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RANGI: a fast list-colored graph motif finding algorithm

RANGI: a fast list-colored graph motif finding algorithm

Ieee/Acm Transactions on Computational Biology and Bioinformatics 10(2): 504-513

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.

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Accession: 055333124

Download citation: RISBibTeXText

PMID: 23929873

DOI: 10.1109/TCBB.2012.167

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