Improved Parameterized Algorithms for Network Query Problems

Ron Y. Pinter, Hadas Shachnai, Meirav Zehavi

Abstract: In the Partial Information Network Query (PINQ) problem, we are given a host graph \(H\), and a pattern \(\mathcal P\) whose topology is partially known. We seek a subgraph of \(H\) that resembles \(\mathcal{P}\). PINQ is a generalization of Subgraph Isomorphism, where the topology of \(\mathcal P\) is known, and Graph Motif, where the topology of \(\mathcal P\) is unknown. This generalization has important applications to bioinformatics, since it addresses the major challenge of analyzing biological networks in the absence of certain topological data. In this paper, we use a non-standard part-algebraic/part-combinatorial hybridization strategy to develop an exact parameterized algorithm as well as an FPT-approximation scheme for PINQ, allowing near resemblance between \(H\) and \(\mathcal P\). We thus unify and significantly improve previous results related to network queries.