Time–space trade-offs for longest common extensions

Philip Bille, Inge Li Gørtz, Benjamin Sach, Hjalte Wedel Vildhøj

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Abstract

We revisit the longest common extension (LCE) problem, that is, preprocess a string T into a compact data structure that supports fast LCE queries. An LCE query takes a pair (i,j) of indices in T and returns the length of the longest common prefix of the suffixes of T starting at positions i and j. We study the time–space trade-offs for the problem, that is, the space used for the data structure vs. the worst-case time for answering an LCE query. Let n be the length of T. Given a parameter τ, 1⩽τ⩽n, we show how to achieve either O(n/τ) space and O(τ) query time, or O(n/τ) space and O(τlog(|LCE(i,j)|/τ)) query time, where |LCE(i,j)| denotes the length of the LCE returned by the query. These bounds provide the first smooth trade-offs for the LCE problem and almost match the previously known bounds at the extremes when τ=1 or τ=n. We apply the result to obtain improved bounds for several applications where the LCE problem is the computational bottleneck, including approximate string matching and computing palindromes. We also present an efficient technique to reduce LCE queries on two strings to one string. Finally, we give a lower bound on the time–space product for LCE data structures in the non-uniform cell probe model showing that our second trade-off is nearly optimal.
Original languageEnglish
JournalJournal of Discrete Algorithms
Volume25
Pages (from-to)42-50
ISSN1570-8667
DOIs
Publication statusPublished - 2014

Keywords

  • Longest common extension
  • Approximate string matching
  • Palindrome
  • Tandem repeat
  • Time–space trade-off

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