On Entropy-Compressed Text Indexing in External Memory View Full Text


Ontology type: schema:Chapter      Open Access: True


Chapter Info

DATE

2009

AUTHORS

Wing-Kai Hon , Rahul Shah , Sharma V. Thankachan , Jeffrey Scott Vitter

ABSTRACT

A new trend in the field of pattern matching is to design indexing data structures which take space very close to that required by the indexed text (in entropy-compressed form) and also simultaneously achieve good query performance. Two popular indexes, namely the FM-index [Ferragina and Manzini, 2005] and the CSA [Grossi and Vitter 2005], achieve this goal by exploiting the Burrows-Wheeler transform (BWT) [Burrows and Wheeler, 1994]. However, due to the intricate permutation structure of BWT, no locality of reference can be guaranteed when we perform pattern matching with these indexes. Chien et al. [2008] gave an alternative text index which is based on sparsifying the traditional suffix tree and maintaining an auxiliary 2-D range query structure. Given a text T of length n drawn from a σ-sized alphabet set, they achieved O(n logσ)-bit index for T and showed that this index can preserve locality in pattern matching and hence is amenable to be used in external-memory settings. We improve upon this index and show how to apply entropy compression to reduce index space. Our index takes O(n(H k + 1)) + o(nlogσ) bits of space where H k is the kth-order empirical entropy of the text. This is achieved by creating variable length blocks of text using arithmetic coding. More... »

PAGES

75-89

References to SciGraph publications

  • 2007-12. Compressed Suffix Trees with Full Functionality in THEORY OF COMPUTING SYSTEMS
  • 1996. Sparse suffix trees in COMPUTING AND COMBINATORICS
  • 2006. Position-Restricted Substring Searching in LATIN 2006: THEORETICAL INFORMATICS
  • 2007. A Lempel-Ziv Text Index on Secondary Storage in COMBINATORIAL PATTERN MATCHING
  • Book

    TITLE

    String Processing and Information Retrieval

    ISBN

    978-3-642-03783-2
    978-3-642-03784-9

    From Grant

    Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1007/978-3-642-03784-9_8

    DOI

    http://dx.doi.org/10.1007/978-3-642-03784-9_8

    DIMENSIONS

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