Abstract
We introduce the guided forest edit distance problem, which measures the similarity of two forests under the guidance of a third forest. We give an efficient algorithm for the problem. Our problem is a natural generalization of many important structure comparison problems such as the forest edit distance problem, constrained sequence alignment problem and the longest constrained common subsequence problem. Our algorithm matches the performance of the best known algorithms for these problems.
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References
Chin, F.Y.L., Santis, A.D., Ferrara, A.L., Ho, N.L., Kim, S.K.: A simple algorithm for the constrained sequence problems. Information Processing Letters 90(4), 175–179 (2004)
Cobena, G., Abiteboul, S., Marian, A.: Detecting changes in XML documents. In: Proc. of the 18th IEEE International Conference on Data Engineering, pp. 41–52 (2002)
Jiang, T., Lin, G., Ma, B., Zhang, K.: A general edit distance between RNA structures. Journal of Molecular Biology 9(2), 371–388 (2002)
Kilpelainen, P., Mannila, H.: Ordered and unordered tree inclusion. SIAM Journal on Computing 24(2), 340–356 (1995)
Klein, P.N.: Computing the edit-distance between unrooted ordered trees. In: Proc. of the 6th European Symposium on Algorithms (ESA 1998), pp. 91–102 (1998)
Lin, G.H., Ma, B., Zhang, K.: Edit distance between two RNA structures. In: Proc. of the 5th international conference on Computational molecular biology, pp. 211–220 (2001)
Lu, C.L., Huang, Y.P.: A memory-efficient algorithm for multiple sequence alignment with constraints. Bioinformatics 21(1), 20–30 (2004)
Nierman, A., Jagadish, H.V.: Evaluating structural similarity in XML documents. In: Proc. of the 5th International Workshop on the Web and Databases, pp. 61–66 (2002)
Peng, Z.S., Ting, H.F.: Time and space efficient algorithms for constrained sequence alignment. In: Proc. of the 9th International Conference on Implementation and Application of Automata, pp. 237–246 (2004)
Shapiro, B.A., Zhang, K.: Comparing multiple RNA secondary structures using tree comparisons. Bioinformatics 6, 309–318 (1990)
Tai, K.C.: The tree-to-tree correction problem. Journal of the ACM 26(3), 422–433 (1979)
Tsai, Y.T.: The constrained longest common subsequence problem. Information Processing Letters, 88(4) (2003)
Zhang, K., Shasha, D.: Simple fast algorithms for the editing distance between trees and related problems. SIAM Journal on Computing 18(6), 1245–1262 (1989)
Zuker, M., Sankoff, D.: RNA secondary structures and their prediction. Bull. Math. Biol. 46, 591–621 (1984)
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Peng, Z., Ting, Hf. (2007). Guided Forest Edit Distance: Better Structure Comparisons by Using Domain-knowledge. In: Ma, B., Zhang, K. (eds) Combinatorial Pattern Matching. CPM 2007. Lecture Notes in Computer Science, vol 4580. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-73437-6_21
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DOI: https://doi.org/10.1007/978-3-540-73437-6_21
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-73436-9
Online ISBN: 978-3-540-73437-6
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