[Colloquium] Reminder: Santerre/Dissertation Defense/Nov 6, 2017

[Margaret Jaffey via Colloquium]

This is a reminder about John Santerre's dissertation defense on
Monday.

       Department of Computer Science/The University of Chicago

                     *** Dissertation Defense ***


Candidate:  John Santerre

Date:  Monday, November 6, 2017

Time:  10:30 AM

Place:  Ryerson 352 -- "The Barn"

Title: Machine Learning for the Phenotype to Genotype Problem

Abstract:
The rise of machine learning to augment or replace human judgments has
grown at an astounding pace. In the broadest of terms, these
techniques look to discern structure from data and are productive when
order can be discerned using statistical techniques. Here we will
explore the genotype to phenotype problem. The goal of this general
problem is to predict the behavior of a sample of bacterial using its
sequenced DNA. The inverse is also important; with a known behavior of
a sample of bacteria, is it possible to make a good prediction about
the genetic structure? The very basis of the genotype to phenotype
problem is one of constructing and conserving inherited structure
through and across generations. We propose to analyze two different
genotype to phenotype problems to illustrate similarities and
differences. The first data set we consider is antimicrobial
resistance (AMR). AMR is topic of critical importance as outcomes are
expected to be dramatically effected by the rise of AMR bacteria over
the next several decades. The second data set we propose to analysis
is predicted growth rates on standard medium types for a variety of
bacterial. These two data sets are complimentary because AMR is
typically a function of a small number of individual mutations, while
growth of an organism on substrates is often a collection of fitness
functions mutations that result in overall fitness.

John's advisor is Prof. Rick Stevens

Login to the Computer Science Department website for details,
including a draft copy of the dissertation:

 https://www.cs.uchicago.edu/phd/phd_announcements#santerre

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Margaret P. Jaffey            margaret at cs.uchicago.edu
Department of Computer Science
Student Support Rep (Ry 156)               (773) 702-6011
The University of Chicago      http://www.cs.uchicago.edu
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