Multi-surface coding simulations of the restricted solid-on-solid model in four dimensions

We study the Restricted Solid on Solid (RSOS) model for surface growth in spatial dimension d=4 by means of a multi-surface coding technique that allows to analyze samples to analyze samples of size up to $256^4$ in the steady state regime. For such large systems we are able to achieve a controlled asymptotic regime where the typical scale of the fluctuations are larger than the lattice spacing used in the simulations. A careful finite-size scaling analysis of the critical exponents clearly indicate that d=4 is not the upper critical dimension of the model.Comment: 6 pages, 3 pdf figures, changed title and minor changes in the abstract, added some references. This is the published versio

Numerical estimate of the Kardar Parisi Zhang universality class in (2 + 1) dimensions

We study the Restricted Solid on Solid model for surface growth in spatial dimension $d=2$ by means of a multi-surface coding technique that allows to produce a large number of samples of samples in the stationary regime in a reasonable computational time. Thanks to: (i) a careful finite-size scaling analysis of the critical exponents, (ii) the accurate estimate of the first three moments of the height fluctuations, we can quantify the wandering exponent with unprecedented precision: $\chi_{d=2} = 0.3869(4)$. This figure is incompatible with the long-standing conjecture due to Kim and Koesterlitz that hypothesized $\chi_{d=2}=2/5$.Comment: 4 pages, 4 figure

Threshold values, stability analysis and high-q asymptotics for the coloring problem on random graphs

We consider the problem of coloring Erdos-Renyi and regular random graphs of finite connectivity using q colors. It has been studied so far using the cavity approach within the so-called one-step replica symmetry breaking (1RSB) ansatz. We derive a general criterion for the validity of this ansatz and, applying it to the ground state, we provide evidence that the 1RSB solution gives exact threshold values c_q for the q-COL/UNCOL phase transition. We also study the asymptotic thresholds for q >> 1 finding c_q = 2qlog(q)-log(q)-1+o(1) in perfect agreement with rigorous mathematical bounds, as well as the nature of excited states, and give a global phase diagram of the problem.Comment: 23 pages, 10 figures. Replaced with accepted versio

Estimating the size of the solution space of metabolic networks

In this work we propose a novel algorithmic strategy that allows for an efficient characterization of the whole set of stable fluxes compatible with the metabolic constraints. The algorithm, based on the well-known Bethe approximation, allows the computation in polynomial time of the volume of a non full-dimensional convex polytope in high dimensions. The result of our algorithm match closely the prediction of Monte Carlo based estimations of the flux distributions of the Red Blood Cell metabolic network but in incomparably shorter time. We also analyze the statistical properties of the average fluxes of the reactions in the E-Coli metabolic network and finally to test the effect of gene knock-outs on the size of the solution space of the E-Coli central metabolism.Comment: 8 pages, 7 pdf figure

Statistical mechanics of sparse generalization and model selection

One of the crucial tasks in many inference problems is the extraction of sparse information out of a given number of high-dimensional measurements. In machine learning, this is frequently achieved using, as a penality term, the $L_p$ norm of the model parameters, with $p\leq 1$ for efficient dilution. Here we propose a statistical-mechanics analysis of the problem in the setting of perceptron memorization and generalization. Using a replica approach, we are able to evaluate the relative performance of naive dilution (obtained by learning without dilution, following by applying a threshold to the model parameters), $L_1$ dilution (which is frequently used in convex optimization) and $L_0$ dilution (which is optimal but computationally hard to implement). Whereas both $L_p$ diluted approaches clearly outperform the naive approach, we find a small region where $L_0$ works almost perfectly and strongly outperforms the simpler to implement $L_1$ dilution.Comment: 18 pages, 9 eps figure

An analytic approximation of the feasible space of metabolic networks

Assuming a steady-state condition within a cell, metabolic fluxes satisfy an under-determined linear system of stoichiometric equations. Characterizing the space of fluxes that satisfy such equations along with given bounds (and possibly additional relevant constraints) is considered of utmost importance for the understanding of cellular metabolism. Extreme values for each individual flux can be computed with Linear Programming (as Flux Balance Analysis), and their marginal distributions can be approximately computed with Monte-Carlo sampling. Here we present an approximate analytic method for the latter task based on Expectation Propagation equations that does not involve sampling and can achieve much better predictions than other existing analytic methods. The method is iterative, and its computation time is dominated by one matrix inversion per iteration. With respect to sampling, we show through extensive simulation that it has some advantages including computation time, and the ability to efficiently fix empirically estimated distributions of fluxes

Propagation of external regulation and asynchronous dynamics in random Boolean networks

Boolean Networks and their dynamics are of great interest as abstract modeling schemes in various disciplines, ranging from biology to computer science. Whereas parallel update schemes have been studied extensively in past years, the level of understanding of asynchronous updates schemes is still very poor. In this paper we study the propagation of external information given by regulatory input variables into a random Boolean network. We compute both analytically and numerically the time evolution and the asymptotic behavior of this propagation of external regulation (PER). In particular, this allows us to identify variables which are completely determined by this external information. All those variables in the network which are not directly fixed by PER form a core which contains in particular all non-trivial feedback loops. We design a message-passing approach allowing to characterize the statistical properties of these cores in dependence of the Boolean network and the external condition. At the end we establish a link between PER dynamics and the full random asynchronous dynamics of a Boolean network.Comment: 19 pages, 14 figures, to appear in Chao

Stability of the replica symmetric solution in diluted perceptron learning

We study the role played by the dilution in the average behavior of a perceptron model with continuous coupling with the replica method. We analyze the stability of the replica symmetric solution as a function of the dilution field for the generalization and memorization problems. Thanks to a Gardner like stability analysis we show that at any fixed ratio $\alpha$ between the number of patterns M and the dimension N of the perceptron ($\alpha=M/N$), there exists a critical dilution field $h_c$ above which the replica symmetric ansatz becomes unstable.Comment: Stability of the solution in arXiv:0907.3241, 13 pages, (some typos corrected