Parameterized Algorithmics for Finding Connected Motifs in Biological Networks

N. Betzler, R. van Bevern, M. R. Fellows, C. Komusiewicz, R. Niedermeier
2011 IEEE/ACM Transactions on Computational Biology & Bioinformatics  
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
more » ... ize |M | and solution size |S| we present fixedparameter 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 |.
doi:10.1109/tcbb.2011.19 pmid:21282862 fatcat:7njunkcrnnfwrotq4xmhlukwgi