Participants and Mentors, during the poster session
Project News
-
Program announced, to be held virtually. May 17 – July 23, 2021.
-
The REU begins Monday, May 17 with the one week workshop.
- National presentation of posters:
- Modeling Cortical Neural Surround Effects Using Deep Neural Networks,
A. DeForge, X. Pan , O. Schwartz.
- Expanding the Horizons of Rehabilitative Neuroscience With Deep Neural Networks,
M. Murry, N. O'Neill, K. Mah, B. Rosenberg, Z. Wang, J. Bixby, V. Lemmon.
were competitively selected to be presented at the
Research Experience for Undergraduates Symposium October 25, 2021,
held virtually.
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 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.
Our 2021 REU student researchers,
- Santiago Cortes, Johns Hopkins University, with Prof. Acevedo
- Annie DeForge, Bentley University, with Prof. Schwartz
- Christian Jerry, Indiana University, guest researcher with Prof. Messinger
- Maya Murry, Cornell University, with Prof. Lemmon
- Nestor Orozco-Llamas, Middlebury College, with Prof. Messinger
- Thomas Spangler, University of North Carolina Wilmington, with Prof. Acevedo
- Kevin Wu, University of Miami, with Prof. Ogihara
The REU experience concluded with a poster presentation and closing ceremonies,
on Friday, July 23, 2021. This presentation was held virtually in
coordination with the Summer Undergraduate Research Fellowship Program (SURF).
- Modeling Cortical Neural Surround Effects Using Deep Neural Networks,
A. DeForge, X. Pan , O. Schwartz.
(PPT)
- Incorporating the GAMESS Program Into the GAML Software,
Santiago Cortes, Thomas Spangler, Orlando Acevedo.
(PPT)
- Language During Covid-19: The Effects of Masks on Preschoolers Proximity & Vocalizations,
Christian Jerry, Sam Mitsven, Lynn Perry, Laura Vitale, Yudong Tao,
Nestor Enrique Orozco-Llamas, Daniel Messinger.
(PPT)
- Expanding the Horizons of Rehabilitative Neuroscience With Deep Neural Networks,
M. Murry, N. O'Neill, K. Mah, B. Rosenberg, Z. Wang, J. Bixby, V. Lemmon.
(PPT)
- Denoising of RFID Recordings Using Kalman Filters,
N. Orozco-Llamas, Y. Tao, L. Vitale, Christian Jerry, D. Messinger.
(PPT)
- Integrated Computational Gestural and Timbral Mapping for Musical Expressions,
K. Wu, M. Ogihara, G. Ren.
(PPT)
There was a judged competition for the top three presentations:
- Annie DeForge, First Place.
- Maya Murry, Second Place.
- Nestor Enrique Orozco-LLamas, Third Place.
REU Program
- Monday, 17 May
- Boot camp begins, 11:00am EST on Zoom.
- Tuesday, 18 May
- Meet the Mentors, 5:0pm EST on Zoom.
- Monday, 24 May
- Research program with mentor begins
- May 18 – July 13
- SURF co-activities. As scheduled.
- Monday ,June 7
- Pegasus at CCS Workshop
- Tuesday–Friday, June 8–10
- TACC Workshop (joint with TACC REU)
- Tuesday–Friday, June 22–24
- Softward Carpentry: Scientific Computing (UM Libraries and CCS)
- Thursday, July 22
- Virtual Poster Presentation
- Friday, July 23
- Join REU/SURF Concluding Conference
The
Welcome Page gives information about places to go and restaurants; as
well as the todo list for program onboard.
The
recruitment page is archived.
Boot Camp:
The Boot Camp Morning Sessions are 11:00am – 3:00pm Miami time, and are
remote by Zoom. The Zoom link will be posted in Slack shortly before the hour.
See my github
for the templates.
Workshop:
- Monday:
- Python programming with Jupyter
- git, and github
- Tuesday:
- Fun Python programs
- SURF co-activity: Intro to Interdisciplinary Research, Dr. Nagi Ayad 1:00-2:00pm
- Numpy and Matplotlib: Scientific Computing in Python
- Meet the Mentors, 5:00pm
- Wednesday:
- Unix Environment
- ssh and make
- SURF co-activity: Acquisition and Interpretation of Genomic Data, Dr. Aristeidis Telonis 1:00-2:30pm
- Thursday:
- Numpy and Matplotlib
- Linear Regression
- SURF co-activity: Acquisition and Interpretation of Genomic Data, Dr. Aristeidis Telonis 1:00-2:00pm
- Friday:
- Bayesian Inference
- SURF co-activity: UNIX and Bioinformatics Tools, Dr. Aristeidis Telonis 1:00-2:30pm
- Projects Due:
- To commit to github:
- Discussion_E, completed (pay attention to loop invariants)
- Fun_Programs, completed
- Exercise-Numpy, completed
Special Continuations:
- Pegasus Workshop:
- Monday, June 7, 10:00am EST
- Pedro Davila, CCS.
- Quick Intro: to Pegasus, JupyterHub and Triton.
- CI (cyber-infrastructure) Research 4 Change: REU at TACC
- Tuesday, June 8, 2:00pm–7:00pm EST
- TACC Overview (intro to TACC resources),
- TACC Onboarding (students create TACC portal account),
- Intro to Linux/Unix
- Wednesday, June 9, 2:00pm–7:00pm EST
- Intro to Linux/Unix cont.,
- Jupyter Notebooks and Python, Matplotlib and Pandas
- Thursday, June 10, 2:00–5:30pm EST
- Intro to Data Science, Intro to R Studio
- Thank you Rosalia Gomez, PI of the REU at TACC, Univ of Texas at Austin, for inviting us into these sessions.
- Software Carpentry Workshop: Scientific Computing
- June 21–24.
- Instructors: Timothy Norris, Elizabeth Overstreet, Cameron Riopelle of CCS and UM Libraries.
- Topics: Unix shell, Python, Git and R.
- An implementation of the Software Carpentry curriculum.
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.
The Zoom links will be posted in Slack shortly before the hour.
- Tuesday, 18 May
- Intro to Interdisciplinary Research, Dr. Nagi Ayad
― 1:00pm–2:00pm.
- Wednesday, 19 May
- Acquisition and Interpretation of Genomic Data, Dr. Aristeidis Telonis
― 1:00pm–2:30pm.
- Thursday, 20 May
- Acquisition and Interpretation of Genomic Data, Dr. Aristeidis Telonis
― 1:00pm–2:00pm.
- Friday, 21 May
- UNIX and Bioinformatics Tools, Dr. Aristeidis Telonis
― 1:00pm–2:30pm.
- Friday, 28 May
- How to Pick an Appropriate Graduate School Mentor, Drs. Larsson, Slepak, Welford, Brambilla.
― 1:00pm–2:30pm.
- Friday, 4 June
- Life as a Graduate Student, many.
― 1:00pm–2:30pm.
- Tuesday, 8 June
- Graduate and Medical School Opportunities
― 1:00pm–2:30pm.
- Friday, 11 June
- Reading and Critiquing Scientific Literature, Drs. Diaz, Maiti
― 1:00pm–2:30pm.
- Tuesday, 15 June
- Effective Writing, Chelsea Skelly
― 1:00pm–2:30pm.
- Thursday, 17 June
- Tips for an Effective Research Presentation, Dr Gaines
― 1:00pm–2:30pm.
- Friday, 18 June
- Diversity and Inclusion in the Sciences, Dr. Symes,
― 1:00pm–2:30pm.
- Friday, 25 June
- Navigating a Career in Academia, Dean Prado
― 1:00pm–2:30pm.
- Thursday, 1 July
- Balancing leadeship and academic careers, Dr. Kerry Burnstein.
― 12:00pm–2:00pm.
- Tuesday, 6 July
- Destination - Passion. My road to a Career in Academia. Dr Sophia George,
― 1:00pm–2:30pm.
- Wednesday, 7 July
- Scientific Ethics and Misconduct, Dr. Salas.
― 1:00pm–2:30pm.
- Thursday, 8 July
- Notes from Cancer Center Director, Dr Nimer
― 1:00pm–2:30pm.
- Friday, 9 July
- Research Outside of Academia: Industry, Dr. Ali
― 1:00pm–2:30pm.
- Balancing clinical, research and leadership, Dr Schulman
― 4:00pm–5:00pm.
- Tuesday, 13 July
- Mental Health Awareness, Dr. Karunaratne
― 1:00pm–2:30pm.
- Friday, 23 July
- Virtual Research Symposium for SURF
― 8:45am–11:30am.
― 1:00pm–3:30pm.
Concluding Programming:
Virtual Poster Fair. Thursday, July 22.
Joint REU/SURF conference. Friday, July 23.
Mentorships
- Computational Chemistry
- Prof Acevado
- Digital Humanities
- Prof Mitsunori Ogihara
- Miami Project to Cure Paralysis
- Prof Lemmon
- Neural Networks
- Prof Schwartz
- Psychology
- Prof Messinger
- Laura Vitale
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
- CI Research 4 Change REU
- Rosalia Gomez, Univ of Texas at Austin TACC
- Charlie Dey, Univ of Texas at Austin TACC
- National Science Foundation Award #1852538
- Center for Computational Science
- Dr. Tsinoremas, Director CCS
- Pedro Davila
- Software Carpentry: Scientific Computer @ UM.
- Timothy Norris
- Elizabeth Overstreet
- Cameron Riopelle
- Department of Computer Science
- Prof. Milenkovic, Chair Computer Science
- Julie Garcia, Project Administration and Manager CSC
- Poster Judges
- Victor Milenkovic, Department of Computer Science, UM
- Huseyin Kocak, Department of Computer Science, UM
- Vanessa Aguiar-Pulido, Department of Computer Science, UM
- Office of Research
- Tracy Ehrlich
- Norma Cajina
- Sarah Thompson
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-1949972,
program solicitation NSF 13-582,
Research Experiences for Undergraduates (REU).