REU: Computing for Structure
Poster Day Presentations
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. On July 28, 2017, the REU concluded the 10 week research activity with poster presentations of the results. The event combined two REUs and the SURF project, see the brochure.
Here are the REU-CFS research results.
★ Congratulations to Seraphina Gibson for her presentation of her poster at the The Twentieth Annual Nebraska Conference for Undergraduate Women in Mathematics,, Lincoln, Nebraska, January 26–28, 2018.
- Exploring Brain Meta Activation Patterns Using Neuroimaging Data,
Rachel Arens, Kenyon College.
Mentors: Prof Lucina Uddin, Psychology and Taylor Bolt, Chemistry. - Visualizing Classroom Social Networks of Hearing Impaired and Non-impaired Children with Real-time Automated Measurements,
Samuel Cooper, Fayetteville State University and Leon Lei, Brown University.
Mentors Prof. Daniel Messinger, Psychology, Prof. Mahsa Mirzargar, Computer Science and Laura Vitali, Psychology. - Uncovering New Knowledge About Nerve Growth Using Clustering and
Thresholding: Distinguishing Responders From Nonresponders,
Robert Costales, Bard College at Simon's Rock.
Mentors: Prof. Vance Lemmon MD, Neurological Surgery, Prof. John Bixby MD, Molecular and Cellular Pharmacology and Neurological Surgery, Matt Danzi. - Techniques for Extracting and Analyzing Axon Paths in 3D Images of Mouse Optic Nerves,
Alexander Fischer, University of Massachusetts, Amherst.
Mentors: Prof. Vance Lemmon MD, Neurological Surgery, Prof. Victor Milenkovic, Computer Science, Prof. Mahsa Mirzargar, Computer Science. - Path planning in approximations to 3D and 4D configuration spaces,
Seraphina Gibson, Oberlin College.
Mentors: Prof. Victor Milenkovic, Computer Science, Prof. Elisha Sacks, Purdue and Chloe Arluck. - Properties of Texture in Convolutional Neural Networks,
David Grossman, University of Miami.
Mentors: Prof. Odelia Schwartz, Computer Science. - Texture Selectivity in Deep Convolutional Neural Nets,
Ariel Lavi, University of California at Los Angles.
Mentors: Prof. Odelia Schwartz, Computer Science. - Visualizing Classroom Social Networks of Hearing Impaired and Non-impaired Children with Real-time Automated Measurements,
Leon Lei, Brown University and Samuel Cooper, Fayetteville State University.
Mentors Prof. Daniel Messinger, Psychology, Prof. Mahsa Mirzargar, Computer Science and Laura Vitali, Psychology. - Exploratory analysis of diabetes data using R and Shiny,
Markanday Ravi, Barrett Honors College, Arizona State University, Tempe.
Mentors: Prof. Mahsa Mirzargar, Computer Science, Prof. Burton Rosenberg, Computer Science. - Development of an OPLS-AA Force Field for Molecular Dynamic Simulations of Pyridinium-based Ionic Liquids,
Forrest Wang, University of Pittsburgh.
Mentors: Prof. Orlando Acevedo, Chemistry, Brian Doherty, Chemistry.
REU 2017: Leon Lei, Rachel Arens, Robert Costales, Samuel Cooper, Alex Fischer.
General Information
- Poster day brochure.
- Our slack channel
- Our calendar
- Participant emails: first.last@cs.miami.edu
Boot Camp, first week
The first week was an intensive program to present skills in computers and mathematics, needed in the mentorships. Covered were: Matlab, Python, Unix and High Performance Computing. The camp was held Monday–Friday, May 22–26 in the Ungar Building computer lab, third floor, except Friday was an AM meeting only.
AM series: 9:30am – 12:00
- Mon: Getting started in lab and with unix. Burt R.
- Tues–Wed: Scientific Python with statistics. Athina H.
- Thur–Fri: Matlab with neural nets. Odelia S. and Luis S.
- Mon: Python. Burt R.
- Tues: Unix and HPC Joel Z.
- Wed: Big Data at CCS. ZongJun Hu
- Thur: Power Unix Joel Z / Mentor Meet-up
Nature of Science Lecture Series / Research Seminars
A series of Wednesdays afternoon lectures with a historical or conceptual viewpoint of the development or practice of science. Some lectures in the series were devoted to an overview of specific research topics, relevant to the REU theme, by active researchers in those fields.
- Thursday, 1 June.
- Prof. Alvarez, Physics. Science and Physics
- Wednesday, 7 June.
- Prof. Kirtman,Marine Sciences (RSMA). Science and Computation
- Wednesday, 14 June.
- Prof. Ogihara, Computer Science. Science and Humanities
- Wednesday, 21 June.
- Prof. Goodman, Program on Ethics. Science and Ethics
- Wednesday, 28 June.
- Prof. Visser, Computer Science. Research: The Semantic Web
- Thursday, 6 July.
- Profs. Rosenberg and Schwartz, Project Reports
- Wednesday, 12 July.
- Prof. Sutcliffe, Computer Science. Research: Automated Theorem Proving
- Wednesday, 19 July.
- Prof. Rosenberg, Computer Science. Science and Information
- Wednesday, 26 July.
- Profs. Mirzargar, Rosenberg and Schwartz, Poster Presentation Preview
Lectures are also announce on our CFS-REU calendar.
Professional Development Workshop
In coordination with the REU at the Chem Dept, we had a series of weekly workshops to help new scientist develop in their field and understand their future options.
Date and time: 3pm–5pm Fridays, (except 9 and 27 June) either in the Cox science building, next to Ungar, or downtown on the Medical Campus, at the Gautier building.
- Friday, 26 May
- Introduction to Interdisciplinary Research, Prof. Knecht. Cox 166.
- Friday, 2 June
- Giving an Effective Research Presentation, Prof. Nawaz. Gautier 118.
- Friday, 9 June 4pm–5:30pm
- Scientific Ethics and Misconduct, Prof. Gaines. Cox 145.
- Friday, 16 June
- Reading and Critiquing Scientific Literature, TBA. Cox 166.
- Friday, 23 June
- Graduate School Opportunities, Dr. Captain, Dr. Salas, and Dr. Deo. Gautier 118.
- Tuesday, 27 June 9am–10am
- M.D./Ph.D. Opportunities, Prof Lemmon. Lois Pope Center, 7th flr Conf Rm. Note day of the week
- Friday, 30 June
- Life as a Graduate Student, Panel discussion. Cox 166.
- Friday, 7 July
- Reading and Critiquing Scientific Literature, TBA. Cox 166.
- Friday, 14 July
- Graduate and Postdoctoral Opportunities, Prof. Rai. Cox 166.
- Friday, 21 July
- Program wrap-up, Prof. Knecht, Cox 166.
- Friday, 28 July
- Research Symposium and Luncheon. 9:30am–3:00pm Cox Atrium.
Mentorships
- Computational Chemistry
- Prof Acevado
- Cryptography
- Prof. Rosenberg
- Neural Networks
- Prof Schwartz
- Neuroscience
- Prof Uddin
- Protein Networks
- Prof Wuchty
- Psychology
- Prof Messinger
- Laura Vitale
- Visualization
- Prof Mirzarga
- Prof Milenkovic
- Prof Lemmon
- Prof Milenkovic
With help and guidance from:
- Statistics
- Dr. Hadjixenofontos
- High Performance Computing
- Joel Zysman
- Administration
- Evelyn Cruz, Senior Manager CCS
Julie Garcia, Project Administration and Manager CSC
Prof. Sutcliffe, Chair Computer Science
Dr. Tsinoremas, Director CCS
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.
The full title of this program is REU Site: Scientific Computing for Structure in Big or Complex Datasets and it is NSF grant CNS-1659144. The REU program is described in program solicitation NSF 13-542, Research Experiences for Undergraduates (REU).