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Seminar Speaker: Marc Suchard

Institution: David Geffen School of Medicine, University of California at Los Angeles (UCLA)
Wednesday Seminar Title: "Phylogenetic likelihoods 100-fold faster, or ridiculously parallel statistical inference" 4:00 PM, CLAS 344
Faculty or Student Contact: Paul Lewis

Important note: Because this is a joint EEB/Statistics seminar, the days of Marc's visit and the location of his seminar are unusual. He will be in the EEB department on Tuesday, but will give his seminar on Wednesday in the CLAS building (home of the Statistics Department).


Massive numerical integration plagues the statistical inference of partially observed stochastic processes and high dimensional data modeling. An important biological example entertains partially observed continuous-time Markov chains (CTMCs) to model molecular sequence evolution. Joint inference of phylogenetic trees and codon-based substitution models of sequence evolution remains computationally impractical. Parallelizing data likelihood calculations is an obvious strategy; however, across a cluster-computer, this scales with the total number of processing cores, incurring considerable cost to achieve reasonable run-time.

To solve this problem, I describe many-core computing algorithms that harness inexpensive graphics processing units (GPUs) for calculation of the likelihood under CTMC models of evolution. High-end GPUs containing hundreds of cores and are low-cost. These novel algorithms are particularly efficient for large state-spaces, including codon models, and large data sets, such as full genome alignments where we demonstrate up to 150-fold speed-up. I conclude with a discussion of the future of many-core computing in statistics and touch upon recent experiences with massively large and high-dimensional mixture models.

Tuesday, September 21, 2010

Time Name Room
12:00pm Lunch, with Grad Students Torrey Life Science (TLS) Bamford Room 171b
3:00pm Simon BioPharm 305D
3:30pm Simon BioPharm 305D
4:00pm Systematics Seminar
(visitors welcome!)
Bamford Room (TLS 171b)
6-8 Dinner, Willimantic Brewing Co. Paul Lewis, Louise Lewis, others?

Wednesday, September 22, 2010

Time Name Room
8am-4pm Statistics Department meetings
4:00pm Seminar CLAS 344