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Schedule of Events – Summer
2019 |
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Schedule Subject
to Change |
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All activities and events will be held
in the Millennia Boardroom (room 723, CDM building, Loop campus) unless
otherwise noted. |
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Monday June 17,
2019 |
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REU Welcome, Introduction & Tutorials, Logistics (Orientation Day) |
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09:30
AM |
10:00
AM |
Breakfast |
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10:00
AM |
10:45
AM |
Welcome
to CDM and DePaul —Dr. Miller, Dean of CDM |
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Overview
of the summer program—Drs. Furst & Raicu |
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10:45
AM |
11:15
AM |
Mentors
& Students Introductions |
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11:15
AM |
12:15
PM |
REU
MedIX Experiences – Previous REU participants – Part I Reilley
Grant – REU Participant 2017 Chufan
Gao – REU Participant 2018 Sam
Berglin – REU Participant 2018 |
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12:15
PM |
02:00
PM |
Lunch |
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02:00
PM |
03:30
PM |
Introduction
to Image Processing – Dr. Furst |
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03:30
PM |
04:00
PM |
Logistics
(email accounts, lab access, pictures) |
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Evaluation
Process during the MedIX Program – Dr. Furst |
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Entry
Survey of Expectations and Preferences I – online survey – REU students |
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04:00
PM |
04:30
PM |
Responsible
conduct of research training, offered online by the Collaborative
Institutional Training Initiative (CITI) – Dr. Furst |
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04:30
PM |
05:30
PM |
Tour
of SoC and of the DePaul Center – Dr. Furst |
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Tuesday June 18,
2019 |
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Logistics, Tutorials, Research seminar and Research Training (Orientation
Day) |
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08:30
AM |
9:00
AM |
Breakfast |
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09:00
AM |
10:30
AM |
Lab
session: Introduction to Matlab and Image Processing in Matlab tutorial –Part
I - Dr. Furst (room 819) |
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10:30
AM |
12:00
PM |
Introduction
to Data Mining and Machine Learning– Dr. Jonathan Gemmell |
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12:00
PM |
1:30
PM |
Lunch |
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01:30
PM |
3:00
PM |
DePaul
Project Descriptions – Dr. Gemmell |
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03:30
PM |
04:30
PM |
Developing
a research career – Dr. Furst |
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04:30
PM |
05:30
PM |
Responsible
conduct of research training, offered online by the Collaborative
Institutional Training Initiative (CITI) – Dr. Furst |
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Wednesday June
19, 2019 |
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Project Descriptions and Visit to University of Chicago (Orientation
Day) |
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09:30
AM |
12:30
PM |
Visit
to University of Chicago (UofC) Research
Projects’ Descriptions – Dr. Armato & Dr. Carroll |
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12:30
PM |
2:00
PM |
Lunch
and Travel from University of Chicago to DePaul |
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2:00
PM |
5:00
PM |
Research
Projects’ Descriptions –Dr. Furst and Dr. Raicu |
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Thursday June 20,
2019 |
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Tutorials, Project Selection & Research seminar (Orientation Day) |
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08:30
AM |
09:00
AM |
Breakfast |
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09:00
AM |
10:30
PM |
Lab
session: Introduction to Matlab and Image Processing in Matlab –Part II - Dr.
Furst (room 819) |
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10:30
AM |
12:00
PM |
Lab
session: Introduction to SPSS - Dr. Raicu (room 819) |
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12:00
PM |
12:30
PM |
REU
MedIX Experiences – Previous REU participants – Part II (Dante
Dettori Dante Chakravorti, REU Participant 2018) |
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12:30
PM |
02:00
PM |
Lunch |
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02:00
PM |
03:00
PM |
Open
Discussion/ Project Assignment |
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03:00
PM |
04:30
PM |
Retrieving
and reading research papers – Dr. Raicu |
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04:30
PM |
05:
30 PM |
Introduction
to Deep learning – Dr. Gemmell |
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Friday June 21,
2019 |
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Lab work and team meetings |
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09:00
AM |
05:00
PM |
Lab
Work and team meetings at UofC and DePaul |
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Friday June 28,
2019 |
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Lab work, REU group meeting and seminar |
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09:00
AM |
01:30
PM |
Lab
work at UofC and DePaul (UofC
students go to UofC until 12:30pm and then come to
DePaul) |
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01:30 PM |
05:30 PM |
Group meeting at DePaul |
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01:30
PM |
2:30
PM |
pizza
lunch and progress report: a) the problem you are working on (including goals
for the project), b) motivation for the problem, and c) some interesting
facts you discovered (1) about the data based your preliminary analysis of
the data and (2) papers you read so far; |
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02:30
PM |
3:00
PM |
Paper
presentation: "Distributed representations of words and phrases and
their compositionality" by Elisa and Alex |
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03:00
PM |
04:00
PM |
How
to give a research presentation – Dr. Gemmell |
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04:00
PM |
05:00
PM |
Creating
TED-style Talks - Dr. Gemmell |
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Tuesday July 2,
2019 |
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Lab work and visit to UofC (room Q 207) |
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02:30
PM |
04:30
PM |
Imaging
Modalities lecture at UofC (Dr. Armato) |
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Friday July 5,
2019 |
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Lab work, REU group meeting, and Survey |
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09:00
AM |
01:30
PM |
Lab
work at UofC and DePaul |
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01:30 PM |
05:00 PM |
Group meeting at DePaul |
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01:30
PM |
02:30
PM |
pizza
lunch and progress report: a) (refined) goals for the project, b) research
hypothesis, c) literature review – part 1, and d) preliminary data analysis |
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Survey
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02:30
PM |
03:00
PM |
MedIX
Team II paper presentation and discussion, "Automated assessment of
early hypoxic brain edema in non-enhanced CT predicts outcome in patients
after cardiac arrest" by Ashely and Nicole |
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03:00
PM |
04:00
PM |
Graduate
Funding - Dr. Furst |
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04:00
PM |
05:00
PM |
How
to write a research paper – Dr. Furst |
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Thursday July 9,
2019 |
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02:30
PM |
04:30
PM |
Imaging
Modalities lecture at UofC (Dr. Armato) |
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Friday July 12,
2019 |
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09:00
AM |
01:00
PM |
Lab
work at UofC and DePaul |
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01:00 PM |
05:00 PM |
Group meeting at DePaul |
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01:00
PM |
02:
00 PM |
pizza
lunch and progress report: a) any new relevant literature review, b)
methodology, c) preliminary results |
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02:00
PM |
02:30
PM |
MedIX Team II paper
presentation and discussion, "Automated assessment of early hypoxic
brain edema in non-enhanced CT predicts outcome in patients after cardiac
arrest" by Ashely and Nicole |
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02:30
PM |
03:00
PM |
Travel
to IIT |
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03:00
PM |
05:00
PM |
“A
day in the life of a PhD student” – event by REU site @IIT Speakers:
Roselyne Tchoua, recent PhD graduate from University of Chicago Yiyang
Wang, PhD student at DePaul University since 09/2018 Brian
Tauro, PhD student at IIT since 09/2018 |
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Saturday July
13, 2019 |
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Picnic
@ Gillson Park, Wilmette, 3PM REU students, graduate students and
faculty from DePaul, UofC, IIT Picnic Pictures: https://www.icloud.com/sharedalbum/#B0w5tzEA5ckJfO |
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Tuesday July 16,
2019 |
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02:30
PM |
04:00
PM |
Imaging
Modalities lecture at UofC: CT (Dr. La Riviere) |
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Friday July 19,
2019 |
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Survey and midterm presentations |
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08:30
AM |
09:00
AM |
Breakfast
(Room 723, CDM building) |
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09:00
AM |
09:45
AM |
Presentation
1: “Applying Topic Modeling Techniques to Detect Trends in Mental Health
Discussion” Elise
Glaser (Colorado College) Alex
Morain (University of Illinois at Urbana-Champaign) Mentor:
Dr. Gemmell |
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09:45
AM |
10:30
AM |
Presentation
2: “Modelling Uncertainty in Medical Reports” Yilan Dong (Grinnell
College) Kathleen
Isenegger (Amherst College) Mentor:
Dr. Furst |
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10:30
AM |
10:40
AM |
Break |
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10:40
AM |
11:25
AM |
Presentation
3: “Predicting Age-Related Macular Degeneration Disease from SD-OCT Images
Using Machine Learning” Abum Okemgbo (University of Pennsylvania) David
Rein (Duke University) Mentor:
Dr. Raicu |
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11:25
PM |
12:10
PM |
Presentation
4: “Radiomics-Based Texture Analysis of Idiopathic
Pulmonary Fibrosis” Ahmed
Rashid (Valencia College, Rollins College) Jorie Budzikowski (Vanderbilt University) Mentor:
Dr. Armato |
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12:15
PM |
01:15
PM |
Lunch
(DePaul Center 11013) |
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01:10
PM |
02:00
PM |
Presentation
5: “Medical Imaging: Predicting Comatose Patient Outcomes” Ashley
Sjurson (University of Iowa) Nicole
Kuznetsov (University of Rochester) Mentor
Dr. Carroll |
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02:00
PM |
02:20
PM |
Presentation
6: “Machine Learning for User Experience Design” Ally Theodorescu
(DePaul University) Yan
Yu (DePaul University) Mentor
Dr. Raicu |
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02:20
PM |
02:30
PM |
Survey
(Room 723) |
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Thursday July
26, 2019 |
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Visit
to Argonne National Labs |
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08:15
AM |
08:45
AM |
Arrive
at Argonne visitor center to pick up badge |
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08:45
AM |
09:00
AM |
Meet
in Building 240, Room 1406/1407 Introductions
[Ioan Raicu & Kyle
Chard] |
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09:
00 AM |
10:00
AM |
Building
240, Room 4312 Visualization
Lab Tour with Joseph Insley |
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10:00
AM |
11:00
AM |
Building
240, Room 2208 Tour
of ALCF machine room |
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11:00
AM |
02:30
PM |
Building
240, Room 2208 |
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11:00
AM |
12:00
PM |
Research
Talks: Bogdan Nicolae and Joaquin Chung |
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12:00
PM |
12:30
PM |
Lunch/Pizza
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12:30
PM |
01:30
PM |
Computer
Science Focused Competitions [Ioan Raicu] |
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01:30
PM |
02:00
PM |
Research
Talk [Rob Latham] |
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02:00
PM |
02:30
PM |
Leave
for APS Building (with cars) |
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03:00
PM |
05:00
PM |
Building
401, Lobby |
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05:00
PM |
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Adjourn |
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Friday July 26,
2019 |
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Lab work, REU group meeting |
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09:00
AM |
01:00
PM |
Lab
work at UofC and DePaul |
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01:00
PM |
02:45
PM |
Pizza
lunch, progress report: a) methodology, b) results, and c) TED talks |
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02:45
PM |
03:15
PM |
MedIX Team 3 paper
presentation: “Individual
Drusen Segmentation and Repeatability and
Reproducibility of Their Automated Quantification in Optical Coherence
Tomography Images” by Abum and David |
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03:15
PM |
03:30
PM |
Break |
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03:30
PM |
05:30
PM |
Women
in Science and Technology Panel Speakers:
Dr. Rujia Wang (Assistant Professor at IIT) Dr.
Sheena Erete (Associate Professor at DePaul) Dr.
Irina Matveeva (Head of Machine Learning, NexLP & Adjunct Professor at IIT) |
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Tuesday July 30,
2019 |
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02:30
PM |
04:00
PM |
Imaging
Modalities lecture at UofC: MRI (Dr. Carroll) |
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Friday August 2,
2019 |
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NSF REU MedIX
Program 15 Year Anniversary |
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9:30
AM |
10:00
AM |
Breakfast |
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10:00
AM |
10:15
AM |
Opening
Remarks and Introductions: Dr.
Salma Ghanem, Provost, DePaul University Dr.
Harriet Taylor, Program Director, National Science Foundation |
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10:15AM |
12:15
PM |
REU
student presentations |
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10:15AM |
10:40AM |
Medical
Imaging: Predicting Comatose Patient Outcomes Students:
Ashley Sjurson (University of Iowa) Nicole
Kuznetsov (University of Rochester) Mentor:
Dr. Carroll |
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10:40
PM |
11:05
AM |
Predicting
Age-Related Macular Degeneration Disease from SD-OCT Images Students:
Abum Okemgbo (University
of Pennsylvania) David
Rein (Duke University) Mentor:
Dr. Raicu |
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11:05
AM |
11:30
AM |
Radiomics-Based Texture
Analysis of Idiopathic Pulmonary Fibrosis Students:
Ahmed Rashid (Valencia College, Rollins College) Jorie Budzikowski (Vanderbilt University) Mentor:
Dr. Armato |
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11:30
AM |
11:35
AM |
Break |
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11:35
AM |
12:00
PM |
Modelling
Uncertainty in Medical Reports Students:
Yilan Dong (Grinnell College) Kathleen
Isenegger (Amherst College) Mentor:
Dr. Furst |
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12:00
PM |
12:
25 PM |
Applying
Topic Modeling Techniques to Detect Trends in Mental Discussion Students:
Elise Glaser (Colorado College) Alex
Morain (University of Illinois at Urbana-Champaign) Mentor:
Dr. Gemmell |
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12:30
PM |
02:30
PM |
Lunch
and Invited talks (DePaul Center Room 11013): Dr.
Harriet Taylor, Program Director, National Science Foundation Dr.
Daniela Raicu & Jacob Furst,
Overview of the MedIX Program & DePaul Dr.
Sam Armato, Overview of the MedIX
Program & The University of Chicago Dr.
Jonathan Gemmell, Dr. Lucia Dettori,
Dr. Sheena Erete (Mentoring experiences) |
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02:30
PM |
03:00
PM |
MedIX Team 4 paper
presentation: “CT
Imaging Phenotypes of Pulmonary Fibrosis in the MUC5B Promoter Site Polymorphism”
by Jorie and Ahmed |
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03:00
PM |
05:00
PM |
Workshop
Session: Preparing a successful NSF Graduate Fellowship Application |
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Tuesday August
6, 2019 |
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02:30
PM |
04:00
PM |
Imaging
Modalities lecture at UofC: Texture analysis and
machine learning (Dr. Giger) |
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01:30 PM |
05:00 PM |
Group meeting at DePaul (CDM Room 723) |
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01:30
PM |
03:00
PM |
Pizza
lunch and progress report: a) detailed results and how they relate to your
research questions/hypothesis, 2) research plan for the last two weeks, and
3) TED-style presentations. |
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03:00
PM |
03:30
PM |
MedIX Team 5 paper
presentation: “The BioScope corpus: biomedical
texts annotated for uncertainty, negation and their scopes” by Kathleen and Yilan |
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03:30
PM |
03:45
PM |
Break |
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03:45
PM |
04:00
PM |
Poster
presentation – first draft (Abum and Ashley) |
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04:00
PM |
05:00
PM |
Professional
and student organizations (Dr. Gemmell) |
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Friday August 9,
2019 |
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Lab work, REU group meeting and seminars |
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09:00
AM |
01:30
PM |
Lab
work at UofC and DePaul |
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01:30 PM |
05:00 PM |
Group meeting at DePaul |
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01:30
PM |
02:30
PM |
MedIX
teams progress report |
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02:30
PM |
03:00
PM |
Paper
Presentation by MedIX Team V |
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03:00
PM |
03:30
PM |
Unveiling
of poster draft |
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03:30
PM |
05:00
PM |
Student
organizations and professional organizations (Dr. Gemmell) |
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Friday August
16, 2019 |
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Lab work, REU group meeting and seminar + survey |
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09:00
AM |
01:30
PM |
Lab
work at UofC and DePaul |
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01:30 PM |
05:00 PM |
Group meeting at DePaul (CDM Room 723) |
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01:30
PM |
03:00
PM |
Lunch
and Progress report: provide an overview of your research, hypotheses, and
summary of your results on how they relate to your research
questions/hypothesis; final Ted-style presentations |
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03:00
PM |
03:30
PM |
Survey
week 9 & poster last draft review |
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03:30
PM |
05:00
PM |
Research
@CDM; Moderators: Alex & Ahmed |
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Friday August
23, 2019 |
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Final Presentation and Deliverables |
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09:00
AM |
09:30
AM |
Breakfast
(Room 723, CDM building) |
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09:30
AM |
10:05
AM |
Predicting
Age-Related Macular Degeneration Disease from SD-OCT Images Students:
Abum Okemgbo (University
of Pennsylvania) David
Rein (Duke University) Mentor:
Dr. Raicu |
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10:05
AM |
10:40
AM |
Radiomics-Based Texture
Analysis of Idiopathic Pulmonary Fibrosis Students:
Ahmed Rashid (Valencia College, Rollins College) Jorie Budzikowski (Vanderbilt University) Mentor:
Dr. Armato |
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10:40
AM |
11:15
AM |
Medical
Imaging: Predicting Comatose Patient Outcomes Students:
Ashley Sjurson (University of Iowa) Nicole
Kuznetsov (University of Rochester) Mentor:
Dr. Carroll |
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11:15
AM |
11:20
AM |
Break |
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11:20
AM |
11:55
AM |
Applying
Topic Modeling Techniques to Detect Trends in Mental Discussion Students:
Elise Glaser (Colorado College) Alex
Morain (University of Illinois at Urbana-Champaign) Mentor:
Dr. Gemmell |
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11:55
AM |
12:30
PM |
Modelling
Uncertainty in Medical Reports Students:
Yilan Dong (Grinnell College) Kathleen
Isenegger (Amherst College) Mentor:
Dr. Furst |
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12:30
PM |
02:00
PM |
Lunch
(Exchequer Restaurant) |
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02:00
PM |
05:00
PM |
Deliverables
and individual student interview |
