Finding Supported Paths in Heterogeneous Networks

• Published in: Algorithms Vol. 8; no. 4; pp. 810 - 831
• Main Authors: Fertin, Guillaume, Komusiewicz, Christian, Mohamed-Babou, Hafedh, Rusu, Irena
• Format: Journal Article
• Language: English
• Published: MDPI 09.10.2015; MDPI AG
• Subjects: Bioinformatics; Computational Complexity; Computer Science; Data Structures and Algorithms; directed acyclic graphs; longest path problem; metabolic networks; NP-hard problems; protein interaction networks; shortest path problem; longest path problem; shortest path problem; protein interaction networks; metabolic networks; directed acyclic graphs; NP-hard problems
• ISSN: 1999-4893; 1999-4893
• DOI: 10.3390/a8040810

Subnetwork mining is an essential issue in the analysis of biological, social and communication networks. Recent applications require the simultaneous mining of several networks on the same or a similar vertex set. That is, one searches for subnetworks fulfilling different properties in each input network. We study the case that the input consists of a directed graph D and an undirected graph G on the same vertex set, and the sought pattern is a path P in D whose vertex set induces a connected subgraph of G. In this context, three concrete problems arise, depending on whether the existence of P is questioned or whether the length of P is to be optimized: in that case, one can search for a longest path or (maybe less intuitively) a shortest one. These problems have immediate applications in biological networks and predictable applications in social, information and communication networks. We study the classic and parameterized complexity of the problem, thus identifying polynomial and NP-complete cases, as well as fixed-parameter tractable and W[1]-hard cases. We also propose two enumeration algorithms that we evaluate on synthetic and biological data.