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Issue No.02 - March-April (2013 vol.10)
pp: 504-513
Ali Gholami Rudi , Fac. of Electr. & Comput. Eng., Tarbiat Modares Univ., Tehran, Iran
Saeed Shahrivari , Fac. of Electr. & Comput. Eng., Tarbiat Modares Univ., Tehran, Iran
Saeed Jalili , Fac. of Electr. & Comput. Eng., Tarbiat Modares Univ., Tehran, Iran
Zahra Razaghi Moghadam Kashani , Fac. of Electr. & Comput. Eng., Tarbiat Modares Univ., Tehran, Iran
ABSTRACT
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
CITATION
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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