EECS Department Colloquium Series
Using Computer Science to Help Save Lives 
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Wednesday, September 10, 2014 David Patterson |
ABSTRACT:
A team of computer scientists, statisticians, doctors, and biologists are applying modern CS techniques to fight deadly diseases. This talk will start with a quick introduction to genetics, describe our approach to the challenges of fast genetic processing, describe how such processing helps discover infectious diseases, show results from a recent collaboration with cancer researchers fighting Acute Myeloid Leukemia, and conclude with opportunities for others to participate.
When we got started in genetics in 2011, I wrote a somewhat optimistic essay in the New York Times that computer scientists have a lot to bring to the fight deadly diseases like cancer, in part by making much better software tools. (This hypothesis was not universally heralded by everyone in all fields.) The good news is that we have already helped save one life, as documented in the same newspaper.
Using cloud computing and open source development, we believe we can build new tools that will accelerate genetics processing from the current one week per genome to one hour, which would help many patients with genetics-based diseases. For example:
● SNAP is one of the most accurate and by 3X-10X the fastest sequencing aligner.
● ADAM is a cluster friendly storage format for genetic information that executes two other expensive steps 110X faster on an 82-node cluster.
● SMaSH is a genetics processing benchmark that measures progress and thereby accelerates it.
BIOGRAPHY:
David Patterson is the Pardee Professor of Computer Science at the University of California at Berkeley, which he joined after graduating from UCLA in 1977.
Dave's research style is to identify critical questions for the IT industry and gather inter-disciplinary groups of faculty and graduate students to answer them. The answer is typically embodied in demonstration systems, and these demonstration systems are later mirrored in commercial products. In addition to research impact, these projects train leaders of our field. The best known projects were Reduced Instruction Set Computers (RISC), Redundant Array of Inexpensive Disks (RAID), and Networks of Workstations (NOW), each of which helped lead to billion dollar industries.
A measure of the success of projects is the list of awards won by Patterson and as his teammates: the C & C Prize, the IEEE von Neumann Medal, the IEEE Johnson Storage Award, the SIGMOD Test of Time award, the ACM-IEEE Eckert-Mauchly Award, and the Katayanagi Prize. He was also elected to both AAAS societies, the National Academy of Engineering, the National Academy of Sciences, the Silicon Valley Engineering Hall of Fame, and to be a Fellow of the Computer History Museum. The full list includes about 35 awards for research, teaching, and service.
In his spare time he coauthored six books, including two with John Hennessy, who is President of Stanford University. Patterson also served as Chair of the Computer Science Division at UC Berkeley, Chair of the Computing Research Association, and President of ACM.
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