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RANGI: A Fast List-Colored Graph Motif Finding Algorithm
March-April 2013 (vol. 10 no. 2)
pp. 504-513
Ali Gholami Rudi, Tarbiat Modares University
Saeed Shahrivari, Tarbiat Modares University
Saeed Jalili, Tarbiat Modares University
Zahra Razaghi Moghadam Kashani, Tarbiat Modares University
Given a multiset of colors as the query and a list-colored graph, i.e., an undirected graph with a set of colors assigned to each of its vertices, in the NP-hard list-colored graph motif problem the goal is to find the largest connected subgraph such that one can select a color from the set of colors assigned to each of its vertices to obtain a subset of the query. This problem was introduced to find functional motifs in biological networks. We present a branch-and-bound algorithm named RANGI for finding and enumerating list-colored graph motifs. As our experimental results show, RANGI's pruning methods and heuristics make it quite fast in practice compared to the algorithms presented in the literature. We also present a parallel version of RANGI that achieves acceptable scalability.
Index Terms:
Color,Heuristic algorithms,Computational biology,Bioinformatics,Proteins,list-colored graphs,Color,Heuristic algorithms,Computational biology,Bioinformatics,Proteins,protein-interaction networks,Branch-and-bound algorithms,parallel algorithms
Ali Gholami Rudi, Saeed Shahrivari, Saeed Jalili, Zahra Razaghi Moghadam Kashani, "RANGI: A Fast List-Colored Graph Motif Finding Algorithm," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 10, no. 2, pp. 504-513, March-April 2013, doi:10.1109/TCBB.2012.167
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