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A Class of Heuristics for Reducing the Number of BWT-Runs in the String Ordering Problem

Authors Gianmarco Bertola, Anthony J. Cox, Veronica Guerrini , Giovanna Rosone

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Author Details

Gianmarco Bertola
  • Department of Computer Science, University of Pisa, Italy
Anthony J. Cox
  • Independent Researcher, Cambridge, UK
Veronica Guerrini
  • Department of Computer Science, University of Pisa, Italy
Giovanna Rosone
  • Department of Computer Science, University of Pisa, Italy

Funding

Work partially supported by PNRR - M4C2 - Investimento 1.5, Ecosistema dell'Innovazione ECS00000017 - "THE - Tuscany Health Ecosystem" - Spoke 6 "Precision medicine & personalized healthcare", funded by the European Commission under the NextGeneration EU programme, by the MUR PRIN 2022YRB97K PINC and by INdAM - GNCS Project, codice CUP_E53C23001670001.

Cite AsGet BibTex

Gianmarco Bertola, Anthony J. Cox, Veronica Guerrini, and Giovanna Rosone. A Class of Heuristics for Reducing the Number of BWT-Runs in the String Ordering Problem. In 35th Annual Symposium on Combinatorial Pattern Matching (CPM 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 296, pp. 7:1-7:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
https://doi.org/10.4230/LIPIcs.CPM.2024.7

Abstract

The Burrows-Wheeler transform (BWT) is a famous text transformation that rearranges the symbols of the input strings so that occurrences of a same symbol tend to occur in runs. The number of runs is an important parameter in the BWT output string, historically associated with its high compressibility and more recently used as a measure for the space complexity of efficient data structures. It is a known fact that reordering the strings in the input collection 𝒮 affects the number of runs in the output string bwt(𝒮) produced by applying the BWT to the string collection. In this paper, we define a class of transformed strings where symbols in particular blocks of the bwt(𝒮) can be reordered according to a different adaptive alphabet order. Then, we introduce new heuristics to reduce the number of runs in the BWT output of a string collection that improve on the two existing heuristics introduced in Cox et al. [Anthony J. Cox et al., 2012]. These new heuristics are computed when applying the BWT to a string collection assuming no a priori order on the input strings and without requiring any pre- and/or post- processing of the collection 𝒮 or of the BWT string. In this paper, we also face the problem of reconstructing the input collection 𝒮 from the string bwt(𝒮) together with the string permutation realized when applying an alphabetical reordering of symbols during the construction of bwt(𝒮).

Subject Classification

ACM Subject Classification
  • Theory of computation → Data compression
  • Applied computing → Bioinformatics
Keywords
  • Burrows-Wheeler Transform
  • SAP-interval
  • repetitive text
  • string compression

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References

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