Awesome
Prompt-DDG
Learning to Predict Mutational Effects of Protein-Protein Interactions by Microenvironment-aware Hierarchical Prompt Learning
Lirong Wu, Yijun Tian, Haitao Lin, Yufei Huang, Siyuan Li, Nitesh V Chawla, Stan Z. Li. In ICML, 2024.
<p align="center"> <img src='./assets/framework.PNG' width="800"> </p>Dependencies
conda env create -f environment.yml
conda activate Prompt-DDG
The default PyTorch version is 1.8.1 and cudatoolkit version is 11.3. They can be changed in environment.yml
.
Dataset
Dataset | Download Script |
---|---|
SKEMPI v2 | data/get_skempi_v2.sh |
Usage
Codebook Pre-training and DDG Prediction
python -B train.py
The customized hyperparameters are available in ./configs/param_config.json
.
Loading the Pre-trained Model and Making Inference
We provide a pre-trained model in Google Drive for DDG prediction on SKEMPI v2. To use it, please download it to ./trained_models/
and run
python -B train.py --ckpt_path ../trained_models/ddg_model.ckpt
Citation
If you are interested in our repository and our paper, please cite the following paper:
@article{wu2024learning,
title={Learning to Predict Mutation Effects of Protein-Protein Interactions by Microenvironment-aware Hierarchical Prompt Learning},
author={Wu, Lirong and Tian, Yijun and Lin, Haitao and Huang, Yufei and Li, Siyuan and Chawla, Nitesh V and Li, Stan Z},
journal={arXiv preprint arXiv:2405.10348},
year={2024}
}
@article{wu2024mape,
title={MAPE-PPI: Towards Effective and Efficient Protein-Protein Interaction Prediction via Microenvironment-Aware Protein Embedding},
author={Wu, Lirong and Tian, Yijun and Huang, Yufei and Li, Siyuan and Lin, Haitao and Chawla, Nitesh V and Li, Stan Z},
journal={arXiv preprint arXiv:2402.14391},
year={2024}
}
Feedback
If you have any issue about this work, please feel free to contact me by email:
- Lirong Wu: wulirong@westlake.edu.cn