4,505 research outputs found
Inference algorithms for gene networks: a statistical mechanics analysis
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
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
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
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
- …