A Global Network Alignment Method Using Discrete Particle Swarm Optimization

Molecular interactions data increase exponentially with the advance of biotechnology. This makes it possible and necessary to comparatively analyze the different data at a network level. Global network alignment is an important network comparison approach to identify conserved subnetworks and get insight into evolutionary relationship across species. Network alignment which is analogous to subgraph isomorphism is known to be an NP-hard problem. In this paper, we introduce a novel heuristic Particle-Swarm-Optimization based Network Aligner (PSONA), which optimizes a weighted global alignment model considering both protein sequence similarity and interaction conservations. The particle statuses and status updating rules are redefined in a discrete form by using permutation. A seed-and-extend strategy is employed to guide the searching for the superior alignment. The proposed initialization method “seeds” matches with high sequence similarity into the alignment, which guarantees the functional coherence of the mapping nodes. A greedy local search method is designed as the “extension” procedure to iteratively optimize the edge conservations. PSONA is compared with several state-of-art methods on ten network pairs combined by five species. The experimental results demonstrate that the proposed aligner can map the proteins with high functional coherence and can be used as a booster to effectively refine the well-studied aligners.