iSCoder: Mitigating Genomic Sequencing Data Compression Bottlenecks via In-SRAM Computing
文献类型：期刊论文
| 作者 | Liu, Wan-Qi1; Li, Ye-Wen2; Tan, Guang-Min1,3 |
| 刊名 | JOURNAL OF COMPUTER SCIENCE AND TECHNOLOGY
 |
| 出版日期 | 2026-01-21 |
| 页码 | 18 |
| 关键词 | genomic sequencing data compression in-SRAM computing hardware accelerator |
| ISSN号 | 1000-9000 |
| DOI | 10.1007/s11390-025-5022-y |
| 英文摘要 | With the rapid expansion of genomic sequencing data over the years, the costs associated with storage, transmission, and bandwidth are becoming the primary bottlenecks in genomic research and applications. Data compression is widely used to alleviate this burden, provided it achieves a sufficiently high compression ratio and fast compression speed. MPEG-G is a genome-specific compression standard that offers a higher compression ratio than general-purpose compression tools (4.3x), however, at the cost of performance reduction (5x). Following common strategies in compression acceleration, we design to the best of our knowledge, the first hardware accelerator for the MPEG-G genomic data compression pipeline utilizing in-SRAM (Static Random-Access Memory) computing, referred to as iSCoder. We identify and analyze MatchC (Match Coding) and LutC (Lut Coding) as two bottleneck algorithms within this pipeline, propose two optimized in-SRAM algorithms, and design a unified hardware architecture for these algorithms, considering the characteristics of genomic data. Compared with 72-core Intel processors operating at 3.0 GHz, experimental results demonstrate that iSCoder achieves an average speedup of 131x for MatchC and 191x for LutC. |
| 资助项目 | National Natural Science Foundation of China[62032023] ; National Natural Science Foundation of China[T2125013] |
| WOS研究方向 | Computer Science |
| 语种 | 英语 |
| WOS记录号 | WOS:001666429600001 |
| 出版者 | SPRINGER SINGAPORE PTE LTD |
| 源URL | [http://119.78.100.204/handle/2XEOYT63/42883]  |
| 专题 | 中国科学院计算技术研究所 |
| 通讯作者 | Tan, Guang-Min |
| 作者单位 | 1.Inst Comp Technol, Chinese Acad Sci, State Key Lab Processors, Beijing 100190, Peoples R China 2.Hong Kong Univ Sci & Technol, Hong Kong 999077, Peoples R China 3.Univ Chinese Acad Sci, Sch Comp Sci & Technol, Beijing 100049, Peoples R China |
| 推荐引用方式 GB/T 7714 | Liu, Wan-Qi,Li, Ye-Wen,Tan, Guang-Min. iSCoder: Mitigating Genomic Sequencing Data Compression Bottlenecks via In-SRAM Computing[J]. JOURNAL OF COMPUTER SCIENCE AND TECHNOLOGY,2026:18. |
| APA | Liu, Wan-Qi,Li, Ye-Wen,&Tan, Guang-Min.(2026).iSCoder: Mitigating Genomic Sequencing Data Compression Bottlenecks via In-SRAM Computing.JOURNAL OF COMPUTER SCIENCE AND TECHNOLOGY,18. |
| MLA | Liu, Wan-Qi,et al."iSCoder: Mitigating Genomic Sequencing Data Compression Bottlenecks via In-SRAM Computing".JOURNAL OF COMPUTER SCIENCE AND TECHNOLOGY (2026):18. |
入库方式： OAI收割
来源：计算技术研究所
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