Practical Random Access to SLP-Compressed Texts

Gagie, Travis; Sakamoto, Hiroshi; Benkner, Louisa Seelbach; Takabatake, Yoshimasa; Thankachan, SV

Abstract

Grammar-based compression is a popular and powerful approach to compressing repetitive texts but until recently its relatively poor time-space trade-offs during real-life construction made it impractical for truly massive datasets such as genomic databases. In a recent paper (SPIRE 2019) we showed how simple pre-processing can dramatically improve those trade-offs, and in this paper we turn our attention to one of the features that make grammar-based compression so attractive: the possibility of supporting fast random access. This is an essential primitive in many algorithms that process grammar-compressed texts without decompressing them and so many theoretical bounds have been published about it, but experimentation has lagged behind. We give a new encoding of grammars that is about as small as the practical state of the art (Maruyama et al., SPIRE 2013) but with significantly faster queries.

Más información

Título según WOS: ID WOS:001344660300016 Not found in local WOS DB
Título de la Revista: STRING PROCESSING AND INFORMATION RETRIEVAL, SPIRE 2020
Volumen: 12303
Editorial: SPRINGER INTERNATIONAL PUBLISHING AG
Fecha de publicación: 2020
Página de inicio: 221
Página final: 231
DOI:

10.1007/978-3-030-59212-7_16

Notas: ISI