Networks , modules and breeding schedules

Data on molecular interactions is increasing at a tremendous pace, while the development of solid methods for analyzing this network data is lagging behind. This holds in particular for the field of comparative network analysis, where one wants to identify commonalities between biological networks. Since biological functionality primarily operates at the network level, there is a clear need for topology-aware comparisonmethods. In this paper we present amethod for global network alignment that is fast and robust, and can flexibly deal with various scoring schemes taking both node-to-node correspondences as well as network topologies into account. It is based on an integer linear programming formulation, generalizing the well-studied quadratic assignment problem. We obtain strong upper and lower bounds for the problem by improving a Lagrangian relaxation approach and introduce the software tool natalie 2.0, a publicly available implementation of our method. In an extensive computational study on protein interaction networks for six different species, we find that our newmethod outperforms alternative state-of-the-art methods with respect to quality and running time. 2.