REU: Computing for Structure

An almost group picture: Allison Dusek, Bruno Mochi, Julia Brzac, Ellie Dawson
Not pictured: Abraham Abel Arias, Alicia Bilbao Martinez

Project News

Program housing opens on Saturday, May 21 (new date) and closes Sunday, July 31, 2022.
Program begins Monday May 23 and closes Friday, July 29, 2022.
You should receive an email from housing about housing-onboarding.
You will be at the Lakeside Village complex.
The housing will be a 4/2 with a kitchen.
The program begins in the third floor of Ungar. You will need a canecard for access.
National presentation of posters:
- Investigation into the Cannizzaro Reaction of HMF Utilizing Computational Chemistry Methods, Bruno Mochi, Orlando Acevedo.
was presented at the of American Chemical Society, Spring 2023 Conference, March 26-30, 2023.

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 2022 REU student researchers,

Bruno Mochi, Lebanon Valley College, with Prof. Acevedo
Abraham Abel Arias, Pomona College, with with Prof. Messinger and Dr. Vitale
Allison Dusek, Samford University, with Prof. Aguiar-Pulido
Alicia Bilbao Martinez, University of Miami, with Prof. Aguiar-Pulido
Julia Brzac, Clarkson University, with Prof. Lemmon
Ellie Dawson, Cornell University, with Prof. Lemmon

Poster Day

The REU experience concluded with a poster presentation and closing ceremonies, on Friday, July 29, 2022.

Poster presentation in the Cox Science Center lobby, 9:30 am – 12:00 pm, was open to the public with all students presenting in round, and two judges to award a first and second place prize.

Investigation into the Cannizzaro Reaction of HMF Utilizing Computational Chemistry Methods, Bruno Mochi, Orlando Acevedo.
Facilitating Data Collection for Activity Logging, Abraham Arias, Dr. Perry, Dr. Vitale, Dr. Messinger
Unsupervised learning for the analysis of cancer data, Allison J. Dusek, Alicia Bilbao Martinez, Alexander Claman, Daniel Bilbao Cortes, Vanessa Aguiar-Pulido.
Deep Learning as a Cancer Diagnosis Tool, Alicia Bilbao Martinez, Allison J. Dusek, Alexander Claman, Daniel Bilbao Cortes, Vanessa Aguiar-Pulido.
Markerless Tracking Identifies Behavioral Changes After Spinal Cord Injury, Julia Brzac, N. O'Neil, K. Mah, B. Rosenberg, J. Bixby, V. Lemmon.
Machine Learning as a Validation Tool for Qualitative Difference Analysis, Ellie Dawson, N. O'Neil, B. Rosenberg, Z. Wang, T. Liu, J. Bixby, V. Lemmon.

Invited Speaker

For this year's event Professor Alberto Cairo of the University of Miami school of communications, expert and evangelist for visualizing data, has agreed to give a one hour talk, by zoom, 1 pm – 2 pm Cox room 145.

Alberto has also generously gifted each participant an autographed copy of his book, How Charts Lie: Getting smarter about visual information, which was presented to the participants during the closing ceremonies.

Poster judging and concluding ceremonies

There was a judged competition for the top two presentations:

Abraham Abel Arias, First Place.
Julia Brzac, Second Place.

The day concluded with presentation of certificates of participation, Cairo's book, additional books and certificates for our two winners, and some farewells.

Left to right: Alicia Bilbao Martinez, Bruno Mochi, Abraham Abel Arias, Allison Dusek, Julia Brzac, Ellie Dawson.

REU Program

Monday, 23 May: Boot camp begins in the Ungar Building Computer Science Laboratory.
Friday, July 29: Virtual Poster Presentation and Project Conclusion.

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 10:00am – 3:00pm Miami time, in Ungar 305.

The workshop Jupyter notebook are on github.com/burt/reu-cfs.

Workshop:

Monday:
- Anaconda, conda, and Jupyter
- git, and github
- Python programming with Jupyter
  - Exercise A: Iteration
  - Exercise B: Lists
- Further reading
  - Discussion A: Defs and the execution model
  - Discussion C: Iterators and Mutability
Tuesday:
- Exercises:
  - Exercise C: Recursion
  - Loop Invariants
- Further reading
  - Discussion B: Classes and Inheritance
  - Discussion D: Loop invariants and Assertions
Wednesday:
- Exercises:
  - Slicing Homework
  - Exercise D: Classes
  - Connected Graph Homework
  - Logging onto pegasus
Thursday:
- Lecture on Scientific Computing in Python:
  - Numpy
  - Matplotlib
  - Pandas
  - Linear Regression
  - Using ssh public-key and config file
  - Presentation by Prof. Aguiar-Pulido
Friday:
- Bayesian and Maximum Likelihood Estimation
  - Bayesian
Monday: Memorial Day
Tuesday:
- Random Walk on a Markov Chain
- Triton, modules, conda and installation.
- BSUB and jobs.
List of exercises:
- From Exercise C,
  - `gcd`
  - `count_the_vowels`
  - `list_uniq`
- From Loop Invariants
  - `is_inorder`
  - `is_smallest_elements`
  - `selection_sort`
- From Connected Graph Homework
  - `is_connected`
- From Slicing Homework
  - `max_interval`
  - `perfect_shuffle`
- From Bayesian and Maximum Likelihood Estimation
  - `MandM`
  - `Train`
- From Random Walk on a Markov Chain
  - `is_clause_satisfied`
  - `change_one`

Special Continuations:

As we plan this years Boot Camp, Special Continuations, and Professional Development Workshops, please visit the last year's page for and idea of what we will plan for this year.

Software Carpentry Workshop:

June 23–24.
Scientific Computing With R

Poster presentation preparation

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.

☆ Monday, 30 May: Memorial Day
― University Closed
Wednesday, 1 June: Research Ethics and Rigor , Dr. Pedro Salas
― 12:00pm–1:30pm. 3rd floor auditorium
Friday, 3 June: Summer Undergraduate Social Evening, SURF Staff
~~― 6:00pm–8:00pm. Lakeside Village Quad~~
― awaiting new date.
Monday, 6 June: Conversation with Leadership, Dr Erin Kobetz
― 12:00pm–1:00pm. RMSB 6018
Tuesday, 7 June: Posbaccalaureate Program, Drs Lemmon, Munson, Lee, Halhotra
― 12:00pm–4:00pm. RMSB 6018
Thursday, 9 June: Conflict Resolution, Dr Ralf Landgraf
― 12:00pm–1:00pm. RMSB 6018
Monday, 13 June: How to pick good mentors, Drs. Brambilla, Weiford, Slepak
― 12:00pm–1:30pm. RMSB 6018
Tuesday, 14 June: Life as a Grad Student, Panel of Graduate Students
― 12:00pm–1:30pm. RMSB 6018
☆ Monday, 20 June: Juneteenth
― University Closed
Thursday, 23 June: ODICE, Drs Vega, Gatewood, and team
― 12:00pm–1:30pm. RMSB 6018
Friday, 24 June: Careers in Academic Biotech, Dr Hassan Al-Ali
― 1:00pm–2:30pm. RMSB 6018
Thursday, 30 June: Research Presentation, Dr Sophia George
― 12:00pm–1:00pm. RMSB 6018
Friday, 1 July: Research Presentation, Dr Barrientos
― 12:00pm–1:30pm. RMSB 6018
☆ Monday, 4 July: Independence Day
― University Closed
Thursday, 7 July: Effective Scientific Writing, Dr Adina Sanchez-Garcia
― 3:30pm–5:00pm. Cox 145
Friday, 8 July: Good Interviewing Skills, Drs Dann Liebl and Marie Denise Gervais
― 12:00pm–1:30pm. RMSB 6018
Monday, 11 July: Effective Scientific Presentations, Drs Michael Gaines and Jane Indorf
― 3:30pm–5:00pm. Cox 145
Tuesday, 12 July: Transitioning to an Independent Career, Drs Tuesta, Mahai, Cimmino, Sanghvi
― 12:00pm–1:30pm. RMSB 6018
Friday, 15 July: Research Presentation, Drs Brandon Mahai and Carl Shulman
― 12:00pm–1:30pm. RMSB 6018

Mentorships

Computational Chemistry: Prof. Orlando Acevado
Miami Project to Cure Paralysis: Prof. Vance Lemmon; Prof. Stefan Wuchty; Prof. Zhang Wang
Neural Networks: Prof. Odelia Schwartz
Psychology: Prof. Daniel Messinger; Laura Vitale
Data Sciences: Prof. Vanessa Aguiar-Pulido; Alexander Claman

With help from:

Department of Computer Science: Prof. Milenkovic, Chair Computer Science; Ms. Ebony Gallagher, Department Manager; Ms. Arce, Department Manager
University of Miami Institute for Data Science and Computing: Dr. Tsinoremas, Director iDSC; Prof. Yelena Yesha, CSC and Area Director iDSC; Pedro Davila
The SURF Program at the Miller School of Medicine: Priyamvada Rai, Ph.D., Director of SURF; Laura Fields, Summer Programs Manager, Sylvester Comprehensive Cancer Center
Department of Biology, Office of the Provost: Prof Michael Gaines
Software Carpentry: Scientific Computer @ UM.: Timothy Norris; Cameron Riopelle; Gabriel Odom
Office of Research: Tracy Ehrlich; Norma Cajina; Sarah Thompson