More time-space tradeoffs for finding a shortest unique substring

Hideo Bannai, Travis Gagie, Gary Hoppenworth, Simon J. Puglisi, Luís M.S. Russo

Research output: Contribution to journalArticlepeer-review

Abstract

We extend recent results regarding finding shortest unique substrings (SUSs) to obtain new time-space tradeoffs for this problem and the generalization of finding k-mismatch SUSs. Our new results include the first algorithm for finding a k-mismatch SUS in sublinear space, which we obtain by extending an algorithm by Senanayaka (2019) and combining it with a result on sketching by Gawrychowski and Starikovskaya (2019). We first describe how, given a text T of length n and m words of workspace, with high probability we can find an SUS of length L in O(n(L/m) log L) time using random access to T, or in O(n(L/m) log2(L) log log σ) time using O((L/m) log2 L) sequential passes over T. We then describe how, for constant k, with high probability, we can find a k-mismatch SUS in O(n1+eL/m) time using O(neL/m) sequential passes over T, again using only m words of workspace. Finally, we also describe a deterministic algorithm that takes O(nτ log σ log n) time to find an SUS using O(n/τ) words of workspace, where τ is a parameter.

Original languageEnglish
Article number234
JournalAlgorithms
Volume13
Issue number9
DOIs
Publication statusPublished - Sep 2020

All Science Journal Classification (ASJC) codes

  • Theoretical Computer Science
  • Numerical Analysis
  • Computational Theory and Mathematics
  • Computational Mathematics

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