CAREER: System Support for Scalable, Fast, and Power-Efficient Genome Sequencing

基因组测序是增进公众健康、优化个性医学和促进病毒监测的关键。然而，目前的基因组测序流水线缺乏全栈系统支持，消耗数十甚至数百个CPU小时，导致治疗延误、患者病情恶化，甚至死亡。本项目集成了四项协同研究任务，以实现可扩展、快速和高能效的基因组测序：(1)本项目将创建一个基准测试套件，以确定流水线中的性能/功率瓶颈；(2)本项目为基因组测序流水线中最耗时的种子和扩展操作提供一个可扩展的算法；(3)本项目将设计一个超低功耗内存处理架构，用于加速基因组测序流水线中的密集操作员；(4)本项目将开发一个自动化编译框架，以将基因组测序流水线部署到CPU/加速器异质系统。这项提议的结果将降低基因组测序开发的进入门槛，使下一代用户、开发人员、企业家和科学家能够使用基因组测序，而不需要软件和硬件专家的帮助。这项研究将启发未来计算机系统和计算生物学的研究，为专门的基因组测序流水线加速。这项建议整合了研究和教育，包括研究生和本科生课程开发以及研究指导，这是一个高中实习生计划，使早期学习者能够使用基因组测序并培养对STEM的兴趣。该奖项反映了NSF的法定使命，并通过使用基金会的智力优势和更广泛的影响审查标准进行评估，被认为值得支持。

Genome sequencing is the key to enhancing public health, optimizing personality medicine, and facilitating viral surveillance. However, the current genome sequencing pipeline lacks full-stack system support and consumes tens or even hundreds of CPU hours, causing delays in treatment, patient deterioration, or even mortality. This project integrates four synergistic research tasks to enable scalable, fast, and power-efficient genome sequencing: (1) This project will create a benchmark suite to identify the performance/power bottlenecks in the pipeline; (2) This project presents a scalable algorithm for the most time-consuming Seed-and-Extension operations in the genome sequencing pipeline; (3) This project will design an ultra-low power processing-in-memory architecture for accelerating intensive operators in the genome sequencing pipeline; (4) This project will develop an automated compilation framework to deploy the genome sequencing pipeline to a CPU/accelerator heterogeneous system. The outcomes of this proposal will lower the barrier to entry for genome sequencing development, equipping the next generation of users, developers, entrepreneurs, and scientists to use genome sequencing, without help from software and hardware experts. The research will inspire future computer systems and computational biology research for specialized genome sequencing pipeline acceleration. This proposal integrates research and education including graduate and undergraduate curriculum development and research mentoring, a high school intern program to enable early learners to use genome sequencing and develop an interest in STEM.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.