@article{1929,
  abstract     = {We propose an algorithm for the generalization of cartographic objects that can be used to represent maps on different scales.},
  author       = {Alexeev, V V and Bogaevskaya, V G and Preobrazhenskaya, M M and Ukhalov, A Y and Edelsbrunner, Herbert and Yakimova, Olga},
  issn         = {1573-8795},
  journal      = {Journal of Mathematical Sciences},
  number       = {6},
  pages        = {754 -- 760},
  publisher    = {Springer},
  title        = {{An algorithm for cartographic generalization that preserves global topology}},
  doi          = {10.1007/s10958-014-2165-8},
  volume       = {203},
  year         = {2014},
}

@article{1930,
  abstract     = {(Figure Presented) Data acquisition, numerical inaccuracies, and sampling often introduce noise in measurements and simulations. Removing this noise is often necessary for efficient analysis and visualization of this data, yet many denoising techniques change the minima and maxima of a scalar field. For example, the extrema can appear or disappear, spatially move, and change their value. This can lead to wrong interpretations of the data, e.g., when the maximum temperature over an area is falsely reported being a few degrees cooler because the denoising method is unaware of these features. Recently, a topological denoising technique based on a global energy optimization was proposed, which allows the topology-controlled denoising of 2D scalar fields. While this method preserves the minima and maxima, it is constrained by the size of the data. We extend this work to large 2D data and medium-sized 3D data by introducing a novel domain decomposition approach. It allows processing small patches of the domain independently while still avoiding the introduction of new critical points. Furthermore, we propose an iterative refinement of the solution, which decreases the optimization energy compared to the previous approach and therefore gives smoother results that are closer to the input. We illustrate our technique on synthetic and real-world 2D and 3D data sets that highlight potential applications.},
  author       = {Günther, David and Jacobson, Alec and Reininghaus, Jan and Seidel, Hans and Sorkine Hornung, Olga and Weinkauf, Tino},
  journal      = {IEEE Transactions on Visualization and Computer Graphics},
  number       = {12},
  pages        = {2585 -- 2594},
  publisher    = {IEEE},
  title        = {{Fast and memory-efficient topological denoising of 2D and 3D scalar fields}},
  doi          = {10.1109/TVCG.2014.2346432},
  volume       = {20},
  year         = {2014},
}

@article{1931,
  abstract     = {A wealth of experimental evidence suggests that working memory circuits preferentially represent information that is behaviorally relevant. Still, we are missing a mechanistic account of how these representations come about. Here we provide a simple explanation for a range of experimental findings, in light of prefrontal circuits adapting to task constraints by reward-dependent learning. In particular, we model a neural network shaped by reward-modulated spike-timing dependent plasticity (r-STDP) and homeostatic plasticity (intrinsic excitability and synaptic scaling). We show that the experimentally-observed neural representations naturally emerge in an initially unstructured circuit as it learns to solve several working memory tasks. These results point to a critical, and previously unappreciated, role for reward-dependent learning in shaping prefrontal cortex activity.},
  author       = {Savin, Cristina and Triesch, Jochen},
  journal      = {Frontiers in Computational Neuroscience},
  number       = {MAY},
  publisher    = {Frontiers Research Foundation},
  title        = {{Emergence of task-dependent representations in working memory circuits}},
  doi          = {10.3389/fncom.2014.00057},
  volume       = {8},
  year         = {2014},
}

@article{1932,
  abstract     = {The existence of complex (multiple-step) genetic adaptations that are "irreducible" (i.e., all partial combinations are less fit than the original genotype) is one of the longest standing problems in evolutionary biology. In standard genetics parlance, these adaptations require the crossing of a wide adaptive valley of deleterious intermediate stages. Here, we demonstrate, using a simple model, that evolution can cross wide valleys to produce "irreducibly complex" adaptations by making use of previously cryptic mutations. When revealed by an evolutionary capacitor, previously cryptic mutants have higher initial frequencies than do new mutations, bringing them closer to a valley-crossing saddle in allele frequency space. Moreover, simple combinatorics implies an enormous number of candidate combinations exist within available cryptic genetic variation. We model the dynamics of crossing of a wide adaptive valley after a capacitance event using both numerical simulations and analytical approximations. Although individual valley crossing events become less likely as valleys widen, by taking the combinatorics of genotype space into account, we see that revealing cryptic variation can cause the frequent evolution of complex adaptations.},
  author       = {Trotter, Meredith and Weissman, Daniel and Peterson, Grant and Peck, Kayla and Masel, Joanna},
  journal      = {Evolution},
  number       = {12},
  pages        = {3357 -- 3367},
  publisher    = {Wiley-Blackwell},
  title        = {{Cryptic genetic variation can make "irreducible complexity" a common mode of adaptation in sexual populations}},
  doi          = {10.1111/evo.12517},
  volume       = {68},
  year         = {2014},
}

@article{1933,
  abstract     = {The development of the vertebrate brain requires an exquisite balance between proliferation and differentiation of neural progenitors. Notch signaling plays a pivotal role in regulating this balance, yet the interaction between signaling and receiving cells remains poorly understood. We have found that numerous nascent neurons and/or intermediate neurogenic progenitors expressing the ligand of Notch retain apical endfeet transiently at the ventricular lumen that form adherens junctions (AJs) with the endfeet of progenitors. Forced detachment of the apical endfeet of those differentiating cells by disrupting AJs resulted in precocious neurogenesis that was preceded by the downregulation of Notch signaling. Both Notch1 and its ligand Dll1 are distributed around AJs in the apical endfeet, and these proteins physically interact with ZO-1, a constituent of the AJ. Furthermore, live imaging of a fluorescently tagged Notch1 demonstrated its trafficking from the apical endfoot to the nucleus upon cleavage. Our results identified the apical endfoot as the central site of active Notch signaling to securely prohibit inappropriate differentiation of neural progenitors.},
  author       = {Hatakeyama, Jun and Wakamatsu, Yoshio and Nagafuchi, Akira and Kageyama, Ryoichiro and Shigemoto, Ryuichi and Shimamura, Kenji},
  journal      = {Development},
  number       = {8},
  pages        = {1671 -- 1682},
  publisher    = {Company of Biologists},
  title        = {{Cadherin-based adhesions in the apical endfoot are required for active Notch signaling to control neurogenesis in vertebrates}},
  doi          = {10.1242/dev.102988},
  volume       = {141},
  year         = {2014},
}

@article{1934,
  abstract     = {The plant hormones auxin and cytokinin mutually coordinate their activities to control various aspects of development [1-9], and their crosstalk occurs at multiple levels [10, 11]. Cytokinin-mediated modulation of auxin transport provides an efficient means to regulate auxin distribution in plant organs. Here, we demonstrate that cytokinin does not merely control the overall auxin flow capacity, but might also act as a polarizing cue and control the auxin stream directionality during plant organogenesis. Cytokinin enhances the PIN-FORMED1 (PIN1) auxin transporter depletion at specific polar domains, thus rearranging the cellular PIN polarities and directly regulating the auxin flow direction. This selective cytokinin sensitivity correlates with the PIN protein phosphorylation degree. PIN1 phosphomimicking mutations, as well as enhanced phosphorylation in plants with modulated activities of PIN-specific kinases and phosphatases, desensitize PIN1 to cytokinin. Our results reveal conceptually novel, cytokinin-driven polarization mechanism that operates in developmental processes involving rapid auxin stream redirection, such as lateral root organogenesis, in which a gradual PIN polarity switch defines the growth axis of the newly formed organ.},
  author       = {Marhavy, Peter and Duclercq, Jérôme and Weller, Benjamin and Feraru, Elena and Bielach, Agnieszka and Offringa, Remko and Friml, Jirí and Schwechheimer, Claus and Murphy, Angus and Benková, Eva},
  journal      = {Current Biology},
  number       = {9},
  pages        = {1031 -- 1037},
  publisher    = {Cell Press},
  title        = {{Cytokinin controls polarity of PIN1-dependent Auxin transport during lateral root organogenesis}},
  doi          = {10.1016/j.cub.2014.04.002},
  volume       = {24},
  year         = {2014},
}

@article{1935,
  abstract     = {We consider Ising models in d = 2 and d = 3 dimensions with nearest neighbor ferromagnetic and long-range antiferromagnetic interactions, the latter decaying as (distance)-p, p > 2d, at large distances. If the strength J of the ferromagnetic interaction is larger than a critical value J c, then the ground state is homogeneous. It has been conjectured that when J is smaller than but close to J c, the ground state is periodic and striped, with stripes of constant width h = h(J), and h → ∞ as J → Jc -. (In d = 3 stripes mean slabs, not columns.) Here we rigorously prove that, if we normalize the energy in such a way that the energy of the homogeneous state is zero, then the ratio e 0(J)/e S(J) tends to 1 as J → Jc -, with e S(J) being the energy per site of the optimal periodic striped/slabbed state and e 0(J) the actual ground state energy per site of the system. Our proof comes with explicit bounds on the difference e 0(J)-e S(J) at small but positive J c-J, and also shows that in this parameter range the ground state is striped/slabbed in a certain sense: namely, if one looks at a randomly chosen window, of suitable size ℓ (very large compared to the optimal stripe size h(J)), one finds a striped/slabbed state with high probability.},
  author       = {Giuliani, Alessandro and Lieb, Élliott and Seiringer, Robert},
  issn         = {1432-0916},
  journal      = {Communications in Mathematical Physics},
  pages        = {333 -- 350},
  publisher    = {Springer},
  title        = {{Formation of stripes and slabs near the ferromagnetic transition}},
  doi          = {10.1007/s00220-014-1923-2},
  volume       = {331},
  year         = {2014},
}

@article{1936,
  abstract     = {The social intelligence hypothesis states that the need to cope with complexities of social life has driven the evolution of advanced cognitive abilities. It is usually invoked in the context of challenges arising from complex intragroup structures, hierarchies, and alliances. However, a fundamental aspect of group living remains largely unexplored as a driving force in cognitive evolution: the competition between individuals searching for resources (producers) and conspecifics that parasitize their findings (scroungers). In populations of social foragers, abilities that enable scroungers to steal by outsmarting producers, and those allowing producers to prevent theft by outsmarting scroungers, are likely to be beneficial and may fuel a cognitive arms race. Using analytical theory and agent-based simulations, we present a general model for such a race that is driven by the producer-scrounger game and show that the race's plausibility is dramatically affected by the nature of the evolving abilities. If scrounging and scrounging avoidance rely on separate, strategy-specific cognitive abilities, arms races are short-lived and have a limited effect on cognition. However, general cognitive abilities that facilitate both scrounging and scrounging avoidance undergo stable, long-lasting arms races. Thus, ubiquitous foraging interactions may lead to the evolution of general cognitive abilities in social animals, without the requirement of complex intragroup structures.},
  author       = {Arbilly, Michal and Weissman, Daniel and Feldman, Marcus and Grodzinski, Uri},
  journal      = {Behavioral Ecology},
  number       = {3},
  pages        = {487 -- 495},
  publisher    = {Oxford University Press},
  title        = {{An arms race between producers and scroungers can drive the evolution of social cognition}},
  doi          = {10.1093/beheco/aru002},
  volume       = {25},
  year         = {2014},
}

@article{1937,
  abstract     = {We prove the edge universality of the beta ensembles for any β ≥ 1, provided that the limiting spectrum is supported on a single interval, and the external potential is C4 and regular. We also prove that the edge universality holds for generalized Wigner matrices for all symmetry classes. Moreover, our results allow us to extend bulk universality for beta ensembles from analytic potentials to potentials in class C4.},
  author       = {Bourgade, Paul and Erdös, László and Yau, Horngtzer},
  journal      = {Communications in Mathematical Physics},
  number       = {1},
  pages        = {261 -- 353},
  publisher    = {Springer},
  title        = {{Edge universality of beta ensembles}},
  doi          = {10.1007/s00220-014-2120-z},
  volume       = {332},
  year         = {2014},
}

@inproceedings{475,
  abstract     = {First cycle games (FCG) are played on a finite graph by two players who push a token along the edges until a vertex is repeated, and a simple cycle is formed. The winner is determined by some fixed property Y of the sequence of labels of the edges (or nodes) forming this cycle. These games are traditionally of interest because of their connection with infinite-duration games such as parity and mean-payoff games. We study the memory requirements for winning strategies of FCGs and certain associated infinite duration games. We exhibit a simple FCG that is not memoryless determined (this corrects a mistake in Memoryless determinacy of parity and mean payoff games: a simple proof by Bj⋯orklund, Sandberg, Vorobyov (2004) that claims that FCGs for which Y is closed under cyclic permutations are memoryless determined). We show that θ (n)! memory (where n is the number of nodes in the graph), which is always sufficient, may be necessary to win some FCGs. On the other hand, we identify easy to check conditions on Y (i.e., Y is closed under cyclic permutations, and both Y and its complement are closed under concatenation) that are sufficient to ensure that the corresponding FCGs and their associated infinite duration games are memoryless determined. We demonstrate that many games considered in the literature, such as mean-payoff, parity, energy, etc., satisfy these conditions. On the complexity side, we show (for efficiently computable Y) that while solving FCGs is in PSPACE, solving some families of FCGs is PSPACE-hard. },
  author       = {Aminof, Benjamin and Rubin, Sasha},
  booktitle    = {Electronic Proceedings in Theoretical Computer Science, EPTCS},
  location     = {Grenoble, France},
  pages        = {83 -- 90},
  publisher    = {Open Publishing Association},
  title        = {{First cycle games}},
  doi          = {10.4204/EPTCS.146.11},
  volume       = {146},
  year         = {2014},
}

@article{535,
  abstract     = {Energy games belong to a class of turn-based two-player infinite-duration games played on a weighted directed graph. It is one of the rare and intriguing combinatorial problems that lie in NP∩co-NP, but are not known to be in P. The existence of polynomial-time algorithms has been a major open problem for decades and apart from pseudopolynomial algorithms there is no algorithm that solves any non-trivial subclass in polynomial time. In this paper, we give several results based on the weight structures of the graph. First, we identify a notion of penalty and present a polynomial-time algorithm when the penalty is large. Our algorithm is the first polynomial-time algorithm on a large class of weighted graphs. It includes several worst-case instances on which previous algorithms, such as value iteration and random facet algorithms, require at least sub-exponential time. Our main technique is developing the first non-trivial approximation algorithm and showing how to convert it to an exact algorithm. Moreover, we show that in a practical case in verification where weights are clustered around a constant number of values, the energy game problem can be solved in polynomial time. We also show that the problem is still as hard as in general when the clique-width is bounded or the graph is strongly ergodic, suggesting that restricting the graph structure does not necessarily help.},
  author       = {Chatterjee, Krishnendu and Henzinger, Monika H and Krinninger, Sebastian and Nanongkai, Danupon},
  journal      = {Algorithmica},
  number       = {3},
  pages        = {457 -- 492},
  publisher    = {Springer},
  title        = {{Polynomial-time algorithms for energy games with special weight structures}},
  doi          = {10.1007/s00453-013-9843-7},
  volume       = {70},
  year         = {2014},
}

@article{537,
  abstract     = {Transgenerational effects are broader than only parental relationships. Despite mounting evidence that multigenerational effects alter phenotypic and life-history traits, our understanding of how they combine to determine fitness is not well developed because of the added complexity necessary to study them. Here, we derive a quantitative genetic model of adaptation to an extraordinary new environment by an additive genetic component, phenotypic plasticity, maternal and grandmaternal effects. We show how, at equilibrium, negative maternal and negative grandmaternal effects maximize expected population mean fitness. We define negative transgenerational effects as those that have a negative effect on trait expression in the subsequent generation, that is, they slow, or potentially reverse, the expected evolutionary dynamic. When maternal effects are positive, negative grandmaternal effects are preferred. As expected under Mendelian inheritance, the grandmaternal effects have a lower impact on fitness than the maternal effects, but this dual inheritance model predicts a more complex relationship between maternal and grandmaternal effects to constrain phenotypic variance and so maximize expected population mean fitness in the offspring.},
  author       = {Prizak, Roshan and Ezard, Thomas and Hoyle, Rebecca},
  journal      = {Ecology and Evolution},
  number       = {15},
  pages        = {3139 -- 3145},
  publisher    = {Wiley-Blackwell},
  title        = {{Fitness consequences of maternal and grandmaternal effects}},
  doi          = {10.1002/ece3.1150},
  volume       = {4},
  year         = {2014},
}

@misc{5411,
  abstract     = {Model-based testing is a promising technology for black-box software and hardware testing, in which test cases are generated automatically from high-level specifications. Nowadays, systems typically consist of multiple interacting components and, due to their complexity, testing presents a considerable portion of the effort and cost in the design process. Exploiting the compositional structure of system specifications can considerably reduce the effort in model-based testing. Moreover, inferring properties about the system from testing its individual components allows the designer to reduce the amount of integration testing.
In this paper, we study compositional properties of the IOCO-testing theory. We propose a new approach to composition and hiding operations, inspired by contract-based design and interface theories. These operations preserve behaviors that are compatible under composition and hiding, and prune away incompatible ones. The resulting specification characterizes the input sequences for which the unit testing of components is sufficient to infer the correctness of component integration without the need for further tests. We provide a methodology that uses these results to minimize integration testing effort, but also to detect potential weaknesses in specifications. While we focus on asynchronous models and the IOCO conformance relation, the resulting methodology can be applied to a broader class of systems.},
  author       = {Daca, Przemyslaw and Henzinger, Thomas A and Krenn, Willibald and Nickovic, Dejan},
  issn         = {2664-1690},
  pages        = {20},
  publisher    = {IST Austria},
  title        = {{Compositional specifications for IOCO testing}},
  doi          = {10.15479/AT:IST-2014-148-v2-1},
  year         = {2014},
}

@misc{5412,
  abstract     = {We consider Markov decision processes (MDPs) which are a standard model for probabilistic systems. We focus on qualitative properties for MDPs that can express that desired behaviors of the system arise almost-surely (with probability 1) or with positive probability.
We introduce a new simulation relation to capture the refinement relation of MDPs with respect to qualitative properties, and present discrete graph theoretic algorithms with quadratic complexity to compute the simulation relation.
We present an automated technique for assume-guarantee style reasoning for compositional analysis of MDPs with qualitative properties by giving a counter-example guided abstraction-refinement approach to compute our new simulation relation. We have implemented our algorithms and show that the compositional analysis leads to significant improvements. },
  author       = {Chatterjee, Krishnendu and Daca, Przemyslaw and Chmelik, Martin},
  issn         = {2664-1690},
  pages        = {31},
  publisher    = {IST Austria},
  title        = {{CEGAR for qualitative analysis of probabilistic systems}},
  doi          = {10.15479/AT:IST-2014-153-v1-1},
  year         = {2014},
}

@misc{5413,
  abstract     = {We consider Markov decision processes (MDPs) which are a standard model for probabilistic systems. We focus on qualitative properties for MDPs that can express that desired behaviors of the system arise almost-surely (with probability 1) or with positive probability.
We introduce a new simulation relation to capture the refinement relation of MDPs with respect to qualitative properties, and present discrete graph theoretic algorithms with quadratic complexity to compute the simulation relation.
We present an automated technique for assume-guarantee style reasoning for compositional analysis of MDPs with qualitative properties by giving a counter-example guided abstraction-refinement approach to compute our new simulation relation. We have implemented our algorithms and show that the compositional analysis leads to significant improvements. },
  author       = {Chatterjee, Krishnendu and Daca, Przemyslaw and Chmelik, Martin},
  issn         = {2664-1690},
  pages        = {33},
  publisher    = {IST Austria},
  title        = {{CEGAR for qualitative analysis of probabilistic systems}},
  doi          = {10.15479/AT:IST-2014-153-v2-2},
  year         = {2014},
}

@misc{5414,
  abstract     = {We consider Markov decision processes (MDPs) which are a standard model for probabilistic systems. We focus on qualitative properties for MDPs that can express that desired behaviors of the system arise almost-surely (with probability 1) or with positive probability.
We introduce a new simulation relation to capture the refinement relation of MDPs with respect to qualitative properties, and present discrete graph theoretic algorithms with quadratic complexity to compute the simulation relation.
We present an automated technique for assume-guarantee style reasoning for compositional analysis of MDPs with qualitative properties by giving a counter-example guided abstraction-refinement approach to compute our new simulation relation. 
We have implemented our algorithms and show that the compositional analysis leads to significant improvements. },
  author       = {Chatterjee, Krishnendu and Daca, Przemyslaw and Chmelik, Martin},
  issn         = {2664-1690},
  pages        = {33},
  publisher    = {IST Austria},
  title        = {{CEGAR for qualitative analysis of probabilistic systems}},
  doi          = {10.15479/AT:IST-2014-153-v3-1},
  year         = {2014},
}

@misc{5415,
  abstract     = {Recently there has been a significant effort to add quantitative properties in formal verification and synthesis. While weighted automata over finite and infinite words provide a natural and flexible framework to express quantitative properties, perhaps surprisingly, several basic system properties such as average response time cannot be expressed with weighted automata. In this work, we introduce nested weighted automata as a new formalism for expressing important quantitative properties such as average response time. We establish an almost complete decidability picture for the basic decision problems for nested weighted automata, and illustrate its applicability in several domains.  },
  author       = {Chatterjee, Krishnendu and Henzinger, Thomas A and Otop, Jan},
  issn         = {2664-1690},
  pages        = {27},
  publisher    = {IST Austria},
  title        = {{Nested weighted automata}},
  doi          = {10.15479/AT:IST-2014-170-v1-1},
  year         = {2014},
}

@misc{5416,
  abstract     = {As hybrid systems involve continuous behaviors, they should be evaluated by quantitative methods, rather than qualitative methods. In this paper we adapt a quantitative framework, called model measuring, to the hybrid systems domain. The model-measuring problem asks, given a model M and a specification, what is the maximal distance such that all models within that distance from M satisfy (or violate) the specification. A distance function on models is given as part of the input of the problem. Distances, especially related to continuous behaviors are more natural in the hybrid case than the discrete case. We are interested in distances represented by monotonic hybrid automata, a hybrid counterpart of (discrete) weighted automata, whose recognized timed languages are monotone (w.r.t. inclusion) in the values of parameters.The contributions of this paper are twofold. First, we give sufficient conditions under which the model-measuring problem can be solved. Second, we discuss the modeling of distances and applications of the model-measuring problem.},
  author       = {Henzinger, Thomas A and Otop, Jan},
  issn         = {2664-1690},
  pages        = {22},
  publisher    = {IST Austria},
  title        = {{Model measuring for hybrid systems}},
  doi          = {10.15479/AT:IST-2014-171-v1-1},
  year         = {2014},
}

@misc{5417,
  abstract     = {We define the model-measuring problem: given a model M and specification φ, what is the maximal distance ρ such that all models M'within distance ρ from M satisfy (or violate)φ. The model measuring problem presupposes a distance function on models. We concentrate on automatic distance functions, which are defined by weighted automata.
The model-measuring problem subsumes several generalizations of the classical model-checking problem, in particular, quantitative model-checking problems that measure the degree of satisfaction of a specification, and robustness problems that measure how much a model can be perturbed without violating the specification.
We show that for automatic distance functions, and ω-regular linear-time and branching-time specifications, the model-measuring problem can be solved.
We use automata-theoretic model-checking methods for model measuring, replacing the emptiness question for standard word and tree automata by the optimal-weight question for the weighted versions of these automata. We consider weighted automata that accumulate weights by maximizing, summing, discounting, and limit averaging. 
We give several examples of using the model-measuring problem to compute various notions of robustness and quantitative satisfaction for temporal specifications.},
  author       = {Henzinger, Thomas A and Otop, Jan},
  issn         = {2664-1690},
  pages        = {14},
  publisher    = {IST Austria},
  title        = {{From model checking to model measuring}},
  doi          = {10.15479/AT:IST-2014-172-v1-1},
  year         = {2014},
}

@misc{5418,
  abstract     = {We consider multi-player graph games with partial-observation and parity objective. While the decision problem for three-player games with a coalition of the first and second players against the third player is undecidable, we present a decidability result for partial-observation games where the first and third player are in a coalition against the second player, thus where the second player is adversarial but weaker due to partial-observation. We establish tight complexity bounds in the case where player 1 is less informed than player 2, namely 2-EXPTIME-completeness for parity objectives. The symmetric case of player 1 more informed than player 2 is much more complicated, and we show that already in the case where player 1 has perfect observation, memory of size non-elementary is necessary in general for reachability objectives, and the problem is decidable for safety and reachability objectives. Our results have tight connections with partial-observation stochastic games for which we derive new complexity results.},
  author       = {Chatterjee, Krishnendu and Doyen, Laurent},
  issn         = {2664-1690},
  pages        = {18},
  publisher    = {IST Austria},
  title        = {{Games with a weak adversary}},
  doi          = {10.15479/AT:IST-2014-176-v1-1},
  year         = {2014},
}