ProMotE: an efficient algorithm for counting independent motifs in uncertain network topologies

Abstract Background Identifying motifs in biological networks is essential in uncovering key functions served by these networks. Finding non-overlapping motif instances is however a computationally challenging task. The fact that biological interactions are uncertain events further complicates the problem, as it makes the existence of an embedding of a given motif an uncertain event as well. Results In this paper, we develop a novel method, ProMotE (Probabilistic Motif Embedding), to count non-overlapping embeddings of a given motif in probabilistic networks. We utilize a polynomial model to capture the uncertainty. We develop three strategies to scale our algorithm to large networks. Conclusions Our experiments demonstrate that our method scales to large networks in practical time with high accuracy where existing methods fail. Moreover, our experiments on cancer and degenerative disease networks show that our method helps in uncovering key functional characteristics of biological networks