A multithreaded algorithm for network alignment via approximate matching

Arif M. Khan, David F. Gleich, Alex Pothen, Mahantesh Halappanavar
2012 2012 International Conference for High Performance Computing, Networking, Storage and Analysis  
Network alignment is an optimization problem to find the best one-to-one map between the vertices of a pair of graphs that overlaps as many edges as possible. It is a relaxation of the graph isomorphism problem and is closely related to the subgraph isomorphism problem. The best current approaches are entirely heuristic and iterative in nature. They generate real-valued heuristic weights that must be rounded to find integer solutions. This rounding requires solving a bipartite maximum weight
more » ... ching problem at each iteration in order to avoid missing high quality solutions. We investigate substituting a parallel, half-approximation for maximum weight matching instead of an exact computation. Our experiments show that the resulting difference in solution quality is negligible. We demonstrate almost a 20-fold speedup using 40 threads on an 8 processor Intel Xeon E7-8870 system and now solve real-world problems in 36 seconds instead of 10 minutes.
doi:10.1109/sc.2012.8 dblp:conf/sc/KhanGPH12 fatcat:besb76g6cfbwlj5ppakwgr45fy