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Algorithms for Finding a Minimum Repetition Representation of a String

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Title: Algorithms for Finding a Minimum Repetition Representation of a String
Authors: Nakamura, Atsuyoshi Browse this author →KAKEN DB
Saito, Tomoya Browse this author
Takigawa, Ichigaku Browse this author
Mamitsuka, Hiroshi Browse this author
Kudo, Mineichi Browse this author
Keywords: tandem repeat
string algorithm
Issue Date: 2010
Publisher: Springer Berlin / Heidelberg
Citation: String Processing and Information Retrieval (17th International Symposium, SPIRE 2010, Los Cabos, Mexico, October 11-13, 2010. Proceedings), ed. by Edgar Chavez; Stefano Lonardi, ISBN: 978-3-642-16320-3, (Lecture Notes in Computer Science; 6393/2010), pp. 185-190
Publisher DOI: 10.1007/978-3-642-16321-0_18
Abstract: A string with many repetitions can be written compactly by replacing h-fold contiguous repetitions of substring r with (r)h. We refer to such a compact representation as a repetition representation string or RRS, by which a set of disjoint or nested tandem arrays can be compacted. In this paper, we study the problem of finding a minimum RRS or MRRS, where the size of an RRS is defined to be the sum of its component letter sizes and the sizes needed to describe the repetitions (・)h which are defined as wR(h) using a repetition weight function wR. We develop two dynamic programming algorithms to solve the problem. One is CMR that works for any repetition weight function, and the other is CMR-C that is faster but can be applied only when the repetition weight function is constant. CMR-C is an O(w(n + z))-time algorithm using O(n + z) space for a given string with length n, where w and z are the number of distinct primitive tandem repeats and the number of their occurrences, respectively. Since w = O(n) and z = O(n log n) in the worst case, CMR-C is an O(n2 log n)-time O(n log n)-space algorithm, which is faster than CMR by ((log n)/n)-factor.
Rights: The original publication is available at
Type: bookchapter (author version)
Appears in Collections:情報科学院・情報科学研究院 (Graduate School of Information Science and Technology / Faculty of Information Science and Technology) > 雑誌発表論文等 (Peer-reviewed Journal Articles, etc)

Submitter: 中村 篤祥

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