Hardware acceleration of genomics data analysis: challenges and opportunities

T Robinson, J Harkin, P Shukla - Bioinformatics, 2021 - academic.oup.com
The significant decline in the cost of genome sequencing has dramatically changed the
typical bioinformatics pipeline for analysing sequencing data. Where traditionally, the …

AccuReD: High accuracy training of CNNs on ReRAM/GPU heterogeneous 3-D architecture

BK Joardar, JR Doppa, PP Pande, H Li… - … on Computer-Aided …, 2020 - ieeexplore.ieee.org
The growing popularity of convolutional neural networks (CNNs) along with their complexity
has led to the search for efficient computational platforms suitable for them. Resistive …

Beacon: Scalable near-data-processing accelerators for genome analysis near memory pool with the cxl support

W Huangfu, KT Malladi, A Chang… - 2022 55th IEEE/ACM …, 2022 - ieeexplore.ieee.org
Genome analysis benefits precise medical care, wildlife conservation, pandemic treatment
(eg, COVID-19), and so on. Unfortunately, in genome analysis, the speed of data processing …

Machine learning-based Rowhammer mitigation

BK Joardar, TK Bletsch… - IEEE Transactions on …, 2022 - ieeexplore.ieee.org
Rowhammer is a security vulnerability that arises due to the undesirable electrical
interaction between physically adjacent rows in DRAMs. Bit flips caused by Rowhammer …

[หนังสือ][B] In-/near-memory Computing

D Fujiki, X Wang, A Subramaniyan, R Das - 2021 - Springer
This book provides a structured introduction of the key concepts and techniques that enable
in-/near-memory computing. For decades, processing-in-memory or near-memory …

Nest: Dimm based near-data-processing accelerator for k-mer counting

W Huangfu, KT Malladi, S Li, P Gu, Y **e - Proceedings of the 39th …, 2020 - dl.acm.org
With the ability to help wildlife conservation, precise medical care, and disease
understanding, genomics analysis is becoming more and moe important. Recently, with the …

Abakus: Accelerating k-mer Counting with Storage Technology

L Wu, M Zhou, W Xu, A Venkat, T Rosing… - ACM Transactions on …, 2024 - dl.acm.org
This work seeks to leverage Processing-with-storage-technology (PWST) to accelerate a key
bioinformatics kernel called k-mer counting, which involves processing large files of …

3D++: Unlocking the next generation of high-performance and energy-efficient architectures using M3D integration

BK Joardar, AI Arka, JR Doppa… - … Design, Automation & …, 2021 - ieeexplore.ieee.org
Three-dimensional (3D) integration has frequently been described as a means to overcome
scaling bottlenecks, and advance both “More Moore” and “More Than Moore” through the …

A Survey of Processing Systems for Phylogenetics and Population Genetics

R Corts, N Alachiotis - ACM Transactions on Reconfigurable …, 2023 - dl.acm.org
The COVID-19 pandemic brought Bioinformatics into the spotlight, revealing that several
existing methods, algorithms, and tools were not well prepared to handle large amounts of …

Noc-enabled 3d heterogeneous manycore systems for big-data applications

BK Joardar, JR Doppa, PP Pande… - … on Quality Electronic …, 2022 - ieeexplore.ieee.org
High-performance heterogeneous computing systems are suitable for big-data applications.
However, the use of off-chip interconnects (eg, PCIe in discrete CPU and GPU based …