@article{3846,
  abstract     = {We summarize classical and recent results about two-player games played on graphs with ω-regular objectives. These games have applications in the verification and synthesis of reactive systems. Important distinctions are whether a graph game is turn-based or concurrent; deterministic or stochastic; zero-sum or not. We cluster known results and open problems according to these classifications.},
  author       = {Chatterjee, Krishnendu and Henzinger, Thomas A},
  journal      = {Journal of Computer and System Sciences},
  number       = {2},
  pages        = {394 -- 413},
  publisher    = {Elsevier},
  title        = {{A survey of stochastic ω regular games}},
  doi          = {10.1016/j.jcss.2011.05.002},
  volume       = {78},
  year         = {2012},
}

@article{493,
  abstract     = {The BCI competition IV stands in the tradition of prior BCI competitions that aim to provide high quality neuroscientific data for open access to the scientific community. As experienced already in prior competitions not only scientists from the narrow field of BCI compete, but scholars with a broad variety of backgrounds and nationalities. They include high specialists as well as students.The goals of all BCI competitions have always been to challenge with respect to novel paradigms and complex data. We report on the following challenges: (1) asynchronous data, (2) synthetic, (3) multi-class continuous data, (4) sessionto-session transfer, (5) directionally modulated MEG, (6) finger movements recorded by ECoG. As after past competitions, our hope is that winning entries may enhance the analysis methods of future BCIs.},
  author       = {Tangermann, Michael and Müller, Klaus and Aertsen, Ad and Birbaumer, Niels and Braun, Christoph and Brunner, Clemens and Leeb, Robert and Mehring, Carsten and Miller, Kai and Müller Putz, Gernot and Nolte, Guido and Pfurtscheller, Gert and Preissl, Hubert and Schalk, Gerwin and Schlögl, Alois and Vidaurre, Carmen and Waldert, Stephan and Blankertz, Benjamin},
  journal      = {Frontiers in Neuroscience},
  publisher    = {Frontiers Research Foundation},
  title        = {{Review of the BCI competition IV}},
  doi          = {10.3389/fnins.2012.00055},
  volume       = {6},
  year         = {2012},
}

@article{494,
  abstract     = {We solve the longstanding open problems of the blow-up involved in the translations, when possible, of a nondeterministic Büchi word automaton (NBW) to a nondeterministic co-Büchi word automaton (NCW) and to a deterministic co-Büchi word automaton (DCW). For the NBW to NCW translation, the currently known upper bound is 2o(nlog n) and the lower bound is 1.5n. We improve the upper bound to n2n and describe a matching lower bound of 2ω(n). For the NBW to DCW translation, the currently known upper bound is 2o(nlog n). We improve it to 2 o(n), which is asymptotically tight. Both of our upper-bound constructions are based on a simple subset construction, do not involve intermediate automata with richer acceptance conditions, and can be implemented symbolically. We continue and solve the open problems of translating nondeterministic Streett, Rabin, Muller, and parity word automata to NCW and to DCW. Going via an intermediate NBW is not optimal and we describe direct, simple, and asymptotically tight constructions, involving a 2o(n) blow-up. The constructions are variants of the subset construction, providing a unified approach for translating all common classes of automata to NCW and DCW. Beyond the theoretical importance of the results, we point to numerous applications of the new constructions. In particular, they imply a simple subset-construction based translation, when possible, of LTL to deterministic Büchi word automata.},
  author       = {Boker, Udi and Kupferman, Orna},
  journal      = {ACM Transactions on Computational Logic (TOCL)},
  number       = {4},
  publisher    = {ACM},
  title        = {{Translating to Co-Büchi made tight, unified, and useful}},
  doi          = {10.1145/2362355.2362357},
  volume       = {13},
  year         = {2012},
}

@inproceedings{495,
  abstract     = {An automaton with advice is a finite state automaton which has access to an additional fixed infinite string called an advice tape. We refine the Myhill-Nerode theorem to characterize the languages of finite strings that are accepted by automata with advice. We do the same for tree automata with advice.},
  author       = {Kruckman, Alex and Rubin, Sasha and Sheridan, John and Zax, Ben},
  booktitle    = {Proceedings GandALF 2012},
  location     = {Napoli, Italy},
  pages        = {238 -- 246},
  publisher    = {Open Publishing Association},
  title        = {{A Myhill Nerode theorem for automata with advice}},
  doi          = {10.4204/EPTCS.96.18},
  volume       = {96},
  year         = {2012},
}

@inproceedings{496,
  abstract     = {We study the expressive power of logical interpretations on the class of scattered trees, namely those with countably many infinite branches. Scattered trees can be thought of as the tree analogue of scattered linear orders. Every scattered tree has an ordinal rank that reflects the structure of its infinite branches. We prove, roughly, that trees and orders of large rank cannot be interpreted in scattered trees of small rank. We consider a quite general notion of interpretation: each element of the interpreted structure is represented by a set of tuples of subsets of the interpreting tree. Our trees are countable, not necessarily finitely branching, and may have finitely many unary predicates as labellings. We also show how to replace injective set-interpretations in (not necessarily scattered) trees by 'finitary' set-interpretations.},
  author       = {Rabinovich, Alexander and Rubin, Sasha},
  location     = {Dubrovnik, Croatia},
  publisher    = {IEEE},
  title        = {{Interpretations in trees with countably many branches}},
  doi          = {10.1109/LICS.2012.65},
  year         = {2012},
}

@inproceedings{497,
  abstract     = {One central issue in the formal design and analysis of reactive systems is the notion of refinement that asks whether all behaviors of the implementation is allowed by the specification. The local interpretation of behavior leads to the notion of simulation. Alternating transition systems (ATSs) provide a general model for composite reactive systems, and the simulation relation for ATSs is known as alternating simulation. The simulation relation for fair transition systems is called fair simulation. In this work our main contributions are as follows: (1) We present an improved algorithm for fair simulation with Büchi fairness constraints; our algorithm requires O(n 3·m) time as compared to the previous known O(n 6)-time algorithm, where n is the number of states and m is the number of transitions. (2) We present a game based algorithm for alternating simulation that requires O(m2)-time as compared to the previous known O((n·m)2)-time algorithm, where n is the number of states and m is the size of transition relation. (3) We present an iterative algorithm for alternating simulation that matches the time complexity of the game based algorithm, but is more space efficient than the game based algorithm. © Krishnendu Chatterjee, Siddhesh Chaubal, and Pritish Kamath.},
  author       = {Chatterjee, Krishnendu and Chaubal, Siddhesh and Kamath, Pritish},
  location     = {Fontainebleau, France},
  pages        = {167 -- 182},
  publisher    = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
  title        = {{Faster algorithms for alternating refinement relations}},
  doi          = {10.4230/LIPIcs.CSL.2012.167},
  volume       = {16},
  year         = {2012},
}

@article{498,
  abstract     = {Understanding patterns and correlates of local adaptation in heterogeneous landscapes can provide important information in the selection of appropriate seed sources for restoration. We assessed the extent of local adaptation of fitness components in 12 population pairs of the perennial herb Rutidosis leptorrhynchoides (Asteraceae) and examined whether spatial scale (0.7-600 km), environmental distance, quantitative (QST) and neutral (FST) genetic differentiation, and size of the local and foreign populations could predict patterns of adaptive differentiation. Local adaptation varied among populations and fitness components. Including all population pairs, local adaptation was observed for seedling survival, but not for biomass, while foreign genotype advantage was observed for reproduction (number of inflorescences). Among population pairs, local adaptation increased with QST and local population size for biomass. QST was associated with environmental distance, suggesting ecological selection for phenotypic divergence. However, low FST and variation in population structure in small populations demonstrates the interaction of gene flow and drift in constraining local adaptation in R. leptorrhynchoides. Our study indicates that for species in heterogeneous landscapes, collecting seed from large populations from similar environments to candidate sites is likely to provide the most appropriate seed sources for restoration.},
  author       = {Pickup, Melinda and Field, David and Rowell, David and Young, Andrew},
  journal      = {Evolutionary Applications},
  number       = {8},
  pages        = {913 -- 924},
  publisher    = {Wiley-Blackwell},
  title        = {{Predicting local adaptation in fragmented plant populations: Implications for restoration genetics}},
  doi          = {10.1111/j.1752-4571.2012.00284.x},
  volume       = {5},
  year         = {2012},
}

@article{506,
  author       = {Sixt, Michael K},
  journal      = {Journal of Cell Biology},
  number       = {3},
  pages        = {347 -- 349},
  publisher    = {Rockefeller University Press},
  title        = {{Cell migration: Fibroblasts find a new way to get ahead}},
  doi          = {10.1083/jcb.201204039},
  volume       = {197},
  year         = {2012},
}

@misc{5377,
  abstract     = {Two-player games on graphs are central in many problems in formal verification and program analysis such as synthesis and verification of open systems. In this work we consider solving recursive game graphs (or pushdown game graphs) that can model the control flow of sequential programs with recursion. While pushdown games have been studied before with qualitative objectives, such as reachability and ω-regular objectives, in this work we study for the first time such games with the most well-studied quantitative objective, namely, mean-payoff objectives. In pushdown games two types of strategies are relevant: (1) global strategies, that depend on the entire global history; and (2) modular strategies, that have only local memory and thus do not depend on the context of invocation, but only on the history of the current invocation of the module. Our main results are as follows: (1) One-player pushdown games with mean-payoff objectives under global strategies are decidable in polynomial time. (2) Two- player pushdown games with mean-payoff objectives under global strategies are undecidable. (3) One-player pushdown games with mean-payoff objectives under modular strategies are NP- hard. (4) Two-player pushdown games with mean-payoff objectives under modular strategies can be solved in NP (i.e., both one-player and two-player pushdown games with mean-payoff objectives under modular strategies are NP-complete). We also establish the optimal strategy complexity showing that global strategies for mean-payoff objectives require infinite memory even in one-player pushdown games; and memoryless modular strategies are sufficient in two- player pushdown games. Finally we also show that all the problems have the same complexity if the stack boundedness condition is added, where along with the mean-payoff objective the player must also ensure that the stack height is bounded.},
  author       = {Chatterjee, Krishnendu and Velner, Yaron},
  issn         = {2664-1690},
  pages        = {33},
  publisher    = {IST Austria},
  title        = {{Mean-payoff pushdown games}},
  doi          = {10.15479/AT:IST-2012-0002},
  year         = {2012},
}

@misc{5378,
  abstract     = {One central issue in the formal design and analysis of reactive systems is the notion of refinement that asks whether all behaviors of the implementation is allowed by the specification. The local interpretation of behavior leads to the notion of simulation. Alternating transition systems (ATSs) provide a general model for composite reactive systems, and the simulation relation for ATSs is known as alternating simulation. The simulation relation for fair transition systems is called fair simulation. In this work our main contributions are as follows: (1) We present an improved algorithm for fair simulation with Büchi fairness constraints; our algorithm requires O(n3 · m) time as compared to the previous known O(n6)-time algorithm, where n is the number of states and m is the number of transitions. (2) We present a game based algorithm for alternating simulation that requires O(m2)-time as compared to the previous known O((n · m)2)-time algorithm, where n is the number of states and m is the size of transition relation. (3) We present an iterative algorithm for alternating simulation that matches the time complexity of the game based algorithm, but is more space efficient than the game based algorithm.},
  author       = {Chatterjee, Krishnendu and Chaubal, Siddhesh and Kamath, Pritish},
  issn         = {2664-1690},
  pages        = {21},
  publisher    = {IST Austria},
  title        = {{Faster algorithms for alternating refinement relations}},
  doi          = {10.15479/AT:IST-2012-0001},
  year         = {2012},
}

@article{2263,
  abstract     = {Nestin-cre transgenic mice have been widely used to direct recombination to neural stem cells (NSCs) and intermediate neural progenitor cells (NPCs). Here we report that a readily utilized, and the only commercially available, Nestin-cre line is insufficient for directing recombination in early embryonic NSCs and NPCs. Analysis of recombination efficiency in multiple cre-dependent reporters and a genetic mosaic line revealed consistent temporal and spatial patterns of recombination in NSCs and NPCs. For comparison we utilized a knock-in Emx1cre line and found robust recombination in NSCs and NPCs in ventricular and subventricular zones of the cerebral cortices as early as embryonic day 12.5. In addition we found that the rate of Nestin-cre driven recombination only reaches sufficiently high levels in NSCs and NPCs during late embryonic and early postnatal periods. These findings are important when commercially available cre lines are considered for directing recombination to embryonic NSCs and NPCs.},
  author       = {Liang, Huixuan and Hippenmeyer, Simon and Ghashghaei, H.},
  journal      = {Biology open},
  number       = {12},
  pages        = {1200 -- 1203},
  publisher    = {The Company of Biologists},
  title        = {{A Nestin-cre transgenic mouse is insufficient for recombination in early embryonic neural progenitors}},
  doi          = {10.1242/bio.20122287},
  volume       = {1},
  year         = {2012},
}

@article{2302,
  abstract     = {We introduce propagation models (PMs), a formalism able to express several kinds of equations that describe the behavior of biochemical reaction networks. Furthermore, we introduce the propagation abstract data type (PADT), which separates concerns regarding different numerical algorithms for the transient analysis of biochemical reaction networks from concerns regarding their implementation, thus allowing for portable and efficient solutions. The state of a propagation abstract data type is given by a vector that assigns mass values to a set of nodes, and its (next) operator propagates mass values through this set of nodes. We propose an approximate implementation of the (next) operator, based on threshold abstraction, which propagates only "significant" mass values and thus achieves a compromise between efficiency and accuracy. Finally, we give three use cases for propagation models: the chemical master equation (CME), the reaction rate equation (RRE), and a hybrid method that combines these two equations. These three applications use propagation models in order to propagate probabilities and/or expected values and variances of the model's variables.},
  author       = {Henzinger, Thomas A and Mateescu, Maria},
  journal      = {IEEE ACM Transactions on Computational Biology and Bioinformatics},
  number       = {2},
  pages        = {310 -- 322},
  publisher    = {IEEE},
  title        = {{The propagation approach for computing biochemical reaction networks}},
  doi          = {10.1109/TCBB.2012.91},
  volume       = {10},
  year         = {2012},
}

@article{2318,
  abstract     = {We show that bosons interacting via pair potentials with negative scattering length form bound states for a suitable number of particles. In other words, the absence of many-particle bound states of any kind implies the non-negativity of the scattering length of the interaction potential. },
  author       = {Seiringer, Robert},
  journal      = {Journal of Spectral Theory},
  number       = {3},
  pages        = {321--328},
  publisher    = {European Mathematical Society},
  title        = {{Absence of bound states implies non-negativity of the scattering length}},
  doi          = {10.4171/JST/31},
  volume       = {2},
  year         = {2012},
}

@article{2411,
  abstract     = {The kingdom of fungi provides model organisms for biotechnology, cell biology, genetics, and life sciences in general. Only when their phylogenetic relationships are stably resolved, can individual results from fungal research be integrated into a holistic picture of biology. However, and despite recent progress, many deep relationships within the fungi remain unclear. Here, we present the first phylogenomic study of an entire eukaryotic kingdom that uses a consistency criterion to strengthen phylogenetic conclusions. We reason that branches (splits) recovered with independent data and different tree reconstruction methods are likely to reflect true evolutionary relationships. Two complementary phylogenomic data sets based on 99 fungal genomes and 109 fungal expressed sequence tag (EST) sets analyzed with four different tree reconstruction methods shed light from different angles on the fungal tree of life. Eleven additional data sets address specifically the phylogenetic position of Blastocladiomycota, Ustilaginomycotina, and Dothideomycetes, respectively. The combined evidence from the resulting trees supports the deep-level stability of the fungal groups toward a comprehensive natural system of the fungi. In addition, our analysis reveals methodologically interesting aspects. Enrichment for EST encoded data-a common practice in phylogenomic analyses-introduces a strong bias toward slowly evolving and functionally correlated genes. Consequently, the generalization of phylogenomic data sets as collections of randomly selected genes cannot be taken for granted. A thorough characterization of the data to assess possible influences on the tree reconstruction should therefore become a standard in phylogenomic analyses.},
  author       = {Ebersberger, Ingo and De Matos Simoes, Ricardo and Kupczok, Anne and Gube, Matthias and Kothe, Erika and Voigt, Kerstin and Von Haeseler, Arndt},
  journal      = {Molecular Biology and Evolution},
  number       = {5},
  pages        = {1319 -- 1334},
  publisher    = {Oxford University Press},
  title        = {{A consistent phylogenetic backbone for the fungi}},
  doi          = {10.1093/molbev/msr285},
  volume       = {29},
  year         = {2012},
}

@inproceedings{2715,
  abstract     = {We consider Markov decision processes (MDPs) with specifications given as Büchi (liveness) objectives. We consider the problem of computing the set of almost-sure winning vertices from where the objective can be ensured with probability 1. We study for the first time the average case complexity of the classical algorithm for computing the set of almost-sure winning vertices for MDPs with Büchi objectives. Our contributions are as follows: First, we show that for MDPs with constant out-degree the expected number of iterations is at most logarithmic and the average case running time is linear (as compared to the worst case linear number of iterations and quadratic time complexity). Second, for the average case analysis over all MDPs we show that the expected number of iterations is constant and the average case running time is linear (again as compared to the worst case linear number of iterations and quadratic time complexity). Finally we also show that given that all MDPs are equally likely, the probability that the classical algorithm requires more than constant number of iterations is exponentially small.},
  author       = {Chatterjee, Krishnendu and Joglekar, Manas and Shah, Nisarg},
  location     = {Hyderabad, India},
  pages        = {461 -- 473},
  publisher    = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
  title        = {{Average case analysis of the classical algorithm for Markov decision processes with Büchi objectives}},
  doi          = {10.4230/LIPIcs.FSTTCS.2012.461},
  volume       = {18},
  year         = {2012},
}

@inproceedings{2825,
  abstract     = {We study the problem of maximum marginal prediction (MMP) in probabilistic graphical models, a task that occurs, for example, as the Bayes optimal decision rule under a Hamming loss. MMP is typically performed as a two-stage procedure: one estimates each variable's marginal probability and then forms a prediction from the states of maximal probability. In this work we propose a simple yet effective technique for accelerating MMP when inference is sampling-based: instead of the above two-stage procedure we directly estimate the posterior probability of each decision variable. This allows us to identify the point of time when we are sufficiently certain about any individual decision. Whenever this is the case, we dynamically prune the variables we are confident about from the underlying factor graph. Consequently, at any time only samples of variables whose decision is still uncertain need to be created. Experiments in two prototypical scenarios, multi-label classification and image inpainting, show that adaptive sampling can drastically accelerate MMP without sacrificing prediction accuracy.},
  author       = {Lampert, Christoph},
  location     = {Lake Tahoe, NV, United States},
  pages        = {82 -- 90},
  publisher    = {Neural Information Processing Systems},
  title        = {{Dynamic pruning of factor graphs for maximum marginal prediction}},
  volume       = {1},
  year         = {2012},
}

@article{2848,
  abstract     = {We study evolutionary game theory in a setting where individuals learn from each other. We extend the traditional approach by assuming that a population contains individuals with different learning abilities. In particular, we explore the situation where individuals have different search spaces, when attempting to learn the strategies of others. The search space of an individual specifies the set of strategies learnable by that individual. The search space is genetically given and does not change under social evolutionary dynamics. We introduce a general framework and study a specific example in the context of direct reciprocity. For this example, we obtain the counter intuitive result that cooperation can only evolve for intermediate benefit-to-cost ratios, while small and large benefit-to-cost ratios favor defection. Our paper is a step toward making a connection between computational learning theory and evolutionary game dynamics.},
  author       = {Chatterjee, Krishnendu and Zufferey, Damien and Nowak, Martin},
  journal      = {Journal of Theoretical Biology},
  pages        = {161 -- 173},
  publisher    = {Elsevier},
  title        = {{Evolutionary game dynamics in populations with different learners}},
  doi          = {10.1016/j.jtbi.2012.02.021},
  volume       = {301},
  year         = {2012},
}

@article{2849,
  author       = {Edelsbrunner, Herbert and Strelkova, Nataliya},
  journal      = {Russian Mathematical Surveys},
  number       = {6},
  pages        = {1167 -- 1168},
  publisher    = {IOP Publishing Ltd.},
  title        = {{On the configuration space of Steiner minimal trees}},
  doi          = {10.1070/RM2012v067n06ABEH004820},
  volume       = {67},
  year         = {2012},
}

@inproceedings{2888,
  abstract     = {Formal verification aims to improve the quality of hardware and software by detecting errors before they do harm. At the basis of formal verification lies the logical notion of correctness, which purports to capture whether or not a circuit or program behaves as desired. We suggest that the boolean partition into correct and incorrect systems falls short of the practical need to assess the behavior of hardware and software in a more nuanced fashion against multiple criteria.},
  author       = {Henzinger, Thomas A},
  booktitle    = {Conference proceedings MODELS 2012},
  location     = {Innsbruck, Austria},
  pages        = {1 -- 2},
  publisher    = {Springer},
  title        = {{Quantitative reactive models}},
  doi          = {10.1007/978-3-642-33666-9_1},
  volume       = {7590},
  year         = {2012},
}

@inproceedings{2890,
  abstract     = {Systems are often specified using multiple requirements on their behavior. In practice, these requirements can be contradictory. The classical approach to specification, verification, and synthesis demands more detailed specifications that resolve any contradictions in the requirements. These detailed specifications are usually large, cumbersome, and hard to maintain or modify. In contrast, quantitative frameworks allow the formalization of the intuitive idea that what is desired is an implementation that comes "closest" to satisfying the mutually incompatible requirements, according to a measure of fit that can be defined by the requirements engineer. One flexible framework for quantifying how "well" an implementation satisfies a specification is offered by simulation distances that are parameterized by an error model. We introduce this framework, study its properties, and provide an algorithmic solution for the following quantitative synthesis question: given two (or more) behavioral requirements specified by possibly incompatible finite-state machines, and an error model, find the finite-state implementation that minimizes the maximal simulation distance to the given requirements. Furthermore, we generalize the framework to handle infinite alphabets (for example, realvalued domains). We also demonstrate how quantitative specifications based on simulation distances might lead to smaller and easier to modify specifications. Finally, we illustrate our approach using case studies on error correcting codes and scheduler synthesis.},
  author       = {Cerny, Pavol and Gopi, Sivakanth and Henzinger, Thomas A and Radhakrishna, Arjun and Totla, Nishant},
  booktitle    = {Proceedings of the tenth ACM international conference on Embedded software},
  location     = {Tampere, Finland},
  pages        = {53 -- 62},
  publisher    = {ACM},
  title        = {{Synthesis from incompatible specifications}},
  doi          = {10.1145/2380356.2380371},
  year         = {2012},
}