Medfusion - Medical Denoising Diffusion Probabilistic Model

Paper

Please see: Diffusion Probabilistic Models beat GANs on Medical 2D Images

Figure: Medfusion

Figure: Eye fundus, chest X-ray and colon histology images generated with Medfusion (Warning color quality limited by .gif)

Demo

Link to streamlit app.

Install

Create virtual environment and install packages:
python -m venv venv
source venv/bin/activate
pip install -e .

Get Started

1 Prepare Data

• Go to medical_diffusion/data/datasets/dataset_simple_2d.py and create a new SimpleDataset2D or write your own Dataset.

2 Train Autoencoder

• Go to scripts/train_latent_embedder_2d.py and import your Dataset.
• Load your dataset with eg. SimpleDataModule
• Customize VAE to your needs
• (Optional): Train a VAEGAN instead or load a pre-trained VAE and set start_gan_train_step=-1 to start training of GAN immediately.

2.1 Evaluate Autoencoder

• Use scripts/evaluate_latent_embedder.py to evaluate the performance of the Autoencoder.

3 Train Diffusion

• Go to scripts/train_diffusion.py and import/load your Dataset as before.
• Load your pre-trained VAE or VAEGAN with latent_embedder_checkpoint=...
• Use cond_embedder = LabelEmbedder for conditional training, otherwise cond_embedder = None

3.1 Evaluate Diffusion

• Go to scripts/sample.py to sample a test image.
• Go to scripts/helpers/sample_dataset.py to sample a more reprensative sample size.
• Use scripts/evaluate_images.py to evaluate performance of sample (FID, Precision, Recall)

Acknowledgment

• Code builds upon https://github.com/lucidrains/denoising-diffusion-pytorch