BMI 702 | Biomedical Artificial Intelligence
Harvard - Foundations of Biomedical Informatics II, Spring 2024
Artificial intelligence is poised to reshape medicine. This course provides a survey of artificial intelligence for biomedical informatics, covering methods for key data modalities: clinical data, networks, language, and images. It introduces machine learning problems from a practical perspective, focusing on tasks that drive the adoption of machine learning in biology and medicine.
The course covers foundational algorithms and highlights the nuances of handling biomedical data. It places a strong emphasis on strategies for evaluating and seamlessly integrating machine learning methods into biomedical research and clinical practice. This includes critical discussions on topics such as trustworthiness, interpretability, evaluation, and the ethical and legal challenges associated with biomedical artificial intelligence.
Week 1
Course overview and introduction to biomedical AI
- Jan 25
- 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
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
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
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
Week 12
Introduction to ethical frameworks, data privacy, regulation and liability aspects of AI (Guest lecture by Dr. Sara Gerke)
- April 18
- 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
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