Shared Memory Parallel Subgraph Enumeration

The subgraph enumeration problem asks us to find all subgraphs of a target graph that are isomorphic to a given pattern graph. Determining whether even one such isomorphic subgraph exists is NP-complete---and therefore finding all such subgraphs (if they exist) is a time-consuming task. Subgraph enumeration has applications in many fields, including biochemistry and social networks, and interestingly the fastest algorithms for solving the problem for biochemical inputs are sequential. Since they depend on depth-first tree traversal, an efficient parallelization is far from trivial. Nevertheless, since important applications produce data sets with increasing difficulty, parallelism seems beneficial. We thus present here a shared-memory parallelization of the state-of-the-art subgraph enumeration algorithms RI and RI-DS (a variant of RI for dense graphs) by Bonnici et al. [BMC Bioinformatics, 2013]. Our strategy uses work stealing and our implementation demonstrates a significant speedup on real-world biochemical data---despite a highly irregular data access pattern. We also improve RI-DS by pruning the search space better; this further improves the empirical running times compared to the already highly tuned RI-DS.Comment: 18 pages, 12 figures, To appear at the 7th IEEE Workshop on Parallel / Distributed Computing and Optimization (PDCO 2017

Performance Comparison of Five Exact Graph Matching Algorithms on Biological Databases

Graphs are a powerful data structure that can be applied to several problems in bioinformatics. Graph matching, in its diverse forms, is an important operation on graphs, involved when there is the need to compare two graphs or to find substructures into larger structures. Many graph matching algorithms exist, and their relative efficiency depends on the kinds of graphs they are applied to. In this paper we will consider some popular and freely available matching algorithms, and will experimentally compare them on graphs derived from bioinformatics applications, in order to help the researchers in this field to choose the right tool for the problem at hand