G4003: Symbolic Methods in Biomedical Informatics

topics to be covered:

Next Offering: 2018 fall semester

The course is customized for 1st-year PhD and MA students in the biomedical informatics program and also open to other interested students at Columbia. It provides an in-depth overview of symbolic methods. Topics include:


       Semantic Interoperability

       Knowledge & Concept Representation

       Terminologies & Ontologies

       Natural Language Processing

       Data / Information Models

       Concept Mapping & Clinical Phenotyping


Lectures: Lectures are interactive, and an emphasis is put on class participation in discussions. We will use the PollEverywhere web application to facilitate discussion and help evaluate class participation. Please bring a laptop or smartphone to class to participate in PollEverywhere. Please note the schedule of lectures may be subject to change. Students will be informed of changes if/when they occur.


Lab Sessions: Sessions are conducted using a group-based format; see the "lab group assignments" document for your group assignment for the entire semester. Please bring a laptop. Sessions will take place in two parts: (1) quiz, (2) lab.


Quiz: Students will have 10 minutes to work on the quiz individually, then 15 minutes to revise their answers as per discussion with their group and the TAs. Quizzes are open book. Quizzes will not be graded, but students will receive a participation grade for answering all the quiz questions.


Lab: The remaining 50 minutes will be spent on the lab assignment. Labs are due on the following Sunday at 11:59PM (midnight) by uploading them into CourseWorks. Students should work on the lab with their group members, but labs must be submitted individually. See the grading rubric below for details on grading.


Readings: Readings are posted on CourseWorks. Each week includes on average 30 pages (2 hours) of required reading. Please complete the required readings for each week in advance of the Tuesday morning lecture. Supplemental reading is included for ease-of-reference, and is not required.


Final Project: Students may work in a team of 2 or individually.

Office Hours: Instructor: by appointment only

TAs: 12:00 - 1:00 PM on Fridays (after lab) in the collaboration room