[HTML][HTML] From GPUs to AI and quantum: three waves of acceleration in bioinformatics

B Schmidt, A Hildebrandt - Drug Discovery Today, 2024 - Elsevier
The enormous growth in the amount of data generated by the life sciences is continuously
shifting the field from model-driven science towards data-driven science. The need for …

Evaluating the potential of disaggregated memory systems for HPC applications

N Ding, P Maris, HA Nam, T Groves… - Concurrency and …, 2024 - Wiley Online Library
Disaggregated memory is a promising approach that addresses the limitations of traditional
memory architectures by enabling memory to be decoupled from compute nodes and …

cuSZp2: A GPU Lossy Compressor with Extreme Throughput and Optimized Compression Ratio

Y Huang, S Di, G Li, F Cappello - … : International Conference for …, 2024 - ieeexplore.ieee.org
Existing GPU lossy compressors suffer from expensive data movement overheads,
inefficient memory access patterns, and high synchronization latency, resulting in limited …

Rapid GPU-Based Pangenome Graph Layout

J Li, JN Schmelzle, Y Du, S Heumos… - … Conference for High …, 2024 - ieeexplore.ieee.org
Computational Pangenomics is an emerging field that studies genetic variation using a
graph structure encompassing multiple genomes. Visualizing pangenome graphs is vital for …

A configurable hierarchical architecture for parallel dynamic contingency analysis on gpus

C Wang, S Jin, R Huang, Q Huang… - IEEE Open Access …, 2022 - ieeexplore.ieee.org
Dynamic contingency analysis (DCA) for modern power systems is fundamental to help
researchers and operators look ahead of potential issues, arrange operational plans, and …

Methodology for Evaluating the Potential of Disaggregated Memory Systems

N Ding, S Williams, HA Nam, T Groves… - 2022 IEEE/ACM …, 2022 - ieeexplore.ieee.org
Tightly-coupled HPC systems have rigid memory allocation and can result in expensive
memory resource underutilization. As novel memory and network technologies mature …

High-Performance Sorting-Based K-mer Counting in Distributed Memory with Flexible Hybrid Parallelism

Y Li, G Guidi - Proceedings of the 53rd International Conference on …, 2024 - dl.acm.org
In generating large quantities of DNA data, high-throughput sequencing technologies
require advanced bioinformatics infrastructures for efficient data analysis. k-mer counting …

Performance Modeling and Analysis of a de Bruijn Graph Based Local Assembly Kernel on Multiple Vendor GPUs

LAM Lindsey, N Ding, J Deslippe… - SC24-W: Workshops of …, 2024 - ieeexplore.ieee.org
Bioinformatics workloads differ significantly from traditional scientific computing and AI
workloads because they consist primarily of integer-only operations and string comparisons …

iPuma: High-Performance Sequence Alignment on the Graphcore IPU

M Zhao, L Burchard, DT Schroeder… - ISC High …, 2024 - ieeexplore.ieee.org
String alignment algorithms are an essential tool for understanding DNA and protein
sequences. They demand substantial computation in real-world applications, and are thus a …

Overcoming the Limitations of Si-CMOS and Von Neuman Architectures by Adopting Beyond-Si Devices and Near-Memory Computation

HW Kim - 2024 - deepblue.lib.umich.edu
The advancement of Silicon CMOS technology has led to information technology innovation
for decades. Transistor density, computation frequency, and storage capacity have been …