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| + | '''Seminar Speaker:''' Christophe Dupraz <br> |
| − | |'''To schedule a meeting:''' Click the 'edit' tab above. Enter '''your name''' to the right of the first pair of vertical lines <nowiki>(||)</nowiki> for the desired meeting time and the '''meeting location''' after the second pair of vertical lines.
| + | '''Institution:''' UConn, Center for Integrative Geosciences and Dept. of Marine Sciences <br> |
| − | | + | '''Seminar Title:''' Biosignatures in carbonate rocks: organomineralization processes in microbial ecosystems <br> |
| − | '''For seminar hosts:''' This page should be updated in order to reflect the schedule of the current week's seminar speaker. For an empty template of the source text, click [[Template:Seminar speaker sign-up|here]]. Customize the schedule to match the speaker's availability, and add events like meals and airport arrival/departure times as necessary.
| + | '''Faculty or Student Contact:''' Andrew Bush |
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| − | Click [[EEB Department Seminar|here]] for the EEB Department Seminar page.
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| − | |}
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| − | '''Seminar Speaker:''' [http://www.biomath.ucla.edu/msuchard/ Marc Suchard]<br> | + | |
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| − | '''Institution:''' [http://dgsom.healthsciences.ucla.edu/ David Geffen School of Medicine, University of California at Los Angeles (UCLA)]<br> | + | |
| − | '''Wednesday Seminar Title: "Phylogenetic likelihoods 100-fold faster, or ridiculously parallel statistical inference" 4:00 PM, CLAS 344''' <br> | + | |
| − | '''Faculty or Student Contact:''' [mailto:paul.lewis@uconn.edu Paul Lewis]'''<br> | + | |
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| + | ==Thursday, 30 September== |
| − | |<span style="color:crimson">'''Important note:'''</span> 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 <span style="color:crimson">'''Tuesday'''</span>, but will give his seminar on <span style="color:crimson">'''Wednesday'''</span> in the <span style="color:crimson">'''CLAS building'''</span> (home of the Statistics Department).
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| − | |}
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| − | | + | |
| − | '''Abstract'''
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| − | 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.
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| − | 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.
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| − | | + | |
| − | ==<span style="color:crimson">Tuesday</span>, September 21, 2010==
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| | {|border=1 cellpadding=8 | | {|border=1 cellpadding=8 |
| | | '''Time''' || '''Name''' || '''Room''' | | | '''Time''' || '''Name''' || '''Room''' |
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| − | | 10:00am || Paul Lewis || TLS 166a | + | | 2:00pm || || |
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| − | | 10:30am || || | + | | 2:30pm || || |
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| − | | 11:00am || || | + | | 3:00pm || EEB 3894 || Bamford |
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| − | | 11:30am || || | + | | 3:30pm || Seminar Setup || |
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| − | | 12:00pm || Lunch, with Grad Students || Torrey Life Science (TLS) Bamford Room 171b
| + | | 4:00pm || Seminar || BPB 130 |
| − | |-
| + | |
| − | | 1:30pm || ||
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| − | |-
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| − | | 2:00pm || Yu (Daniel) Fan || TLS 162
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| − | |-
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| − | | 2:30pm || Chris Simon|| Biopharm 305d
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| − | |-
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| − | | 3:00pm || Simon Lab || BioPharm 323
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| − | |-
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| − | | 3:30pm || Simon Lab || BioPharm 323
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| − | |-
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| − | | 4:00pm || Systematics Seminar<br/>(visitors welcome!) || Bamford Room (TLS 171b) | + | |
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| + | |
| − | | 6-8 || Dinner, [http://www.willibrew.com/ Willimantic Brewing Co.] || Paul Lewis, Louise Lewis, Chris Simon, Chris Owen, Dave Marshall, Kathy Hill, others?
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| − | |-
| + | |
| − | |}
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| − | ==<span style="color:crimson">Wednesday</span>, September 22, 2010==
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| − | {|border=1 cellpadding=8
| + | |
| − | | '''Time''' || '''Name''' || '''Room'''
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| − | | 8am-4pm || colspan="2" align="center" | Statistics Department meetings | + | | 4:30pm || || |
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| − | | 4:00pm || Seminar || CLAS 344
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| − | |-
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| | |} | | |} |
