Calendar

Week 1

Course overview and introduction to biomedical AI

Jan 25

LectureWhat makes biomedical problems unique: Slides, Reading List

Jan 26

QuizWeek 2 pre-class quiz (due Feb 1): Canvas

Week 2

Machine learning using electronic health records, subtype discovery, disease diagnosis and prognosis prediction

Feb 1

Module 1LectureClinical AI Part I: Slides, Reading List

Feb 2

QuizWeek 3 pre-class quiz (due Feb 8): Canvas

Week 3

Machine learning on clinico-genetic datasets, diagnostic odyssey and therapy selection

Feb 8

Module 1LectureClinical AI Part II: Slides, Reading List

Feb 9

QuizWeek 4 pre-class quiz (due Feb 15): Canvas

Week 4

Interpretability and explainability

Feb 15

Module 2LectureTrustworthy & Efficient AI Part I: Slides, Reading List

Feb 16

QuizWeek 5 pre-class quiz (due Feb 22): Canvas

Week 5

Fairness, bias, distribution shifts, and robustness

Feb 22

Module 2LectureTrustworthy & Efficient AI Part II: Slides, Reading List

Feb 23

QuizWeek 6 pre-class quiz (due Feb 29): Canvas

Feb 23

PSet releasedPSet 1: Bias, trustworthiness, and fairness: Canvas

Week 6

Foundations of graph representation learning, link prediction, node classification, graph clustering, graph classification, semi-supervised learning, label propagation, network medicine, and disease modules.

Feb 29

Module 3LectureBiomedical graph learning Part I: Slides, Reading List

Mar 1

QuizWeek 7 pre-class quiz (due Mar 7): Canvas

Week 7

Machine learning with heterogeneous graphs, graph neural networks, knowledge graph embeddings, prediction and reasoning using knowledge graphs

Mar 7

Module 3LectureBiomedical graph learning Part II: Slides, Reading List

Mar 8

QuizWeek 8 pre-class quiz (due Mar 21): Canvas

Mar 8

PSet duePSet 1: Bias, trustworthiness, and fairness: Canvas

Week 8

Large language models (Guest lecture by Dr. Jonathan Richard Schwarz)

Mar 21

Module 4LectureMedical language modeling Part I: Slides, Reading List

Mar 22

QuizWeek 9 pre-class quiz (due Mar 28): Canvas

Mar 22

PSet releasedPSet 2: Knowledge graphs and geometric deep learning: Canvas

Week 9

Natural language processing across clinical domains and tasks

Mar 28

Module 4LectureMedical language modeling Part II: Slides, Reading List

Apr 29

QuizWeek 10 pre-class quiz (due Apr 4): Canvas

Week 10

Vision and vision-language pre-training, towards generic vision interface, multimodal LLMs

Apr 4

Module 5LectureBiomedical imaging Part I: Slides, Reading List

Apr 5

QuizWeek 11 pre-class quiz (due Apr 11): Canvas

Apr 5

PSet duePSet 2: Knowledge graphs and geometric deep learning: Canvas

Week 11

Multimodal learning, computational pathology with applications to oncology, analysis of histopathology slides

Apr 11

Module 5LectureBiomedical imaging Part II: Slides, Reading List

Apr 12

QuizWeek 12 pre-class quiz (due Apr 18): Canvas

Apr 12

PSet releasedPSet 3: Biomedical imaging methods and applications: Canvas

Week 12

Introduction to ethical frameworks, data privacy, regulation and liability aspects of AI (Guest lecture by Dr. Sara Gerke)

April 18

LectureEthical and legal considerations for biomedical AI: Slides, Reading List

Apr 19

QuizWeek 13 pre-class quiz (due Apr 25): Canvas

Week 13

AI-guided drug design, small-molecule generation, molecule optimization, drug target identification

Apr 25

Module 6LectureGenerative AI Part I: Slides, Reading List

Apr 26

QuizWeek 14 pre-class quiz (due May 2): Canvas

Apr 26

PSet duePSet 3: Biomedical imaging methods and applications: Canvas

Week 14

Design of chemical and genetic perturbations, drug repurposing, emerging uses of generative AI (protein design and generative agents)

May 2

Module 6LectureGenerative AI Part II: Slides - Part 1, Slides - Part 2, Reading List