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Construction of Sparse Suffix Trees and LCE Indexes in Optimal Time and Space

Authors Dmitry Kosolobov , Nikita Sivukhin

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Author Details

Dmitry Kosolobov
  • Ural Federal University, Ekaterinburg, Russia
Nikita Sivukhin
  • Ural Federal University, Ekaterinburg, Russia

Funding

Supported by the Russian Science Foundation (RSF), project 20-71-00050.

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Dmitry Kosolobov and Nikita Sivukhin. Construction of Sparse Suffix Trees and LCE Indexes in Optimal Time and Space. In 35th Annual Symposium on Combinatorial Pattern Matching (CPM 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 296, pp. 20:1-20:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024) https://doi.org/10.4230/LIPIcs.CPM.2024.20

Abstract

The notions of synchronizing and partitioning sets are recently introduced variants of locally consistent parsings with a great potential in problem-solving. In this paper we propose a deterministic algorithm that constructs for a given readonly string of length n over the alphabet {0,1,…,n^{𝒪(1)}} a variant of a τ-partitioning set with size 𝒪(b) and τ = n/b using 𝒪(b) space and 𝒪(1/(ε)n) time provided b ≥ n^ε, for ε > 0. As a corollary, for b ≥ n^ε and constant ε > 0, we obtain linear time construction algorithms with 𝒪(b) space on top of the string for two major small-space indexes: a sparse suffix tree, which is a compacted trie built on b chosen suffixes of the string, and a longest common extension (LCE) index, which occupies 𝒪(b) space and allows us to compute the longest common prefix for any pair of substrings in 𝒪(n/b) time. For both, the 𝒪(b) construction storage is asymptotically optimal since the tree itself takes 𝒪(b) space and any LCE index with 𝒪(n/b) query time must occupy at least 𝒪(b) space by a known trade-off (at least for b ≥ Ω(n / log n)). In case of arbitrary b ≥ Ω(log² n), we present construction algorithms for the partitioning set, sparse suffix tree, and LCE index with 𝒪(nlog_b n) running time and 𝒪(b) space, thus also improving the state of the art.

Subject Classification

ACM Subject Classification
  • Theory of computation → Design and analysis of algorithms
Keywords
  • (τ,δ)-partitioning set
  • longest common extension
  • sparse suffix tree

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