@inproceedings{3858, abstract = {We consider two-player zero-sum games on graphs. On the basis of the information available to the players these games can be classified as follows: (a) partial-observation (both players have partial view of the game); (b) one-sided partial-observation (one player has partial-observation and the other player has complete-observation); and (c) complete-observation (both players have com- plete view of the game). We survey the complexity results for the problem of de- ciding the winner in various classes of partial-observation games with ω-regular winning conditions specified as parity objectives. We present a reduction from the class of parity objectives that depend on sequence of states of the game to the sub-class of parity objectives that only depend on the sequence of observations. We also establish that partial-observation acyclic games are PSPACE-complete.}, author = {Chatterjee, Krishnendu and Doyen, Laurent}, location = {Yogyakarta, Indonesia}, pages = {1 -- 14}, publisher = {Springer}, title = {{The complexity of partial-observation parity games}}, doi = {10.1007/978-3-642-16242-8_1}, volume = {6397}, year = {2010}, } @proceedings{3859, abstract = {This book constitutes the proceedings of the 8th International Conference on Formal Modeling and Analysis of Timed Systems, FORMATS 2010, held in Klosterneuburg, Austria in September 2010. The 14 papers presented were carefully reviewed and selected from 31 submissions. In addition, the volume contains 3 invited talks and 2 invited tutorials.The aim of FORMATS is to promote the study of fundamental and practical aspects of timed systems, and to bring together researchers from different disciplines that share an interest in the modeling and analysis of timed systems. Typical topics include foundations and semantics, methods and tools, and applications.}, editor = {Chatterjee, Krishnendu and Henzinger, Thomas A}, location = {Klosterneuburg, Austria}, publisher = {Springer}, title = {{Formal modeling and analysis of timed systems}}, doi = {10.1007/978-3-642-15297-9}, volume = {6246}, year = {2010}, } @inproceedings{3860, abstract = {In mean-payoff games, the objective of the protagonist is to ensure that the limit average of an infinite sequence of numeric weights is nonnegative. In energy games, the objective is to ensure that the running sum of weights is always nonnegative. Generalized mean-payoff and energy games replace individual weights by tuples, and the limit average (resp. running sum) of each coordinate must be (resp. remain) nonnegative. These games have applications in the synthesis of resource-bounded processes with multiple resources. We prove the finite-memory determinacy of generalized energy games and show the inter- reducibility of generalized mean-payoff and energy games for finite-memory strategies. We also improve the computational complexity for solving both classes of games with finite-memory strategies: while the previously best known upper bound was EXPSPACE, and no lower bound was known, we give an optimal coNP-complete bound. For memoryless strategies, we show that the problem of deciding the existence of a winning strategy for the protagonist is NP-complete.}, author = {Chatterjee, Krishnendu and Doyen, Laurent and Henzinger, Thomas A and Raskin, Jean}, location = {Chennai, India}, pages = {505 -- 516}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Generalized mean-payoff and energy games}}, doi = {10.4230/LIPIcs.FSTTCS.2010.505}, volume = {8}, year = {2010}, } @article{3861, abstract = {We introduce strategy logic, a logic that treats strategies in two-player games as explicit first-order objects. The explicit treatment of strategies allows us to specify properties of nonzero-sum games in a simple and natural way. We show that the one-alternation fragment of strategy logic is strong enough to express the existence of Nash equilibria and secure equilibria, and subsumes other logics that were introduced to reason about games, such as ATL, ATL*, and game logic. We show that strategy logic is decidable, by constructing tree automata that recognize sets of strategies. While for the general logic, our decision procedure is nonelementary, for the simple fragment that is used above we show that the complexity is polynomial in the size of the game graph and optimal in the size of the formula (ranging from polynomial to 2EXPTIME depending on the form of the formula).}, author = {Chatterjee, Krishnendu and Henzinger, Thomas A and Piterman, Nir}, journal = {Information and Computation}, number = {6}, pages = {677 -- 693}, publisher = {Elsevier}, title = {{Strategy logic}}, doi = {10.1016/j.ic.2009.07.004}, volume = {208}, year = {2010}, } @article{3863, abstract = {We consider two-player parity games with imperfect information in which strategies rely on observations that provide imperfect information about the history of a play. To solve such games, i.e., to determine the winning regions of players and corresponding winning strategies, one can use the subset construction to build an equivalent perfect-information game. Recently, an algorithm that avoids the inefficient subset construction has been proposed. The algorithm performs a fixed-point computation in a lattice of antichains, thus maintaining a succinct representation of state sets. However, this representation does not allow to recover winning strategies. In this paper, we build on the antichain approach to develop an algorithm for constructing the winning strategies in parity games of imperfect information. One major obstacle in adapting the classical procedure is that the complementation of attractor sets would break the invariant of downward-closedness on which the antichain representation relies. We overcome this difficulty by decomposing problem instances recursively into games with a combination of reachability, safety, and simpler parity conditions. We also report on an experimental implementation of our algorithm: to our knowledge, this is the first implementation of a procedure for solving imperfect-information parity games on graphs.}, author = {Berwanger, Dietmar and Chatterjee, Krishnendu and De Wulf, Martin and Doyen, Laurent and Henzinger, Thomas A}, journal = {Information and Computation}, number = {10}, pages = {1206 -- 1220}, publisher = {Elsevier}, title = {{Strategy construction for parity games with imperfect information}}, doi = {10.1016/j.ic.2009.09.006}, volume = {208}, year = {2010}, } @inproceedings{3864, abstract = {Often one has a preference order among the different systems that satisfy a given specification. Under a probabilistic assumption about the possible inputs, such a preference order is naturally expressed by a weighted automaton, which assigns to each word a value, such that a system is preferred if it generates a higher expected value. We solve the following optimal-synthesis problem: given an omega-regular specification, a Markov chain that describes the distribution of inputs, and a weighted automaton that measures how well a system satisfies the given specification tinder the given input assumption, synthesize a system that optimizes the measured value. For safety specifications and measures that are defined by mean-payoff automata, the optimal-synthesis problem amounts to finding a strategy in a Markov decision process (MDP) that is optimal for a long-run average reward objective, which can be done in polynomial time. For general omega-regular specifications, the solution rests on a new, polynomial-time algorithm for computing optimal strategies in MDPs with mean-payoff parity objectives. We present some experimental results showing optimal systems that were automatically generated in this way.}, author = {Chatterjee, Krishnendu and Henzinger, Thomas A and Jobstmann, Barbara and Singh, Rohit}, location = {Edinburgh, United Kingdom}, pages = {380 -- 395}, publisher = {Springer}, title = {{Measuring and synthesizing systems in probabilistic environments}}, doi = {10.1007/978-3-642-14295-6_34}, volume = {6174}, year = {2010}, } @inproceedings{3865, abstract = {We introduce a technique for debugging multi-threaded C programs and analyzing the impact of source code changes, and its implementation in the prototype tool DIRECT. Our approach uses a combination of source code instrumentation and runtime management. The source code along with a test harness is instrumented to monitor Operating System (OS) and user defined function calls. DIRECT tracks all concurrency control primitives and, optionally, data from the program. DIRECT maintains an abstract global state that combines information from every thread, including the sequence of function calls and concurrency primitives executed. The runtime manager can insert delays, provoking thread inter-leavings that may exhibit bugs that are difficult to reach otherwise. The runtime manager collects an approximation of the reachable state space and uses this approximation to assess the impact of change in a new version of the program.}, author = {Chatterjee, Krishnendu and De Alfaro, Luca and Raman, Vishwanath and Sánchez, César}, booktitle = {13th International Conference on Fundamental Approaches to Software Engineering}, issn = {1611-3349}, location = {Paphos, Cyprus}, pages = {293 -- 307}, publisher = {Springer}, title = {{Analyzing the impact of change in multi-threaded programs}}, doi = {10.1007/978-3-642-12029-9_21}, volume = {6013}, year = {2010}, } @inproceedings{3866, abstract = {Systems ought to behave reasonably even in circumstances that are not anticipated in their specifications. We propose a definition of robustness for liveness specifications which prescribes, for any number of environment assumptions that are violated, a minimal number of system guarantees that must still be fulfilled. This notion of robustness can be formulated and realized using a Generalized Reactivity formula. We present an algorithm for synthesizing robust systems from such formulas. For the important special case of Generalized Reactivity formulas of rank 1, our algorithm improves the complexity of [PPS06] for large specifications with a small number of assumptions and guarantees.}, author = {Bloem, Roderick and Chatterjee, Krishnendu and Greimel, Karin and Henzinger, Thomas A and Jobstmann, Barbara}, editor = {Touili, Tayssir and Cook, Byron and Jackson, Paul}, location = {Edinburgh, UK}, pages = {410 -- 424}, publisher = {Springer}, title = {{Robustness in the presence of liveness}}, doi = {10.1007/978-3-642-14295-6_36}, volume = {6174}, year = {2010}, } @article{3901, abstract = {We are interested in 3-dimensional images given as arrays of voxels with intensity values. Extending these values to acontinuous function, we study the robustness of homology classes in its level and interlevel sets, that is, the amount of perturbationneeded to destroy these classes. The structure of the homology classes and their robustness, over all level and interlevel sets, can bevisualized by a triangular diagram of dots obtained by computing the extended persistence of the function. We give a fast hierarchicalalgorithm using the dual complexes of oct-tree approximations of the function. In addition, we show that for balanced oct-trees, thedual complexes are geometrically realized in $R^3$ and can thus be used to construct level and interlevel sets. We apply these tools tostudy 3-dimensional images of plant root systems.}, author = {Bendich, Paul and Edelsbrunner, Herbert and Kerber, Michael}, journal = {IEEE Transactions of Visualization and Computer Graphics}, number = {6}, pages = {1251 -- 1260}, publisher = {IEEE}, title = {{Computing robustness and persistence for images}}, doi = {10.1109/TVCG.2010.139}, volume = {16}, year = {2010}, } @phdthesis{3962, author = {Pflicke, Holger}, issn = {2663-337X}, publisher = {Institute of Science and Technology Austria}, title = {{Dendritic cell migration across basement membranes in the skin}}, year = {2010}, } @article{4134, abstract = {All species are restricted in their distribution. Currently, ecological models can only explain such limits if patches vary in quality, leading to asymmetrical dispersal, or if genetic variation is too low at the margins for adaptation. However, population genetic models suggest that the increase in genetic variance resulting from dispersal should allow adaptation to almost any ecological gradient. Clearly therefore, these models miss something that prevents evolution in natural populations. We developed an individual-based simulation to explore stochastic effects in these models. At high carrying capacities, our simulations largely agree with deterministic predictions. However, when carrying capacity is low, the population fails to establish for a wide range of parameter values where adaptation was expected from previous models. Stochastic or transient effects appear critical around the boundaries in parameter space between simulation behaviours. Dispersal, gradient steepness, and population density emerge as key factors determining adaptation on an ecological gradient. }, author = {Bridle, Jon and Polechova, Jitka and Kawata, Masakado and Butlin, Roger}, journal = {Ecology Letters}, number = {4}, pages = {485 -- 494}, publisher = {Wiley-Blackwell}, title = {{Why is adaptation prevented at ecological margins? New insights from individual-based simulations}}, doi = {10.1111/j.1461-0248.2010.01442.x}, volume = {13}, year = {2010}, } @article{4157, abstract = {Integrin- and cadherin-mediated adhesion is central for cell and tissue morphogenesis, allowing cells and tissues to change shape without loosing integrity. Studies predominantly in cell culture showed that mechanosensation through adhesion structures is achieved by force-mediated modulation of their molecular composition. The specific molecular composition of adhesion sites in turn determines their signalling activity and dynamic reorganization. Here, we will review how adhesion sites respond to mecanical stimuli, and how spatially and temporally regulated signalling from different adhesion sites controls cell migration and tissue morphogenesis.}, author = {Papusheva, Ekaterina and Heisenberg, Carl-Philipp J}, journal = {EMBO Journal}, number = {16}, pages = {2753 -- 2768}, publisher = {Wiley-Blackwell}, title = {{Spatial organization of adhesion: force-dependent regulation and function in tissue morphogenesis}}, doi = {10.1038/emboj.2010.182}, volume = {29}, year = {2010}, } @article{4243, abstract = {We investigate a new model for populations evolving in a spatial continuum. This model can be thought of as a spatial version of the Lambda-Fleming-Viot process. It explicitly incorporates both small scale reproduction events and large scale extinction-recolonisation events. The lineages ancestral to a sample from a population evolving according to this model can be described in terms of a spatial version of the Lambda-coalescent. Using a technique of Evans (1997), we prove existence and uniqueness in law for the model. We then investigate the asymptotic behaviour of the genealogy of a finite number of individuals sampled uniformly at random (or more generally `far enough apart') from a two-dimensional torus of sidelength L as L tends to infinity. Under appropriate conditions (and on a suitable timescale) we can obtain as limiting genealogical processes a Kingman coalescent, a more general Lambda-coalescent or a system of coalescing Brownian motions (with a non-local coalescence mechanism).}, author = {Barton, Nicholas H and Etheridge, Alison and Véber, Amandine}, journal = {Electronic Journal of Probability}, number = {7}, pages = {162 -- 216}, publisher = {Institute of Mathematical Statistics}, title = {{A new model for evolution in a spatial continuum}}, doi = {10.1214/EJP.v15-741}, volume = {15}, year = {2010}, } @article{3867, abstract = {Weighted automata are nondeterministic automata with numerical weights on transitions. They can define quantitative languages L that assign to each word w a real number L(w). In the case of infinite words, the value of a run is naturally computed as the maximum, limsup, liminf, limit-average, or discounted-sum of the transition weights. The value of a word w is the supremum of the values of the runs over w. We study expressiveness and closure questions about these quantitative languages. We first show that the set of words with value greater than a threshold can be omega-regular for deterministic limit-average and discounted-sum automata, while this set is always omega-regular when the threshold is isolated (i.e., some neighborhood around the threshold contains no word). In the latter case, we prove that the omega-regular language is robust against small perturbations of the transition weights. We next consider automata with transition weights 0 or 1 and show that they are as expressive as general weighted automata in the limit-average case, but not in the discounted-sum case. Third, for quantitative languages L-1 and L-2, we consider the operations max(L-1, L-2), min(L-1, L-2), and 1 - L-1, which generalize the boolean operations on languages, as well as the sum L-1 + L-2. We establish the closure properties of all classes of quantitative languages with respect to these four operations.}, author = {Chatterjee, Krishnendu and Doyen, Laurent and Henzinger, Thomas A}, journal = {Logical Methods in Computer Science}, number = {3}, pages = {1 -- 23}, publisher = {International Federation for Computational Logic}, title = {{Expressiveness and closure properties for quantitative languages}}, doi = {10.2168/LMCS-6(3:10)2010}, volume = {6}, year = {2010}, } @article{3868, abstract = {Simulation and bisimulation metrics for stochastic systems provide a quantitative generalization of the classical simulation and bisimulation relations. These metrics capture the similarity of states with respect to quantitative specifications written in the quantitative mu-calculus and related probabilistic logics. We first show that the metrics provide a bound for the difference in long-run average and discounted average behavior across states, indicating that the metrics can be used both in system verification, and in performance evaluation. For turn-based games and MDPs, we provide a polynomial-time algorithm for the computation of the one-step metric distance between states. The algorithm is based on linear programming; it improves on the previous known exponential-time algorithm based on a reduction to the theory of reals. We then present PSPACE algorithms for both the decision problem and the problem of approximating the metric distance between two states, matching the best known algorithms for Markov chains. For the bisimulation kernel of the metric our algorithm works in time O(n(4)) for both turn-based games and MDPs; improving the previously best known O(n(9).log(n)) time algorithm for MDPs. For a concurrent game G, we show that computing the exact distance be tween states is at least as hard as computing the value of concurrent reachability games and the square-root-sum problem in computational geometry. We show that checking whether the metric distance is bounded by a rational r, can be done via a reduction to the theory of real closed fields, involving a formula with three quantifier alternations, yielding O(vertical bar G vertical bar(O(vertical bar G vertical bar 5))) time complexity, improving the previously known reduction, which yielded O(vertical bar G vertical bar(O(vertical bar G vertical bar 7))) time complexity. These algorithms can be iterated to approximate the metrics using binary search}, author = {Chatterjee, Krishnendu and De Alfaro, Luca and Majumdar, Ritankar and Raman, Vishwanath}, journal = {Logical Methods in Computer Science}, number = {3}, pages = {1 -- 27}, publisher = {International Federation for Computational Logic}, title = {{Algorithms for game metrics}}, doi = {10.2168/LMCS-6(3:13)2010}, volume = {6}, year = {2010}, } @inproceedings{3782, abstract = {In cortex surface segmentation, the extracted surface is required to have a particular topology, namely, a two-sphere. We present a new method for removing topology noise of a curve or surface within the level set framework, and thus produce a cortical surface with correct topology. We define a new energy term which quantifies topology noise. We then show how to minimize this term by computing its functional derivative with respect to the level set function. This method differs from existing methods in that it is inherently continuous and not digital; and in the way that our energy directly relates to the topology of the underlying curve or surface, versus existing knot-based measures which are related in a more indirect fashion. The proposed flow is validated empirically.}, author = {Chen, Chao and Freedman, Daniel}, booktitle = {Conference proceedings MCV 2010}, location = {Beijing, China}, pages = {31 -- 42}, publisher = {Springer}, title = {{Topology noise removal for curve and surface evolution}}, doi = {10.1007/978-3-642-18421-5_4}, volume = {6533}, year = {2010}, } @article{3789, abstract = {The development of multicellular organisms is dependent on the tight coordination between tissue growth and morphogenesis. The stereotypical orientation of cell divisions has been proposed to be a fundamental mechanism by which proliferating and growing tissues take shape. However, the actual contribution of stereotypical division orientation (SDO) to tissue morphogenesis is unclear. In zebrafish, cell divisions with stereotypical orientation have been implicated in both body-axis elongation and neural rod formation [1, 2], although there is little direct evidence for a critical function of SDO in either of these processes. Here we show that SDO is required for formation of the neural rod midline during neurulation but dispensable for elongation of the body axis during gastrulation. Our data indicate that SDO during both gastrulation and neurulation is dependent on the noncanonical Wnt receptor Frizzled 7 (Fz7) and that interfering with cell division orientation leads to severe defects in neural rod midline formation but not body-axis elongation. These findings suggest a novel function for Fz7-controlled cell division orientation in neural rod midline formation during neurulation. }, author = {Quesada-Hernández, Elena and Caneparo, Luca and Schneider, Sylvia and Winkler, Sylke and Liebling, Michael and Fraser, Scott and Heisenberg, Carl-Philipp J}, journal = {Current Biology}, number = {21}, pages = {1966 -- 1972}, publisher = {Cell Press}, title = {{Stereotypical cell division orientation controls neural rod midline formation in zebrafish}}, doi = {10.1016/j.cub.2010.10.009}, volume = {20}, year = {2010}, } @inproceedings{4542, abstract = {Weighted automata are finite automata with numerical weights on transitions. Nondeterministic weighted automata define quantitative languages L that assign to each word w a real number L(w) computed as the maximal value of all runs over w, and the value of a run r is a function of the sequence of weights that appear along r. There are several natural functions to consider such as Sup, LimSup, LimInf, limit average, and discounted sum of transition weights. We introduce alternating weighted automata in which the transitions of the runs are chosen by two players in a turn-based fashion. Each word is assigned the maximal value of a run that the first player can enforce regardless of the choices made by the second player. We survey the results about closure properties, expressiveness, and decision problems for nondeterministic weighted automata, and we extend these results to alternating weighted automata. For quantitative languages L 1 and L 2, we consider the pointwise operations max(L 1,L 2), min(L 1,L 2), 1 − L 1, and the sum L 1 + L 2. We establish the closure properties of all classes of alternating weighted automata with respect to these four operations. We next compare the expressive power of the various classes of alternating and nondeterministic weighted automata over infinite words. In particular, for limit average and discounted sum, we show that alternation brings more expressive power than nondeterminism. Finally, we present decidability results and open questions for the quantitative extension of the classical decision problems in automata theory: emptiness, universality, language inclusion, and language equivalence.}, author = {Chatterjee, Krishnendu and Doyen, Laurent and Henzinger, Thomas A}, location = {Wroclaw, Poland}, pages = {3 -- 13}, publisher = {Springer}, title = {{Alternating weighted automata}}, doi = {10.1007/978-3-642-03409-1_2}, volume = {5699}, year = {2009}, } @inproceedings{4543, abstract = {The synthesis of a reactive system with respect to all omega-regular specification requires the solution of a graph game. Such games have been extended in two natural ways. First, a game graph can be equipped with probabilistic choices between alternative transitions, thus allowing the, modeling of uncertain behaviour. These are called stochastic games. Second, a liveness specification can he strengthened to require satisfaction within all unknown but bounded amount of time. These are called finitary objectives. We study. for the first time, the, combination of Stochastic games and finitary objectives. We characterize the requirements on optimal strategies and provide algorithms for Computing the maximal achievable probability of winning stochastic games with finitary parity or Street, objectives. Most notably the set of state's from which a player can win with probability . for a finitary parity objective can he computed in polynomial time even though no polynomial-time algorithm is known in the nonfinitary case.}, author = {Chatterjee, Krishnendu and Henzinger, Thomas A and Horn, Florian}, location = {High Tatras, Slovakia}, pages = {34 -- 54}, publisher = {Springer}, title = {{Stochastic games with finitary objectives}}, doi = {10.1007/978-3-642-03816-7_4}, volume = {5734}, year = {2009}, } @inproceedings{4545, abstract = {A stochastic game is a two-player game played oil a graph, where in each state the successor is chosen either by One of the players, or according to a probability distribution. We Survey Stochastic games with limsup and liminf objectives. A real-valued re-ward is assigned to each state, and the value of all infinite path is the limsup (resp. liminf) of all rewards along the path. The value of a stochastic game is the maximal expected value of an infinite path that call he achieved by resolving the decisions of the first player. We present the complexity of computing values of Stochastic games and their subclasses, and the complexity, of optimal strategies in such games. }, author = {Chatterjee, Krishnendu and Doyen, Laurent and Henzinger, Thomas A}, location = {Rhodos, Greece}, pages = {1 -- 15}, publisher = {Springer}, title = {{A survey of stochastic games with limsup and liminf objectives}}, doi = {10.1007/978-3-642-02930-1_1}, volume = {5556}, year = {2009}, }