Giovanni Manzini | DeepAI

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∙ 07/05/2023

Compressibility measures for two-dimensional data

In this paper we extend to two-dimensional data two recently introduced ...

0 Lorenzo Carfagna, et al. ∙

∙ 01/13/2023

Computing matching statistics on Wheeler DFAs

Matching statistics were introduced to solve the approximate string matc...

0 Alessio Conte, et al. ∙

∙ 08/21/2022

Teaching the Burrows-Wheeler Transform via the Positional Burrows-Wheeler Transform

The Burrows-Wheeler Transform (BWT) is often taught in undergraduate cou...

0 Travis Gagie, et al. ∙

∙ 05/11/2022

A New Class of String Transformations for Compressed Text Indexing

Introduced about thirty years ago in the field of Data Compression, the ...

0 Raffaele Giancarlo, et al. ∙

∙ 03/28/2022

Improving Matrix-vector Multiplication via Lossless Grammar-Compressed Matrices

As nowadays Machine Learning (ML) techniques are generating huge data co...

0 Paolo Ferragina, et al. ∙

∙ 11/11/2020

PHONI: Streamed Matching Statistics with Multi-Genome References

Computing the matching statistics of patterns with respect to a text is ...

0 Christina Boucher, et al. ∙

∙ 09/05/2020

Space efficient merging of de Bruijn graphs and Wheeler graphs

The merging of succinct data structures is a well established technique ...

0 Lavinia Egidi, et al. ∙

∙ 06/21/2020

PFP Data Structures

Prefix-free parsing (PFP) was introduced by Boucher et al. (2019) as a p...

0 Christina Boucher, et al. ∙

∙ 10/16/2019

Tree-Shape Grammars for Random Access

Shape grammars are well known in the graphics and design communities but...

0 Travis Gagie, et al. ∙

∙ 08/04/2019

Matching reads to many genomes with the r-index

The r-index is a tool for compressed indexing of genomic databases for e...

0 Taher Mun, et al. ∙

∙ 07/04/2019

The Alternating BWT: an algorithmic perspective

The Burrows-Wheeler Transform (BWT) is a word transformation introduced ...

0 Raffaele Giancarlo, et al. ∙

∙ 06/03/2019

Rpair: Rescaling RePair with Rsync

Data compression is a powerful tool for managing massive but repetitive ...

0 Travis Gagie, et al. ∙

∙ 05/30/2019

Inducing the Lyndon Array

In this paper we propose a variant of the induced suffix sorting algorit...

0 Felipe A. Louza, et al. ∙

∙ 03/04/2019

Lightweight merging of compressed indices based on BWT variants

In this paper we propose a flexible and lightweight technique for mergin...

0 Lavinia Egidi, et al. ∙

∙ 02/07/2019

Space-efficient merging of succinct de Bruijn graphs

We propose a new algorithm for merging succinct representations of de Br...

0 Lavinia Egidi, et al. ∙

∙ 02/04/2019

A New Class of Searchable and Provably Highly Compressible String Transformations

The Burrows-Wheeler Transform is a string transformation that plays a fu...

0 Raffaele Giancarlo, et al. ∙

∙ 11/16/2018

Efficient Construction of a Complete Index for Pan-Genomics Read Alignment

While short read aligners, which predominantly use the FM-index, are abl...

0 Alan Kuhnle, et al. ∙

∙ 05/17/2018

External memory BWT and LCP computation for sequence collections with applications

We propose an external memory algorithm for the computation of the BWT a...

0 Lavinia Egidi, et al. ∙

∙ 03/29/2018

Prefix-Free Parsing for Building Big BWTs

High-throughput sequencing technologies have led to explosive growth of ...

0 Travis Gagie, et al. ∙

∙ 10/27/2017

Lyndon Array Construction during Burrows-Wheeler Inversion

In this paper we present an algorithm to compute the Lyndon array of a s...

0 Felipe A. Louza, et al. ∙

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