Related papers: A New Class of String Transformations for Compress…
Mantaci et al. [TCS 2007] defined the eBWT to extend the definition of the BWT to a collection of strings, however, since this introduction, it has been used more generally to describe any BWT of a collection of strings and the fundamental…
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…
We show how to merge two run-length compressed Burrows-Wheeler Transforms (RLBWTs) into a run-length compressed extended Burrows-Wheeler Transform (eBWT) in $O (r)$ space and $O ((r + L) \log (m + n))$ time, where $m$ and $n$ are the…
Enumerating characteristic substrings (e.g., maximal repeats, minimal unique substrings, and minimal absent words) in a given string has been an important research topic because there are a wide variety of applications in various areas such…
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…
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…
Ordering the collection of states of a given automaton starting from an order of the underlying alphabet is a natural move towards a computational treatment of the language accepted by the automaton. Along this path, Wheeler \emph{graphs}…
We investigate various connections between the clustering for the Burrows-Wheeler transform, a lossless algorithm used in data compression, and languages of interval exchange transformations. We show that a primitive word $u$ clusters for a…
We propose a novel transformer-based styled handwritten text image generation approach, HWT, that strives to learn both style-content entanglement as well as global and local writing style patterns. The proposed HWT captures the long and…
In this paper, we describe a new type of match between a pattern and a text that aren't necessarily maximal in the query, but still contain useful matching information: locally maximal exact matches (LEMs). There are usually a large amount…
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…
A self-index is a compressed data structure that supports locate queries -- reporting all positions where a given pattern occurs in a string while maintaining the string in compressed form. While many self-indexes have been proposed,…
Converting a compressed format of a string into another compressed format without an explicit decompression is one of the central research topics in string processing. We discuss the problem of converting the run-length Burrows-Wheeler…
We describe a grammar for DNA sequencing reads from which we can compute the BWT directly. Our motivation is to perform in succinct space genomic analyses that require complex string queries not yet supported by repetition-based…
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…
An indexed sequence of strings is a data structure for storing a string sequence that supports random access, searching, range counting and analytics operations, both for exact matches and prefix search. String sequences lie at the core of…
Consider an input text string T[1,N] drawn from an unbounded alphabet. We study partial computation in suffix-based problems for Data Compression and Text Indexing such as (I) retrieve any segment of K<=N consecutive symbols from the…
The rise of repetitive datasets has lately generated a lot of interest in compressed self-indexes based on dictionary compression, a rich and heterogeneous family that exploits text repetitions in different ways. For each such compression…
Advances in DNA sequencing technology have stimulated the development of algorithms and tools for processing very large collections of short strings (reads). Short-read alignment and assembly are among the most well-studied problems. Many…
Transformer architectures, underpinned by the self-attention mechanism, have achieved state-of-the-art results across numerous natural language processing (NLP) tasks by effectively modeling long-range dependencies. However, the…