[{"oa_version":"Submitted Version","month":"08","has_accepted_license":"1","conference":{"name":"ACSD: Application of Concurrency to System Design"},"language":[{"iso":"eng"}],"oa":1,"publist_id":"1069","date_published":"2010-08-23T00:00:00Z","type":"conference","file":[{"date_created":"2018-12-12T10:09:10Z","checksum":"42b2952bfc6b6974617bd554842b904a","file_size":159920,"date_updated":"2020-07-14T12:46:28Z","file_name":"IST-2012-44-v1+1_Robustness_of_sequential_circuits.pdf","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"4733","creator":"system"}],"status":"public","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publication_status":"published","department":[{"_id":"ToHe"}],"date_created":"2018-12-11T12:08:36Z","pubrep_id":"44","title":"Robustness of sequential circuits","_id":"4389","scopus_import":1,"author":[{"full_name":"Doyen, Laurent","first_name":"Laurent","last_name":"Doyen"},{"last_name":"Henzinger","first_name":"Thomas A","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Legay, Axel","first_name":"Axel","last_name":"Legay"},{"id":"41BCEE5C-F248-11E8-B48F-1D18A9856A87","full_name":"Nickovic, Dejan","last_name":"Nickovic","first_name":"Dejan"}],"publisher":"IEEE","page":"77 - 84","quality_controlled":"1","file_date_updated":"2020-07-14T12:46:28Z","doi":"10.1109/ACSD.2010.26","day":"23","abstract":[{"lang":"eng","text":"Digital components play a central role in the design of complex embedded systems. These components are interconnected with other, possibly analog, devices and the physical environment. This environment cannot be entirely captured and can provide inaccurate input data to the component. It is thus important for digital components to have a robust behavior, i.e. the presence of a small change in the input sequences should not result in a drastic change in the output sequences. In this paper, we study a notion of robustness for sequential circuits. However, since sequential circuits may have parts that are naturally discontinuous (e.g., digital controllers with switching behavior), we need a flexible framework that accommodates this fact and leaves discontinuous parts of the circuit out from the robustness analysis. As a consequence, we consider sequential circuits that have their input variables partitioned into two disjoint sets: control and disturbance variables. Our contributions are (1) a definition of robustness for sequential circuits as a form of continuity with respect to disturbance variables, (2) the characterization of the exact class of sequential circuits that are robust according to our definition, (3) an algorithm to decide whether a sequential circuit is robust or not."}],"date_updated":"2021-01-12T07:56:36Z","citation":{"mla":"Doyen, Laurent, et al. <i>Robustness of Sequential Circuits</i>. IEEE, 2010, pp. 77–84, doi:<a href=\"https://doi.org/10.1109/ACSD.2010.26\">10.1109/ACSD.2010.26</a>.","short":"L. Doyen, T.A. Henzinger, A. Legay, D. Nickovic, in:, IEEE, 2010, pp. 77–84.","ista":"Doyen L, Henzinger TA, Legay A, Nickovic D. 2010. Robustness of sequential circuits. ACSD: Application of Concurrency to System Design, 77–84.","apa":"Doyen, L., Henzinger, T. A., Legay, A., &#38; Nickovic, D. (2010). Robustness of sequential circuits (pp. 77–84). Presented at the ACSD: Application of Concurrency to System Design, IEEE. <a href=\"https://doi.org/10.1109/ACSD.2010.26\">https://doi.org/10.1109/ACSD.2010.26</a>","ama":"Doyen L, Henzinger TA, Legay A, Nickovic D. Robustness of sequential circuits. In: IEEE; 2010:77-84. doi:<a href=\"https://doi.org/10.1109/ACSD.2010.26\">10.1109/ACSD.2010.26</a>","chicago":"Doyen, Laurent, Thomas A Henzinger, Axel Legay, and Dejan Nickovic. “Robustness of Sequential Circuits,” 77–84. IEEE, 2010. <a href=\"https://doi.org/10.1109/ACSD.2010.26\">https://doi.org/10.1109/ACSD.2010.26</a>.","ieee":"L. Doyen, T. A. Henzinger, A. Legay, and D. Nickovic, “Robustness of sequential circuits,” presented at the ACSD: Application of Concurrency to System Design, 2010, pp. 77–84."},"year":"2010","ddc":["004"]},{"language":[{"iso":"eng"}],"conference":{"start_date":"2010-07-15","name":"CAV: Computer Aided Verification","end_date":"2010-07-17","location":"Edinburgh, UK"},"has_accepted_license":"1","oa_version":"Submitted Version","month":"07","file":[{"relation":"main_file","access_level":"open_access","file_id":"7873","creator":"dernst","date_created":"2020-05-19T16:31:56Z","file_size":3633276,"checksum":"2eb211ce40b3c4988bce3a3592980704","date_updated":"2020-07-14T12:46:28Z","content_type":"application/pdf","file_name":"2010_CAV_Cerny.pdf"}],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"relation":"earlier_version","id":"5391","status":"public"}]},"date_published":"2010-07-01T00:00:00Z","type":"conference","publist_id":"1066","oa":1,"page":"465 - 479","quality_controlled":"1","file_date_updated":"2020-07-14T12:46:28Z","publisher":"Springer","_id":"4390","author":[{"id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87","full_name":"Cerny, Pavol","last_name":"Cerny","first_name":"Pavol"},{"id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87","first_name":"Arjun","last_name":"Radhakrishna","full_name":"Radhakrishna, Arjun"},{"id":"4397AC76-F248-11E8-B48F-1D18A9856A87","last_name":"Zufferey","first_name":"Damien","full_name":"Zufferey, Damien","orcid":"0000-0002-3197-8736"},{"last_name":"Chaudhuri","first_name":"Swarat","full_name":"Chaudhuri, Swarat"},{"last_name":"Alur","first_name":"Rajeev","full_name":"Alur, Rajeev"}],"publication_status":"published","date_created":"2018-12-11T12:08:36Z","department":[{"_id":"ToHe"}],"article_processing_charge":"No","title":"Model checking of linearizability of concurrent list implementations","pubrep_id":"27","alternative_title":["LNCS"],"intvolume":"      6174","volume":6174,"ddc":["000"],"date_updated":"2023-02-23T12:24:12Z","citation":{"short":"P. Cerny, A. Radhakrishna, D. Zufferey, S. Chaudhuri, R. Alur, in:, Springer, 2010, pp. 465–479.","mla":"Cerny, Pavol, et al. <i>Model Checking of Linearizability of Concurrent List Implementations</i>. Vol. 6174, Springer, 2010, pp. 465–79, doi:<a href=\"https://doi.org/10.1007/978-3-642-14295-6_41\">10.1007/978-3-642-14295-6_41</a>.","ista":"Cerny P, Radhakrishna A, Zufferey D, Chaudhuri S, Alur R. 2010. Model checking of linearizability of concurrent list implementations. CAV: Computer Aided Verification, LNCS, vol. 6174, 465–479.","ama":"Cerny P, Radhakrishna A, Zufferey D, Chaudhuri S, Alur R. Model checking of linearizability of concurrent list implementations. In: Vol 6174. Springer; 2010:465-479. doi:<a href=\"https://doi.org/10.1007/978-3-642-14295-6_41\">10.1007/978-3-642-14295-6_41</a>","apa":"Cerny, P., Radhakrishna, A., Zufferey, D., Chaudhuri, S., &#38; Alur, R. (2010). Model checking of linearizability of concurrent list implementations (Vol. 6174, pp. 465–479). Presented at the CAV: Computer Aided Verification, Edinburgh, UK: Springer. <a href=\"https://doi.org/10.1007/978-3-642-14295-6_41\">https://doi.org/10.1007/978-3-642-14295-6_41</a>","ieee":"P. Cerny, A. Radhakrishna, D. Zufferey, S. Chaudhuri, and R. Alur, “Model checking of linearizability of concurrent list implementations,” presented at the CAV: Computer Aided Verification, Edinburgh, UK, 2010, vol. 6174, pp. 465–479.","chicago":"Cerny, Pavol, Arjun Radhakrishna, Damien Zufferey, Swarat Chaudhuri, and Rajeev Alur. “Model Checking of Linearizability of Concurrent List Implementations,” 6174:465–79. Springer, 2010. <a href=\"https://doi.org/10.1007/978-3-642-14295-6_41\">https://doi.org/10.1007/978-3-642-14295-6_41</a>."},"year":"2010","doi":"10.1007/978-3-642-14295-6_41","day":"01","abstract":[{"text":"Concurrent data structures with fine-grained synchronization are notoriously difficult to implement correctly. The difficulty of reasoning about these implementations does not stem from the number of variables or the program size, but rather from the large number of possible interleavings. These implementations are therefore prime candidates for model checking. We introduce an algorithm for verifying linearizability of singly-linked heap-based concurrent data structures. We consider a model consisting of an unbounded heap where each vertex stores an element from an unbounded data domain, with a restricted set of operations for testing and updating pointers and data elements. Our main result is that linearizability is decidable for programs that invoke a fixed number of methods, possibly in parallel. This decidable fragment covers many of the common implementation techniques — fine-grained locking, lazy synchronization, and lock-free synchronization. We also show how the technique can be used to verify optimistic implementations with the help of programmer annotations. We developed a verification tool CoLT and evaluated it on a representative sample of Java implementations of the concurrent set data structure. The tool verified linearizability of a number of implementations, found a known error in a lock-free implementation and proved that the corrected version is linearizable.","lang":"eng"}]},{"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","status":"public","date_published":"2010-07-29T00:00:00Z","type":"book_chapter","publist_id":"1064","language":[{"iso":"eng"}],"publication":"Time For Verification: Essays in Memory of Amir Pnueli","oa_version":"None","project":[{"grant_number":"215543","name":"COMponent-Based Embedded Systems design Techniques","call_identifier":"FP7","_id":"25EFB36C-B435-11E9-9278-68D0E5697425"},{"grant_number":"214373","name":"Design for Embedded Systems","_id":"25F1337C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"month":"07","volume":6200,"date_updated":"2021-01-12T07:56:38Z","year":"2010","citation":{"ista":"Cerny P, Henzinger TA, Radhakrishna A. 2010.Quantitative Simulation Games. In: Time For Verification: Essays in Memory of Amir Pnueli. LNCS, vol. 6200, 42–60.","short":"P. Cerny, T.A. Henzinger, A. Radhakrishna, in:, Z. Manna, D. Peled (Eds.), Time For Verification: Essays in Memory of Amir Pnueli, Springer, 2010, pp. 42–60.","mla":"Cerny, Pavol, et al. “Quantitative Simulation Games.” <i>Time For Verification: Essays in Memory of Amir Pnueli</i>, edited by Zohar Manna and Doron Peled, vol. 6200, Springer, 2010, pp. 42–60, doi:<a href=\"https://doi.org/10.1007/978-3-642-13754-9_3\">10.1007/978-3-642-13754-9_3</a>.","ieee":"P. Cerny, T. A. Henzinger, and A. Radhakrishna, “Quantitative Simulation Games,” in <i>Time For Verification: Essays in Memory of Amir Pnueli</i>, vol. 6200, Z. Manna and D. Peled, Eds. Springer, 2010, pp. 42–60.","chicago":"Cerny, Pavol, Thomas A Henzinger, and Arjun Radhakrishna. “Quantitative Simulation Games.” In <i>Time For Verification: Essays in Memory of Amir Pnueli</i>, edited by Zohar Manna and Doron Peled, 6200:42–60. Essays in Memory of Amir Pnueli. Springer, 2010. <a href=\"https://doi.org/10.1007/978-3-642-13754-9_3\">https://doi.org/10.1007/978-3-642-13754-9_3</a>.","apa":"Cerny, P., Henzinger, T. A., &#38; Radhakrishna, A. (2010). Quantitative Simulation Games. In Z. Manna &#38; D. Peled (Eds.), <i>Time For Verification: Essays in Memory of Amir Pnueli</i> (Vol. 6200, pp. 42–60). Springer. <a href=\"https://doi.org/10.1007/978-3-642-13754-9_3\">https://doi.org/10.1007/978-3-642-13754-9_3</a>","ama":"Cerny P, Henzinger TA, Radhakrishna A. Quantitative Simulation Games. In: Manna Z, Peled D, eds. <i>Time For Verification: Essays in Memory of Amir Pnueli</i>. Vol 6200. Essays in Memory of Amir Pnueli. Springer; 2010:42-60. doi:<a href=\"https://doi.org/10.1007/978-3-642-13754-9_3\">10.1007/978-3-642-13754-9_3</a>"},"doi":"10.1007/978-3-642-13754-9_3","day":"29","abstract":[{"text":"While a boolean notion of correctness is given by a preorder on systems and properties, a quantitative notion of correctness is defined by a distance function on systems and properties, where the distance between a system and a property provides a measure of “fit” or “desirability.” In this article, we explore several ways how the simulation preorder can be generalized to a distance function. This is done by equipping the classical simulation game between a system and a property with quantitative objectives. In particular, for systems that satisfy a property, a quantitative simulation game can measure the “robustness” of the satisfaction, that is, how much the system can deviate from its nominal behavior while still satisfying the property. For systems that violate a property, a quantitative simulation game can measure the “seriousness” of the violation, that is, how much the property has to be modified so that it is satisfied by the system. These distances can be computed in polynomial time, since the computation reduces to the value problem in limit average games with constant weights. Finally, we demonstrate how the robustness distance can be used to measure how many transmission errors are tolerated by error correcting codes. ","lang":"eng"}],"page":"42 - 60","quality_controlled":"1","series_title":"Essays in Memory of Amir Pnueli","ec_funded":1,"publisher":"Springer","editor":[{"full_name":"Manna, Zohar","first_name":"Zohar","last_name":"Manna"},{"full_name":"Peled, Doron","last_name":"Peled","first_name":"Doron"}],"_id":"4392","scopus_import":1,"author":[{"full_name":"Cerny, Pavol","last_name":"Cerny","first_name":"Pavol","id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","first_name":"Thomas A","last_name":"Henzinger"},{"first_name":"Arjun","last_name":"Radhakrishna","full_name":"Radhakrishna, Arjun","id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","date_created":"2018-12-11T12:08:37Z","department":[{"_id":"ToHe"}],"alternative_title":["LNCS"],"title":"Quantitative Simulation Games","intvolume":"      6200"},{"date_created":"2018-12-11T12:08:37Z","department":[{"_id":"ToHe"}],"publication_status":"published","intvolume":"      6269","title":"Simulation distances","pubrep_id":"42","alternative_title":["LNCS"],"scopus_import":1,"_id":"4393","author":[{"last_name":"Cerny","first_name":"Pavol","full_name":"Cerny, Pavol","id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger","first_name":"Thomas A"},{"id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87","full_name":"Radhakrishna, Arjun","first_name":"Arjun","last_name":"Radhakrishna"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","quality_controlled":"1","ec_funded":1,"page":"235 - 268","file_date_updated":"2020-07-14T12:46:28Z","day":"01","doi":"10.1007/978-3-642-15375-4_18","abstract":[{"text":"Boolean notions of correctness are formalized by preorders on systems. Quantitative measures of correctness can be formalized by real-valued distance functions between systems, where the distance between implementation and specification provides a measure of “fit” or “desirability.” We extend the simulation preorder to the quantitative setting, by making each player of a simulation game pay a certain price for her choices. We use the resulting games with quantitative objectives to define three different simulation distances. The correctness distance measures how much the specification must be changed in order to be satisfied by the implementation. The coverage distance measures how much the implementation restricts the degrees of freedom offered by the specification. The robustness distance measures how much a system can deviate from the implementation description without violating the specification. We consider these distances for safety as well as liveness specifications. The distances can be computed in polynomial time for safety specifications, and for liveness specifications given by weak fairness constraints. We show that the distance functions satisfy the triangle inequality, that the distance between two systems does not increase under parallel composition with a third system, and that the distance between two systems can be bounded from above and below by distances between abstractions of the two systems. These properties suggest that our simulation distances provide an appropriate basis for a quantitative theory of discrete systems. We also demonstrate how the robustness distance can be used to measure how many transmission errors are tolerated by error correcting codes.","lang":"eng"}],"citation":{"ista":"Cerny P, Henzinger TA, Radhakrishna A. 2010. Simulation distances. CONCUR: Concurrency Theory, LNCS, vol. 6269, 235–268.","mla":"Cerny, Pavol, et al. <i>Simulation Distances</i>. Vol. 6269, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2010, pp. 235–68, doi:<a href=\"https://doi.org/10.1007/978-3-642-15375-4_18\">10.1007/978-3-642-15375-4_18</a>.","short":"P. Cerny, T.A. Henzinger, A. Radhakrishna, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2010, pp. 235–268.","ieee":"P. Cerny, T. A. Henzinger, and A. Radhakrishna, “Simulation distances,” presented at the CONCUR: Concurrency Theory, Paris, France, 2010, vol. 6269, pp. 235–268.","chicago":"Cerny, Pavol, Thomas A Henzinger, and Arjun Radhakrishna. “Simulation Distances,” 6269:235–68. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2010. <a href=\"https://doi.org/10.1007/978-3-642-15375-4_18\">https://doi.org/10.1007/978-3-642-15375-4_18</a>.","apa":"Cerny, P., Henzinger, T. A., &#38; Radhakrishna, A. (2010). Simulation distances (Vol. 6269, pp. 235–268). 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_18\">https://doi.org/10.1007/978-3-642-15375-4_18</a>","ama":"Cerny P, Henzinger TA, Radhakrishna A. Simulation distances. In: Vol 6269. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2010:235-268. doi:<a href=\"https://doi.org/10.1007/978-3-642-15375-4_18\">10.1007/978-3-642-15375-4_18</a>"},"year":"2010","date_updated":"2023-02-23T12:24:04Z","volume":6269,"acknowledgement":"This work was partially supported by the European Union project COMBEST and the European Network of Excellence ArtistDesign.","ddc":["005"],"project":[{"name":"COMponent-Based Embedded Systems design Techniques","grant_number":"215543","_id":"25EFB36C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"grant_number":"214373","name":"Design for Embedded Systems","call_identifier":"FP7","_id":"25F1337C-B435-11E9-9278-68D0E5697425"}],"oa_version":"Submitted Version","month":"11","has_accepted_license":"1","conference":{"name":"CONCUR: Concurrency Theory","start_date":"2010-08-31","location":"Paris, France","end_date":"2010-09-03"},"language":[{"iso":"eng"}],"oa":1,"publist_id":"1065","type":"conference","date_published":"2010-11-01T00:00:00Z","file":[{"relation":"main_file","access_level":"open_access","file_id":"5130","creator":"system","date_created":"2018-12-12T10:15:12Z","checksum":"ea567903676ba8afe0507ee11313dce5","file_size":198913,"date_updated":"2020-07-14T12:46:28Z","file_name":"IST-2012-42-v1+1_Simulation_distances.pdf","content_type":"application/pdf"}],"related_material":{"record":[{"status":"public","relation":"later_version","id":"3249"},{"status":"public","id":"5389","relation":"earlier_version"}]},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","status":"public"},{"oa":1,"publist_id":"1061","type":"conference","date_published":"2010-04-21T00:00:00Z","file":[{"file_size":312147,"checksum":"7d26e59a9681487d7283eba337292b2c","date_created":"2018-12-12T10:18:13Z","file_name":"IST-2012-41-v1+1_Shape_refinement_through_explicit_heap_analysis.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:46:29Z","relation":"main_file","access_level":"open_access","creator":"system","file_id":"5332"}],"status":"public","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","project":[{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"oa_version":"Submitted Version","month":"04","has_accepted_license":"1","conference":{"location":"Paphos, Cyprus","end_date":"2010-03-28","start_date":"2010-03-20","name":"FASE: Fundamental Approaches To Software Engineering"},"language":[{"iso":"eng"}],"day":"21","doi":"10.1007/978-3-642-12029-9_19","abstract":[{"text":"Shape analysis is a promising technique to prove program properties about recursive data structures. The challenge is to automatically determine the data-structure type, and to supply the shape analysis with the necessary information about the data structure. We present a stepwise approach to the selection of instrumentation predicates for a TVLA-based shape analysis, which takes us a step closer towards the fully automatic verification of data structures. The approach uses two techniques to guide the refinement of shape abstractions: (1) during program exploration, an explicit heap analysis collects sample instances of the heap structures, which are used to identify the data structures that are manipulated by the program; and (2) during abstraction refinement along an infeasible error path, we consider different possible heap abstractions and choose the coarsest one that eliminates the infeasible path. We have implemented this combined approach for automatic shape refinement as an extension of the software model checker BLAST. Example programs from a data-structure library that manipulate doubly-linked lists and trees were successfully verified by our tool.","lang":"eng"}],"year":"2010","citation":{"ieee":"D. Beyer, T. A. Henzinger, G. Théoduloz, and D. Zufferey, “Shape refinement through explicit heap analysis,” presented at the FASE: Fundamental Approaches To Software Engineering, Paphos, Cyprus, 2010, vol. 6013, pp. 263–277.","chicago":"Beyer, Dirk, Thomas A Henzinger, Grégory Théoduloz, and Damien Zufferey. “Shape Refinement through Explicit Heap Analysis.” edited by David Rosenblum and Gabriele Taenzer, 6013:263–77. Springer, 2010. <a href=\"https://doi.org/10.1007/978-3-642-12029-9_19\">https://doi.org/10.1007/978-3-642-12029-9_19</a>.","ama":"Beyer D, Henzinger TA, Théoduloz G, Zufferey D. Shape refinement through explicit heap analysis. In: Rosenblum D, Taenzer G, eds. Vol 6013. Springer; 2010:263-277. doi:<a href=\"https://doi.org/10.1007/978-3-642-12029-9_19\">10.1007/978-3-642-12029-9_19</a>","apa":"Beyer, D., Henzinger, T. A., Théoduloz, G., &#38; Zufferey, D. (2010). Shape refinement through explicit heap analysis. In D. Rosenblum &#38; G. Taenzer (Eds.) (Vol. 6013, pp. 263–277). Presented at the FASE: Fundamental Approaches To Software Engineering, Paphos, Cyprus: Springer. <a href=\"https://doi.org/10.1007/978-3-642-12029-9_19\">https://doi.org/10.1007/978-3-642-12029-9_19</a>","ista":"Beyer D, Henzinger TA, Théoduloz G, Zufferey D. 2010. Shape refinement through explicit heap analysis. FASE: Fundamental Approaches To Software Engineering, LNCS, vol. 6013, 263–277.","short":"D. Beyer, T.A. Henzinger, G. Théoduloz, D. Zufferey, in:, D. Rosenblum, G. Taenzer (Eds.), Springer, 2010, pp. 263–277.","mla":"Beyer, Dirk, et al. <i>Shape Refinement through Explicit Heap Analysis</i>. Edited by David Rosenblum and Gabriele Taenzer, vol. 6013, Springer, 2010, pp. 263–77, doi:<a href=\"https://doi.org/10.1007/978-3-642-12029-9_19\">10.1007/978-3-642-12029-9_19</a>."},"date_updated":"2021-01-12T07:56:40Z","volume":6013,"ddc":["004"],"date_created":"2018-12-11T12:08:38Z","department":[{"_id":"ToHe"}],"publication_status":"published","intvolume":"      6013","title":"Shape refinement through explicit heap analysis","alternative_title":["LNCS"],"pubrep_id":"41","scopus_import":1,"_id":"4396","author":[{"first_name":"Dirk","last_name":"Beyer","full_name":"Beyer, Dirk"},{"last_name":"Henzinger","first_name":"Thomas A","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Théoduloz","first_name":"Grégory","full_name":"Théoduloz, Grégory"},{"last_name":"Zufferey","first_name":"Damien","full_name":"Zufferey, Damien","orcid":"0000-0002-3197-8736","id":"4397AC76-F248-11E8-B48F-1D18A9856A87"}],"editor":[{"first_name":"David","last_name":"Rosenblum","full_name":"Rosenblum, David"},{"first_name":"Gabriele","last_name":"Taenzer","full_name":"Taenzer, Gabriele"}],"publisher":"Springer","quality_controlled":"1","page":"263 - 277","file_date_updated":"2020-07-14T12:46:29Z"},{"publisher":"Springer","page":"140 - 156","ec_funded":1,"quality_controlled":"1","alternative_title":["LNCS"],"title":"Better quality in synthesis through quantitative objectives","intvolume":"      5643","publication_status":"published","date_created":"2018-12-11T12:09:31Z","department":[{"_id":"KrCh"}],"author":[{"first_name":"Roderick","last_name":"Bloem","full_name":"Bloem, Roderick"},{"first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Henzinger","first_name":"Thomas A","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Barbara","last_name":"Jobstmann","full_name":"Jobstmann, Barbara"}],"_id":"4569","acknowledgement":"This research was supported by the Swiss National Science Foundation (Indo-Swiss Research Program and NCCR MICS) and the European Union projects COMBEST and COCONUT.","volume":5643,"abstract":[{"lang":"eng","text":"Most specification languages express only qualitative constraints. However, among two implementations that satisfy a given specification, one may be preferred to another. For example, if a specification asks that every request is followed by a response, one may prefer an implementation that generates responses quickly but does not generate unnecessary responses. We use quantitative properties to measure the “goodness” of an implementation. Using games with corresponding quantitative objectives, we can synthesize “optimal” implementations, which are preferred among the set of possible implementations that satisfy a given specification.\r\nIn particular, we show how automata with lexicographic mean-payoff conditions can be used to express many interesting quantitative properties for reactive systems. In this framework, the synthesis of optimal implementations requires the solution of lexicographic mean-payoff games (for safety requirements), and the solution of games with both lexicographic mean-payoff and parity objectives (for liveness requirements). We present algorithms for solving both kinds of novel graph games."}],"arxiv":1,"doi":"10.1007/978-3-642-02658-4_14","day":"19","external_id":{"arxiv":["0904.2638"]},"date_updated":"2021-01-12T07:59:46Z","year":"2009","citation":{"short":"R. Bloem, K. Chatterjee, T.A. Henzinger, B. Jobstmann, in:, Springer, 2009, pp. 140–156.","mla":"Bloem, Roderick, et al. <i>Better Quality in Synthesis through Quantitative Objectives</i>. Vol. 5643, Springer, 2009, pp. 140–56, doi:<a href=\"https://doi.org/10.1007/978-3-642-02658-4_14\">10.1007/978-3-642-02658-4_14</a>.","ista":"Bloem R, Chatterjee K, Henzinger TA, Jobstmann B. 2009. Better quality in synthesis through quantitative objectives. CAV: Computer Aided Verification, LNCS, vol. 5643, 140–156.","apa":"Bloem, R., Chatterjee, K., Henzinger, T. A., &#38; Jobstmann, B. (2009). Better quality in synthesis through quantitative objectives (Vol. 5643, pp. 140–156). Presented at the CAV: Computer Aided Verification, Grenoble, France: Springer. <a href=\"https://doi.org/10.1007/978-3-642-02658-4_14\">https://doi.org/10.1007/978-3-642-02658-4_14</a>","ama":"Bloem R, Chatterjee K, Henzinger TA, Jobstmann B. Better quality in synthesis through quantitative objectives. In: Vol 5643. Springer; 2009:140-156. doi:<a href=\"https://doi.org/10.1007/978-3-642-02658-4_14\">10.1007/978-3-642-02658-4_14</a>","ieee":"R. Bloem, K. Chatterjee, T. A. Henzinger, and B. Jobstmann, “Better quality in synthesis through quantitative objectives,” presented at the CAV: Computer Aided Verification, Grenoble, France, 2009, vol. 5643, pp. 140–156.","chicago":"Bloem, Roderick, Krishnendu Chatterjee, Thomas A Henzinger, and Barbara Jobstmann. “Better Quality in Synthesis through Quantitative Objectives,” 5643:140–56. Springer, 2009. <a href=\"https://doi.org/10.1007/978-3-642-02658-4_14\">https://doi.org/10.1007/978-3-642-02658-4_14</a>."},"conference":{"location":"Grenoble, France","end_date":"2009-07-02","start_date":"2009-06-26","name":"CAV: Computer Aided Verification"},"language":[{"iso":"eng"}],"month":"06","oa_version":"Preprint","project":[{"call_identifier":"FP7","_id":"25EFB36C-B435-11E9-9278-68D0E5697425","grant_number":"215543","name":"COMponent-Based Embedded Systems design Techniques"}],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"url":"http://arxiv.org/abs/0904.2638","open_access":"1"}],"publist_id":"141","oa":1,"date_published":"2009-06-19T00:00:00Z","type":"conference"},{"doi":"10.15479/AT:IST-2009-0004","day":"02","publication_identifier":{"issn":["2664-1690"]},"abstract":[{"text":"We consider probabilistic automata on infinite words with acceptance defined by safety, reachability, Büchi, coBüchi and limit-average conditions. We consider quantitative and qualitative decision problems. We present extensions and adaptations of proofs of [GO09] and present a precise characterization of the decidability and undecidability frontier of the quantitative and qualitative decision problems.","lang":"eng"}],"oa":1,"date_updated":"2023-02-23T11:45:44Z","year":"2009","citation":{"ieee":"K. Chatterjee, <i>Probabilistic automata on infinite words: Decidability and undecidability results</i>. IST Austria, 2009.","chicago":"Chatterjee, Krishnendu. <i>Probabilistic Automata on Infinite Words: Decidability and Undecidability Results</i>. IST Austria, 2009. <a href=\"https://doi.org/10.15479/AT:IST-2009-0004\">https://doi.org/10.15479/AT:IST-2009-0004</a>.","apa":"Chatterjee, K. (2009). <i>Probabilistic automata on infinite words: Decidability and undecidability results</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2009-0004\">https://doi.org/10.15479/AT:IST-2009-0004</a>","ama":"Chatterjee K. <i>Probabilistic Automata on Infinite Words: Decidability and Undecidability Results</i>. IST Austria; 2009. doi:<a href=\"https://doi.org/10.15479/AT:IST-2009-0004\">10.15479/AT:IST-2009-0004</a>","ista":"Chatterjee K. 2009. Probabilistic automata on infinite words: Decidability and undecidability results, IST Austria, 17p.","short":"K. Chatterjee, Probabilistic Automata on Infinite Words: Decidability and Undecidability Results, IST Austria, 2009.","mla":"Chatterjee, Krishnendu. <i>Probabilistic Automata on Infinite Words: Decidability and Undecidability Results</i>. IST Austria, 2009, doi:<a href=\"https://doi.org/10.15479/AT:IST-2009-0004\">10.15479/AT:IST-2009-0004</a>."},"date_published":"2009-11-02T00:00:00Z","type":"technical_report","file":[{"file_size":311065,"checksum":"fb7563150231325b00b1718d956f687b","date_created":"2018-12-12T11:54:08Z","content_type":"application/pdf","file_name":"IST-2009-0004_IST-2009-0004.pdf","date_updated":"2020-07-14T12:46:43Z","relation":"main_file","access_level":"open_access","creator":"system","file_id":"5530"}],"related_material":{"record":[{"status":"public","relation":"later_version","id":"3857"}]},"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["005"],"oa_version":"Published Version","publication_status":"published","department":[{"_id":"KrCh"}],"date_created":"2018-12-12T11:39:04Z","alternative_title":["IST Austria Technical Report"],"pubrep_id":"28","title":"Probabilistic automata on infinite words: Decidability and undecidability results","month":"11","_id":"5392","has_accepted_license":"1","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"}],"publisher":"IST Austria","page":"17","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:46:43Z"},{"pubrep_id":"29","alternative_title":["IST Austria Technical Report"],"title":"Gist: A solver for probabilistic games","month":"10","publication_status":"published","oa_version":"Published Version","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"date_created":"2018-12-12T11:39:05Z","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger","first_name":"Thomas A"},{"full_name":"Jobstmann, Barbara","first_name":"Barbara","last_name":"Jobstmann"},{"full_name":"Radhakrishna, Arjun","last_name":"Radhakrishna","first_name":"Arjun","id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87"}],"_id":"5393","has_accepted_license":"1","publisher":"IST Austria","file_date_updated":"2020-07-14T12:46:43Z","language":[{"iso":"eng"}],"page":"12","abstract":[{"lang":"eng","text":"Gist is a tool that (a) solves the qualitative analysis problem of turn-based probabilistic games with ω-regular objectives; and (b) synthesizes reasonable environment assumptions for synthesis of unrealizable specifications. Our tool provides efficient implementations of several reduction based techniques to solve turn-based probabilistic games, and uses the analysis of turn-based probabilistic games for synthesizing environment assumptions for unrealizable specifications."}],"oa":1,"doi":"10.15479/AT:IST-2009-0003","day":"09","publication_identifier":{"issn":["2664-1690"]},"date_published":"2009-10-09T00:00:00Z","type":"technical_report","date_updated":"2023-02-23T12:09:01Z","citation":{"ista":"Chatterjee K, Henzinger TA, Jobstmann B, Radhakrishna A. 2009. Gist: A solver for probabilistic games, IST Austria, 12p.","mla":"Chatterjee, Krishnendu, et al. <i>Gist: A Solver for Probabilistic Games</i>. IST Austria, 2009, doi:<a href=\"https://doi.org/10.15479/AT:IST-2009-0003\">10.15479/AT:IST-2009-0003</a>.","short":"K. Chatterjee, T.A. Henzinger, B. Jobstmann, A. Radhakrishna, Gist: A Solver for Probabilistic Games, IST Austria, 2009.","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, Barbara Jobstmann, and Arjun Radhakrishna. <i>Gist: A Solver for Probabilistic Games</i>. IST Austria, 2009. <a href=\"https://doi.org/10.15479/AT:IST-2009-0003\">https://doi.org/10.15479/AT:IST-2009-0003</a>.","ieee":"K. Chatterjee, T. A. Henzinger, B. Jobstmann, and A. Radhakrishna, <i>Gist: A solver for probabilistic games</i>. IST Austria, 2009.","ama":"Chatterjee K, Henzinger TA, Jobstmann B, Radhakrishna A. <i>Gist: A Solver for Probabilistic Games</i>. IST Austria; 2009. doi:<a href=\"https://doi.org/10.15479/AT:IST-2009-0003\">10.15479/AT:IST-2009-0003</a>","apa":"Chatterjee, K., Henzinger, T. A., Jobstmann, B., &#38; Radhakrishna, A. (2009). <i>Gist: A solver for probabilistic games</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2009-0003\">https://doi.org/10.15479/AT:IST-2009-0003</a>"},"year":"2009","ddc":["000","005"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","related_material":{"record":[{"relation":"later_version","id":"4388","status":"public"}]},"file":[{"relation":"main_file","access_level":"open_access","file_id":"5459","creator":"system","date_created":"2018-12-12T11:52:58Z","checksum":"49551ac552915b17593a14c993845274","file_size":386866,"date_updated":"2020-07-14T12:46:43Z","file_name":"IST-2009-0003_IST-2009-0003.pdf","content_type":"application/pdf"}]},{"_id":"5394","has_accepted_license":"1","author":[{"first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Thomas A","last_name":"Henzinger","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Horn, Florian","first_name":"Florian","last_name":"Horn","id":"37327ACE-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","oa_version":"Published Version","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"date_created":"2018-12-12T11:39:05Z","title":"Improved lower bounds for request-response and finitary Streett games","pubrep_id":"30","month":"09","alternative_title":["IST Austria Technical Report"],"page":"11","file_date_updated":"2020-07-14T12:46:43Z","language":[{"iso":"eng"}],"publisher":"IST Austria","date_updated":"2020-07-14T23:07:47Z","year":"2009","citation":{"ieee":"K. Chatterjee, T. A. Henzinger, and F. Horn, <i>Improved lower bounds for request-response and finitary Streett games</i>. IST Austria, 2009.","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, and Florian Horn. <i>Improved Lower Bounds for Request-Response and Finitary Streett Games</i>. IST Austria, 2009. <a href=\"https://doi.org/10.15479/AT:IST-2009-0002\">https://doi.org/10.15479/AT:IST-2009-0002</a>.","apa":"Chatterjee, K., Henzinger, T. A., &#38; Horn, F. (2009). <i>Improved lower bounds for request-response and finitary Streett games</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2009-0002\">https://doi.org/10.15479/AT:IST-2009-0002</a>","ama":"Chatterjee K, Henzinger TA, Horn F. <i>Improved Lower Bounds for Request-Response and Finitary Streett Games</i>. IST Austria; 2009. doi:<a href=\"https://doi.org/10.15479/AT:IST-2009-0002\">10.15479/AT:IST-2009-0002</a>","ista":"Chatterjee K, Henzinger TA, Horn F. 2009. Improved lower bounds for request-response and finitary Streett games, IST Austria, 11p.","mla":"Chatterjee, Krishnendu, et al. <i>Improved Lower Bounds for Request-Response and Finitary Streett Games</i>. IST Austria, 2009, doi:<a href=\"https://doi.org/10.15479/AT:IST-2009-0002\">10.15479/AT:IST-2009-0002</a>.","short":"K. Chatterjee, T.A. Henzinger, F. Horn, Improved Lower Bounds for Request-Response and Finitary Streett Games, IST Austria, 2009."},"date_published":"2009-09-09T00:00:00Z","type":"technical_report","doi":"10.15479/AT:IST-2009-0002","day":"09","publication_identifier":{"issn":["2664-1690"]},"abstract":[{"lang":"eng","text":"We consider two-player games played on graphs with request-response and finitary Streett objectives. We show these games are PSPACE-hard, improving the previous known NP-hardness. We also improve the lower bounds on memory required by the winning strategies for the players."}],"oa":1,"file":[{"date_created":"2018-12-12T11:53:50Z","checksum":"1c50a9723fbae1b2c46d18138968efb3","file_size":238091,"date_updated":"2020-07-14T12:46:43Z","content_type":"application/pdf","file_name":"IST-2009-0002_IST-2009-0002.pdf","relation":"main_file","access_level":"open_access","file_id":"5511","creator":"system"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","ddc":["004"]},{"status":"public","related_material":{"record":[{"status":"public","id":"3855","relation":"later_version"}]},"ddc":["005"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"creator":"system","file_id":"5486","relation":"main_file","access_level":"open_access","file_name":"IST-2009-0001_IST-2009-0001.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:46:43Z","file_size":342088,"checksum":"04d9cc065cc19598a4e8631c47f1a562","date_created":"2018-12-12T11:53:25Z"}],"oa":1,"abstract":[{"text":"We study observation-based strategies for partially-observable Markov decision processes (POMDPs) with omega-regular objectives. An observation-based strategy relies on partial information about the history of a play, namely, on the past sequence of observa- tions. We consider the qualitative analysis problem: given a POMDP with an omega-regular objective, whether there is an observation-based strategy to achieve the objective with probability 1 (almost-sure winning), or with positive probability (positive winning). Our main results are twofold. First, we present a complete picture of the computational complexity of the qualitative analysis of POMDPs with parity objectives (a canonical form to express omega-regular objectives) and its subclasses. Our contribution consists in establishing several upper and lower bounds that were not known in literature. Second, we present optimal bounds (matching upper and lower bounds) on the memory required by pure and randomized observation-based strategies for the qualitative analysis of POMDPs with parity objectives and its subclasses.","lang":"eng"}],"day":"09","publication_identifier":{"issn":["2664-1690"]},"doi":"10.15479/AT:IST-2009-0001","type":"technical_report","date_published":"2009-09-09T00:00:00Z","year":"2009","citation":{"short":"K. Chatterjee, L. Doyen, T.A. Henzinger, Qualitative Analysis of Partially-Observable Markov Decision Processes, IST Austria, 2009.","mla":"Chatterjee, Krishnendu, et al. <i>Qualitative Analysis of Partially-Observable Markov Decision Processes</i>. IST Austria, 2009, doi:<a href=\"https://doi.org/10.15479/AT:IST-2009-0001\">10.15479/AT:IST-2009-0001</a>.","ista":"Chatterjee K, Doyen L, Henzinger TA. 2009. Qualitative analysis of partially-observable Markov decision processes, IST Austria, 20p.","apa":"Chatterjee, K., Doyen, L., &#38; Henzinger, T. A. (2009). <i>Qualitative analysis of partially-observable Markov decision processes</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2009-0001\">https://doi.org/10.15479/AT:IST-2009-0001</a>","ama":"Chatterjee K, Doyen L, Henzinger TA. <i>Qualitative Analysis of Partially-Observable Markov Decision Processes</i>. IST Austria; 2009. doi:<a href=\"https://doi.org/10.15479/AT:IST-2009-0001\">10.15479/AT:IST-2009-0001</a>","ieee":"K. Chatterjee, L. Doyen, and T. A. Henzinger, <i>Qualitative analysis of partially-observable Markov decision processes</i>. IST Austria, 2009.","chicago":"Chatterjee, Krishnendu, Laurent Doyen, and Thomas A Henzinger. <i>Qualitative Analysis of Partially-Observable Markov Decision Processes</i>. IST Austria, 2009. <a href=\"https://doi.org/10.15479/AT:IST-2009-0001\">https://doi.org/10.15479/AT:IST-2009-0001</a>."},"date_updated":"2023-02-23T11:45:39Z","publisher":"IST Austria","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:46:43Z","page":"20","title":"Qualitative analysis of partially-observable Markov decision processes","alternative_title":["IST Austria Technical Report"],"pubrep_id":"31","month":"09","date_created":"2018-12-12T11:39:05Z","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"publication_status":"published","oa_version":"Published Version","author":[{"last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Doyen, Laurent","first_name":"Laurent","last_name":"Doyen"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","first_name":"Thomas A","last_name":"Henzinger"}],"has_accepted_license":"1","_id":"5395"},{"article_type":"original","publisher":"American Association for the Advancement of Science","page":"1451-1454","quality_controlled":"1","title":"Genome-wide demethylation of Arabidopsis endosperm","intvolume":"       324","publication_status":"published","date_created":"2021-06-04T08:55:41Z","article_processing_charge":"No","department":[{"_id":"DaZi"}],"author":[{"full_name":"Hsieh, Tzung-Fu","last_name":"Hsieh","first_name":"Tzung-Fu"},{"last_name":"Ibarra","first_name":"Christian A.","full_name":"Ibarra, Christian A."},{"first_name":"Pedro","last_name":"Silva","full_name":"Silva, Pedro"},{"full_name":"Zemach, Assaf","first_name":"Assaf","last_name":"Zemach"},{"full_name":"Eshed-Williams, Leor","first_name":"Leor","last_name":"Eshed-Williams"},{"first_name":"Robert L.","last_name":"Fischer","full_name":"Fischer, Robert L."},{"id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649","last_name":"Zilberman","first_name":"Daniel"}],"issue":"5933","_id":"9453","pmid":1,"scopus_import":"1","extern":"1","volume":324,"abstract":[{"text":"Parent-of-origin-specific (imprinted) gene expression is regulated in Arabidopsis thaliana endosperm by cytosine demethylation of the maternal genome mediated by the DNA glycosylase DEMETER, but the extent of the methylation changes is not known. Here, we show that virtually the entire endosperm genome is demethylated, coupled with extensive local non-CG hypermethylation of small interfering RNA–targeted sequences. Mutation of DEMETER partially restores endosperm CG methylation to levels found in other tissues, indicating that CG demethylation is specific to maternal sequences. Endosperm demethylation is accompanied by CHH hypermethylation of embryo transposable elements. Our findings demonstrate extensive reconfiguration of the endosperm methylation landscape that likely reinforces transposon silencing in the embryo.","lang":"eng"}],"doi":"10.1126/science.1172417","day":"12","external_id":{"pmid":["19520962"]},"date_updated":"2021-12-14T08:53:26Z","year":"2009","citation":{"mla":"Hsieh, Tzung-Fu, et al. “Genome-Wide Demethylation of Arabidopsis Endosperm.” <i>Science</i>, vol. 324, no. 5933, American Association for the Advancement of Science, 2009, pp. 1451–54, doi:<a href=\"https://doi.org/10.1126/science.1172417\">10.1126/science.1172417</a>.","short":"T.-F. Hsieh, C.A. Ibarra, P. Silva, A. Zemach, L. Eshed-Williams, R.L. Fischer, D. Zilberman, Science 324 (2009) 1451–1454.","ista":"Hsieh T-F, Ibarra CA, Silva P, Zemach A, Eshed-Williams L, Fischer RL, Zilberman D. 2009. Genome-wide demethylation of Arabidopsis endosperm. Science. 324(5933), 1451–1454.","apa":"Hsieh, T.-F., Ibarra, C. A., Silva, P., Zemach, A., Eshed-Williams, L., Fischer, R. L., &#38; Zilberman, D. (2009). Genome-wide demethylation of Arabidopsis endosperm. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.1172417\">https://doi.org/10.1126/science.1172417</a>","ama":"Hsieh T-F, Ibarra CA, Silva P, et al. Genome-wide demethylation of Arabidopsis endosperm. <i>Science</i>. 2009;324(5933):1451-1454. doi:<a href=\"https://doi.org/10.1126/science.1172417\">10.1126/science.1172417</a>","ieee":"T.-F. Hsieh <i>et al.</i>, “Genome-wide demethylation of Arabidopsis endosperm,” <i>Science</i>, vol. 324, no. 5933. American Association for the Advancement of Science, pp. 1451–1454, 2009.","chicago":"Hsieh, Tzung-Fu, Christian A. Ibarra, Pedro Silva, Assaf Zemach, Leor Eshed-Williams, Robert L. Fischer, and Daniel Zilberman. “Genome-Wide Demethylation of Arabidopsis Endosperm.” <i>Science</i>. American Association for the Advancement of Science, 2009. <a href=\"https://doi.org/10.1126/science.1172417\">https://doi.org/10.1126/science.1172417</a>."},"language":[{"iso":"eng"}],"keyword":["Multidisciplinary"],"month":"06","oa_version":"Submitted Version","publication":"Science","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","status":"public","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4044190/"}],"oa":1,"publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"date_published":"2009-06-12T00:00:00Z","type":"journal_article"},{"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":74,"acknowledgement":"Royal Society and the Engineering and Physical Sciences for support (GR/ T11753/01)","date_published":"2009-11-10T00:00:00Z","type":"book_chapter","date_updated":"2021-01-12T07:45:04Z","citation":{"mla":"Barton, Nicholas H. “Why Sex and Recombination? .” <i>Cold Spring Harbor Symposia on Quantitative Biology</i>, vol. 74, Cold Spring Harbor Laboratory Press, 2009, pp. 187–95, doi:<a href=\"https://doi.org/10.1101/sqb.2009.74.030\">10.1101/sqb.2009.74.030</a>.","short":"N.H. Barton, in:, Cold Spring Harbor Symposia on Quantitative Biology, Cold Spring Harbor Laboratory Press, 2009, pp. 187–195.","ista":"Barton NH. 2009.Why sex and recombination? . In: Cold Spring Harbor Symposia on Quantitative Biology. vol. 74, 187–195.","ama":"Barton NH. Why sex and recombination? . In: <i>Cold Spring Harbor Symposia on Quantitative Biology</i>. Vol 74. Cold Spring Harbor Laboratory Press; 2009:187-195. doi:<a href=\"https://doi.org/10.1101/sqb.2009.74.030\">10.1101/sqb.2009.74.030</a>","apa":"Barton, N. H. (2009). Why sex and recombination? . In <i>Cold Spring Harbor Symposia on Quantitative Biology</i> (Vol. 74, pp. 187–195). Cold Spring Harbor Laboratory Press. <a href=\"https://doi.org/10.1101/sqb.2009.74.030\">https://doi.org/10.1101/sqb.2009.74.030</a>","ieee":"N. H. Barton, “Why sex and recombination? ,” in <i>Cold Spring Harbor Symposia on Quantitative Biology</i>, vol. 74, Cold Spring Harbor Laboratory Press, 2009, pp. 187–195.","chicago":"Barton, Nicholas H. “Why Sex and Recombination? .” In <i>Cold Spring Harbor Symposia on Quantitative Biology</i>, 74:187–95. Cold Spring Harbor Laboratory Press, 2009. <a href=\"https://doi.org/10.1101/sqb.2009.74.030\">https://doi.org/10.1101/sqb.2009.74.030</a>."},"year":"2009","abstract":[{"text":"Sex and recombination have long been seen as adaptations that facilitate natural selection by generating favorable variations. If recombination is to aid selection, there must be negative linkage disequilibria—favorable alleles must be found together less often than expected by chance. These negative linkage disequilibria can be generated directly by selection, but this must involve negative epistasis of just the right strength, which is not expected, from either experiment or theory. Random drift provides a more general source of negative associations: Favorable mutations almost always arise on different genomes, and negative associations tend to persist, precisely because they shield variation from selection.\r\n\r\nWe can understand how recombination aids adaptation by determining the maximum possible rate of adaptation. With unlinked loci, this rate increases only logarithmically with the influx of favorable mutations. With a linear genome, a scaling argument shows that in a large population, the rate of adaptive substitution depends only on the expected rate in the absence of interference, divided by the total rate of recombination. A two-locus approximation predicts an upper bound on the rate of substitution, proportional to recombination rate.\r\n\r\nIf associations between linked loci do impede adaptation, there can be substantial selection for modifiers that increase recombination. Whether this can account for the maintenance of high rates of sex and recombination depends on the extent of selection. It is clear that the rate of species-wide substitutions is typically far too low to generate appreciable selection for recombination. However, local sweeps within a subdivided population may be effective.","lang":"eng"}],"publist_id":"2708","doi":"10.1101/sqb.2009.74.030","day":"10","language":[{"iso":"eng"}],"page":"187 - 195","quality_controlled":"1","publisher":"Cold Spring Harbor Laboratory Press","author":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"}],"publication":"Cold Spring Harbor Symposia on Quantitative Biology","_id":"3675","scopus_import":1,"title":"Why sex and recombination? ","month":"11","intvolume":"        74","publication_status":"published","oa_version":"None","department":[{"_id":"NiBa"}],"date_created":"2018-12-11T12:04:33Z"},{"acknowledgement":"This work was supported by a Royal Society/Wolfson Award, and by grants EP/T11753/01, EP/C546318/01 from the EPSRC.\r\nWe are grateful to M. Cates, H.P. de Vladar and G. Sella, and to two anonymous referees, for their helpful comments.","volume":259,"day":"21","doi":"10.1016/j.jtbi.2009.03.019","abstract":[{"lang":"eng","text":"There is a close analogy between statistical thermodynamics and the evolution of allele frequencies under mutation, selection and random drift. Wright's formula for the stationary distribution of allele frequencies is analogous to the Boltzmann distribution in statistical physics. Population size, 2N, plays the role of the inverse temperature, 1/kT, and determines the magnitude of random fluctuations. Log mean fitness, View the MathML source, tends to increase under selection, and is analogous to a (negative) energy; a potential function, U, increases under mutation in a similar way. An entropy, SH, can be defined which measures the deviation from the distribution of allele frequencies expected under random drift alone; the sum View the MathML source gives a free fitness that increases as the population evolves towards its stationary distribution. Usually, we observe the distribution of a few quantitative traits that depend on the frequencies of very many alleles. The mean and variance of such traits are analogous to observable quantities in statistical thermodynamics. Thus, we can define an entropy, SΩ, which measures the volume of allele frequency space that is consistent with the observed trait distribution. The stationary distribution of the traits is View the MathML source; this applies with arbitrary epistasis and dominance. The entropies SΩ, SH are distinct, but converge when there are so many alleles that traits fluctuate close to their expectations. Populations tend to evolve towards states that can be realised in many ways (i.e., large SΩ), which may lead to a substantial drop below the adaptive peak; we illustrate this point with a simple model of genetic redundancy. This analogy with statistical thermodynamics brings together previous ideas in a general framework, and justifies a maximum entropy approximation to the dynamics of quantitative traits."}],"year":"2009","citation":{"ista":"Barton NH, Coe J. 2009. On the application of statistical physics to evolutionary biology. Journal of Theoretical Biology. 259(2), 317–324.","mla":"Barton, Nicholas H., and Jason Coe. “On the Application of Statistical Physics to Evolutionary Biology.” <i>Journal of Theoretical Biology</i>, vol. 259, no. 2, Elsevier, 2009, pp. 317–24, doi:<a href=\"https://doi.org/10.1016/j.jtbi.2009.03.019\">10.1016/j.jtbi.2009.03.019</a>.","short":"N.H. Barton, J. Coe, Journal of Theoretical Biology 259 (2009) 317–324.","ieee":"N. H. Barton and J. Coe, “On the application of statistical physics to evolutionary biology,” <i>Journal of Theoretical Biology</i>, vol. 259, no. 2. Elsevier, pp. 317–324, 2009.","chicago":"Barton, Nicholas H, and Jason Coe. “On the Application of Statistical Physics to Evolutionary Biology.” <i>Journal of Theoretical Biology</i>. Elsevier, 2009. <a href=\"https://doi.org/10.1016/j.jtbi.2009.03.019\">https://doi.org/10.1016/j.jtbi.2009.03.019</a>.","apa":"Barton, N. H., &#38; Coe, J. (2009). On the application of statistical physics to evolutionary biology. <i>Journal of Theoretical Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jtbi.2009.03.019\">https://doi.org/10.1016/j.jtbi.2009.03.019</a>","ama":"Barton NH, Coe J. On the application of statistical physics to evolutionary biology. <i>Journal of Theoretical Biology</i>. 2009;259(2):317-324. doi:<a href=\"https://doi.org/10.1016/j.jtbi.2009.03.019\">10.1016/j.jtbi.2009.03.019</a>"},"date_updated":"2021-01-12T07:52:06Z","publisher":"Elsevier","quality_controlled":"1","page":"317 - 324","department":[{"_id":"NiBa"}],"date_created":"2018-12-11T12:05:06Z","publication_status":"published","intvolume":"       259","title":"On the application of statistical physics to evolutionary biology","scopus_import":1,"_id":"3775","issue":"2","author":[{"last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Coe, Jason","first_name":"Jason","last_name":"Coe"}],"main_file_link":[{"url":"https://hal.archives-ouvertes.fr/hal-00554594/document","open_access":"1"}],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"publist_id":"2452","type":"journal_article","date_published":"2009-07-21T00:00:00Z","language":[{"iso":"eng"}],"oa_version":"Submitted Version","month":"07","publication":"Journal of Theoretical Biology"},{"oa_version":"Submitted Version","month":"08","has_accepted_license":"1","publication":"Journal of Evolutionary Biology","language":[{"iso":"eng"}],"publist_id":"2447","oa":1,"type":"journal_article","date_published":"2009-08-01T00:00:00Z","file":[{"content_type":"application/pdf","file_name":"Davison_JEB_v31_2009.pdf","date_updated":"2020-07-14T12:46:15Z","checksum":"f70c15c6ab9306121d4153a3be0d2346","file_size":2583812,"date_created":"2019-02-22T09:21:44Z","creator":"dernst","file_id":"6044","access_level":"open_access","relation":"main_file"}],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"NiBa"}],"date_created":"2018-12-11T12:05:08Z","publication_status":"published","intvolume":"        22","pubrep_id":"553","title":"The effect of chirality phenotype and genotype on the fecundity and viability of Partula suturalis and Lymnaea stagnalis: Implications for the evolution of sinistral snails","scopus_import":1,"_id":"3780","issue":"8","author":[{"full_name":"Davison, Angus","last_name":"Davison","first_name":"Angus"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"},{"full_name":"Clarke, Bryan","last_name":"Clarke","first_name":"Bryan"}],"publisher":"Wiley","quality_controlled":"1","page":"1624 - 1635","file_date_updated":"2020-07-14T12:46:15Z","day":"01","doi":"10.1111/j.1420-9101.2009.01770.x","abstract":[{"lang":"eng","text":"Why are sinistral snails so rare? Two main hypotheses are that selection acts against the establishment of new coiling morphs, because dextral and sinistral snails have trouble mating, or else a developmental constraint prevents the establishment of sinistrals. We therefore used an isolate of the snail Lymnaea stagnalis, in which sinistrals are rare, and populations of Partula suturalis, in which sinistrals are common, as well as a mathematical model, to understand the circumstances by which new morphs evolve. The main finding is that the sinistral genotype is associated with reduced egg viability in L. stagnalis, but in P. suturalis individuals of sinistral and dextral genotype appear equally fecund, implying a lack of a constraint. As positive frequency-dependent selection against the rare chiral morph in P. suturalis also operates over a narrow range (&lt; 3%), the results suggest a model for chiral evolution in snails in which weak positive frequency-dependent selection may be overcome by a negative frequency-dependent selection, such as reproductive character displacement. In snails, there is not always a developmental constraint. As the direction of cleavage, and thus the directional asymmetry of the entire body, does not generally vary in other Spiralia (annelids, echiurans, vestimentiferans, sipunculids and nemerteans), it remains an open question as to whether this is because of a constraint and/or because most taxa do not have a conspicuous external asymmetry (like a shell) upon which selection can act."}],"year":"2009","citation":{"ista":"Davison A, Barton NH, Clarke B. 2009. The effect of chirality phenotype and genotype on the fecundity and viability of Partula suturalis and Lymnaea stagnalis: Implications for the evolution of sinistral snails. Journal of Evolutionary Biology. 22(8), 1624–1635.","mla":"Davison, Angus, et al. “The Effect of Chirality Phenotype and Genotype on the Fecundity and Viability of Partula Suturalis and Lymnaea Stagnalis: Implications for the Evolution of Sinistral Snails.” <i>Journal of Evolutionary Biology</i>, vol. 22, no. 8, Wiley, 2009, pp. 1624–35, doi:<a href=\"https://doi.org/10.1111/j.1420-9101.2009.01770.x\">10.1111/j.1420-9101.2009.01770.x</a>.","short":"A. Davison, N.H. Barton, B. Clarke, Journal of Evolutionary Biology 22 (2009) 1624–1635.","ieee":"A. Davison, N. H. Barton, and B. Clarke, “The effect of chirality phenotype and genotype on the fecundity and viability of Partula suturalis and Lymnaea stagnalis: Implications for the evolution of sinistral snails,” <i>Journal of Evolutionary Biology</i>, vol. 22, no. 8. Wiley, pp. 1624–1635, 2009.","chicago":"Davison, Angus, Nicholas H Barton, and Bryan Clarke. “The Effect of Chirality Phenotype and Genotype on the Fecundity and Viability of Partula Suturalis and Lymnaea Stagnalis: Implications for the Evolution of Sinistral Snails.” <i>Journal of Evolutionary Biology</i>. Wiley, 2009. <a href=\"https://doi.org/10.1111/j.1420-9101.2009.01770.x\">https://doi.org/10.1111/j.1420-9101.2009.01770.x</a>.","ama":"Davison A, Barton NH, Clarke B. The effect of chirality phenotype and genotype on the fecundity and viability of Partula suturalis and Lymnaea stagnalis: Implications for the evolution of sinistral snails. <i>Journal of Evolutionary Biology</i>. 2009;22(8):1624-1635. doi:<a href=\"https://doi.org/10.1111/j.1420-9101.2009.01770.x\">10.1111/j.1420-9101.2009.01770.x</a>","apa":"Davison, A., Barton, N. H., &#38; Clarke, B. (2009). The effect of chirality phenotype and genotype on the fecundity and viability of Partula suturalis and Lymnaea stagnalis: Implications for the evolution of sinistral snails. <i>Journal of Evolutionary Biology</i>. Wiley. <a href=\"https://doi.org/10.1111/j.1420-9101.2009.01770.x\">https://doi.org/10.1111/j.1420-9101.2009.01770.x</a>"},"date_updated":"2021-01-12T07:52:09Z","volume":22,"acknowledgement":"We owe a great debt to Jim Murray for his many contributions to the study of Partula, in the field, in the laboratory, in the interpretation of data, and in generating new ideas about evolution. With pleasure and respect we dedicate this paper to him. Jim Murray played a leading role in making the collections used here. We are very grateful also to Ann Clarke and Elizabeth Murray for help with collecting, to Lorna Stewart for snail dissections, to Joris Koene for the gift of snails, to Natasha Constant for entering the data, and Takahiro Asami, Edmund Gittenberger and Gerhard Falkner for establishing the sinistral stock of L. stagnalis. Comments from an anonymous referee, A. Richard Palmer and the editorial board improved the manuscript. Work in the field was supported by the Royal Society, The Carnegie Trust, the Percy Sladen Trust and the National Science Foundation. The Science Research Council (B/SR/4144), the National Science Foundation (GB-4188), the Royal Society and the University of Nottingham supported work in the laboratory.","ddc":["570"]},{"title":"On relational interfaces","pubrep_id":"70","date_created":"2018-12-11T12:05:26Z","department":[{"_id":"ToHe"}],"publication_status":"published","author":[{"full_name":"Tripakis, Stavros","first_name":"Stavros","last_name":"Tripakis"},{"last_name":"Lickly","first_name":"Ben","full_name":"Lickly, Ben"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","first_name":"Thomas A","last_name":"Henzinger"},{"last_name":"Lee","first_name":"Edward","full_name":"Lee, Edward"}],"_id":"3837","publisher":"ACM","file_date_updated":"2020-07-14T12:46:16Z","quality_controlled":"1","ec_funded":1,"page":"67 - 76","abstract":[{"lang":"eng","text":"In this paper we extend the work of Alfaro, Henzinger et al. on interface theories for component-based design. Existing interface theories often fail to capture functional relations between the inputs and outputs of an interface. For example, a simple synchronous interface that takes as input a number n ≥ 0 and returns, at the same time, as output n + 1, cannot be expressed in existing theories. In this paper we provide a theory of relational interfaces, where such input-output relations can be captured. Our theory supports synchronous interfaces, both stateless and stateful. It includes explicit notions of environments and pluggability, and satisfies fundamental properties such as preservation of refinement by composition, and characterization of pluggability by refinement. We achieve these properties by making reasonable restrictions on feedback loops in interface compositions."}],"day":"01","doi":"10.1145/1629335.1629346","year":"2009","citation":{"short":"S. Tripakis, B. Lickly, T.A. Henzinger, E. Lee, in:, EMSOFT ’09 Proceedings of the Seventh ACM International Conference on Embedded Software, ACM, 2009, pp. 67–76.","mla":"Tripakis, Stavros, et al. “On Relational Interfaces.” <i>EMSOFT ’09 Proceedings of the Seventh ACM International Conference on Embedded Software</i>, ACM, 2009, pp. 67–76, doi:<a href=\"https://doi.org/10.1145/1629335.1629346\">10.1145/1629335.1629346</a>.","ista":"Tripakis S, Lickly B, Henzinger TA, Lee E. 2009. On relational interfaces. EMSOFT ’09 Proceedings of the seventh ACM international conference on Embedded software. EMSOFT: Embedded Software , 67–76.","ama":"Tripakis S, Lickly B, Henzinger TA, Lee E. On relational interfaces. In: <i>EMSOFT ’09 Proceedings of the Seventh ACM International Conference on Embedded Software</i>. ACM; 2009:67-76. doi:<a href=\"https://doi.org/10.1145/1629335.1629346\">10.1145/1629335.1629346</a>","apa":"Tripakis, S., Lickly, B., Henzinger, T. A., &#38; Lee, E. (2009). On relational interfaces. In <i>EMSOFT ’09 Proceedings of the seventh ACM international conference on Embedded software</i> (pp. 67–76). Grenoble, France: ACM. <a href=\"https://doi.org/10.1145/1629335.1629346\">https://doi.org/10.1145/1629335.1629346</a>","chicago":"Tripakis, Stavros, Ben Lickly, Thomas A Henzinger, and Edward Lee. “On Relational Interfaces.” In <i>EMSOFT ’09 Proceedings of the Seventh ACM International Conference on Embedded Software</i>, 67–76. ACM, 2009. <a href=\"https://doi.org/10.1145/1629335.1629346\">https://doi.org/10.1145/1629335.1629346</a>.","ieee":"S. Tripakis, B. Lickly, T. A. Henzinger, and E. Lee, “On relational interfaces,” in <i>EMSOFT ’09 Proceedings of the seventh ACM international conference on Embedded software</i>, Grenoble, France, 2009, pp. 67–76."},"date_updated":"2021-01-12T07:52:33Z","ddc":["004"],"acknowledgement":"This work is supported by the Center for Hybrid and Embedded Software Systems (CHESS) at UC Berkeley, which receives support from the National Science Foundation (NSF awards #0720882 (CSR-EHS: PRET) and #0720841 (CSR-CPS)), the U.S. Army Research Office (ARO #W911NF-07-2-0019), the U.S. Air Force Office of Scientific Research (MURI #FA9550-06-0312), the Air Force Research Lab (AFRL), the State of California Micro Program, and the following companies: Agilent, Bosch, Lockheed-Martin, National Instruments, Thales and Toyota. This work is also supported by the COMBEST and ArtistDesign projects of the European Union, and the Swiss National Science Foundation. ","month":"01","project":[{"grant_number":"215543","name":"COMponent-Based Embedded Systems design Techniques","_id":"25EFB36C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"_id":"25F1337C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Design for Embedded Systems","grant_number":"214373"}],"oa_version":"Submitted Version","has_accepted_license":"1","publication":"EMSOFT '09 Proceedings of the seventh ACM international conference on Embedded software","conference":{"location":"Grenoble, France","end_date":"2009-10-16","start_date":"2009-10-12","name":"EMSOFT: Embedded Software "},"language":[{"iso":"eng"}],"publist_id":"2360","oa":1,"type":"conference","date_published":"2009-01-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","file":[{"creator":"system","file_id":"5045","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"IST-2012-70-v1+1_On_Relational_Interfaces.pdf","date_updated":"2020-07-14T12:46:16Z","checksum":"3a70e21527dfaad2f198549ae5710786","file_size":310902,"date_created":"2018-12-12T10:13:57Z"}]},{"publisher":"Springer","file_date_updated":"2020-07-14T12:46:16Z","quality_controlled":"1","page":"3 - 23","intvolume":"      5797","title":"Formalisms for specifying Markovian population models","pubrep_id":"67","alternative_title":["LNCS"],"department":[{"_id":"ToHe"}],"date_created":"2018-12-11T12:05:28Z","publication_status":"published","author":[{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724"},{"last_name":"Jobstmann","first_name":"Barbara","full_name":"Jobstmann, Barbara"},{"full_name":"Wolf, Verena","first_name":"Verena","last_name":"Wolf"}],"scopus_import":1,"_id":"3841","ddc":["005"],"acknowledgement":"This research was supported in part by the Excellence Cluster on Multimodal Computing and Interaction and the Swiss National Science Foundation.","volume":5797,"abstract":[{"lang":"eng","text":"We compare several languages for specifying Markovian population models such as queuing networks and chemical reaction networks. These languages —matrix descriptions, stochastic Petri nets, stoichiometric equations, stochastic process algebras, and guarded command models— all describe continuous-time Markov chains, but they differ according to important properties, such as compositionality, expressiveness and succinctness, executability, ease of use, and the support they provide for checking the well-formedness of a model and for analyzing a model. "}],"day":"07","doi":"10.1007/978-3-642-04420-5_2","year":"2009","citation":{"short":"T.A. Henzinger, B. Jobstmann, V. Wolf, in:, Springer, 2009, pp. 3–23.","mla":"Henzinger, Thomas A., et al. <i>Formalisms for Specifying Markovian Population Models</i>. Vol. 5797, Springer, 2009, pp. 3–23, doi:<a href=\"https://doi.org/10.1007/978-3-642-04420-5_2\">10.1007/978-3-642-04420-5_2</a>.","ista":"Henzinger TA, Jobstmann B, Wolf V. 2009. Formalisms for specifying Markovian population models. RP: Reachability Problems, LNCS, vol. 5797, 3–23.","apa":"Henzinger, T. A., Jobstmann, B., &#38; Wolf, V. (2009). Formalisms for specifying Markovian population models (Vol. 5797, pp. 3–23). Presented at the RP: Reachability Problems, Palaiseau, France: Springer. <a href=\"https://doi.org/10.1007/978-3-642-04420-5_2\">https://doi.org/10.1007/978-3-642-04420-5_2</a>","ama":"Henzinger TA, Jobstmann B, Wolf V. Formalisms for specifying Markovian population models. In: Vol 5797. Springer; 2009:3-23. doi:<a href=\"https://doi.org/10.1007/978-3-642-04420-5_2\">10.1007/978-3-642-04420-5_2</a>","ieee":"T. A. Henzinger, B. Jobstmann, and V. Wolf, “Formalisms for specifying Markovian population models,” presented at the RP: Reachability Problems, Palaiseau, France, 2009, vol. 5797, pp. 3–23.","chicago":"Henzinger, Thomas A, Barbara Jobstmann, and Verena Wolf. “Formalisms for Specifying Markovian Population Models,” 5797:3–23. Springer, 2009. <a href=\"https://doi.org/10.1007/978-3-642-04420-5_2\">https://doi.org/10.1007/978-3-642-04420-5_2</a>."},"date_updated":"2023-02-23T11:24:49Z","conference":{"start_date":"2009-09-23","name":"RP: Reachability Problems","location":"Palaiseau, France","end_date":"2009-09-25"},"language":[{"iso":"eng"}],"month":"09","oa_version":"Submitted Version","has_accepted_license":"1","related_material":{"record":[{"status":"public","relation":"later_version","id":"3381"}]},"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"date_updated":"2020-07-14T12:46:16Z","content_type":"application/pdf","file_name":"IST-2012-67-v1+1_Formalisms_for_specifying_Markovian_population_models.pdf","date_created":"2018-12-12T10:08:41Z","checksum":"df88431872586c773fbcfea37d7b36a2","file_size":222840,"file_id":"4702","creator":"system","relation":"main_file","access_level":"open_access"}],"oa":1,"publist_id":"2352","type":"conference","date_published":"2009-09-07T00:00:00Z"},{"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).\r\nStandard Uniformization (SU) is an efficient method for the transient analysis of CTMCs. For systems with very different time scales, such as biochemical reaction networks, SU is computationally expensive. In these cases, a variant of SU, called adaptive uniformization (AU), is known to reduce the large number of iterations needed by SU. The additional difficulty of AU is that it requires the solution of a birth process.\r\nIn this paper we present an on-the-fly variant of AU, where we improve the original algorithm for AU 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."}],"doi":"10.1109/HiBi.2009.23","day":"30","date_updated":"2023-02-23T11:45:05Z","year":"2009","citation":{"short":"F. Didier, T.A. Henzinger, M. Mateescu, V. Wolf, in:, IEEE, 2009, pp. 118–127.","mla":"Didier, Frédéric, et al. <i>Fast Adaptive Uniformization of the Chemical Master Equation</i>. Vol. 4, no. 6, IEEE, 2009, pp. 118–27, doi:<a href=\"https://doi.org/10.1109/HiBi.2009.23\">10.1109/HiBi.2009.23</a>.","ista":"Didier F, Henzinger TA, Mateescu M, Wolf V. 2009. Fast adaptive uniformization of the chemical master equation. HIBI: High-Performance Computational Systems Biology vol. 4, 118–127.","ama":"Didier F, Henzinger TA, Mateescu M, Wolf V. Fast adaptive uniformization of the chemical master equation. In: Vol 4. IEEE; 2009:118-127. doi:<a href=\"https://doi.org/10.1109/HiBi.2009.23\">10.1109/HiBi.2009.23</a>","apa":"Didier, F., Henzinger, T. A., Mateescu, M., &#38; Wolf, V. (2009). Fast adaptive uniformization of the chemical master equation (Vol. 4, pp. 118–127). Presented at the HIBI: High-Performance Computational Systems Biology, Trento, Italy: IEEE. <a href=\"https://doi.org/10.1109/HiBi.2009.23\">https://doi.org/10.1109/HiBi.2009.23</a>","ieee":"F. Didier, T. A. Henzinger, M. Mateescu, and V. Wolf, “Fast adaptive uniformization of the chemical master equation,” presented at the HIBI: High-Performance Computational Systems Biology, Trento, Italy, 2009, vol. 4, no. 6, pp. 118–127.","chicago":"Didier, Frédéric, Thomas A Henzinger, Maria Mateescu, and Verena Wolf. “Fast Adaptive Uniformization of the Chemical Master Equation,” 4:118–27. IEEE, 2009. <a href=\"https://doi.org/10.1109/HiBi.2009.23\">https://doi.org/10.1109/HiBi.2009.23</a>."},"ddc":["000"],"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.","volume":4,"title":"Fast adaptive uniformization of the chemical master equation","intvolume":"         4","publication_status":"published","date_created":"2018-12-11T12:05:28Z","department":[{"_id":"ToHe"},{"_id":"CaGu"}],"article_processing_charge":"No","author":[{"full_name":"Didier, Frédéric","last_name":"Didier","first_name":"Frédéric"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"},{"id":"3B43276C-F248-11E8-B48F-1D18A9856A87","last_name":"Mateescu","first_name":"Maria","full_name":"Mateescu, Maria"},{"full_name":"Wolf, Verena","last_name":"Wolf","first_name":"Verena"}],"issue":"6","_id":"3843","scopus_import":1,"publisher":"IEEE","file_date_updated":"2020-07-14T12:46:17Z","page":"118 - 127","quality_controlled":"1","oa":1,"publist_id":"2348","date_published":"2009-10-30T00:00:00Z","type":"conference","related_material":{"record":[{"status":"public","id":"3842","relation":"later_version"}]},"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"content_type":"application/pdf","file_name":"2009_HIBI_Didier.pdf","date_updated":"2020-07-14T12:46:17Z","checksum":"9a3bde48f43203991a0b3c6a277c2f5b","file_size":222890,"date_created":"2020-05-19T16:33:55Z","creator":"dernst","file_id":"7874","access_level":"open_access","relation":"main_file"}],"month":"10","oa_version":"Submitted Version","has_accepted_license":"1","conference":{"start_date":"2009-10-14","name":"HIBI: High-Performance Computational Systems Biology","end_date":"2009-10-16","location":"Trento, Italy"},"language":[{"iso":"eng"}]},{"acknowledgement":"Supported by the EU ArtistDesign Network of Excellence on Embedded Systems Design, the EU project COMBEST, the Austrian Science Funds P18913-N15 and V00125, and Fundacao para a Ciencia e Tecnologia funds SFRH/BD/29461/2006 and PTDC/EIA/71462/2006","ddc":["000"],"doi":"10.1109/RTSS.2009.9","day":"01","abstract":[{"text":"The Hierarchical Timing Language (HTL) is a real-time coordination language for distributed control systems. HTL programs must be checked for well-formedness, race freedom, transmission safety (schedulability of inter-host communication), and time safety (schedulability of host computation). We present a modular abstract syntax and semantics for HTL, modular checks of well-formedness, race freedom, and transmission safety, and modular code distribution. Our contributions here complement previous results on HTL time safety and modular code generation. Modularity in HTL can be utilized in easy program composition as well as fast program analysis and code generation, but also in so-called runtime patching, where program components may be modified at runtime.","lang":"eng"}],"date_updated":"2021-01-12T07:52:36Z","year":"2009","citation":{"mla":"Henzinger, Thomas A., et al. <i>Distributed, Modular HTL</i>. IEEE, 2009, pp. 171–80, doi:<a href=\"https://doi.org/10.1109/RTSS.2009.9\">10.1109/RTSS.2009.9</a>.","short":"T.A. Henzinger, C. Kirsch, E. Marques, A. Sokolova, in:, IEEE, 2009, pp. 171–180.","ista":"Henzinger TA, Kirsch C, Marques E, Sokolova A. 2009. Distributed, modular HTL. RTSS: Real-Time Systems Symposium, 171–180.","ama":"Henzinger TA, Kirsch C, Marques E, Sokolova A. Distributed, modular HTL. In: IEEE; 2009:171-180. doi:<a href=\"https://doi.org/10.1109/RTSS.2009.9\">10.1109/RTSS.2009.9</a>","apa":"Henzinger, T. A., Kirsch, C., Marques, E., &#38; Sokolova, A. (2009). Distributed, modular HTL (pp. 171–180). Presented at the RTSS: Real-Time Systems Symposium, Washington, DC, United States: IEEE. <a href=\"https://doi.org/10.1109/RTSS.2009.9\">https://doi.org/10.1109/RTSS.2009.9</a>","chicago":"Henzinger, Thomas A, Christoph Kirsch, Eduardo Marques, and Ana Sokolova. “Distributed, Modular HTL,” 171–80. IEEE, 2009. <a href=\"https://doi.org/10.1109/RTSS.2009.9\">https://doi.org/10.1109/RTSS.2009.9</a>.","ieee":"T. A. Henzinger, C. Kirsch, E. Marques, and A. Sokolova, “Distributed, modular HTL,” presented at the RTSS: Real-Time Systems Symposium, Washington, DC, United States, 2009, pp. 171–180."},"publisher":"IEEE","page":"171 - 180","ec_funded":1,"quality_controlled":"1","file_date_updated":"2020-07-14T12:46:17Z","publication_status":"published","department":[{"_id":"ToHe"}],"date_created":"2018-12-11T12:05:28Z","title":"Distributed, modular HTL","pubrep_id":"65","_id":"3844","author":[{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger","first_name":"Thomas A"},{"last_name":"Kirsch","first_name":"Christoph","full_name":"Kirsch, Christoph"},{"first_name":"Eduardo","last_name":"Marques","full_name":"Marques, Eduardo"},{"full_name":"Sokolova, Ana","first_name":"Ana","last_name":"Sokolova"}],"file":[{"access_level":"open_access","relation":"main_file","file_id":"4655","creator":"system","date_created":"2018-12-12T10:07:56Z","checksum":"b2b15a5ef71eb50d62eaa5aea7efd8c4","file_size":526458,"date_updated":"2020-07-14T12:46:17Z","content_type":"application/pdf","file_name":"IST-2012-65-v1+1_Distributed_modular_Htl.pdf"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","oa":1,"publist_id":"2346","date_published":"2009-01-01T00:00:00Z","type":"conference","conference":{"start_date":"2009-12-01","name":"RTSS: Real-Time Systems Symposium","end_date":"2009-12-04","location":"Washington, DC, United States"},"language":[{"iso":"eng"}],"oa_version":"Submitted Version","project":[{"grant_number":"214373","name":"Design for Embedded Systems","_id":"25F1337C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"call_identifier":"FP7","_id":"25EFB36C-B435-11E9-9278-68D0E5697425","name":"COMponent-Based Embedded Systems design Techniques","grant_number":"215543"}],"month":"01","has_accepted_license":"1"},{"publist_id":"2309","oa":1,"date_published":"2009-10-01T00:00:00Z","type":"journal_article","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"date_updated":"2020-07-14T12:46:20Z","file_name":"IST-2012-53-v1+1_Finitary_winning_in_omega-regular_games.pdf","content_type":"application/pdf","date_created":"2018-12-12T10:15:08Z","file_size":180082,"checksum":"139c4586d24f11e5da31fb3a0cf96ef4","file_id":"5125","creator":"system","access_level":"open_access","relation":"main_file"}],"month":"10","article_number":"1","oa_version":"Submitted Version","project":[{"call_identifier":"FP7","_id":"25EFB36C-B435-11E9-9278-68D0E5697425","grant_number":"215543","name":"COMponent-Based Embedded Systems design Techniques"}],"publication":"ACM Transactions on Computational Logic (TOCL)","has_accepted_license":"1","language":[{"iso":"eng"}],"abstract":[{"text":"Games on graphs with omega-regular objectives provide a model for the control and synthesis of reactive systems. Every omega-regular objective can be decomposed into a safety part and a liveness part. The liveness part ensures that something good happens “eventually.” Two main strengths of the classical, infinite-limit formulation of liveness are robustness (independence from the granularity of transitions) and simplicity (abstraction of complicated time bounds). However, the classical liveness formulation suffers from the drawback that the time until something good happens may be unbounded. A stronger formulation of liveness, so-called finitary liveness, overcomes this drawback, while still retaining robustness and simplicity. Finitary liveness requires that there exists an unknown, fixed bound b such that something good happens within b transitions. While for one-shot liveness (reachability) objectives, classical and finitary liveness coincide, for repeated liveness (Buchi) objectives, the finitary formulation is strictly stronger. In this work we study games with finitary parity and Streett objectives. We prove the determinacy of these games, present algorithms for solving these games, and characterize the memory requirements of winning strategies. We show that finitary parity games can be solved in polynomial time, which is not known for infinitary parity games. For finitary Streett games, we give an EXPTIME algorithm and show that the problem is NP-hard. Our algorithms can be used, for example, for synthesizing controllers that do not let the response time of a system increase without bound.","lang":"eng"}],"doi":"10.1145/1614431.1614432","day":"01","date_updated":"2021-01-12T07:52:50Z","citation":{"ieee":"K. Chatterjee, T. A. Henzinger, and F. Horn, “Finitary winning in omega-regular games,” <i>ACM Transactions on Computational Logic (TOCL)</i>, vol. 11, no. 1. ACM, 2009.","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, and Florian Horn. “Finitary Winning in Omega-Regular Games.” <i>ACM Transactions on Computational Logic (TOCL)</i>. ACM, 2009. <a href=\"https://doi.org/10.1145/1614431.1614432\">https://doi.org/10.1145/1614431.1614432</a>.","apa":"Chatterjee, K., Henzinger, T. A., &#38; Horn, F. (2009). Finitary winning in omega-regular games. <i>ACM Transactions on Computational Logic (TOCL)</i>. ACM. <a href=\"https://doi.org/10.1145/1614431.1614432\">https://doi.org/10.1145/1614431.1614432</a>","ama":"Chatterjee K, Henzinger TA, Horn F. Finitary winning in omega-regular games. <i>ACM Transactions on Computational Logic (TOCL)</i>. 2009;11(1). doi:<a href=\"https://doi.org/10.1145/1614431.1614432\">10.1145/1614431.1614432</a>","ista":"Chatterjee K, Henzinger TA, Horn F. 2009. Finitary winning in omega-regular games. ACM Transactions on Computational Logic (TOCL). 11(1), 1.","short":"K. Chatterjee, T.A. Henzinger, F. Horn, ACM Transactions on Computational Logic (TOCL) 11 (2009).","mla":"Chatterjee, Krishnendu, et al. “Finitary Winning in Omega-Regular Games.” <i>ACM Transactions on Computational Logic (TOCL)</i>, vol. 11, no. 1, 1, ACM, 2009, doi:<a href=\"https://doi.org/10.1145/1614431.1614432\">10.1145/1614431.1614432</a>."},"year":"2009","ddc":["004"],"acknowledgement":"This research was supported in part by the AFOSR MURI grant F49620-00-1-0327, the NSF grants CCR-0132780, CNS-0720884, and CCR- 225610, by the Swiss National Science Foundation, by the COMBEST project of the European Union, and EU-TMR network Games.\r\nWe thank anonymous reviewers for useful comments.","volume":11,"pubrep_id":"53","title":"Finitary winning in omega-regular games","intvolume":"        11","publication_status":"published","date_created":"2018-12-11T12:05:37Z","department":[{"_id":"KrCh"}],"author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"id":"37327ACE-F248-11E8-B48F-1D18A9856A87","last_name":"Horn","first_name":"Florian","full_name":"Horn, Florian"}],"issue":"1","_id":"3870","scopus_import":1,"publisher":"ACM","file_date_updated":"2020-07-14T12:46:20Z","quality_controlled":"1","ec_funded":1},{"conference":{"location":"Bologna, Italy","end_date":"2009-09-04","name":"CONCUR: Concurrency Theory","start_date":"2009-09-01"},"language":[{"iso":"eng"}],"project":[{"grant_number":"214373","name":"Design for Embedded Systems","call_identifier":"FP7","_id":"25F1337C-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","_id":"25EFB36C-B435-11E9-9278-68D0E5697425","grant_number":"215543","name":"COMponent-Based Embedded Systems design Techniques"}],"oa_version":"Submitted Version","month":"09","has_accepted_license":"1","file":[{"date_created":"2018-12-12T10:09:46Z","checksum":"af973ddbcf131b8810c6bff2c055ff56","file_size":200161,"date_updated":"2020-07-14T12:46:20Z","file_name":"IST-2012-52-v1+1_Probabilistic_Weighted_Automata.pdf","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"4771","creator":"system"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","oa":1,"publist_id":"2304","type":"conference","date_published":"2009-09-01T00:00:00Z","publisher":"Springer","ec_funded":1,"quality_controlled":"1","page":"244 - 258","file_date_updated":"2020-07-14T12:46:20Z","department":[{"_id":"KrCh"}],"date_created":"2018-12-11T12:05:37Z","publication_status":"published","intvolume":"      5710","title":"Probabilistic weighted automata","alternative_title":["LNCS"],"pubrep_id":"52","scopus_import":1,"_id":"3871","author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Doyen, Laurent","last_name":"Doyen","first_name":"Laurent"},{"last_name":"Henzinger","first_name":"Thomas A","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"}],"volume":5710,"acknowledgement":"This research was supported in part by the Swiss National Science Foundation under the Indo-Swiss Joint Research Programme, by the European Network of Excellence on Embedded Systems Design (ArtistDesign), by the European projects Combest, Quasimodo, and Gasics, by the PAI program Moves funded by the Belgian Federal Government, and by the CFV (Federated Center in Verification ) funded by the F.R.S.-FNRS.","ddc":["000","005"],"day":"01","doi":"10.1007/978-3-642-04081-8_17","abstract":[{"lang":"eng","text":"Nondeterministic weighted automata are finite automata with numerical weights oil transitions. They define quantitative languages 1, that assign to each word v; a real number L(w). The value of ail infinite word w is computed as the maximal value of all runs over w, and the value of a run as the supremum, limsup liminf, limit average, or discounted sum of the transition weights. We introduce probabilistic weighted antomata, in which the transitions are chosen in a randomized (rather than nondeterministic) fashion. Under almost-sure semantics (resp. positive semantics), the value of a word v) is the largest real v such that the runs over w have value at least v with probability I (resp. positive probability). We study the classical questions of automata theory for probabilistic weighted automata: emptiness and universality, expressiveness, and closure under various operations oil languages. For quantitative languages, emptiness university axe defined as whether the value of some (resp. every) word exceeds a given threshold. We prove some, of these questions to he decidable, and others undecidable. Regarding expressive power, we show that probabilities allow its to define a wide variety of new classes of quantitative languages except for discounted-sum automata, where probabilistic choice is no more expressive than nondeterminism. Finally we live ail almost complete picture of the closure of various classes of probabilistic weighted automata for the following, provide, is operations oil quantitative languages: maximum, sum. and numerical complement."}],"citation":{"chicago":"Chatterjee, Krishnendu, Laurent Doyen, and Thomas A Henzinger. “Probabilistic Weighted Automata,” 5710:244–58. Springer, 2009. <a href=\"https://doi.org/10.1007/978-3-642-04081-8_17\">https://doi.org/10.1007/978-3-642-04081-8_17</a>.","ieee":"K. Chatterjee, L. Doyen, and T. A. Henzinger, “Probabilistic weighted automata,” presented at the CONCUR: Concurrency Theory, Bologna, Italy, 2009, vol. 5710, pp. 244–258.","ama":"Chatterjee K, Doyen L, Henzinger TA. Probabilistic weighted automata. In: Vol 5710. Springer; 2009:244-258. doi:<a href=\"https://doi.org/10.1007/978-3-642-04081-8_17\">10.1007/978-3-642-04081-8_17</a>","apa":"Chatterjee, K., Doyen, L., &#38; Henzinger, T. A. (2009). Probabilistic weighted automata (Vol. 5710, pp. 244–258). Presented at the CONCUR: Concurrency Theory, Bologna, Italy: Springer. <a href=\"https://doi.org/10.1007/978-3-642-04081-8_17\">https://doi.org/10.1007/978-3-642-04081-8_17</a>","ista":"Chatterjee K, Doyen L, Henzinger TA. 2009. Probabilistic weighted automata. CONCUR: Concurrency Theory, LNCS, vol. 5710, 244–258.","mla":"Chatterjee, Krishnendu, et al. <i>Probabilistic Weighted Automata</i>. Vol. 5710, Springer, 2009, pp. 244–58, doi:<a href=\"https://doi.org/10.1007/978-3-642-04081-8_17\">10.1007/978-3-642-04081-8_17</a>.","short":"K. Chatterjee, L. Doyen, T.A. Henzinger, in:, Springer, 2009, pp. 244–258."},"year":"2009","date_updated":"2021-01-12T07:52:50Z"}]