Related papers: A survey of BWT variants for string collections
The nondecimated or translation-invariant wavelet transform (NDWT) is a central tool in classical multiscale signal analysis, valued for its stability, redundancy, and shift invariance. This paper develops two complementary quantum…
Summary: BGT is a compact format, a fast command line tool and a simple web application for efficient and convenient query of whole-genome genotypes and frequencies across tens to hundreds of thousands of samples. On real data, it encodes…
With the rapid advancement of Neural Machine Translation (NMT), enhancing translation efficiency and quality has become a focal point of research. Despite the commendable performance of general models such as the Transformer in various…
The goal of this work is to develop an application that enables music producers to use their voice to create drum patterns when composing in Digital Audio Workstations (DAWs). An easy-to-use and user-oriented system capable of automatically…
We propose a Bayesian method to detect change points for functional data. We extract the features of a sequence of functional data by the discrete wavelet transform (DWT), and treat each sequence of feature independently. We believe there…
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…
Software development is inherently incremental. Nowadays, many software companies adopt an agile process and a shorter release cycle, where software needs to be delivered faster with quality assurances. On the other hand, the majority of…
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…
We describe an adaptive context tree weighting (ACTW) algorithm, as an extension to the standard context tree weighting (CTW) algorithm. Unlike the standard CTW algorithm, which weights all observations equally regardless of the depth, ACTW…
This paper presents a method for background removal in experimental data processing using the Dual-Tree Complex Wavelet Transform (DTCWT). The technique is based on discrete wavelet theory (DWT) and addresses limitations of commonly used…
In this paper, we revisit the use of spectrograms in neural networks, by making the window length a continuous parameter optimizable by gradient descent instead of an empirically tuned integer-valued hyperparameter. The contribution is…
Dynamic Time Warping (DTW) is a widely used similarity measure for comparing strings that encode time series data, with applications to areas including bioinformatics, signature verification, and speech recognition. The standard…
The paper describes a member of the Symbiotic toolbox called sbt-instrumentation, which is a tool for configurable instrumentation of LLVM bitcode. The tool enables a user to specify patterns of instructions and to define functions whose…
We present a solver for a many-sorted first-order quantifier-free theory $T_{w,bv}$ of string equations, string length represented as bit-vectors, and bit-vector arithmetic aimed at formal verification, automated testing, and security…
We present a new fast Chase decoding algorithm for binary BCH codes. The new algorithm reduces the complexity in comparison to a recent fast Chase decoding algorithm for Reed--Solomon (RS) codes by the authors (IEEE Trans. IT, 2022), by…
Vision Transformers (ViTs) and Swin Transformers (Swin) are currently state-of-the-art in computational pathology. However, domain experts are still reluctant to use these models due to their lack of interpretability. This is not…
Many language generation models are now available for a wide range of generation tasks, including machine translation and summarization. Combining such diverse models may lead to further progress, but ensembling generation models is…
Alternative splicing is crucial in gene regulation, with significant implications in clinical settings and biotechnology. This review article compiles bioinformatics RNA-seq tools for investigating differential splicing; offering a detailed…
The Positional Burrows-Wheeler Transform (PBWT) is a fundamental data structure for the efficient representation and analysis of large-scale haplotype panels. For a panel of $h$ sequences $\{S_1, \dots, S_h\}$ over $m$ sites, a key…
Summary: With the rapid development of long-read sequencing technologies, the era of individual complete genomes is approaching. We have developed wgatools, a cross-platform, ultrafast toolkit that supports a range of whole genome alignment…