REU: Computing for Structure
REU 2019: Courtney, Giulia, Juliana, Angela, Nicholas, Alexis, Azhar, Gregory, Chris, Victor
Project News
- National presentation of a talk: Analyzing Facial Expression Data in Autism Research, Chris Fagin, Yudong Tao, Yeojin Amy Ahn, Laura Vitale, Daniel Messinger. 2020 National Joint Mathematics Meeting, MAA General Contributed Paper Session on Interdisciplinary Topics in Mathematics, Denver, Colorado, January 15–18 2020.
- National presentation of a poster: An Investigation of Congenital Agenesis of the Corpus Callosum, Alexis Delgado, Jason S. Nomi, Bryce Dirks, Lucina Q. Uddin. Research Experience for Undergraduates Symposium, Alexandria, VA. October 27-28, 2019.
- REU-CFS in the news: Students gain valuable research experience, by Janette Neuwahl Tannen. News@TheU. July 25, 2019.
Project Summary
Computing for Structure is an NSF Funded Research Experience for Undergraduates, created and directed by the University of Miami Department of Computer Science and Center for Computational Science. The program ran from Sunday, May 19 to Sundary, July 28, 2019 with the following REU student researchers:
- Giulia Bronzi, Wellesley College
- Nicholas Cimaszewski, University of Rochester
- Alexis Delgado, Avila University
- Chris Fagin, Christian Brothers University
- Juliana Hemela, UNC Chapel Hill
- Gregory Hubbard, Old Dominion University
- Victor Jann, University of California, Berkeley
- Angela Kihiko, Spelman College
- Azhar Moihdeen, Georgia Institute of Technology
- Courtney Sever, Florida State University
Joining us for the poster session were two young researchers from Prof. Milenkovic's REU Supplement NSF grant,
- Allan Gelman, MIT
- Danny Gelman, MIT
The REU experience concluded with a poster presentation and closing ceremonies, on Friday, July 26, 2019. This presentation was held at Schoninger Quadrangle on the UM Medical School campus, in coordination with the Summer Undergraduate Research Fellowship Program (SURF).
- Responsivity in Children with Hearing Loss, Giulia Bronzi, Laura Vitale, Samantha Mitsven, Daniel Messinger.
- The Effect of Divisive Normalization in Deep Convolutional Neural Networks on Figure Ground Assignment, Nicholas Cimaszewski, Luis G. Sanchez Giraldo, Odelia Schwartz.
- An Investigation of Congenital Agenesis of the Corpus Callosum, Alexis Delgado, Jason S. Nomi, Bryce Dirks, Lucina Q. Uddin. (Selected presentation)
- Analyzing Facial Expression Data in Autism Research, Chris Fagin, Yudong Tao, Yeojin Amy Ahn, Laura Vitale, Daniel Messinger.
- CPU versus GPU Based 3D Visualization of Algebraic Surfaces, Allan Gelman, Danny Gelman, Joseph Masterjohn, Victor Milenkovic, Nancy Newlin.
- Single Cell RNA-Sequencing to Identify and Examine Cell-Types within the Motor Cortex, Juliana Hemela, Z. Wang, J. Lowell, J. Bixby, V. Lemmon.
- Normalization on Visual Data for Categorization, Gregory Hubbard, Luis G. Sanchez Giraldo, Odelia Schwartz.
- Implementing Machine Learning Techniques to Quantify Mouse Behavioral Assays, V. Jann, N. O’Neill, K. M. Mah, Z. Wang, J. Bixby, V. Lemmon.
- The Dark Energy between Sonic Partials: Modeling and Visualization of Weak Spectral Components for Musical Sound Analysis and Synthesis, A. Kihiko, G. Ren, J. W. Beauchamp, M. Ogihara.
- Training Machine Learning Models of Ionic Liquids using Ab Initio Molecular Dynamics, Azhar B. Moihdeen, Kun Yue, Orlando Acevedo.
- Development of an Enhanced Machine Learning Based QM/MM Method, Courtney Sever, Caroline Velez, Xiang Zhong, Orlando Acevedo.
There was a judged competition for the top three posters:
- Guilia Bronzi, First Place.
- Chris Fagin, Second Place.
- Victor Jann, Third Place.
The P.I. for the REU is Prof. Rosenberg of the Computer Science Department, but the real work went to the many mentors, listed as co-authors of the student presentations. These mentors were drawn from across the university, and volunteered to mentor the participants.
REU Program
- Sunday, 19 May
- Housing Opens
- Monday, 20 May
- Boot camp begins, 9:30am at Ungar 330.
- Monday, 27 May
- Memorial Day!
- Wednesday, 29 May
- Afternoon: Meet the Mentors
- Thursday, 30 May
- Research program with mentor begins
- Tuesdays, 4 June–9 July
- Mentor Seminars, 3:30pm–5:00pm Ungar 330.
- Wednesdays, 5 June–TBA
- Workshops in Computation / Career Development, 9:30am–12:00pm Ungar 330.
- Friday, July 26
- Poster Presentation in the Atrium of Cox Science / Program closes
- Sunday, 28 July
- Housing Closes
The recruitment page is archived.
There is our Calendar
Boot Camp:
The Boot Camp Morning Sessions are 9:30am – 12:00pm and the afternoon sessions are 1:30pm – 4:00pm. Both sessions are at the Computer Science computer lab, on the 3ird floor of the Ungar Building. See my github for the templates. The tentative plan of study:
Week 1:
- Monday:
AM: Welcome program;
PM: Python programming with Jupyter (Rosenberg and Wang) - Tuesday:
AM: Python II (Rosenberg);
PM: Python III (Rosenberg) - Wednesday:
AM: Unix environment (Wang);
PM: Numpy: Scientific Computing in Python (Rosenberg) - Thursday:
AM: Matplotlib (Wang);
PM: Scientific Programming DNA (Kocak and Basar) - Friday:
AM: Intro to Bioinformatics (Wang);
PM: Scientific Programming DNA (Kocak and Basar)
Week 2:
- Monday: Memorial Day!
- Tuesday: Machine Learning (Odelia and Garcia) github
- Wednesday: see Special Continuation for May 29th.
PM: Meet the Mentors 2:30pm–4:00pm
Special Continuation:
- Wednesday, 29 May
- Prof. Donald Olson, RSMAS, Climate Forecasting Problem 9:30am–1:00pm;
- Wednesday, 5 June
- Prof. Donald Olson, RSMAS, Modeling Life and Evolution 9:30am–1:00pm;
- Wednesday, 12 June
- Prof. Rosenberg, Python Workshop 9:30am–1:00pm;
- Wednesday, 19 June
- Prof. Rosenberg, GPU/Cuda Workshop 9:30am–1:00pm;
- Wednesday, 26 June
- Prof. Rosenberg, GPU/Cuda Workshop (Part 2) 9:30am–1:00pm;
Mentors Seminars
A series of afternoon lectures devoted to an overview of specific research topics, relevant to the REU theme, by mentors. On Tuesdays at 3:30pm—5:00pm, in Ungar 300.
- 4 June
- Prof. Orland Acevedo, Chemistry. Chemistry and Computation
- 11 June
- Prof. Odelia Schwartz, Computer Science. Learning and Computation
- 18 June
- Prof. Uddin, Psychology.
- 25 June
- Prof. Mitsu Ogihara, Computer Science. Humanities and Computation
- 2 July
- Prof. Daniel Messinger and Prof. Laura Vitale, Psychology.
- 9 July
- Prof. Vance Lemon
- 16 July
- Prof. Milenkovic
Professional Development Workshop
In coordination with SURF, Summer Undergraduate Research Fellowship, a series of weekly workshops to help new scientist develop in their field and understand their future options. Generally Friday, with exceptions underlined.
- Friday, 31 May
- Reading and Critiquing Scientific Literature, OGPS Panel.
― SCCC 1301, 12:00pm–1:30pm. - Friday, 7 June
- Graduate and Medical School Opportunities,
― RMSB 6018, 12:00pm–2:00pm. - Thursday, 13 June
- Advice and Lessons from my Career Trajectory, Dean Guillermo Prado
― RMSB 1121-B, 12:00pm–1:30pm. - Friday, 21 June
- Diversity and Inclusion in the Sciences, Dr. Symes,
― SCCC 1301, 12:00pm–1:30pm. - Friday, 28 June
- Transitioning to an Independent Academic Career, Dr. Rai,
― SCCC 1301, 12:00pm–1:30pm. - Monday, 1 July
- Scientific Ethics and Misconduct, Dr. Salas,
― RMSB 1121-B, 12:00pm–1:30pm. - Tuesday, 2 July
- Tips for an Effective Research Presentation, Dr. Emre Dikici.
― RMSB 1121-B, 12:00pm–1:30pm. - Thursday, 11 July
- Destination - Passion. My road to a Career in Academia. Dr Sophia George,
―RMSB 1121-BSCCC 1301, 12:00pm–1:00pm. - Friday, 19 July
- Research Outside of Academia: Industry, Dr. Head and David Robbins.
― SCCC 1301, 12:00pm–1:30pm. - Friday, 26 July
- REU/SURF Poster Session.
― 9:00am–3:00pm TBA
Room Locations:
- SCCC 1301
- Sylvester Comprehensive Cancer Center 1475 NW 12th Avenue, 33136
- RMSB 6018
- Rosensteil Medical Science Building, 1600 NW 10th Avenue, 33136
- RMSB 1121-B
- Rosensteil Medical Science Building, 1600 NW 10th Avenue, 33136 (1st Floor)
Mentorships
- Computational Chemistry
- Prof Acevado
- Digital Humanities
- Prof Mitsunori Ogihara
- Miami Project to Cure Paralysis
- Prof Lemmon
- Prof Wang
- Neural Networks
- Prof Schwartz
- Luis Gonzales
- Neuroscience
- Prof Uddin
- Jason Naomi
- Psychology
- Prof Messinger
- Laura Vitale
- Visualization
- Prof Milenkovic
With help and guidance from:
- The SURF Program at the Miller School of Medicine
- Priyamvada Rai, Ph.D., Director of SURF
- Sarah Sandiford
- Santos Cayetano
- Theresa Votolato
- Rositsa Kalinova
- Sarah Sandiford
- Center for Computational Science
- Dr. Tsinoremas, Director CCS
- Joel Zysman, Director of Advanced Computing at CCS
- Kalan Dawson
- Pedro Davila
- Joel Zysman, Director of Advanced Computing at CCS
- Department of Computer Science
- Prof. Sutcliffe, Chair Computer Science
- Prof. Huseyin Kocak
- Prof. Basar Koc, Stetson University
- Julie Garcia, Project Administration and Manager CSC
- Prof. Huseyin Kocak
- Poster Judges
- Batya Elbaum, Department of Teaching and Learning, Department of Psychology
- Salome Kornfeld, Department of Psychology
- Lynn Perry, Department of Psychology
- Yudong Tao
- Stefan Wuchty, Computer Science
- Salome Kornfeld, Department of Psychology
- Office of Research
- Tracy Ehrlich
- Norma Cajina
Sponsored by the National Science Foundation
The NSF has set up the REU program in order to involve students in meaningful ways in ongoing research programs so as to attract talented students into careers in science and engineering.
Support for the program REU Site: Scientific Computing for Structure in Big or Complex Datasets is by the NSF grant CNS-1659144, program solicitation NSF 13-542, Research Experiences for Undergraduates (REU).
Prof. Milenkovic's REU Supplement was funded by NSF grant CCF-1526335.