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Title: A Multithreaded Algorithm for Network Alignment Via Approximate Matching

Abstract

Network alignment is an optimization problem to find the best one-to-one map between the vertices of a pair of graphs that overlaps in 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 are iterative in nature. They generate real-valued heuristic approximations that must be rounded to find integer solutions. This rounding requires solving a bipartite maximum weight matching problem at each step 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 (from 10 minutes to 36 seconds).

Authors:
; ; ;
Publication Date:
Research Org.:
Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1089096
Report Number(s):
PNNL-SA-87964
400470000
DOE Contract Number:  
AC05-76RL01830
Resource Type:
Conference
Resource Relation:
Conference: International Conference for High Performance Computing, Networking, Storage and Analysis (SC), November 10-16, 2012, Salt Lake City, Utah
Country of Publication:
United States
Language:
English
Subject:
network alignment, matching, multicore

Citation Formats

Khan, Arif, Gleich, David F., Pothen, Alex, and Halappanavar, Mahantesh. A Multithreaded Algorithm for Network Alignment Via Approximate Matching. United States: N. p., 2012. Web. doi:10.1109/SC.2012.8.
Khan, Arif, Gleich, David F., Pothen, Alex, & Halappanavar, Mahantesh. A Multithreaded Algorithm for Network Alignment Via Approximate Matching. United States. doi:10.1109/SC.2012.8.
Khan, Arif, Gleich, David F., Pothen, Alex, and Halappanavar, Mahantesh. Fri . "A Multithreaded Algorithm for Network Alignment Via Approximate Matching". United States. doi:10.1109/SC.2012.8.
@article{osti_1089096,
title = {A Multithreaded Algorithm for Network Alignment Via Approximate Matching},
author = {Khan, Arif and Gleich, David F. and Pothen, Alex and Halappanavar, Mahantesh},
abstractNote = {Network alignment is an optimization problem to find the best one-to-one map between the vertices of a pair of graphs that overlaps in 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 are iterative in nature. They generate real-valued heuristic approximations that must be rounded to find integer solutions. This rounding requires solving a bipartite maximum weight matching problem at each step 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 (from 10 minutes to 36 seconds).},
doi = {10.1109/SC.2012.8},
journal = {},
number = ,
volume = ,
place = {United States},
year = {2012},
month = {11}
}

Conference:
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