Message Passing Algorithms for Sparse Network Alignment

Details Message Passing Algorithms for Sparse Network Alignment Message Passing Algorithms for Sparse Network Alignment

2009-07-20

arxiv.org/abs/0907.3338v2

Mathematics

Optimization and Control

supporting programs available from http://www.cs.purdue.edu/homes/dgleich/codes/netalign

Scientific paper

Network alignment generalizes and unifies several approaches for forming a matching or alignment between the vertices of two graphs. We study a mathematical programming framework for network alignment problem and a sparse variation of it where only a small number of matches between the vertices of the two graphs are possible. We propose a new message passing algorithm that allows us to compute, very efficiently, approximate solutions to the sparse network alignment problems with graph sizes as large as hundreds of thousands of vertices. We also provide extensive simulations comparing our algorithms with two of the best solvers for network alignment problems on two synthetic matching problems, two bioinformatics problems, and three large ontology alignment problems including a multilingual problem with a known labeled alignment.

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