194). Presented at the QEST: Quantitative Evaluation of Systems, Williamsburg, USA: IEEE. <a href=\"https://doi.org/10.1109/QEST.2010.33\">https://doi.org/10.1109/QEST.2010.33</a>","ista":"Didier F, Henzinger TA, Mateescu M, Wolf V. 2010. SABRE: A tool for the stochastic analysis of biochemical reaction networks. QEST: Quantitative Evaluation of Systems, 193–194."},"publication_status":"published"},{"status":"public","type":"conference","scopus_import":1,"date_updated":"2024-10-09T20:54:09Z","volume":6346,"date_published":"2010-09-01T00:00:00Z","date_created":"2018-12-11T12:05:30Z","publist_id":"2336","intvolume":"      6346","day":"01","doi":"10.1007/978-3-642-15775-2_1","department":[{"_id":"HeEd"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","conference":{"location":"Liverpool, UK","end_date":"2010-09-08","start_date":"2010-09-06","name":"ESA: European Symposium on Algorithms"},"language":[{"iso":"eng"}],"month":"09","title":"The robustness of level sets","corr_author":"1","_id":"3848","oa_version":"None","alternative_title":["LNCS"],"abstract":[{"lang":"eng","text":"We define the robustness of a level set homology class of a function f:XR as the magnitude of a perturbation necessary to kill the class. Casting this notion into a group theoretic framework, we compute the robustness for each class, using a connection to extended persistent homology. The special case X=R3 has ramifications in medical imaging and scientific visualization."}],"citation":{"short":"P. Bendich, H. Edelsbrunner, D. Morozov, A. Patel, in:, Springer, 2010, pp. 1–10.","ama":"Bendich P, Edelsbrunner H, Morozov D, Patel A. The robustness of level sets. In: Vol 6346. Springer; 2010:1-10. doi:<a href=\"https://doi.org/10.1007/978-3-642-15775-2_1\">10.1007/978-3-642-15775-2_1</a>","mla":"Bendich, Paul, et al. <i>The Robustness of Level Sets</i>. Vol. 6346, Springer, 2010, pp. 1–10, doi:<a href=\"https://doi.org/10.1007/978-3-642-15775-2_1\">10.1007/978-3-642-15775-2_1</a>.","chicago":"Bendich, Paul, Herbert Edelsbrunner, Dmitriy Morozov, and Amit Patel. “The Robustness of Level Sets,” 6346:1–10. Springer, 2010. <a href=\"https://doi.org/10.1007/978-3-642-15775-2_1\">https://doi.org/10.1007/978-3-642-15775-2_1</a>.","ista":"Bendich P, Edelsbrunner H, Morozov D, Patel A. 2010. The robustness of level sets. ESA: European Symposium on Algorithms, LNCS, vol. 6346, 1–10.","apa":"Bendich, P., Edelsbrunner, H., Morozov, D., &#38; Patel, A. (2010). The robustness of level sets (Vol. 6346, pp. 1–10). Presented at the ESA: European Symposium on Algorithms, Liverpool, UK: Springer. <a href=\"https://doi.org/10.1007/978-3-642-15775-2_1\">https://doi.org/10.1007/978-3-642-15775-2_1</a>","ieee":"P. Bendich, H. Edelsbrunner, D. Morozov, and A. Patel, “The robustness of level sets,” presented at the ESA: European Symposium on Algorithms, Liverpool, UK, 2010, vol. 6346, pp. 1–10."},"author":[{"full_name":"Bendich, Paul","first_name":"Paul","id":"43F6EC54-F248-11E8-B48F-1D18A9856A87","last_name":"Bendich"},{"last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert","first_name":"Herbert"},{"full_name":"Morozov, Dmitriy","first_name":"Dmitriy","last_name":"Morozov"},{"id":"34A254A0-F248-11E8-B48F-1D18A9856A87","last_name":"Patel","full_name":"Patel, Amit","first_name":"Amit"}],"publisher":"Springer","quality_controlled":"1","publication_status":"published","year":"2010","page":"1 - 10"},{"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","doi":"10.1007/978-3-642-15155-2_2","date_created":"2018-12-11T12:05:30Z","scopus_import":1,"volume":6281,"type":"conference","publication_status":"published","quality_controlled":"1","citation":{"short":"P. Bendich, H. Edelsbrunner, M. Kerber, A. Patel, in:, Springer, 2010, pp. 12–23.","ama":"Bendich P, Edelsbrunner H, Kerber M, Patel A. Persistent homology under non-uniform error. In: Vol 6281. Springer; 2010:12-23. doi:<a href=\"https://doi.org/10.1007/978-3-642-15155-2_2\">10.1007/978-3-642-15155-2_2</a>","chicago":"Bendich, Paul, Herbert Edelsbrunner, Michael Kerber, and Amit Patel. “Persistent Homology under Non-Uniform Error,” 6281:12–23. Springer, 2010. <a href=\"https://doi.org/10.1007/978-3-642-15155-2_2\">https://doi.org/10.1007/978-3-642-15155-2_2</a>.","mla":"Bendich, Paul, et al. <i>Persistent Homology under Non-Uniform Error</i>. Vol. 6281, Springer, 2010, pp. 12–23, doi:<a href=\"https://doi.org/10.1007/978-3-642-15155-2_2\">10.1007/978-3-642-15155-2_2</a>.","apa":"Bendich, P., Edelsbrunner, H., Kerber, M., &#38; Patel, A. (2010). Persistent homology under non-uniform error (Vol. 6281, pp. 12–23). Presented at the MFCS: Mathematical Foundations of Computer Science, Brno, Czech Republic: Springer. <a href=\"https://doi.org/10.1007/978-3-642-15155-2_2\">https://doi.org/10.1007/978-3-642-15155-2_2</a>","ieee":"P. Bendich, H. Edelsbrunner, M. Kerber, and A. Patel, “Persistent homology under non-uniform error,” presented at the MFCS: Mathematical Foundations of Computer Science, Brno, Czech Republic, 2010, vol. 6281, pp. 12–23.","ista":"Bendich P, Edelsbrunner H, Kerber M, Patel A. 2010. Persistent homology under non-uniform error. MFCS: Mathematical Foundations of Computer Science, LNCS, vol. 6281, 12–23."},"has_accepted_license":"1","alternative_title":["LNCS"],"oa":1,"oa_version":"Submitted Version","title":"Persistent homology under non-uniform error","month":"08","language":[{"iso":"eng"}],"conference":{"end_date":"2010-08-27","location":"Brno, Czech Republic","name":"MFCS: Mathematical Foundations of Computer Science","start_date":"2010-08-23"},"department":[{"_id":"HeEd"}],"day":"10","intvolume":"      6281","date_published":"2010-08-10T00:00:00Z","publist_id":"2333","date_updated":"2021-01-12T07:52:38Z","ddc":["000"],"status":"public","year":"2010","page":"12 - 23","file_date_updated":"2020-07-14T12:46:17Z","publisher":"Springer","abstract":[{"lang":"eng","text":"Using ideas from persistent homology, the robustness of a level set of a real-valued function is defined in terms of the magnitude of the perturbation necessary to kill the classes. Prior work has shown that the homology and robustness information can be read off the extended persistence diagram of the function. This paper extends these results to a non-uniform error model in which perturbations vary in their magnitude across the domain."}],"author":[{"first_name":"Paul","full_name":"Bendich, Paul","id":"43F6EC54-F248-11E8-B48F-1D18A9856A87","last_name":"Bendich"},{"full_name":"Edelsbrunner, Herbert","first_name":"Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner"},{"last_name":"Kerber","orcid":"0000-0002-8030-9299","id":"36E4574A-F248-11E8-B48F-1D18A9856A87","full_name":"Kerber, Michael","first_name":"Michael"},{"id":"34A254A0-F248-11E8-B48F-1D18A9856A87","last_name":"Patel","first_name":"Amit","full_name":"Patel, Amit"}],"_id":"3849","file":[{"checksum":"af61e1c2bb42f3d556179d4692caeb1b","date_created":"2018-12-12T10:13:13Z","creator":"system","file_id":"4994","access_level":"open_access","content_type":"application/pdf","file_size":142357,"date_updated":"2020-07-14T12:46:17Z","relation":"main_file","file_name":"IST-2016-537-v1+1_2010-P-05-NonuniformError.pdf"}],"pubrep_id":"537"},{"date_created":"2018-12-11T11:46:10Z","publist_id":"7444","date_published":"2010-01-04T00:00:00Z","intvolume":"       104","day":"04","doi":"10.1103/PhysRevLett.104.016401","status":"public","type":"journal_article","volume":104,"date_updated":"2021-01-12T07:52:39Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Physical Review Letters","oa_version":"None","issue":"1","_id":"385","oa":1,"extern":"1","language":[{"iso":"eng"}],"month":"01","title":"STM imaging of electronic waves on the surface of Bi2Te3 Topologically protected surface states and hexagonal warping effects","publication_status":"published","main_file_link":[{"url":"https://arxiv.org/pdf/0908.0371.pdf","open_access":"1"}],"year":"2010","author":[{"full_name":"Alpichshev, Zhanybek","first_name":"Zhanybek","orcid":"0000-0002-7183-5203","id":"45E67A2A-F248-11E8-B48F-1D18A9856A87","last_name":"Alpichshev"},{"full_name":"Analytis, James","first_name":"James","last_name":"Analytis"},{"full_name":"Chu, Jiunhaw","first_name":"Jiunhaw","last_name":"Chu"},{"first_name":"Ian","full_name":"Fisher, Ian","last_name":"Fisher"},{"last_name":"Chen","full_name":"Chen, Yulin","first_name":"Yulin"},{"last_name":"Shen","full_name":"Shen, Zhixun","first_name":"Zhixun"},{"first_name":"Aiping","full_name":"Fang, Aiping","last_name":"Fang"},{"first_name":"Aharon","full_name":"Kapitulnik, Aharon","last_name":"Kapitulnik"}],"abstract":[{"text":"Scanning tunneling spectroscopy studies on high-quality Bi2Te3 crystals exhibit perfect correspondence to angle-resolved photoemission spectroscopy data, hence enabling identification of different regimes measured in the local density of states (LDOS). Oscillations of LDOS near a step are analyzed. Within the main part of the surface band oscillations are strongly damped, supporting the hypothesis of topological protection. At higher energies, as the surface band becomes concave, oscillations appear, dispersing with a wave vector that may result from a hexagonal warping term. ","lang":"eng"}],"citation":{"chicago":"Alpichshev, Zhanybek, James Analytis, Jiunhaw Chu, Ian Fisher, Yulin Chen, Zhixun Shen, Aiping Fang, and Aharon Kapitulnik. “STM Imaging of Electronic Waves on the Surface of Bi2Te3 Topologically Protected Surface States and Hexagonal Warping Effects.” <i>Physical Review Letters</i>. American Physical Society, 2010. <a href=\"https://doi.org/10.1103/PhysRevLett.104.016401\">https://doi.org/10.1103/PhysRevLett.104.016401</a>.","mla":"Alpichshev, Zhanybek, et al. “STM Imaging of Electronic Waves on the Surface of Bi2Te3 Topologically Protected Surface States and Hexagonal Warping Effects.” <i>Physical Review Letters</i>, vol. 104, no. 1, American Physical Society, 2010, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.104.016401\">10.1103/PhysRevLett.104.016401</a>.","ista":"Alpichshev Z, Analytis J, Chu J, Fisher I, Chen Y, Shen Z, Fang A, Kapitulnik A. 2010. STM imaging of electronic waves on the surface of Bi2Te3 Topologically protected surface states and hexagonal warping effects. Physical Review Letters. 104(1).","apa":"Alpichshev, Z., Analytis, J., Chu, J., Fisher, I., Chen, Y., Shen, Z., … Kapitulnik, A. (2010). STM imaging of electronic waves on the surface of Bi2Te3 Topologically protected surface states and hexagonal warping effects. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.104.016401\">https://doi.org/10.1103/PhysRevLett.104.016401</a>","ieee":"Z. Alpichshev <i>et al.</i>, “STM imaging of electronic waves on the surface of Bi2Te3 Topologically protected surface states and hexagonal warping effects,” <i>Physical Review Letters</i>, vol. 104, no. 1. American Physical Society, 2010.","short":"Z. Alpichshev, J. Analytis, J. Chu, I. Fisher, Y. Chen, Z. Shen, A. Fang, A. Kapitulnik, Physical Review Letters 104 (2010).","ama":"Alpichshev Z, Analytis J, Chu J, et al. STM imaging of electronic waves on the surface of Bi2Te3 Topologically protected surface states and hexagonal warping effects. <i>Physical Review Letters</i>. 2010;104(1). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.104.016401\">10.1103/PhysRevLett.104.016401</a>"},"publisher":"American Physical Society"},{"author":[{"full_name":"Berberich, Eric","first_name":"Eric","last_name":"Berberich"},{"first_name":"Dan","full_name":"Halperin, Dan","last_name":"Halperin"},{"orcid":"0000-0002-8030-9299","id":"36E4574A-F248-11E8-B48F-1D18A9856A87","last_name":"Kerber","full_name":"Kerber, Michael","first_name":"Michael"},{"last_name":"Pogalnikova","full_name":"Pogalnikova, Roza","first_name":"Roza"}],"citation":{"ista":"Berberich E, Halperin D, Kerber M, Pogalnikova R. 2010. Polygonal reconstruction from approximate offsets. EuroCG: European Workshop on Computational Geometry, 12–23.","apa":"Berberich, E., Halperin, D., Kerber, M., &#38; Pogalnikova, R. (2010). Polygonal reconstruction from approximate offsets (pp. 12–23). Presented at the EuroCG: European Workshop on Computational Geometry, Dortmund, Germany: TU Dortmund.","ieee":"E. Berberich, D. Halperin, M. Kerber, and R. Pogalnikova, “Polygonal reconstruction from approximate offsets,” presented at the EuroCG: European Workshop on Computational Geometry, Dortmund, Germany, 2010, pp. 12–23.","mla":"Berberich, Eric, et al. <i>Polygonal Reconstruction from Approximate Offsets</i>. TU Dortmund, 2010, pp. 12–23.","chicago":"Berberich, Eric, Dan Halperin, Michael Kerber, and Roza Pogalnikova. “Polygonal Reconstruction from Approximate Offsets,” 12–23. TU Dortmund, 2010.","ama":"Berberich E, Halperin D, Kerber M, Pogalnikova R. Polygonal reconstruction from approximate offsets. In: TU Dortmund; 2010:12-23.","short":"E. Berberich, D. Halperin, M. Kerber, R. Pogalnikova, in:, TU Dortmund, 2010, pp. 12–23."},"abstract":[{"lang":"eng","text":"Given a polygonal shape Q with n vertices, can it be expressed, up to a tolerance ε in Hausdorff distance, as the Minkowski sum of another polygonal shape with a disk of fixed radius? If it does, we also seek a preferably simple solution shape P;P’s offset constitutes an accurate, vertex-reduced, and smoothened approximation of Q. We give a decision algorithm for fixed radius in O(nlogn) time that handles any polygonal shape. For convex shapes, the complexity drops to O(n), which is also the time required to compute a solution shape P with at most one more vertex than a vertex-minimal one."}],"publisher":"TU Dortmund","quality_controlled":"1","publication_status":"published","year":"2010","page":"12 - 23","language":[{"iso":"eng"}],"title":"Polygonal reconstruction from approximate offsets","month":"01","oa_version":"None","_id":"3850","department":[{"_id":"HeEd"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","conference":{"end_date":"2010-03-24","location":"Dortmund, Germany","name":"EuroCG: European Workshop on Computational Geometry","start_date":"2010-03-22"},"type":"conference","status":"public","date_updated":"2021-01-12T07:52:39Z","date_created":"2018-12-11T12:05:30Z","publist_id":"2334","date_published":"2010-01-01T00:00:00Z","day":"01"},{"doi":"10.1007/978-3-642-14162-1_50","date_created":"2018-12-11T12:05:31Z","arxiv":1,"volume":6199,"scopus_import":"1","type":"conference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"status":"public","id":"2972","relation":"later_version"}]},"alternative_title":["LNCS"],"oa_version":"Preprint","oa":1,"title":"Energy parity games","month":"09","language":[{"iso":"eng"}],"publication_status":"published","article_processing_charge":"No","quality_controlled":"1","citation":{"ieee":"K. Chatterjee and L. Doyen, “Energy parity games,” presented at the ICALP: Automata, Languages and Programming, Bordeaux, France, 2010, vol. 6199, pp. 599–610.","apa":"Chatterjee, K., &#38; Doyen, L. (2010). Energy parity games (Vol. 6199, pp. 599–610). Presented at the ICALP: Automata, Languages and Programming, Bordeaux, France: Springer. <a href=\"https://doi.org/10.1007/978-3-642-14162-1_50\">https://doi.org/10.1007/978-3-642-14162-1_50</a>","ista":"Chatterjee K, Doyen L. 2010. Energy parity games. ICALP: Automata, Languages and Programming, LNCS, vol. 6199, 599–610.","chicago":"Chatterjee, Krishnendu, and Laurent Doyen. “Energy Parity Games,” 6199:599–610. Springer, 2010. <a href=\"https://doi.org/10.1007/978-3-642-14162-1_50\">https://doi.org/10.1007/978-3-642-14162-1_50</a>.","mla":"Chatterjee, Krishnendu, and Laurent Doyen. <i>Energy Parity Games</i>. Vol. 6199, Springer, 2010, pp. 599–610, doi:<a href=\"https://doi.org/10.1007/978-3-642-14162-1_50\">10.1007/978-3-642-14162-1_50</a>.","ama":"Chatterjee K, Doyen L. Energy parity games. In: Vol 6199. Springer; 2010:599-610. doi:<a href=\"https://doi.org/10.1007/978-3-642-14162-1_50\">10.1007/978-3-642-14162-1_50</a>","short":"K. Chatterjee, L. Doyen, in:, Springer, 2010, pp. 599–610."},"intvolume":"      6199","day":"10","publist_id":"2330","date_published":"2010-09-10T00:00:00Z","external_id":{"arxiv":["1001.5183"]},"date_updated":"2025-09-30T08:02:20Z","status":"public","conference":{"end_date":"2010-07-10","location":"Bordeaux, France","name":"ICALP: Automata, Languages and Programming","start_date":"2010-07-06"},"department":[{"_id":"KrCh"}],"_id":"3851","corr_author":"1","page":"599 - 610","year":"2010","main_file_link":[{"url":"http://arxiv.org/abs/1001.5183","open_access":"1"}],"publisher":"Springer","author":[{"last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"last_name":"Doyen","full_name":"Doyen, Laurent","first_name":"Laurent"}],"abstract":[{"lang":"eng","text":"Energy parity games are infinite two-player turn-based games played on weighted graphs. The objective of the game combines a (qualitative) parity condition with the (quantitative) requirement that the sum of the weights (i.e., the level of energy in the game) must remain positive. Beside their own interest in the design and synthesis of resource-constrained omega-regular specifications, energy parity games provide one of the simplest model of games with combined qualitative and quantitative objective. Our main results are as follows: (a) exponential memory is sufficient and may be necessary for winning strategies in energy parity games; (b) the problem of deciding the winner in energy parity games can be solved in NP ∩ coNP; and (c) we give an algorithm to solve energy parity by reduction to energy games. We also show that the problem of deciding the winner in energy parity games is polynomially equivalent to the problem of deciding the winner in mean-payoff parity games, which can thus be solved in NP ∩ coNP. As a consequence we also obtain a conceptually simple algorithm to solve mean-payoff parity games."}]},{"publication_status":"published","citation":{"ama":"Chatterjee K, Majumdar R. Discounting in games across time scales. In: Vol 25. EPTCS; 2010:22-29. doi:<a href=\"https://doi.org/10.4204/EPTCS.25.6\">10.4204/EPTCS.25.6</a>","short":"K. Chatterjee, R. Majumdar, in:, EPTCS, 2010, pp. 22–29.","ista":"Chatterjee K, Majumdar R. 2010. Discounting in games across time scales. GandALF: Games, Automata, Logic, and Formal Verification, EPTCS, vol. 25, 22–29.","ieee":"K. Chatterjee and R. Majumdar, “Discounting in games across time scales,” presented at the GandALF: Games, Automata, Logic, and Formal Verification, Minori, Italy, 2010, vol. 25, pp. 22–29.","apa":"Chatterjee, K., &#38; Majumdar, R. (2010). Discounting in games across time scales (Vol. 25, pp. 22–29). Presented at the GandALF: Games, Automata, Logic, and Formal Verification, Minori, Italy: EPTCS. <a href=\"https://doi.org/10.4204/EPTCS.25.6\">https://doi.org/10.4204/EPTCS.25.6</a>","mla":"Chatterjee, Krishnendu, and Ritankar Majumdar. <i>Discounting in Games across Time Scales</i>. Vol. 25, EPTCS, 2010, pp. 22–29, doi:<a href=\"https://doi.org/10.4204/EPTCS.25.6\">10.4204/EPTCS.25.6</a>.","chicago":"Chatterjee, Krishnendu, and Ritankar Majumdar. “Discounting in Games across Time Scales,” 25:22–29. EPTCS, 2010. <a href=\"https://doi.org/10.4204/EPTCS.25.6\">https://doi.org/10.4204/EPTCS.25.6</a>."},"article_processing_charge":"No","quality_controlled":"1","oa":1,"oa_version":"Published Version","has_accepted_license":"1","alternative_title":["EPTCS"],"language":[{"iso":"eng"}],"title":"Discounting in games across time scales","month":"06","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T12:05:31Z","doi":"10.4204/EPTCS.25.6","type":"conference","scopus_import":"1","volume":25,"arxiv":1,"file_date_updated":"2020-07-14T12:46:17Z","year":"2010","page":"22 - 29","abstract":[{"text":"We introduce two-level discounted games played by two players on a perfect-information stochastic game graph. The upper level game is a discounted game and the lower level game is an undiscounted reachability game. Two-level games model hierarchical and sequential decision making under uncertainty across different time scales. We show the existence of pure memoryless optimal strategies for both players and an ordered field property for such games. We show that if there is only one player (Markov decision processes), then the values can be computed in polynomial time. It follows that whether the value of a player is equal to a given rational constant in two-level discounted games can be decided in NP intersected coNP. We also give an alternate strategy improvement algorithm to compute the value. ","lang":"eng"}],"author":[{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee"},{"last_name":"Majumdar","full_name":"Majumdar, Ritankar","first_name":"Ritankar"}],"publisher":"EPTCS","_id":"3852","file":[{"file_id":"4937","checksum":"2bdf1e9103710555c6251ca4153cb5e9","date_created":"2018-12-12T10:12:19Z","creator":"system","date_updated":"2020-07-14T12:46:17Z","file_size":74598,"access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_name":"IST-2016-491-v1+1_1006.1403v1.pdf"}],"pubrep_id":"491","corr_author":"1","conference":{"start_date":"2010-06-17","name":"GandALF: Games, Automata, Logic, and Formal Verification","location":"Minori, Italy","end_date":"2010-06-18"},"department":[{"_id":"KrCh"}],"date_published":"2010-06-08T00:00:00Z","publist_id":"2329","day":"08","intvolume":"        25","ddc":["000"],"status":"public","date_updated":"2024-10-09T20:54:08Z","external_id":{"arxiv":["1006.1403"]}},{"oa":1,"oa_version":"Submitted Version","has_accepted_license":"1","alternative_title":["LNCS"],"language":[{"iso":"eng"}],"month":"11","title":"Mean-payoff automaton expressions","ec_funded":1,"publication_status":"published","citation":{"chicago":"Chatterjee, Krishnendu, Laurent Doyen, Herbert Edelsbrunner, Thomas A Henzinger, and Philippe Rannou. “Mean-Payoff Automaton Expressions,” 6269:269–83. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2010. <a href=\"https://doi.org/10.1007/978-3-642-15375-4_19\">https://doi.org/10.1007/978-3-642-15375-4_19</a>.","mla":"Chatterjee, Krishnendu, et al. <i>Mean-Payoff Automaton Expressions</i>. Vol. 6269, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2010, pp. 269–83, doi:<a href=\"https://doi.org/10.1007/978-3-642-15375-4_19\">10.1007/978-3-642-15375-4_19</a>.","ista":"Chatterjee K, Doyen L, Edelsbrunner H, Henzinger TA, Rannou P. 2010. Mean-payoff automaton expressions. CONCUR: Concurrency Theory, LNCS, vol. 6269, 269–283.","ieee":"K. Chatterjee, L. Doyen, H. Edelsbrunner, T. A. Henzinger, and P. Rannou, “Mean-payoff automaton expressions,” presented at the CONCUR: Concurrency Theory, Paris, France, 2010, vol. 6269, pp. 269–283.","apa":"Chatterjee, K., Doyen, L., Edelsbrunner, H., Henzinger, T. A., &#38; Rannou, P. (2010). Mean-payoff automaton expressions (Vol. 6269, pp. 269–283). Presented at the CONCUR: Concurrency Theory, Paris, France: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.1007/978-3-642-15375-4_19\">https://doi.org/10.1007/978-3-642-15375-4_19</a>","short":"K. Chatterjee, L. Doyen, H. Edelsbrunner, T.A. Henzinger, P. Rannou, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2010, pp. 269–283.","ama":"Chatterjee K, Doyen L, Edelsbrunner H, Henzinger TA, Rannou P. Mean-payoff automaton expressions. In: Vol 6269. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2010:269-283. doi:<a href=\"https://doi.org/10.1007/978-3-642-15375-4_19\">10.1007/978-3-642-15375-4_19</a>"},"project":[{"grant_number":"215543","call_identifier":"FP7","_id":"25EFB36C-B435-11E9-9278-68D0E5697425","name":"COMponent-Based Embedded Systems design Techniques"},{"call_identifier":"FP7","grant_number":"214373","name":"Design for Embedded Systems","_id":"25F1337C-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","date_created":"2018-12-11T12:05:31Z","doi":"10.1007/978-3-642-15375-4_19","type":"conference","scopus_import":1,"volume":6269,"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"3853","file":[{"file_name":"IST-2012-62-v1+1_Mean-payoff_automaton_expressions.pdf","relation":"main_file","content_type":"application/pdf","access_level":"open_access","date_updated":"2020-07-14T12:46:17Z","file_size":233260,"creator":"system","date_created":"2018-12-12T10:15:41Z","checksum":"4f753ae99d076553fb8733e2c8b390e2","file_id":"5163"}],"pubrep_id":"62","corr_author":"1","file_date_updated":"2020-07-14T12:46:17Z","year":"2010","page":"269 - 283","abstract":[{"text":"Quantitative languages are an extension of boolean languages that assign to each word a real number. Mean-payoff automata are finite automata with numerical weights on transitions that assign to each infinite path the long-run average of the transition weights. When the mode of branching of the automaton is deterministic, nondeterministic, or alternating, the corresponding class of quantitative languages is not robust as it is not closed under the pointwise operations of max, min, sum, and numerical complement. Nondeterministic and alternating mean-payoff automata are not decidable either, as the quantitative generalization of the problems of universality and language inclusion is undecidable. We introduce a new class of quantitative languages, defined by mean-payoff automaton expressions, which is robust and decidable: it is closed under the four pointwise operations, and we show that all decision problems are decidable for this class. Mean-payoff automaton expressions subsume deterministic meanpayoff automata, and we show that they have expressive power incomparable to nondeterministic and alternating mean-payoff automata. We also present for the first time an algorithm to compute distance between two quantitative languages, and in our case the quantitative languages are given as mean-payoff automaton expressions.","lang":"eng"}],"author":[{"first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"},{"last_name":"Doyen","full_name":"Doyen, Laurent","first_name":"Laurent"},{"first_name":"Herbert","full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833"},{"last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","first_name":"Thomas A","full_name":"Henzinger, Thomas A"},{"last_name":"Rannou","full_name":"Rannou, Philippe","first_name":"Philippe"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","date_published":"2010-11-18T00:00:00Z","publist_id":"2328","intvolume":"      6269","day":"18","ddc":["000","005"],"status":"public","date_updated":"2024-10-09T20:54:08Z","conference":{"name":"CONCUR: Concurrency Theory","start_date":"2010-08-31","location":"Paris, France","end_date":"2010-09-03"},"department":[{"_id":"KrCh"},{"_id":"HeEd"},{"_id":"ToHe"}]},{"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"KrCh"}],"conference":{"location":"Paris, France","end_date":"2010-09-03","start_date":"2010-08-31","name":"CONCUR: Concurrency Theory"},"type":"conference","status":"public","volume":6269,"scopus_import":1,"date_updated":"2024-10-09T20:54:07Z","date_created":"2018-12-11T12:05:32Z","publist_id":"2327","date_published":"2010-09-08T00:00:00Z","day":"08","doi":"10.1007/978-3-642-15375-4_20","intvolume":"      6269","author":[{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee"},{"last_name":"Horn","id":"37327ACE-F248-11E8-B48F-1D18A9856A87","first_name":"Florian","full_name":"Horn, Florian"},{"full_name":"Löding, Christof","first_name":"Christof","last_name":"Löding"}],"abstract":[{"lang":"eng","text":"Graph games of infinite length provide a natural model for open reactive systems: one player (Eve) represents the controller and the other player (Adam) represents the environment. The evolution of the system depends on the decisions of both players. The specification for the system is usually given as an ω-regular language L over paths and Eve’s goal is to ensure that the play belongs to L irrespective of Adam’s behaviour. The classical notion of winning strategies fails to capture several interesting scenarios. For example, strong fairness (Streett) conditions are specified by a number of request-grant pairs and require every pair that is requested infinitely often to be granted infinitely often: Eve might win just by preventing Adam from making any new request, but a “better” strategy would allow Adam to make as many requests as possible and still ensure fairness. To address such questions, we introduce the notion of obliging games, where Eve has to ensure a strong condition Φ, while always allowing Adam to satisfy a weak condition Ψ. We present a linear time reduction of obliging games with two Muller conditions Φ and Ψ to classical Muller games. We consider obliging Streett games and show they are co-NP complete, and show a natural quantitative optimisation problem for obliging Streett games is in FNP. We also show how obliging games can provide new and interesting semantics for multi-player games."}],"citation":{"ama":"Chatterjee K, Horn F, Löding C. Obliging games. In: Vol 6269. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2010:284-296. doi:<a href=\"https://doi.org/10.1007/978-3-642-15375-4_20\">10.1007/978-3-642-15375-4_20</a>","short":"K. Chatterjee, F. Horn, C. Löding, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2010, pp. 284–296.","ista":"Chatterjee K, Horn F, Löding C. 2010. Obliging games. CONCUR: Concurrency Theory, LNCS, vol. 6269, 284–296.","ieee":"K. Chatterjee, F. Horn, and C. Löding, “Obliging games,” presented at the CONCUR: Concurrency Theory, Paris, France, 2010, vol. 6269, pp. 284–296.","apa":"Chatterjee, K., Horn, F., &#38; Löding, C. (2010). Obliging games (Vol. 6269, pp. 284–296). Presented at the CONCUR: Concurrency Theory, Paris, France: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.1007/978-3-642-15375-4_20\">https://doi.org/10.1007/978-3-642-15375-4_20</a>","mla":"Chatterjee, Krishnendu, et al. <i>Obliging Games</i>. Vol. 6269, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2010, pp. 284–96, doi:<a href=\"https://doi.org/10.1007/978-3-642-15375-4_20\">10.1007/978-3-642-15375-4_20</a>.","chicago":"Chatterjee, Krishnendu, Florian Horn, and Christof Löding. “Obliging Games,” 6269:284–96. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2010. <a href=\"https://doi.org/10.1007/978-3-642-15375-4_20\">https://doi.org/10.1007/978-3-642-15375-4_20</a>."},"quality_controlled":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","publication_status":"published","page":"284 - 296","year":"2010","language":[{"iso":"eng"}],"corr_author":"1","month":"09","title":"Obliging games","oa_version":"None","_id":"3854","alternative_title":["LNCS"]}]