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Searching Long Repeats in Streams

Authors Oleg Merkurev, Arseny M. Shur

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Author Details

Oleg Merkurev
  • Ural Federal University, Ekaterinburg, Russia
Arseny M. Shur
  • Ural Federal University, Ekaterinburg, Russia

Funding

  • Merkurev, Oleg: Supported by the Russian Ministry of Education and Science, project 1.3253.2017.
  • Shur, Arseny M.: Supported by the Russian Ministry of Education and Science, project 1.3253.2017.

Acknowledgements

The authors are grateful to D. Kosolobov for very useful comments.

Cite AsGet BibTex

Oleg Merkurev and Arseny M. Shur. Searching Long Repeats in Streams. In 30th Annual Symposium on Combinatorial Pattern Matching (CPM 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 128, pp. 31:1-31:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)
https://doi.org/10.4230/LIPIcs.CPM.2019.31

Abstract

We consider two well-known related problems: Longest Repeated Substring (LRS) and Longest Repeated Reversed Substring (LRRS). Their streaming versions cannot be solved exactly; we show that only approximate solutions by Monte Carlo algorithms are possible, and prove a lower bound on consumed memory. For both problems, we present purely linear-time Monte Carlo algorithms working in O(E + n/E) space, where E is the additive approximation error. Within the same space bounds, we then present nearly real-time solutions, which require O(log n) time per symbol and O(n + n/E log n) time overall. The working space exactly matches the lower bound whenever E=O(n^{0.5}) and the size of the alphabet is Omega(n^{0.01}).

Subject Classification

ACM Subject Classification
  • Theory of computation → Streaming, sublinear and near linear time algorithms
Keywords
  • Longest repeated substring
  • longest repeated reversed substring
  • streaming algorithm
  • Karp
  • Rabin fingerprint
  • suffix tree

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