Computing longest common square subsequences

Takafumi Inoue, Shunsuke Inenaga, Heikki Hyyrö, Hideo Bannai, Masayuki Takeda

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

A square is a non-empty string of form Y Y. 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(n6) time or O(|M|n4) time with O(n4) 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(σ|M|3 + n) time and O(|M|2 + n) space, or in O(|M|3 log2 n log log n + n) time with O(|M|3 + n) space, where σ 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.

Original languageEnglish
Title of host publication29th Annual Symposium on Combinatorial Pattern Matching, CPM 2018
EditorsBinhai Zhu, Gonzalo Navarro, David Sankoff
PublisherSchloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing
Pages151-1513
Number of pages1363
ISBN (Electronic)9783959770743
DOIs
Publication statusPublished - May 1 2018
Event29th Annual Symposium on Combinatorial Pattern Matching, CPM 2018 - Qingdao, China
Duration: Jul 2 2018Jul 4 2018

Publication series

NameLeibniz International Proceedings in Informatics, LIPIcs
Volume105
ISSN (Print)1868-8969

Other

Other29th Annual Symposium on Combinatorial Pattern Matching, CPM 2018
CountryChina
CityQingdao
Period7/2/187/4/18

All Science Journal Classification (ASJC) codes

  • Software

Cite this

Inoue, T., Inenaga, S., Hyyrö, H., Bannai, H., & Takeda, M. (2018). Computing longest common square subsequences. In B. Zhu, G. Navarro, & D. Sankoff (Eds.), 29th Annual Symposium on Combinatorial Pattern Matching, CPM 2018 (pp. 151-1513). (Leibniz International Proceedings in Informatics, LIPIcs; Vol. 105). Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing. https://doi.org/10.4230/LIPIcs.CPM.2018.15

Computing longest common square subsequences. / Inoue, Takafumi; Inenaga, Shunsuke; Hyyrö, Heikki; Bannai, Hideo; Takeda, Masayuki.

29th Annual Symposium on Combinatorial Pattern Matching, CPM 2018. ed. / Binhai Zhu; Gonzalo Navarro; David Sankoff. Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing, 2018. p. 151-1513 (Leibniz International Proceedings in Informatics, LIPIcs; Vol. 105).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Inoue, T, Inenaga, S, Hyyrö, H, Bannai, H & Takeda, M 2018, Computing longest common square subsequences. in B Zhu, G Navarro & D Sankoff (eds), 29th Annual Symposium on Combinatorial Pattern Matching, CPM 2018. Leibniz International Proceedings in Informatics, LIPIcs, vol. 105, Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing, pp. 151-1513, 29th Annual Symposium on Combinatorial Pattern Matching, CPM 2018, Qingdao, China, 7/2/18. https://doi.org/10.4230/LIPIcs.CPM.2018.15
Inoue T, Inenaga S, Hyyrö H, Bannai H, Takeda M. Computing longest common square subsequences. In Zhu B, Navarro G, Sankoff D, editors, 29th Annual Symposium on Combinatorial Pattern Matching, CPM 2018. Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing. 2018. p. 151-1513. (Leibniz International Proceedings in Informatics, LIPIcs). https://doi.org/10.4230/LIPIcs.CPM.2018.15
Inoue, Takafumi ; Inenaga, Shunsuke ; Hyyrö, Heikki ; Bannai, Hideo ; Takeda, Masayuki. / Computing longest common square subsequences. 29th Annual Symposium on Combinatorial Pattern Matching, CPM 2018. editor / Binhai Zhu ; Gonzalo Navarro ; David Sankoff. Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing, 2018. pp. 151-1513 (Leibniz International Proceedings in Informatics, LIPIcs).
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