Parameterized algorithmics for finding connected motifs in biological networks

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|.