Protein A-like Peptide Generation Based on a Generalized Diffusion Model

August 11, 2025 ยท View on GitHub

This repository contains the code for the paper "Protein A-like Peptide Generation Based on a Generalized Diffusion Model". The core functionality is implemented in a Jupyter Notebook (GDM.ipynb).

Requirements

Install the required dependencies to run the code:

  • Python 3.8+
  • PyTorch 1.10+
  • NumPy
  • pandas
  • matplotlib
  • Jupyter Notebook
  • torchgeometry
  • einops
  • tqdm
  • comet_ml (optional, for experiment tracking)

Install via pip:pip install torch numpy pandas matplotlib jupyter torchgeometry einops tqdm comet_ml

Quick Start

The main entry point is GDM.ipynb. Follow these steps:

  1. Clone the repository:

    git clone <repository-url>
cd ProteinGeneration-GeneralizedDiffusion

  2. Launch Jupyter Notebook:

    jupyter notebook

  3. Open GDM.ipynb and run all cells sequentially. This will:

    • Handle data loading and preprocessing
    • Initialize the diffusion model
    • Support training (from scratch) or loading pre-trained checkpoints
    • Generate Protein A-like peptides
    • Include basic evaluation and visualization of results

License

This project is licensed under the MIT License - see the LICENSE file for details.

Citation

If you use this code in your research, please cite our paper

Contact

For questions, please contact us or open an issue in the repository.