We present a novel solution called Cluster-based Steiner Tree Miner (CST-Miner) to instantly identify multi-entity topological relationships in biological networks.  Given a list of user-specific entities, CST-Miner decomposes a biological network into nested cluster-based subgraphs, on which multiple minimum Steiner trees are identified.  Experimental results showed that CST-Miner can finish in nearly log-linear time and the tree constructed by CST-Miner is close to the global minimum.
CST-Miner