Discovering Entities Similarities in Biological Networks Using a Hybrid Immune Algorithm

Disease phenotypes are generally caused by the failure of gene modules which often have similar biological roles. Through the study of biological networks, it is possible to identify the intrinsic structure of molecular interactions in order to identify the so-called “disease modules”. Community detection is an interesting and valuable approach to discovering the structure of the community in a complex network, revealing the internal organization of the nodes, and has become a leading research topic in the analysis of complex networks. This work investigates the link between biological modules and network communities in test-case biological networks that are commonly used as a reference point and which include Protein–Protein Interaction Networks, Metabolic Networks and Transcriptional Regulation Networks. In order to identify small and structurally well-defined communities in the biological context, a hybrid immune metaheuristic algorithm Hybrid-IA is proposed and compared with several metaheuristics, hyper-heuristics, and the well-known greedy algorithm Louvain, with respect to modularity maximization. Considering the limitation of modularity optimization, which can fail to identify smaller communities, the reliability of Hybrid-IA was also analyzed with respect to three well-known sensitivity analysis measures (NMI, ARI and NVI) that assess how similar the detected communities are to real ones. By inspecting all outcomes and the performed comparisons, we will see that on one hand Hybrid-IA finds slightly lower modularity values than Louvain, but outperforms all other metaheuristics, while on the other hand, it can detect communities more similar to the real ones when compared to those detected by Louvain.