ProtGO: Multi-Modal Protein Function Prediction using Large-Scale Protein Language Models

Requirements

pip install fair-esm
pip install git+https://github.com/facebookresearch/esm.git
python -m pip install ankh
pip install SwissArmyTransformer

Datasets

• Train set: /main/data/cafa5_train_1.txt + /main/data/cafa5_train_2.txt
• Test set: /main/data/cafa5_test.txt

Usage

• Linear Probing with MLP:

python model/ProtGO_linear.py

• Fine-tuning with LoRA:

python model/ProtGO_LoRA.py