Computational Medicine (Fall 2021)

Instructor

• Christopher James Langmead - cjl@cs.cmu.edu

  • Associate Professor

  • Computational Biology Department, School of Computer Science, Carnegie Mellon University

  • Office hours: Wednesdays, 9-10 am (Eastern time) via Zoom (see Canvas for link), or by appointment

Teaching Assistant

• Tianqin Li: tianqinl@andrew.cmu.edu

  • Office hours: Mondays 6:30 - 7:30pm, GHC 7607

Lectures

Tu,Th 11:50am-1:10 pm, GHC 4102

Remote-only option (REO): Fridays 10:10 - 11am via Zoom (see Canvas for links)

Course resources

Canvas and Piazza and this website

Course Description

CMU 02-518 (12 units) & CMU 02-718 (12 units)

This course examines computational methods that enhance our ability to diagnose, treat, and understand human diseases. Topics will include techniques for learning models from clinical data types, including: proteomics, genomics, metabolomics, transcriptomics, imaging, and electronic medical records. Most of the techniques will involve Machine Learning. The course is organized into modules. The first module will be an introduction to the field of Medicine, and how it differs from the basic sciences. Subsequent modules will focus specific clinical tasks, including: phenotyping, biomarker discovery, predictive and causal modeling, and the design and optimization of medical interventions. Personalized and precision medicine will also be discussed. Students will be assessed based on quizzes and a course project. Students are allowed to work in small teams (2-3 students) for the project. Students are not allowed to work in teams for quizzes.

This course uses a flipped classroom model of instruction. Students will complete reading and watch videos on the reading before the live sessions on Tuesdays and Thursdays. The first part of each live session will be devoted to answering any questions on that lecture's material. The second part of each live session will be devoted to in-class team-based data analysis exercises or, when necessary, going over remedial material. Students are not required to attend the live sessions, but are strongly encouraged to.

Students enrolled in the REO section on Fridays will get the same content as those who attend the live session from the preceding Tuesday and Thursday.

Pre/Co-requisites

The course is designed for graduate and upper-level undergraduate students from a wide variety of backgrounds. Students should have some background in Machine Learning, but no prior background in Medicine is required. Students must also understand and agree to comply with Carnegie Mellon University's policies on academic integrity (see also here).

Related Course

If you are interested in SARS-CoV-2/COVID-19, I created a mini-course on the topic called SARS-Wars. Enjoy!

Syllabus

Course Outline (see here for detailed schedule)

1. Introduction to medicine (2 weeks)

   1. Branches of medicine

• • Disease categories

  • The hierarchy of medical evidence (meta reviews; randomized clinical trials, etc)

  • Medical Education

  • The Healthcare Industry

  • Clinical data types

2. Computational challenges (10 weeks)

• • Phenotyping

  • Biomarker discovery

  • Predictive Modeling

  • Causal Modeling

  • Optimizing and/or selecting interventions

3. Advanced topics (2 weeks)

There is no required textbook.

Course outcomes

Students who complete the course successfully will be able to:

• Explain the core computational challenges in medicine

• Discuss and critique computational methods used to address these challenges

• Explain common clinical data types, and what they are used for

• Use software to analyze clinical data and build predictive models

Assessments

• Surveys and 'One Minute Papers' (ungraded)

  • We will be using a flipped classroom model of instruction.

    • Students will complete assigned readings and watch a prerecorded lecture videos on that reading before the live sessions on Tuesdays and Thursdays.

    • Students will be invited to complete a short online survey to assess their understanding of the material for the lecture.

      • Each survey will have a handful of multiple choice questions and a "One Minute Paper"

      • The 'One Minute Paper' involves providing short responses to two questions:

        • What is the most important concept from today's paper/lecture?

        • Which concept from today's paper/lecture was the hardest for you to understand?

      • These should be completed by 9am on the day of the live session.

      • The surveys are ungraded

      • The instructor will review the responses before each lecture and go over any topics that require additional discussion.

• Quizzes (60% of your final grade)

  • Six quizzes will be given online via canvas.

    • Students must complete the quizzes alone.

    • See Canvas for due dates.

• Course Project (40% of your final grade)

  • Students are allowed to work in small teams (2-3 students), or individually.

  • Students/Teams will submit a project proposal mid-semester (see Canvas for due date).

  • Students/Teams will record and submit a video presentation detailing their project.

  • The recorded presentations are due on the final day of classes.

Attendance and participation

Class attendance and participation are important parts of the learning in this course, although you will not be graded on either. Historically, the students who do best in this course come to lecture and ask questions. If you find that you are doing poorly on the surveys and quizzes, I strongly recommend that you start attending class and ask questions.

Your well-being

Be sure to take care of yourself. Do your best to maintain a healthy lifestyle this semester by eating well, exercising, avoiding drugs and alcohol, getting enough sleep and taking some time to relax. This will help you achieve your goals and cope with stress.

All of us benefit from support during times of struggle. You are not alone. There are many helpful resources available on campus and an important part of the college experience is learning how to ask for help. Asking for support sooner rather than later is often helpful.

If you or anyone you know experiences any academic stress, difficult life events, or feelings like anxiety or depression, we strongly encourage you to seek support. Counseling and Psychological Services (CaPS) is here to help: call 412-268-2922 and visit their website at http://www.cmu.edu/counseling/. Consider reaching out to a friend, faculty or family member you trust for help getting connected to the support that can help.

If you or someone you know is feeling suicidal or in danger of self-harm, call someone immediately, day or night:

CaPS: 412-268-2922

Re:solve Crisis Network: 888-796-8226

If the situation is life threatening, call the police:

On campus: CMU Police: 412-268-2323

Off campus: 911

Food Insecurity

If you are worried about affording food or feeling insecure about food, there are resources on campus who can help. Email the CMU Food Pantry Coordinator to schedule an appointment:

Pantry Coordinator

cmu-pantry@andrew.cmu.edu

412-268-8704 (SLICE office)

If you have questions about this or your coursework, please let me know.

Diversity Statement

We must treat every individual with respect. We are diverse in many ways, and this diversity is fundamental to building and maintaining an equitable and inclusive campus community. Diversity can refer to multiple ways that we identify ourselves, including but not limited to race, color, national origin, language, sex, disability, age, sexual orientation, gender identity, religion, creed, ancestry, belief, veteran status, or genetic information. Each of these diverse identities, along with many others not mentioned here, shape the perspectives our students, faculty, and staff bring to our campus. We, at CMU, will work to promote diversity, equity and inclusion not only because diversity fuels excellence and innovation, but because we want to pursue justice. We acknowledge our imperfections while we also fully commit to the work, inside and outside of our classrooms, of building and sustaining a campus community that increasingly embraces these core values.

Each of us is responsible for creating a safer, more inclusive environment.

Unfortunately, incidents of bias or discrimination do occur, whether intentional or unintentional. They contribute to creating an unwelcoming environment for individuals and groups at the university. Therefore, the university encourages anyone who experiences or observes unfair or hostile treatment on the basis of identity to speak out for justice and support, within the moment of the incident or after the incident has passed. Anyone can share these experiences using the following resources:

• Center for Student Diversity and Inclusion: csdi@andrew.cmu.edu, (412) 268-2150

• Report-It online anonymous reporting platform: reportit.net username: tartans password: plaid

All reports will be documented and deliberated to determine if there should be any following actions. Regardless of incident type, the university will use all shared experiences to transform our campus climate to be more equitable and just.

Accommodations

If you have a disability and have an accommodations letter from the Disability Resources office, I encourage you to discuss your accommodations and needs with me as early in the semester as possible. I will work with you to ensure that accommodations are provided as appropriate. If you suspect that you may have a disability and would benefit from accommodations but are not yet registered with the Office of Disability Resources, I encourage you to contact them at access@andrew.cmu.edu.

Pandemic-specific policies

Some sections are in person. In order to attend those session in person, we expect that you will abide by all behaviors indicated in A Tartan’s Responsibility, including any timely updates based on the current conditions. In terms of specific expectations for in-person students, this includes:

• entering the classroom via the designated ingress route with appropriate physical distancing,

• wearing a facial covering throughout class,

• sitting in the seats with appropriate spacing (and not moving furniture),

• using the sanitizing wipes available in the classroom to wipe surfaces (e.g., your desk, tablet arm) upon entry and exit,

• exit the classroom at her direction, proceeding in a row-by-row fashion, following the designated egress route and maintaining proper distancing.

Facial coverings. If you do not wear a facial covering to class, we will ask you to put one on (and if you don’t have one with you, we will direct you to a distribution location on campus). If you do not comply, please remember that you will be subject to student conduct proceedings, up to and including removal from CMU. Accordingly, I will be obliged to take other measures for the safety of the whole class.

Contingency plan, should the class need to go fully remote

If the class needs to go fully remote, you will receive an email from me (the instructor) and an announcement will be published on our course website on Canvas. The primary change will be that the live sessions will move to zoom.