Efficient computation of substring equivalence classes with suffix arrays

  • Authors:

  • Kazuyuki Narisawa;Shunsuke Inenaga;Hideo Bannai;Masayuki Takeda

  • Affiliations:

  • Department of Informatics, Kyushu University, Fukuoka, Japan;Department of Computer Science and Communication Engineering, Kyushu University, Fukuoka, Japan;Department of Informatics, Kyushu University, Fukuoka, Japan;Department of Informatics, Kyushu University, Fukuoka, Japan and SORST, Japan Science and Technology Agency

  • Venue:
  • CPM'07 Proceedings of the 18th annual conference on Combinatorial Pattern Matching
  • Year:
  • 2007

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Abstract

This paper considers enumeration of substring equivalence classes introduced by Blumer et al. [1]. They used the equivalence classes to define an index structure called compact directed acyclic word graphs (CDAWGs). In text analysis, considering these equivalence classes is useful since they group together redundant substrings with essentially identical occurrences. In this paper, we present how to enumerate those equivalence classes using suffix arrays. Our algorithm uses rank and lcp arrays for traversing the corresponding suffix trees, but does not need any other additional data structure. The algorithm runs in linear time in the length of the input string. We show experimental results comparing the running times and space consumptions of our algorithm, suffix tree and CDAWG based approaches.