Calendar
Introduction
- Jan 09
- Introduction & Logistics
Algorithms in computational biology
- Jan 11
- Molecular biology
- Jan 16
- No class (MLK day)
- Jan 18
- Sequence alignment I
- Jan 23
- Sequence alignment II
ML foundations
- Jan 25
- Classification and regression
- HW1 out
- Jan 30
- Optimization & Evaluation
- Feb 01
- Deep learning and neural networks
- Presentation paper signup
- Feb 06
- CNNs
- Feb 08
- RNN & Transformers
- HW1 due
- Feb 13
- Generative models
Learning from high-dim data
- Feb 15
- Clustering
- HW2 out
- Feb 20
- Dimensionality reduction
Learning from sequence data
- Feb 22
- Protein/DNA sequences and language models
Learning from network data
- Feb 27
- Network basics & ML for graphs
- Mar 01
- Graph neural network
- HW2 due
Learning from structure data
- Mar 06
- Protein structure prediction & generation (AlphaFold, diffusion models)
Paper discussion: ML for sequence data
- Mar 08
- Protein language models
- HW3 out
- Mar 13
- Disease variant prediction
- Mar 15
- Protein sequence design
- Project proposal due
Paper discussion: ML for structure data
- Mar 27
- Deep learning for structure prediction
- Mar 29
- Deep learning for structure generation
- HW3 due
- Apr 03
- GNN for 3D structures
Paper discussion: ML for network data
- Apr 05
- Biological network embeddings
- Apr 10
- ML for network biology
- Apr 12
- ML for drug discovery
Paper discussion: ML for high-D data
- Apr 17
- Dim reduction in bio data
- Apr 19
- Latent generative models
- Apr 24
- ML-guided biological discovery
Project report