CSEP 590 AI for Medicine (Fall 2022)

General information

Course Logistics

Instructors:
Sheng Wang

Office hours

TA:
Yilun Sheng

Office hours

Lecture (hybrid mode): https://washington.zoom.us/j/99459769251 (need UW email to access) or in-person at CSE2 G10 (GATES CTR.)
Piazza discussion board: All questions that are not of a personal nature should be posted to the discussion board.

Grading

Grading: Your grade will be based on two parts: course project (80%) and discussion in four research showcase lectures (5% each, 20% in total). There is no credit given for attending other lectures that are offered by the instructor. There is no exam. There is no homework.

Guest lectures: 45-minute invited presentation about ongoing AI for medicine research in the Allen School (see schedule below). The instructor will then lead the discussion about the potential improvement and future directions.

Projects:

Option 1. Literature review (AI for drug discovery). Review 3-5 papers in AI for drug discovery/medicine in NeurIPS/ICML/ICLR in the past five years.

Option 2. A project related to AI for medicine/drug discovery. Any topic is fine.

Grading the project: Mid-term presentation (20%). Final presentation (20%). Final project report (40%). These add up to 80% in total.

Tentative Schedule

Date Theme Reading/Content in Drug discovery Reading/Content in Machine learning Slides

AI for Drug Discovery

9/29 Overview of drug discovery pipeline. Deep learning for DDR1 inhibitors
Another AI Drug Announcement

10/06 Precision medicine Multi-omics data integration (Unpaired) data integration, Batch correction

10/13 Graph-based drug discovery Modeling polypharmacy side effects with graph convolutional networks
Drug repositioning by integrating target information through a heterogeneous network model
Neural Message Passing for Quantum Chemistry

10/20 Structure-based drug discovery Protein Docking, Drug Binding Structure Prediction, Molecular 3D Conformer E(n) Equivariant Graph Neural Networks
EQUIBIND: Geometric Deep Learning for Drug Binding Structure Prediction
INDEPENDENT SE(3)-EQUIVARIANT MODELS FOR END-TO-END RIGID PROTEIN DOCKING

10/27 Mid-term project presentation

AI for medicine

11/03 Algorithm for medicine First half: Research showcase (gene expression time series analysis)
Second half: Algorithm for medicine (sequence analysis)

11/10 Algorithm for medicine First half: Research showcase (text generation in biomedicine)
Second half: Natural language processing for medicine

11/17 Algorithm for medicine First half: Research showcase (hi-c super-resolution)
Second half: Computer vision for medicine

12/01 Algorithm for medicine First half: Research showcase (protein design)
Second half: Graph analysis for medicine
12/08 Final project presentation

Date	Theme	Reading/Content in Drug discovery	Reading/Content in Machine learning
	AI for Drug Discovery
9/29	Overview of drug discovery pipeline.		Deep learning for DDR1 inhibitors Another AI Drug Announcement
10/06	Precision medicine	Multi-omics data integration	(Unpaired) data integration, Batch correction
10/13	Graph-based drug discovery	Modeling polypharmacy side effects with graph convolutional networks Drug repositioning by integrating target information through a heterogeneous network model	Neural Message Passing for Quantum Chemistry
10/20	Structure-based drug discovery	Protein Docking, Drug Binding Structure Prediction, Molecular 3D Conformer	E(n) Equivariant Graph Neural Networks EQUIBIND: Geometric Deep Learning for Drug Binding Structure Prediction INDEPENDENT SE(3)-EQUIVARIANT MODELS FOR END-TO-END RIGID PROTEIN DOCKING
10/27	Mid-term project presentation
	AI for medicine
11/03	Algorithm for medicine	First half: Research showcase (gene expression time series analysis) Second half: Algorithm for medicine (sequence analysis)
11/10	Algorithm for medicine	First half: Research showcase (text generation in biomedicine) Second half: Natural language processing for medicine
11/17	Algorithm for medicine	First half: Research showcase (hi-c super-resolution) Second half: Computer vision for medicine
12/01	Algorithm for medicine	First half: Research showcase (protein design) Second half: Graph analysis for medicine
12/08	Final project presentation