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Gapped Indexing for Consecutive Occurrences

Authors Philip Bille , Inge Li Gørtz , Max Rishøj Pedersen , Teresa Anna Steiner

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Author Details

Philip Bille
  • Technical University of Denmark, DTU Compute, Lyngby, Denmark
Inge Li Gørtz
  • Technical University of Denmark, DTU Compute, Lyngby, Denmark
Max Rishøj Pedersen
  • Technical University of Denmark, DTU Compute, Lyngby, Denmark
Teresa Anna Steiner
  • Technical University of Denmark, DTU Compute, Lyngby, Denmark

Funding

  • Bille, Philip: Supported by the Danish Research Council grant DFF-8021-002498.
  • Gørtz, Inge Li: Supported by the Danish Research Council grant DFF-8021-002498.
  • Pedersen, Max Rishøj: Supported by the Danish Research Council grant DFF-8021-002498.

Cite As Get BibTex

Philip Bille, Inge Li Gørtz, Max Rishøj Pedersen, and Teresa Anna Steiner. Gapped Indexing for Consecutive Occurrences. In 32nd Annual Symposium on Combinatorial Pattern Matching (CPM 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 191, pp. 10:1-10:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021) https://doi.org/10.4230/LIPIcs.CPM.2021.10

Abstract

The classic string indexing problem is to preprocess a string S into a compact data structure that supports efficient pattern matching queries. Typical queries include existential queries (decide if the pattern occurs in S), reporting queries (return all positions where the pattern occurs), and counting queries (return the number of occurrences of the pattern). In this paper we consider a variant of string indexing, where the goal is to compactly represent the string such that given two patterns P₁ and P₂ and a gap range [α, β] we can quickly find the consecutive occurrences of P₁ and P₂ with distance in [α, β], i.e., pairs of subsequent occurrences with distance within the range. We present data structures that use Õ(n) space and query time Õ(|P₁|+|P₂|+n^{2/3}) for existence and counting and Õ(|P₁|+|P₂|+n^{2/3}occ^{1/3}) for reporting. We complement this with a conditional lower bound based on the set intersection problem showing that any solution using Õ(n) space must use Ω̃(|P₁| + |P₂| + √n) query time. To obtain our results we develop new techniques and ideas of independent interest including a new suffix tree decomposition and hardness of a variant of the set intersection problem.

Subject Classification

ACM Subject Classification
  • Theory of computation → Data structures design and analysis
  • Theory of computation → Pattern matching
Keywords
  • String indexing
  • two patterns
  • consecutive occurrences
  • conditional lower bound

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