Artificial Fish Swarm Optimization Based Method to Identify Essential Proteins

摘要

It is well known that essential proteins play an extremely important role in controlling cellular activities in living organisms. Identifying essential proteins from protein protein interaction (PPI) networks is conducive to the understanding of cellular functions and molecular mechanisms. Hitherto, many essential proteins detection methods have been proposed. Nevertheless, those existing identification methods are not satisfactory because of low efficiency and low sensitivity to noisy data. This paper presents a novel computational approach based on artificial fish swarm optimization for essential proteins prediction in PPI networks (called AFSO_EP). In AFSO_EP, first, a part of known essential proteins are randomly chosen as artificial fishes of priori knowledge. Then, detecting essential proteins by imitating four principal biological behaviors of artificial fishes when searching for food or companions, including foraging behavior, following behavior, swarming behavior, and random behavior, in which process, the network topology, gene expression, gene ontology (GO) annotation, and subcellular localization information are utilized. To evaluate the performance of AFSO_EP, we conduct experiments on two species (Saccharomyces cerevisiae and Drosophila melanogaster), the experimental results show that our method AFSO_EP achieves a better performance for identifying essential proteins in comparison with several other well-known identification methods, which confirms the effectiveness of AFSO_EP.