Global Biological Network Alignment by Using Efficient Memetic Algorithm

High-throughput experimental screening techniques have resulted in a large number of biological network data such as protein-protein interactions (PPI) data. The analysis of these data can enhance our understanding of cellular processes. PPI network alignment is one of the comparative analysis methods for analyzing biological networks. Research on PPI networks can identify conserved subgraphs and help us to understand evolutionary trajectories across species. Some evolutionary algorithms have been proposed for coping with PPI network alignment, but most of them are limited by the lower search efficiency due to the lack of the priori knowledge. In this paper, we propose a memetic algorithm, denoted as MeAlgn, to solve the biological network alignment by optimizing an objective function which introduces topological structure and sequence similarities. MeAlign combines genetic algorithm with a local search refinement. The genetic algorithm is to find interesting alignment solution regions, and the local search is to find optimal solutions around the regions. The proposed algorithm first develops a coarse similarity score matrix for initialization and then it uses a specific neighborhood heuristic local search strategy to find an optimal alignment. In MeAlign, the information of topological structure and sequence similarities is used to guide our mapping. Experimental results demonstrate that our algorithm can achieve a better mapping than some state-of-the-art algorithms and it makes a better balance between the network topology and nodes sequence similarities.