Presents innovative approaches to computational problems in the life sciences focusing on deep learning based approaches with comparisons to conventional methods. Topics include protein-DNA interaction, chromatin accessibility, regulatory variant interpretation, medical image understanding, medical record understanding, therapeutic design, and experiment design (the choice and interpretation of interventions). Lecture presentations will be given by faculty and topic specific student groups. Multidisciplinary team-oriented final research project, and teams will complete their project using TensorFlow or other framework. Provides a comprehensive introduction to each life sciences problems, but relies upon students understanding probabilistic problem formulations.
| Lecture | Date | Topic | Deadlines |
|---|---|---|---|
| 1 | February 7 | Machine Learning in the Computational Life Sciences | |
| 2 | February 9 | Introduction to TensorFlow | |
| 3 | February 14 | Dimensionality Reduction | |
| 4 | February 16 | Autoencoders | |
| February 21 | No Class - President's Day | ||
| 5 | February 23 | Protein-DNA Interactions | |
| 6 | February 28 | Deep Learning for Protein-DNA Interactions | |
| 7 | March 2 | Predicting Chromatin Data | |
| 8 | March 7 | Deep Learning for Predicting Chromatin Data | |
| 9 | March 9 | eQTL Prediction and Variant Prioritization | |
| 10 | March 14 | Deep Learning for eQTL Prediction and Variant Prioritization | |
| 11 | March 16 | Medical Image Understanding | |
| 12 | March 21 | Medical Record Understanding | |
| 13 | March 23 | Experimental Design - Bayesian Networks | |
| March 28 | No Class - Spring Vacation | ||
| March 30 | No Class - Spring Vacation | ||
| 14 | April 4 | Bayesian Optimization | |
| 15 | April 6 | Project Proposals | Project Proposals due |
| 16 | April 11 | Project Proposals | |
| 17 | April 13 | Guest Lectures and/or Meetings with Mentors | |
| April 18 | No Class - Patriot's Day | ||
| 18 | April 20 | Guest Lectures and/or Meetings with Mentors | |
| 19 | April 25 | Guest Lectures and/or Meetings with Mentors | |
| 20 | April 27 | Guest Lectures and/or Meetings with Mentors | |
| 21 | May 2 | Guest Lectures and/or Meetings with Mentors | |
| 22 | May 4 | Guest Lectures and/or Meetings with Mentors | |
| 23 | May 9 | Guest Lectures and/or Meetings with Mentors | |
| 24 | May 11 | Guest Lectures and/or Meetings with Mentors | |
| 25 | May 16 | Final Project Presentations | Final Projects due |
| 26 | May 18 | Final Project Presentations | Last Day of Class! |