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Efficient processing of graph similarity queries with edit distance constraints

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Abstract

Graphs are widely used to model complicated data semantics in many applications in bioinformatics, chemistry, social networks, pattern recognition, etc. A recent trend is to tolerate noise arising from various sources such as erroneous data entries and find similarity matches. In this paper, we study graph similarity queries with edit distance constraints. Inspired by the \(q\)-gram idea for string similarity problems, our solution extracts paths from graphs as features for indexing. We establish a lower bound of common features to generate candidates. Efficient algorithms are proposed to handle three types of graph similarity queries by exploiting both matching and mismatching features as well as degree information to improve the filtering and verification on candidates. We demonstrate the proposed algorithms significantly outperform existing approaches with extensive experiments on real and synthetic datasets.

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Notes

  1. \(q\)-Grams in strings are accompanied by their starting positions in the string, and thus there is no duplicate.

  2. Rare cases are observed that tree-based \(q\)-grams deliver identical or even tighter count filtering lower bound than path-based \(q\)-grams.

  3. Two sequential scans on \(w_s\) if the sequences are symmetric.

  4. http://dtp.nci.nih.gov/docs/aids/aids_data.html.

  5. http://www.iam.unibe.ch/fki/databases/iam-graph-database/download-the-iam-graph-database.

  6. http://www.cse.ust.hk/graphgen/.

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Acknowledgments

X. Lin is supported by ARC DP0987557, DP110102937, DP120104168, NSFC61232006 and NSFC61021004. W. Wang is supported by ARC DP130103401 and DP130103405. C. Xiao and Y. Ishikawa are supported by FIRST Program, Japan.

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Authors and Affiliations

  1. The University of New South Wales, Sydney, Australia

    Xiang Zhao, Xuemin Lin & Wei Wang

  2. NICTA, Sydney, Australia

    Xiang Zhao

  3. Nagoya University, Nagoya, Japan

    Chuan Xiao & Yoshiharu Ishikawa

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  1. Xiang Zhao
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  2. Chuan Xiao
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  3. Xuemin Lin
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  4. Wei Wang
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  5. Yoshiharu Ishikawa
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Correspondence to Xiang Zhao.

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Zhao, X., Xiao, C., Lin, X. et al. Efficient processing of graph similarity queries with edit distance constraints. The VLDB Journal 22, 727–752 (2013). https://doi.org/10.1007/s00778-013-0306-1

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