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Track A: Algorithms, Complexity and Games
Streaming k-Edit Approximate Pattern Matching via String Decomposition

Authors: Sudatta Bhattacharya and Michal Koucký

Published in: LIPIcs, Volume 261, 50th International Colloquium on Automata, Languages, and Programming (ICALP 2023)


Abstract
In this paper we give an algorithm for streaming k-edit approximate pattern matching which uses space Õ(k²) and time Õ(k²) per arriving symbol. This improves substantially on the recent algorithm of Kociumaka, Porat and Starikovskaya [Kociumaka et al., 2022] which uses space Õ(k⁵) and time Õ(k⁸) per arriving symbol. In the k-edit approximate pattern matching problem we get a pattern P and text T and we want to identify all substrings of the text T that are at edit distance at most k from P. In the streaming version of this problem both the pattern and the text arrive in a streaming fashion symbol by symbol and after each symbol of the text we need to report whether there is a current suffix of the text with edit distance at most k from P. We measure the total space needed by the algorithm and time needed per arriving symbol.

Cite as

Sudatta Bhattacharya and Michal Koucký. Streaming k-Edit Approximate Pattern Matching via String Decomposition. In 50th International Colloquium on Automata, Languages, and Programming (ICALP 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 261, pp. 22:1-22:14, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2023)


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@InProceedings{bhattacharya_et_al:LIPIcs.ICALP.2023.22,
  author =	{Bhattacharya, Sudatta and Kouck\'{y}, Michal},
  title =	{{Streaming k-Edit Approximate Pattern Matching via String Decomposition}},
  booktitle =	{50th International Colloquium on Automata, Languages, and Programming (ICALP 2023)},
  pages =	{22:1--22:14},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-278-5},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{261},
  editor =	{Etessami, Kousha and Feige, Uriel and Puppis, Gabriele},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ICALP.2023.22},
  URN =		{urn:nbn:de:0030-drops-180741},
  doi =		{10.4230/LIPIcs.ICALP.2023.22},
  annote =	{Keywords: Approximate pattern matching, edit distance, streaming algorithms}
}
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