Papers by Valery Van Kerrebroeck
22pVC-12 Probabilistic Model for Cycles in Planar Graph
Meeting Abstracts of the Physical Society of Japan (Nihon Butsuri Gakkai koen gaiyoshu), 2008
22pVC-12 平面グラフ上の閉路と確率モデル(22pVC 情報統計力学,領域11(統計力学,物性基礎論,応用数学,力学,流体物理))
日本物理学会講演概要集, Aug 25, 2008
Journal of Biomedicine and Biotechnology, 2010
Characterizing the capabilities, key dependencies, and response to perturbations of genome-scale ... more Characterizing the capabilities, key dependencies, and response to perturbations of genome-scale metabolic networks is a basic problem with important applications. A key question concerns the identification of the potentially most harmful reaction knockouts. The integration of combinatorial methods with sampling techniques to explore the space of viable flux states may provide crucial insights on this issue. We assess the replaceability of every metabolic conversion in the human red blood cell by enumerating the alternative paths from substrate to product, obtaining a complete map of he potential damage of single enzymopathies. Sampling the space of optimal steady state fluxes in the healthy and in the mutated cell reveals both correlations and complementarity between topologic and dynamical aspects.
Motivation: Characterizing the capabilities, criticalities and response to perturbations of genom... more Motivation: Characterizing the capabilities, criticalities and response to perturbations of genome-scale metabolic networks is a basic problem with important applications. A key question concerns the identification of the potentially most harmful knockouts. The integration of combinatorial methods with sampling techniques to explore the space of viable flux states may provide crucial insights on this issue. Results: We assess the replaceability of every metabolic conversion in the human red blood cell by enumerating the alternative paths from substrate to product, obtaining a complete map of the potential damage of single enzymopathies. Sampling the space of optimal flux states in the healthy and in the mutated cell reveals both correlations and complementarity between topologic and dynamical aspects. Availability: Related material (stoichiometric matrices, C codes, optimal flux configurations and the detailed structure of alternative paths) is available from
Physical Review Letters, Aug 1, 2008
We introduce Loop Ranking, a new ranking measure based on the detection of closed paths, which ca... more We introduce Loop Ranking, a new ranking measure based on the detection of closed paths, which can be computed in an efficient way. We analyze it with respect to several ranking measures which have been proposed in the past, and are widely used to capture the relative importance of the vertices in complex networks. We argue that Loop Ranking is a very appropriate measure to quantify the role of both vertices and edges in the network traffic.
We introduce Loop Ranking, a new ranking measure based on the detection of closed paths, which ca... more We introduce Loop Ranking, a new ranking measure based on the detection of closed paths, which can be computed in an efficient way. We analyze it with respect to several ranking measures which have been proposed in the past, and are widely used to capture the relative importance of the vertices in complex networks. We argue that Loop Ranking is a very appropriate measure to quantify the role of both vertices and edges in the network traffic.
Interdisciplinary Information Sciences, 2009
We study a probabilistic model for single connected cycles on an undirected planar graph for whic... more We study a probabilistic model for single connected cycles on an undirected planar graph for which the degree of every vertex is restricted to two or three. By using a diagrammatical method to solve a free fermion model, we derive the exact expression of the partition function as well as marginal probabilities. We compare the exact results for the marginals with the approximations obtained with Loopy Belief Propagation allowing us to evaluate the efficacy of the latter.
Physical Review Letters, 2008
We introduce Loop Ranking, a new ranking measure based on the detection of closed paths, which ca... more We introduce Loop Ranking, a new ranking measure based on the detection of closed paths, which can be computed in an efficient way. We analyze it with respect to several ranking measures which have been proposed in the past, and are widely used to capture the relative importance of the vertices in complex networks. We argue that Loop Ranking is a very appropriate measure to quantify the role of both vertices and edges in the network traffic.
Journal of Statistical Mechanics: Theory and Experiment, 2010
We analyze the limits inherent to the inverse reconstruction of a pairwise Ising spin glass based... more We analyze the limits inherent to the inverse reconstruction of a pairwise Ising spin glass based on susceptibility propagation. We establish the conditions under which the susceptibility propagation algorithm is able to reconstruct the characteristics of the network given first-and second-order local observables, evaluate eventual errors due to various types of noise in the originally observed data, and discuss the scaling of the problem with the number of degrees of freedom.
Journal of Physics: Conference Series, 2008
We study the cycles in sparse random graphs by treating them as a constraint satisfaction problem... more We study the cycles in sparse random graphs by treating them as a constraint satisfaction problem. We discuss how the model is defined, and the results that can be obtained in this way. In particular, we introduce and discuss an approximation to the self-avoiding walk-sum which emerges naturally from a slightly engineered version of the original problem.
Dynamical behavior of the Biroli-Mezard model
Journal of Physics: Conference Series, 2006
Some essential dynamical features of the Biroli-Mezard model are discussed. We observe a dynamica... more Some essential dynamical features of the Biroli-Mezard model are discussed. We observe a dynamical slowing down which for higher densities depends both on the observation time and the age of the system. We relate this aging behavior to the real space dynamics of the system, where due to some essential initial restructuring the system gains mobility. This allows us to get a better understanding of what is causing the two-time dependence of the correlation function. Finally, we quantify how heterogenous the slow dynamics of the BM model is by investigating the dynamical susceptibility and discuss its dependence on the age of the system.
Europhysics Letters (EPL), 2006
We discuss a number of essential dynamical features of the Biroli-Mezard model. We observe a dyna... more We discuss a number of essential dynamical features of the Biroli-Mezard model. We observe a dynamical slowing down which for high densities depends both on the observation time and on the age of the system. We relate this ageing behavior to the real space dynamics of the system, from which it is clear that the system initially gains mobility due to some essential initial restructuring. We discuss crystallization, its relevant time scales and connection with ageing. We quantify how heterogeneous the slow dynamics of the BM model is by investigating the dynamical susceptibility and discussing its dependence on the age of the system. We establish a number of quantitative evidences that are in good agreement with a recent analysis.
Motivation: Characterizing the capabilities, criticalities and response to perturbations of genom... more Motivation: Characterizing the capabilities, criticalities and response to perturbations of genome-scale metabolic networks is a basic problem with important applications. A key question concerns the identification of the potentially most harmful knockouts. The integration of combinatorial methods with sampling techniques to explore the space of viable flux states may provide crucial insights on this issue. Results: We assess the replaceability of every metabolic conversion in the human red blood cell by enumerating the alternative paths from substrate to product, obtaining a complete map of the potential damage of single enzymopathies. Sampling the space of optimal flux states in the healthy and in the mutated cell reveals both correlations and complementarity between topologic and dynamical aspects. Availability: Related material (stoichiometric matrices, C codes, optimal flux configurations and the detailed structure of alternative paths) is available from http://chimera.roma1.infn.it/SYSBIO
Europhys. Lett Phys Rev E
We analyze the problem of discovering long cycles inside a graph. We propose and test two algorit... more We analyze the problem of discovering long cycles inside a graph. We propose and test two algorithms for this task. The first one is based on recent advances in statistical mechanics and relies on a message passing procedure. The second follows a more standard Monte Carlo Markov Chain strategy. Special attention is devoted to Hamiltonian cycles of (non-regular) random graphs of minimal connectivity equal to three.
Europhys. Lett Phys Rev E
We analyze the problem of discovering long cycles inside a graph. We propose and test two algorit... more We analyze the problem of discovering long cycles inside a graph. We propose and test two algorithms for this task. The first one is based on recent advances in statistical mechanics and relies on a message passing procedure. The second follows a more standard Monte Carlo Markov Chain strategy. Special attention is devoted to Hamiltonian cycles of (non-regular) random graphs of minimal connectivity equal to three.
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Papers by Valery Van Kerrebroeck