Related papers: MUSIC: A Hybrid Computing Environment for Burrows-…
Music structure analysis (MSA) underpins music understanding and controllable generation, yet progress has been limited by small, inconsistent corpora. We present SongFormer, a scalable framework that learns from heterogeneous supervision.…
Background: The huge quantity of data produced in Biomedical research needs sophisticated algorithmic methodologies for its storage, analysis, and processing. High Performance Computing (HPC) appears as a magic bullet in this challenge.…
Advances in data acquisition and computational methods have accelerated the use of differential equation based modelling for complex systems. Such systems are often described by coupled (or more) variables, yet governing equation is…
We provide a view on high-dimensional statistical inference for genome-wide association studies (GWAS). It is in part a review but covers also new developments for meta analysis with multiple studies and novel software in terms of an…
In this work, we propose a subspace-based algorithm for direction-of-arrival (DOA) estimation applied to the signals impinging on a two-level nested array, referred to as multi-step knowledge-aided iterative nested MUSIC method…
Genome analysis fundamentally starts with a process known as read mapping, where sequenced fragments of an organism's genome are compared against a reference genome. Read mapping is currently a major bottleneck in the entire genome analysis…
Drug development is a very costly and lengthy process, while repositioned or repurposed drugs could be brought into clinical practice within a shorter time-frame and at a much reduced cost. The past decade has observed a massive growth in…
Cutting planes (cuts) play an important role in solving mixed-integer linear programs (MILPs), which formulate many important real-world applications. Cut selection heavily depends on (P1) which cuts to prefer and (P2) how many cuts to…
A major hindrance to studies of microbial diversity has been that the vast majority of microbes cannot be cultured in the laboratory and thus are not amenable to traditional methods of characterization. Environmental shotgun sequencing…
We present a new scalable, lightweight algorithm to incrementally construct the BWT and FM-index of large string sets such as those produced by Next Generation Sequencing. The algorithm is designed for massive parallelism and can…
DNA sequence classification is a fundamental task in computational biology with vast implications for applications such as disease prevention and drug design. Therefore, fast high-quality sequence classifiers are significantly important.…
Next-generation sequencing (NGS) technologies have enabled affordable sequencing of billions of short DNA fragments at high throughput, paving the way for population-scale genomics. Genomics data analytics at this scale requires overcoming…
We present an assignment for a full Parallel Computing course. Since 2017/2018, we have proposed a different problem each academic year to illustrate various methodologies for approaching the same computational problem using different…
The Burrows-Wheeler Transform is a string transformation that plays a fundamental role for the design of self-indexing compressed data structures. Over the years, researchers have successfully extended this transformation outside the…
This paper presents an unsupervised machine learning algorithm that identifies recurring patterns -- referred to as ``music-words'' -- from symbolic music data. These patterns are fundamental to musical structure and reflect the cognitive…
DNA read mapping is a ubiquitous task in bioinformatics, and many tools have been developed to solve the read mapping problem. However, there are two trends that are changing the landscape of readmapping: First, new sequencing technologies…
Prior work inspired by compression algorithms has described how the Burrows Wheeler Transform can be used to create a distance measure for bioinformatics problems. We describe issues with this approach that were not widely known, and…
Metagenomic studies have increasingly utilized sequencing technologies in order to analyze DNA fragments found in environmental samples.One important step in this analysis is the taxonomic classification of the DNA fragments. Conventional…
Neuroscience is moving towards a more integrative discipline, where understanding brain function requires consolidating the accumulated evidence seen across experiments, species, and measurement techniques. A remaining challenge on that…
Music Structure Analysis (MSA) is a Music Information Retrieval task consisting of representing a song in a simplified, organized manner by breaking it down into sections typically corresponding to ``chorus'', ``verse'', ``solo'', etc. In…