Related papers: Bit catastrophes for the Burrows-Wheeler Transform
Compression algorithms and streaming algorithms are both powerful tools for dealing with massive data sets, but many of the best compression algorithms -- e.g., those based on the Burrows-Wheeler Transform -- at first seem incompatible with…
We study the sensitivity of the Lempel-Ziv 77 compression algorithm to edits, showing how modifying a string $w$ can deteriorate or improve its compression. Our first result is a tight upper bound for $k$ edits: $\forall w' \in B(w,k)$, we…
The compact directed acyclic word graph (CDAWG) of a string $T$ is an index occupying $O(\mathsf{e})$ space, where $\mathsf{e}$ is the number of right extensions of maximal repeats in $T$. For highly repetitive datasets, the measure…
In 1994, Burrows and Wheeler developed a data compression algorithm which performs significantly better than Lempel-Ziv based algorithms. Since then, a lot of work has been done in order to improve their algorithm, which is based on a…
Consider a binary string $x$ of length $n$ whose Kolmogorov complexity is $\alpha n$ for some $\alpha<1$. We want to increase the complexity of $x$ by changing a small fraction of bits in $x$. This is always possible: Buhrman, Fortnow,…
A wavelet forest for a text $T [1..n]$ over an alphabet $\sigma$ takes $n H_0 (T) + o (n \log \sigma)$ bits of space and supports access and rank on $T$ in $O (\log \sigma)$ time. K\"arkk\"ainen and Puglisi (2011) implicitly introduced…
In the field of compressed string indexes, recent work has introduced suffixient sets and their corresponding repetitiveness measure $\chi$. In particular, researchers have explored its relationship to other repetitiveness measures, notably…
This paper provides an upper bound for several subsets of maximal repeats and maximal pairs in compressed strings and also presents a formerly unknown relationship between maximal pairs and the run-length Burrows-Wheeler transform. This…
A degenerate or indeterminate string on an alphabet $\Sigma$ is a sequence of non-empty subsets of $\Sigma$. Given a degenerate string $t$ of length $n$, we present a new method based on the Burrows--Wheeler transform for searching for a…
The Burrows Wheeler transform has applications in data compression as well as full text indexing. Despite its important applications and various existing algorithmic approaches the construction of the transform for large data sets is still…
Large-alphabet strings are common in scenarios such as information retrieval and natural-language processing. The efficient storage and processing of such strings usually introduces several challenges that are not witnessed in…
Compressed suffix arrays (CSAs) index large repetitive collections and are key in many text applications. The r-index and its derivatives combine the run-length Burrows-Wheeler Transform (BWT) with suffix array sampling to achieve space…
With the rapid growing of data and number of applications, there is a crucial need of dictionary based reversible transformation techniques to increase the efficiency of the compression algorithms and hence contribute towards the…
Entropy quantifies the number of bits required to store objects under certain given assumptions. While this is a well established concept for strings, in the context of tries the state-of-the-art regarding entropies is less developed. The…
We study the maximum size of a set system on $n$ elements whose trace on any $b$ elements has size at most $k$. We show that if for some $b \ge i \ge 0$ the shatter function $f_R$ of a set system $([n],R)$ satisfies $f_R(b) < 2^i(b-i+1)$…
Indexing highly repetitive texts --- such as genomic databases, software repositories and versioned text collections --- has become an important problem since the turn of the millennium. A relevant compressibility measure for repetitive…
A weight based dynamic compression method has recently been proposed, which is especially suitable for the encoding of files with locally skewed distributions. Its main idea is to assign larger weights to closer to be encoded symbols by…
The Positional Burrows--Wheeler Transform (PBWT) is a data structure designed for efficiently representing and querying large collections of sequences, such as haplotype panels in genomics. Forward and backward stepping operations --…
We show that the Longest Common Prefix Array of a text collection of total size n on alphabet [1, {\sigma}] can be computed from the Burrows-Wheeler transformed collection in O(n log {\sigma}) time using o(n log {\sigma}) bits of working…
Assuming we are in a Word-RAM model with word size $w$, we show that we can construct in $o(w)$ time an error correcting code with a constant relative positive distance that maps numbers of $w$ bits into $\Theta(w)$-bit numbers, and such…