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An improved algorithm for tree edit distance with applications for RNA secondary structure comparison

Author

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  • Shihyen Chen

    (The University of Western Ontario)

  • Kaizhong Zhang

    (The University of Western Ontario)

Abstract

An ordered labeled tree is a tree in which the nodes are labeled and the left-to-right order among siblings is relevant. The edit distance between two ordered labeled trees is the minimum cost of transforming one tree into the other through a sequence of edit operations. We present techniques for speeding up the tree edit distance computation which are applicable to a family of algorithms based on closely related recursion strategies. These techniques aim to reduce repetitious steps in the original algorithms by exploring certain structural features in the tree. When these features exist in a large portion of the tree, the speedup due to our techniques would be significant. Viable examples for application include RNA secondary structure comparison and structured text comparison.

Suggested Citation

  • Shihyen Chen & Kaizhong Zhang, 2014. "An improved algorithm for tree edit distance with applications for RNA secondary structure comparison," Journal of Combinatorial Optimization, Springer, vol. 27(4), pages 778-797, May.
    • Handle: RePEc:spr:jcomop:v:27:y:2014:i:4:d:10.1007_s10878-012-9552-1
    DOI: 10.1007/s10878-012-9552-1
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