One 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 protein. Then, it is possible for each of the remaining proteins associated with the original coarse-grained complex to repulse from one of the new generated complexes while attracted by the core protein of the second complex. The topology-based complex detection models presented in the literature are adopted to inter-play with the proposed heuristic operator inside the EA general framework. To assess the performance of the EA when coupled with the proposed heuristic operator, the well known Saccaromycaes Cerevisiae yeast PPI network and one reference set of benchmark complexes created from MIPS are used in the experiments. The results prove the positive impact of the heuristic operator to harness the strength of almost all adopted EA models.
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 optim
... Show MoreDetecting protein complexes in protein-protein interaction (PPI) networks is a challenging problem in computational biology. To uncover a PPI network into a complex structure, different meta-heuristic algorithms have been proposed in the literature. Unfortunately, many of such methods, including evolutionary algorithms (EAs), are based solely on the topological information of the network rather than on biological information. Despite the effectiveness of EAs over heuristic methods, more inherent biological properties of proteins are rarely investigated and exploited in these approaches. In this paper, we proposed an EA with a new mutation operator for complex detection problems. The proposed mutation operator is formulated und
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Finding communities of connected individuals in complex networks is challenging, yet crucial for understanding different real-world societies and their interactions. Recently attention has turned to discover the dynamics of such communities. However, detecting accurate community structures that evolve over time adds additional challenges. Almost all the state-of-the-art algorithms are designed based on seemingly the same principle while treating the problem as a coupled optimization model to simultaneously identify community structures and their evolution over time. Unlike all these studies, the current work aims to individually consider this three measures, i.e. intra-community score, inter-community score, and evolution of community over
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Detecting protein complexes in protein-protein interaction (PPI) networks is a challenging problem in computational biology. To uncover a PPI network into a complex structure, different meta-heuristic algorithms have been proposed in the literature. Unfortunately, many of such methods, including evolutionary algorithms (EAs), are based solely on the topological information of the network rather than on biological information. Despite the effectiveness of EAs over heuristic methods, more inherent biological properties of proteins are rarely investigated and exploited in these approaches. In this paper, we proposed an EA with a new mutation operator for complex detection problems. The proposed mutation operator is formulate
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Nowad ays, with the development of internet communication that provides many facilities to the user leads in turn to growing unauthorized access. As a result, intrusion detection system (IDS) becomes necessary to provide a high level of security for huge amount of information transferred in the network to protect them from threats. One of the main challenges for IDS is the high dimensionality of the feature space and how the relevant features to distinguish the normal network traffic from attack network are selected. In this paper, multi-objective evolutionary algorithm with decomposition (MOEA/D) and MOEA/D with the injection of a proposed local search operator are adopted to solve the Multi-objective optimization (MOO) followed by Naï
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Community detection is an important and interesting topic for better understanding and analyzing complex network structures. Detecting hidden partitions in complex networks is proven to be an NP-hard problem that may not be accurately resolved using traditional methods. So it is solved using evolutionary computation methods and modeled in the literature as an optimization problem. In recent years, many researchers have directed their research efforts toward addressing the problem of community structure detection by developing different algorithms and making use of single-objective optimization methods. In this study, we have continued that research line by improving the Particle Swarm Optimization (PSO) algorithm using a local
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