General information

Course Logistics


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.


  • 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
    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