Finding optimal pairs of cooperative and competing patterns with bounded distance

Shunsuke Inenaga, Hideo Bannai, Heikki Hyyrö, Ayumi Shinohara, Masayuki Takeda, Kenta Nakai, Satoru Miyano

Research output: Chapter in Book/Report/Conference proceedingChapter

10 Citations (Scopus)

Abstract

We consider the problem of discovering the optimal pair of substring patterns with bounded distance α, from a given set S of strings. We study two kinds of pattern classes, one is in form p ∧α q that are interpreted as cooperative patterns within α distance, and the other is in form p ∧α ¬q representing competing patterns, with respect to S. We show an efficient algorithm to find the optimal pair of patterns in O(N2) time using O(N) space. We also present an O(m 2N2) time and O(m2N) space solution to a more difficult version of the optimal pattern pair discovery problem, where m denotes the number of strings in S.

Original languageEnglish
Title of host publicationLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
EditorsEinoshin Suzuki, Setsuo Arikawa
PublisherSpringer Verlag
Pages32-46
Number of pages15
ISBN (Print)9783540233572
DOIs
Publication statusPublished - Jan 1 2004

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume3245
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

All Science Journal Classification (ASJC) codes

  • Theoretical Computer Science
  • Computer Science(all)

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  • Cite this

    Inenaga, S., Bannai, H., Hyyrö, H., Shinohara, A., Takeda, M., Nakai, K., & Miyano, S. (2004). Finding optimal pairs of cooperative and competing patterns with bounded distance. In E. Suzuki, & S. Arikawa (Eds.), Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (pp. 32-46). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 3245). Springer Verlag. https://doi.org/10.1007/978-3-540-30214-8_3