An algorithm for orienting graphs based on cause-effect pairs and its applications to orienting protein networks

Abstract

We consider a graph orientation problem arising in the study of biological networks. Given an undirected graph and a list of ordered source-target pairs, the goal is to orient the graph so that a maximum number of pairs will admit a directed path from the source to the target. We show that the problem is NP-hard and hard to approximate to within a constant ratio. We then study restrictions of the problem to various graph classes, and provide an O(logn) approximation algorithm for the general case. We show that this algorithm achieves very tight approximation ratios in practice and is able to infer edge directions with high accuracy on both simulated and real network data. © 2008 Springer-Verlag Berlin Heidelberg.