ShanghaiTech-CS177H-MSA-Scoring

Author: Lian Yihang, Yang Xuchu & Teng Yue

Content

• explore.ipynb pre-processing with HH-Filter; explore dataset & models
• extract_embedding.ipynb extract MSA embeddings using MSA Transformer
• subsampling.py subsampling utilities
• dataset.py dataset utilities (pointwise + pairwise)
• mlp.ipynb MLP models & training
• CNN.ipynb CNN models & training
• dataset/ MSA data & dataset split file
• embeddings/ extracted MSA embeddings
• model/ training checkpoints
• report/ presentations

Reference

• https://github.com/facebookresearch/esm MSA Transformer = ESM-MSA-1b

• https://github.com/axelmarmet/protein_protein_interaction MSA Transformer Example Jupyter Notebooks

  • https://github.com/axelmarmet/protein_protein_interaction/blob/main/src/msa_to_embeddings/MSA%20to%20embeddings.ipynb MSA Embeddings

  • https://github.com/axelmarmet/protein_protein_interaction/blob/main/src/ppi_pred/dataset/embedding_seq_dataset.py Embedding Feature Map Dataset

  • https://github.com/axelmarmet/protein_protein_interaction/blob/main/src/ppi_pred/dataset/pooling_baseline_dataset.py Embedding Vector Dataset