1,721,024 research outputs found
From random point processes to hierarchical cavity master equations for stochastic dynamics of disordered systems in random graphs: Ising models and epidemics
Get PDFWe start from the theory of random point processes to derive n-point coupled master equations describing the continuous dynamics of discrete variables in random graphs. These equations constitute a hierarchical set of approximations that generalize and improve the cavity master equation (CME), a recently obtained closure for the usual master equation representing the dynamics. Our derivation clarifies some of the hypotheses and approximations that originally led to the CME, considered now as the first order of a more general technique. We tested the scheme in the dynamics of three models defined over diluted graphs: the Ising ferromagnet, the Viana-Bray spin-glass, and the susceptible-infectious-susceptible model for epidemics. In the first two, the equations perform similarly to the best-known approaches in literature. In the latter, they outperform the well-known pair quenched mean-field approximation
The cavity master equation: average and fixed point of the ferromagnetic model in random graphs
No full textThe cavity master equation (CME) is a closure scheme to the usual master equation representing the dynamics of discrete variables in continuous time. In this work we explore the CME for a ferromagnetic model in a random graph. We first derive and average equation of the CME that describes the dynamics of mean magnetization of the system. We show that the numerical results compare remarkably well with the Monte Carlo simulations. Then, we show that the stationary state of the CME is well described by BP-like equations (independently of the dynamic rules that let the system toward the stationary state). These equations may be rewritten exactly as the fixed point solutions of the cavity equation if one also assumes that the stationary state is well described by a Boltzmann distribution
Estimating the size of the solution space of metabolic networks
Get PDFAbstract Background Cellular metabolism is one of the most investigated system of biological interactions. While the topological nature of individual reactions and pathways in the network is quite well understood there is still a lack of comprehension regarding the global functional behavior of the system. In the last few years flux-balance analysis (FBA) has been the most successful and widely used technique for studying metabolism at system level. This method strongly relies on the hypothesis that the organism maximizes an objective function. However only under very specific biological conditions (e.g. maximization of biomass for E. coli in reach nutrient medium) the cell seems to obey such optimization law. A more refined analysis not assuming extremization remains an elusive task for large metabolic systems due to algorithmic limitations. Results In this work we propose a novel algorithmic strategy that provides an efficient characterization of the whole set of stable fluxes compatible with the metabolic constraints. Using a technique derived from the fields of statistical physics and information theory we designed a message-passing algorithm to estimate the size of the affine space containing all possible steady-state flux distributions of metabolic networks. The algorithm, based on the well known Bethe approximation, can be used to approximately compute the volume of a non full-dimensional convex polytope in high dimensions. We first compare the accuracy of the predictions with an exact algorithm on small random metabolic networks. We also verify that the predictions of the algorithm match closely those of Monte Carlo based methods in the case of the Red Blood Cell metabolic network. Then we test the effect of gene knock-outs on the size of the solution space in the case of E. coli central metabolism. Finally we analyze the statistical properties of the average fluxes of the reactions in the E. coli metabolic network. Conclusion We propose a novel efficient distributed algorithmic strategy to estimate the size and shape of the affine space of a non full-dimensional convex polytope in high dimensions. The method is shown to obtain, quantitatively and qualitatively compatible results with the ones of standard algorithms (where this comparison is possible) being still efficient on the analysis of large biological systems, where exact deterministic methods experience an explosion in algorithmic time. The algorithm we propose can be considered as an alternative to Monte Carlo sampling methods.</p
Modeling the neural activity of Caenorhabditis elegans through neural message passing
Get PDFThe great complexity of the human connectome motivates the study of a simpler neural network. For that purpose, the Ising Model was applied on experimental data on the synaptic connectivity of Caenorhabditis elegans (C. elegans) in resting-state, assigning a binary variable (representing active or inactive states) to each neuron in the network. The dynamics of this system is postulated as a message passing network, encoded by the Belief Propagation algorithm (BP) in its criticality region. The inferences of neuronal activity maps were obtained for different times of the nematode’s life cycle. We determined the network susceptibilities as a measure of correlations in the system through the Susceptibility Propagation algorithm (SP). Finally, we applied clustering methods to obtain functional clusters and analyze similarities between them and the real functional clusters (sensory, interneurons and motor). All this contributed to the analysis of structure-function relationship in the C. elegans neural network
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
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