[Colloquium] Reminder: [masters-presentation] Assaf/MS Presentation/Feb 18, 2020

[Margaret Jaffey]

This is a reminder about Rida Assaf's MS Presentation tomorrow
morning.

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Date:  Tuesday, February 18, 2020

Time:  9:00 AM

Place:  John Crerar Library 298

M.S. Candidate:  Rida Assaf

M.S. Paper Title: Identifying Genomic Islands with Deep Neural
Networks

Abstract:
Horizontal gene transfer is the main source of adaptability for
bacteria, through which genes are obtained from different sources
including bacteria, archaea, viruses, and eukaryotes. This process
promotes the rapid spread of genetic information across lineages,
typically in the form of clusters of genes referred to as genomic
islands (GIs). Different types of GIs exist, often classified by the
content of their cargo genes or their means of integration and
mobility. Various computational methods have been devised to detect
different types of GIs, but no single method currently is capable of
detecting all GIs. We propose a method, which we call Shutter Island,
that uses a deep learning model (Inception V3, widely used in computer
vision) to detect genomic islands. The intrinsic value of deep
learning methods lies in their ability to generalize. Via a technique
called transfer learning, the model is pre-trained on a large generic
dataset and then re-trained on images that we generate to represent
genomic fragments. We demonstrate that this image-based approach
generalizes better than the existing tools.

Rida's advisor is Prof. Rick Stevens

Login to the Computer Science Department website for details:
 https://newtraell.cs.uchicago.edu/phd/ms_announcements#rida

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Margaret P. Jaffey            margaret at cs.uchicago.edu
Department of Computer Science
Student Support Rep (JCL 350)              (773) 702-6011
The University of Chicago      http://www.cs.uchicago.edu
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