[{"oa":1,"_id":"1838","title":"Assume-guarantee synthesis for concurrent reactive programs with partial information","publication_status":"published","abstract":[{"text":"Synthesis of program parts is particularly useful for concurrent systems. However, most approaches do not support common design tasks, like modifying a single process without having to re-synthesize or verify the whole system. Assume-guarantee synthesis (AGS) provides robustness against modifications of system parts, but thus far has been limited to the perfect information setting. This means that local variables cannot be hidden from other processes, which renders synthesis results cumbersome or even impossible to realize.We resolve this shortcoming by defining AGS under partial information. We analyze the complexity and decidability in different settings, showing that the problem has a high worstcase complexity and is undecidable in many interesting cases. Based on these observations, we present a pragmatic algorithm based on bounded synthesis, and demonstrate its practical applicability on several examples.","lang":"eng"}],"project":[{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23"},{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"}],"author":[{"first_name":"Roderick","last_name":"Bloem","full_name":"Bloem, Roderick"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee"},{"full_name":"Jacobs, Swen","last_name":"Jacobs","first_name":"Swen"},{"full_name":"Könighofer, Robert","last_name":"Könighofer","first_name":"Robert"}],"citation":{"mla":"Bloem, Roderick, et al. <i>Assume-Guarantee Synthesis for Concurrent Reactive Programs with Partial Information</i>. Vol. 9035, Springer, 2015, pp. 517–32, doi:<a href=\"https://doi.org/10.1007/978-3-662-46681-0_50\">10.1007/978-3-662-46681-0_50</a>.","apa":"Bloem, R., Chatterjee, K., Jacobs, S., &#38; 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. <a href=\"https://doi.org/10.1007/978-3-662-46681-0_50\">https://doi.org/10.1007/978-3-662-46681-0_50</a>","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.","short":"R. Bloem, K. Chatterjee, S. Jacobs, R. Könighofer, in:, Springer, 2015, pp. 517–532.","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. <a href=\"https://doi.org/10.1007/978-3-662-46681-0_50\">https://doi.org/10.1007/978-3-662-46681-0_50</a>.","ieee":"R. Bloem, K. Chatterjee, S. Jacobs, and R. Könighofer, “Assume-guarantee synthesis for concurrent reactive programs with partial information,” presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, London, United Kingdom, 2015, vol. 9035, pp. 517–532.","ama":"Bloem R, Chatterjee K, Jacobs S, Könighofer R. Assume-guarantee synthesis for concurrent reactive programs with partial information. In: Vol 9035. Springer; 2015:517-532. doi:<a href=\"https://doi.org/10.1007/978-3-662-46681-0_50\">10.1007/978-3-662-46681-0_50</a>"},"main_file_link":[{"url":"http://arxiv.org/abs/1411.4604","open_access":"1"}],"year":"2015","publist_id":"5264","intvolume":"      9035","status":"public","date_created":"2018-12-11T11:54:17Z","conference":{"end_date":"2015-04-18","name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems","location":"London, United Kingdom","start_date":"2015-04-11"},"month":"01","volume":9035,"publisher":"Springer","language":[{"iso":"eng"}],"doi":"10.1007/978-3-662-46681-0_50","department":[{"_id":"KrCh"}],"ec_funded":1,"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).","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","date_updated":"2021-01-12T06:53:32Z","type":"conference","oa_version":"Preprint","scopus_import":1,"alternative_title":["LNCS"],"page":"517 - 532","date_published":"2015-01-01T00:00:00Z"},{"alternative_title":["LNCS"],"date_published":"2015-01-01T00:00:00Z","page":"181 - 187","ec_funded":1,"department":[{"_id":"KrCh"}],"doi":"10.1007/978-3-662-46681-0_12","language":[{"iso":"eng"}],"oa_version":"Preprint","date_updated":"2020-01-21T13:18:52Z","series_title":"Lecture Notes in Computer Science","type":"conference","day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","conference":{"end_date":"2015-04-18","name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems","location":"London, United Kingdom","start_date":"2015-04-11"},"month":"01","date_created":"2018-12-11T11:54:18Z","status":"public","intvolume":"      9035","publist_id":"5263","publisher":"Springer","volume":9035,"project":[{"grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"}],"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."}],"publication_status":"published","title":"Multigain: A controller synthesis tool for MDPs with multiple mean-payoff objectives","_id":"1839","oa":1,"year":"2015","main_file_link":[{"url":"http://arxiv.org/abs/1501.03093","open_access":"1"}],"citation":{"apa":"Brázdil, T., Chatterjee, K., Forejt, V., &#38; 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. <a href=\"https://doi.org/10.1007/978-3-662-46681-0_12\">https://doi.org/10.1007/978-3-662-46681-0_12</a>","mla":"Brázdil, Tomáš, et al. <i>Multigain: A Controller Synthesis Tool for MDPs with Multiple Mean-Payoff Objectives</i>. Vol. 9035, Springer, 2015, pp. 181–87, doi:<a href=\"https://doi.org/10.1007/978-3-662-46681-0_12\">10.1007/978-3-662-46681-0_12</a>.","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.","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:<a href=\"https://doi.org/10.1007/978-3-662-46681-0_12\">10.1007/978-3-662-46681-0_12</a>","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.","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. <a href=\"https://doi.org/10.1007/978-3-662-46681-0_12\">https://doi.org/10.1007/978-3-662-46681-0_12</a>.","short":"T. Brázdil, K. Chatterjee, V. Forejt, A. Kučera, 9035 (2015) 181–187."},"author":[{"full_name":"Brázdil, Tomáš","first_name":"Tomáš","last_name":"Brázdil"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee"},{"full_name":"Forejt, Vojtěch","first_name":"Vojtěch","last_name":"Forejt"},{"first_name":"Antonín","last_name":"Kučera","full_name":"Kučera, Antonín"}],"quality_controlled":"1"},{"publication_identifier":{"issn":["0018-9286"]},"scopus_import":1,"page":"1010 - 1022","date_published":"2015-04-01T00:00:00Z","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","language":[{"iso":"eng"}],"doi":"10.1109/TAC.2014.2364971","department":[{"_id":"CaGu"},{"_id":"ToHe"}],"day":"01","type":"journal_article","date_updated":"2021-01-12T06:53:33Z","oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","date_created":"2018-12-11T11:54:18Z","month":"04","publist_id":"5262","intvolume":"        60","publisher":"IEEE","issue":"4","volume":60,"publication_status":"published","abstract":[{"text":"In this paper, we present a method for reducing a regular, discrete-time Markov chain (DTMC) to another DTMC with a given, typically much smaller number of states. The cost of reduction is defined as the Kullback-Leibler divergence rate between a projection of the original process through a partition function and a DTMC on the correspondingly partitioned state space. Finding the reduced model with minimal cost is computationally expensive, as it requires an exhaustive search among all state space partitions, and an exact evaluation of the reduction cost for each candidate partition. Our approach deals with the latter problem by minimizing an upper bound on the reduction cost instead of minimizing the exact cost. The proposed upper bound is easy to compute and it is tight if the original chain is lumpable with respect to the partition. Then, we express the problem in the form of information bottleneck optimization, and propose using the agglomerative information bottleneck algorithm for searching a suboptimal partition greedily, rather than exhaustively. The theory is illustrated with examples and one application scenario in the context of modeling bio-molecular interactions.","lang":"eng"}],"oa":1,"_id":"1840","title":"Optimal Kullback-Leibler aggregation via information bottleneck","publication":"IEEE Transactions on Automatic Control","year":"2015","author":[{"full_name":"Geiger, Bernhard","first_name":"Bernhard","last_name":"Geiger"},{"id":"3D5811FC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9041-0905","full_name":"Petrov, Tatjana","first_name":"Tatjana","last_name":"Petrov"},{"last_name":"Kubin","first_name":"Gernot","full_name":"Kubin, Gernot"},{"full_name":"Koeppl, Heinz","first_name":"Heinz","last_name":"Koeppl"}],"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1304.6603"}],"citation":{"apa":"Geiger, B., Petrov, T., Kubin, G., &#38; Koeppl, H. (2015). Optimal Kullback-Leibler aggregation via information bottleneck. <i>IEEE Transactions on Automatic Control</i>. IEEE. <a href=\"https://doi.org/10.1109/TAC.2014.2364971\">https://doi.org/10.1109/TAC.2014.2364971</a>","mla":"Geiger, Bernhard, et al. “Optimal Kullback-Leibler Aggregation via Information Bottleneck.” <i>IEEE Transactions on Automatic Control</i>, vol. 60, no. 4, IEEE, 2015, pp. 1010–22, doi:<a href=\"https://doi.org/10.1109/TAC.2014.2364971\">10.1109/TAC.2014.2364971</a>.","short":"B. Geiger, T. Petrov, G. Kubin, H. Koeppl, IEEE Transactions on Automatic Control 60 (2015) 1010–1022.","chicago":"Geiger, Bernhard, Tatjana Petrov, Gernot Kubin, and Heinz Koeppl. “Optimal Kullback-Leibler Aggregation via Information Bottleneck.” <i>IEEE Transactions on Automatic Control</i>. IEEE, 2015. <a href=\"https://doi.org/10.1109/TAC.2014.2364971\">https://doi.org/10.1109/TAC.2014.2364971</a>.","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.","ama":"Geiger B, Petrov T, Kubin G, Koeppl H. Optimal Kullback-Leibler aggregation via information bottleneck. <i>IEEE Transactions on Automatic Control</i>. 2015;60(4):1010-1022. doi:<a href=\"https://doi.org/10.1109/TAC.2014.2364971\">10.1109/TAC.2014.2364971</a>","ieee":"B. Geiger, T. Petrov, G. Kubin, and H. Koeppl, “Optimal Kullback-Leibler aggregation via information bottleneck,” <i>IEEE Transactions on Automatic Control</i>, vol. 60, no. 4. IEEE, pp. 1010–1022, 2015."}},{"date_published":"2015-05-01T00:00:00Z","page":"919 - 930","scopus_import":1,"type":"journal_article","date_updated":"2021-01-12T06:53:33Z","oa_version":"Preprint","day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ec_funded":1,"doi":"10.1109/TPAMI.2014.2363465","language":[{"iso":"eng"}],"department":[{"_id":"VlKo"}],"publisher":"IEEE","issue":"5","volume":37,"date_created":"2018-12-11T11:54:18Z","month":"05","status":"public","intvolume":"        37","publist_id":"5261","year":"2015","citation":{"apa":"Kolmogorov, V. (2015). A new look at reweighted message passing. <i>IEEE Transactions on Pattern Analysis and Machine Intelligence</i>. IEEE. <a href=\"https://doi.org/10.1109/TPAMI.2014.2363465\">https://doi.org/10.1109/TPAMI.2014.2363465</a>","mla":"Kolmogorov, Vladimir. “A New Look at Reweighted Message Passing.” <i>IEEE Transactions on Pattern Analysis and Machine Intelligence</i>, vol. 37, no. 5, IEEE, 2015, pp. 919–30, doi:<a href=\"https://doi.org/10.1109/TPAMI.2014.2363465\">10.1109/TPAMI.2014.2363465</a>.","ista":"Kolmogorov V. 2015. A new look at reweighted message passing. IEEE Transactions on Pattern Analysis and Machine Intelligence. 37(5), 919–930.","chicago":"Kolmogorov, Vladimir. “A New Look at Reweighted Message Passing.” <i>IEEE Transactions on Pattern Analysis and Machine Intelligence</i>. IEEE, 2015. <a href=\"https://doi.org/10.1109/TPAMI.2014.2363465\">https://doi.org/10.1109/TPAMI.2014.2363465</a>.","short":"V. Kolmogorov, IEEE Transactions on Pattern Analysis and Machine Intelligence 37 (2015) 919–930.","ama":"Kolmogorov V. A new look at reweighted message passing. <i>IEEE Transactions on Pattern Analysis and Machine Intelligence</i>. 2015;37(5):919-930. doi:<a href=\"https://doi.org/10.1109/TPAMI.2014.2363465\">10.1109/TPAMI.2014.2363465</a>","ieee":"V. Kolmogorov, “A new look at reweighted message passing,” <i>IEEE Transactions on Pattern Analysis and Machine Intelligence</i>, vol. 37, no. 5. IEEE, pp. 919–930, 2015."},"main_file_link":[{"url":"http://arxiv.org/abs/1309.5655","open_access":"1"}],"quality_controlled":"1","author":[{"last_name":"Kolmogorov","first_name":"Vladimir","full_name":"Kolmogorov, Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"}],"project":[{"grant_number":"616160","name":"Discrete Optimization in Computer Vision: Theory and Practice","_id":"25FBA906-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"publication_status":"published","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."}],"title":"A new look at reweighted message passing","publication":"IEEE Transactions on Pattern Analysis and Machine Intelligence","oa":1,"_id":"1841"},{"department":[{"_id":"PeJo"}],"has_accepted_license":"1","doi":"10.1016/j.neuron.2015.03.006","language":[{"iso":"eng"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_processing_charge":"No","day":"18","oa_version":"Published Version","date_updated":"2021-10-08T09:07:34Z","type":"journal_article","scopus_import":"1","page":"1149 - 1151","file":[{"date_created":"2018-12-12T10:16:07Z","relation":"main_file","content_type":"application/pdf","creator":"system","file_size":411832,"file_id":"5192","date_updated":"2020-07-14T12:45:19Z","access_level":"open_access","checksum":"d1808550e376a0eca2a950fda017cfa6","file_name":"IST-2017-822-v1+1_Perspective_Fig__Final.pdf"},{"date_updated":"2020-07-14T12:45:19Z","file_id":"5193","access_level":"open_access","file_name":"IST-2017-822-v1+2_Perspective_Final2.pdf","checksum":"a279f4ae61e6c8f33d68f69a0d02097d","date_created":"2018-12-12T10:16:07Z","relation":"main_file","content_type":"application/pdf","creator":"system","file_size":100769}],"date_published":"2015-03-18T00:00:00Z","_id":"1845","ddc":["570"],"oa":1,"title":"Excitement about inhibitory presynaptic terminals","publication":"Neuron","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."}],"publication_status":"published","author":[{"full_name":"Vandael, David H","orcid":"0000-0001-7577-1676","id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87","first_name":"David H","last_name":"Vandael"},{"id":"31FFEE2E-F248-11E8-B48F-1D18A9856A87","full_name":"Espinoza Martinez, Claudia ","orcid":"0000-0003-4710-2082","last_name":"Espinoza Martinez","first_name":"Claudia "},{"last_name":"Jonas","first_name":"Peter M","orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"}],"quality_controlled":"1","citation":{"apa":"Vandael, D. H., Espinoza Martinez, C., &#38; Jonas, P. M. (2015). Excitement about inhibitory presynaptic terminals. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2015.03.006\">https://doi.org/10.1016/j.neuron.2015.03.006</a>","mla":"Vandael, David H., et al. “Excitement about Inhibitory Presynaptic Terminals.” <i>Neuron</i>, vol. 85, no. 6, Elsevier, 2015, pp. 1149–51, doi:<a href=\"https://doi.org/10.1016/j.neuron.2015.03.006\">10.1016/j.neuron.2015.03.006</a>.","short":"D.H. Vandael, C. Espinoza Martinez, P.M. Jonas, Neuron 85 (2015) 1149–1151.","chicago":"Vandael, David H, Claudia  Espinoza Martinez, and Peter M Jonas. “Excitement about Inhibitory Presynaptic Terminals.” <i>Neuron</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.neuron.2015.03.006\">https://doi.org/10.1016/j.neuron.2015.03.006</a>.","ista":"Vandael DH, Espinoza Martinez C, Jonas PM. 2015. Excitement about inhibitory presynaptic terminals. Neuron. 85(6), 1149–1151.","ama":"Vandael DH, Espinoza Martinez C, Jonas PM. Excitement about inhibitory presynaptic terminals. <i>Neuron</i>. 2015;85(6):1149-1151. doi:<a href=\"https://doi.org/10.1016/j.neuron.2015.03.006\">10.1016/j.neuron.2015.03.006</a>","ieee":"D. H. Vandael, C. Espinoza Martinez, and P. M. Jonas, “Excitement about inhibitory presynaptic terminals,” <i>Neuron</i>, vol. 85, no. 6. Elsevier, pp. 1149–1151, 2015."},"year":"2015","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"},"publist_id":"5256","intvolume":"        85","status":"public","month":"03","date_created":"2018-12-11T11:54:19Z","pubrep_id":"822","volume":85,"issue":"6","publisher":"Elsevier","file_date_updated":"2020-07-14T12:45:19Z"},{"volume":52,"issue":"2-3","article_type":"original","publisher":"Springer","file_date_updated":"2020-07-14T12:45:19Z","publist_id":"5255","intvolume":"        52","status":"public","month":"04","date_created":"2018-12-11T11:54:20Z","quality_controlled":"1","author":[{"full_name":"Beneš, Nikola","last_name":"Beneš","first_name":"Nikola"},{"first_name":"Jan","last_name":"Kretinsky","orcid":"0000-0002-8122-2881","full_name":"Kretinsky, Jan","id":"44CEF464-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Larsen, Kim","first_name":"Kim","last_name":"Larsen"},{"first_name":"Mikael","last_name":"Möller","full_name":"Möller, Mikael"},{"first_name":"Salomon","last_name":"Sickert","full_name":"Sickert, Salomon"},{"full_name":"Srba, Jiří","first_name":"Jiří","last_name":"Srba"}],"citation":{"mla":"Beneš, Nikola, et al. “Refinement Checking on Parametric Modal Transition Systems.” <i>Acta Informatica</i>, vol. 52, no. 2–3, Springer, 2015, pp. 269–97, doi:<a href=\"https://doi.org/10.1007/s00236-015-0215-4\">10.1007/s00236-015-0215-4</a>.","apa":"Beneš, N., Kretinsky, J., Larsen, K., Möller, M., Sickert, S., &#38; Srba, J. (2015). Refinement checking on parametric modal transition systems. <i>Acta Informatica</i>. Springer. <a href=\"https://doi.org/10.1007/s00236-015-0215-4\">https://doi.org/10.1007/s00236-015-0215-4</a>","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.","chicago":"Beneš, Nikola, Jan Kretinsky, Kim Larsen, Mikael Möller, Salomon Sickert, and Jiří Srba. “Refinement Checking on Parametric Modal Transition Systems.” <i>Acta Informatica</i>. Springer, 2015. <a href=\"https://doi.org/10.1007/s00236-015-0215-4\">https://doi.org/10.1007/s00236-015-0215-4</a>.","short":"N. Beneš, J. Kretinsky, K. Larsen, M. Möller, S. Sickert, J. Srba, Acta Informatica 52 (2015) 269–297.","ama":"Beneš N, Kretinsky J, Larsen K, Möller M, Sickert S, Srba J. Refinement checking on parametric modal transition systems. <i>Acta Informatica</i>. 2015;52(2-3):269-297. doi:<a href=\"https://doi.org/10.1007/s00236-015-0215-4\">10.1007/s00236-015-0215-4</a>","ieee":"N. Beneš, J. Kretinsky, K. Larsen, M. Möller, S. Sickert, and J. Srba, “Refinement checking on parametric modal transition systems,” <i>Acta Informatica</i>, vol. 52, no. 2–3. Springer, pp. 269–297, 2015."},"year":"2015","_id":"1846","oa":1,"ddc":["000"],"publication":"Acta Informatica","title":"Refinement checking on parametric modal transition systems","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."}],"publication_status":"published","project":[{"grant_number":"267989","name":"Quantitative Reactive Modeling","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"page":"269 - 297","file":[{"checksum":"fb4037ddc4fc05f33080dd3547ede350","file_name":"2015_ActaInfo_Benes.pdf","access_level":"open_access","date_updated":"2020-07-14T12:45:19Z","file_id":"7854","creator":"dernst","content_type":"application/pdf","file_size":488482,"relation":"main_file","date_created":"2020-05-15T08:57:44Z"}],"date_published":"2015-04-01T00:00:00Z","scopus_import":1,"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","oa_version":"Submitted Version","type":"journal_article","date_updated":"2021-01-12T06:53:35Z","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"has_accepted_license":"1","language":[{"iso":"eng"}],"doi":"10.1007/s00236-015-0215-4","ec_funded":1},{"_id":"1847","department":[{"_id":"JiFr"}],"doi":"10.1016/j.molp.2014.12.013","language":[{"iso":"eng"}],"publication":"Molecular Plant","title":"ABP1: Finally docking","publication_status":"published","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).","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Grones","first_name":"Peter","id":"399876EC-F248-11E8-B48F-1D18A9856A87","full_name":"Grones, Peter"},{"first_name":"Jiřĺ","last_name":"Friml","full_name":"Friml, Jiřĺ","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"citation":{"ieee":"P. Grones and J. Friml, “ABP1: Finally docking,” <i>Molecular Plant</i>, vol. 8, no. 3. Elsevier, pp. 356–358, 2015.","ama":"Grones P, Friml J. ABP1: Finally docking. <i>Molecular Plant</i>. 2015;8(3):356-358. doi:<a href=\"https://doi.org/10.1016/j.molp.2014.12.013\">10.1016/j.molp.2014.12.013</a>","ista":"Grones P, Friml J. 2015. ABP1: Finally docking. Molecular Plant. 8(3), 356–358.","chicago":"Grones, Peter, and Jiří Friml. “ABP1: Finally Docking.” <i>Molecular Plant</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.molp.2014.12.013\">https://doi.org/10.1016/j.molp.2014.12.013</a>.","short":"P. Grones, J. Friml, Molecular Plant 8 (2015) 356–358.","apa":"Grones, P., &#38; Friml, J. (2015). ABP1: Finally docking. <i>Molecular Plant</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.molp.2014.12.013\">https://doi.org/10.1016/j.molp.2014.12.013</a>","mla":"Grones, Peter, and Jiří Friml. “ABP1: Finally Docking.” <i>Molecular Plant</i>, vol. 8, no. 3, Elsevier, 2015, pp. 356–58, doi:<a href=\"https://doi.org/10.1016/j.molp.2014.12.013\">10.1016/j.molp.2014.12.013</a>."},"year":"2015","day":"02","oa_version":"None","type":"journal_article","date_updated":"2021-01-12T06:53:35Z","scopus_import":1,"publist_id":"5254","intvolume":"         8","status":"public","month":"03","date_created":"2018-12-11T11:54:20Z","page":"356 - 358","volume":8,"issue":"3","date_published":"2015-03-02T00:00:00Z","publisher":"Elsevier"},{"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."}],"publication_status":"published","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.).","department":[{"_id":"JiFr"}],"_id":"1849","language":[{"iso":"eng"}],"doi":"10.1016/j.bbamcr.2015.02.017","publication":"Biochimica et Biophysica Acta - Molecular Cell Research","title":"Calcium is an organizer of cell polarity in plants","year":"2015","day":"01","oa_version":"None","date_updated":"2021-01-12T06:53:36Z","type":"journal_article","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Himschoot, Ellie","last_name":"Himschoot","first_name":"Ellie"},{"last_name":"Beeckman","first_name":"Tom","full_name":"Beeckman, Tom"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiřĺ","orcid":"0000-0002-8302-7596","first_name":"Jiřĺ","last_name":"Friml"},{"last_name":"Vanneste","first_name":"Steffen","full_name":"Vanneste, Steffen"}],"citation":{"ama":"Himschoot E, Beeckman T, Friml J, Vanneste S. Calcium is an organizer of cell polarity in plants. <i>Biochimica et Biophysica Acta - Molecular Cell Research</i>. 2015;1853(9):2168-2172. doi:<a href=\"https://doi.org/10.1016/j.bbamcr.2015.02.017\">10.1016/j.bbamcr.2015.02.017</a>","ieee":"E. Himschoot, T. Beeckman, J. Friml, and S. Vanneste, “Calcium is an organizer of cell polarity in plants,” <i>Biochimica et Biophysica Acta - Molecular Cell Research</i>, 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.","short":"E. Himschoot, T. Beeckman, J. Friml, S. Vanneste, Biochimica et Biophysica Acta - Molecular Cell Research 1853 (2015) 2168–2172.","chicago":"Himschoot, Ellie, Tom Beeckman, Jiří Friml, and Steffen Vanneste. “Calcium Is an Organizer of Cell Polarity in Plants.” <i>Biochimica et Biophysica Acta - Molecular Cell Research</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.bbamcr.2015.02.017\">https://doi.org/10.1016/j.bbamcr.2015.02.017</a>.","mla":"Himschoot, Ellie, et al. “Calcium Is an Organizer of Cell Polarity in Plants.” <i>Biochimica et Biophysica Acta - Molecular Cell Research</i>, vol. 1853, no. 9, Elsevier, 2015, pp. 2168–72, doi:<a href=\"https://doi.org/10.1016/j.bbamcr.2015.02.017\">10.1016/j.bbamcr.2015.02.017</a>.","apa":"Himschoot, E., Beeckman, T., Friml, J., &#38; Vanneste, S. (2015). Calcium is an organizer of cell polarity in plants. <i>Biochimica et Biophysica Acta - Molecular Cell Research</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.bbamcr.2015.02.017\">https://doi.org/10.1016/j.bbamcr.2015.02.017</a>"},"status":"public","month":"09","date_created":"2018-12-11T11:54:21Z","scopus_import":1,"publist_id":"5252","intvolume":"      1853","publisher":"Elsevier","page":"2168 - 2172","volume":1853,"issue":"9","date_published":"2015-09-01T00:00:00Z"},{"intvolume":"       372","publist_id":"5251","date_created":"2018-12-11T11:54:21Z","month":"05","status":"public","volume":372,"issue":"5","pubrep_id":"329","file_date_updated":"2020-07-14T12:45:19Z","publisher":"Elsevier","publication":"Journal of Theoretical Biology","title":"Fungal disease dynamics in insect societies: Optimal killing rates and the ambivalent effect of high social interaction rates","ddc":["576"],"oa":1,"_id":"1850","project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation"},{"name":"Social Vaccination in Ant Colonies: from Individual Mechanisms to Society Effects","grant_number":"243071","_id":"25DC711C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"publication_status":"published","abstract":[{"text":"Entomopathogenic fungi are potent biocontrol agents that are widely used against insect pests, many of which are social insects. Nevertheless, theoretical investigations of their particular life history are scarce. We develop a model that takes into account the main distinguishing features between traditionally studied diseases and obligate killing pathogens, like the (biocontrol-relevant) insect-pathogenic fungi Metarhizium and Beauveria. First, obligate killing entomopathogenic fungi produce new infectious particles (conidiospores) only after host death and not yet on the living host. Second, the killing rates of entomopathogenic fungi depend strongly on the initial exposure dosage, thus we explicitly consider the pathogen load of individual hosts. Further, we make the model applicable not only to solitary host species, but also to group living species by incorporating social interactions between hosts, like the collective disease defences of insect societies. Our results identify the optimal killing rate for the pathogen that minimises its invasion threshold. Furthermore, we find that the rate of contact between hosts has an ambivalent effect: dense interaction networks between individuals are considered to facilitate disease outbreaks because of increased pathogen transmission. In social insects, this is compensated by their collective disease defences, i.e., social immunity. For the type of pathogens considered here, we show that even without social immunity, high contact rates between live individuals dilute the pathogen in the host colony and hence can reduce individual pathogen loads below disease-causing levels.","lang":"eng"}],"citation":{"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.","chicago":"Novak, Sebastian, and Sylvia Cremer. “Fungal Disease Dynamics in Insect Societies: Optimal Killing Rates and the Ambivalent Effect of High Social Interaction Rates.” <i>Journal of Theoretical Biology</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.jtbi.2015.02.018\">https://doi.org/10.1016/j.jtbi.2015.02.018</a>.","short":"S. Novak, S. Cremer, Journal of Theoretical Biology 372 (2015) 54–64.","ieee":"S. Novak and S. Cremer, “Fungal disease dynamics in insect societies: Optimal killing rates and the ambivalent effect of high social interaction rates,” <i>Journal of Theoretical Biology</i>, vol. 372, no. 5. Elsevier, pp. 54–64, 2015.","ama":"Novak S, Cremer S. Fungal disease dynamics in insect societies: Optimal killing rates and the ambivalent effect of high social interaction rates. <i>Journal of Theoretical Biology</i>. 2015;372(5):54-64. doi:<a href=\"https://doi.org/10.1016/j.jtbi.2015.02.018\">10.1016/j.jtbi.2015.02.018</a>","apa":"Novak, S., &#38; Cremer, S. (2015). Fungal disease dynamics in insect societies: Optimal killing rates and the ambivalent effect of high social interaction rates. <i>Journal of Theoretical Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jtbi.2015.02.018\">https://doi.org/10.1016/j.jtbi.2015.02.018</a>","mla":"Novak, Sebastian, and Sylvia Cremer. “Fungal Disease Dynamics in Insect Societies: Optimal Killing Rates and the Ambivalent Effect of High Social Interaction Rates.” <i>Journal of Theoretical Biology</i>, vol. 372, no. 5, Elsevier, 2015, pp. 54–64, doi:<a href=\"https://doi.org/10.1016/j.jtbi.2015.02.018\">10.1016/j.jtbi.2015.02.018</a>."},"quality_controlled":"1","author":[{"full_name":"Novak, Sebastian","orcid":"0000-0002-2519-824X","id":"461468AE-F248-11E8-B48F-1D18A9856A87","last_name":"Novak","first_name":"Sebastian"},{"last_name":"Cremer","first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia"}],"year":"2015","scopus_import":1,"date_published":"2015-05-07T00:00:00Z","file":[{"content_type":"application/pdf","creator":"system","file_size":1546914,"date_created":"2018-12-12T10:18:07Z","relation":"main_file","access_level":"open_access","checksum":"3c0dcacc900bc45cc65a453dfda4ca43","file_name":"IST-2015-329-v1+1_manuscript.pdf","date_updated":"2020-07-14T12:45:19Z","file_id":"5326"}],"page":"54 - 64","ec_funded":1,"doi":"10.1016/j.jtbi.2015.02.018","language":[{"iso":"eng"}],"has_accepted_license":"1","department":[{"_id":"NiBa"},{"_id":"SyCr"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2025-05-28T11:42:49Z","type":"journal_article","oa_version":"Submitted Version","day":"07"},{"department":[{"_id":"NiBa"},{"_id":"KrCh"}],"has_accepted_license":"1","doi":"10.1111/evo.12618","language":[{"iso":"eng"}],"ec_funded":1,"day":"09","oa_version":"Submitted Version","date_updated":"2022-06-07T10:52:37Z","type":"journal_article","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","publication_identifier":{"issn":["0014-3820"],"eissn":["1558-5646"]},"page":"1015 - 1026","external_id":{"pmid":["25662095"]},"file":[{"date_created":"2020-05-15T09:05:34Z","relation":"main_file","file_size":967214,"content_type":"application/pdf","creator":"dernst","file_id":"7855","date_updated":"2020-07-14T12:45:19Z","access_level":"open_access","checksum":"1e8be0b1d7598a78cd2623d8ee8e7798","file_name":"2015_Evolution_Priklopil.pdf"}],"date_published":"2015-02-09T00:00:00Z","abstract":[{"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.","lang":"eng"}],"publication_status":"published","project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"_id":"1851","oa":1,"ddc":["570"],"pmid":1,"title":"Evolutionarily stable mating decisions for sequentially searching females and the stability of reproductive isolation by assortative mating","publication":"Evolution","year":"2015","quality_controlled":"1","author":[{"full_name":"Priklopil, Tadeas","id":"3C869AA0-F248-11E8-B48F-1D18A9856A87","last_name":"Priklopil","first_name":"Tadeas"},{"full_name":"Kisdi, Eva","first_name":"Eva","last_name":"Kisdi"},{"full_name":"Gyllenberg, Mats","last_name":"Gyllenberg","first_name":"Mats"}],"citation":{"mla":"Priklopil, Tadeas, et al. “Evolutionarily Stable Mating Decisions for Sequentially Searching Females and the Stability of Reproductive Isolation by Assortative Mating.” <i>Evolution</i>, vol. 69, no. 4, Wiley, 2015, pp. 1015–26, doi:<a href=\"https://doi.org/10.1111/evo.12618\">10.1111/evo.12618</a>.","apa":"Priklopil, T., Kisdi, E., &#38; Gyllenberg, M. (2015). Evolutionarily stable mating decisions for sequentially searching females and the stability of reproductive isolation by assortative mating. <i>Evolution</i>. Wiley. <a href=\"https://doi.org/10.1111/evo.12618\">https://doi.org/10.1111/evo.12618</a>","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.” <i>Evolution</i>. Wiley, 2015. <a href=\"https://doi.org/10.1111/evo.12618\">https://doi.org/10.1111/evo.12618</a>.","short":"T. Priklopil, E. Kisdi, M. Gyllenberg, Evolution 69 (2015) 1015–1026.","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.","ama":"Priklopil T, Kisdi E, Gyllenberg M. Evolutionarily stable mating decisions for sequentially searching females and the stability of reproductive isolation by assortative mating. <i>Evolution</i>. 2015;69(4):1015-1026. doi:<a href=\"https://doi.org/10.1111/evo.12618\">10.1111/evo.12618</a>","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,” <i>Evolution</i>, vol. 69, no. 4. Wiley, pp. 1015–1026, 2015."},"status":"public","month":"02","date_created":"2018-12-11T11:54:21Z","publist_id":"5249","intvolume":"        69","publisher":"Wiley","article_type":"original","file_date_updated":"2020-07-14T12:45:19Z","issue":"4","volume":69},{"intvolume":"        84","publist_id":"5245","month":"03","date_created":"2018-12-11T11:54:23Z","status":"public","pubrep_id":"460","issue":"3","volume":84,"file_date_updated":"2020-07-14T12:45:19Z","publisher":"Wiley","article_type":"original","pmid":1,"publication":"Journal of Animal Ecology","title":"A sting in the spit: Widespread cross-infection of multiple RNA viruses across wild and managed bees","_id":"1855","related_material":{"record":[{"status":"public","relation":"research_data","id":"9720"}]},"ddc":["570"],"oa":1,"abstract":[{"text":"Summary: Declining populations of bee pollinators are a cause of concern, with major repercussions for biodiversity loss and food security. RNA viruses associated with honeybees represent a potential threat to other insect pollinators, but the extent of this threat is poorly understood. This study aims to attain a detailed understanding of the current and ongoing risk of emerging infectious disease (EID) transmission between managed and wild pollinator species across a wide range of RNA viruses. Within a structured large-scale national survey across 26 independent sites, we quantify the prevalence and pathogen loads of multiple RNA viruses in co-occurring managed honeybee (Apis mellifera) and wild bumblebee (Bombus spp.) populations. We then construct models that compare virus prevalence between wild and managed pollinators. Multiple RNA viruses associated with honeybees are widespread in sympatric wild bumblebee populations. Virus prevalence in honeybees is a significant predictor of virus prevalence in bumblebees, but we remain cautious in speculating over the principle direction of pathogen transmission. We demonstrate species-specific differences in prevalence, indicating significant variation in disease susceptibility or tolerance. Pathogen loads within individual bumblebees may be high and in the case of at least one RNA virus, prevalence is higher in wild bumblebees than in managed honeybee populations. Our findings indicate widespread transmission of RNA viruses between managed and wild bee pollinators, pointing to an interconnected network of potential disease pressures within and among pollinator species. In the context of the biodiversity crisis, our study emphasizes the importance of targeting a wide range of pathogens and defining host associations when considering potential drivers of population decline.","lang":"eng"}],"publication_status":"published","citation":{"chicago":"Mcmahon, Dino, Matthias Fürst, Jesicca Caspar, Panagiotis Theodorou, Mark Brown, and Robert Paxton. “A Sting in the Spit: Widespread Cross-Infection of Multiple RNA Viruses across Wild and Managed Bees.” <i>Journal of Animal Ecology</i>. Wiley, 2015. <a href=\"https://doi.org/10.1111/1365-2656.12345\">https://doi.org/10.1111/1365-2656.12345</a>.","short":"D. Mcmahon, M. Fürst, J. Caspar, P. Theodorou, M. Brown, R. Paxton, Journal of Animal Ecology 84 (2015) 615–624.","ista":"Mcmahon D, Fürst M, Caspar J, Theodorou P, Brown M, Paxton R. 2015. A sting in the spit: Widespread cross-infection of multiple RNA viruses across wild and managed bees. Journal of Animal Ecology. 84(3), 615–624.","ama":"Mcmahon D, Fürst M, Caspar J, Theodorou P, Brown M, Paxton R. A sting in the spit: Widespread cross-infection of multiple RNA viruses across wild and managed bees. <i>Journal of Animal Ecology</i>. 2015;84(3):615-624. doi:<a href=\"https://doi.org/10.1111/1365-2656.12345\">10.1111/1365-2656.12345</a>","ieee":"D. Mcmahon, M. Fürst, J. Caspar, P. Theodorou, M. Brown, and R. Paxton, “A sting in the spit: Widespread cross-infection of multiple RNA viruses across wild and managed bees,” <i>Journal of Animal Ecology</i>, vol. 84, no. 3. Wiley, pp. 615–624, 2015.","mla":"Mcmahon, Dino, et al. “A Sting in the Spit: Widespread Cross-Infection of Multiple RNA Viruses across Wild and Managed Bees.” <i>Journal of Animal Ecology</i>, vol. 84, no. 3, Wiley, 2015, pp. 615–24, doi:<a href=\"https://doi.org/10.1111/1365-2656.12345\">10.1111/1365-2656.12345</a>.","apa":"Mcmahon, D., Fürst, M., Caspar, J., Theodorou, P., Brown, M., &#38; Paxton, R. (2015). A sting in the spit: Widespread cross-infection of multiple RNA viruses across wild and managed bees. <i>Journal of Animal Ecology</i>. Wiley. <a href=\"https://doi.org/10.1111/1365-2656.12345\">https://doi.org/10.1111/1365-2656.12345</a>"},"author":[{"first_name":"Dino","last_name":"Mcmahon","full_name":"Mcmahon, Dino"},{"last_name":"Fürst","first_name":"Matthias","id":"393B1196-F248-11E8-B48F-1D18A9856A87","full_name":"Fürst, Matthias","orcid":"0000-0002-3712-925X"},{"last_name":"Caspar","first_name":"Jesicca","full_name":"Caspar, Jesicca"},{"full_name":"Theodorou, Panagiotis","last_name":"Theodorou","first_name":"Panagiotis"},{"full_name":"Brown, Mark","first_name":"Mark","last_name":"Brown"},{"full_name":"Paxton, Robert","first_name":"Robert","last_name":"Paxton"}],"quality_controlled":"1","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2015","scopus_import":"1","file":[{"date_updated":"2020-07-14T12:45:19Z","file_id":"5350","checksum":"542a0b9b07e78050a81b35f26f0b82da","file_name":"IST-2016-460-v1+1_McMahon_et_al-2015-Journal_of_Animal_Ecology.pdf","access_level":"open_access","relation":"main_file","date_created":"2018-12-12T10:18:29Z","creator":"system","content_type":"application/pdf","file_size":1823045}],"external_id":{"pmid":["25646973"]},"date_published":"2015-03-03T00:00:00Z","page":"615 - 624","has_accepted_license":"1","department":[{"_id":"SyCr"}],"language":[{"iso":"eng"}],"doi":"10.1111/1365-2656.12345","acknowledgement":"We thank J.R. de Miranda, L. De Smet and D. de Graaf for supplying qRT-PCR and MLPA positive controls, respectively, in the form of plasmids. This work was supported by the Insect Pollinators Initiative (IPI grants BB/1000100/1 and BB/I000151/1). The IPI is funded jointly by the Biotechnology and Biological Sciences Research Council, the Department for Environment, Food and Rural Affairs, the Natural Environment Research Council, The Scottish Government and The Wellcome Trust, under the Living with Environmental Change Partnership.","article_processing_charge":"No","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","oa_version":"Published Version","date_updated":"2023-02-23T14:06:09Z","type":"journal_article","day":"03"},{"date_published":"2015-02-01T00:00:00Z","scopus_import":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","type":"journal_article","date_updated":"2023-02-23T11:46:04Z","day":"01","ec_funded":1,"department":[{"_id":"KrCh"},{"_id":"ToHe"}],"language":[{"iso":"eng"}],"doi":"10.1145/2699430","volume":62,"issue":"1","publisher":"ACM","intvolume":"        62","publist_id":"5244","month":"02","date_created":"2018-12-11T11:54:23Z","article_number":"9","status":"public","citation":{"mla":"Chatterjee, Krishnendu, et al. “Measuring and Synthesizing Systems in Probabilistic Environments.” <i>Journal of the ACM</i>, vol. 62, no. 1, 9, ACM, 2015, doi:<a href=\"https://doi.org/10.1145/2699430\">10.1145/2699430</a>.","apa":"Chatterjee, K., Henzinger, T. A., Jobstmann, B., &#38; Singh, R. (2015). Measuring and synthesizing systems in probabilistic environments. <i>Journal of the ACM</i>. ACM. <a href=\"https://doi.org/10.1145/2699430\">https://doi.org/10.1145/2699430</a>","ama":"Chatterjee K, Henzinger TA, Jobstmann B, Singh R. Measuring and synthesizing systems in probabilistic environments. <i>Journal of the ACM</i>. 2015;62(1). doi:<a href=\"https://doi.org/10.1145/2699430\">10.1145/2699430</a>","ieee":"K. Chatterjee, T. A. Henzinger, B. Jobstmann, and R. Singh, “Measuring and synthesizing systems in probabilistic environments,” <i>Journal of the ACM</i>, 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.","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, Barbara Jobstmann, and Rohit Singh. “Measuring and Synthesizing Systems in Probabilistic Environments.” <i>Journal of the ACM</i>. ACM, 2015. <a href=\"https://doi.org/10.1145/2699430\">https://doi.org/10.1145/2699430</a>.","short":"K. Chatterjee, T.A. Henzinger, B. Jobstmann, R. Singh, Journal of the ACM 62 (2015)."},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1004.0739"}],"quality_controlled":"1","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu"},{"orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A"},{"full_name":"Jobstmann, Barbara","first_name":"Barbara","last_name":"Jobstmann"},{"full_name":"Singh, Rohit","last_name":"Singh","first_name":"Rohit"}],"year":"2015","publication":"Journal of the ACM","title":"Measuring and synthesizing systems in probabilistic environments","_id":"1856","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"3864"}]},"oa":1,"project":[{"call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","name":"Quantitative Reactive Modeling"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Game Theory","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"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 &gt; 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."}],"publication_status":"published"},{"year":"2015","day":"01","oa_version":"Preprint","type":"conference","date_updated":"2023-02-23T10:17:31Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"42E87FC6-F248-11E8-B48F-1D18A9856A87","full_name":"Pentina, Anastasia","last_name":"Pentina","first_name":"Anastasia"},{"full_name":"Sharmanska, Viktoriia","orcid":"0000-0003-0192-9308","id":"2EA6D09E-F248-11E8-B48F-1D18A9856A87","last_name":"Sharmanska","first_name":"Viktoriia"},{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","first_name":"Christoph","last_name":"Lampert"}],"quality_controlled":"1","citation":{"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.","ama":"Pentina A, Sharmanska V, Lampert C. Curriculum learning of multiple tasks. In: IEEE; 2015:5492-5500. doi:<a href=\"https://doi.org/10.1109/CVPR.2015.7299188\">10.1109/CVPR.2015.7299188</a>","short":"A. Pentina, V. Sharmanska, C. Lampert, in:, IEEE, 2015, pp. 5492–5500.","chicago":"Pentina, Anastasia, Viktoriia Sharmanska, and Christoph Lampert. “Curriculum Learning of Multiple Tasks,” 5492–5500. IEEE, 2015. <a href=\"https://doi.org/10.1109/CVPR.2015.7299188\">https://doi.org/10.1109/CVPR.2015.7299188</a>.","ista":"Pentina A, Sharmanska V, Lampert C. 2015. Curriculum learning of multiple tasks. CVPR: Computer Vision and Pattern Recognition, 5492–5500.","apa":"Pentina, A., Sharmanska, V., &#38; 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. <a href=\"https://doi.org/10.1109/CVPR.2015.7299188\">https://doi.org/10.1109/CVPR.2015.7299188</a>","mla":"Pentina, Anastasia, et al. <i>Curriculum Learning of Multiple Tasks</i>. IEEE, 2015, pp. 5492–500, doi:<a href=\"https://doi.org/10.1109/CVPR.2015.7299188\">10.1109/CVPR.2015.7299188</a>."},"main_file_link":[{"url":"http://arxiv.org/abs/1412.1353","open_access":"1"}],"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. "}],"publication_status":"published","_id":"1857","department":[{"_id":"ChLa"}],"doi":"10.1109/CVPR.2015.7299188","language":[{"iso":"eng"}],"oa":1,"title":"Curriculum learning of multiple tasks","publisher":"IEEE","page":"5492 - 5500","date_published":"2015-06-01T00:00:00Z","status":"public","month":"06","conference":{"name":"CVPR: Computer Vision and Pattern Recognition","end_date":"2015-06-12","start_date":"2015-06-07","location":"Boston, MA, United States"},"date_created":"2018-12-11T11:54:23Z","scopus_import":1,"publist_id":"5243"},{"page":"942 - 950","date_published":"2015-10-15T00:00:00Z","external_id":{"arxiv":["1406.5362"]},"publisher":"IEEE","publist_id":"5241","scopus_import":1,"status":"public","date_created":"2018-12-11T11:54:24Z","conference":{"location":"Boston, MA, United States","start_date":"2015-06-07","name":"CVPR: Computer Vision and Pattern Recognition","end_date":"2015-06-12"},"arxiv":1,"month":"10","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","author":[{"first_name":"Christoph","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph"}],"citation":{"mla":"Lampert, Christoph. <i>Predicting the Future Behavior of a Time-Varying Probability Distribution</i>. IEEE, 2015, pp. 942–50, doi:<a href=\"https://doi.org/10.1109/CVPR.2015.7298696\">10.1109/CVPR.2015.7298696</a>.","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. <a href=\"https://doi.org/10.1109/CVPR.2015.7298696\">https://doi.org/10.1109/CVPR.2015.7298696</a>","ama":"Lampert C. Predicting the future behavior of a time-varying probability distribution. In: IEEE; 2015:942-950. doi:<a href=\"https://doi.org/10.1109/CVPR.2015.7298696\">10.1109/CVPR.2015.7298696</a>","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.","chicago":"Lampert, Christoph. “Predicting the Future Behavior of a Time-Varying Probability Distribution,” 942–50. IEEE, 2015. <a href=\"https://doi.org/10.1109/CVPR.2015.7298696\">https://doi.org/10.1109/CVPR.2015.7298696</a>.","short":"C. Lampert, in:, IEEE, 2015, pp. 942–950.","ista":"Lampert C. 2015. Predicting the future behavior of a time-varying probability distribution. CVPR: Computer Vision and Pattern Recognition, 942–950."},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1406.5362"}],"day":"15","year":"2015","date_updated":"2021-01-12T06:53:40Z","type":"conference","oa_version":"Preprint","language":[{"iso":"eng"}],"doi":"10.1109/CVPR.2015.7298696","oa":1,"department":[{"_id":"ChLa"}],"_id":"1858","title":"Predicting the future behavior of a time-varying probability distribution","publication_status":"published","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."}]},{"publist_id":"5240","scopus_import":1,"date_created":"2018-12-11T11:54:24Z","month":"06","conference":{"end_date":"2015-06-12","name":"CVPR: Computer Vision and Pattern Recognition","start_date":"2015-06-07","location":"Boston, MA, USA"},"status":"public","date_published":"2015-06-01T00:00:00Z","page":"2737 - 2745","publisher":"IEEE","title":"A multi-plane block-coordinate Frank-Wolfe algorithm for training structural SVMs with a costly max-oracle","ec_funded":1,"language":[{"iso":"eng"}],"oa":1,"doi":"10.1109/CVPR.2015.7298890","department":[{"_id":"VlKo"},{"_id":"ChLa"}],"_id":"1859","project":[{"name":"Lifelong Learning of Visual Scene Understanding","grant_number":"308036","_id":"2532554C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"grant_number":"616160","name":"Discrete Optimization in Computer Vision: Theory and Practice","_id":"25FBA906-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"publication_status":"published","abstract":[{"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. ","lang":"eng"}],"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1408.6804"}],"citation":{"mla":"Shah, Neel, et al. <i>A Multi-Plane Block-Coordinate Frank-Wolfe Algorithm for Training Structural SVMs with a Costly Max-Oracle</i>. IEEE, 2015, pp. 2737–45, doi:<a href=\"https://doi.org/10.1109/CVPR.2015.7298890\">10.1109/CVPR.2015.7298890</a>.","apa":"Shah, N., Kolmogorov, V., &#38; 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. <a href=\"https://doi.org/10.1109/CVPR.2015.7298890\">https://doi.org/10.1109/CVPR.2015.7298890</a>","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.","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. <a href=\"https://doi.org/10.1109/CVPR.2015.7298890\">https://doi.org/10.1109/CVPR.2015.7298890</a>.","short":"N. Shah, V. Kolmogorov, C. Lampert, in:, IEEE, 2015, pp. 2737–2745.","ieee":"N. Shah, V. Kolmogorov, and C. Lampert, “A multi-plane block-coordinate Frank-Wolfe algorithm for training structural SVMs with a costly max-oracle,” presented at the CVPR: Computer Vision and Pattern Recognition, Boston, MA, USA, 2015, pp. 2737–2745.","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:<a href=\"https://doi.org/10.1109/CVPR.2015.7298890\">10.1109/CVPR.2015.7298890</a>"},"quality_controlled":"1","author":[{"full_name":"Shah, Neel","id":"31ABAF80-F248-11E8-B48F-1D18A9856A87","last_name":"Shah","first_name":"Neel"},{"full_name":"Kolmogorov, Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","last_name":"Kolmogorov","first_name":"Vladimir"},{"first_name":"Christoph","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"conference","date_updated":"2021-01-12T06:53:40Z","oa_version":"Preprint","day":"01","year":"2015"},{"page":"1401 - 1409","date_published":"2015-06-01T00:00:00Z","publisher":"IEEE","scopus_import":1,"publist_id":"5239","status":"public","month":"06","conference":{"name":"CVPR: Computer Vision and Pattern Recognition","end_date":"2015-06-12","start_date":"2015-06-07","location":"Boston, MA, United States"},"date_created":"2018-12-11T11:54:24Z","author":[{"last_name":"Royer","first_name":"Amélie","full_name":"Royer, Amélie"},{"last_name":"Lampert","first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887"}],"quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"open_access":"1","url":"http://www.cv-foundation.org/openaccess/content_cvpr_2015/papers/Royer_Classifier_Adaptation_at_2015_CVPR_paper.pdf"}],"citation":{"ama":"Royer A, Lampert C. Classifier adaptation at prediction time. In: IEEE; 2015:1401-1409. doi:<a href=\"https://doi.org/10.1109/CVPR.2015.7298746\">10.1109/CVPR.2015.7298746</a>","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.","short":"A. Royer, C. Lampert, in:, IEEE, 2015, pp. 1401–1409.","chicago":"Royer, Amélie, and Christoph Lampert. “Classifier Adaptation at Prediction Time,” 1401–9. IEEE, 2015. <a href=\"https://doi.org/10.1109/CVPR.2015.7298746\">https://doi.org/10.1109/CVPR.2015.7298746</a>.","ista":"Royer A, Lampert C. 2015. Classifier adaptation at prediction time. CVPR: Computer Vision and Pattern Recognition, 1401–1409.","apa":"Royer, A., &#38; 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. <a href=\"https://doi.org/10.1109/CVPR.2015.7298746\">https://doi.org/10.1109/CVPR.2015.7298746</a>","mla":"Royer, Amélie, and Christoph Lampert. <i>Classifier Adaptation at Prediction Time</i>. IEEE, 2015, pp. 1401–09, doi:<a href=\"https://doi.org/10.1109/CVPR.2015.7298746\">10.1109/CVPR.2015.7298746</a>."},"year":"2015","day":"01","oa_version":"Submitted Version","date_updated":"2021-01-12T06:53:41Z","type":"conference","_id":"1860","department":[{"_id":"ChLa"}],"doi":"10.1109/CVPR.2015.7298746","language":[{"iso":"eng"}],"oa":1,"title":"Classifier adaptation at prediction time","ec_funded":1,"abstract":[{"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.","lang":"eng"}],"publication_status":"published","project":[{"grant_number":"308036","name":"Lifelong Learning of Visual Scene Understanding","_id":"2532554C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}]},{"citation":{"apa":"Ruess, J., &#38; Lygeros, J. (2015). Moment-based methods for parameter inference and experiment design for stochastic biochemical reaction networks. <i>ACM Transactions on Modeling and Computer Simulation</i>. ACM. <a href=\"https://doi.org/10.1145/2688906\">https://doi.org/10.1145/2688906</a>","mla":"Ruess, Jakob, and John Lygeros. “Moment-Based Methods for Parameter Inference and Experiment Design for Stochastic Biochemical Reaction Networks.” <i>ACM Transactions on Modeling and Computer Simulation</i>, vol. 25, no. 2, 8, ACM, 2015, doi:<a href=\"https://doi.org/10.1145/2688906\">10.1145/2688906</a>.","chicago":"Ruess, Jakob, and John Lygeros. “Moment-Based Methods for Parameter Inference and Experiment Design for Stochastic Biochemical Reaction Networks.” <i>ACM Transactions on Modeling and Computer Simulation</i>. ACM, 2015. <a href=\"https://doi.org/10.1145/2688906\">https://doi.org/10.1145/2688906</a>.","short":"J. Ruess, J. Lygeros, ACM Transactions on Modeling and Computer Simulation 25 (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.","ieee":"J. Ruess and J. Lygeros, “Moment-based methods for parameter inference and experiment design for stochastic biochemical reaction networks,” <i>ACM Transactions on Modeling and Computer Simulation</i>, vol. 25, no. 2. ACM, 2015.","ama":"Ruess J, Lygeros J. Moment-based methods for parameter inference and experiment design for stochastic biochemical reaction networks. <i>ACM Transactions on Modeling and Computer Simulation</i>. 2015;25(2). doi:<a href=\"https://doi.org/10.1145/2688906\">10.1145/2688906</a>"},"author":[{"full_name":"Ruess, Jakob","orcid":"0000-0003-1615-3282","id":"4A245D00-F248-11E8-B48F-1D18A9856A87","first_name":"Jakob","last_name":"Ruess"},{"last_name":"Lygeros","first_name":"John","full_name":"Lygeros, John"}],"quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","type":"journal_article","date_updated":"2021-01-12T06:53:41Z","year":"2015","day":"01","title":"Moment-based methods for parameter inference and experiment design for stochastic biochemical reaction networks","publication":"ACM Transactions on Modeling and Computer Simulation","department":[{"_id":"ToHe"},{"_id":"GaTk"}],"_id":"1861","language":[{"iso":"eng"}],"doi":"10.1145/2688906","acknowledgement":"HYCON2; EC; European Commission\r\n","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."}],"publication_status":"published","date_published":"2015-02-01T00:00:00Z","issue":"2","volume":25,"publisher":"ACM","intvolume":"        25","scopus_import":1,"publist_id":"5238","month":"02","date_created":"2018-12-11T11:54:25Z","article_number":"8","status":"public"},{"publication_status":"published","abstract":[{"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","lang":"eng"}],"project":[{"grant_number":"338804","name":"Random matrices, universality and disordered quantum systems","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"oa":1,"_id":"1864","publication":"Annales Henri Poincare","title":"The Altshuler–Shklovskii formulas for random band matrices II: The general case","year":"2015","author":[{"last_name":"Erdös","first_name":"László","full_name":"Erdös, László","orcid":"0000-0001-5366-9603","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Knowles, Antti","last_name":"Knowles","first_name":"Antti"}],"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1309.5107"}],"citation":{"chicago":"Erdös, László, and Antti Knowles. “The Altshuler–Shklovskii Formulas for Random Band Matrices II: The General Case.” <i>Annales Henri Poincare</i>. Springer, 2015. <a href=\"https://doi.org/10.1007/s00023-014-0333-5\">https://doi.org/10.1007/s00023-014-0333-5</a>.","short":"L. Erdös, A. Knowles, Annales Henri Poincare 16 (2015) 709–799.","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.","ama":"Erdös L, Knowles A. The Altshuler–Shklovskii formulas for random band matrices II: The general case. <i>Annales Henri Poincare</i>. 2015;16(3):709-799. doi:<a href=\"https://doi.org/10.1007/s00023-014-0333-5\">10.1007/s00023-014-0333-5</a>","ieee":"L. Erdös and A. Knowles, “The Altshuler–Shklovskii formulas for random band matrices II: The general case,” <i>Annales Henri Poincare</i>, vol. 16, no. 3. Springer, pp. 709–799, 2015.","apa":"Erdös, L., &#38; Knowles, A. (2015). The Altshuler–Shklovskii formulas for random band matrices II: The general case. <i>Annales Henri Poincare</i>. Springer. <a href=\"https://doi.org/10.1007/s00023-014-0333-5\">https://doi.org/10.1007/s00023-014-0333-5</a>","mla":"Erdös, László, and Antti Knowles. “The Altshuler–Shklovskii Formulas for Random Band Matrices II: The General Case.” <i>Annales Henri Poincare</i>, vol. 16, no. 3, Springer, 2015, pp. 709–99, doi:<a href=\"https://doi.org/10.1007/s00023-014-0333-5\">10.1007/s00023-014-0333-5</a>."},"status":"public","date_created":"2018-12-11T11:54:26Z","month":"03","publist_id":"5233","intvolume":"        16","publisher":"Springer","volume":16,"issue":"3","doi":"10.1007/s00023-014-0333-5","language":[{"iso":"eng"}],"department":[{"_id":"LaEr"}],"ec_funded":1,"day":"01","type":"journal_article","date_updated":"2021-01-12T06:53:42Z","oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":1,"page":"709 - 799","date_published":"2015-03-01T00:00:00Z"},{"citation":{"mla":"Robert, Hélène, et al. “Plant Embryogenesis Requires AUX/LAX-Mediated Auxin Influx.” <i>Development</i>, vol. 142, no. 4, Company of Biologists, 2015, pp. 702–11, doi:<a href=\"https://doi.org/10.1242/dev.115832\">10.1242/dev.115832</a>.","apa":"Robert, H., Grunewald, W., Sauer, M., Cannoot, B., Soriano, M., Swarup, R., … Friml, J. (2015). Plant embryogenesis requires AUX/LAX-mediated auxin influx. <i>Development</i>. Company of Biologists. <a href=\"https://doi.org/10.1242/dev.115832\">https://doi.org/10.1242/dev.115832</a>","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.","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.","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.” <i>Development</i>. Company of Biologists, 2015. <a href=\"https://doi.org/10.1242/dev.115832\">https://doi.org/10.1242/dev.115832</a>.","ieee":"H. Robert <i>et al.</i>, “Plant embryogenesis requires AUX/LAX-mediated auxin influx,” <i>Development</i>, vol. 142, no. 4. Company of Biologists, pp. 702–711, 2015.","ama":"Robert H, Grunewald W, Sauer M, et al. Plant embryogenesis requires AUX/LAX-mediated auxin influx. <i>Development</i>. 2015;142(4):702-711. doi:<a href=\"https://doi.org/10.1242/dev.115832\">10.1242/dev.115832</a>"},"quality_controlled":"1","author":[{"full_name":"Robert, Hélène","first_name":"Hélène","last_name":"Robert"},{"full_name":"Grunewald, Wim","first_name":"Wim","last_name":"Grunewald"},{"full_name":"Sauer, Michael","last_name":"Sauer","first_name":"Michael"},{"full_name":"Cannoot, Bernard","last_name":"Cannoot","first_name":"Bernard"},{"first_name":"Mercedes","last_name":"Soriano","full_name":"Soriano, Mercedes"},{"full_name":"Swarup, Ranjan","last_name":"Swarup","first_name":"Ranjan"},{"last_name":"Weijers","first_name":"Dolf","full_name":"Weijers, Dolf"},{"full_name":"Bennett, Malcolm","last_name":"Bennett","first_name":"Malcolm"},{"full_name":"Boutilier, Kim","first_name":"Kim","last_name":"Boutilier"},{"last_name":"Friml","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí"}],"year":"2015","publication":"Development","title":"Plant embryogenesis requires AUX/LAX-mediated auxin influx","_id":"1865","project":[{"_id":"25716A02-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"282300","name":"Polarity and subcellular dynamics in plants"}],"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."}],"publication_status":"published","issue":"4","volume":142,"publisher":"Company of Biologists","intvolume":"       142","publist_id":"5231","month":"02","date_created":"2018-12-11T11:54:26Z","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","type":"journal_article","date_updated":"2021-01-12T06:53:43Z","day":"15","ec_funded":1,"department":[{"_id":"JiFr"}],"doi":"10.1242/dev.115832","language":[{"iso":"eng"}],"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","date_published":"2015-02-15T00:00:00Z","page":"702 - 711","scopus_import":1},{"_id":"1866","department":[{"_id":"ToHe"}],"doi":"10.1145/2701001","language":[{"iso":"eng"}],"publication":"Communications of the ACM","title":"The equivalence problem for finite automata: Technical perspective","publication_status":"published","author":[{"full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger"},{"full_name":"Raskin, Jean","first_name":"Jean","last_name":"Raskin"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Henzinger TA, Raskin J. The equivalence problem for finite automata: Technical perspective. <i>Communications of the ACM</i>. 2015;58(2):86-86. doi:<a href=\"https://doi.org/10.1145/2701001\">10.1145/2701001</a>","ieee":"T. A. Henzinger and J. Raskin, “The equivalence problem for finite automata: Technical perspective,” <i>Communications of the ACM</i>, vol. 58, no. 2. ACM, pp. 86–86, 2015.","short":"T.A. Henzinger, J. Raskin, Communications of the ACM 58 (2015) 86–86.","chicago":"Henzinger, Thomas A, and Jean Raskin. “The Equivalence Problem for Finite Automata: Technical Perspective.” <i>Communications of the ACM</i>. ACM, 2015. <a href=\"https://doi.org/10.1145/2701001\">https://doi.org/10.1145/2701001</a>.","ista":"Henzinger TA, Raskin J. 2015. The equivalence problem for finite automata: Technical perspective. Communications of the ACM. 58(2), 86–86.","apa":"Henzinger, T. A., &#38; Raskin, J. (2015). The equivalence problem for finite automata: Technical perspective. <i>Communications of the ACM</i>. ACM. <a href=\"https://doi.org/10.1145/2701001\">https://doi.org/10.1145/2701001</a>","mla":"Henzinger, Thomas A., and Jean Raskin. “The Equivalence Problem for Finite Automata: Technical Perspective.” <i>Communications of the ACM</i>, vol. 58, no. 2, ACM, 2015, pp. 86–86, doi:<a href=\"https://doi.org/10.1145/2701001\">10.1145/2701001</a>."},"year":"2015","day":"28","oa_version":"None","date_updated":"2021-01-12T06:53:43Z","type":"journal_article","scopus_import":1,"publist_id":"5232","intvolume":"        58","status":"public","month":"01","date_created":"2018-12-11T11:54:26Z","page":"86-86","volume":58,"issue":"2","date_published":"2015-01-28T00:00:00Z","publisher":"ACM"}]