Parameterized Algorithmics for Finding Connected Motifs in Biological Networks

Nadja Betzler, Rene Van Bevern, Michael Fellows, Christian Komusiewicz, Rolf Niedermeier

    Research output: Contribution to journalArticle

    Abstract

    We study the NP-hard List-Colored Graph Motif problem which, given an undirected list-colored graph G=(V,E) and a multiset M of colors, asks for maximum-cardinality sets S ? V and M? ? M such that G[S] is connected and contains exactly (with respect to multiplicity) the colors in M?. List-Colored Graph Motif has applications in the analysis of biological networks. We study List-Colored Graph Motif with respect to three different parameterizations. For the parameters motif size |M| and solution size |S|, we present fixed-parameter algorithms, whereas for the parameter |V|-|M|, we show W[1]-hardness for general instances and achieve fixed-parameter tractability for a special case of List-Colored Graph Motif. We implemented the fixed-parameter algorithms for parameters |M|and |S|, developed further speed-up heuristics for these algorithms, and applied them in the context of querying protein-interaction networks, demonstrating their usefulness for realistic instances. Furthermore, we show that extending the request for motif connectedness to stronger demands, such as biconnectedness or bridge-connectedness leads to W[1]-hard problems when the parameter is the motif size |M|.
    Original languageEnglish
    Pages (from-to)1296-1308
    Number of pages13
    JournalIEEE/ACM Transactions on Computational Biology and Bioinformatics
    Volume8
    Issue number5
    DOIs
    Publication statusPublished - 2011

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