Many applications in precision medicine present significant computational challenges. For example, the computation demand for personalized cancer treatment is prohibitively high for the general-purpose computing technologies, as tumor heterogeneity requires great sequencing depths, structural aberrations are difficult to detect with today’s algorithms, and the tumor has the ability to evolve, meaning the same tumor might be assayed a great many times during the course of treatment. The goal of this research project is to make apply the domain-specific customized computing techniques developed by the Center for Domain-Specific Computing (CDSC) to greatly accelerate computation for multiple key healthcare applications.
CDSC develops a general methodology for creating novel customizable computing platforms and the associated compilation tools and runtime management environment to support domain-specific computing. The recent focus is on design and implementation of accelerator-rich architectures, from single chips to data centers. It also includes highly automated compilation tools and runtime management software systems for customizable heterogeneous platforms, including multi-core CPUs, many-core GPUs, and FPGAs, as well as a general, reusable methodology for customizable computing applicable across different domains. By combining these critical capabilities, the goal is to deliver a supercomputer-in-a-box or supercomputer-in-a-cluster (for data center level deployment) that can be customized to an application domain to enable disruptive innovations. Our approach has been successfully demonstrated in the domain of genomic processing (BWA-mem + GATK) and medical image processing with over 10X improvement in performance and 100X in energy efficiency.
NSF and Intel support the development of domain-specific hardware to address health care needs.
In partnership with Intel Corporation, NSF announced the first InTrans award of $3 million to a team of researchers who are designing customizable, domain-specific computing technologies for use in healthcare. The work could lead to less exposure to dangerous radiation during x-rays by speeding up the computing side of medicine. It also could result in patient-specific cancer treatments.Led by the University of California, Los Angeles, the research team includes experts in computer science and engineering, electrical engineering and medicine from Rice University and Oregon Health and Science University. The team comes mainly from the Center of Domain-Specific Computing (CDSC), which was supported by an NSF Expeditions in Computing Award in 2009.
In the project, the researchers looked beyond parallelization (the process of working on a problem with more than one processor at the same time) and instead focused on domain-specific customization, a disruptive technology with the potential to bring orders-of-magnitude improvements to important applications. Domain-specific computing systems work efficiently on specific problems - in this case, medical imaging and DNA sequencing of tumors - or a set of problems with similar features, reducing the time to solution and bringing down costs.The InTrans program not only advances important fundamental research and integrates it into industry, it also benefits society by improving medical imaging technologies and cancer treatments, helping to extend lives.
Intrans Project Sponsored by NSF and Intel
"Datacenter-Scale Customizable Computing", first International Workshop on Heterogeneous High-performance Reconfigurable Computing (H2RC'15) Held in conjunction with Super Computing 2015, November 22, 2015(Keynote Speech)
"Characterization and Acceleration for Genomic Sequencing and Analysis", IEEE International Symposium on Workload Characterization, Seattle, WA, October 2017 (Keynote Speech)