AntNetAlign: Ant colony optimization for network alignment

Abstract

Network Alignment (NA) is a hard optimization problem with important applications such as, for example, the identification of orthologous relationships between different proteins and of phylogenetic relationships between species. Given two (or more) networks, the goal is to find an alignment between them, that is, a mapping between their respective nodes such that the topological and functional structure is well preserved. Although the problem has received great interest in recent years, there is still a need to unify the different trends that have emerged from diverse research areas. In this paper, we introduce AntNetAlign, an Ant Colony Optimization (ACO) approach for solving the problem. The proposed approach makes use of similarity information extracted from the input networks to guide the construction process. Combined with an improvement measure that depends on the current construction state, it is able to optimize any of the three main topological quality measures. We provide an extensive experimental evaluation using real-world instances that range from Protein–Protein Interaction (PPI) networks to Social Networks. Results show that our method outperforms other state-of-the-art approaches in two out of three of the tested scores within a reasonable amount of time, specially in the important score. Moreover, it is able to obtain near-optimal results when aligning networks with themselves. Furthermore, in larger instances, our algorithm was still able to compete with the best performing method in this regard.