RANGI: a fast list-colored graph motif finding algorithm

IEEE/ACM Trans Comput Biol Bioinform. 2013 Mar-Apr;10(2):504-13. doi: 10.1109/TCBB.2012.167.


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.

MeSH terms

  • Algorithms*
  • Animals
  • Cattle
  • Color
  • Computational Biology / methods*
  • Humans
  • Image Processing, Computer-Assisted / methods*
  • Mice
  • Protein Interaction Maps
  • Rats
  • Reproducibility of Results
  • Software*