A network (or formally a graph) can be described by a set of nodes and a set of edges connecting these nodes. Networks model many real-world phenomena in various research domains, such as biology, engineering and sociology. Community mining is discovering the groups in a network where individuals group of membership are not explicitly given. Detecting natural divisions in such complex networks is proved to be extremely NP-hard problem that recently enjoyed a considerable interest. Among the proposed methods, the field of evolutionary algorithms (EAs) takes a remarkable interest. To this end, the aim of this paper is to present the general statement of community detection problem in social networks. Then, it visits the problem as an optimization problem where a modularity-based ( ) and normalized mutual information ( ) metrics are formulated to describe the problem. An evolutionary algorithm is then expressed in the light of its characteristic components to tackle the problem. The presentation will highlight the possible alternative that can be adopted in this study for individual representation, fitness evaluations, and crossover and mutation operators. The results point out that adopting as a fitness function carries out more correct solutions than adopting the modularity function . Moreover, the strength of mutation has a background role. When coupled with non elite selection, increasing mutation probability could results in better solutions. However, when elitism is used, increasing mutation probability could bewilder the behavior of EA.
A network (or formally a graph) can be described by a set of nodes and a set of edges connecting these nodes. Networks model many real-world phenomena in various research domains, such as biology, engineering and sociology. Community mining is discovering the groups in a network where individuals group of membership are not explicitly given. Detecting natural divisions in such complex networks is proved to be extremely NP-hard problem that recently enjoyed a considerable interest. Among the proposed methods, the field of evolutionary algorithms (EAs) takes a remarkable interest. To this end, the aim of this paper is to present the general statement of community detection problem in social networks. Then, it visits the problem as an optimization problem where a modularity-based ( ) and normalized mutual information ( ) metrics are formulated to describe the problem. An evolutionary algorithm is then expressed in the light of its characteristic components to tackle the problem. The presentation will highlight the possible alternative that can be adopted in this study for individual representation, fitness evaluations, and crossover and mutation operators. The results point out that adopting as a fitness function carries out more correct solutions than adopting the modularity function . Moreover, the strength of mutation has a background role. When coupled with non elite selection, increasing mutation probability could results in better solutions. However, when elitism is used, increasing mutation probability could bewilder the behavior of EA.
Evolutionary algorithms (EAs), as global search methods, are proved to be more robust than their counterpart local heuristics for detecting protein complexes in protein-protein interaction (PPI) networks. Typically, the source of robustness of these EAs comes from their components and parameters. These components are solution representation, selection, crossover, and mutation. Unfortunately, almost all EA based complex detection methods suggested in the literature were designed with only canonical or traditional components. Further, topological structure of the protein network is the main information that is used in the design of almost all such components. The main contribution of this paper is to formulate a more robust EA wit
... Show MoreEvolutionary algorithms (EAs), as global search methods, are proved to be more robust than their counterpart local heuristics for detecting protein complexes in protein-protein interaction (PPI) networks. Typically, the source of robustness of these EAs comes from their components and parameters. These components are solution representation, selection, crossover, and mutation. Unfortunately, almost all EA based complex detection methods suggested in the literature were designed with only canonical or traditional components. Further, topological structure of the protein network is the main information that is used in the design of almost all such components. The main contribution of this paper is to formulate a more robust E
... Show MoreOne of the most interested problems that recently attracts many research investigations in Protein-protein interactions (PPI) networks is complex detection problem. Detecting natural divisions in such complex networks is proved to be extremely NP-hard problem wherein, recently, the field of Evolutionary Algorithms (EAs) reveals positive results. The contribution of this work is to introduce a heuristic operator, called protein-complex attraction and repulsion, which is especially tailored for the complex detection problem and to enable the EA to improve its detection ability. The proposed heuristic operator is designed to fine-grain the structure of a complex by dividing it into two more complexes, each being distinguished with a core pr
... Show MoreIdentification of complex communities in biological networks is a critical and ongoing challenge since lots of network-related problems correspond to the subgraph isomorphism problem known in the literature as NP-hard. Several optimization algorithms have been dedicated and applied to solve this problem. The main challenge regarding the application of optimization algorithms, specifically to handle large-scale complex networks, is their relatively long execution time. Thus, this paper proposes a parallel extension of the PSO algorithm to detect communities in complex biological networks. The main contribution of this study is summarized in three- fold; Firstly, a modified PSO algorithm with a local search operator is proposed to d
... Show MoreOne of the recent significant but challenging research studies in computational biology and bioinformatics is to unveil protein complexes from protein-protein interaction networks (PPINs). However, the development of a reliable algorithm to detect more complexes with high quality is still ongoing in many studies. The main contribution of this paper is to improve the effectiveness of the well-known modularity density ( ) model when used as a single objective optimization function in the framework of the canonical evolutionary algorithm (EA). To this end, the design of the EA is modified with a gene ontology-based mutation operator, where the aim is to make a positive collaboration between the modularity density model and the proposed
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