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Top-k Similar Graph Matching Using TraM in Biological Networks
Nov.-Dec. 2012 (vol. 9 no. 6)
pp. 1790-1804
M. S. Amin, Dept. of Comput. Sci., Wayne State Univ., Sunnyvale, CA, USA
R. L. Finley, Center for Mol. Med. & Genetics, Wayne State Univ., Detroit, MI, USA
H. M. Jamil, Dept. of Comput. Sci., Univ. of Idaho, Moscow, ID, USA
Many emerging database applications entail sophisticated graph-based query manipulation, predominantly evident in large-scale scientific applications. To access the information embedded in graphs, efficient graph matching tools and algorithms have become of prime importance. Although the prohibitively expensive time complexity associated with exact subgraph isomorphism techniques has limited its efficacy in the application domain, approximate yet efficient graph matching techniques have received much attention due to their pragmatic applicability. Since public domain databases are noisy and incomplete in nature, inexact graph matching techniques have proven to be more promising in terms of inferring knowledge from numerous structural data repositories. In this paper, we propose a novel technique called TraM for approximate graph matching that off-loads a significant amount of its processing on to the database making the approach viable for large graphs. Moreover, the vector space embedding of the graphs and efficient filtration of the search space enables computation of approximate graph similarity at a throw-away cost. We annotate nodes of the query graphs by means of their global topological properties and compare them with neighborhood biased segments of the data-graph for proper matches. We have conducted experiments on several real data sets, and have demonstrated the effectiveness and efficiency of the proposed method.
Index Terms:
tree searching,bioinformatics,genetics,graphs,isomorphism,genetics,top-k similar graph matching,TraM,biological networks,database applications,sophisticated graph-based query manipulation,large-scale scientific,expensive time complexity,exact subgraph isomorphism techniques,pragmatic applicability,noisy public domain databases,structural data repository,vector space embedding,query graphs,global topological properties,neighborhood biased segments,bioinformatics,Proteins,Databases,Graphics,Bioinformatics,Computational biology,Diseases,Bioinformatics,Genetics,biology and genetics,Graphs and networks,knowledge and data engineering tools and techniques,bioinformatics,graph and tree search strategies
Citation:
M. S. Amin, R. L. Finley, H. M. Jamil, "Top-k Similar Graph Matching Using TraM in Biological Networks," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 9, no. 6, pp. 1790-1804, Nov.-Dec. 2012, doi:10.1109/TCBB.2012.90
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