|
Schedule of Events - Summer 2023 |
||
|
Schedule
Subject to Change |
||
|
All
activities and events will be held in the Millennia Boardroom (room 723, CDM
building, 243 South Wabash, Chicago, IL 60604 Loop campus) unless otherwise
noted. All
times are Central Time. |
||
|
Monday
June 12, 2023 |
||
|
REU Welcome, Introduction & Tutorials, Logistics
(Orientation Day) |
||
|
08:30 AM |
9:00 AM |
Breakfast |
|
9:00AM |
9:55AM |
Welcome to CDM and DePaul - Dr. Dettori, Interim CDM Dean |
|
|
|
Overview of the summer program -
Drs. Furst & Raicu |
|
9:55AM |
10:25AM |
Mentors & Students
Introductions |
|
10:25AM |
10:30AM |
Break |
|
10:30AM |
11:15AM |
REU MedIX
Experiences - Jorie Budzikowski,
PhD student, Northwestern University (REU participant, Summer 2023) |
|
11:15AM |
11:45AM |
Evaluation Process during the MedIX Program - Dr. Furst |
|
Entry Survey of Expectations and
Preferences I - online survey -REU students |
||
|
11:45 AM |
1:15 PM |
Lunch Break |
|
1:15 PM |
3:00 PM |
Tutorial 1: Introduction to Image
Processing, Part 1 - Dr. Furst |
|
3:00 PM |
3:15 PM |
Logistics (DePaul username
accounts, computer lab remote access, pictures, website, hiring paper work) |
|
3:15 PM |
4:00 PM |
Responsible conduct of research
training, offered online by the Collaborative Institutional Training
Initiative (CITI), Part 1 - Dr. Furst |
|
4:00 PM |
5:00PM |
Tutorial 2: Data Analysis
Review - Dr. Ian Wang |
|
|
||
|
Tuesday
June 13, 2023 |
||
|
Logistics, Tutorials, Research seminar and Research Training
(Orientation Day) |
||
|
08:30 AM |
9:00 AM |
Breakfast |
|
09:00 AM |
10:30 AM |
Tutorial 3: Lab session:
Introduction to Matlab and Image Processing in Matlab
tutorial - Part I - Dr. Furst, CDM Lab
801 |
|
10:30 AM |
12:00 PM |
Tutorial 4: Introduction to Data
Science and Machine Learning-Dr. Tchoua |
|
12:00 PM |
1:00 PM |
Lunch Break |
|
1:00 PM |
2:30 PM |
DePaul Research Project
Descriptions - Dr. Tchoua |
|
2:30 PM |
4:00 PM |
DePaul Research Project
Descriptions - Dr. Furst |
|
4:00 PM |
4:30 PM |
Responsible conduct of research
training, offered online by the Collaborative Institutional Training
Initiative (CITI) -Part 2-Dr. Furst |
|
04:30 PM |
05:00 PM |
Tour of CDM and of the DePaul
Center (including the Jarvis Innovation and Collaboration Center) -Dr. Furst |
|
|
||
|
Wednesday
June 14, 2023 |
||
|
Tutorials, Project Descriptions and Visit to University of
Chicago (Orientation Day) |
||
|
09:30 AM |
12:30 PM |
Tutorial 5: Computer-aided
diagnosis UofC Research Project Descriptions
-Mena, Shenouda, Dr. Armato & Dr. Bader |
|
12:30 PM |
1:30 PM |
Lunch break and travel back to
DePaul |
|
1:30 PM |
3:00 PM |
DePaul Research Project Descriptions
-Dr. Raicu |
|
3:00 PM |
5:00 PM |
Tutorial 6: Lab session:
Introduction to SPSS/Python, and Data Analysis in SPSS/Python -Yiyang(Ian)
Wang, CDM Lab 801) |
|
|
||
|
Thursday
June 15, 2023 |
||
|
Tutorials, Project Selection & Research seminar
(Orientation Day) |
||
|
08:30 AM |
9:00 AM |
Breakfast |
|
09:00 AM |
10:30 AM |
Tutorial 7: Lab session:
Introduction to Matlab and Image Processing in Matlab
-Part II - Dr. Furst, CDM Lab
801 |
|
10:30 AM |
12:00 PM |
Tutorial 8: Introduction to Deep
Learning -Dr. Furst, CDM Lab 801 |
|
12:00 PM |
1:00 PM |
Lunch Break |
|
1:00 PM |
2:00 PM |
Open Discussion/ Project
Assignment |
|
2:00 PM |
2:30 PM |
Professional Organizations in
Computing, Medical Physics, and Medical Imaging -Dr. Raicu |
|
2:30 PM |
4:00 PM |
Retrieving and reading research
papers -Dr. Raicu |
|
4:00 PM |
5:00 PM |
Developing a research career
-Dr. Raicu |
|
|
||
|
Friday
June 16, 2023 |
||
|
Lab work and team meetings |
||
|
9:00 AM |
5:00 PM |
Lab Work and team meetings
at UofC and DePaul Projects kick off |
|
|
||
|
Tuesday
June 20, 2023 |
||
|
Lab work and visit to UofC |
||
|
3:00 PM |
5:00 PM |
UofC Lecture: Radiographic imaging modalities (Dr. Armato) Location: UChicago
Medical Center Q207 |
|
|
||
|
Friday
June 23, 2023 |
||
|
Lab work, REU group meeting and seminar |
||
|
9:00 AM |
1:00 PM |
Lab work at UofC and
DePaul |
|
1:00 PM |
5:00 PM |
Group REU activities |
|
1:00 PM |
3:00 PM |
Pizza lunch and progress report – each team
will put together a 10-minute PPT presentation that will describe 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 your
project data based your preliminary analysis of the data and (2) papers you
read so far |
|
3:00 PM |
3:30 PM |
Paper
presentation by MedIX Team I – Nicole and Nuvia; please read the paper
and be prepared to discuss strengths and weaknesses Sharma, A., Vans, E., Shigemizu,
D. et al. DeepInsight: A methodology to
transform a non-image data to an image for convolution neural network
architecture. Sci Rep 9, 11399 (2019). https://doi.org/10.1038/s41598-019-47765-6 |
|
3:30 PM |
4:30 PM |
How to give a research
presentation -- Dr. Raicu |
|
4:30 PM |
5:00 PM |
Creating TED-style Talks
--Dr. Raicu |
|
|
||
|
Lab work and visit to UofC |
||
|
3:00
PM |
05:00
PM |
UofC Lecture: Computed Tomography (Dr. La Riviere) Location:
UChicago Medical Center Q207 |
|
|
||
|
Friday
June 30, 2023 |
||
|
Lab work, REU group meeting, and Survey |
||
|
9:00 AM |
1:00 PM |
Lab work at UofC and
DePaul |
|
1:00 PM |
5:00 PM |
Group REU activities |
|
1:00 PM |
2:55 PM |
Lunch and progress reports |
|
2:55 PM |
3:10 PM |
Survey -Week 3 |
|
3:10 PM |
3:15 PM |
Break |
|
3:15 PM |
3:45 PM |
Paper presentation by MedIX Team II – Abheet and
Avery; please read the paper and be prepared to discuss strengths and
weaknesses Liu, L.Y., Bush, W.S., Koyutürk, M. et al. Interplay between traumatic brain
injury and intimate partner violence: data driven analysis utilizing
electronic health records. BMC Women's Health 20, 269 (2020). https://doi.org/10.1186/s12905-020-01104-4 |
|
3:45 PM |
4:15 PM |
Graduate Funding Opportunities -
Dr. Furst |
|
4:15 PM |
5:00 PM |
How to write a research paper -Dr.
Furst |
|
|
||
|
Wednesday
July 05, 2023 |
||
|
Lab work and visit to UofC |
||
|
3:00 PM |
05:00 PM |
UofC Lecture: Introduction to medical image processing
(Dr. Armato) Location: UChicago
Medical Center Q207 |
|
|
||
|
Friday
July 7, 2023 |
||
|
9:00 AM |
1:00 PM |
Lab work at UofC and
DePaul |
|
1:00 PM |
5:00 PM |
Group REU activities |
|
1:00 PM |
2:45 PM |
Lunch and progress reports |
|
2:45 PM |
3:15 PM |
Travel to IIT |
|
3:15 PM |
3:30 PM |
Meet and Greet with the REU
students from BigDataX at IIT/UChicago |
|
3:30 PM |
5:00 PM |
“A day in the life of a PhD
student” (joint with IIT REU Program) |
|
|
||
|
Saturday
July 8, 2023 |
||
|
Picnic @Gilson Park, Wilmette |
||
|
|
||
|
Tuesday
July 11, 2023 |
||
|
Lab work and visit to UofC |
||
|
3:00 PM |
5:00 PM |
UofC Lecture: The ABCs of CAD (Dr. Armato) Location: UChicago
Medical Center Q207 |
|
|
||
|
Friday
July 14, 2023 |
||
|
Survey and midterm presentations |
||
|
08:30 AM |
9:00 AM |
Breakfast |
|
9:00 AM |
9:40 AM |
Presentation
1: "Real-Time Histotripsy with Robot Arm Based on Improved
SURF Algorithm" Emmanuel Rosa Delgado (University of Puerto Rico
at Humacao) and Nina Soofi (University
of Illinois at Urbana Champaign) Mentor:
Dr. Bader |
|
9:40 AM |
10:20 AM |
Presentation 2: "Identification of Undiagnosed Traumatic Brain Injuries
through Semi-Supervised Clustering of Clinical Reports" Abheet Singh Sachdeva (Baylor University) and Avery Bell (Northern Arizona University) Mentor:
Dr. Furst |
|
10:20 AM |
10:30 AM |
Break |
|
10:30 AM |
11:10 AM |
Presentation
3: "Texture Analysis for Differentiation of BAP1 Mutation
Status from CT Scans" Abbas Shaikh (Rice
University) and Illana
Deutsch (Northwestern University) Mentor:
Dr. Armato |
|
11:10 AM |
11:50 PM |
Presentation 4: "Enhancing
Subtype Discovery through Latent Representation Learning" Julia
Gugulski (Brown
University) and Alicia Tee (University of
Wisconsin -Madison) Mentor: Dr. Raicu |
|
11:50 PM |
1:30 PM |
Lunch Location: DePaul Center (DPC 11013)
|
|
1:30 PM |
1:45 PM |
Survey -week 5 |
|
1:45 PM |
2:25 PM |
Presentation 5: "Transforming
Data to Images for CNN Classification of High-Risk Patients Return to the
Emergency Department" Nicole
Baugh (North Carolina State
University, University of North Carolina Chapel-Hill) and Nuvia Hernandez (Lewis University) Mentor: Dr. Tchoua |
|
2:25 PM |
3:05 PM |
Presentation
6: "Extracting
Important Symptoms of Long Haul Covid through
Machine Learning Algorithms" Machelle
Le (Swarthmore
College) and Amelia Nelson (University of Utah) Mentor:
Dr. Furst |
|
|
||
|
Tuesday
July 18, 2023 |
||
|
Lab work and visit to UofC |
||
|
3:00 PM |
5:00 PM |
UofC Lecture: Texture analysis, machine learning, and big
data (Dr. Giger) Location: UChicago
Medical Center Q207 |
|
|
||
|
Friday
July 21, 2023 |
||
|
Lab work, REU group meeting |
||
|
9:00 AM |
1:00 PM |
Lab work at UofC and
DePaul |
|
1:00 PM |
5:00 PM |
Group REU activities |
|
1:00 PM |
2:45 PM |
Lunch & MedIX teams
progress reports |
|
2:45 PM |
3:15 PM |
Paper presentation by
MedIX Team III - Emmanuel and
Nina Abdouni A, Presles B, Fargier-Voiron M, Rit S, Sarrut D.
Development of 2D+T tracking algorithm in ultrasound images for radiotherapy.
Annu Int Conf IEEE Eng Med Biol Soc. 2015 Aug;2015:2916-9. PMID: 26736902. https://doi.org/10.1109/EMBC.2015.73190024 |
|
3:15 PM |
3:30 PM |
Break |
|
3:30 PM |
5:30 PM |
“Women in Science and Technology” (Event Moderators: Nuvia and Nicole) |
|
|
||
|
Tuesday
July 25, 2023 |
||
|
9:00 AM |
5:00 PM |
|
|
|
||
|
Friday
July 28, 2023 |
||
|
REU group meeting, seminars + survey |
||
|
9:00 AM |
1:00 PM |
Lab work at UofC and
DePaul |
|
1:00 PM |
5:00 PM |
Group REU activities |
|
1:00 PM |
2:55 PM |
Lunch & MedIX teams
progress reports |
|
2:55 PM |
3:25 PM |
Rescheduled Paper presentation by
MedIX Team III - Emmanuel and
Nina Abdouni A, Presles B, Fargier-Voiron M, Rit S, Sarrut D.
Development of 2D+T tracking algorithm in ultrasound images for radiotherapy.
Annu Int Conf IEEE Eng Med Biol Soc. 2015 Aug;2015:2916-9. PMID: 26736902. https://doi.org/10.1109/EMBC.2015.73190024 |
|
3:25 PM |
3:30 PM |
Break |
|
3:30 PM |
5:00 PM |
Professional Organizations and Computing Competitions - Dr. Tchoua |
|
|
||
|
Tuesday
August 1, 2023 |
||
|
Lab work and visit to UofC |
||
|
3:00 PM |
05:00 PM |
UofC Lecture: Ultrasound (Dr. Bader) Location: UChicago
Medical Center Q207 |
|
|
||
|
Friday
August 4, 2023 |
||
|
Lab work, REU group meeting and seminars |
||
|
9:00 AM |
1:00 PM |
Lab work at UofC and DePaul |
|
1:00 PM |
5:00 PM |
Group REU activities |
|
1:00 PM |
2:55 PM |
Lunch, Poster Draft Presentation & MedIX teams
progress reports |
|
2:55 PM |
3:55 PM |
Paper presentation by
MedIX Team IV - Illana and
Abbas Zwanenburg, A., Leger, S., Agolli, L. et al.
Assessing robustness of radiomic features by image perturbation. Sci Rep 9, 614 (2019). https://doi.org/10.1038/s41598-018-36938-4 Paper presentation by
MedIX Team V - Alicia and
Julia Schulz MA, Chapman-Rounds M, Verma M, Bzdok D, Georgatzis K.
Inferring disease subtypes from clusters in explanation space. Sci Rep. 2020 Jul 30;10(1):12900. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7393364/ |
|
3:55 PM |
4:00 PM |
Break |
|
4:00 PM |
5:00 PM |
|
|
|
||
|
Friday
August 11, 2023 |
||
|
Lab work, REU group meeting and seminar + survey |
||
|
9:00 AM |
1:00 PM |
Lab work at UofC and
DePaul |
|
1:00 PM |
5:00 PM |
Group REU activities |
|
1:00 PM |
2:55 PM |
Lunch MedIX teams’
progress reports |
|
2:55 PM |
3:15 PM |
Survey for week 9 |
|
3:15 PM |
3:45 PM |
Paper presentation by
MedIX Team VI - Amelia and
Machelle Thaweethai, T., Jolley, S.E., Karlson, E.W., Levitan, E.B., Levy, B., McComsey, G.A., McCorkell, L.,
Nadkarni, G.N., Parthasarathy, S., Singh, U. and Walker, T.A., 2023. Development of a definition of postacute sequelae of SARS-CoV-2 infection.
Jama, 329(22), pp.1934-1946. https://jamanetwork.com/journals/jama/fullarticle/2805540 |
|
3:45 PM |
4:00 PM |
Break |
|
4:00 PM |
5:00 PM |
Research at CDM Seminar |
|
|
||
|
Friday
August 18, 2023 |
||
|
Final Presentation and Deliverables |
||
|
08:30 AM |
9:00 AM |
Breakfast |
|
9:00 AM |
9:40 AM |
Presentation
1: "Extracting
Important Symptoms of Long Haul Covid through
Machine Learning Algorithms" Machelle
Le (Swarthmore
College) and Amelia Nelson (University of Utah) Mentor:
Dr. Furst |
|
9:40 AM |
10:20 AM |
Presentation 2: "Enhancing
Subtype Discovery through Latent Representation Learning" Julia
Gugulski (Brown
University) and Alicia Tee (University of
Wisconsin -Madison) Mentor: Dr. Raicu |
|
10:20 AM |
11:00 AM |
Presentation
3: "Real-Time Histotripsy with Robot Arm Based on Improved
SURF Algorithm" Emmanuel Rosa Delgado (University of Puerto Rico
at Humacao) and Nina Soofi (University
of Illinois at Urbana Champaign) Mentor:
Dr. Bader |
|
11:00 AM |
11:15 AM |
Break |
|
11:15 AM |
11:55 AM |
Presentation
4: "Texture Analysis for Differentiation of BAP1 Mutation
Status from CT Scans" Abbas Shaikh (Rice
University) and Illana
Deutsch (Northwestern University) Mentor:
Dr. Armato |
|
11:55 AM |
12:15 PM |
Exit Surveys |
|
12:15 PM |
1:45 PM |
Lunch |
|
1:45 PM |
2:25 PM |
Presentation 5: "Transforming
Data to Images for CNN Classification of High-Risk Patients Return to the
Emergency Department" Nicole
Baugh (North Carolina State
University, University of North Carolina Chapel-Hill) and Nuvia Hernandez (Lewis University) Mentor: Dr. Tchoua |
|
2:25 PM |
3:05 PM |
Presentation 6: "Identification of Undiagnosed Traumatic Brain Injuries
through Semi-Supervised Clustering of Clinical Reports" Abheet Singh Sachdeva (Baylor University) and Avery Bell (Northern Arizona University) Mentor:
Dr. Furst |
|
3:05 PM |
3:15 PM |
Break |
|
3:15 PM |
5:00 PM |
Deliverables saved on
the MedIX server |
.png){kind=link}