@article{3775,
  abstract     = {There is a close analogy between statistical thermodynamics and the evolution of allele frequencies under mutation, selection and random drift. Wright's formula for the stationary distribution of allele frequencies is analogous to the Boltzmann distribution in statistical physics. Population size, 2N, plays the role of the inverse temperature, 1/kT, and determines the magnitude of random fluctuations. Log mean fitness, View the MathML source, tends to increase under selection, and is analogous to a (negative) energy; a potential function, U, increases under mutation in a similar way. An entropy, SH, can be defined which measures the deviation from the distribution of allele frequencies expected under random drift alone; the sum View the MathML source gives a free fitness that increases as the population evolves towards its stationary distribution. Usually, we observe the distribution of a few quantitative traits that depend on the frequencies of very many alleles. The mean and variance of such traits are analogous to observable quantities in statistical thermodynamics. Thus, we can define an entropy, SΩ, which measures the volume of allele frequency space that is consistent with the observed trait distribution. The stationary distribution of the traits is View the MathML source; this applies with arbitrary epistasis and dominance. The entropies SΩ, SH are distinct, but converge when there are so many alleles that traits fluctuate close to their expectations. Populations tend to evolve towards states that can be realised in many ways (i.e., large SΩ), which may lead to a substantial drop below the adaptive peak; we illustrate this point with a simple model of genetic redundancy. This analogy with statistical thermodynamics brings together previous ideas in a general framework, and justifies a maximum entropy approximation to the dynamics of quantitative traits.},
  author       = {Barton, Nicholas H and Coe, Jason},
  journal      = {Journal of Theoretical Biology},
  number       = {2},
  pages        = {317 -- 324},
  publisher    = {Elsevier},
  title        = {{On the application of statistical physics to evolutionary biology}},
  doi          = {10.1016/j.jtbi.2009.03.019},
  volume       = {259},
  year         = {2009},
}

@article{3780,
  abstract     = {Why are sinistral snails so rare? Two main hypotheses are that selection acts against the establishment of new coiling morphs, because dextral and sinistral snails have trouble mating, or else a developmental constraint prevents the establishment of sinistrals. We therefore used an isolate of the snail Lymnaea stagnalis, in which sinistrals are rare, and populations of Partula suturalis, in which sinistrals are common, as well as a mathematical model, to understand the circumstances by which new morphs evolve. The main finding is that the sinistral genotype is associated with reduced egg viability in L. stagnalis, but in P. suturalis individuals of sinistral and dextral genotype appear equally fecund, implying a lack of a constraint. As positive frequency-dependent selection against the rare chiral morph in P. suturalis also operates over a narrow range (< 3%), the results suggest a model for chiral evolution in snails in which weak positive frequency-dependent selection may be overcome by a negative frequency-dependent selection, such as reproductive character displacement. In snails, there is not always a developmental constraint. As the direction of cleavage, and thus the directional asymmetry of the entire body, does not generally vary in other Spiralia (annelids, echiurans, vestimentiferans, sipunculids and nemerteans), it remains an open question as to whether this is because of a constraint and/or because most taxa do not have a conspicuous external asymmetry (like a shell) upon which selection can act.},
  author       = {Davison, Angus and Barton, Nicholas H and Clarke, Bryan},
  journal      = {Journal of Evolutionary Biology},
  number       = {8},
  pages        = {1624 -- 1635},
  publisher    = {Wiley},
  title        = {{The effect of chirality phenotype and genotype on the fecundity and viability of Partula suturalis and Lymnaea stagnalis: Implications for the evolution of sinistral snails}},
  doi          = {10.1111/j.1420-9101.2009.01770.x},
  volume       = {22},
  year         = {2009},
}

@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},
}

@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 (TOCL)},
  number       = {1},
  publisher    = {ACM},
  title        = {{Finitary winning in omega-regular games}},
  doi          = {10.1145/1614431.1614432},
  volume       = {11},
  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},
}

@article{3946,
  abstract     = {We compare anti-parasite defences at the level of multicellular organisms and insect societies, and find that selection by parasites at these two organisational levels is often very similar and has created a number of parallel evolutionary solutions in the host's immune response. The defence mechanisms of both individuals and insect colonies start with border defences to prevent parasite intake and are followed by soma defences that prevent the establishment and spread of the parasite between the body's cells or the social insect workers. Lastly, germ line defences are employed to inhibit infection of the reproductive tissue of organisms or the reproductive individuals in colonies. We further find sophisticated self/non-self-recognition systems operating at both levels, which appear to be vital in maintaining the integrity of the body or colony as a reproductive entity. We then expand on the regulation of immune responses and end with a contemplation of how evolution may shape the different immune components, both within and between levels. The aim of this review is to highlight common evolutionary principles acting in disease defence at the level of both individual organisms and societies, thereby linking the fields of physiological and ecological immunology.},
  author       = {Cremer, Sylvia and Sixt, Michael K},
  journal      = {Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences},
  number       = {1513},
  pages        = {129 -- 142},
  publisher    = {Royal Society, The},
  title        = {{Analogies in the evolution of individual and social immunity}},
  doi          = {10.1098/rstb.2008.0166},
  volume       = {364},
  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{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},
}

@inproceedings{4383,
  abstract     = {Pseudo-code descriptions of STMs assume sequentially consistent program execution and atomicity of high-level STM operations like read, write, and commit. These assumptions are often violated in realistic settings, as STM implementations run on relaxed memory models, with the atomicity of operations as provided by the hardware. This paper presents the first approach to verify STMs under relaxed memory models with atomicity of 32 bit loads and stores, and read-modify-write operations. We present RML, a new high-level language for expressing concurrent algorithms with a hardware-level atomicity of instructions, and whose semantics is parametrized by various relaxed memory models. We then present our tool, FOIL, which takes as input the RML description of an STM algorithm and the description of a memory model, and automatically determines the locations of fences, which if inserted, ensure the correctness of the STM algorithm under the given memory model. We use FOIL to verify DSTM, TL2, and McRT STM under the memory models of sequential consistency, total store order, partial store order, and relaxed memory order.},
  author       = {Guerraoui, Rachid and Thomas Henzinger and Vasu Singh},
  pages        = {321 -- 336},
  publisher    = {Springer},
  title        = {{Software transactional memory on relaxed memory models}},
  doi          = {10.1007/978-3-642-02658-4_26},
  volume       = {5643},
  year         = {2009},
}

@inproceedings{4403,
  abstract     = {For programs whose data variables range over boolean or finite domains, program verification is decidable, and this forms the basis of recent tools for software model checking. In this paper, we consider algorithmic verification of programs that use boolean variables, and in addition, access a single read-only array whose length is potentially unbounded, and whose elements range over a potentially unbounded data domain. We show that the reachability problem, while undecidable in general, is (1) Pspace-complete for programs in which the array-accessing for-loops are not nested, (2) decidable for a restricted class of programs with doubly-nested loops. The second result establishes connections to automata and logics defining languages over data words.},
  author       = {Alur, Rajeev and Cerny, Pavol and Weinstein, Scott},
  location     = {Coimbra, Portugal},
  pages        = {86 -- 101},
  publisher    = {Springer},
  title        = {{Algorithmic analysis of array-accessing programs}},
  doi          = {10.1007/978-3-642-04027-6_9},
  volume       = {5771},
  year         = {2009},
}

@inproceedings{4453,
  abstract     = {We present an on-the-fly abstraction technique for infinite-state continuous -time Markov chains. We consider Markov chains that are specified by a finite set of transition classes. Such models naturally represent biochemical reactions and therefore play an important role in the stochastic modeling of biological systems. We approximate the transient probability distributions at various time instances by solving a sequence of dynamically constructed abstract models, each depending on the previous one. Each abstract model is a finite Markov chain that represents the behavior of the original, infinite chain during a specific time interval. Our approach provides complete information about probability distributions, not just about individual parameters like the mean. The error of each abstraction can be computed, and the precision of the abstraction refined when desired. We implemented the algorithm and demonstrate its usefulness and efficiency on several case studies from systems biology.},
  author       = {Thomas Henzinger and Maria Mateescu and Wolf, Verena},
  pages        = {337 -- 352},
  publisher    = {Springer},
  title        = {{Sliding-window abstraction for infinite Markov chains}},
  doi          = {10.1007/978-3-642-02658-4_27},
  volume       = {5643},
  year         = {2009},
}

@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{4544,
  abstract     = {We consider concurrent games played on graphs. At every round of a game, each player simultaneously and independently selects a move; the moves jointly determine the transition to a successor state. Two basic objectives are the safety objective to stay forever in a given set of states, and its dual, the reachability objective to reach a given set of states. We present in this paper a strategy improvement algorithm for computing the value of a concurrent safety game, that is, the maximal probability with which player 1 can enforce the safety objective. The algorithm yields a sequence of player-1 strategies which ensure probabilities of winning that converge monotonically to the value of the safety game. Our result is significant because the strategy improvement algorithm provides, for the first time, a way to approximate the value of a concurrent safety game from below. Since a value iteration algorithm, or a strategy improvement algorithm for reachability games, can be used to approximate the same value from above, the combination of both algorithms yields a method for computing a converging sequence of upper and lower bounds for the values of concurrent reachability and safety games. Previous methods could approximate the values of these games only from one direction, and as no rates of convergence are known, they did not provide a practical way to solve these games.},
  author       = {Krishnendu Chatterjee and de Alfaro, Luca and Thomas Henzinger},
  pages        = {197 -- 206},
  publisher    = {SIAM},
  title        = {{Termination criteria for solving concurrent safety and reachability games}},
  doi          = {10.1137/1.9781611973068.23},
  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},
}

@inproceedings{4569,
  abstract     = {Most specification languages express only qualitative constraints. However, among two implementations that satisfy a given specification, one may be preferred to another. For example, if a specification asks that every request is followed by a response, one may prefer an implementation that generates responses quickly but does not generate unnecessary responses. We use quantitative properties to measure the “goodness” of an implementation. Using games with corresponding quantitative objectives, we can synthesize “optimal” implementations, which are preferred among the set of possible implementations that satisfy a given specification.
In particular, we show how automata with lexicographic mean-payoff conditions can be used to express many interesting quantitative properties for reactive systems. In this framework, the synthesis of optimal implementations requires the solution of lexicographic mean-payoff games (for safety requirements), and the solution of games with both lexicographic mean-payoff and parity objectives (for liveness requirements). We present algorithms for solving both kinds of novel graph games.},
  author       = {Bloem, Roderick and Chatterjee, Krishnendu and Henzinger, Thomas A and Jobstmann, Barbara},
  location     = {Grenoble, France},
  pages        = {140 -- 156},
  publisher    = {Springer},
  title        = {{Better quality in synthesis through quantitative objectives}},
  doi          = {10.1007/978-3-642-02658-4_14},
  volume       = {5643},
  year         = {2009},
}

@inproceedings{4580,
  abstract     = {Alpaga is a solver for two-player parity games with imperfect information. Given the description of a game, it determines whether the first player can ensure to win and, if so, it constructs a winning strategy. The tool provides a symbolic implementation of a recent algorithm based on antichains.},
  author       = {Berwanger, Dietmar and Krishnendu Chatterjee and De Wulf, Martin and Doyen, Laurent and Thomas Henzinger},
  pages        = {58 -- 61},
  publisher    = {Springer},
  title        = {{Alpaga: A tool for solving parity games with imperfect information}},
  doi          = {10.1007/978-3-642-00768-2_7},
  volume       = {5505},
  year         = {2009},
}