Related papers: Tag arrays
Due to the exponential growth of genomic data, constructing dedicated data structures has become the principal bottleneck in common bioinformatics applications. In particular, the Burrows-Wheeler Transform (BWT) is the basis of some of the…
In recent years, robots are used in an increasing variety of tasks, especially by small- and medium- sized enterprises. These tasks are usually fast-changing, they have a collaborative scenario and happen in unpredictable environments with…
Highly-repetitive collections of strings are increasingly being amassed by genome sequencing and genetic variation experiments, as well as by storing all versions of human-generated files, like webpages and source code. Existing indexes for…
Constructing the Burrows-Wheeler transform (BWT) for long strings poses significant challenges regarding construction time and memory usage. We use a prefix of the suffix array to partition a long string into shorter substrings, thereby…
The sort transform (ST) is a modification of the Burrows-Wheeler transform (BWT). Both transformations map an arbitrary word of length n to a pair consisting of a word of length n and an index between 1 and n. The BWT sorts all rotation…
The positional Burrows-Wheeler Transform (PBWT) is commonly used to store haplotype panels compactly in such a way that, given a query haplotype, we can quickly find the set maximal exact matches (SMEMs) between the query and the haplotypes…
Abstract Contextuality is a property of systems of random variables. The identity of a random variable in a system is determined by its joint distribution with all other random variables in the same context. When context changes, a variable…
Recently, there has been growing interest in the ability of Transformer-based models to produce meaningful embeddings of text with several applications, such as text similarity. Despite significant progress in the field, the explanations…
Modern genomic analyses increasingly rely on pangenomes, that is, representations of the genome of entire populations. The simplest representation of a pangenome is a set of individual genome sequences. Compared to e.g. sequence graphs,…
In highly repetitive strings, like collections of genomes from the same species, distinct measures of repetition all grow sublinearly in the length of the text, and indexes targeted to such strings typically depend only on one of these…
In order to avoid the reference bias introduced by mapping reads to a reference genome, bioinformaticians are investigating reference-free methods for analyzing sequenced genomes. With large projects sequencing thousands of individuals,…
Many of language models' impressive capabilities originate from their in-context learning: based on instructions or examples, they can infer and perform new tasks without weight updates. In this work, we investigate when representations for…
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…
An important question concerning contextualized word embedding (CWE) models like BERT is how well they can represent different word senses, especially those in the long tail of uncommon senses. Rather than build a WSD system as in previous…
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 texts…
When coping with literary texts such as novels or short stories, the extraction of structured information in the form of a knowledge graph might be hindered by the huge number of possible relations between the entities corresponding to the…
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…
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}…
It is well known that attributed tree transducers can be equipped with "regular look-around" in order to obtain a more robust class of translations. We present two characterizations of this class in terms of macro tree transducers (MTTs):…
We propose algorithms that, given the input string of length $n$ over integer alphabet of size $\sigma$, construct the Burrows-Wheeler transform (BWT), the permuted longest-common-prefix (PLCP) array, and the LZ77 parsing in…