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Computing longest common square subsequences

Authors: Takafumi Inoue, Shunsuke Inenaga, Heikki Hyyrö, Hideo Bannai, and Masayuki Takeda

Published in: LIPIcs, Volume 105, 29th Annual Symposium on Combinatorial Pattern Matching (CPM 2018)


Abstract
A square is a non-empty string of form YY. The longest common square subsequence (LCSqS) problem is to compute a longest square occurring as a subsequence in two given strings A and B. We show that the problem can easily be solved in O(n^6) time or O(|M|n^4) time with O(n^4) space, where n is the length of the strings and M is the set of matching points between A and B. Then, we show that the problem can also be solved in O(sigma |M|^3 + n) time and O(|M|^2 + n) space, or in O(|M|^3 log^2 n log log n + n) time with O(|M|^3 + n) space, where sigma is the number of distinct characters occurring in A and B. We also study lower bounds for the LCSqS problem for two or more strings.

Cite as

Takafumi Inoue, Shunsuke Inenaga, Heikki Hyyrö, Hideo Bannai, and Masayuki Takeda. Computing longest common square subsequences. In 29th Annual Symposium on Combinatorial Pattern Matching (CPM 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 105, pp. 15:1-15:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)


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@InProceedings{inoue_et_al:LIPIcs.CPM.2018.15,
  author =	{Inoue, Takafumi and Inenaga, Shunsuke and Hyyr\"{o}, Heikki and Bannai, Hideo and Takeda, Masayuki},
  title =	{{Computing longest common square subsequences}},
  booktitle =	{29th Annual Symposium on Combinatorial Pattern Matching (CPM 2018)},
  pages =	{15:1--15:13},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-074-3},
  ISSN =	{1868-8969},
  year =	{2018},
  volume =	{105},
  editor =	{Navarro, Gonzalo and Sankoff, David and Zhu, Binhai},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2018.15},
  URN =		{urn:nbn:de:0030-drops-86946},
  doi =		{10.4230/LIPIcs.CPM.2018.15},
  annote =	{Keywords: squares, subsequences, matching rectangles, dynamic programming}
}
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