TY - JOUR AB - 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. AU - Chatterjee, Krishnendu AU - Zufferey, Damien AU - Nowak, Martin ID - 2848 JF - Journal of Theoretical Biology TI - Evolutionary game dynamics in populations with different learners VL - 301 ER - TY - JOUR AU - Edelsbrunner, Herbert AU - Strelkova, Nataliya ID - 2849 IS - 6 JF - Russian Mathematical Surveys TI - On the configuration space of Steiner minimal trees VL - 67 ER - TY - JOUR AB - Cytokinin (CK) activity is regulated by the complex interplay of their metabolism, transport, stability and cellular/tissue localization. O-glucosides of zeatin-type CKs are postulated to be storage and/or transport forms. Active CK levels are determined in part by their differential distribution of CK metabolites across different subcellular compartments. We have previously shown that overexpressing chloroplast-localized Zm-p60.1, a maize β-glucosidase capable of releasing active cytokinins from their O- and N3-glucosides, perturbs CK homeostasis in transgenic tobacco. We obtained tobacco (Nicotiana tabacum L., cv Petit Havana SR1) plants overexpressing a recombinant Zm-p60.1 that is targeted to the vacuole. The protein is correctly processed and localized to the vacuole. When grown on medium containing exogenous zeatin, transgenic seedlings rapidly accumulate fresh weight due to ectopic growths at the base of the hypocotyl. The presence of the enzyme in these ectopic structures is shown by histochemical staining. CK quantification reveals that these transgenic seedlings are unable to accumulate zeatin-O-glucoside to levels similar to those observed in the wild type. When crossed with tobacco overexpressing the zeatin-O-glucosyltransferase gene from Phaseolus, the vacuolar variant shows an almost complete reversion in the root elongation assay. This is the first evidence from intact plants that the vacuole is the storage organelle for CK O-glucosides and that they are available to attack by Zm-p60.1. We propose the use of Zm-p60.1 as a robust molecular tool that exploits the reversibility of O-glucosylation and enables delicate manipulations of active CK content at the cellular level. AU - Kiran, Nagavalli S AU - Eva Benková AU - Reková, Alena AU - Dubová, Jaroslava AU - Malbeck, Jiří AU - Palme, Klaus AU - Brzobohatý, Břetislav ID - 2876 JF - Phytochemistry TI - Retargeting a maize β-glucosidase to the vacuole - Evidence from intact plants that zeatin-O-glucoside is stored in the vacuole VL - 79 ER - TY - JOUR AB - Phytohormones are important plant growth regulators that control many developmental processes, such as cell division, cell differentiation, organogenesis and morphogenesis. They regulate a multitude of apparently unrelated physiological processes, often with overlapping roles, and they mutually modulate their effects. These features imply important synergistic and antagonistic interactions between the various plant hormones. Auxin and cytokinin are central hormones involved in the regulation of plant growth and development, including processes determining root architecture, such as root pole establishment during early embryogenesis, root meristem maintenance and lateral root organogenesis. Thus, to control root development both pathways put special demands on the mechanisms that balance their activities and mediate their interactions. Here, we summarize recent knowledge on the role of auxin and cytokinin in the regulation of root architecture with special focus on lateral root organogenesis, discuss the latest findings on the molecular mechanisms of their interactions, and present forward genetic screen as a tool to identify novel molecular components of the auxin and cytokinin crosstalk. AU - Bielach, Agnieszka AU - Duclercq, Jérôme AU - Peter Marhavy AU - Eva Benková ID - 2875 IS - 1595 JF - Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences TI - Genetic approach towards the identification of auxin - cytokinin crosstalk components involved in root development VL - 367 ER - TY - JOUR AB - Phyllotaxis, the regular arrangement of leaves and flowers around the stem, is a key feature of plant architecture. Current models propose that the spatiotemporal regulation of organ initiation is controlled by a positive feedback loop between the plant hormone auxin and its efflux carrier PIN-FORMED1 (PIN1). Consequently, pin1 mutants give rise to naked inflorescence stalks with few or no flowers, indicating that PIN1 plays a crucial role in organ initiation. However, pin1 mutants do produce leaves. In order to understand the regulatory mechanisms controlling leaf initiation in Arabidopsis (Arabidopsis thaliana) rosettes, we have characterized the vegetative pin1 phenotype in detail. We show that although the timing of leaf initiation in vegetative pin1 mutants is variable and divergence angles clearly deviate from the canonical 137° value, leaves are not positioned at random during early developmental stages. Our data further indicate that other PIN proteins are unlikely to explain the persistence of leaf initiation and positioning during pin1 vegetative development. Thus, phyllotaxis appears to be more complex than suggested by current mechanistic models. AU - Guenot, Bernadette AU - Bayer, Emmanuelle AU - Kierzkowski, Daniel AU - Smith, Richard S AU - Mandel, Therese AU - Žádníková, Petra AU - Eva Benková AU - Kuhlemeier, Cris ID - 2878 IS - 4 JF - Plant Physiology TI - Pin1 independent leaf initiation in Arabidopsis VL - 159 ER - TY - JOUR AB - Hormones, such as auxin and cytokinin, are involved in the complex molecular network that regulates the coordinated development of plant organs. Genes controlling ovule patterning have been identified and studied in detail; however, the roles of auxin and cytokinin in ovule development are largely unknown. Here we show that key cytokinin pathway genes, such as isopentenyltransferase and cytokinin receptors, are expressed during ovule development. Also, in a cre1-12 ahk2-2 ahk3-3 triple mutant with severely reduced cytokinin perception, expression of the auxin efflux facilitator PIN-FORMED 1 (PIN1) was severely reduced. In sporocyteless/nozzle (spl/nzz) mutants, which show a similar phenotype to the cre1-12 ahk2-2 ahk3-3 triple mutant, PIN1 expression is also reduced. Treatment with the exogenous cytokinin N6-benzylaminopurine also altered both auxin distribution and patterning of the ovule; this process required the homeodomain transcription factor BELL1 (BEL1). Thus, this article shows that cytokinin regulates ovule development through the regulation of PIN1. Furthermore, the transcription factors BEL1 and SPL/NZZ, previously described as key regulators of ovule development, are needed for the auxin and cytokinin signaling pathways for the correct patterning of the ovule. AU - Bencivenga, Stefano AU - Simonini, Sara AU - Eva Benková AU - Colombo, Lucia ID - 2879 IS - 7 JF - Plant Cell TI - The transcription factors BEL1 and SPL are required for cytokinin and auxin signaling during ovule development in Arabidopsis VL - 24 ER - TY - CONF AB - Quantitative automata are nondeterministic finite automata with edge weights. They value a run by some function from the sequence of visited weights to the reals, and value a word by its minimal/maximal run. They generalize boolean automata, and have gained much attention in recent years. Unfortunately, important automaton classes, such as sum, discounted-sum, and limit-average automata, cannot be determinized. Yet, the quantitative setting provides the potential of approximate determinization. We define approximate determinization with respect to a distance function, and investigate this potential. We show that sum automata cannot be determinized approximately with respect to any distance function. However, restricting to nonnegative weights allows for approximate determinization with respect to some distance functions. Discounted-sum automata allow for approximate determinization, as the influence of a word’s suffix is decaying. However, the naive approach, of unfolding the automaton computations up to a sufficient level, is shown to be doubly exponential in the discount factor. We provide an alternative construction that is singly exponential in the discount factor, in the precision, and in the number of states. We prove matching lower bounds, showing exponential dependency on each of these three parameters. Average and limit-average automata are shown to prohibit approximate determinization with respect to any distance function, and this is the case even for two weights, 0 and 1. AU - Boker, Udi AU - Henzinger, Thomas A ID - 2891 T2 - Leibniz International Proceedings in Informatics TI - Approximate determinization of quantitative automata VL - 18 ER - TY - CONF AB - 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. AU - Cerny, Pavol AU - Gopi, Sivakanth AU - Henzinger, Thomas A AU - Radhakrishna, Arjun AU - Totla, Nishant ID - 2890 T2 - Proceedings of the tenth ACM international conference on Embedded software TI - Synthesis from incompatible specifications ER - TY - CONF AB - 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. AU - Henzinger, Thomas A ID - 2888 T2 - Conference proceedings MODELS 2012 TI - Quantitative reactive models VL - 7590 ER - TY - CONF AB - In order to enjoy a digital version of the Jordan Curve Theorem, it is common to use the closed topology for the foreground and the open topology for the background of a 2-dimensional binary image. In this paper, we introduce a single topology that enjoys this theorem for all thresholds decomposing a real-valued image into foreground and background. This topology is easy to construct and it generalizes to n-dimensional images. AU - Edelsbrunner, Herbert AU - Symonova, Olga ID - 2903 TI - The adaptive topology of a digital image ER - TY - CONF AB - The classical (boolean) notion of refinement for behavioral interfaces of system components is the alternating refinement preorder. In this paper, we define a quantitative measure for interfaces, called interface simulation distance. It makes the alternating refinement preorder quantitative by, intu- itively, tolerating errors (while counting them) in the alternating simulation game. We show that the interface simulation distance satisfies the triangle inequality, that the distance between two interfaces does not increase under parallel composition with a third interface, and that the distance between two interfaces can be bounded from above and below by distances between abstractions of the two interfaces. We illustrate the framework, and the properties of the distances under composition of interfaces, with two case studies. AU - Cerny, Pavol AU - Chmelik, Martin AU - Henzinger, Thomas A AU - Radhakrishna, Arjun ID - 2916 T2 - Electronic Proceedings in Theoretical Computer Science TI - Interface Simulation Distances VL - 96 ER - TY - JOUR AB - The search for extra-terrestrial intelligence (SETI) has been performed principally as a one-way survey, listening of radio frequencies across the Milky Way and other galaxies. However, scientists have engaged in an active messaging only rarely. This suggests the simple rationale that if other civilizations exist and take a similar approach to ours, namely listening but not broadcasting, the result is a silent universe. A simple game theoretical model, the prisoner's dilemma, explains this situation: each player (civilization) can passively search (defect), or actively search and broadcast (cooperate). In order to maximize the payoff (or, equivalently, minimize the risks) the best strategy is not to broadcast. In fact, the active search has been opposed on the basis that it might be dangerous to expose ourselves. However, most of these ideas have not been based on objective arguments, and ignore accounting of the possible gains and losses. Thus, the question stands: should we perform an active search? I develop a game-theoretical framework where civilizations can be of different types, and explicitly apply it to a situation where societies are either interested in establishing a two-way communication or belligerent and in urge to exploit ours. The framework gives a quantitative solution (a mixed-strategy), which is how frequent we should perform the active SETI. This frequency is roughly proportional to the inverse of the risk, and can be extremely small. However, given the immense amount of stars being scanned, it supports active SETI. The model is compared with simulations, and the possible actions are evaluated through the San Marino scale, measuring the risks of messaging. AU - Vladar, Harold ID - 2917 IS - 1 JF - International Journal of Astrobiology TI - The game of active search for extra terrestrial intelligence Breaking the Great Silence VL - 12 ER - TY - JOUR AB - We have selected problems that may not yet be well known, but have the potential to push the research in interesting directions. In particular, we state problems that do not require specific knowledge outside the standard circle of ideas in discrete geometry. Despite the relatively simple statements, these problems are related to current research and their solutions are likely to require new ideas and approaches. We have chosen problems from different fields to make this short paper attractive to a wide range of specialists. AU - Herbert Edelsbrunner AU - Ivanov, Alexander AU - Karasev, Roman ID - 2911 JF - Automatic Control and Computer Sciences TI - Open problems in discrete and computational geometry VL - in print ER - TY - CONF AB - In this paper we investigate k-submodular functions. This natural family of discrete functions includes submodular and bisubmodular functions as the special cases k = 1 and k = 2 respectively. In particular we generalize the known Min-Max-Theorem for submodular and bisubmodular functions. This theorem asserts that the minimum of the (bi)submodular function can be found by solving a maximization problem over a (bi)submodular polyhedron. We define a k-submodular polyhedron, prove a Min-Max-Theorem for k-submodular functions, and give a greedy algorithm to construct the vertices of the polyhedron. AU - Huber, Anna AU - Kolmogorov, Vladimir ID - 2930 TI - Towards minimizing k-submodular functions VL - 7422 ER - TY - GEN AB - This paper addresses the problem of approximate MAP-MRF inference in general graphical models. Following [36], we consider a family of linear programming relaxations of the problem where each relaxation is specified by a set of nested pairs of factors for which the marginalization constraint needs to be enforced. We develop a generalization of the TRW-S algorithm [9] for this problem, where we use a decomposition into junction chains, monotonic w.r.t. some ordering on the nodes. This generalizes the monotonic chains in [9] in a natural way. We also show how to deal with nested factors in an efficient way. Experiments show an improvement over min-sum diffusion, MPLP and subgradient ascent algorithms on a number of computer vision and natural language processing problems. AU - Kolmogorov, Vladimir AU - Schoenemann, Thomas ID - 2928 T2 - arXiv TI - Generalized sequential tree-reweighted message passing ER - TY - GEN AU - Vladimir Kolmogorov ID - 2929 TI - The power of linear programming for valued CSPs: a constructive characterization ER - TY - CONF AB - Developers building cryptography into security-sensitive applications face a daunting task. Not only must they understand the security guarantees delivered by the constructions they choose, they must also implement and combine them correctly and efficiently. Cryptographic compilers free developers from this task by turning high-level specifications of security goals into efficient implementations. Yet, trusting such tools is hard as they rely on complex mathematical machinery and claim security properties that are subtle and difficult to verify. In this paper we present ZKCrypt, an optimizing cryptographic compiler achieving an unprecedented level of assurance without sacrificing practicality for a comprehensive class of cryptographic protocols, known as Zero-Knowledge Proofs of Knowledge. The pipeline of ZKCrypt integrates purpose-built verified compilers and verifying compilers producing formal proofs in the CertiCrypt framework. By combining the guarantees delivered by each stage, ZKCrypt provides assurance that the output implementation securely realizes the abstract proof goal given as input. We report on the main characteristics of ZKCrypt, highlight new definitions and concepts at its foundations, and illustrate its applicability through a representative example of an anonymous credential system. AU - Almeida, José AU - Barbosa, Manuel AU - Bangerter, Endre AU - Barthe, Gilles AU - Krenn, Stephan AU - Béguelin, Santiago ID - 2937 T2 - Proceedings of the 2012 ACM conference on Computer and communications security TI - Full proof cryptography: Verifiable compilation of efficient zero-knowledge protocols ER - TY - CONF AB - The notion of delays arises naturally in many computational models, such as, in the design of circuits, control systems, and dataflow languages. In this work, we introduce automata with delay blocks (ADBs), extending finite state automata with variable time delay blocks, for deferring individual transition output symbols, in a discrete-time setting. We show that the ADB languages strictly subsume the regular languages, and are incomparable in expressive power to the context-free languages. We show that ADBs are closed under union, concatenation and Kleene star, and under intersection with regular languages, but not closed under complementation and intersection with other ADB languages. We show that the emptiness and the membership problems are decidable in polynomial time for ADBs, whereas the universality problem is undecidable. Finally we consider the linear-time model checking problem, i.e., whether the language of an ADB is contained in a regular language, and show that the model checking problem is PSPACE-complete. Copyright 2012 ACM. AU - Chatterjee, Krishnendu AU - Henzinger, Thomas A AU - Prabhu, Vinayak ID - 2936 T2 - roceedings of the tenth ACM international conference on Embedded software TI - Finite automata with time delay blocks ER - TY - JOUR AB - Social insects have a very high potential to become invasive pest species. Here, we explore how their social lifestyle and their interaction with parasites may contribute to this invasive success. Similar to solitary species, parasite release followed by the evolution of increased competitive ability can promote establishment of introduced social insect hosts in their introduced range. Genetic bottlenecks during introduction of low numbers of founder individuals decrease the genetic diversity at three levels: the population, the colony and the individual, with the colony level being specific to social insects. Reduced genetic diversity can affect both the individual immune system and the collective colony-level disease defences (social immunity). Still, the dual immune system is likely to make social insects more robust to parasite attack. Changes in social structure from small, family-based, territorially aggressive societies in native populations towards huge networks of cooperating nests (unicoloniality) occur in some invasive social insects, for example, most invasive ants and some termites. Unicoloniality is likely to affect disease dynamics in multiple ways. The free exchange of individuals within the population leads to an increased genetic heterogeneity among individuals of a single nest, thereby decreasing disease transmission. However, the multitude of reproductively active queens per colony buffers the effect of individual diseased queens and their offspring, which may result in a higher level of vertical disease transmission in unicolonial societies. Lastly, unicoloniality provides a competitive advantage over native species, allowing them to quickly become the dominant species in the habitat, which in turn selects for parasite adaptation to this common host genotype and thus eventually a high parasite pressure. Overall, invasions by insect societies are characterized by general features applying to all introduced species, as well as idiosyncrasies that emerge from their social lifestyle. It is important to study these effects in concert to be able to develop efficient management and biocontrol strategies. © 2012 British Ecological Society. AU - Ugelvig, Line V AU - Cremer, Sylvia ID - 2938 IS - 6 JF - Functional Ecology TI - Effects of social immunity and unicoloniality on host parasite interactions in invasive insect societies VL - 26 ER - TY - JOUR AB - In this paper, we present a new approach for establishing correspondences between sparse image features related by an unknown nonrigid mapping and corrupted by clutter and occlusion, such as points extracted from images of different instances of the same object category. We formulate this matching task as an energy minimization problem by defining an elaborate objective function of the appearance and the spatial arrangement of the features. Optimization of this energy is an instance of graph matching, which is in general an NP-hard problem. We describe a novel graph matching optimization technique, which we refer to as dual decomposition (DD), and demonstrate on a variety of examples that this method outperforms existing graph matching algorithms. In the majority of our examples, DD is able to find the global minimum within a minute. The ability to globally optimize the objective allows us to accurately learn the parameters of our matching model from training examples. We show on several matching tasks that our learned model yields results superior to those of state-of-the-art methods. AU - Torresani, Lorenzo AU - Kolmogorov, Vladimir AU - Rother, Carsten ID - 2931 IS - 2 JF - IEEE Transactions on Pattern Analysis and Machine Intelligence TI - A dual decomposition approach to feature correspondence VL - 35 ER -