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Structural Pattern Matching - Succinctly

Authors Arnab Ganguly, Rahul Shah, Sharma V. Thankachan

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Arnab Ganguly
Rahul Shah
Sharma V. Thankachan

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Arnab Ganguly, Rahul Shah, and Sharma V. Thankachan. Structural Pattern Matching - Succinctly. In 28th International Symposium on Algorithms and Computation (ISAAC 2017). Leibniz International Proceedings in Informatics (LIPIcs), Volume 92, pp. 35:1-35:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2017)
https://doi.org/10.4230/LIPIcs.ISAAC.2017.35

Abstract

Let T be a text of length n containing characters from an alphabet \Sigma, which is the union of two disjoint sets: \Sigma_s containing static characters (s-characters) and \Sigma_p containing parameterized characters (p-characters). Each character in \Sigma_p has an associated complementary character from \Sigma_p. A pattern P (also over \Sigma) matches an equal-length substring $S$ of T iff the s-characters match exactly, there exists a one-to-one function that renames the p-characters in S to the p-characters in P, and if a p-character x is renamed to another p-character y then the complement of x is renamed to the complement of y. The task is to find the starting positions (occurrences) of all such substrings S. Previous indexing solution [Shibuya, SWAT 2000], known as Structural Suffix Tree, requires \Theta(n\log n) bits of space, and can find all occ occurrences in time O(|P|\log \sigma+ occ), where \sigma = |\Sigma|. In this paper, we present the first succinct index for this problem, which occupies n \log \sigma + O(n) bits and offers O(|P|\log\sigma+ occ\cdot \log n \log\sigma) query time.
Keywords
  • Parameterized Pattern Matching
  • Suffix tree
  • Burrows-Wheeler Transform
  • Wavelet Tree
  • Fully-functional succinct tree

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