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Counting on General Run-Length Grammars

Authors Gonzalo Navarro , Alejandro Pacheco

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Subject Classification

ACM Subject Classification
  • Theory of computation → Data structures design and analysis
Keywords
  • Grammar-based indexing
  • Run-length context-free grammars
  • Counting pattern occurrences
  • Periods in strings

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Abstract

We introduce a data structure for counting pattern occurrences in texts compressed with any run-length context-free grammar. Our structure uses space proportional to the grammar size and counts the occurrences of a pattern of length m in a text of length n in time O(mlog^{2+ε} n), for any constant ε > 0 chosen at indexing time. This is the first solution to an open problem posed by Christiansen et al. [ACM TALG 2020] and enhances our abilities for computation over compressed data; we give an example application.

Cite As Get BibTex

Gonzalo Navarro and Alejandro Pacheco. Counting on General Run-Length Grammars. In 36th Annual Symposium on Combinatorial Pattern Matching (CPM 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 331, pp. 3:1-3:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025) https://doi.org/10.4230/LIPIcs.CPM.2025.3

Author Details

Gonzalo Navarro
  • Center for Biotechnology and Bioengineering (CeBiB), Department of Computer Science, University of Chile, Santiago, Chile
Alejandro Pacheco
  • Center for Biotechnology and Bioengineering (CeBiB), Department of Computer Science, University of Chile, Santiago, Chile

Funding

  • Navarro, Gonzalo: Funded by Basal Funds FB0001 and AFB240001, Mideplan, Chile, and Fondecyt Grant 1-230755, Chile.
  • Pacheco, Alejandro: Funded by Basal Funds FB0001 and AFB240001, Mideplan, Chile, Fondecyt Grant 1-230755, Chile, and ANID/Scholarship Program/DOCTORADO BECAS CHILE/2018-21180760.

Acknowledgements

We thank the reviewers for their comments, particularly one that did an exhaustive and thoughtful job to improve our presentation.

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