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mathpluscode committed Dec 11, 2023
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Expand Up @@ -4,7 +4,7 @@ ImgX-DiffSeg is a Jax-based deep learning toolkit using Flax for biomedical imag

This repository includes the implementation of the following work

- [A Recycling Training Strategy for Medical Image Segmentation with Diffusion Denoising Models](https://arxiv.org/abs/2308.16355)
- [A Recycling Training Strategy for Medical Image Segmentation with Diffusion Denoising Models](https://melba-journal.org/2023:016)
- [Importance of Aligning Training Strategy with Evaluation for Diffusion Models in 3D Multiclass Segmentation](https://arxiv.org/abs/2303.06040)

:construction: **The codebase is still under active development for more enhancements and
Expand All @@ -29,7 +29,7 @@ applications.** :construction:
features or [reach out](https://orcid.org/0000-0002-1184-7421) for collaborations. :mailbox:

<div>
<img src="images/diffusion_training_strategy_diagram.png" width="600" alt="diffusion_training_strategy_diagram"></img>
<img src="images/melba_graphic_abstract.png" width="600" alt="graphic_abstract"></img>
</div>

## Features
Expand All @@ -54,7 +54,7 @@ See the [readme](imgx_datasets/README.md) for further details.
prediction ([x0-parameterization](https://arxiv.org/abs/2102.09672)).
- [Importance sampling](https://arxiv.org/abs/2102.09672) for timestep.
- Recycling training strategies, including [xt-recycling](https://arxiv.org/abs/2303.06040) and
[xT-recycling](https://arxiv.org/abs/2308.16355).
[xT-recycling](https://melba-journal.org/2023:016).
- Self-conditioning training strategies, including
[Chen et al. 2022](https://arxiv.org/abs/2208.04202) and
[Watson et al. 2023.](https://www.nature.com/articles/s41586-023-06415-8).
Expand Down Expand Up @@ -311,13 +311,17 @@ London and the University of Manchester, and Cloud TPUs from Google's TPU Resear
If you find the code base and method useful in your research, please cite the relevant paper:
```bibtex
@article{fu2023recycling,
title={A Recycling Training Strategy for Medical Image Segmentation with Diffusion Denoising Models},
author={Fu, Yunguan and Li, Yiwen and Saeed, Shaheer U and Clarkson, Matthew J and Hu, Yipeng},
journal={arXiv preprint arXiv:2308.16355},
year={2023},
doi={10.48550/arXiv.2308.16355},
url={https://arxiv.org/abs/2308.16355},
@article{melba:2023:016:fu,
title = "A Recycling Training Strategy for Medical Image Segmentation with Diffusion Denoising Models",
author = "Fu, Yunguan and Li, Yiwen and Saeed, Shaheer U. and Clarkson, Matthew J. and Hu, Yipeng",
journal = "Machine Learning for Biomedical Imaging",
volume = "2",
issue = "Special Issue for Generative Models",
year = "2023",
pages = "507--546",
issn = "2766-905X",
doi = "https://doi.org/10.59275/j.melba.2023-fbe4",
url = "https://melba-journal.org/2023:016"
}
@article{fu2023importance,
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