Hierarchical DNN with Heterogeneous Computing Enabled High-Performance DNA Sequencing

Shaobo Luo,1; Zhiyuan Xie1; Gengxin Chen1; Lei Cui1; Mei Yan1; Xiwei Huang3; Shuwei Li2; Changhai Man2; Wei Mao2; Hao Yu2

10.1109/APCCAS55924.2022.10090281

2022

IEEE Asia Pacific Conference on Circuits and Systems (APCCAS)

978-1-6654-5080-5

2022 IEEE ASIA PACIFIC CONFERENCE ON CIRCUITS AND SYSTEMS, APCCAS

35-40

NOV 11-13, 2022

So Univ Sci & Technol,Shenzhen,PEOPLES R CHINA

345 E 47TH ST, NEW YORK, NY 10017 USA

IEEE

DNA sequencing is a popular tool to demystify the code of living organisms and is reforming the medical, pharmaceutical and biotech industries. The Next-Generation Sequencing (NGS) plays a vital role in high-throughput DNA sequencing with massively parallel data generation. Nevertheless, the massive amount of data imposes great challenges for data analysis. It is arduous to reach a low error rate for handling noisy and/or biased signals owing to the imperfect biochemical reactions and imaging systems. Furthermore, a homogeneous computing system lacks computing power and memory bandwidth. Therefore, in this work, a heterogeneous computing platform with a hierarchical deep neural network sequencing pipeline is proposed to improve the sequencing quality and increase processing speed. Experiments demonstrate that the proposed work reached higher effective throughput (12.18% more clusters found), lower error rate (0.0175%), higher quality score (%Q30 99.27%), and 19% faster. The reported work empowers virus detection, diseases diagnostic, and other potential biomedical applications.

DNA NGS Base-calling Deep neural network

Corresponding

English

CPCI-S

Computer Science ; Engineering

Computer Science, Hardware & Architecture ; Engineering, Electrical & Electronic

WOS:000987045300008

Web of Science

1.GeneSense Technology Inc., Shanghai 201210
2.School of Microelectronics, Southern University of Science and Technology
3.Ministry of Education Key Laboratory of RF Circuits and Systems, Hangzhou Dianzi University

Shaobo Luo,,Zhiyuan Xie,Gengxin Chen,et al. Hierarchical DNN with Heterogeneous Computing Enabled High-Performance DNA Sequencing[C]. 345 E 47TH ST, NEW YORK, NY 10017 USA:IEEE,2022:35-40.