@inproceedings{3838,
abstract = {We present a numerical approximation technique for the analysis of continuous-time Markov chains that describe net- works of biochemical reactions and play an important role in the stochastic modeling of biological systems. Our approach is based on the construction of a stochastic hybrid model in which certain discrete random variables of the original Markov chain are approximated by continuous deterministic variables. We compute the solution of the stochastic hybrid model using a numerical algorithm that discretizes time and in each step performs a mutual update of the transient prob- ability distribution of the discrete stochastic variables and the values of the continuous deterministic variables. We im- plemented the algorithm and we demonstrate its usefulness and efficiency on several case studies from systems biology.},
author = {Henzinger, Thomas A and Mateescu, Maria and Mikeev, Linar and Wolf, Verena},
location = {Trento, Italy},
pages = {55 -- 65},
publisher = {Springer},
title = {{Hybrid numerical solution of the chemical master equation}},
doi = {10.1145/1839764.1839772},
year = {2010},
}
@inproceedings{3840,
abstract = {Classical formalizations of systems and properties are boolean: given a system and a property, the property is either true or false of the system. Correspondingly, classical methods for system analysis determine the truth value of a property, preferably giving a proof if the property is true, and a counterexample if the property is false; classical methods for system synthesis construct a system for which a property is true; classical methods for system transformation, composition, and abstraction aim to preserve the truth of properties. The boolean view is prevalent even if the system, the property, or both refer to numerical quantities, such as the times or probabilities of events. For example, a timed automaton either satisfies or violates a formula of a real-time logic; a stochastic process either satisfies or violates a formula of a probabilistic logic. The classical black-and-white view partitions the world into "correct" and "incorrect" systems, offering few nuances. In reality, of several systems that satisfy a property in the boolean sense, often some are more desirable than others, and of the many systems that violate a property, usually some are less objectionable than others. For instance, among the systems that satisfy the response property that every request be granted, we may prefer systems that grant requests quickly (the quicker, the better), or we may prefer systems that issue few unnecessary grants (the fewer, the better); and among the systems that violate the response property, we may prefer systems that serve many initial requests (the more, the better), or we may prefer systems that serve many requests in the long run (the greater the fraction of served to unserved requests, the better). Formally, while a boolean notion of correctness is given by a preorder on systems and properties, a quantitative notion of correctness is defined by a directed metric on systems and properties, where the distance between a system and a property provides a measure of "fit" or "desirability." There are many ways how such distances can be defined. In a linear-time framework, one assigns numerical values to individual behaviors before assigning values to systems and properties, which are sets of behaviors. For example, the value of a single behavior may be a discounted value, which is largely determined by a prefix of the behavior, e.g., by the number of requests that are granted before the first request that is not granted; or a limit value, which is independent of any finite prefix. A limit value may be an average, such as the average response time over an infinite sequence of requests and grants, or a supremum, such as the worst-case response time. Similarly, the value of a set of behaviors may be an extremum or an average across the values of all behaviors in the set: in this way one can measure the worst of all possible average-case response times, or the average of all possible worst-case response times, etc. Accordingly, the distance between two sets of behaviors may be defined as the worst or average difference between the values of corresponding behaviors. In summary, we propagate replacing boolean specifications for the correctness of systems with quantitative measures for the desirability of systems. In quantitative analysis, the aim is to compute the distance between a system and a property (or between two systems, or two properties); in quantitative synthesis, the objective is to construct a system that has minimal distance from a given property. Multiple quantitative measures can be prioritized (e.g., combined lexicographically into a single measure) or studied along the Pareto curve. Quantitative transformations, compositions, and abstractions of systems are useful if they allow us to bound the induced change in distance from a property. We present some initial results in some of these directions. We also give some potential applications, which not only generalize tradiditional correctness concerns in the functional, timed, and probabilistic domains, but also capture such system measures as resource use, performance, cost, reliability, and robustness.},
author = {Henzinger, Thomas A},
location = {Madrid, Spain},
number = {1},
pages = {157 -- 158},
publisher = {ACM},
title = {{From boolean to quantitative notions of correctness}},
doi = {10.1145/1706299.1706319},
volume = {45},
year = {2010},
}
@inproceedings{3852,
abstract = {We introduce two-level discounted games played by two players on a perfect-information stochastic game graph. The upper level game is a discounted game and the lower level game is an undiscounted reachability game. Two-level games model hierarchical and sequential decision making under uncertainty across different time scales. We show the existence of pure memoryless optimal strategies for both players and an ordered field property for such games. We show that if there is only one player (Markov decision processes), then the values can be computed in polynomial time. It follows that whether the value of a player is equal to a given rational constant in two-level discounted games can be decided in NP intersected coNP. We also give an alternate strategy improvement algorithm to compute the value. },
author = {Chatterjee, Krishnendu and Majumdar, Ritankar},
location = {Minori, Italy},
pages = {22 -- 29},
publisher = {EPTCS},
title = {{Discounting in games across time scales}},
doi = {10.4204/EPTCS.25.6},
volume = {25},
year = {2010},
}
@inproceedings{3845,
abstract = {This paper presents Aligators, a tool for the generation of universally quantified array invariants. Aligators leverages recurrence solving and algebraic techniques to carry out inductive reasoning over array content. The Aligators’ loop extraction module allows treatment of multi-path loops by exploiting their commutativity and serializability properties. Our experience in applying Aligators on a collection of loops from open source software projects indicates the applicability of recurrence and algebraic solving techniques for reasoning about arrays.},
author = {Henzinger, Thomas A and Hottelier, Thibaud and Kovács, Laura and Rybalchenko, Andrey},
location = {Yogyakarta, Indonesia},
pages = {348 -- 356},
publisher = {Springer},
title = {{Aligators for arrays}},
doi = {10.1007/978-3-642-16242-8_25},
volume = {6397},
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},
}
@inproceedings{4362,
abstract = {Software transactional memories (STMs) promise simple and efficient concurrent programming. Several correctness properties have been proposed for STMs. Based on a bounded conflict graph algorithm for verifying correctness of STMs, we develop TRACER, a tool for runtime verification of STM implementations. The novelty of TRACER lies in the way it combines coarse and precise runtime analyses to guarantee sound and complete verification in an efficient manner. We implement TRACER in the TL2 STM implementation. We evaluate the performance of TRACER on STAMP benchmarks. While a precise runtime verification technique based on conflict graphs results in an average slowdown of 60x, the two-level approach of TRACER performs complete verification with an average slowdown of around 25x across different benchmarks.},
author = {Singh, Vasu},
editor = {Sokolsky, Oleg and Rosu, Grigore and Tilmann, Nikolai and Barringer, Howard and Falcone, Ylies and Finkbeiner, Bernd and Havelund, Klaus and Lee, Insup and Pace, Gordon},
location = {St. Julians, Malta},
pages = {421 -- 435},
publisher = {Springer},
title = {{Runtime verification for software transactional memories}},
doi = {10.1007/978-3-642-16612-9_32},
volume = {6418},
year = {2010},
}
@inproceedings{4381,
abstract = {Cloud computing aims to give users virtually unlimited pay-per-use computing resources without the burden of managing the underlying infrastructure. We claim that, in order to realize the full potential of cloud computing, the user must be presented with a pricing model that offers flexibility at the requirements level, such as a choice between different degrees of execution speed and the cloud provider must be presented with a programming model that offers flexibility at the execution level, such as a choice between different scheduling policies. In such a flexible framework, with each job, the user purchases a virtual computer with the desired speed and cost characteristics, and the cloud provider can optimize the utilization of resources across a stream of jobs from different users. We designed a flexible framework to test our hypothesis, which is called FlexPRICE (Flexible Provisioning of Resources in a Cloud Environment) and works as follows. A user presents a job to the cloud. The cloud finds different schedules to execute the job and presents a set of quotes to the user in terms of price and duration for the execution. The user then chooses a particular quote and the cloud is obliged to execute the job according to the chosen quote. FlexPRICE thus hides the complexity of the actual scheduling decisions from the user, but still provides enough flexibility to meet the users actual demands. We implemented FlexPRICE in a simulator called PRICES that allows us to experiment with our framework. We observe that FlexPRICE provides a wide range of execution options-from fast and expensive to slow and cheap-- for the whole spectrum of data-intensive and computation-intensive jobs. We also observe that the set of quotes computed by FlexPRICE do not vary as the number of simultaneous jobs increases.},
author = {Henzinger, Thomas A and Tomar, Anmol and Singh, Vasu and Wies, Thomas and Zufferey, Damien},
location = {Miami, USA},
pages = {83 -- 90},
publisher = {IEEE},
title = {{FlexPRICE: Flexible provisioning of resources in a cloud environment}},
doi = {10.1109/CLOUD.2010.71 },
year = {2010},
}
@inproceedings{489,
abstract = {Graph games of infinite length are a natural model for open reactive processes: one player represents the controller, trying to ensure a given specification, and the other represents a hostile environment. The evolution of the system depends on the decisions of both players, supplemented by chance. In this work, we focus on the notion of randomised strategy. More specifically, we show that three natural definitions may lead to very different results: in the most general cases, an almost-surely winning situation may become almost-surely losing if the player is only allowed to use a weaker notion of strategy. In more reasonable settings, translations exist, but they require infinite memory, even in simple cases. Finally, some traditional problems becomes undecidable for the strongest type of strategies.},
author = {Cristau, Julien and David, Claire and Horn, Florian},
booktitle = {Proceedings of GandALF 2010},
location = {Minori, Amalfi Coast, Italy},
pages = {30 -- 39},
publisher = {Open Publishing Association},
title = {{How do we remember the past in randomised strategies? }},
doi = {10.4204/EPTCS.25.7},
volume = {25},
year = {2010},
}
@inproceedings{3857,
abstract = {We consider probabilistic automata on infinite words with acceptance defined by safety, reachability, Büchi, coBüchi, and limit-average conditions. We consider quantitative and qualitative decision problems. We present extensions and adaptations of proofs for probabilistic finite automata and present an almost complete characterization of the decidability and undecidability frontier of the quantitative and qualitative decision problems for probabilistic automata on infinite words.},
author = {Chatterjee, Krishnendu and Henzinger, Thomas A},
location = {Singapore, Singapore},
pages = {1 -- 16},
publisher = {Springer},
title = {{Probabilistic Automata on infinite words: decidability and undecidability results}},
doi = {10.1007/978-3-642-15643-4_1},
volume = {6252},
year = {2010},
}
@misc{5391,
abstract = {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.},
author = {Cerny, Pavol and Radhakrishna, Arjun and Zufferey, Damien and Chaudhuri, Swarat and Alur, Rajeev},
issn = {2664-1690},
pages = {27},
publisher = {IST Austria},
title = {{Model checking of linearizability of concurrent list implementations}},
doi = {10.15479/AT:IST-2010-0001},
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{4393,
abstract = {Boolean notions of correctness are formalized by preorders on systems. Quantitative measures of correctness can be formalized by real-valued distance functions between systems, where the distance between implementation and specification provides a measure of “fit” or “desirability.” We extend the simulation preorder to the quantitative setting, by making each player of a simulation game pay a certain price for her choices. We use the resulting games with quantitative objectives to define three different simulation distances. The correctness distance measures how much the specification must be changed in order to be satisfied by the implementation. The coverage distance measures how much the implementation restricts the degrees of freedom offered by the specification. The robustness distance measures how much a system can deviate from the implementation description without violating the specification. We consider these distances for safety as well as liveness specifications. The distances can be computed in polynomial time for safety specifications, and for liveness specifications given by weak fairness constraints. We show that the distance functions satisfy the triangle inequality, that the distance between two systems does not increase under parallel composition with a third system, and that the distance between two systems can be bounded from above and below by distances between abstractions of the two systems. These properties suggest that our simulation distances provide an appropriate basis for a quantitative theory of discrete systems. We also demonstrate how the robustness distance can be used to measure how many transmission errors are tolerated by error correcting codes.},
author = {Cerny, Pavol and Henzinger, Thomas A and Radhakrishna, Arjun},
location = {Paris, France},
pages = {235 -- 268},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
title = {{Simulation distances}},
doi = {10.1007/978-3-642-15375-4_18},
volume = {6269},
year = {2010},
}
@misc{5389,
abstract = {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.},
author = {Cerny, Pavol and Henzinger, Thomas A and Radhakrishna, Arjun},
issn = {2664-1690},
pages = {24},
publisher = {IST Austria},
title = {{Simulation distances}},
doi = {10.15479/AT:IST-2010-0003},
year = {2010},
}
@article{3303,
abstract = {Biological traits result in part from interactions between different genetic loci. This can lead to sign epistasis, in which a beneficial adaptation involves a combination of individually deleterious or neutral mutations; in this case, a population must cross a “fitness valley” to adapt. Recombination can assist this process by combining mutations from different individuals or retard it by breaking up the adaptive combination. Here, we analyze the simplest fitness valley, in which an adaptation requires one mutation at each of two loci to provide a fitness benefit. We present a theoretical analysis of the effect of recombination on the valley-crossing process across the full spectrum of possible parameter regimes. We find that low recombination rates can speed up valley crossing relative to the asexual case, while higher recombination rates slow down valley crossing, with the transition between the two regimes occurring when the recombination rate between the loci is approximately equal to the selective advantage provided by the adaptation. In large populations, if the recombination rate is high and selection against single mutants is substantial, the time to cross the valley grows exponentially with population size, effectively meaning that the population cannot acquire the adaptation. Recombination at the optimal (low) rate can reduce the valley-crossing time by up to several orders of magnitude relative to that in an asexual population. },
author = {Weissman, Daniel and Feldman, Marcus and Fisher, Daniel},
journal = {Genetics},
number = {4},
pages = {1389 -- 1410},
publisher = {Genetics Society of America},
title = {{The rate of fitness-valley crossing in sexual populations}},
doi = {10.1534/genetics.110.123240},
volume = {186},
year = {2010},
}
@inproceedings{3719,
abstract = {The induction of a signaling pathway is characterized by transient complex formation and mutual posttranslational modification of proteins. To faithfully capture this combinatorial process in a math- ematical model is an important challenge in systems biology. Exploiting the limited context on which most binding and modification events are conditioned, attempts have been made to reduce the com- binatorial complexity by quotienting the reachable set of molecular species, into species aggregates while preserving the deterministic semantics of the thermodynamic limit. Recently we proposed a quotienting that also preserves the stochastic semantics and that is complete in the sense that the semantics of individual species can be recovered from the aggregate semantics. In this paper we prove that this quotienting yields a sufficient condition for weak lumpability and that it gives rise to a backward Markov bisimulation between the original and aggregated transition system. We illustrate the framework on a case study of the EGF/insulin receptor crosstalk.},
author = {Feret, Jérôme and Henzinger, Thomas A and Koeppl, Heinz and Petrov, Tatjana},
location = {Jena, Germany},
pages = {142--161},
publisher = {Open Publishing Association},
title = {{Lumpability abstractions of rule-based systems}},
volume = {40},
year = {2010},
}
@article{3776,
abstract = {The prevalence of recombination in eukaryotes poses one of the most puzzling questions in biology. The most compelling general explanation is that recombination facilitates selection by breaking down the negative associations generated by random drift (i.e. Hill-Robertson interference, HRI). I classify the effects of HRI owing to: deleterious mutation, balancing selection and selective sweeps on: neutral diversity, rates of adaptation and the mutation load. These effects are mediated primarily by the density of deleterious mutations and of selective sweeps. Sequence polymorphism and divergence suggest that these rates may be high enough to cause significant interference even in genomic regions of high recombination. However, neither seems able to generate enough variance in fitness to select strongly for high rates of recombination. It is plausible that spatial and temporal fluctuations in selection generate much more fitness variance, and hence selection for recombination, than can be explained by uniformly deleterious mutations or species-wide selective sweeps.},
author = {Barton, Nicholas H},
journal = {Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences},
number = {1552},
pages = {2559 -- 2569},
publisher = {Royal Society},
title = {{Genetic linkage and natural selection}},
doi = {10.1098/rstb.2010.0106},
volume = {365},
year = {2010},
}
@article{3783,
abstract = {MICROSATELIGHT is a Perl/Tk pipeline with a graphical user interface that facilitates several tasks when scoring microsatellites. It implements new subroutines in R and PERL and takes advantage of features provided by previously developed freeware. MICROSATELIGHT takes raw genotype data and automates the peak identification through PeakScanner. The PeakSelect subroutine assigns peaks to different microsatellite markers according to their multiplex group, fluorochrome type, and size range. After peak selection, binning of alleles can be carried out 1) automatically through AlleloBin or 2) by manual bin definition through Binator. In both cases, several features for quality checking and further binning improvement are provided. The genotype table can then be converted into input files for several population genetics programs through CREATE. Finally, Hardy–Weinberg equilibrium tests and confidence intervals for null allele frequency can be obtained through GENEPOP. MICROSATELIGHT is the only freely available public-domain software that facilitates full multiplex microsatellite scoring, from electropherogram files to user-defined text files to be used with population genetics software. MICROSATELIGHT has been created for the Windows XP operating system and has been successfully tested under Windows 7. It is available at http://sourceforge.net/projects/microsatelight/.},
author = {Palero, Ferran and González Candelas, Fernando and Pascual, Marta},
journal = {Journal of Heredity},
number = {2},
pages = {247 -- 249},
publisher = {Oxford University Press},
title = {{Microsatelight – Pipeline to expedite microsatellite analysis}},
doi = {10.1093/jhered/esq111},
volume = {102},
year = {2010},
}
@article{3788,
abstract = {Cell sorting is a widespread phenomenon pivotal to the early development of multicellular organisms. In vitro cell sorting studies have been instrumental in revealing the cellular properties driving this process. However, these studies have as yet been limited to two-dimensional analysis of three-dimensional cell sorting events. Here we describe a method to record the sorting of primary zebrafish ectoderm and mesoderm germ layer progenitor cells in three dimensions over time, and quantitatively analyze their sorting behavior using an order parameter related to heterotypic interface length. We investigate the cell population size dependence of sorted aggregates and find that the germ layer progenitor cells engulfed in the final configuration display a relationship between total interfacial length and system size according to a simple geometrical argument, subject to a finite-size effect.},
author = {Klopper, Abigail and Krens, Gabriel and Grill, Stephan and Heisenberg, Carl-Philipp J},
journal = {The European Physical Journal E: Soft Matter and Biological Physics},
number = {2},
pages = {99 -- 103},
publisher = {Springer},
title = {{Finite-size corrections to scaling behavior in sorted cell aggregates}},
doi = {10.1140/epje/i2010-10642-y},
volume = {33},
year = {2010},
}
@article{3790,
abstract = {Cell shape and motility are primarily controlled by cellular mechanics. The attachment of the plasma membrane to the underlying actomyosin cortex has been proposed to be important for cellular processes involving membrane deformation. However, little is known about the actual function of membrane-to-cortex attachment (MCA) in cell protrusion formation and migration, in particular in the context of the developing embryo. Here, we use a multidisciplinary approach to study MCA in zebrafish mesoderm and endoderm (mesendoderm) germ layer progenitor cells, which migrate using a combination of different protrusion types, namely, lamellipodia, filopodia, and blebs, during zebrafish gastrulation. By interfering with the activity of molecules linking the cortex to the membrane and measuring resulting changes in MCA by atomic force microscopy, we show that reducing MCA in mesendoderm progenitors increases the proportion of cellular blebs and reduces the directionality of cell migration. We propose that MCA is a key parameter controlling the relative proportions of different cell protrusion types in mesendoderm progenitors, and thus is key in controlling directed migration during gastrulation.},
author = {Diz Muñoz, Alba and Krieg, Michael and Bergert, Martin and Ibarlucea Benitez, Itziar and Müller, Daniel and Paluch, Ewa and Heisenberg, Carl-Philipp J},
journal = {PLoS Biology},
number = {11},
publisher = {Public Library of Science},
title = {{Control of directed cell migration in vivo by membrane-to-cortex attachment}},
doi = {10.1371/journal.pbio.1000544},
volume = {8},
year = {2010},
}
@inbook{3795,
abstract = {The (apparent) contour of a smooth mapping from a 2-manifold to the plane, f: M → R2 , is the set of critical values, that is, the image of the points at which the gradients of the two component functions are linearly dependent. Assuming M is compact and orientable and measuring difference with the erosion distance, we prove that the contour is stable.},
author = {Edelsbrunner, Herbert and Morozov, Dmitriy and Patel, Amit},
booktitle = {Topological Data Analysis and Visualization: Theory, Algorithms and Applications},
pages = {27 -- 42},
publisher = {Springer},
title = {{The stability of the apparent contour of an orientable 2-manifold}},
doi = {10.1007/978-3-642-15014-2_3},
year = {2010},
}
@article{3834,
abstract = {Background
The chemical master equation (CME) is a system of ordinary differential equations that describes the evolution of a network of chemical reactions as a stochastic process. Its solution yields the probability density vector of the system at each point in time. Solving the CME numerically is in many cases computationally expensive or even infeasible as the number of reachable states can be very large or infinite. We introduce the sliding window method, which computes an approximate solution of the CME by performing a sequence of local analysis steps. In each step, only a manageable subset of states is considered, representing a "window" into the state space. In subsequent steps, the window follows the direction in which the probability mass moves, until the time period of interest has elapsed. We construct the window based on a deterministic approximation of the future behavior of the system by estimating upper and lower bounds on the populations of the chemical species.
Results
In order to show the effectiveness of our approach, we apply it to several examples previously described in the literature. The experimental results show that the proposed method speeds up the analysis considerably, compared to a global analysis, while still providing high accuracy.
Conclusions
The sliding window method is a novel approach to address the performance problems of numerical algorithms for the solution of the chemical master equation. The method efficiently approximates the probability distributions at the time points of interest for a variety of chemically reacting systems, including systems for which no upper bound on the population sizes of the chemical species is known a priori.},
author = {Wolf, Verena and Goel, Rushil and Mateescu, Maria and Henzinger, Thomas A},
journal = {BMC Systems Biology},
number = {42},
pages = {1 -- 19},
publisher = {BioMed Central},
title = {{Solving the chemical master equation using sliding windows}},
doi = {10.1186/1752-0509-4-42},
volume = {4},
year = {2010},
}
@inproceedings{3839,
abstract = {We present a loop property generation method for loops iterating over multi-dimensional arrays. When used on matrices, our method is able to infer their shapes (also called types), such as upper-triangular, diagonal, etc. To gen- erate loop properties, we first transform a nested loop iterating over a multi- dimensional array into an equivalent collection of unnested loops. Then, we in- fer quantified loop invariants for each unnested loop using a generalization of a recurrence-based invariant generation technique. These loop invariants give us conditions on matrices from which we can derive matrix types automatically us- ing theorem provers. Invariant generation is implemented in the software package Aligator and types are derived by theorem provers and SMT solvers, including Vampire and Z3. When run on the Java matrix package JAMA, our tool was able to infer automatically all matrix types describing the matrix shapes guaranteed by JAMA’s API.},
author = {Henzinger, Thomas A and Hottelier, Thibaud and Kovács, Laura and Voronkov, Andrei},
location = {Madrid, Spain},
pages = {163 -- 179},
publisher = {Springer},
title = {{Invariant and type inference for matrices}},
doi = {10.1007/978-3-642-11319-2_14},
volume = {5944},
year = {2010},
}
@inproceedings{3853,
abstract = {Quantitative languages are an extension of boolean languages that assign to each word a real number. Mean-payoff automata are finite automata with numerical weights on transitions that assign to each infinite path the long-run average of the transition weights. When the mode of branching of the automaton is deterministic, nondeterministic, or alternating, the corresponding class of quantitative languages is not robust as it is not closed under the pointwise operations of max, min, sum, and numerical complement. Nondeterministic and alternating mean-payoff automata are not decidable either, as the quantitative generalization of the problems of universality and language inclusion is undecidable. We introduce a new class of quantitative languages, defined by mean-payoff automaton expressions, which is robust and decidable: it is closed under the four pointwise operations, and we show that all decision problems are decidable for this class. Mean-payoff automaton expressions subsume deterministic meanpayoff automata, and we show that they have expressive power incomparable to nondeterministic and alternating mean-payoff automata. We also present for the first time an algorithm to compute distance between two quantitative languages, and in our case the quantitative languages are given as mean-payoff automaton expressions.},
author = {Chatterjee, Krishnendu and Doyen, Laurent and Edelsbrunner, Herbert and Henzinger, Thomas A and Rannou, Philippe},
location = {Paris, France},
pages = {269 -- 283},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
title = {{Mean-payoff automaton expressions}},
doi = {10.1007/978-3-642-15375-4_19},
volume = {6269},
year = {2010},
}
@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},
editor = {Fermüller, Christian and Voronkov, Andrei},
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},
}
@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},
}
@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},
editor = {Rosenblum, David and Taenzer, Gabriele},
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},
}
@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},
}
@inproceedings{4382,
abstract = {Transactional memory (TM) has shown potential to simplify the task of writing concurrent programs. Inspired by classical work on databases, formal definitions of the semantics of TM executions have been proposed. Many of these definitions assumed that accesses to shared data are solely performed through transactions. In practice, due to legacy code and concurrency libraries, transactions in a TM have to share data with non-transactional operations. The semantics of such interaction, while widely discussed by practitioners, lacks a clear formal specification. Those interactions can vary, sometimes in subtle ways, between TM implementations and underlying memory models. We propose a correctness condition for TMs, parametrized opacity, to formally capture the now folklore notion of strong atomicity by stipulating the two following intuitive requirements: first, every transaction appears as if it is executed instantaneously with respect to other transactions and non-transactional operations, and second, non-transactional operations conform to the given underlying memory model. We investigate the inherent cost of implementing parametrized opacity. We first prove that parametrized opacity requires either instrumenting non-transactional operations (for most memory models) or writing to memory by transactions using potentially expensive read-modify-write instructions (such as compare-and-swap). Then, we show that for a class of practical relaxed memory models, parametrized opacity can indeed be implemented with constant-time instrumentation of non-transactional writes and no instrumentation of non-transactional reads. We show that, in practice, parametrizing the notion of correctness allows developing more efficient TM implementations.},
author = {Guerraoui, Rachid and Henzinger, Thomas A and Kapalka, Michal and Singh, Vasu},
location = {Santorini, Greece},
pages = {263 -- 272},
publisher = {ACM},
title = {{Transactions in the jungle}},
doi = {10.1145/1810479.1810529},
year = {2010},
}
@article{3772,
author = {Barton, Nicholas H},
journal = {PLoS Genetics},
number = {6},
publisher = {Public Library of Science},
title = {{Understanding adaptation in large populations}},
doi = {10.1371/journal.pgen.1000987},
volume = {6},
year = {2010},
}
@article{3777,
abstract = {Under the classical view, selection depends more or less directly on mutation: standing genetic variance is maintained by a balance between selection and mutation, and adaptation is fuelled by new favourable mutations. Recombination is favoured if it breaks negative associations among selected alleles, which interfere with adaptation. Such associations may be generated by negative epistasis, or by random drift (leading to the Hill-Robertson effect). Both deterministic and stochastic explanations depend primarily on the genomic mutation rate, U. This may be large enough to explain high recombination rates in some organisms, but seems unlikely to be so in general. Random drift is a more general source of negative linkage disequilibria, and can cause selection for recombination even in large populations, through the chance loss of new favourable mutations. The rate of species-wide substitutions is much too low to drive this mechanism, but local fluctuations in selection, combined with gene flow, may suffice. These arguments are illustrated by comparing the interaction between good and bad mutations at unlinked loci under the infinitesimal model.},
author = {Barton, Nicholas H},
journal = {Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences},
number = {1544},
pages = {1281 -- 1294},
publisher = {Royal Society},
title = {{Mutation and the evolution of recombination}},
doi = {10.1098/rstb.2009.0320},
volume = {365},
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},
}
@article{3498,
abstract = {Purpose
Calcifying tendinitis is a common condition of the shoulder. In many cases, arthroscopic reduction in the deposit is indicated. The localization of the deposit is sometimes challenging and time-consuming. Pre-operative ultrasound (US)-guided needle placement in the deposit and pre-operative US marking of the deposit at the skin with a ballpoint are described and recommended methods to alleviate the procedure without using ionizing radiation by fluoroscopy.
Methods
Intra-operative sonography of the shoulder is introduced as a new method to localize the calcific deposit with high accuracy. After standard arthroscopic buresectomy, the surgeon performs an ultrasound examination under sterile conditions to localize the deposits. A ventral longitudinal US section is recommended, and the upper arm is rotated until the deposit is visible. Subsequently, perpendicular to the skin at the position of the transducer, a needle is introduced under arthroscopic and ultrasound visualization to puncture the deposit.
Results
The presence of snow-white crystals at the tip of the needle proves the exact localization. Consecutively, the curettage can be accomplished. Another intra-operative sonography evaluates possible calcific remnants and the tendon structure.
Conclusion
This new technique may alleviate arthroscopic calcific deposit curettage by visualizing the deposit without using ionizing radiation. Additionally, soft tissue damage due to decreased number of punctures to detect the deposit may be achieved. Both factors may contribute to reduced operation time.},
author = {Sabeti Aschraf, M. and Gonano, C. and Nemecek, E. and Cichocki, Lisa and Schueller Weidekamm, C.},
journal = {Knee Surgery, Sports Traumatology, Arthroscopy},
number = {12},
pages = {1792 -- 1794},
publisher = {Springer},
title = {{Intra-operative ultrasound facilitates the localization of the calcific deposit during arthroscopic treatment of calcifying tendinitis}},
doi = {10.1007/s00167-010-1227-9},
volume = {18},
year = {2010},
}
@inproceedings{3847,
abstract = {The importance of stochasticity within biological systems has been shown repeatedly during the last years and has raised the need for efficient stochastic tools. We present SABRE, a tool for stochastic analysis of biochemical reaction networks. SABRE implements fast adaptive uniformization (FAU), a direct numerical approximation algorithm for computing transient solutions of biochemical reaction networks. Biochemical reactions networks represent biological systems studied at a molecular level and these reactions can be modeled as transitions of a Markov chain. SABRE accepts as input the formalism of guarded commands, which it interprets either as continuous-time or as discrete-time Markov chains. Besides operating in a stochastic mode, SABRE may also perform a deterministic analysis by directly computing a mean-field approximation of the system under study. We illustrate the different functionalities of SABRE by means of biological case studies.},
author = {Didier, Frédéric and Henzinger, Thomas A and Mateescu, Maria and Wolf, Verena},
location = {Williamsburg, USA},
pages = {193 -- 194},
publisher = {IEEE},
title = {{SABRE: A tool for the stochastic analysis of biochemical reaction networks}},
doi = {10.1109/QEST.2010.33},
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{3842,
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). The uniformization technique is an efficient method to compute probability distributions of a CTMC if the number of states is manageable. However, the size of a CTMC that represents a biochemical reaction network is usually far beyond what is feasible. In this paper we present an on-the-fly variant of uniformization, where we improve the original algorithm 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},
journal = {IET Systems Biology},
number = {6},
pages = {441 -- 452},
publisher = {Institution of Engineering and Technology},
title = {{Fast adaptive uniformization of the chemical master equation}},
doi = {10.1049/iet-syb.2010.0005},
volume = {4},
year = {2010},
}
@inproceedings{3854,
abstract = {Graph games of infinite length provide a natural model for open reactive systems: one player (Eve) represents the controller and the other player (Adam) represents the environment. The evolution of the system depends on the decisions of both players. The specification for the system is usually given as an ω-regular language L over paths and Eve’s goal is to ensure that the play belongs to L irrespective of Adam’s behaviour. The classical notion of winning strategies fails to capture several interesting scenarios. For example, strong fairness (Streett) conditions are specified by a number of request-grant pairs and require every pair that is requested infinitely often to be granted infinitely often: Eve might win just by preventing Adam from making any new request, but a “better” strategy would allow Adam to make as many requests as possible and still ensure fairness. To address such questions, we introduce the notion of obliging games, where Eve has to ensure a strong condition Φ, while always allowing Adam to satisfy a weak condition Ψ. We present a linear time reduction of obliging games with two Muller conditions Φ and Ψ to classical Muller games. We consider obliging Streett games and show they are co-NP complete, and show a natural quantitative optimisation problem for obliging Streett games is in FNP. We also show how obliging games can provide new and interesting semantics for multi-player games.},
author = {Chatterjee, Krishnendu and Horn, Florian and Löding, Christof},
location = {Paris, France},
pages = {284 -- 296},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
title = {{Obliging games}},
doi = {10.1007/978-3-642-15375-4_20},
volume = {6269},
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},
}
@phdthesis{3962,
author = {Pflicke, Holger},
publisher = {IST Austria},
title = {{Dendritic cell migration across basement membranes in the skin}},
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},
}
@inproceedings{4369,
abstract = {In this paper we propose a novel technique for constructing timed automata from properties expressed in the logic mtl, under bounded-variability assumptions. We handle full mtl and include all future operators. Our construction is based on separation of the continuous time monitoring of the input sequence and discrete predictions regarding the future. The separation of the continuous from the discrete allows us to determinize our automata in an exponential construction that does not increase the number of clocks. This leads to a doubly exponential construction from mtl to deterministic timed automata, compared with triply exponential using existing approaches. We offer an alternative to the existing approach to linear real-time model checking, which has never been implemented. It further offers a unified framework for model checking, runtime monitoring, and synthesis, in an approach that can reuse tools, implementations, and insights from the discrete setting.},
author = {Nickovic, Dejan and Piterman, Nir},
editor = {Henzinger, Thomas A. and Chatterjee, Krishnendu},
location = {Klosterneuburg, Austria},
pages = {152 -- 167},
publisher = {Springer},
title = {{From MTL to deterministic timed automata}},
doi = {10.1007/978-3-642-15297-9_13},
volume = {6246},
year = {2010},
}
@article{474,
abstract = {Classical models of gene flow fail in three ways: they cannot explain large-scale patterns; they predict much more genetic diversity than is observed; and they assume that loosely linked genetic loci evolve independently. We propose a new model that deals with these problems. Extinction events kill some fraction of individuals in a region. These are replaced by offspring from a small number of parents, drawn from the preexisting population. This model of evolution forwards in time corresponds to a backwards model, in which ancestral lineages jump to a new location if they are hit by an event, and may coalesce with other lineages that are hit by the same event. We derive an expression for the identity in allelic state, and show that, over scales much larger than the largest event, this converges to the classical value derived by Wright and Malécot. However, rare events that cover large areas cause low genetic diversity, large-scale patterns, and correlations in ancestry between unlinked loci.},
author = {Barton, Nicholas H and Kelleher, Jerome and Etheridge, Alison},
journal = {Evolution},
number = {9},
pages = {2701 -- 2715},
publisher = {Wiley-Blackwell},
title = {{A new model for extinction and recolonization in two dimensions: Quantifying phylogeography}},
doi = {10.1111/j.1558-5646.2010.01019.x},
volume = {64},
year = {2010},
}
@inproceedings{4388,
abstract = {GIST is a tool that (a) solves the qualitative analysis problem of turn-based probabilistic games with ω-regular objectives; and (b) synthesizes reasonable environment assumptions for synthesis of unrealizable specifications. Our tool provides the first and efficient implementations of several reduction-based techniques to solve turn-based probabilistic games, and uses the analysis of turn-based probabilistic games for synthesizing environment assumptions for unrealizable specifications.},
author = {Chatterjee, Krishnendu and Henzinger, Thomas A and Jobstmann, Barbara and Radhakrishna, Arjun},
location = {Edinburgh, UK},
pages = {665 -- 669},
publisher = {Springer},
title = {{GIST: A solver for probabilistic games}},
doi = {10.1007/978-3-642-14295-6_57},
volume = {6174},
year = {2010},
}
@inproceedings{4390,
abstract = {Concurrent data structures with fine-grained synchronization are notoriously difficult to implement correctly. The difficulty of reasoning about these implementations does not stem from the number of variables or the program size, but rather from the large number of possible interleavings. These implementations are therefore prime candidates for model checking. We introduce an algorithm for verifying linearizability of singly-linked heap-based concurrent data structures. We consider a model consisting of an unbounded heap where each vertex stores an element from an unbounded data domain, with a restricted set of operations for testing and updating pointers and data elements. Our main result is that linearizability is decidable for programs that invoke a fixed number of methods, possibly in parallel. This decidable fragment covers many of the common implementation techniques — fine-grained locking, lazy synchronization, and lock-free synchronization. We also show how the technique can be used to verify optimistic implementations with the help of programmer annotations. We developed a verification tool CoLT and evaluated it on a representative sample of Java implementations of the concurrent set data structure. The tool verified linearizability of a number of implementations, found a known error in a lock-free implementation and proved that the corrected version is linearizable.},
author = {Cerny, Pavol and Radhakrishna, Arjun and Zufferey, Damien and Chaudhuri, Swarat and Alur, Rajeev},
location = {Edinburgh, UK},
pages = {465 -- 479},
publisher = {Springer},
title = {{Model checking of linearizability of concurrent list implementations}},
doi = {10.1007/978-3-642-14295-6_41},
volume = {6174},
year = {2010},
}
@article{3773,
abstract = {If distinct biological species are to coexist in sympatry, they must be reproductively isolated and must exploit different limiting resources. A two-niche Levene model is analysed, in which habitat preference and survival depend on underlying additive traits. The population genetics of preference and viability are equivalent. However, there is a linear trade-off between the chances of settling in either niche, whereas viabilities may be constrained arbitrarily. With a convex trade-off, a sexual population evolves a single generalist genotype, whereas with a concave trade-off, disruptive selection favours maximal variance. A pure habitat preference evolves to global linkage equilibrium if mating occurs in a single pool, but remarkably, evolves to pairwise linkage equilibrium within niches if mating is within those niches--independent of the genetics. With a concave trade-off, the population shifts sharply between a unimodal distribution with high gene flow and a bimodal distribution with strong isolation, as the underlying genetic variance increases. However, these alternative states are only simultaneously stable for a narrow parameter range. A sharp threshold is only seen if survival in the 'wrong' niche is low; otherwise, strong isolation is impossible. Gene flow from divergent demes makes speciation much easier in parapatry than in sympatry.},
author = {Barton, Nicholas H},
journal = {Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences},
number = {1547},
pages = {1825 -- 1840},
publisher = {Royal Society},
title = {{What role does natural selection play in speciation?}},
doi = {10.1098/rstb.2010.0001},
volume = {365},
year = {2010},
}
@article{3785,
abstract = {Most fisheries involving spiny lobsters of the genus Palinurus have been over exploited during the last decades, so there is a raising concern about management decisions for these valuable resources. A total of 13 microsatellite DNA loci recently developed in Palinurus elephas were assayed in order to assess genetic diversity levels in every known species of the genus. Microsatellite markers gave amplifications and showed polymorphism in all species, with gene diversity values varying from 0.65060.077 SD (Palinurus barbarae) to 0.79260.051 SD (Palinurus elephas). Most importantly, when depth distribution was taken into account, shallower waters pecies consistently showed larger historical effective population sizes than their deeper-water counterparts. This could explain why deeper-water species are more sensitive to overfishing, and would indicate that overexploitation may have a larger impact on their long-term genetic diversity.},
author = {Palero, Ferran and Abello, Pere and Macpherson, E. and Matthee, C. and Pascual, Marta},
journal = {Journal of Crustacean Biology},
number = {4},
pages = {658 -- 663},
publisher = {BioOne},
title = {{Genetic diversity levels in fishery-exploited spiny lobsters of the Genus Palinurus (Decapoda: Achelata)}},
doi = {10.1651/09-3192.1 },
volume = {30},
year = {2010},
}
@article{3792,
abstract = {The yolk syncytial layer (YSL) plays crucial roles in early zebrafish development. The YSL is a transient extra-embryonic syncytial tissue that forms during early cleavage stages and persists until larval stages. During gastrulation, the YSL undergoes highly dynamic movements, which are tightly coordinated with the movements of the overlying germ layer progenitor cells, and has critical functions in cell fate specification and morphogenesis of the early germ layers. Movement coordination between the YSL and blastoderm cells is dependent on contact between these tissues, and is probably required for the patterning and morphogenetic function of the YSL. In this review, we will discuss recent advances in elucidating the molecular and cellular mechanisms underlying the YSL morphogenesis and movement coordination between the YSL and blastoderm during early development.},
author = {Carvalho, Lara and Heisenberg, Carl-Philipp J},
journal = {Trends in Cell Biology},
number = {10},
pages = {586 -- 592},
publisher = {Cell Press},
title = {{The yolk syncytial layer in early, zebrafish development}},
doi = {10.1016/j.tcb.2010.06.009},
volume = {20},
year = {2010},
}
@inproceedings{3848,
abstract = {We define the robustness of a level set homology class of a function f:XR as the magnitude of a perturbation necessary to kill the class. Casting this notion into a group theoretic framework, we compute the robustness for each class, using a connection to extended persistent homology. The special case X=R3 has ramifications in medical imaging and scientific visualization.},
author = {Bendich, Paul and Edelsbrunner, Herbert and Morozov, Dmitriy and Patel, Amit},
location = {Liverpool, UK},
pages = {1 -- 10},
publisher = {Springer},
title = {{The robustness of level sets}},
doi = {10.1007/978-3-642-15775-2_1},
volume = {6346},
year = {2010},
}
@inproceedings{3850,
abstract = {Given a polygonal shape Q with n vertices, can it be expressed, up to a tolerance ε in Hausdorff distance, as the Minkowski sum of another polygonal shape with a disk of fixed radius? If it does, we also seek a preferably simple solution shape P;P’s offset constitutes an accurate, vertex-reduced, and smoothened approximation of Q. We give a decision algorithm for fixed radius in O(nlogn) time that handles any polygonal shape. For convex shapes, the complexity drops to O(n), which is also the time required to compute a solution shape P with at most one more vertex than a vertex-minimal one.},
author = {Berberich, Eric and Halperin, Dan and Kerber, Michael and Pogalnikova, Roza},
location = {Dortmund, Germany},
pages = {12 -- 23},
publisher = {TU Dortmund},
title = {{Polygonal reconstruction from approximate offsets}},
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},
}
@book{4346,
abstract = {With the term "Library 2.0" the editors mean an institution which applies the principles of the Web 2.0 such as openness, re-use, collaboration and interaction in the entire organization. Libraries are extending their service offerings and work processes to include the potential of Web 2.0 technologies. This changes the job description and self-image of librarians. The collective volume offers a complete overview of the topic Library 2.0 and the current state of developments from a technological, sociological, information theoretical and practice-oriented perspective.},
author = {Danowski, Patrick and Bergmann, Julia},
publisher = {De Gruyter},
title = {{Handbuch Bibliothek 2.0}},
year = {2010},
}