Machine Learning in Computational Biology
Machine Learning in Computational Biology
Time: Tuesdays 10-12
Location: BA 2179
Instructor office: 686 Bay St. Rm 12-9708
Instructor availability: meeting pre-arranged by email
Prerequisites: background in machine learning (at least an introductory course) and
basic probability and statistics are required
Course Overview
The goal of this graduate seminar course is to investigate the areas of computational biology where machine learning can make the most difference. We will cover many topics in such diverse areas as variation in the genome, regulation, epigenetics and microbiome, etc with relation to human disease. Together we will read and discuss the most recent computational developments in these areas and brainstorm about what can be done to improve current performance.
Importantly, this will not be an introduction to molecular biology nor machine learning. This course is intended for people with machine learning background (or at least an introductory course) who will be able to develop new methods or modify and apply existing algorithms to problems in computational biology. Thus the emphasis in my lectures will be on introducing the areas and framing the problems in compbio and computational medicine.
Each lecture will be divided into a discussion hour of relevant literature led by assigned students and a brief introduction to the new topic.
Grading Scheme
Paper presentations 30%
Written summaries 20%
Project 50%
Paper presentations: each student will present ~ 3 papers on 3 different topics throughout the duration of the course. Each presentation will be 20-25min + question/answer portion
Written summaries: each student is required to submit a 1 (max 2) paragraphs on the topic that was covered in the previous lecture and the presented papers by 5pm on the day of the presentations. The paragraphs should reflect student’s understanding of the area covered. It should list definition and advantages and disadvantages of existing methods. The summaries should be submitted by email from a uoft account in plain text (or as a pdf attachment if formulas are included) to anna dot goldenberg at utoronto dot ca with the subject “CSC2431 summary”.
Project (in teams of 1-2 people): the goal of the project is to produce a machine learning contribution (preferably publishable) addressing an area of computational biology/medicine. Each student will be evaluated on proposal, midterm report, final paper and presentation. Each paper should be written using a conference template of your choice with the goal to publish at a conference.
Proposal: goals, division of work (in team projects), aims, methods, datasets, challenges and
alternatives, competitors (methods you will compare to)
Midterm report: adjusted aims, draft of the final paper with placeholders for figures (which figures
and tables you expect to generate in the final draft)
Final draft: paper written in a conference format
(pick your conference style - ISMB, RECOMB, ICML, NIPS)
CSC 2431