相关论文: Prefix-free parsing for building large tunnelled W…

When building Burrows-Wheeler Transforms (BWTs) of truly huge datasets, prefix-free parsing (PFP) can use an unreasonable amount of memory. In this paper we show how if a dataset can be broken down into small datasets that are not very…

Prefix-free parsing (PFP) was introduced by Boucher et al. (2019) as a preprocessing step to ease the computation of Burrows-Wheeler Transforms (BWTs) of genomic databases. Given a string $S$, it produces a dictionary $D$ and a parse $P$ of…

High-throughput sequencing technologies have led to explosive growth of genomic databases; one of which will soon reach hundreds of terabytes. For many applications we want to build and store indexes of these databases but constructing such…

Motivated by challenges in pangenomic read alignment, we propose a generalization of Wheeler graphs that we call Wheeler maps. A Wheeler map stores a text $T[1..n]$ and an assignment of tags to the characters of $T$ such that we can…

A recent paradigm shift in bioinformatics from a single reference genome to a pangenome brought with it several graph structures. These graph structures must implement operations, such as efficient construction from multiple genomes and…

In recent years several compressed indexes based on variants of the Burrows-Wheeler transformation have been introduced. Some of these index structures far more complex than a single string, as was originally done with the FM-index…

The Burrows-Wheeler Transform (BWT) is an important technique both in data compression and in the design of compact indexing data structures. It has been generalized from single strings to collections of strings and some classes of labeled…

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…

The Burrows-Wheeler Transform (BWT) has been an essential tool in text compression and indexing. First introduced in 1994, it went on to provide the backbone for the first encoding of the classic suffix tree data structure in space close to…

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 --…

FM-indexes are a crucial data structure in DNA alignment, for example, but searching with them usually takes at least one random access per character in the query pattern. Ferragina and Fischer observed in 2007 that word-based indexes often…

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…

Prefix parsing asks whether an input prefix can be extended to a complete string generated by a given grammar. In the weighted setting, it also provides prefix probabilities, which are central to context-free language modeling,…

Recently, Cenzato et al.\ proposed a new text index, called the \emph{suffixient array}, which is a subset of the suffix array and supports locating a single pattern occurrence or finding its maximal exact matches (MEMs), assuming random…

Indexing strings via prefix (or suffix) sorting is, arguably, one of the most successful algorithmic techniques developed in the last decades. Can indexing be extended to languages? The main contribution of this paper is to initiate the…

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}…

Large graph datasets make training graph neural networks (GNNs) computationally costly. Graph condensation methods address this by generating small synthetic graphs that approximate the original data. However, existing approaches rely on…

Graph plays a vital role in representing entities and their relationships in a variety of fields, such as e-commerce networks, social networks and biological networks. Given two vertices s and t, one of the fundamental problems in graph…

Indexing labeled graphs for pattern matching is a central challenge of pangenomics. Equi et al. (Algorithmica, 2022) developed the Elastic Founder Graph ($\mathsf{EFG}$) representing an alignment of $m$ sequences of length $n$, drawn from…

Word sense induction (WSI), which addresses polysemy by unsupervised discovery of multiple word senses, resolves ambiguities for downstream NLP tasks and also makes word representations more interpretable. This paper proposes an accurate…