@inproceedings{3837, abstract = {In this paper we extend the work of Alfaro, Henzinger et al. on interface theories for component-based design. Existing interface theories often fail to capture functional relations between the inputs and outputs of an interface. For example, a simple synchronous interface that takes as input a number n ≥ 0 and returns, at the same time, as output n + 1, cannot be expressed in existing theories. In this paper we provide a theory of relational interfaces, where such input-output relations can be captured. Our theory supports synchronous interfaces, both stateless and stateful. It includes explicit notions of environments and pluggability, and satisfies fundamental properties such as preservation of refinement by composition, and characterization of pluggability by refinement. We achieve these properties by making reasonable restrictions on feedback loops in interface compositions.}, author = {Tripakis, Stavros and Lickly, Ben and Henzinger, Thomas A and Lee, Edward}, booktitle = {EMSOFT '09 Proceedings of the seventh ACM international conference on Embedded software}, location = {Grenoble, France}, pages = {67 -- 76}, publisher = {ACM}, title = {{On relational interfaces}}, doi = {10.1145/1629335.1629346}, year = {2009}, } @inproceedings{3841, abstract = {We compare several languages for specifying Markovian population models such as queuing networks and chemical reaction networks. These languages —matrix descriptions, stochastic Petri nets, stoichiometric equations, stochastic process algebras, and guarded command models— all describe continuous-time Markov chains, but they differ according to important properties, such as compositionality, expressiveness and succinctness, executability, ease of use, and the support they provide for checking the well-formedness of a model and for analyzing a model. }, author = {Henzinger, Thomas A and Jobstmann, Barbara and Wolf, Verena}, location = {Palaiseau, France}, pages = {3 -- 23}, publisher = {Springer}, title = {{Formalisms for specifying Markovian population models}}, doi = {10.1007/978-3-642-04420-5_2}, volume = {5797}, year = {2009}, } @inproceedings{3843, abstract = {Within systems biology there is an increasing interest in the stochastic behavior of biochemical reaction networks. An appropriate stochastic description is provided by the chemical master equation, which represents a continuous- time Markov chain (CTMC). Standard Uniformization (SU) is an efficient method for the transient analysis of CTMCs. For systems with very different time scales, such as biochemical reaction networks, SU is computationally expensive. In these cases, a variant of SU, called adaptive uniformization (AU), is known to reduce the large number of iterations needed by SU. The additional difficulty of AU is that it requires the solution of a birth process. In this paper we present an on-the-fly variant of AU, where we improve the original algorithm for AU at the cost of a small approximation error. By means of several examples, we show that our approach is particularly well-suited for biochemical reaction networks.}, author = {Didier, Frédéric and Henzinger, Thomas A and Mateescu, Maria and Wolf, Verena}, location = {Trento, Italy}, number = {6}, pages = {118 -- 127}, publisher = {IEEE}, title = {{Fast adaptive uniformization of the chemical master equation}}, doi = {10.1109/HiBi.2009.23}, volume = {4}, year = {2009}, } @inproceedings{3844, abstract = {The Hierarchical Timing Language (HTL) is a real-time coordination language for distributed control systems. HTL programs must be checked for well-formedness, race freedom, transmission safety (schedulability of inter-host communication), and time safety (schedulability of host computation). We present a modular abstract syntax and semantics for HTL, modular checks of well-formedness, race freedom, and transmission safety, and modular code distribution. Our contributions here complement previous results on HTL time safety and modular code generation. Modularity in HTL can be utilized in easy program composition as well as fast program analysis and code generation, but also in so-called runtime patching, where program components may be modified at runtime.}, author = {Henzinger, Thomas A and Kirsch, Christoph and Marques, Eduardo and Sokolova, Ana}, location = {Washington, DC, United States}, pages = {171 -- 180}, publisher = {IEEE}, title = {{Distributed, modular HTL}}, doi = {10.1109/RTSS.2009.9}, year = {2009}, } @inproceedings{3871, abstract = {Nondeterministic weighted automata are finite automata with numerical weights oil transitions. They define quantitative languages 1, that assign to each word v; a real number L(w). The value of ail infinite word w is computed as the maximal value of all runs over w, and the value of a run as the supremum, limsup liminf, limit average, or discounted sum of the transition weights. We introduce probabilistic weighted antomata, in which the transitions are chosen in a randomized (rather than nondeterministic) fashion. Under almost-sure semantics (resp. positive semantics), the value of a word v) is the largest real v such that the runs over w have value at least v with probability I (resp. positive probability). We study the classical questions of automata theory for probabilistic weighted automata: emptiness and universality, expressiveness, and closure under various operations oil languages. For quantitative languages, emptiness university axe defined as whether the value of some (resp. every) word exceeds a given threshold. We prove some, of these questions to he decidable, and others undecidable. Regarding expressive power, we show that probabilities allow its to define a wide variety of new classes of quantitative languages except for discounted-sum automata, where probabilistic choice is no more expressive than nondeterminism. Finally we live ail almost complete picture of the closure of various classes of probabilistic weighted automata for the following, provide, is operations oil quantitative languages: maximum, sum. and numerical complement.}, author = {Chatterjee, Krishnendu and Doyen, Laurent and Henzinger, Thomas A}, location = {Bologna, Italy}, pages = {244 -- 258}, publisher = {Springer}, title = {{Probabilistic weighted automata}}, doi = {10.1007/978-3-642-04081-8_17}, volume = {5710}, year = {2009}, } @inproceedings{3968, abstract = {We describe an algorithm for segmenting three-dimensional medical imaging data modeled as a continuous function on a 3-manifold. It is related to watershed algorithms developed in image processing but is closer to its mathematical roots, which are Morse theory and homological algebra. It allows for the implicit treatment of an underlying mesh, thus combining the structural integrity of its mathematical foundations with the computational efficiency of image processing.}, author = {Edelsbrunner, Herbert and Harer, John}, location = {Zermatt, Switzerland}, pages = {36 -- 50}, publisher = {Springer}, title = {{The persistent Morse complex segmentation of a 3-manifold}}, doi = {10.1007/978-3-642-10470-1_4}, volume = {5903}, year = {2009}, } @article{4136, abstract = {Populations living in a spatially and temporally changing environment can adapt to the changing optimum and/or migrate toward favorable habitats. Here we extend previous analyses with a static optimum to allow the environment to vary in time as well as in space. The model follows both population dynamics and the trait mean under stabilizing selection, and the outcomes can be understood by comparing the loads due to genetic variance, dispersal, and temporal change. With fixed genetic variance, we obtain two regimes: (1) adaptation that is uniform along the environmental gradient and that responds to the moving optimum as expected for panmictic populations and when the spatial gradient is sufficiently steep, and (2) a population with limited range that adapts more slowly than the environmental optimum changes in both time and space; the population therefore becomes locally extinct and migrates toward suitable habitat. We also use a population‐genetic model with many loci to allow genetic variance to evolve, and we show that the only solution now has uniform adaptation.}, author = {Polechova, Jitka and Barton, Nicholas H and Marion, Glenn}, journal = {American Naturalist}, number = {5}, pages = {E186 -- E204}, publisher = {University of Chicago Press}, title = {{Species' range: Adaptation in space and time}}, doi = {10.1086/605958}, volume = {174}, year = {2009}, } @article{4231, abstract = {The evolution of quantitative characters depends on the frequencies of the alleles involved, yet these frequencies cannot usually be measured. Previous groups have proposed an approximation to the dynamics of quantitative traits, based on an analogy with statistical mechanics. We present a modified version of that approach, which makes the analogy more precise and applies quite generally to describe the evolution of allele frequencies. We calculate explicitly how the macroscopic quantities (i.e., quantities that depend on the quantitative trait) depend on evolutionary forces, in a way that is independent of the microscopic details. We first show that the stationary distribution of allele frequencies under drift, selection, and mutation maximizes a certain measure of entropy, subject to constraints on the expectation of observable quantities. We then approximate the dynamical changes in these expectations, assuming that the distribution of allele frequencies always maximizes entropy, conditional on the expected values. When applied to directional selection on an additive trait, this gives a very good approximation to the evolution of the trait mean and the genetic variance, when the number of mutations per generation is sufficiently high (4Nμ > 1). We show how the method can be modified for small mutation rates (4Nμ → 0). We outline how this method describes epistatic interactions as, for example, with stabilizing selection.}, author = {Barton, Nicholas H and De Vladar, Harold}, journal = {Genetics}, number = {3}, pages = {997 -- 1011}, publisher = {Genetics Society of America}, title = {{Statistical mechanics and the evolution of polygenic quantitative traits}}, doi = {10.1534/genetics.108.099309}, volume = {181}, year = {2009}, } @article{4242, abstract = {Felsenstein distinguished two ways by which selection can directly strengthen isolation. First, a modifier that strengthens prezygotic isolation can be favored everywhere. This fits with the traditional view of reinforcement as an adaptation to reduce deleterious hybridization by strengthening assortative mating. Second, selection can favor association between different incompatibilities, despite recombination. We generalize this “two allele” model to follow associations among any number of incompatibilities, which may include both assortment and hybrid inviability. Our key argument is that this process, of coupling between incompatibilities, may be quite different from the usual view of reinforcement: strong isolation can evolve through the coupling of any kind of incompatibility, whether prezygotic or postzygotic. Single locus incompatibilities become coupled because associations between them increase the variance in compatibility, which in turn increases mean fitness if there is positive epistasis. Multiple incompatibilities, each maintained by epistasis, can become coupled in the same way. In contrast, a single-locus incompatibility can become coupled with loci that reduce the viability of haploid hybrids because this reduces harmful recombination. We obtain simple approximations for the limits of tight linkage, and strong assortment, and show how assortment alleles can invade through associations with other components of reproductive isolation.}, author = {Barton, Nicholas H and De Cara, Maria}, journal = {Evolution; International Journal of Organic Evolution}, number = {5}, pages = {1171 -- 1190}, publisher = {Wiley}, title = {{The evolution of strong reproductive isolation}}, doi = {10.1111/j.1558-5646.2009.00622.x}, volume = {63}, year = {2009}, } @article{3870, abstract = {Games on graphs with omega-regular objectives provide a model for the control and synthesis of reactive systems. Every omega-regular objective can be decomposed into a safety part and a liveness part. The liveness part ensures that something good happens “eventually.” Two main strengths of the classical, infinite-limit formulation of liveness are robustness (independence from the granularity of transitions) and simplicity (abstraction of complicated time bounds). However, the classical liveness formulation suffers from the drawback that the time until something good happens may be unbounded. A stronger formulation of liveness, so-called finitary liveness, overcomes this drawback, while still retaining robustness and simplicity. Finitary liveness requires that there exists an unknown, fixed bound b such that something good happens within b transitions. While for one-shot liveness (reachability) objectives, classical and finitary liveness coincide, for repeated liveness (Buchi) objectives, the finitary formulation is strictly stronger. In this work we study games with finitary parity and Streett objectives. We prove the determinacy of these games, present algorithms for solving these games, and characterize the memory requirements of winning strategies. We show that finitary parity games can be solved in polynomial time, which is not known for infinitary parity games. For finitary Streett games, we give an EXPTIME algorithm and show that the problem is NP-hard. Our algorithms can be used, for example, for synthesizing controllers that do not let the response time of a system increase without bound.}, author = {Chatterjee, Krishnendu and Henzinger, Thomas A and Horn, Florian}, journal = {ACM Transactions on Computational Logic}, number = {1}, publisher = {ACM}, title = {{Finitary winning in omega-regular games}}, doi = {10.1145/1614431.1614432}, volume = {11}, year = {2009}, } @article{517, author = {Barton, Nicholas H}, journal = {Genetics Research}, number = {5-6}, pages = {475 -- 477}, publisher = {Cambridge University Press}, title = {{Identity and coalescence in structured populations: A commentary on 'Inbreeding coefficients and coalescence times' by Montgomery Slatkin}}, doi = {10.1017/S0016672308009683}, volume = {89}, year = {2008}, }