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

基因组测序是加强公共卫生、优化人格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，占用数十甚至数百CPU小时，导致治疗延误，患者病情恶化，甚至死亡。该项目整合了四项协同研究任务，以实现可扩展、快速和节能的基因组测序：(1)该项目将创建一个基准套件，以确定管道中的性能/功耗瓶颈；(2)本项目提出了一种可扩展的算法，用于基因组测序流水线中最耗时的播种和推广操作；(3)本项目将设计超低功耗内存处理架构，加速基因组测序流水线中的密集操作；(4)本项目将开发一个自动编译框架，将基因组测序流水线部署到CPU/加速器异构系统。该提案的结果将降低基因组测序开发的进入门槛，使下一代用户、开发者、企业家和科学家能够在没有软件和硬件专家帮助的情况下使用基因组测序。该研究将启发未来的计算机系统和计算生物学研究，用于专门的基因组测序管道加速。该提案整合了研究和教育，包括研究生和本科生课程开发和研究指导，一个高中实习项目，使早期学习者能够使用基因组测序并培养对STEM的兴趣。该奖项反映了美国国家科学基金会的法定使命，并通过使用基金会的知识价值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.