Counting motifs in dynamic networks. Kingshuk Mukherjee, Md Mahmudul Hasan, Christina Boucher and Tamer Kahveci

Background A network motif is a sub-network that occurs frequently in a given network. Detection of such motifs is important since they uncover functions and local properties of the given biological network. Finding motifs is however a computationally challenging task as it requires solving the costly subgraph isomorphism problem. Moreover, the topology of biological networks change over time. These changing networks are called dynamic biological networks. As the network evolves, frequency of each motif in the network also changes. Computing the frequency of a given motif from scratch in a dynamic network as the network topology evolves is infeasible, particularly for large and fast evolving networks. Results In this article, we design and develop a scalable method for counting the number of motifs in a dynamic biological network. Our method incrementally updates the frequency of each motif as the underlying network’s topology evolves. Our experiments demonstrate that our method can update the frequency of each motif in orders of magnitude faster than counting the motif embeddings every time the network changes. If the network evolves more frequently, the margin with which our method outperforms the existing static methods, increases. Conclusions We evaluated our method extensively using synthetic and real datasets, and show that our method is highly accurate (≥ 96%) and that it can be scaled to large dense networks. The results on real data demonstrate the utility of our method in revealing interesting insights on the evolution of biological processes.

Counting motifs in dynamic networks. Kingshuk Mukherjee, Md Mahmudul Hasan, Christina Boucher and Tamer Kahveci. BMC Systems Biology. BMC Systems Biology, 2018, 12(Suppl 1):6.

@article{counting-motifs, title={Counting motifs in dynamic networks}, authors={Mukherjee, K. and Hasan, M.M. and Boucher, C. and Kahveci, T.}, journal={BMC Systems Biology} year={2018}, volume={12}, number={Suppl 1}, pages={6} }