@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},
}
@article{3051,
author = {Weijers, Dolf and Friml, Jirí},
journal = {Cell},
number = {6},
pages = {1172 -- 1172},
publisher = {Cell Press},
title = {{SnapShot: Auxin signaling and transport}},
doi = {10.1016/j.cell.2009.03.009},
volume = {136},
year = {2009},
}
@article{3052,
abstract = {The dynamic, differential distribution of the hormone auxin within plant tissues controls an impressive variety of developmental processes, which tailor plant growth and morphology to environmental conditions. Various environmental and endogenous signals can be integrated into changes in auxin distribution through their effects on local auxin biosynthesis and intercellular auxin transport. Individual cells interpret auxin largely by a nuclear signaling pathway that involves the F box protein TIR1 acting as an auxin receptor. Auxin-dependent TIR1 activity leads to ubiquitination-based degradation of transcriptional repressors and complex transcriptional reprogramming. Thus, auxin appears to be a versatile trigger of preprogrammed developmental changes in plant cells.},
author = {Vanneste, Steffen and Friml, Jirí},
journal = {Cell},
number = {6},
pages = {1005 -- 1016},
publisher = {Cell Press},
title = {{Auxin: A trigger for change in plant development}},
doi = {10.1016/j.cell.2009.03.001},
volume = {136},
year = {2009},
}
@article{3057,
abstract = {The differential distribution of the plant signaling molecule auxin is required for many aspects of plant development. Local auxin maxima and gradients arise as a result of local auxin metabolism and, predominantly, from directional cell-to-cell transport. In this primer, we discuss how the coordinated activity of several auxin influx and efflux systems, which transport auxin across the plasma membrane, mediates directional auxin flow. This activity crucially contributes to the correct setting of developmental cues in embryogenesis, organogenesis, vascular tissue formation and directional growth in response to environmental stimuli.},
author = {Petrášek, Jan and Friml, Jirí},
journal = {Development},
number = {16},
pages = {2675 -- 2688},
publisher = {Company of Biologists},
title = {{Auxin transport routes in plant development}},
doi = {10.1242/dev.030353},
volume = {136},
year = {2009},
}
@article{3061,
abstract = {The PIN-FORMED (PIN) proteins are secondary transporters acting in the efflux of the plant signal molecule auxin from cells. They are asymmetrically localized within cells and their polarity determines the directionality of intercellular auxin flow. PIN genes are found exclusively in the genomes of multicellular plants and play an important role in regulating asymmetric auxin distribution in multiple developmental processes, including embryogenesis, organogenesis, tissue differentiation and tropic responses. All PIN proteins have a similar structure with amino- and carboxy-terminal hydrophobic, membrane-spanning domains separated by a central hydrophilic domain. The structure of the hydrophobic domains is well conserved. The hydrophilic domain is more divergent and it determines eight groups within the protein family. The activity of PIN proteins is regulated at multiple levels, including transcription, protein stability, subcellular localization and transport activity. Different endogenous and environmental signals can modulate PIN activity and thus modulate auxin-distribution-dependent development. A large group of PIN proteins, including the most ancient members known from mosses, localize to the endoplasmic reticulum and they regulate the subcellular compartmentalization of auxin and thus auxin metabolism. Further work is needed to establish the physiological importance of this unexpected mode of auxin homeostasis regulation. Furthermore, the evolution of PIN-based transport, PIN protein structure and more detailed biochemical characterization of the transport function are important topics for further studies.},
author = {Křeček, Pavel and Skůpa, Petr and Libus, Jiří and Naramoto, Satoshi and Tejos, Ricardo and Friml, Jirí and Zažímalová, Eva},
journal = {Genome Biology},
number = {12},
publisher = {BioMed Central},
title = {{The PIN-FORMED (PIN) protein family of auxin transporters}},
doi = {10.1186/gb-2009-10-12-249},
volume = {10},
year = {2009},
}
@article{3197,
abstract = {The problem of obtaining the maximum a posteriori estimate of a general discrete Markov random field (i.e., a Markov random field defined using a discrete set of labels) is known to be NP-hard. However, due to its central importance in many applications, several approximation algorithms have been proposed in the literature. In this paper, we present an analysis of three such algorithms based on convex relaxations: (i) LP-S: the linear programming (LP) relaxation proposed by Schlesinger (1976) for a special case and independently in Chekuri et al. (2001), Koster et al. (1998), and Wainwright et al. (2005) for the general case; (ii) QP-RL: the quadratic programming (QP) relaxation of Ravikumar and Lafferty (2006); and (iii) SOCP-MS: the second order cone programming (SOCP) relaxation first proposed by Muramatsu and Suzuki (2003) for two label problems and later extended by Kumar et al. (2006) for a general label set.
We show that the SOCP-MS and the QP-RL relaxations are equivalent. Furthermore, we prove that despite the flexibility in the form of the constraints/objective function offered by QP and SOCP, the LP-S relaxation strictly dominates (i.e., provides a better approximation than) QP-RL and SOCP-MS. We generalize these results by defining a large class of SOCP (and equivalent QP) relaxations which is dominated by the LP-S relaxation. Based on these results we propose some novel SOCP relaxations which define constraints using random variables that form cycles or cliques in the graphical model representation of the random field. Using some examples we show that the new SOCP relaxations strictly dominate the previous approaches.},
author = {Kumar, M Pawan and Vladimir Kolmogorov and Torr, Philip H},
journal = {Journal of Machine Learning Research},
pages = {71 -- 106},
publisher = {Microtome Publishing},
title = {{An analysis of convex relaxations for MAP estimation of discrete MRFs}},
volume = {10},
year = {2009},
}
@inproceedings{3503,
abstract = {We give polynomial-time algorithms for computing the values of Markov decision processes (MDPs) with limsup and liminf objectives. A real-valued reward is assigned to each state, and the value of an infinite path in the MDP is the limsup (resp. liminf) of all rewards along the path. The value of an MDP is the maximal expected value of an infinite path that can be achieved by resolving the decisions of the MDP. Using our result on MDPs, we show that turn-based stochastic games with limsup and liminf objectives can be solved in NP ∩ coNP. },
author = {Krishnendu Chatterjee and Thomas Henzinger},
pages = {32 -- 45},
publisher = {Springer},
title = {{Probabilistic systems with limsup and liminf objectives}},
doi = {10.1007/978-3-642-03092-5_4},
volume = {5489},
year = {2009},
}
@article{9453,
abstract = {Parent-of-origin-specific (imprinted) gene expression is regulated in Arabidopsis thaliana endosperm by cytosine demethylation of the maternal genome mediated by the DNA glycosylase DEMETER, but the extent of the methylation changes is not known. Here, we show that virtually the entire endosperm genome is demethylated, coupled with extensive local non-CG hypermethylation of small interfering RNA–targeted sequences. Mutation of DEMETER partially restores endosperm CG methylation to levels found in other tissues, indicating that CG demethylation is specific to maternal sequences. Endosperm demethylation is accompanied by CHH hypermethylation of embryo transposable elements. Our findings demonstrate extensive reconfiguration of the endosperm methylation landscape that likely reinforces transposon silencing in the embryo.},
author = {Hsieh, Tzung-Fu and Ibarra, Christian A. and Silva, Pedro and Zemach, Assaf and Eshed-Williams, Leor and Fischer, Robert L. and ZILBERMAN, Daniel},
issn = {1095-9203},
journal = {Science},
keywords = {Multidisciplinary},
number = {5933},
pages = {1451--1454},
publisher = {American Association for the Advancement of Science},
title = {{Genome-wide demethylation of Arabidopsis endosperm}},
doi = {10.1126/science.1172417},
volume = {324},
year = {2009},
}
@inproceedings{2331,
abstract = {We present a review of recent work on the mathematical aspects of the BCS gap equation, covering our results of Ref. 9 as well our recent joint work with Hamza and Solovej and with Frank and Naboko, respectively. In addition, we mention some related new results.},
author = {Hainzl, Christian and Robert Seiringer},
pages = {117 -- 136},
publisher = {World Scientific Publishing},
title = {{ Spectral properties of the BCS gap equation of superfluidity}},
doi = {10.1142/9789812832382_0009},
year = {2008},
}
@inproceedings{2332,
abstract = {We present a rigorous proof of the appearance of quantized vortices in dilute trapped Bose gases with repulsive two-body interactions subject to rotation, which was obtained recently in joint work with Elliott Lieb.14 Starting from the many-body Schrödinger equation, we show that the ground state of such gases is, in a suitable limit, well described by the nonlinear Gross-Pitaevskii equation. In the case of axially symmetric traps, our results show that the appearance of quantized vortices causes spontaneous symmetry breaking in the ground state.},
author = {Robert Seiringer},
pages = {241 -- 254},
publisher = {World Scientific Publishing},
title = {{Vortices and Spontaneous Symmetry Breaking in Rotating Bose Gases}},
doi = {10.1142/9789812832382_0017},
year = {2008},
}