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Finding Optimal Pairs of Cooperative and Competing Patterns with Bounded Distance

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Discovery Science (DS 2004)

Part of the book series: Lecture Notes in Computer Science ((LNAI,volume 3245))

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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 \(p \land_\alpha q\) that are interpreted as cooperative patterns within α distance, and the other is in form \(p \land_\alpha \lnot q\) representing competing patterns, with respect to S. We show an efficient algorithm to find the optimal pair of patterns in O(N 2) time using O(N) space. We also present an O(m 2 N 2) time and O(m 2 N) space solution to a more difficult version of the optimal pattern pair discovery problem, where m denotes the number of strings in S.

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Author information

Authors and Affiliations

  1. Department of Computer Science, University of Helsinki, P.O. Box 26, (Teollisuuskatu 23), FIN-00014, Finland

    Shunsuke Inenaga

  2. Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639, Japan

    Hideo Bannai, Kenta Nakai & Satoru Miyano

  3. PRESTO, Japan Science and Technology Agency (JST),  

    Heikki Hyyrö & Ayumi Shinohara

  4. SORST, Japan Science and Technology Agency (JST),  

    Masayuki Takeda

  5. Department of Informatics, Kyushu University 33, Fukuoka, 812-8581, Japan

    Ayumi Shinohara & Masayuki Takeda

Authors
  1. Shunsuke Inenaga
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  2. Hideo Bannai
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  3. Heikki Hyyrö
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  4. Ayumi Shinohara
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  5. Masayuki Takeda
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  6. Kenta Nakai
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  7. Satoru Miyano
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Editor information

Editors and Affiliations

  1. Department of Informatics, Graduate School of Information Science and Electrical Engineering, Kyushu University, 744 Motooka, Nishi, 819-0395, Fukuoka, Japan

    Einoshin Suzuki

  2. Kyushu University, 6–10–1 Hakozaki Higashi-ku, 812–8581, Fukuoka, Japan

    Setsuo Arikawa

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© 2004 Springer-Verlag Berlin Heidelberg

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Inenaga, S. et al. (2004). Finding Optimal Pairs of Cooperative and Competing Patterns with Bounded Distance. In: Suzuki, E., Arikawa, S. (eds) Discovery Science. DS 2004. Lecture Notes in Computer Science(), vol 3245. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-30214-8_3

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  • DOI: https://doi.org/10.1007/978-3-540-30214-8_3

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-23357-2

  • Online ISBN: 978-3-540-30214-8

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