Related papers: AnySeq/GPU: A Novel Approach for Faster Sequence A…

Sequence alignments are fundamental to bioinformatics which has resulted in a variety of optimized implementations. Unfortunately, the vast majority of them are hand-tuned and specific to certain architectures and execution models. This not…

State-of-the-art multiple sequence alignment (MSA) algorithms are based on progressive approaches that rely on pairwise sequence alignment (PSA) to generate guide trees to align all sequences. Given an evidenced explosion in genomic data…

With the advance in genome sequencing technology, the lengths of deoxyribonucleic acid (DNA) sequencing results are rapidly increasing at lower prices than ever. However, the longer lengths come at the cost of a heavy computational burden…

Sequence alignment forms an important backbone in many sequencing applications. A commonly used strategy for sequence alignment is an approximate string matching with a two-dimensional dynamic programming approach. Although some prior work…

Single-cell sequencing technologies reveal cellular heterogeneity at high resolution, advancing our understanding of biological complexity. As datasets start to scale to tens of millions of cells, computational workflows face substantial…

We present GPU-SLS, a GPU-parallelized framework for safe, robust nonlinear model predictive control (MPC) that scales to high-dimensional uncertain robotic systems and long planning horizons. Our method jointly optimizes an…

Pairwise sequence alignment is one of the most computationally intensive kernels in genomic data analysis, accounting for more than 90% of the runtime for key bioinformatics applications. This method is particularly expensive for…

Leveraging Graphics Processing Units (GPUs) to accelerate scientific software has proven to be highly successful, but in order to extract more performance, GPU programmers must overcome the high latency costs associated with their use. One…

Deep learning (DL) frameworks take advantage of GPUs to improve the speed of DL inference and training. Ideally, DL frameworks should be able to fully utilize the computation power of GPUs such that the running time depends on the amount of…

We improve on GenASM, a recent algorithm for genomic sequence alignment, by significantly reducing its memory footprint and bandwidth requirement. Our algorithmic improvements reduce the memory footprint by 24$\times$ and the number of…

Over the past decade there has been a growing interest in the development of parallel hardware systems for simulating large-scale networks of spiking neurons. Compared to other highly-parallel systems, GPU-accelerated solutions have the…

We study exact sparse linear regression with an $\ell_0-\ell_2$ penalty and develop a branch-and-bound (BnB) algorithm explicitly designed for GPU execution. Starting from a perspective reformulation, we derive an interval relaxation that…

At the last step of short read mapping, the candidate locations of the reads on the reference genome are verified to compute their differences from the corresponding reference segments using sequence alignment algorithms. Calculating the…

Gaussian Process Regression (GPR) is an important type of supervised machine learning model with inherent uncertainty measure in its predictions. We propose a new framework, nuGPR, to address the well-known challenge of high computation…

Graph Neural Networks (GNNs) have shown great superiority on non-Euclidean graph data, achieving ground-breaking performance on various graph-related tasks. As a practical solution to train GNN on large graphs with billions of nodes and…

For large-scale graph analytics on the GPU, the irregularity of data access and control flow, and the complexity of programming GPUs, have presented two significant challenges to developing a programmable high-performance graph library.…

In the acceleration of deep neural network training, the GPU has become the mainstream platform. GPUs face substantial challenges on GNNs, such as workload imbalance and memory access irregularities, leading to underutilized hardware.…

We introduce FastGraph, a novel GPU-optimized k-nearest neighbor algorithm specifically designed to accelerate graph construction in low-dimensional spaces (2-10 dimensions), critical for high-performance graph neural networks. Our method…

GPU accelerators have become an important backbone for scientific high performance computing, and the performance advances obtained from adopting new GPU hardware are significant. In this paper we take a first look at NVIDIA's newest server…

This paper presents a GPU-accelerated framework for solving block tridiagonal linear systems that arise naturally in numerous real-time applications across engineering and scientific computing. Through a multi-stage permutation strategy…