Dynamic dictionary matching and compressed suffix trees

  • Authors:

  • Ho-Leung Chan;Wing-Kai Hon;Tak-Wah Lam;Kunihiko Sadakane

  • Affiliations:

  • The University of Hong Kong, Hong Kong;The University of Hong Kong, Hong Kong;The University of Hong Kong, Hong Kong;Kyushu University, Japan

  • Venue:
  • SODA '05 Proceedings of the sixteenth annual ACM-SIAM symposium on Discrete algorithms
  • Year:
  • 2005

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Abstract

Recent breakthrough in compressed indexing data structures has reduced the space for indexing a text (or a collection of texts) of length n from O(n log n) bits to O(n) bits, while allowing very efficient pattern matching [10, 13]. Yet the compressed nature of such indices also makes them difficult to update dynamically. This paper presents the first O(n)-bit representation of a suffix tree for a dynamic collection of texts whose total length is n, which supports insertion and deletion of a text T in O(|T | log2 n) time, as well as all suffix tree traversal operations, including forward and backward suffix links. This work can be regarded as a generalization of the compressed representation of static texts. Our new suffix tree representation serves as a core part in a compact solution for the dynamic dictionary matching problem, i.e., providing an O(d)-bit data structure for a dynamic collection of patterns of total length d that can support the dictionary matching query efficiently. When compared with the O(d log d)-bit suffix tree based solution of Amir et al., the compact solution increases the query time by roughly a factor of log d only. In the study of the above results, we also derive the first O(n)-bit representation for maintaining n pairs of balanced parentheses in O(log n/log log n) time per operation, matching the time complexity of the previous O(n log n)-bit solution.