Search results for "Burrows"

Burrows–Wheeler transform and Sturmian words

2003

The Myriad Virtues of Wavelet Trees

2009

Wavelet Trees have been introduced in [Grossi, Gupta and Vitter, SODA '03] and have been rapidly recognized as a very flexible tool for the design of compressed full-text indexes and data compressors. Although several papers have investigated the beauty and usefulness of this data structure in the full-text indexing scenario, its impact on data compression has not been fully explored. In this paper we provide a complete theoretical analysis of a wide class of compression algorithms based on Wavelet Trees. We also show how to improve their asymptotic performance by introducing a novel framework, called Generalized Wavelet Trees, that aims for the best combination of binary compressors (like,…

Logarithmic Equal-Letter Runs for BWT of Purely Morphic Words

2022

In this paper we study the number r(bwt) of equal-letter runs produced by the Burrows-Wheeler transform (BWT) when it is applied to purely morphic finite words, which are words generated by iterating prolongable morphisms. Such a parameter r(bwt) is very significant since it provides a measure of the performances of the BWT, in terms of both compressibility and indexing. In particular, we prove that, when BWT is applied to whichever purely morphic finite word on a binary alphabet, r(bwt) is O(log n), where n is the length of the word. Moreover, we prove that r(bwt) is Theta(log n) for the binary words generated by a large class of prolongable binary morphisms. These bounds are proved by pro…

A New Combinatorial Approach to Sequence Comparison

2008

In this paper we introduce a new alignment-free method for comparing sequences which is combinatorial by nature and does not use any compressor nor any information-theoretic notion. Such a method is based on an extension of the Burrows-Wheeler Transform, a transformation widely used in the context of Data Compression. The new extended transformation takes as input a multiset of sequences and produces as output a string obtained by a suitable rearrangement of the characters of all the input sequences. By using such a transformation we give a general method for comparing sequences that takes into account how much the characters coming from the different input sequences are mixed in the output…

From First Principles to the Burrows and Wheeler Transform and Beyond, via Combinatorial Optimization

2007

AbstractWe introduce a combinatorial optimization framework that naturally induces a class of optimal word permutations with respect to a suitably defined cost function taking into account various measures of relatedness between words. The Burrows and Wheeler transform (bwt) (cf. [M. Burrows, D. Wheeler, A block sorting lossless data compression algorithm, Technical Report 124, Digital Equipment Corporation, 1994]), and its analog for labelled trees (cf. [P. Ferragina, F. Luccio, G. Manzini, S. Muthukrishnan, Structuring labeled trees for optimal succinctness, and beyond, in: Proc. of the 45th Annual IEEE Symposium on Foundations of Computer Science, 2005, pp. 198–207]), are special cases i…

Relationships between earthworm communities and burrow numbers under different land use systems

2010

International audience; This study addresses the influence of three different land use systems (continuous maize, pasture/maize rotation, permanent pasture) on the relationships between earthworm populations and the number of earthworm burrows quantified in a soil profile. Quantified burrows were limited to those observable by the naked eye (i.e. >2 mm in diameter) and enumerated earthworms were limited to those which could have created the observable burrows (i.e. >0.3 g). The results were combined with data from the literature coming from different geographical regions. This study showed that earthworm abundance decreased with the increasing land management intensity (maize crop vs. pastu…

Optimal Partitions of Strings: A New Class of Burrows-Wheeler Compression Algorithms

2003

The Burrows-Wheeler transform [1] is one of the mainstays of lossless data compression. In most cases, its output is fed to Move to Front or other variations of symbol ranking compression. One of the main open problems [2] is to establish whether Move to Front, or more in general symbol ranking compression, is an essential part of the compression process. We settle this question positively by providing a new class of Burrows-Wheeler algorithms that use optimal partitions of strings, rather than symbol ranking, for the additional step. Our technique is a quite surprising specialization to strings of partitioning techniques devised by Buchsbaum et al. [3] for two-dimensional table compression…

Computing the Original eBWT Faster, Simpler, and with Less Memory

2021

Mantaci et al. [TCS 2007] defined the \(\mathrm {eBWT}\) to extend the definition of the \(\mathrm {BWT}\) to a collection of strings. However, since this introduction, it has been used more generally to describe any \(\mathrm {BWT}\) of a collection of strings, and the fundamental property of the original definition (i.e., the independence from the input order) is frequently disregarded. In this paper, we propose a simple linear-time algorithm for the construction of the original \(\mathrm {eBWT}\), which does not require the preprocessing of Bannai et al. [CPM 2021]. As a byproduct, we obtain the first linear-time algorithm for computing the \(\mathrm {BWT}\) of a single string that uses …

Lossless and nearly-lossless image compression based on combinatorial transforms

2011

Common image compression standards are usually based on frequency transform such as Discrete Cosine Transform or Wavelets. We present a different approach for loss-less image compression, it is based on combinatorial transform. The main transform is Burrows Wheeler Transform (BWT) which tends to reorder symbols according to their following context. It becomes a promising compression approach based on contextmodelling. BWT was initially applied for text compression software such as BZIP2 ; nevertheless it has been recently applied to the image compression field. Compression scheme based on Burrows Wheeler Transform is usually lossless ; therefore we imple-ment this algorithm in medical imagi…

r-Indexing the eBWT

2021

The extended Burrows Wheeler Transform (\(\mathrm {eBWT}\)) was introduced by Mantaci et al. [TCS 2007] to extend the definition of the \(\mathrm {BWT}\) to a collection of strings. In our prior work [SPIRE 2021], we give a linear-time algorithm for the \(\mathrm {eBWT}\) that preserves the fundamental property of the original definition (i.e., the independence from the input order). The algorithm combines a modification of the Suffix Array Induced Sorting (SAIS) algorithm [IEEE Trans Comput 2011] with Prefix Free Parsing [AMB 2019; JCB 2020]. In this paper, we show how this construction algorithm leads to r-indexing the \(\mathrm {eBWT}\), i.e., run-length encoded \(\mathrm {eBWT}\) and \(…