Related papers: GPU-Accelerated BWT Construction for Large Collect…
Motivation: Read mapping is a computationally expensive process and a major bottleneck in genomics analyses. The performance of read mapping is mainly limited by the performance of three key computational steps: Index Querying, Seed…
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…
Bayesian networks (BNs) are a widely used graphical model in machine learning for representing knowledge with uncertainty. The mainstream BN structure learning methods require performing a large number of conditional independence (CI)…
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…
Existing approaches to train neural networks that use large images require to either crop or down-sample data during pre-processing, use small batch sizes, or split the model across devices mainly due to the prohibitively limited memory…
Range minimum queries are frequently used in string processing and database applications including biological sequence analysis, document retrieval, and web search. Hence, various data structures have been proposed for improving their…
The Burrows-Wheeler transform (BWT) is a reversible transform that converts a string $w$ into another string $\mathsf{BWT}(w)$. The size of the run-length encoded BWT (RLBWT) can be interpreted as a measure of repetitiveness in the class of…
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…
Hash tables are ubiquitous. Properties such as an amortized constant time complexity for insertion and querying as well as a compact memory layout make them versatile associative data structures with manifold applications. The rapidly…
GPUs are uniquely suited to accelerate (SQL) analytics workloads thanks to their massive compute parallelism and High Bandwidth Memory (HBM) -- when datasets fit in the GPU HBM, performance is unparalleled. Unfortunately, GPU HBMs remain…
A concurrent binary tree (CBT) is a GPU-friendly data-structure suitable for the generation of bisection based terrain tessellations, i.e., adaptive triangulations over square domains. In this paper, we expand the benefits of this…
Our formulation reveals that the reduction across the sequence axis can be efficiently computed in parallel through a tree reduction. Our algorithm, called Tree Attention, for parallelizing exact attention computation across multiple GPUs…
The Burrows-Wheeler Transform (BWT) is an invertible text transformation that permutes symbols of a text according to the lexicographical order of its suffixes. BWT is the main component of popular lossless compression programs (such as…
Motivation: Single Molecule Real-Time (SMRT) sequencing technology and Oxford Nanopore technologies (ONT) produce reads over 10kbp in length, which have enabled high-quality genome assembly at an affordable cost. However, at present, long…
The click-through rate (CTR) prediction task is to predict whether a user will click on the recommended item. As mind-boggling amounts of data are produced online daily, accelerating CTR prediction model training is critical to ensuring an…
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…
Continuous Wavelet Transform (CWT) is frequently used for waveform analysis. For example, in the field of neuroscience research, CWT is performed to analyze electroencephalograms (EEG) and calculate the index of brain activity. Recent…
Modern genomic analyses increasingly rely on pangenomes, that is, representations of the genome of entire populations. The simplest representation of a pangenome is a set of individual genome sequences. Compared to e.g. sequence graphs,…
Computational Pangenomics is an emerging field that studies genetic variation using a graph structure encompassing multiple genomes. Visualizing pangenome graphs is vital for understanding genome diversity. Yet, handling large graphs can be…
In this work we propose an accelerated stochastic learning system for very large-scale applications. Acceleration is achieved by mapping the training algorithm onto massively parallel processors: we demonstrate a parallel, asynchronous GPU…