Community detection by consensus genetic-based algorithm for directed networks

Finding communities in networks is a commonly used form of network analysis. There is a myriad of community detection algorithms in the literature to perform this task. In spite of that, the number of community detection algorithms in directed networks is much lower than in undirected networks. However, evaluation measures to estimate the quality of communities in undirected networks nowadays have its adaptation to directed networks as, for example, the well-known modularity measure. This paper introduces a genetic-based consensus clustering to detect communities in directed networks with the directed modularity as the fitness function. Consensus strategies involve combining computational models to improve the quality of solutions generated by a single model. The reason behind the development of a consensus strategy relies on the fact that recent studies indicate that the modularity may fail in detecting expected clusterings. Computational experiments with artificial LFR networks show that the proposed method was very competitive in comparison to existing strategies in the literature. (C) 2016 The Authors. Published by Elsevier B.V.Instituto de Ciência e Tecnologia, Universidade Federal de São Paulo (UNIFESP) Av. Cesare M. G. Lattes, 1201, Eugênio de Mello, São José dos Campos-SP, CEP: 12247-014, BrasilInstituto de Ciência e Tecnologia, Universidade Federal de São Paulo (UNIFESP) Av. Cesare M. G. Lattes, 1201, Eugênio de Mello, São José dos Campos-SP, CEP: 12247-014, BrasilWeb of Scienc

Detection of regulator genes and eQTLs in gene networks

Genetic differences between individuals associated to quantitative phenotypic traits, including disease states, are usually found in non-coding genomic regions. These genetic variants are often also associated to differences in expression levels of nearby genes (they are "expression quantitative trait loci" or eQTLs for short) and presumably play a gene regulatory role, affecting the status of molecular networks of interacting genes, proteins and metabolites. Computational systems biology approaches to reconstruct causal gene networks from large-scale omics data have therefore become essential to understand the structure of networks controlled by eQTLs together with other regulatory genes, and to generate detailed hypotheses about the molecular mechanisms that lead from genotype to phenotype. Here we review the main analytical methods and softwares to identify eQTLs and their associated genes, to reconstruct co-expression networks and modules, to reconstruct causal Bayesian gene and module networks, and to validate predicted networks in silico.Comment: minor revision with typos corrected; review article; 24 pages, 2 figure

Identifying communities by influence dynamics in social networks

Communities are not static; they evolve, split and merge, appear and disappear, i.e. they are product of dynamical processes that govern the evolution of the network. A good algorithm for community detection should not only quantify the topology of the network, but incorporate the dynamical processes that take place on the network. We present a novel algorithm for community detection that combines network structure with processes that support creation and/or evolution of communities. The algorithm does not embrace the universal approach but instead tries to focus on social networks and model dynamic social interactions that occur on those networks. It identifies leaders, and communities that form around those leaders. It naturally supports overlapping communities by associating each node with a membership vector that describes node's involvement in each community. This way, in addition to overlapping communities, we can identify nodes that are good followers to their leader, and also nodes with no clear community involvement that serve as a proxy between several communities and are equally as important. We run the algorithm for several real social networks which we believe represent a good fraction of the wide body of social networks and discuss the results including other possible applications.Comment: 10 pages, 6 figure