https://github.com/csyfjiang/M4oE

https://github.com/csyfjiang/M4oE

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• Host: GitHub
• URL: https://github.com/csyfjiang/M4oE
• Owner: csyfjiang
• Created: 2024-02-25T02:19:14.000Z (11 months ago)
• Default Branch: master
• Last Pushed: 2024-10-03T14:31:59.000Z (3 months ago)
• Last Synced: 2024-10-17T17:09:55.803Z (3 months ago)
• Language: Python
• Size: 70.3 KB
• Stars: 14
• Watchers: 1
• Forks: 2
• Open Issues: 2
• Metadata Files:
  • Readme: README.md

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README

        
# M4oE

The codes for the work "M4oE: Foundation Model for Medical Multimodal Image Segmentation with Mixture of Experts"([Arxiv](https://arxiv.org/abs/2405.09446)). Our paper has been accepted by MICCAI 2024.

## 1. Pretrained Models: You can choose a pretrained model based on your preference.

### Opt 1.1 Download pre-trained swin transformer model (Swin-T)

* [Get pre-trained model in this link] (https://drive.google.com/drive/folders/1UC3XOoezeum0uck4KBVGa8osahs6rKUY?usp=sharing): Put pretrained Swin-T into folder "pretrained_ckpt/”

### Opt 1.2 Pretraining by using MAE methods on your datasets.

- References: (https://github.com/zian-xu/swin-mae)

## 2. Prepare data

- [AMOS 22](https://amos22.grand-challenge.org/Dataset/)

- [FLARE 22](https://flare22.grand-challenge.org/)

- [ATLAS](https://atlas.grand-challenge.org/)

## 3. Environment

- Please prepare an environment with python=3.8.10, and then use the command "pip install -r requirements.txt" for the dependencies.

## 4. Train/Test

- Run the train script on synapse dataset. The batch size we used is 36. If you do not have enough GPU memory, the bacth size can be reduced to 12 or 6 to save memory.

- Train

```bash

sh train.sh or python train.py --cfg configs/swin_tiny_patch4_window7_224_lite.yaml --root_path your DATA_DIR --max_epochs 150 --output_dir your OUT_DIR  --img_size 224 --base_lr 0.05 --batch_size 24

```

- Test 

```bash

sh test.sh or python test.py --cfg configs/swin_tiny_patch4_window7_224_lite.yaml --is_saveni --volume_path your DATA_DIR --output_dir your OUT_DIR --max_epoch 150 --base_lr 0.05 --img_size 224 --batch_size 24

```

## References

* [SwinUnet](https://github.com/HuCaoFighting/Swin-Unet)

* [Swin-MAE](https://github.com/zian-xu/swin-mae)

* [MAE](https://github.com/facebookresearch/mae)

## Citation

```bibtex

@InProceedings{Jia_M4oE_MICCAI2024,

        author = { Jiang, Yufeng and Shen, Yiqing},

        title = { { M4oE: A Foundation Model for Medical Multimodal Image Segmentation with Mixture of Experts } },

        booktitle = {proceedings of Medical Image Computing and Computer Assisted Intervention -- MICCAI 2024},

        year = {2024},

        publisher = {Springer Nature Switzerland},

        volume = {LNCS 15012},

        month = {October},

        page = {pending}

}

```