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A New Class of Searchable and Provably Highly Compressible String Transformations

Authors Raffaele Giancarlo , Giovanni Manzini , Giovanna Rosone , Marinella Sciortino

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Author Details

Raffaele Giancarlo
  • University of Palermo, Dipartimento di Matematica e Informatica, Italy
Giovanni Manzini
  • University of Eastern Piedmont, Alessandria, Italy
  • IIT-CNR, Pisa, Italy
Giovanna Rosone
  • University of Pisa, Dipartimento di Informatica, Italy
Marinella Sciortino
  • University of Palermo, Dipartimento di Matematica e Informatica, Italy

Funding

GR and SM are partially supported by MIUR-SIR project CMACBioSeq "Combinatorial methods for analysis and compression of biological sequences" grant n. RBSI146R5L; RG and GM are partially supported by INdAM-GNCS project 2018 "Innovative methods for the solution of medical and biological big data" and MIUR-PRIN project "Multicriteria Data Structures and Algorithms: from compressed to learned indexes, and beyond" grant n. 2017WR7SHH.

Cite As Get BibTex

Raffaele Giancarlo, Giovanni Manzini, Giovanna Rosone, and Marinella Sciortino. A New Class of Searchable and Provably Highly Compressible String Transformations. In 30th Annual Symposium on Combinatorial Pattern Matching (CPM 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 128, pp. 12:1-12:12, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019) https://doi.org/10.4230/LIPIcs.CPM.2019.12

Abstract

The Burrows-Wheeler Transform is a string transformation that plays a fundamental role for the design of self-indexing compressed data structures. Over the years, researchers have successfully extended this transformation outside the domains of strings. However, efforts to find non-trivial alternatives of the original, now 25 years old, Burrows-Wheeler string transformation have met limited success. In this paper we bring new lymph to this area by introducing a whole new family of transformations that have all the "myriad virtues" of the BWT: they can be computed and inverted in linear time, they produce provably highly compressible strings, and they support linear time pattern search directly on the transformed string. This new family is a special case of a more general class of transformations based on context adaptive alphabet orderings, a concept introduced here. This more general class includes also the Alternating BWT, another invertible string transforms recently introduced in connection with a generalization of Lyndon words.

Subject Classification

ACM Subject Classification
  • Theory of computation → Data compression
  • Mathematics of computing → Combinatorial algorithms
Keywords
  • Data Indexing and Compression
  • Burrows-Wheeler Transformation
  • Combinatorics on Words

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