Simultaneous Optimization of both Node and Edge Conservation in Network Alignment via WAVE

Network alignment can be used to transfer functional knowledge between conserved regions of different networks. Existing methods use a node cost function (NCF) to compare nodes across networks and an alignment strategy (AS) to find high-scoring alignments with respect to total NCF over all aligned nodes (or node conservation). Then, they evaluate alignments via a measure that is different than node conservation used to guide alignment construction. Typically, one measures edge conservation, but only after alignments are produced. Hence, we recently directly maximized edge conservation while constructing alignments, which improved their quality. Here, we aim to maximize both node and edge conservation during alignment construction to further improve quality. We design a novel measure of edge conservation that (unlike existing measures that treat each conserved edge the same) weighs conserved edges to favor edges with highly NCF-similar end-nodes. As a result, we introduce a novel AS, Weighted Alignment VotEr (WAVE), which can optimize any measures of node and edge conservation. Using WAVE on top of well-established NCFs improves alignments compared to existing methods that optimize only node or edge conservation or treat each conserved edge the same. We evaluate WAVE on biological data, but it is applicable in any domain.