FuHsi: Shifting Base-Calling Closer to Sequencer via In-Cache Acceleration

doi:10.1007/s11390-025-3886-5

	FuHsi: Shifting Base-Calling Closer to Sequencer via In-Cache Acceleration
	Li, Ye-Wen 1,2; Tan, Guang-Ming 1,2; Li, Xue-Qi 1
	2025-03-01
发表期刊	JOURNAL OF COMPUTER SCIENCE AND TECHNOLOGY
ISSN	1000-9000
卷号	40 期号:2 页码:482-499
摘要	Base-calling is an essential step in the analysis of third-generation genome data. Many previous hardware efforts aimed at enhancing processing in the workflow. However, an order of magnitude throughput gap still exists. In this paper, we propose FuHsi to improve the end-to-end throughput of the base-calling process. FuHsi is an in-cache accelerator that only introduces three components to the traditional CPUs in the sequencer. We propose FuHsi Cache, which offloads the bottleneck operations to cache arithmetic. Specifically, we accelerate beam search, string conversion, and MAC (multiply-accumulate) using algorithm/hardware co-design. We also introduce FuHsi APIs and FuHsi Controller to provide coarse-grained control for FuHsi Cache. Experimental results show that FuHsi can achieve 45.7x, 113.1x, and 100x throughput per watt speedup compared with an NVIDIA Jetson baseline, an NVIDIA A100 GPU baseline, and the Helix accelerator, respectively. FuHsi can provide base-calling requests for up to 15 ONT sequencers simultaneously.
关键词	genome base-calling in-cache accelerator domain-specific architecture genome analysis Nanopore sequencing
DOI	10.1007/s11390-025-3886-5
收录类别	SCI
语种	英语
资助项目	National Key Research and Development Program of China[2021YFB0300202] ; National Key Research and Development Program of China[2022YFB4500403] ; National Natural Science Foundation of China[62202454] ; National Natural Science Foundation of China[62032023] ; National Natural Science Foundation of China[T2125013]
WOS研究方向	Computer Science
WOS类目	Computer Science, Hardware & Architecture ; Computer Science, Software Engineering
WOS记录号	WOS:001483026900017
出版者	SPRINGER SINGAPORE PTE LTD
引用统计
文献类型	期刊论文
条目标识符	http://119.78.100.204/handle/2XEOYT63/40637
专题	中国科学院计算技术研究所期刊论文_英文
通讯作者	Tan, Guang-Ming; Li, Xue-Qi
作者单位	1.Chinese Acad Sci, Inst Comp Technol, State Key Lab Proc, Beijing 100190, Peoples R China 2.Univ Chinese Acad Sci, Sch Comp Sci & Technol, Beijing 100049, Peoples R China
推荐引用方式 GB/T 7714	Li, Ye-Wen,Tan, Guang-Ming,Li, Xue-Qi. FuHsi: Shifting Base-Calling Closer to Sequencer via In-Cache Acceleration[J]. JOURNAL OF COMPUTER SCIENCE AND TECHNOLOGY,2025,40(2):482-499.
APA	Li, Ye-Wen,Tan, Guang-Ming,&Li, Xue-Qi.(2025).FuHsi: Shifting Base-Calling Closer to Sequencer via In-Cache Acceleration.JOURNAL OF COMPUTER SCIENCE AND TECHNOLOGY,40(2),482-499.
MLA	Li, Ye-Wen,et al."FuHsi: Shifting Base-Calling Closer to Sequencer via In-Cache Acceleration".JOURNAL OF COMPUTER SCIENCE AND TECHNOLOGY 40.2(2025):482-499.