Related papers: MUSIC: A Hybrid Computing Environment for Burrows-…

The advent of high-throughput sequencing technologies has revolutionized genome analysis by enabling the rapid and cost-effective sequencing of large genomes. Despite these advancements, the increasing complexity and volume of genomic data…

Music structure analysis (MSA) methods traditionally search for musically meaningful patterns in audio: homogeneity, repetition, novelty, and segment-length regularity. Hand-crafted audio features such as MFCCs or chromagrams are often used…

In the Western music tradition, chords are the main constituent components of harmony, a fundamental dimension of music. Despite its relevance for several Music Information Retrieval (MIR) tasks, chord-annotated audio datasets are limited…

Deep shotgun sequencing and analysis of genomes, transcriptomes, amplified single-cell genomes, and metagenomes has enabled investigation of a wide range of organisms and ecosystems. However, sampling variation in short-read data sets and…

The Burrows-Wheeler Transform (BWT) is among the most influential discoveries in text compression and DNA storage. It is a reversible preprocessing step that rearranges an $n$-letter string into runs of identical characters (by exploiting…

The Burrows-Wheeler Transform (BWT) is an efficient invertible text transformation algorithm with the properties of tending to group identical characters together in a run, and enabling search of the text. This transformation has extensive…

In microbiome and genomic studies, the regression of compositional data has been a crucial tool for identifying microbial taxa or genes that are associated with clinical phenotypes. To account for the variation in sequencing depth, the…

Audio-to-score alignment aims at generating an accurate mapping between a performance audio and the score of a given piece. Standard alignment methods are based on Dynamic Time Warping (DTW) and employ handcrafted features. We explore the…

String kernels are typically used to compare genome-scale sequences whose length makes alignment impractical, yet their computation is based on data structures that are either space-inefficient, or incur large slowdowns. We show that a…

Music mixing traditionally involves recording instruments in the form of clean, individual tracks and blending them into a final mixture using audio effects and expert knowledge (e.g., a mixing engineer). The automation of music production…

Multi-channel audio alignment is a key requirement in bioacoustic monitoring, spatial audio systems, and acoustic localization. However, existing methods often struggle to address nonlinear clock drift and lack mechanisms for quantifying…

Recent advancements in web-based audio systems have enabled sufficiently accurate timing control and real-time sound processing capabilities. Numerous specialized music tools, as well as digital audio workstations, are now accessible from…

Next-generation sequencing technologies generate millions of short sequence reads, which are usually aligned to a reference genome. In many applications, the key information required for downstream analysis is the number of reads mapping to…

Background: Several sources of noise obfuscate the identification of single nucleotide variation (SNV) in next generation sequencing data. For instance, errors may be introduced during library construction and sequencing steps. In addition,…

Multiple sequence alignment (MSA) is a core operation for comparing genome sequences and is widely used in bio-informatics. MAFFT, a practical MSA tool, repeatedly shifts a pair of sequences and computes a distance. Because the number of…

Applying new computing paradigms like quantum computing to the field of machine learning has recently gained attention. However, as high-dimensional real-world applications are not yet feasible to be solved using purely quantum hardware,…

Multiple sequence alignment (MSA) is a ubiquitous problem in computational biology. Although it is NP-hard to find an optimal solution for an arbitrary number of sequences, due to the importance of this problem researchers are trying to…

Sequence alignment is a fundamental process in computational biology which identifies regions of similarity in biological sequences. With the exponential growth in the volume of data in bioinformatics databases, the time, processing power,…

Audio-based music structure analysis (MSA) is an essential task in Music Information Retrieval that remains challenging due to the complexity and variability of musical form. Recent advances highlight the potential of fine-tuning…

Multiple matching algorithms are used to locate the occurrences of patterns from a finite pattern set in a large input string. Aho-Corasick and Wu-Manber, two of the most well known algorithms for multiple matching require an increased…