[{"type":"technical_report","publication_status":"published","oa_version":"Published Version","year":"2011","month":"07","pubrep_id":"15","date_created":"2018-12-12T11:38:59Z","title":"An O(n2) time algorithm for alternating Büchi games","has_accepted_license":"1","status":"public","doi":"10.15479/AT:IST-2011-0009","ddc":["000","004"],"abstract":[{"text":"Computing the winning set for Büchi objectives in alternating games on graphs is a central problem in computer aided verification with a large number of applications. The long standing best known upper bound for solving the problem is ̃O(n·m), where n is the number of vertices and m is the number of edges in the graph. We are the first to break the ̃O(n·m) boundary by presenting a new technique that reduces the running time to O(n2). This bound also leads to O(n2) time algorithms for computing the set of almost-sure winning vertices for Büchi objectives (1) in alternating games with probabilistic transitions (improving an earlier bound of O(n·m)), (2) in concurrent graph games with constant actions (improving an earlier bound of O(n3)), and (3) in Markov decision processes (improving for m > n4/3 an earlier bound of O(min(m1.5, m·n2/3)). We also show that the same technique can be used to compute the maximal end-component decomposition of a graph in time O(n2), which is an improvement over earlier bounds for m > n4/3. Finally, we show how to maintain the winning set for Büchi objectives in alternating games under a sequence of edge insertions or a sequence of edge deletions in O(n) amortized time per operation. This is the first dynamic algorithm for this problem.","lang":"eng"}],"publisher":"IST Austria","author":[{"orcid":"0000-0002-4561-241X","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H","last_name":"Henzinger","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","first_name":"Monika H"}],"publication_identifier":{"issn":["2664-1690"]},"date_updated":"2023-02-23T11:15:12Z","department":[{"_id":"KrCh"}],"language":[{"iso":"eng"}],"article_processing_charge":"No","_id":"5379","day":"11","date_published":"2011-07-11T00:00:00Z","file":[{"date_updated":"2020-07-14T12:46:39Z","relation":"main_file","file_size":388665,"creator":"system","file_name":"IST-2011-0009_IST-2011-0009.pdf","file_id":"5504","content_type":"application/pdf","date_created":"2018-12-12T11:53:43Z","checksum":"0b354264229045d982332fd2cb5b9a26","access_level":"open_access"}],"related_material":{"record":[{"id":"3165","relation":"later_version","status":"public"}]},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","alternative_title":["IST Austria Technical Report"],"file_date_updated":"2020-07-14T12:46:39Z","oa":1,"citation":{"ama":"Chatterjee K, Henzinger MH. <i>An O(N2) Time Algorithm for Alternating Büchi Games</i>. IST Austria; 2011. doi:<a href=\"https://doi.org/10.15479/AT:IST-2011-0009\">10.15479/AT:IST-2011-0009</a>","ista":"Chatterjee K, Henzinger MH. 2011. An O(n2) time algorithm for alternating Büchi games, IST Austria, 20p.","short":"K. Chatterjee, M.H. Henzinger, An O(N2) Time Algorithm for Alternating Büchi Games, IST Austria, 2011.","ieee":"K. Chatterjee and M. H. Henzinger, <i>An O(n2) time algorithm for alternating Büchi games</i>. IST Austria, 2011.","mla":"Chatterjee, Krishnendu, and Monika H. Henzinger. <i>An O(N2) Time Algorithm for Alternating Büchi Games</i>. IST Austria, 2011, doi:<a href=\"https://doi.org/10.15479/AT:IST-2011-0009\">10.15479/AT:IST-2011-0009</a>.","apa":"Chatterjee, K., &#38; Henzinger, M. H. (2011). <i>An O(n2) time algorithm for alternating Büchi games</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2011-0009\">https://doi.org/10.15479/AT:IST-2011-0009</a>","chicago":"Chatterjee, Krishnendu, and Monika H Henzinger. <i>An O(N2) Time Algorithm for Alternating Büchi Games</i>. IST Austria, 2011. <a href=\"https://doi.org/10.15479/AT:IST-2011-0009\">https://doi.org/10.15479/AT:IST-2011-0009</a>."},"page":"20"},{"citation":{"mla":"Chatterjee, Krishnendu. <i>Bounded Rationality in Concurrent Parity Games</i>. IST Austria, 2011, doi:<a href=\"https://doi.org/10.15479/AT:IST-2011-0008\">10.15479/AT:IST-2011-0008</a>.","apa":"Chatterjee, K. (2011). <i>Bounded rationality in concurrent parity games</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2011-0008\">https://doi.org/10.15479/AT:IST-2011-0008</a>","chicago":"Chatterjee, Krishnendu. <i>Bounded Rationality in Concurrent Parity Games</i>. IST Austria, 2011. <a href=\"https://doi.org/10.15479/AT:IST-2011-0008\">https://doi.org/10.15479/AT:IST-2011-0008</a>.","ista":"Chatterjee K. 2011. Bounded rationality in concurrent parity games, IST Austria, 53p.","ama":"Chatterjee K. <i>Bounded Rationality in Concurrent Parity Games</i>. IST Austria; 2011. doi:<a href=\"https://doi.org/10.15479/AT:IST-2011-0008\">10.15479/AT:IST-2011-0008</a>","ieee":"K. Chatterjee, <i>Bounded rationality in concurrent parity games</i>. IST Austria, 2011.","short":"K. Chatterjee, Bounded Rationality in Concurrent Parity Games, IST Austria, 2011."},"page":"53","publication_identifier":{"issn":["2664-1690"]},"oa":1,"file_date_updated":"2020-07-14T12:46:39Z","author":[{"first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"}],"publisher":"IST Austria","abstract":[{"text":"We consider 2-player games played on a finite state space for an infinite number of rounds.  The games are concurrent: in each round, the two players (player 1 and player 2) choose their moves independently and simultaneously; the current state and the two moves determine the successor state. We study concurrent games with ω-regular winning conditions specified as parity objectives.  We consider the qualitative analysis problems: the computation of the almost-sure and limit-sure winning set of states, where player 1 can ensure to win with probability 1 and with probability arbitrarily close to 1, respectively. In general the almost-sure and limit-sure winning strategies require both infinite-memory as well as infinite-precision (to describe probabilities). We study the bounded-rationality problem for qualitative analysis of concurrent parity games, where the strategy set for player 1 is restricted to bounded-resource strategies.  In terms of precision, strategies can be deterministic, uniform, finite-precision or infinite-precision;  and in terms of memory, strategies can be memoryless, finite-memory or infinite-memory. We present a precise and complete characterization of the qualitative winning sets for all combinations of classes of strategies. In particular, we show that uniform memoryless strategies are as powerful as finite-precision infinite-memory strategies, and infinite-precision memoryless strategies are as powerful as infinite-precision finite-memory strategies.  We show that the winning sets can be computed in O(n2d+3) time, where n is the size of the game structure and 2d is the number of priorities (or colors), and our algorithms are symbolic. The membership problem of whether a state belongs to a winning set can be decided in NP ∩ coNP. While this complexity is the same as for the simpler class of turn-based parity games, where in each state only one of the two players has a choice of moves, our algorithms,that are obtained by characterization of the winning sets as μ-calculus formulas, are considerably more involved than those for turn-based games.","lang":"eng"}],"alternative_title":["IST Austria Technical Report"],"ddc":["000"],"doi":"10.15479/AT:IST-2011-0008","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Bounded rationality in concurrent parity games","date_created":"2018-12-12T11:39:00Z","has_accepted_license":"1","related_material":{"record":[{"status":"public","relation":"later_version","id":"3338"}]},"pubrep_id":"16","file":[{"checksum":"0fd38186409be819a911c4990fa79d1f","date_created":"2018-12-12T11:54:22Z","access_level":"open_access","content_type":"application/pdf","file_id":"5544","file_name":"IST-2011-0008_IST-2011-0008.pdf","creator":"system","file_size":500399,"relation":"main_file","date_updated":"2020-07-14T12:46:39Z"}],"month":"07","date_published":"2011-07-11T00:00:00Z","year":"2011","day":"11","_id":"5380","oa_version":"Published Version","publication_status":"published","language":[{"iso":"eng"}],"department":[{"_id":"KrCh"}],"date_updated":"2023-02-23T11:22:53Z","type":"technical_report"},{"year":"2011","month":"07","date_published":"2011-07-05T00:00:00Z","pubrep_id":"17","file":[{"date_updated":"2020-07-14T12:46:39Z","relation":"main_file","file_size":574055,"date_created":"2018-12-12T11:53:27Z","access_level":"open_access","checksum":"06bf6dfc97f6006e3fd0e9a3f31bc961","file_id":"5488","file_name":"IST-2011-0007_IST-2011-0007.pdf","creator":"system","content_type":"application/pdf"}],"date_created":"2018-12-12T11:39:00Z","title":"Partial-observation stochastic games: How to win when belief fails","has_accepted_license":"1","related_material":{"record":[{"relation":"later_version","id":"1903","status":"public"},{"relation":"later_version","id":"2211","status":"public"},{"status":"public","id":"2955","relation":"later_version"}]},"language":[{"iso":"eng"}],"type":"technical_report","date_updated":"2023-02-23T11:05:48Z","department":[{"_id":"KrCh"}],"publication_status":"published","_id":"5381","day":"05","oa_version":"Published Version","abstract":[{"lang":"eng","text":"In two-player finite-state stochastic games of partial obser- vation on graphs, in every state of the graph, the players simultaneously choose an action, and their joint actions determine a probability distri- bution over the successor states. The game is played for infinitely many rounds and thus the players construct an infinite path in the graph. We consider reachability objectives where the first player tries to ensure a target state to be visited almost-surely (i.e., with probability 1) or pos- itively (i.e., with positive probability), no matter the strategy of the second player.\r\n\r\nWe classify such games according to the information and to the power of randomization available to the players. On the basis of information, the game can be one-sided with either (a) player 1, or (b) player 2 having partial observation (and the other player has perfect observation), or two- sided with (c) both players having partial observation. On the basis of randomization, (a) the players may not be allowed to use randomization (pure strategies), or (b) they may choose a probability distribution over actions but the actual random choice is external and not visible to the player (actions invisible), or (c) they may use full randomization.\r\n\r\nOur main results for pure strategies are as follows: (1) For one-sided games with player 2 perfect observation we show that (in contrast to full randomized strategies) belief-based (subset-construction based) strate- gies are not sufficient, and present an exponential upper bound on mem- ory both for almost-sure and positive winning strategies; we show that the problem of deciding the existence of almost-sure and positive winning strategies for player 1 is EXPTIME-complete and present symbolic algo- rithms that avoid the explicit exponential construction. (2) For one-sided games with player 1 perfect observation we show that non-elementary memory is both necessary and sufficient for both almost-sure and posi- tive winning strategies. (3) We show that for the general (two-sided) case finite-memory strategies are sufficient for both positive and almost-sure winning, and at least non-elementary memory is required. We establish the equivalence of the almost-sure winning problems for pure strategies and for randomized strategies with actions invisible. Our equivalence re- sult exhibit serious flaws in previous results in the literature: we show a non-elementary memory lower bound for almost-sure winning whereas an exponential upper bound was previously claimed."}],"author":[{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu"},{"first_name":"Laurent","full_name":"Doyen, Laurent","last_name":"Doyen"}],"publisher":"IST Austria","file_date_updated":"2020-07-14T12:46:39Z","page":"43","citation":{"chicago":"Chatterjee, Krishnendu, and Laurent Doyen. <i>Partial-Observation Stochastic Games: How to Win When Belief Fails</i>. IST Austria, 2011. <a href=\"https://doi.org/10.15479/AT:IST-2011-0007\">https://doi.org/10.15479/AT:IST-2011-0007</a>.","mla":"Chatterjee, Krishnendu, and Laurent Doyen. <i>Partial-Observation Stochastic Games: How to Win When Belief Fails</i>. IST Austria, 2011, doi:<a href=\"https://doi.org/10.15479/AT:IST-2011-0007\">10.15479/AT:IST-2011-0007</a>.","apa":"Chatterjee, K., &#38; Doyen, L. (2011). <i>Partial-observation stochastic games: How to win when belief fails</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2011-0007\">https://doi.org/10.15479/AT:IST-2011-0007</a>","ieee":"K. Chatterjee and L. Doyen, <i>Partial-observation stochastic games: How to win when belief fails</i>. IST Austria, 2011.","short":"K. Chatterjee, L. Doyen, Partial-Observation Stochastic Games: How to Win When Belief Fails, IST Austria, 2011.","ama":"Chatterjee K, Doyen L. <i>Partial-Observation Stochastic Games: How to Win When Belief Fails</i>. IST Austria; 2011. doi:<a href=\"https://doi.org/10.15479/AT:IST-2011-0007\">10.15479/AT:IST-2011-0007</a>","ista":"Chatterjee K, Doyen L. 2011. Partial-observation stochastic games: How to win when belief fails, IST Austria, 43p."},"oa":1,"publication_identifier":{"issn":["2664-1690"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","ddc":["000","005"],"doi":"10.15479/AT:IST-2011-0007","alternative_title":["IST Austria Technical Report"]},{"publication_identifier":{"issn":["2664-1690"]},"oa":1,"page":"18","citation":{"ieee":"K. Chatterjee, <i>Robustness of structurally equivalent concurrent parity games</i>. IST Austria, 2011.","short":"K. Chatterjee, Robustness of Structurally Equivalent Concurrent Parity Games, IST Austria, 2011.","ama":"Chatterjee K. <i>Robustness of Structurally Equivalent Concurrent Parity Games</i>. IST Austria; 2011. doi:<a href=\"https://doi.org/10.15479/AT:IST-2011-0006\">10.15479/AT:IST-2011-0006</a>","ista":"Chatterjee K. 2011. Robustness of structurally equivalent concurrent parity games, IST Austria, 18p.","chicago":"Chatterjee, Krishnendu. <i>Robustness of Structurally Equivalent Concurrent Parity Games</i>. IST Austria, 2011. <a href=\"https://doi.org/10.15479/AT:IST-2011-0006\">https://doi.org/10.15479/AT:IST-2011-0006</a>.","mla":"Chatterjee, Krishnendu. <i>Robustness of Structurally Equivalent Concurrent Parity Games</i>. IST Austria, 2011, doi:<a href=\"https://doi.org/10.15479/AT:IST-2011-0006\">10.15479/AT:IST-2011-0006</a>.","apa":"Chatterjee, K. (2011). <i>Robustness of structurally equivalent concurrent parity games</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2011-0006\">https://doi.org/10.15479/AT:IST-2011-0006</a>"},"file_date_updated":"2020-07-14T12:46:40Z","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","first_name":"Krishnendu"}],"publisher":"IST Austria","abstract":[{"text":"We consider two-player stochastic games played on a finite state space for an infinite num- ber of rounds. The games are concurrent: in each round, the two players (player 1 and player 2) choose their moves independently and simultaneously; the current state and the two moves determine a probability distribution over the successor states. We also consider the important special case of turn-based stochastic games where players make moves in turns, rather than concurrently. We study concurrent games with ω-regular winning conditions specified as parity objectives. The value for player 1 for a parity objective is the maximal probability with which the player can guarantee the satisfaction of the objective against all strategies of the opponent. We study the problem of continuity and robustness of the value function in concurrent and turn-based stochastic parity games with respect to imprecision in the transition probabilities. We present quantitative bounds on the difference of the value function (in terms of the imprecision of the transition probabilities) and show the value continuity for structurally equivalent concurrent games (two games are structurally equivalent if the support of the transition func- tion is same and the probabilities differ). We also show robustness of optimal strategies for structurally equivalent turn-based stochastic parity games. Finally we show that the value continuity property breaks without the structurally equivalent assumption (even for Markov chains) and show that our quantitative bound is asymptotically optimal. Hence our results are tight (the assumption is both necessary and sufficient) and optimal (our quantitative bound is asymptotically optimal).","lang":"eng"}],"alternative_title":["IST Austria Technical Report"],"doi":"10.15479/AT:IST-2011-0006","ddc":["000","005"],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"id":"3341","relation":"later_version","status":"public"}]},"title":"Robustness of structurally equivalent concurrent parity games","has_accepted_license":"1","date_created":"2018-12-12T11:39:00Z","pubrep_id":"18","file":[{"date_updated":"2020-07-14T12:46:40Z","relation":"main_file","file_size":335997,"access_level":"open_access","date_created":"2018-12-12T11:54:24Z","checksum":"1322b652d6ab07eb5248298a3f91c1cf","creator":"system","file_id":"5546","file_name":"IST-2011-0006_IST-2011-0006.pdf","content_type":"application/pdf"}],"date_published":"2011-06-27T00:00:00Z","month":"06","year":"2011","oa_version":"Published Version","day":"27","_id":"5382","publication_status":"published","department":[{"_id":"KrCh"}],"date_updated":"2023-02-23T11:23:01Z","type":"technical_report","language":[{"iso":"eng"}]},{"publisher":"IST Austria","author":[{"first_name":"Thomas","full_name":"Wies, Thomas","last_name":"Wies","id":"447BFB88-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Marco","full_name":"Muñiz, Marco","last_name":"Muñiz"},{"full_name":"Kuncak, Viktor","last_name":"Kuncak","first_name":"Viktor"}],"abstract":[{"text":"We present a new decidable logic called TREX for expressing constraints about imperative tree data structures. In particular, TREX supports a transitive closure operator that can express reachability constraints, which often appear in data structure invariants. We show that our logic is closed under weakest precondition computation, which enables its use for automated software verification. We further show that satisfiability of formulas in TREX is decidable in NP. The low complexity makes it an attractive alternative to more expensive logics such as monadic second-order logic (MSOL) over trees, which have been traditionally used for reasoning about tree data structures.","lang":"eng"}],"publication_identifier":{"issn":["2664-1690"]},"oa":1,"citation":{"mla":"Wies, Thomas, et al. <i>On an Efficient Decision Procedure for Imperative Tree Data Structures</i>. IST Austria, 2011, doi:<a href=\"https://doi.org/10.15479/AT:IST-2011-0005\">10.15479/AT:IST-2011-0005</a>.","apa":"Wies, T., Muñiz, M., &#38; Kuncak, V. (2011). <i>On an efficient decision procedure for imperative tree data structures</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2011-0005\">https://doi.org/10.15479/AT:IST-2011-0005</a>","chicago":"Wies, Thomas, Marco Muñiz, and Viktor Kuncak. <i>On an Efficient Decision Procedure for Imperative Tree Data Structures</i>. IST Austria, 2011. <a href=\"https://doi.org/10.15479/AT:IST-2011-0005\">https://doi.org/10.15479/AT:IST-2011-0005</a>.","ama":"Wies T, Muñiz M, Kuncak V. <i>On an Efficient Decision Procedure for Imperative Tree Data Structures</i>. IST Austria; 2011. doi:<a href=\"https://doi.org/10.15479/AT:IST-2011-0005\">10.15479/AT:IST-2011-0005</a>","ista":"Wies T, Muñiz M, Kuncak V. 2011. On an efficient decision procedure for imperative tree data structures, IST Austria, 25p.","short":"T. Wies, M. Muñiz, V. Kuncak, On an Efficient Decision Procedure for Imperative Tree Data Structures, IST Austria, 2011.","ieee":"T. Wies, M. Muñiz, and V. Kuncak, <i>On an efficient decision procedure for imperative tree data structures</i>. IST Austria, 2011."},"page":"25","file_date_updated":"2020-07-14T12:46:40Z","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","alternative_title":["IST Austria Technical Report"],"doi":"10.15479/AT:IST-2011-0005","ddc":["000","006"],"date_published":"2011-04-26T00:00:00Z","month":"04","year":"2011","related_material":{"record":[{"id":"3323","relation":"later_version","status":"public"}]},"has_accepted_license":"1","date_created":"2018-12-12T11:39:01Z","title":"On an efficient decision procedure for imperative tree data structures","pubrep_id":"19","file":[{"access_level":"open_access","checksum":"b20029184c4a819c5f4466a4a3d238b5","date_created":"2018-12-12T11:53:01Z","file_id":"5462","file_name":"IST-2011-0005_IST-2011-0005.pdf","creator":"system","content_type":"application/pdf","date_updated":"2020-07-14T12:46:40Z","relation":"main_file","file_size":619053}],"publication_status":"published","type":"technical_report","date_updated":"2023-02-23T11:22:16Z","department":[{"_id":"ToHe"}],"language":[{"iso":"eng"}],"oa_version":"Published Version","_id":"5383","day":"26"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","doi":"10.15479/AT:IST-2011-0004","ddc":["000","005"],"alternative_title":["IST Austria Technical Report"],"abstract":[{"text":"We consider probabilistic automata on infinite words with acceptance defined by parity conditions. We consider three qualitative decision problems: (i) the positive decision problem asks whether there is a word that is accepted with positive probability; (ii) the almost decision problem asks whether there is a word that is accepted with probability 1; and (iii) the limit decision problem asks whether for every ε > 0 there is a word that is accepted with probability at least 1 − ε. We unify and generalize several decidability results for probabilistic automata over infinite words, and identify a robust (closed under union and intersection) subclass of probabilistic automata for which all the qualitative decision problems are decidable for parity conditions. We also show that if the input words are restricted to lasso shape words, then the positive and almost problems are decidable for all probabilistic automata with parity conditions.","lang":"eng"}],"publisher":"IST Austria","author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X"},{"id":"3F54FA38-F248-11E8-B48F-1D18A9856A87","full_name":"Tracol, Mathieu","last_name":"Tracol","first_name":"Mathieu"}],"file_date_updated":"2020-07-14T12:46:40Z","publication_identifier":{"issn":["2664-1690"]},"oa":1,"page":"30","citation":{"chicago":"Chatterjee, Krishnendu, and Mathieu Tracol. <i>Decidable Problems for Probabilistic Automata on Infinite Words</i>. IST Austria, 2011. <a href=\"https://doi.org/10.15479/AT:IST-2011-0004\">https://doi.org/10.15479/AT:IST-2011-0004</a>.","mla":"Chatterjee, Krishnendu, and Mathieu Tracol. <i>Decidable Problems for Probabilistic Automata on Infinite Words</i>. IST Austria, 2011, doi:<a href=\"https://doi.org/10.15479/AT:IST-2011-0004\">10.15479/AT:IST-2011-0004</a>.","apa":"Chatterjee, K., &#38; Tracol, M. (2011). <i>Decidable problems for probabilistic automata on infinite words</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2011-0004\">https://doi.org/10.15479/AT:IST-2011-0004</a>","ieee":"K. Chatterjee and M. Tracol, <i>Decidable problems for probabilistic automata on infinite words</i>. IST Austria, 2011.","short":"K. Chatterjee, M. Tracol, Decidable Problems for Probabilistic Automata on Infinite Words, IST Austria, 2011.","ama":"Chatterjee K, Tracol M. <i>Decidable Problems for Probabilistic Automata on Infinite Words</i>. IST Austria; 2011. doi:<a href=\"https://doi.org/10.15479/AT:IST-2011-0004\">10.15479/AT:IST-2011-0004</a>","ista":"Chatterjee K, Tracol M. 2011. Decidable problems for probabilistic automata on infinite words, IST Austria, 30p."},"department":[{"_id":"KrCh"}],"type":"technical_report","date_updated":"2023-02-23T11:05:53Z","language":[{"iso":"eng"}],"publication_status":"published","oa_version":"Published Version","day":"11","_id":"5384","year":"2011","date_published":"2011-04-11T00:00:00Z","month":"04","file":[{"file_name":"IST-2011-004_IST-2011-0004.pdf","file_id":"5545","creator":"system","content_type":"application/pdf","access_level":"open_access","date_created":"2018-12-12T11:54:23Z","checksum":"f5a0f664fadc335990f5fcf138df19f1","date_updated":"2020-07-14T12:46:40Z","relation":"main_file","file_size":570827}],"pubrep_id":"20","related_material":{"record":[{"status":"public","id":"2957","relation":"later_version"}]},"date_created":"2018-12-12T11:39:01Z","has_accepted_license":"1","title":"Decidable problems for probabilistic automata on infinite words"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","alternative_title":["IST Austria Technical Report"],"citation":{"ieee":"U. Boker, K. Chatterjee, T. A. Henzinger, and O. Kupferman, <i>Temporal specifications with accumulative values</i>. IST Austria, 2011.","short":"U. Boker, K. Chatterjee, T.A. Henzinger, O. Kupferman, Temporal Specifications with Accumulative Values, IST Austria, 2011.","ista":"Boker U, Chatterjee K, Henzinger TA, Kupferman O. 2011. Temporal specifications with accumulative values, IST Austria, 14p.","ama":"Boker U, Chatterjee K, Henzinger TA, Kupferman O. <i>Temporal Specifications with Accumulative Values</i>. IST Austria; 2011. doi:<a href=\"https://doi.org/10.15479/AT:IST-2011-0003\">10.15479/AT:IST-2011-0003</a>","chicago":"Boker, Udi, Krishnendu Chatterjee, Thomas A Henzinger, and Orna Kupferman. <i>Temporal Specifications with Accumulative Values</i>. IST Austria, 2011. <a href=\"https://doi.org/10.15479/AT:IST-2011-0003\">https://doi.org/10.15479/AT:IST-2011-0003</a>.","mla":"Boker, Udi, et al. <i>Temporal Specifications with Accumulative Values</i>. IST Austria, 2011, doi:<a href=\"https://doi.org/10.15479/AT:IST-2011-0003\">10.15479/AT:IST-2011-0003</a>.","apa":"Boker, U., Chatterjee, K., Henzinger, T. A., &#38; Kupferman, O. (2011). <i>Temporal specifications with accumulative values</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2011-0003\">https://doi.org/10.15479/AT:IST-2011-0003</a>"},"page":"14","oa":1,"file_date_updated":"2020-07-14T12:46:41Z","language":[{"iso":"eng"}],"department":[{"_id":"ToHe"},{"_id":"KrCh"}],"date_updated":"2023-02-23T11:23:41Z","day":"04","_id":"5385","project":[{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"grant_number":"215543","call_identifier":"FP7","name":"COMponent-Based Embedded Systems design Techniques","_id":"25EFB36C-B435-11E9-9278-68D0E5697425"},{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","call_identifier":"FP7","name":"Quantitative Reactive Modeling"},{"_id":"25F1337C-B435-11E9-9278-68D0E5697425","grant_number":"214373","name":"Design for Embedded Systems","call_identifier":"FP7"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"date_published":"2011-04-04T00:00:00Z","related_material":{"record":[{"status":"public","relation":"later_version","id":"2038"},{"status":"public","id":"3356","relation":"later_version"}]},"file":[{"file_size":366281,"date_updated":"2020-07-14T12:46:41Z","relation":"main_file","checksum":"8491d0d48c4911620ecd5350b413c11e","access_level":"open_access","date_created":"2018-12-12T11:53:00Z","content_type":"application/pdf","creator":"system","file_name":"IST-2011-0003_IST-2011-0003.pdf","file_id":"5461"}],"status":"public","ec_funded":1,"ddc":["000","004"],"doi":"10.15479/AT:IST-2011-0003","author":[{"first_name":"Udi","full_name":"Boker, Udi","last_name":"Boker","id":"31E297B6-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-4561-241X","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"},{"last_name":"Kupferman","full_name":"Kupferman, Orna","first_name":"Orna"}],"publisher":"IST Austria","abstract":[{"text":"There is recently a significant effort to add quantitative objectives to formal verification and synthesis. We introduce and investigate the extension of temporal logics with quantitative atomic assertions, aiming for a general and flexible framework for quantitative-oriented specifications. In the heart of quantitative objectives lies the accumulation of values along a computation. It is either the accumulated summation, as with the energy objectives, or the accumulated average, as with the mean-payoff objectives. We investigate the extension of temporal logics with the prefix-accumulation assertions Sum(v) ≥ c and Avg(v) ≥ c, where v is a numeric variable of the system, c is a constant rational number, and Sum(v) and Avg(v) denote the accumulated sum and average of the values of v from the beginning of the computation up to the current point of time. We also allow the path-accumulation assertions LimInfAvg(v) ≥ c and LimSupAvg(v) ≥ c, referring to the average value along an entire computation. We study the border of decidability for extensions of various temporal logics. In particular, we show that extending the fragment of CTL that has only the EX, EF, AX, and AG temporal modalities by prefix-accumulation assertions and extending LTL with path-accumulation assertions, result in temporal logics whose model-checking problem is decidable. The extended logics allow to significantly extend the currently known energy and mean-payoff objectives. Moreover, the prefix-accumulation assertions may be refined with “controlled-accumulation”, allowing, for example, to specify constraints on the average waiting time between a request and a grant. On the negative side, we show that the fragment we point to is, in a sense, the maximal logic whose extension with prefix-accumulation assertions permits a decidable model-checking procedure. Extending a temporal logic that has the EG or EU modalities, and in particular CTL and LTL, makes the problem undecidable.","lang":"eng"}],"publication_identifier":{"issn":["2664-1690"]},"publication_status":"published","type":"technical_report","oa_version":"Published Version","month":"04","year":"2011","has_accepted_license":"1","date_created":"2018-12-12T11:39:02Z","title":"Temporal specifications with accumulative values","pubrep_id":"21"},{"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","alternative_title":["IST Austria Technical Report"],"doi":"10.15479/AT:IST-2011-0002","ddc":["000"],"publisher":"IST Austria","author":[{"id":"3E92416E-F248-11E8-B48F-1D18A9856A87","full_name":"Chen, Chao","last_name":"Chen","first_name":"Chao"},{"first_name":"Daniel","full_name":"Freedman, Daniel","last_name":"Freedman"},{"first_name":"Christoph","full_name":"Lampert, Christoph","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887"}],"abstract":[{"text":"We introduce TopoCut: a new way to integrate knowledge about topological properties (TPs) into random field image segmentation model. Instead of including TPs as additional constraints during minimization of the energy function, we devise an efficient algorithm for modifying the unary potentials such that the resulting segmentation is guaranteed with the desired properties. Our method is more flexible in the sense that it handles more topology constraints than previous methods, which were only able to enforce pairwise or global connectivity. In particular, our method is very fast, making it for the first time possible to enforce global topological properties in practical image segmentation tasks.","lang":"eng"}],"publication_identifier":{"issn":["2664-1690"]},"oa":1,"citation":{"ama":"Chen C, Freedman D, Lampert C. <i>Enforcing Topological Constraints in Random Field Image Segmentation</i>. IST Austria; 2011. doi:<a href=\"https://doi.org/10.15479/AT:IST-2011-0002\">10.15479/AT:IST-2011-0002</a>","ista":"Chen C, Freedman D, Lampert C. 2011. Enforcing topological constraints in random field image segmentation, IST Austria, 69p.","short":"C. Chen, D. Freedman, C. Lampert, Enforcing Topological Constraints in Random Field Image Segmentation, IST Austria, 2011.","ieee":"C. Chen, D. Freedman, and C. Lampert, <i>Enforcing topological constraints in random field image segmentation</i>. IST Austria, 2011.","apa":"Chen, C., Freedman, D., &#38; Lampert, C. (2011). <i>Enforcing topological constraints in random field image segmentation</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2011-0002\">https://doi.org/10.15479/AT:IST-2011-0002</a>","mla":"Chen, Chao, et al. <i>Enforcing Topological Constraints in Random Field Image Segmentation</i>. IST Austria, 2011, doi:<a href=\"https://doi.org/10.15479/AT:IST-2011-0002\">10.15479/AT:IST-2011-0002</a>.","chicago":"Chen, Chao, Daniel Freedman, and Christoph Lampert. <i>Enforcing Topological Constraints in Random Field Image Segmentation</i>. IST Austria, 2011. <a href=\"https://doi.org/10.15479/AT:IST-2011-0002\">https://doi.org/10.15479/AT:IST-2011-0002</a>."},"page":"69","file_date_updated":"2020-07-14T12:46:41Z","publication_status":"published","type":"technical_report","date_updated":"2023-02-23T11:22:48Z","department":[{"_id":"ChLa"}],"language":[{"iso":"eng"}],"oa_version":"Published Version","day":"28","_id":"5386","date_published":"2011-03-28T00:00:00Z","month":"03","year":"2011","related_material":{"record":[{"id":"3336","relation":"later_version","status":"public"}]},"date_created":"2018-12-12T11:39:02Z","title":"Enforcing topological constraints in random field image segmentation","has_accepted_license":"1","file":[{"content_type":"application/pdf","file_name":"IST-2011-0002_IST-2011-0002.pdf","file_id":"5495","creator":"system","date_created":"2018-12-12T11:53:34Z","access_level":"open_access","checksum":"ad64c2add5fe2ad10e9d5c669f3f9526","file_size":26390601,"relation":"main_file","date_updated":"2020-07-14T12:46:41Z"}],"pubrep_id":"22"},{"citation":{"apa":"Feng, X., &#38; Dickinson, H. G. (2010). Tapetal cell fate, lineage and proliferation in the Arabidopsis anther. <i>Development</i>. The Company of Biologists. <a href=\"https://doi.org/10.1242/dev.049320\">https://doi.org/10.1242/dev.049320</a>","mla":"Feng, Xiaoqi, and Hugh G. Dickinson. “Tapetal Cell Fate, Lineage and Proliferation in the Arabidopsis Anther.” <i>Development</i>, vol. 137, no. 14, The Company of Biologists, 2010, pp. 2409–16, doi:<a href=\"https://doi.org/10.1242/dev.049320\">10.1242/dev.049320</a>.","chicago":"Feng, Xiaoqi, and Hugh G. Dickinson. “Tapetal Cell Fate, Lineage and Proliferation in the Arabidopsis Anther.” <i>Development</i>. The Company of Biologists, 2010. <a href=\"https://doi.org/10.1242/dev.049320\">https://doi.org/10.1242/dev.049320</a>.","ama":"Feng X, Dickinson HG. Tapetal cell fate, lineage and proliferation in the Arabidopsis anther. <i>Development</i>. 2010;137(14):2409-2416. doi:<a href=\"https://doi.org/10.1242/dev.049320\">10.1242/dev.049320</a>","ista":"Feng X, Dickinson HG. 2010. Tapetal cell fate, lineage and proliferation in the Arabidopsis anther. Development. 137(14), 2409–2416.","short":"X. Feng, H.G. Dickinson, Development 137 (2010) 2409–2416.","ieee":"X. Feng and H. G. Dickinson, “Tapetal cell fate, lineage and proliferation in the Arabidopsis anther,” <i>Development</i>, vol. 137, no. 14. The Company of Biologists, pp. 2409–2416, 2010."},"page":"2409-2416","external_id":{"pmid":["20570940"]},"issue":"14","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Development","keyword":["Developmental Biology","Molecular Biology","Anther Tapetum","Arabidopsis","Cell Fate Establishment","EMS1","Reproductive Cell Lineage"],"intvolume":"       137","pmid":1,"date_published":"2010-07-15T00:00:00Z","article_processing_charge":"No","day":"15","_id":"12199","language":[{"iso":"eng"}],"department":[{"_id":"XiFe"}],"date_updated":"2023-05-08T10:57:11Z","publication_identifier":{"issn":["1477-9129","0950-1991"]},"scopus_import":"1","abstract":[{"text":"The four microsporangia of the flowering plant anther develop from archesporial cells in the L2 of the primordium. Within each microsporangium, developing microsporocytes are surrounded by concentric monolayers of tapetal, middle layer and endothecial cells. How this intricate array of tissues, each containing relatively few cells, is established in an organ possessing no formal meristems is poorly understood. We describe here the pivotal role of the LRR receptor kinase EXCESS MICROSPOROCYTES 1 (EMS1) in forming the monolayer of tapetal nurse cells in Arabidopsis. Unusually for plants, tapetal cells are specified very early in development, and are subsequently stimulated to proliferate by a receptor-like kinase (RLK) complex that includes EMS1. Mutations in members of this EMS1 signalling complex and its putative ligand result in male-sterile plants in which tapetal initials fail to proliferate. Surprisingly, these cells continue to develop, isolated at the locular periphery. Mutant and wild-type microsporangia expand at similar rates and the ‘tapetal’ space at the periphery of mutant locules becomes occupied by microsporocytes. However, induction of late expression of EMS1 in the few tapetal initials in ems1 plants results in their proliferation to generate a functional tapetum, and this proliferation suppresses microsporocyte number. Our experiments also show that integrity of the tapetal monolayer is crucial for the maintenance of the polarity of divisions within it. This unexpected autonomy of the tapetal ‘lineage’ is discussed in the context of tissue development in complex plant organs, where constancy in size, shape and cell number is crucial.","lang":"eng"}],"extern":"1","author":[{"orcid":"0000-0002-4008-1234","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","full_name":"Feng, Xiaoqi","last_name":"Feng","first_name":"Xiaoqi"},{"last_name":"Dickinson","full_name":"Dickinson, Hugh G.","first_name":"Hugh G."}],"publisher":"The Company of Biologists","quality_controlled":"1","doi":"10.1242/dev.049320","volume":137,"acknowledgement":"We thank the following for providing mutant lines and reagents: Hong Ma, De Ye, Sacco De Vries, and Rod Scott for providing the pA9::Barnase lines and information on A9 expression patterns. Carla Galinha and Paolo Piazza gave valuable help with in situ hybridisation and qRT-PCR, respectively, and we acknowledge Qing Zhang, Helen Prescott and Matthew Dicks for providing excellent technical assistance. We are indebted to Miltos Tsiantis and Angela Hay for helpful discussion, and the research was funded by Oxford University through a Clarendon Scholarship to X.F., with additional financial support from Magdalen College (Oxford).","status":"public","article_type":"original","title":"Tapetal cell fate, lineage and proliferation in the Arabidopsis anther","date_created":"2023-01-16T09:21:54Z","year":"2010","month":"07","oa_version":"None","type":"journal_article","publication_status":"published"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Biochemical Society Transactions","intvolume":"        38","keyword":["Biochemistry","Anther Development","Arabidopsis","Cell Fate","Microsporangium","Polarity","Receptor Kinase"],"external_id":{"pmid":["20298223"]},"issue":"2","citation":{"ista":"Feng X, Dickinson HG. 2010. Cell–cell interactions during patterning of the <i>Arabidopsis</i> anther. Biochemical Society Transactions. 38(2), 571–576.","ama":"Feng X, Dickinson HG. Cell–cell interactions during patterning of the <i>Arabidopsis</i> anther. <i>Biochemical Society Transactions</i>. 2010;38(2):571-576. doi:<a href=\"https://doi.org/10.1042/bst0380571\">10.1042/bst0380571</a>","ieee":"X. Feng and H. G. Dickinson, “Cell–cell interactions during patterning of the <i>Arabidopsis</i> anther,” <i>Biochemical Society Transactions</i>, vol. 38, no. 2. Portland Press Ltd., pp. 571–576, 2010.","short":"X. Feng, H.G. Dickinson, Biochemical Society Transactions 38 (2010) 571–576.","apa":"Feng, X., &#38; Dickinson, H. G. (2010). Cell–cell interactions during patterning of the <i>Arabidopsis</i> anther. <i>Biochemical Society Transactions</i>. Portland Press Ltd. <a href=\"https://doi.org/10.1042/bst0380571\">https://doi.org/10.1042/bst0380571</a>","mla":"Feng, Xiaoqi, and Hugh G. Dickinson. “Cell–Cell Interactions during Patterning of the <i>Arabidopsis</i> Anther.” <i>Biochemical Society Transactions</i>, vol. 38, no. 2, Portland Press Ltd., 2010, pp. 571–76, doi:<a href=\"https://doi.org/10.1042/bst0380571\">10.1042/bst0380571</a>.","chicago":"Feng, Xiaoqi, and Hugh G. Dickinson. “Cell–Cell Interactions during Patterning of the <i>Arabidopsis</i> Anther.” <i>Biochemical Society Transactions</i>. Portland Press Ltd., 2010. <a href=\"https://doi.org/10.1042/bst0380571\">https://doi.org/10.1042/bst0380571</a>."},"page":"571-576","language":[{"iso":"eng"}],"department":[{"_id":"XiFe"}],"date_updated":"2023-05-08T10:57:59Z","article_processing_charge":"No","_id":"12200","day":"22","pmid":1,"date_published":"2010-03-22T00:00:00Z","status":"public","volume":38,"quality_controlled":"1","doi":"10.1042/bst0380571","abstract":[{"lang":"eng","text":"Key steps in the evolution of the angiosperm anther include the patterning of the concentrically organized microsporangium and the incorporation of four such microsporangia into a leaf-like structure. Mutant studies in the model plant Arabidopsis thaliana are leading to an increasingly accurate picture of (i) the cell lineages culminating in the different cell types present in the microsporangium (the microsporocytes, the tapetum, and the middle and endothecial layers), and (ii) some of the genes responsible for specifying their fates. However, the processes that confer polarity on the developing anther and position the microsporangia within it remain unclear. Certainly, data from a range of experimental strategies suggest that hormones play a central role in establishing polarity and the patterning of the anther initial, and may be responsible for locating the microsporangia. But the fact that microsporangia were originally positioned externally suggests that their development is likely to be autonomous, perhaps with the reproductive cells generating signals controlling the growth and division of the investing anther epidermis. These possibilities are discussed in the context of the expression of genes which initiate and maintain male and female reproductive development, and in the perspective of our current views of anther evolution."}],"extern":"1","publisher":"Portland Press Ltd.","author":[{"id":"e0164712-22ee-11ed-b12a-d80fcdf35958","last_name":"Feng","full_name":"Feng, Xiaoqi","orcid":"0000-0002-4008-1234","first_name":"Xiaoqi"},{"full_name":"Dickinson, Hugh G.","last_name":"Dickinson","first_name":"Hugh G."}],"scopus_import":"1","publication_identifier":{"issn":["0300-5127","1470-8752"]},"type":"journal_article","publication_status":"published","oa_version":"None","year":"2010","month":"03","article_type":"original","date_created":"2023-01-16T09:22:18Z","title":"Cell–cell interactions during patterning of the <i>Arabidopsis</i> anther"},{"publication_identifier":{"eisbn":["9783642020919"],"issn":["1612-3018"],"isbn":["9783642020902"]},"abstract":[{"lang":"eng","text":"This chapter tackles a difficult challenge: presenting signal processing material to non-experts. This chapter is meant to be comprehensible to people who have some math background, including a course in linear algebra and basic statistics, but do not specialize in mathematics, engineering, or related fields. Some formulas assume the reader is familiar with matrices and basic matrix operations, but not more advanced material. Furthermore, we tried to make the chapter readable even if you skip the formulas. Nevertheless, we include some simple methods to demonstrate the basics of adaptive data processing, then we proceed with some advanced methods that are fundamental in adaptive signal processing, and are likely to be useful in a variety of applications. The advanced algorithms are also online available [30]. In the second part, these techniques are applied to some real-world BCI data."}],"author":[{"first_name":"Alois","orcid":"0000-0002-5621-8100","last_name":"Schlögl","full_name":"Schlögl, Alois","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Carmen","last_name":"Vidaurre","full_name":"Vidaurre, Carmen"},{"last_name":"Müller","full_name":"Müller, Klaus-Robert","first_name":"Klaus-Robert"}],"publisher":"Springer","doi":"10.1007/978-3-642-02091-9_18","quality_controlled":"1","status":"public","acknowledgement":"This work was supported by the EU grants “BrainCom” (FP6-2004-Mobility-5 Grant No 024259) and “Multi-adaptive BCI” (MEIF-CT-2006 Grant No 040666). Furthermore, we thank Matthias Krauledat for fruitful discussions and tools for generating Fig. 5.","date_created":"2024-02-14T09:56:00Z","title":"Adaptive Methods in BCI Research - An Introductory Tutorial","year":"2010","month":"09","oa_version":"None","type":"book_chapter","series_title":"FRONTCOLL","publication_status":"published","page":"331-355","citation":{"ama":"Schlögl A, Vidaurre C, Müller K-R. Adaptive Methods in BCI Research - An Introductory Tutorial. In: Graimann B, Pfurtscheller G, Allison B, eds. <i>Brain-Computer Interfaces</i>. 1st ed. FRONTCOLL. Berlin, Heidelberg: Springer; 2010:331-355. doi:<a href=\"https://doi.org/10.1007/978-3-642-02091-9_18\">10.1007/978-3-642-02091-9_18</a>","ista":"Schlögl A, Vidaurre C, Müller K-R. 2010.Adaptive Methods in BCI Research - An Introductory Tutorial. In: Brain-Computer Interfaces. The Frontiers Collection, , 331–355.","short":"A. Schlögl, C. Vidaurre, K.-R. Müller, in:, B. Graimann, G. Pfurtscheller, B. Allison (Eds.), Brain-Computer Interfaces, 1st ed., Springer, Berlin, Heidelberg, 2010, pp. 331–355.","ieee":"A. Schlögl, C. Vidaurre, and K.-R. Müller, “Adaptive Methods in BCI Research - An Introductory Tutorial,” in <i>Brain-Computer Interfaces</i>, 1st ed., B. Graimann, G. Pfurtscheller, and B. Allison, Eds. Berlin, Heidelberg: Springer, 2010, pp. 331–355.","mla":"Schlögl, Alois, et al. “Adaptive Methods in BCI Research - An Introductory Tutorial.” <i>Brain-Computer Interfaces</i>, edited by Bernhard Graimann et al., 1st ed., Springer, 2010, pp. 331–55, doi:<a href=\"https://doi.org/10.1007/978-3-642-02091-9_18\">10.1007/978-3-642-02091-9_18</a>.","apa":"Schlögl, A., Vidaurre, C., &#38; Müller, K.-R. (2010). Adaptive Methods in BCI Research - An Introductory Tutorial. In B. Graimann, G. Pfurtscheller, &#38; B. Allison (Eds.), <i>Brain-Computer Interfaces</i> (1st ed., pp. 331–355). Berlin, Heidelberg: Springer. <a href=\"https://doi.org/10.1007/978-3-642-02091-9_18\">https://doi.org/10.1007/978-3-642-02091-9_18</a>","chicago":"Schlögl, Alois, Carmen Vidaurre, and Klaus-Robert Müller. “Adaptive Methods in BCI Research - An Introductory Tutorial.” In <i>Brain-Computer Interfaces</i>, edited by Bernhard Graimann, Gert Pfurtscheller, and Brendan Allison, 1st ed., 331–55. FRONTCOLL. Berlin, Heidelberg: Springer, 2010. <a href=\"https://doi.org/10.1007/978-3-642-02091-9_18\">https://doi.org/10.1007/978-3-642-02091-9_18</a>."},"edition":"1","editor":[{"first_name":"Bernhard","full_name":"Graimann, Bernhard","last_name":"Graimann"},{"first_name":"Gert","full_name":"Pfurtscheller, Gert","last_name":"Pfurtscheller"},{"first_name":"Brendan","full_name":"Allison, Brendan","last_name":"Allison"}],"alternative_title":["The Frontiers Collection"],"publication":"Brain-Computer Interfaces","place":"Berlin, Heidelberg","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2010-09-06T00:00:00Z","article_processing_charge":"No","day":"06","_id":"14983","date_updated":"2024-02-19T09:47:25Z","department":[{"_id":"ScienComp"}],"language":[{"iso":"eng"}]},{"page":"17","citation":{"short":"K. Chatterjee, P. Cerny, T.A. Henzinger, A. Radhakrishna, R. Singh, Quantitative Synthesis for Concurrent Programs, IST Austria, 2010.","ieee":"K. Chatterjee, P. Cerny, T. A. Henzinger, A. Radhakrishna, and R. Singh, <i>Quantitative synthesis for concurrent programs</i>. IST Austria, 2010.","ista":"Chatterjee K, Cerny P, Henzinger TA, Radhakrishna A, Singh R. 2010. Quantitative synthesis for concurrent programs, IST Austria, 17p.","ama":"Chatterjee K, Cerny P, Henzinger TA, Radhakrishna A, Singh R. <i>Quantitative Synthesis for Concurrent Programs</i>. IST Austria; 2010. doi:<a href=\"https://doi.org/10.15479/AT:IST-2010-0004\">10.15479/AT:IST-2010-0004</a>","chicago":"Chatterjee, Krishnendu, Pavol Cerny, Thomas A Henzinger, Arjun Radhakrishna, and Rohit Singh. <i>Quantitative Synthesis for Concurrent Programs</i>. IST Austria, 2010. <a href=\"https://doi.org/10.15479/AT:IST-2010-0004\">https://doi.org/10.15479/AT:IST-2010-0004</a>.","mla":"Chatterjee, Krishnendu, et al. <i>Quantitative Synthesis for Concurrent Programs</i>. IST Austria, 2010, doi:<a href=\"https://doi.org/10.15479/AT:IST-2010-0004\">10.15479/AT:IST-2010-0004</a>.","apa":"Chatterjee, K., Cerny, P., Henzinger, T. A., Radhakrishna, A., &#38; Singh, R. (2010). <i>Quantitative synthesis for concurrent programs</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2010-0004\">https://doi.org/10.15479/AT:IST-2010-0004</a>"},"oa":1,"publication_identifier":{"issn":["2664-1690"]},"file_date_updated":"2020-07-14T12:46:42Z","publisher":"IST Austria","author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"first_name":"Pavol","id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87","last_name":"Cerny","full_name":"Cerny, Pavol"},{"first_name":"Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87","full_name":"Radhakrishna, Arjun","last_name":"Radhakrishna","first_name":"Arjun"},{"first_name":"Rohit","last_name":"Singh","full_name":"Singh, Rohit"}],"abstract":[{"text":"We present an algorithmic method for the synthesis of concurrent programs that are optimal with respect to quantitative performance measures. The input consists of a sequential sketch, that is, a program that does not contain synchronization constructs, and of a parametric performance model that assigns costs to actions such as locking, context switching, and idling. The quantitative synthesis problem is to automatically introduce synchronization constructs into the sequential sketch so that both correctness is guaranteed and worst-case (or average-case) performance is optimized. Correctness is formalized as race freedom or linearizability.\r\n\r\nWe show that for worst-case performance, the problem can be modeled\r\nas a 2-player graph game with quantitative (limit-average) objectives, and\r\nfor average-case performance, as a 2 1/2 -player graph game (with probabilistic transitions). In both cases, the optimal correct program is derived from an optimal strategy in the corresponding quantitative game. We prove that the respective game problems are computationally expensive (NP-complete), and present several techniques that overcome the theoretical difficulty in cases of concurrent programs of practical interest.\r\n\r\nWe have implemented a prototype tool and used it for the automatic syn- thesis of programs that access a concurrent list. For certain parameter val- ues, our method automatically synthesizes various classical synchronization schemes for implementing a concurrent list, such as fine-grained locking or a lazy algorithm. For other parameter values, a new, hybrid synchronization style is synthesized, which uses both the lazy approach and coarse-grained locks (instead of standard fine-grained locks). The trade-off occurs because while fine-grained locking tends to decrease the cost that is due to waiting for locks, it increases cache size requirements.","lang":"eng"}],"alternative_title":["IST Austria Technical Report"],"ddc":["000","005"],"doi":"10.15479/AT:IST-2010-0004","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-12T11:39:03Z","title":"Quantitative synthesis for concurrent programs","has_accepted_license":"1","related_material":{"record":[{"status":"public","relation":"later_version","id":"3366"}]},"pubrep_id":"24","file":[{"date_created":"2018-12-12T11:53:53Z","access_level":"open_access","checksum":"da38782d2388a6fa32109d10bb9bad67","content_type":"application/pdf","file_id":"5515","file_name":"IST-2010-0004_IST-2010-0004.pdf","creator":"system","file_size":429101,"date_updated":"2020-07-14T12:46:42Z","relation":"main_file"}],"month":"10","date_published":"2010-10-07T00:00:00Z","year":"2010","_id":"5388","day":"07","oa_version":"Published Version","publication_status":"published","language":[{"iso":"eng"}],"department":[{"_id":"KrCh"},{"_id":"ToHe"}],"type":"technical_report","date_updated":"2023-02-23T11:24:08Z"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","ddc":["005"],"doi":"10.15479/AT:IST-2010-0003","alternative_title":["IST Austria Technical Report"],"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 im- plementation 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"}],"publisher":"IST Austria","author":[{"last_name":"Cerny","full_name":"Cerny, Pavol","id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87","first_name":"Pavol"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","last_name":"Henzinger","orcid":"0000−0002−2985−7724","first_name":"Thomas A"},{"id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87","full_name":"Radhakrishna, Arjun","last_name":"Radhakrishna","first_name":"Arjun"}],"file_date_updated":"2020-07-14T12:46:42Z","page":"24","citation":{"mla":"Cerny, Pavol, et al. <i>Simulation Distances</i>. IST Austria, 2010, doi:<a href=\"https://doi.org/10.15479/AT:IST-2010-0003\">10.15479/AT:IST-2010-0003</a>.","apa":"Cerny, P., Henzinger, T. A., &#38; Radhakrishna, A. (2010). <i>Simulation distances</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2010-0003\">https://doi.org/10.15479/AT:IST-2010-0003</a>","chicago":"Cerny, Pavol, Thomas A Henzinger, and Arjun Radhakrishna. <i>Simulation Distances</i>. IST Austria, 2010. <a href=\"https://doi.org/10.15479/AT:IST-2010-0003\">https://doi.org/10.15479/AT:IST-2010-0003</a>.","ista":"Cerny P, Henzinger TA, Radhakrishna A. 2010. Simulation distances, IST Austria, 24p.","ama":"Cerny P, Henzinger TA, Radhakrishna A. <i>Simulation Distances</i>. IST Austria; 2010. doi:<a href=\"https://doi.org/10.15479/AT:IST-2010-0003\">10.15479/AT:IST-2010-0003</a>","short":"P. Cerny, T.A. Henzinger, A. Radhakrishna, Simulation Distances, IST Austria, 2010.","ieee":"P. Cerny, T. A. Henzinger, and A. Radhakrishna, <i>Simulation distances</i>. IST Austria, 2010."},"oa":1,"publication_identifier":{"issn":["2664-1690"]},"language":[{"iso":"eng"}],"date_updated":"2023-02-23T12:09:16Z","type":"technical_report","department":[{"_id":"ToHe"}],"publication_status":"published","_id":"5389","day":"04","oa_version":"Published Version","year":"2010","month":"06","date_published":"2010-06-04T00:00:00Z","file":[{"file_name":"IST-2010-0003_IST-2010-0003.pdf","file_id":"5547","creator":"system","content_type":"application/pdf","access_level":"open_access","date_created":"2018-12-12T11:54:25Z","checksum":"284ded99764e32a583a8ea83fcea254b","date_updated":"2020-07-14T12:46:42Z","relation":"main_file","file_size":367246}],"pubrep_id":"25","has_accepted_license":"1","date_created":"2018-12-12T11:39:03Z","title":"Simulation distances","related_material":{"record":[{"id":"3249","relation":"later_version","status":"public"},{"id":"4393","relation":"later_version","status":"public"}]}},{"abstract":[{"text":"The class of ω regular languages provide a robust specification language in verification. Every ω-regular condition 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. In this work we consider the finitary parity and Streett (fairness) conditions. We present the topological, automata-theoretic and logical characterization of finitary languages defined by finitary parity and Streett conditions. We (a) show that the finitary parity and Streett languages are Σ2-complete; (b) present a complete characterization of the expressive power of various classes of automata with finitary and infinitary conditions (in particular we show that non-deterministic finitary parity and Streett automata cannot be determinized to deterministic finitary parity or Streett automata); and (c) show that the languages defined by non-deterministic finitary parity automata exactly characterize the star-free fragment of ωB-regular languages.","lang":"eng"}],"author":[{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"full_name":"Fijalkow, Nathanaël","last_name":"Fijalkow","first_name":"Nathanaël"}],"publisher":"IST Austria","file_date_updated":"2020-07-14T12:46:43Z","oa":1,"publication_identifier":{"issn":["2664-1690"]},"citation":{"chicago":"Chatterjee, Krishnendu, and Nathanaël Fijalkow. <i>Topological, Automata-Theoretic and Logical Characterization of Finitary Languages</i>. IST Austria, 2010. <a href=\"https://doi.org/10.15479/AT:IST-2010-0002\">https://doi.org/10.15479/AT:IST-2010-0002</a>.","mla":"Chatterjee, Krishnendu, and Nathanaël Fijalkow. <i>Topological, Automata-Theoretic and Logical Characterization of Finitary Languages</i>. IST Austria, 2010, doi:<a href=\"https://doi.org/10.15479/AT:IST-2010-0002\">10.15479/AT:IST-2010-0002</a>.","apa":"Chatterjee, K., &#38; Fijalkow, N. (2010). <i>Topological, automata-theoretic and logical characterization of finitary languages</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2010-0002\">https://doi.org/10.15479/AT:IST-2010-0002</a>","ieee":"K. Chatterjee and N. Fijalkow, <i>Topological, automata-theoretic and logical characterization of finitary languages</i>. IST Austria, 2010.","short":"K. Chatterjee, N. Fijalkow, Topological, Automata-Theoretic and Logical Characterization of Finitary Languages, IST Austria, 2010.","ama":"Chatterjee K, Fijalkow N. <i>Topological, Automata-Theoretic and Logical Characterization of Finitary Languages</i>. IST Austria; 2010. doi:<a href=\"https://doi.org/10.15479/AT:IST-2010-0002\">10.15479/AT:IST-2010-0002</a>","ista":"Chatterjee K, Fijalkow N. 2010. Topological, automata-theoretic and logical characterization of finitary languages, IST Austria, 21p."},"page":"21","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","doi":"10.15479/AT:IST-2010-0002","ddc":["000"],"alternative_title":["IST Austria Technical Report"],"year":"2010","date_published":"2010-06-04T00:00:00Z","month":"06","file":[{"file_size":395662,"relation":"main_file","date_updated":"2020-07-14T12:46:43Z","checksum":"283d3604d76dd4d5161585d4c8625fbe","date_created":"2018-12-12T11:54:10Z","access_level":"open_access","content_type":"application/pdf","creator":"system","file_name":"IST-2010-0002_IST-2010-0002.pdf","file_id":"5532"}],"pubrep_id":"26","has_accepted_license":"1","date_created":"2018-12-12T11:39:03Z","title":"Topological, automata-theoretic and logical characterization of finitary languages","date_updated":"2020-07-14T23:04:41Z","department":[{"_id":"KrCh"}],"type":"technical_report","language":[{"iso":"eng"}],"publication_status":"published","oa_version":"Published Version","day":"04","_id":"5390"},{"author":[{"id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87","full_name":"Cerny, Pavol","last_name":"Cerny","first_name":"Pavol"},{"id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87","last_name":"Radhakrishna","full_name":"Radhakrishna, Arjun","first_name":"Arjun"},{"full_name":"Zufferey, Damien","last_name":"Zufferey","id":"4397AC76-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3197-8736","first_name":"Damien"},{"full_name":"Chaudhuri, Swarat","last_name":"Chaudhuri","first_name":"Swarat"},{"last_name":"Alur","full_name":"Alur, Rajeev","first_name":"Rajeev"}],"publisher":"IST Austria","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 node consists 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 imple- mentation and proved that the corrected version is linearizable.","lang":"eng"}],"citation":{"chicago":"Cerny, Pavol, Arjun Radhakrishna, Damien Zufferey, Swarat Chaudhuri, and Rajeev Alur. <i>Model Checking of Linearizability of Concurrent List Implementations</i>. IST Austria, 2010. <a href=\"https://doi.org/10.15479/AT:IST-2010-0001\">https://doi.org/10.15479/AT:IST-2010-0001</a>.","apa":"Cerny, P., Radhakrishna, A., Zufferey, D., Chaudhuri, S., &#38; Alur, R. (2010). <i>Model checking of linearizability of concurrent list implementations</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2010-0001\">https://doi.org/10.15479/AT:IST-2010-0001</a>","mla":"Cerny, Pavol, et al. <i>Model Checking of Linearizability of Concurrent List Implementations</i>. IST Austria, 2010, doi:<a href=\"https://doi.org/10.15479/AT:IST-2010-0001\">10.15479/AT:IST-2010-0001</a>.","short":"P. Cerny, A. Radhakrishna, D. Zufferey, S. Chaudhuri, R. Alur, Model Checking of Linearizability of Concurrent List Implementations, IST Austria, 2010.","ieee":"P. Cerny, A. Radhakrishna, D. Zufferey, S. Chaudhuri, and R. Alur, <i>Model checking of linearizability of concurrent list implementations</i>. IST Austria, 2010.","ista":"Cerny P, Radhakrishna A, Zufferey D, Chaudhuri S, Alur R. 2010. Model checking of linearizability of concurrent list implementations, IST Austria, 27p.","ama":"Cerny P, Radhakrishna A, Zufferey D, Chaudhuri S, Alur R. <i>Model Checking of Linearizability of Concurrent List Implementations</i>. IST Austria; 2010. doi:<a href=\"https://doi.org/10.15479/AT:IST-2010-0001\">10.15479/AT:IST-2010-0001</a>"},"page":"27","publication_identifier":{"issn":["2664-1690"]},"oa":1,"file_date_updated":"2020-07-14T12:46:43Z","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","alternative_title":["IST Austria Technical Report"],"ddc":["004"],"doi":"10.15479/AT:IST-2010-0001","month":"04","date_published":"2010-04-19T00:00:00Z","year":"2010","title":"Model checking of linearizability of concurrent list implementations","date_created":"2018-12-12T11:39:04Z","has_accepted_license":"1","related_material":{"record":[{"status":"public","relation":"later_version","id":"4390"}]},"file":[{"checksum":"986645caad7dd85a6a091488f6c646dc","access_level":"open_access","date_created":"2018-12-12T11:53:44Z","file_id":"5505","file_name":"IST-2010-0001_IST-2010-0001.pdf","creator":"system","content_type":"application/pdf","relation":"main_file","date_updated":"2020-07-14T12:46:43Z","file_size":372286}],"pubrep_id":"27","publication_status":"published","language":[{"iso":"eng"}],"type":"technical_report","department":[{"_id":"ToHe"}],"date_updated":"2023-02-23T12:09:09Z","_id":"5391","day":"19","oa_version":"Published Version"},{"abstract":[{"lang":"eng","text":"Eukaryotic cytosine methylation represses transcription but also occurs in the bodies of active genes, and the extent of methylation biology conservation is unclear. We quantified DNA methylation in 17 eukaryotic genomes and found that gene body methylation is conserved between plants and animals, whereas selective methylation of transposons is not. We show that methylation of plant transposons in the CHG context extends to green algae and that exclusion of histone H2A.Z from methylated DNA is conserved between plants and animals, and we present evidence for RNA-directed DNA methylation of fungal genes. Our data demonstrate that extant DNA methylation systems are mosaics of conserved and derived features, and indicate that gene body methylation is an ancient property of eukaryotic genomes."}],"extern":"1","author":[{"full_name":"Zemach, Assaf ","last_name":"Zemach","first_name":"Assaf "},{"first_name":"Ivy E.","full_name":"McDaniel, Ivy E.","last_name":"McDaniel"},{"first_name":"Pedro","last_name":"Silva","full_name":"Silva, Pedro"},{"first_name":"Daniel","orcid":"0000-0002-0123-8649","last_name":"Zilberman","full_name":"Zilberman, Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1"}],"publisher":"American Association for the Advancement of Science","publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"scopus_import":"1","status":"public","volume":328,"quality_controlled":"1","doi":"10.1126/science.1186366","year":"2010","month":"05","article_type":"original","date_created":"2021-06-04T08:26:08Z","title":"Genome-wide evolutionary analysis of eukaryotic DNA methylation","type":"journal_article","publication_status":"published","oa_version":"None","citation":{"ista":"Zemach A, McDaniel IE, Silva P, Zilberman D. 2010. Genome-wide evolutionary analysis of eukaryotic DNA methylation. Science. 328(5980), 916–919.","ama":"Zemach A, McDaniel IE, Silva P, Zilberman D. Genome-wide evolutionary analysis of eukaryotic DNA methylation. <i>Science</i>. 2010;328(5980):916-919. doi:<a href=\"https://doi.org/10.1126/science.1186366\">10.1126/science.1186366</a>","ieee":"A. Zemach, I. E. McDaniel, P. Silva, and D. Zilberman, “Genome-wide evolutionary analysis of eukaryotic DNA methylation,” <i>Science</i>, vol. 328, no. 5980. American Association for the Advancement of Science, pp. 916–919, 2010.","short":"A. Zemach, I.E. McDaniel, P. Silva, D. Zilberman, Science 328 (2010) 916–919.","apa":"Zemach, A., McDaniel, I. E., Silva, P., &#38; Zilberman, D. (2010). Genome-wide evolutionary analysis of eukaryotic DNA methylation. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.1186366\">https://doi.org/10.1126/science.1186366</a>","mla":"Zemach, Assaf, et al. “Genome-Wide Evolutionary Analysis of Eukaryotic DNA Methylation.” <i>Science</i>, vol. 328, no. 5980, American Association for the Advancement of Science, 2010, pp. 916–19, doi:<a href=\"https://doi.org/10.1126/science.1186366\">10.1126/science.1186366</a>.","chicago":"Zemach, Assaf , Ivy E. McDaniel, Pedro Silva, and Daniel Zilberman. “Genome-Wide Evolutionary Analysis of Eukaryotic DNA Methylation.” <i>Science</i>. American Association for the Advancement of Science, 2010. <a href=\"https://doi.org/10.1126/science.1186366\">https://doi.org/10.1126/science.1186366</a>."},"page":"916-919","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication":"Science","keyword":["Multidisciplinary"],"intvolume":"       328","external_id":{"pmid":["20395474 "]},"issue":"5980","pmid":1,"date_published":"2010-05-14T00:00:00Z","language":[{"iso":"eng"}],"date_updated":"2021-12-14T08:35:37Z","department":[{"_id":"DaZi"}],"article_processing_charge":"No","_id":"9452","day":"14"},{"abstract":[{"lang":"eng","text":"Cytosine methylation silences transposable elements in plants, vertebrates, and fungi but also regulates gene expression. Plant methylation is catalyzed by three families of enzymes, each with a preferred sequence context: CG, CHG (H = A, C, or T), and CHH, with CHH methylation targeted by the RNAi pathway. Arabidopsis thaliana endosperm, a placenta-like tissue that nourishes the embryo, is globally hypomethylated in the CG context while retaining high non-CG methylation. Global methylation dynamics in seeds of cereal crops that provide the bulk of human nutrition remain unknown. Here, we show that rice endosperm DNA is hypomethylated in all sequence contexts. Non-CG methylation is reduced evenly across the genome, whereas CG hypomethylation is localized. CHH methylation of small transposable elements is increased in embryos, suggesting that endosperm demethylation enhances transposon silencing. Genes preferentially expressed in endosperm, including those coding for major storage proteins and starch synthesizing enzymes, are frequently hypomethylated in endosperm, indicating that DNA methylation is a crucial regulator of rice endosperm biogenesis. Our data show that genome-wide reshaping of seed DNA methylation is conserved among angiosperms and has a profound effect on gene expression in cereal crops."}],"author":[{"first_name":"Assaf","full_name":"Zemach, Assaf","last_name":"Zemach"},{"first_name":"M. Yvonne","last_name":"Kim","full_name":"Kim, M. Yvonne"},{"first_name":"Pedro","full_name":"Silva, Pedro","last_name":"Silva"},{"full_name":"Rodrigues, Jessica A.","last_name":"Rodrigues","first_name":"Jessica A."},{"last_name":"Dotson","full_name":"Dotson, Bradley","first_name":"Bradley"},{"last_name":"Brooks","full_name":"Brooks, Matthew D.","first_name":"Matthew D."},{"first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","full_name":"Zilberman, Daniel","last_name":"Zilberman","orcid":"0000-0002-0123-8649"}],"publisher":"National Academy of Sciences","extern":"1","scopus_import":"1","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"status":"public","doi":"10.1073/pnas.1009695107","volume":107,"quality_controlled":"1","year":"2010","month":"10","article_type":"original","date_created":"2021-06-07T09:31:01Z","title":"Local DNA hypomethylation activates genes in rice endosperm","type":"journal_article","publication_status":"published","oa_version":"Published Version","oa":1,"page":"18729-18734","citation":{"chicago":"Zemach, Assaf, M. Yvonne Kim, Pedro Silva, Jessica A. Rodrigues, Bradley Dotson, Matthew D. Brooks, and Daniel Zilberman. “Local DNA Hypomethylation Activates Genes in Rice Endosperm.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2010. <a href=\"https://doi.org/10.1073/pnas.1009695107\">https://doi.org/10.1073/pnas.1009695107</a>.","apa":"Zemach, A., Kim, M. Y., Silva, P., Rodrigues, J. A., Dotson, B., Brooks, M. D., &#38; Zilberman, D. (2010). Local DNA hypomethylation activates genes in rice endosperm. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1009695107\">https://doi.org/10.1073/pnas.1009695107</a>","mla":"Zemach, Assaf, et al. “Local DNA Hypomethylation Activates Genes in Rice Endosperm.” <i>Proceedings of the National Academy of Sciences</i>, vol. 107, no. 43, National Academy of Sciences, 2010, pp. 18729–34, doi:<a href=\"https://doi.org/10.1073/pnas.1009695107\">10.1073/pnas.1009695107</a>.","ieee":"A. Zemach <i>et al.</i>, “Local DNA hypomethylation activates genes in rice endosperm,” <i>Proceedings of the National Academy of Sciences</i>, vol. 107, no. 43. National Academy of Sciences, pp. 18729–18734, 2010.","short":"A. Zemach, M.Y. Kim, P. Silva, J.A. Rodrigues, B. Dotson, M.D. Brooks, D. Zilberman, Proceedings of the National Academy of Sciences 107 (2010) 18729–18734.","ama":"Zemach A, Kim MY, Silva P, et al. Local DNA hypomethylation activates genes in rice endosperm. <i>Proceedings of the National Academy of Sciences</i>. 2010;107(43):18729-18734. doi:<a href=\"https://doi.org/10.1073/pnas.1009695107\">10.1073/pnas.1009695107</a>","ista":"Zemach A, Kim MY, Silva P, Rodrigues JA, Dotson B, Brooks MD, Zilberman D. 2010. Local DNA hypomethylation activates genes in rice endosperm. Proceedings of the National Academy of Sciences. 107(43), 18729–18734."},"intvolume":"       107","publication":"Proceedings of the National Academy of Sciences","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","external_id":{"pmid":["20937895"]},"issue":"43","main_file_link":[{"url":"https://doi.org/10.1073/pnas.1009695107","open_access":"1"}],"pmid":1,"date_published":"2010-10-26T00:00:00Z","department":[{"_id":"DaZi"}],"date_updated":"2021-12-14T08:40:02Z","language":[{"iso":"eng"}],"article_processing_charge":"No","_id":"9485","day":"26"},{"_id":"9489","day":"14","article_processing_charge":"No","department":[{"_id":"DaZi"}],"date_updated":"2021-12-14T08:52:34Z","language":[{"iso":"eng"}],"date_published":"2010-09-14T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cub.2010.07.007"}],"pmid":1,"issue":"17","external_id":{"pmid":["20833323"]},"publication":"Current Biology","intvolume":"        20","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa":1,"citation":{"ieee":"A. Zemach and D. Zilberman, “Evolution of eukaryotic DNA methylation and the pursuit of safer sex,” <i>Current Biology</i>, vol. 20, no. 17. Elsevier, pp. R780–R785, 2010.","short":"A. Zemach, D. Zilberman, Current Biology 20 (2010) R780–R785.","ama":"Zemach A, Zilberman D. Evolution of eukaryotic DNA methylation and the pursuit of safer sex. <i>Current Biology</i>. 2010;20(17):R780-R785. doi:<a href=\"https://doi.org/10.1016/j.cub.2010.07.007\">10.1016/j.cub.2010.07.007</a>","ista":"Zemach A, Zilberman D. 2010. Evolution of eukaryotic DNA methylation and the pursuit of safer sex. Current Biology. 20(17), R780–R785.","chicago":"Zemach, Assaf, and Daniel Zilberman. “Evolution of Eukaryotic DNA Methylation and the Pursuit of Safer Sex.” <i>Current Biology</i>. Elsevier, 2010. <a href=\"https://doi.org/10.1016/j.cub.2010.07.007\">https://doi.org/10.1016/j.cub.2010.07.007</a>.","mla":"Zemach, Assaf, and Daniel Zilberman. “Evolution of Eukaryotic DNA Methylation and the Pursuit of Safer Sex.” <i>Current Biology</i>, vol. 20, no. 17, Elsevier, 2010, pp. R780–85, doi:<a href=\"https://doi.org/10.1016/j.cub.2010.07.007\">10.1016/j.cub.2010.07.007</a>.","apa":"Zemach, A., &#38; Zilberman, D. (2010). Evolution of eukaryotic DNA methylation and the pursuit of safer sex. <i>Current Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cub.2010.07.007\">https://doi.org/10.1016/j.cub.2010.07.007</a>"},"page":"R780-R785","oa_version":"Published Version","publication_status":"published","type":"journal_article","date_created":"2021-06-07T09:45:27Z","title":"Evolution of eukaryotic DNA methylation and the pursuit of safer sex","article_type":"review","month":"09","year":"2010","quality_controlled":"1","volume":20,"doi":"10.1016/j.cub.2010.07.007","status":"public","publication_identifier":{"eissn":["1879-0445"],"issn":["0960-9822"]},"scopus_import":"1","author":[{"first_name":"Assaf","full_name":"Zemach, Assaf","last_name":"Zemach"},{"full_name":"Zilberman, Daniel","last_name":"Zilberman","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","orcid":"0000-0002-0123-8649","first_name":"Daniel"}],"publisher":"Elsevier","extern":"1","abstract":[{"lang":"eng","text":"Cytosine methylation is an ancient process with conserved enzymology but diverse biological functions that include defense against transposable elements and regulation of gene expression. Here we will discuss the evolution and biological significance of eukaryotic DNA methylation, the likely drivers of that evolution, and major remaining mysteries."}]},{"day":"20","_id":"9764","oa_version":"Published Version","article_processing_charge":"No","date_updated":"2023-02-23T11:42:17Z","type":"research_data_reference","department":[{"_id":"NiBa"}],"date_created":"2021-08-02T09:45:39Z","title":"Heterosis and the drift load","related_material":{"record":[{"status":"public","id":"3779","relation":"used_in_publication"}]},"month":"07","date_published":"2010-07-20T00:00:00Z","year":"2010","doi":"10.1371/journal.pbio.1000429.s003","status":"public","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"apa":"Rosas, U., Barton, N. H., Copsey, L., Barbier De Reuille, P., &#38; Coen, E. (2010). Heterosis and the drift load. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.1000429.s003\">https://doi.org/10.1371/journal.pbio.1000429.s003</a>","mla":"Rosas, Ulises, et al. <i>Heterosis and the Drift Load</i>. Public Library of Science, 2010, doi:<a href=\"https://doi.org/10.1371/journal.pbio.1000429.s003\">10.1371/journal.pbio.1000429.s003</a>.","chicago":"Rosas, Ulises, Nicholas H Barton, Lucy Copsey, Pierre Barbier De Reuille, and Enrico Coen. “Heterosis and the Drift Load.” Public Library of Science, 2010. <a href=\"https://doi.org/10.1371/journal.pbio.1000429.s003\">https://doi.org/10.1371/journal.pbio.1000429.s003</a>.","ista":"Rosas U, Barton NH, Copsey L, Barbier De Reuille P, Coen E. 2010. Heterosis and the drift load, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pbio.1000429.s003\">10.1371/journal.pbio.1000429.s003</a>.","ama":"Rosas U, Barton NH, Copsey L, Barbier De Reuille P, Coen E. Heterosis and the drift load. 2010. doi:<a href=\"https://doi.org/10.1371/journal.pbio.1000429.s003\">10.1371/journal.pbio.1000429.s003</a>","short":"U. Rosas, N.H. Barton, L. Copsey, P. Barbier De Reuille, E. Coen, (2010).","ieee":"U. Rosas, N. H. Barton, L. Copsey, P. Barbier De Reuille, and E. Coen, “Heterosis and the drift load.” Public Library of Science, 2010."},"publisher":"Public Library of Science","author":[{"first_name":"Ulises","full_name":"Rosas, Ulises","last_name":"Rosas"},{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H"},{"last_name":"Copsey","full_name":"Copsey, Lucy","first_name":"Lucy"},{"full_name":"Barbier De Reuille, Pierre","last_name":"Barbier De Reuille","first_name":"Pierre"},{"first_name":"Enrico","last_name":"Coen","full_name":"Coen, Enrico"}]},{"oa_version":"Submitted Version","type":"conference","publication_status":"published","series_title":"LNCS","date_created":"2022-03-21T08:14:35Z","title":"ABC: Algebraic Bound Computation for loops","year":"2010","month":"05","doi":"10.1007/978-3-642-17511-4_7","volume":6355,"quality_controlled":"1","acknowledgement":"This work was supported in part by the Swiss NSF. The fourth author is supported by an FWF Hertha Firnberg Research grant (T425-N23).","status":"public","conference":{"name":"LPAR: Conference on Logic for Programming, Artificial Intelligence and Reasoning","location":"Dakar, Senegal","end_date":"2010-05-01","start_date":"2010-04-25"},"publication_identifier":{"eisbn":["9783642175114"],"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["9783642175107"]},"scopus_import":"1","abstract":[{"lang":"eng","text":"We present ABC, a software tool for automatically computing symbolic upper bounds on the number of iterations of nested program loops. The system combines static analysis of programs with symbolic summation techniques to derive loop invariant relations between program variables. Iteration bounds are obtained from the inferred invariants, by replacing variables with bounds on their greatest values. We have successfully applied ABC to a large number of examples. The derived symbolic bounds express non-trivial polynomial relations over loop variables. We also report on results to automatically infer symbolic expressions over harmonic numbers as upper bounds on loop iteration counts."}],"author":[{"last_name":"Blanc","full_name":"Blanc, Régis","first_name":"Régis"},{"first_name":"Thomas A","last_name":"Henzinger","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2985-7724"},{"last_name":"Hottelier","full_name":"Hottelier, Thibaud","first_name":"Thibaud"},{"first_name":"Laura","last_name":"Kovács","full_name":"Kovács, Laura"}],"publisher":"Springer Nature","article_processing_charge":"No","day":"01","_id":"10908","language":[{"iso":"eng"}],"date_updated":"2022-06-13T07:44:21Z","department":[{"_id":"ToHe"}],"main_file_link":[{"open_access":"1","url":"https://infoscience.epfl.ch/record/186096"}],"date_published":"2010-05-01T00:00:00Z","editor":[{"first_name":"Edmund M","full_name":"Clarke, Edmund M","last_name":"Clarke"},{"full_name":"Voronkov, Andrei","last_name":"Voronkov","first_name":"Andrei"}],"place":"Berlin, Heidelberg","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Logic for Programming, Artificial Intelligence, and Reasoning","intvolume":"      6355","citation":{"ama":"Blanc R, Henzinger TA, Hottelier T, Kovács L. ABC: Algebraic Bound Computation for loops. In: Clarke EM, Voronkov A, eds. <i>Logic for Programming, Artificial Intelligence, and Reasoning</i>. Vol 6355. LNCS. Berlin, Heidelberg: Springer Nature; 2010:103-118. doi:<a href=\"https://doi.org/10.1007/978-3-642-17511-4_7\">10.1007/978-3-642-17511-4_7</a>","ista":"Blanc R, Henzinger TA, Hottelier T, Kovács L. 2010. ABC: Algebraic Bound Computation for loops. Logic for Programming, Artificial Intelligence, and Reasoning. LPAR: Conference on Logic for Programming, Artificial Intelligence and ReasoningLNCS vol. 6355, 103–118.","ieee":"R. Blanc, T. A. Henzinger, T. Hottelier, and L. Kovács, “ABC: Algebraic Bound Computation for loops,” in <i>Logic for Programming, Artificial Intelligence, and Reasoning</i>, Dakar, Senegal, 2010, vol. 6355, pp. 103–118.","short":"R. Blanc, T.A. Henzinger, T. Hottelier, L. Kovács, in:, E.M. Clarke, A. Voronkov (Eds.), Logic for Programming, Artificial Intelligence, and Reasoning, Springer Nature, Berlin, Heidelberg, 2010, pp. 103–118.","apa":"Blanc, R., Henzinger, T. A., Hottelier, T., &#38; Kovács, L. (2010). ABC: Algebraic Bound Computation for loops. In E. M. Clarke &#38; A. Voronkov (Eds.), <i>Logic for Programming, Artificial Intelligence, and Reasoning</i> (Vol. 6355, pp. 103–118). Berlin, Heidelberg: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-642-17511-4_7\">https://doi.org/10.1007/978-3-642-17511-4_7</a>","mla":"Blanc, Régis, et al. “ABC: Algebraic Bound Computation for Loops.” <i>Logic for Programming, Artificial Intelligence, and Reasoning</i>, edited by Edmund M Clarke and Andrei Voronkov, vol. 6355, Springer Nature, 2010, pp. 103–18, doi:<a href=\"https://doi.org/10.1007/978-3-642-17511-4_7\">10.1007/978-3-642-17511-4_7</a>.","chicago":"Blanc, Régis, Thomas A Henzinger, Thibaud Hottelier, and Laura Kovács. “ABC: Algebraic Bound Computation for Loops.” In <i>Logic for Programming, Artificial Intelligence, and Reasoning</i>, edited by Edmund M Clarke and Andrei Voronkov, 6355:103–18. LNCS. Berlin, Heidelberg: Springer Nature, 2010. <a href=\"https://doi.org/10.1007/978-3-642-17511-4_7\">https://doi.org/10.1007/978-3-642-17511-4_7</a>."},"page":"103-118","oa":1}]