相关论文: Compressing and Indexing Aligned Readsets

Given a string $T$ on an alphabet of size $\sigma$, we describe a bidirectional Burrows-Wheeler index that takes $O(|T|\log{\sigma})$ bits of space, and that supports the addition \emph{and removal} of one character, on the left or right…

DNA sequencing, especially of microbial genomes and metagenomes, has been at the core of recent research advances in large-scale comparative genomics. The data deluge has resulted in exponential growth in genomic datasets over the past…

The FM-index is a well-known compressed full-text index, based on the Burrows-Wheeler transform (BWT). During a pattern search, the BWT sequence is accessed at "random" locations, which is cache-unfriendly. In this paper, we are interested…

Structured text understanding on Visually Rich Documents (VRDs) is a crucial part of Document Intelligence. Due to the complexity of content and layout in VRDs, structured text understanding has been a challenging task. Most existing…

We propose a new outline for adaptive dictionary learning methods for sparse encoding based on a hierarchical clustering of the training data. Through recursive application of a clustering method, the data is organized into a binary…

This paper reduces discontinuous parsing to sequence labeling. It first shows that existing reductions for constituent parsing as labeling do not support discontinuities. Second, it fills this gap and proposes to encode tree discontinuities…

A chief problem in phylogenetics and database theory is the computation of a maximum consistent tree from a set of rooted or unrooted trees. A standard input are triplets, rooted binary trees on three leaves, or quartets, unrooted binary…

In this paper, we propose Stacked DeBERT, short for Stacked Denoising Bidirectional Encoder Representations from Transformers. This novel model improves robustness in incomplete data, when compared to existing systems, by designing a novel…

We show that the signal-processing paradigm known as compressed sensing (CS) is applicable to genome-wide association studies (GWAS) and genomic selection (GS). The aim of GWAS is to isolate trait-associated loci, whereas GS attempts to…

High-throughput DNA sequencers are becoming indispensable in our understanding of diseases at molecular level, in marker-assisted selection in agriculture and in microbial genetics research. These sequencing instruments produce enormous…

We describe a combinatorial approach for investigating properties of rational numbers. The overall approach rests on structural bijections between rational numbers and familiar combinatorial objects, namely rooted trees. We emphasize that…

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…

In this work, a problem associated with imbalanced text corpora is addressed. A method of converting an imbalanced text corpus into a balanced one is presented. The presented method employs a clustering algorithm for conversion. Initially…

Sublinear time quantum algorithms have been established for many fundamental problems on strings. This work demonstrates that new, faster quantum algorithms can be designed when the string is highly compressible. We focus on two popular and…

Pattern matching is the most central task for text indices. Most recent indices leverage compression techniques to make pattern matching feasible for massive but highly-compressible datasets. Within this kind of indices, we propose a new…

The Transformer has quickly become the dominant architecture for various pattern recognition tasks due to its capacity for long-range representation. However, transformers are data-hungry models and need large datasets for training. In…

In this article we extend the elegant in-place Burrows-Wheeler transform (BWT) algorithm proposed by Crochemore et al. (Crochemore et al., 2015). Our extension is twofold: we first show how to compute simultaneously the longest common…

In this paper we describe algorithms for computing the BWT and for building (compressed) indexes in external memory. The innovative feature of our algorithms is that they are lightweight in the sense that, for an input of size $n$, they use…

To store and search genomic databases efficiently, researchers have recently started building compressed self-indexes based on grammars. In this paper we show how, given a straight-line program with $r$ rules for a string (S [1..n]) whose…

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 --…