Generative modeling of regulatory DNA sequences with diffusion probabilistic models.
Documentation: https://pinellolab.github.io/DNA-Diffusion
Source Code: https://github.com/pinellolab/DNA-Diffusion
DNA-Diffusion is diffusion-based model for generation of 200bp cell type-specific synthetic regulatory elements.
Our preferred package / project manager is uv. To install the necessary packages, run:
uv syncThis will create a virtual environment in .venv and install all dependencies listed in the pyproject.toml file.
We provide a basic config file for generating sequences using the diffusion model resulting in 1000 sequences made per cell type. Base generation utilizes a guidance scale 1.0, however this can be tuned within the sample.py with the cond_weight_to_metric parameter. To generate sequences call:
uv run sample.pyIf you would like to train the model, we provide a basic config file for training the diffusion model. To train the model call:
uv run train.pyThanks goes to these wonderful people (emoji key):
 Lucas Ferreira da Silva 🤔 💻 |
 Luca Pinello 🤔 |
 Simon 🤔 💻 |
This project follows the all-contributors specification. Contributions of any kind welcome!