4,505 research outputs found

    Inference algorithms for gene networks: a statistical mechanics analysis

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    The inference of gene regulatory networks from high throughput gene expression data is one of the major challenges in systems biology. This paper aims at analysing and comparing two different algorithmic approaches. The first approach uses pairwise correlations between regulated and regulating genes; the second one uses message-passing techniques for inferring activating and inhibiting regulatory interactions. The performance of these two algorithms can be analysed theoretically on well-defined test sets, using tools from the statistical physics of disordered systems like the replica method. We find that the second algorithm outperforms the first one since it takes into account collective effects of multiple regulators

    Disappearance of Spurious States in Analog Associative Memories

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    We show that symmetric n-mixture states, when they exist, are almost never stable in autoassociative networks with threshold-linear units. Only with a binary coding scheme we could find a limited region of the parameter space in which either 2-mixtures or 3-mixtures are stable attractors of the dynamics.Comment: 5 pages, 3 figures, accepted for publication in Phys Rev

    Statistical thermodynamics for choice models on graphs

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    Formalism based on equilibrium statistical thermodynamics is applied to communication networks of decision making individuals. It is shown that in statistical ensembles for choice models, properly defined disutility can play the same role as energy in statistical mechanics. We demonstrate additivity and extensivity of disutility and build three types of equilibrium statistical ensembles: the canonical, the grand canonical and the super-canonical. Using Boltzmann-like probability measure one reproduce the logit choice model. We also propose using q-distributions for temperature evolution of moments of stochastic variables. The formalism is applied to three network topologies of different degrees of symmetry, for which in many cases analytic results are obtained and numerical simulations are performed for all of them. Possible applications of the model to airline networks and its usefulness for practical support of economic decisions is pointed out.Comment: 17 pages, 13 figure

    Evolutionary prisoner's dilemma games with optional participation

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    Competition among cooperators, defectors, and loners is studied in an evolutionary prisoner's dilemma game with optional participation. Loners are risk averse i.e. unwilling to participate and rather rely on small but fixed earnings. This results in a rock-scissors-paper type cyclic dominance of the three strategies. The players are located either on square lattices or random regular graphs with the same connectivity. Occasionally, every player reassesses its strategy by sampling the payoffs in its neighborhood. The loner strategy efficiently prevents successful spreading of selfish, defective behavior and avoids deadlocks in states of mutual defection. On square lattices, Monte Carlo simulations reveal self-organizing patterns driven by the cyclic dominance, whereas on random regular graphs different types of oscillatory behavior are observed: the temptation to defect determines whether damped, periodic or increasing oscillations occur. These results are compared to predictions by pair approximation. Although pair approximation is incapable of distinguishing the two scenarios because of the equal connectivity, the average frequencies as well as the oscillations on random regular graphs are well reproduced.Comment: 6 pages, 7 figure
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