Accelerating Biology and Medicine with Hardware Specialization

Yatish Turakhia UC San Diego Thursday, Nov 19, 2020 @ 4:00 pm Virtual Hosted by: Prof. George Candea

Abstract

Genome sequencing data is rising exponentially at a rate (125%/year) that is far higher than our current transistor performance scaling (currently 3%/year). New medical and comparative genomics applications have emerged that ensure that the demand for more sequencing will continue to rise, which threatens to overwhelm our current compute capacities. Domain-specific acceleration (DSA), i.e. using specialized hardware for accelerating a narrow domain of algorithms, will enable us to tap the vast potential of this data by providing massive gains in performance efficiency.

In this talk, I will present the designs of our past co-processors as case-studies for how domain-specific hardware can provide massive speedup (1,000-10,000x) for genomic applications and the various sources of increased efficiency. In the second half of my talk, I will show how this approach would be indispensable to solve a multitude of emerging problems in biology and medicine (including our fight against the current and future pandemics), many of which we will be tackling at my future lab at UC San Diego (UCSD).

Bio

Dr. Yatish Turakhia is a postdoctoral researcher at Genomics Institute, UC Santa Cruz, where he is jointly advised by Prof. David Haussler and Prof. Benedict Paten. He will be joining University of California San Diego (UCSD) next year as an Assistant Professor in the Department of Electrical and Computer Engineering (ECE). His research interests are in developing hardware accelerators and algorithms for faster and cheaper genomic analysis. Dr. Turakhia obtained his PhD from Stanford University in 2019, where he was jointly advised by Prof. Bill Dally and Prof. Gill Bejerano. His work has won the best paper award at ASPLOS 2018 and IEEE Micro Top Picks award 2018. He is also a past recipient of the NVIDIA Graduate Fellowship.