lucascamillomd/cpgpt-models

CpGPT Model Checkpoints

Model weights, configurations, and vocabularies for CpGPT: A Foundation Model for DNA Methylation.

Contents

weights/     # PyTorch Lightning checkpoint files (.ckpt)
config/      # Hydra YAML configuration files
vocab/       # CpG vocabulary files (.json)

Pre-trained Models

Model	Size	Parameters	Model Name
CpGPT-2M	30MB	~2.5M	small
CpGPT-100M	1.1GB	~101M	large

Download

# Install huggingface_hub
pip install huggingface_hub

# Download all model files
huggingface-cli download lucascamillomd/cpgpt-models --local-dir dependencies/model

# Or download a specific model
huggingface-cli download lucascamillomd/cpgpt-models weights/small.ckpt config/small.yaml vocab/small.json --local-dir dependencies/model

Dependencies

You will also need the DNA embeddings for your species of interest:

• Human: lucascamillomd/cpgpt-human-dependencies
• Mammalian (multi-species): lucascamillomd/cpgpt-mammalian-dependencies

Usage

After downloading the model files and species dependencies, follow the tutorials at the CpGPT GitHub repository to get started.

Citation

@article{camillo2024cpgpt,
  title={CpGPT: A Foundation Model for DNA Methylation},
  author={de Lima Camillo, Lucas Paulo et al.},
  journal={bioRxiv},
  year={2024},
  doi={10.1101/2024.10.24.619766}
}

License

MIT License — see the GitHub repository for details.