DNA Diffusion

Generative modeling of regulatory DNA sequences with diffusion probabilistic models.

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Documentation: https://pinellolab.github.io/DNA-Diffusion

Source Code: https://github.com/pinellolab/DNA-Diffusion

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Introduction

DNA-Diffusion is diffusion-based model for generation of 200bp cell type-specific synthetic regulatory elements.

Installation

Our preferred package / project manager is uv. To install the necessary packages, run:

uv sync

This will create a virtual environment in .venv and install all dependencies listed in the pyproject.toml file.

Usage

Sequence Generation

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.py

Training

If 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.py

Contributors ✨

Thanks 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!