A multithreaded algorithm for network alignment via approximate matching

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 a...

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Bibliographic Details
Published in:2012 International Conference for High Performance Computing, Networking, Storage and Analysis pp. 1 - 11
Main Authors: Khan, Arif M., Gleich, David F., Pothen, Alex, Halappanavar, Mahantesh
Format: Conference Proceeding
Language:English
Published: IEEE 01.11.2012
Subjects:
Approximation algorithms
Approximation methods
Bipartite graph
Complexity theory
Multicore processing
Sparse matrices
Vectors
ISBN:1467308056, 9781467308052
ISSN:2167-4329
Online Access:Get full text
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Summary: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 matching 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.
ISBN:1467308056
9781467308052
ISSN:2167-4329
DOI:10.1109/SC.2012.8