REU: Computing for Structure

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 May 22 to July 28 with the following REU student researchers:

Rachel Arens, Kenyon College.
MD, The University of Toledo College of Medicine and Life Sciences
Samuel Cooper, Fayetteville State University
Robert Costales, Bard College at Simon's Rock.
PhD Computer Science, University of Southern California
Alexander Fischer, University of Massachusetts, Amherst.
PhD candidate, Physics, University of New Mexico and Sandia National Labs
Seraphina Gibson, Oberlin College.
David Grossman, University of Miami.
Ariel Lavi, University of California at Los Angles.
Leon Lei, Brown University
Markanday Ravi, Barrett Honors College, Arizona State University, Tempe.
Forrest Wang, University of Pittsburgh.

The REU experience concluded with a poster presentation and closing ceremonies, on Friday, July 28, 2017. This presentation was held in the atrium of the Cox Science center, as was joint with the University of Miami Chemistry REU, PI'ed by Prof. Knecht as well as the Summer Undergraduate Research Fellowship Program (SURF).

See the ★ brochure for all presentations. Below are the presentations funded by REU-CFS 2017.

★ 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.

General Information

Poster day brochure.
Our slack channel
Our calendar
Participant emails: first.last@cs.miami.edu
The Recruitment page is archived.

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.
- Atina's github
Thur–Fri: Matlab with neural nets. Odelia S. and Luis S.

PM series: 1:30pm – 4:00pm

Mon: Python. Burt R.
- Burt's github
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

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