Related papers: Efficient Architecture-Aware Acceleration of BWA-M…
Summary: BWA-MEM is a new alignment algorithm for aligning sequence reads or long query sequences against a large reference genome such as human. It automatically chooses between local and end-to-end alignments, supports paired-end reads…
Genome sequence analysis plays a pivotal role in enabling many medical and scientific advancements in personalized medicine, outbreak tracing, and forensics. However, the analysis of genome sequencing data is currently bottlenecked by the…
DNA sequencing is revolutionising the field of medicine. DNA sequencers, the machines which perform DNA sequencing, have evolved from the size of a fridge to that of a mobile phone over the last two decades. The cost of sequencing a human…
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,…
Asymmetric multicore processors (AMPs) have recently emerged as an appealing technology for severely energy-constrained environments, especially in mobile appliances where heterogeneity in applications is mainstream. In addition, given the…
In this paper, we address the performance degradation of efficient diffusion models by introducing Multi-architecturE Multi-Expert diffusion models (MEME). We identify the need for tailored operations at different time-steps in diffusion…
The GEneral Matrix Multiplication (GEMM) is one of the essential algorithms in scientific computing. Single-thread GEMM implementations are well-optimised with techniques like blocking and autotuning. However, due to the complexity of…
Genome sequence analysis has enabled significant advancements in medical and scientific areas such as personalized medicine, outbreak tracing, and the understanding of evolution. Unfortunately, it is currently bottlenecked by the…
DNA sequencing is the physical/biochemical process of identifying the location of the four bases (Adenine, Guanine, Cytosine, Thymine) in a DNA strand. As semiconductor technology revolutionized computing, modern DNA sequencing technology…
Nanopore genome sequencing is the key to enabling personalized medicine, global food security, and virus surveillance. The state-of-the-art base-callers adopt deep neural networks (DNNs) to translate electrical signals generated by nanopore…
Graph Neural Networks (GNNs) are becoming a promising technique in various domains due to their excellent capabilities in modeling non-Euclidean data. Although a spectrum of accelerators has been proposed to accelerate the inference of…
Sequence alignment is a memory bound computation whose performance in modern systems is limited by the memory bandwidth bottleneck. Processing-in-memory architectures alleviate this bottleneck by providing the memory with computing…
As genome sequencing is finding utility in a wide variety of domains beyond the confines of traditional medical settings, its computational pipeline faces two significant challenges. First, the creation of up to 0.5 GB of data per minute…
Advances in DNA sequencing technology have stimulated the development of algorithms and tools for processing very large collections of short strings (reads). Short-read alignment and assembly are among the most well-studied problems. Many…
A critical step of genome sequence analysis is the mapping of sequenced DNA fragments (i.e., reads) collected from an individual to a known linear reference genome sequence (i.e., sequence-to-sequence mapping). Recent works replace the…
Genome analysis has revolutionized fields such as personalized medicine and forensics. Modern sequencing machines generate vast amounts of fragmented strings of genome data called reads. The alignment of these reads into a complete DNA…
This paper presents the Neural Cache architecture, which re-purposes cache structures to transform them into massively parallel compute units capable of running inferences for Deep Neural Networks. Techniques to do in-situ arithmetic in…
Genome sequences contain hundreds of millions of DNA base pairs. Finding the degree of similarity between two genomes requires executing a compute-intensive dynamic programming algorithm, such as Smith-Waterman. Traditional von Neumann…
The latest trends in high-performance computing systems show an increasing demand on the use of a large scale multicore systems in a efficient way, so that high compute-intensive applications can be executed reasonably well. However, the…
Genome sequence analysis, which examines the DNA sequences of organisms, drives advances in many critical medical and biotechnological fields. Given its importance and the exponentially growing volumes of genomic sequence data, there are…