Simon Fraser University
Engaging the World

Course Outlines

Fall 2021 - CMPT 984 G100

Special Topics in Databases, Data Mining, Computational Biology (3)

Database Systems

Class Number: 4685

Delivery Method: In Person

Overview

  • Course Times + Location:

    Sep 8 – Dec 7, 2021: Tue, 10:30 a.m.–12:20 p.m.
    Burnaby

    Sep 8 – Dec 7, 2021: Fri, 10:30–11:20 a.m.
    Burnaby

Description

COURSE DETAILS:

This course introduces machine learning methods for the life-sciences, focusing on molecular-level data, in particular genomic data. Such data plays a crucial role in precision medicine, e.g. drug response prediction, and in public health, e.g. the tracking of infectious diseases. However, genomic data poses special challenges to machine learning, due to the small number of examples (e.g. patients with clinical information) and great complexity of every example (e.g., SNP, CNV, RNA-seq, omics). The instructors will start the course with a few tutorial-style introductions of foundations. Students will prepare and give presentations on a state-of-the-art research paper. Students will, in small groups, perform a course research project in which they reproduce and extend the results of a recent paper from one of the four given focus areas (see the Topics below). In the last phase of the course, students will present the results of their projects. General guidelines and strategies for writing clearly and giving good talks will be given, and students will receive constructive feedback on their presentations and project reports from the instructor and other students.

COURSE-LEVEL EDUCATIONAL GOALS:

Topics

  • Epigenomics and gene regulation
  • Microbial genomics and antibiotic resistance
  • Precision medicine
  • Single-cell data analysis

Grading

NOTES:

Note the prerequisites: CMPT 726 (Machine Learning) or CMPT 741 (Data Mining) or equivalent. Please, consult with one of the instructors if you have not taken one of these two courses. Grading will be based on participation (10%), research paper presentation (30%), course project presentation (20%), course project report (40%). Details to be discussed in the first class.

Graduate Studies Notes:

Important dates and deadlines for graduate students are found here: http://www.sfu.ca/dean-gradstudies/current/important_dates/guidelines.html. The deadline to drop a course with a 100% refund is the end of week 2. The deadline to drop with no notation on your transcript is the end of week 3.

Registrar Notes:

ACADEMIC INTEGRITY: YOUR WORK, YOUR SUCCESS

SFU’s Academic Integrity web site http://www.sfu.ca/students/academicintegrity.html is filled with information on what is meant by academic dishonesty, where you can find resources to help with your studies and the consequences of cheating.  Check out the site for more information and videos that help explain the issues in plain English.

Each student is responsible for his or her conduct as it affects the University community.  Academic dishonesty, in whatever form, is ultimately destructive of the values of the University. Furthermore, it is unfair and discouraging to the majority of students who pursue their studies honestly. Scholarly integrity is required of all members of the University. http://www.sfu.ca/policies/gazette/student/s10-01.html

TEACHING AT SFU IN FALL 2021

Teaching at SFU in fall 2021 will involve primarily in-person instruction, with approximately 70 to 80 per cent of classes in person/on campus, with safety plans in place.  Whether your course will be in-person or through remote methods will be clearly identified in the schedule of classes.  You will also know at enrollment whether remote course components will be “live” (synchronous) or at your own pace (asynchronous).

Enrolling in a course acknowledges that you are able to attend in whatever format is required.  You should not enroll in a course that is in-person if you are not able to return to campus, and should be aware that remote study may entail different modes of learning, interaction with your instructor, and ways of getting feedback on your work than may be the case for in-person classes.

Students with hidden or visible disabilities who may need class or exam accommodations, including in the context of remote learning, are advised to register with the SFU Centre for Accessible Learning (caladmin@sfu.ca or 778-782-3112) as early as possible in order to prepare for the fall 2021 term.