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

Shihyen Chen () and Kaizhong Zhang ()
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Shihyen Chen: The University of Western Ontario
Kaizhong Zhang: The University of Western Ontario

Journal of Combinatorial Optimization, 2014, vol. 27, issue 4, No 10, 778-797

Abstract: 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.

Keywords: Tree edit distance; RNA secondary structure comparison; Structured text comparison (search for similar items in EconPapers)
Date: 2014
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DOI: 10.1007/s10878-012-9552-1

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