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https://github.com/rmaphoh/RETFound_MAE
RETFound - A foundation model for retinal image
https://github.com/rmaphoh/RETFound_MAE
Last synced: about 2 months ago
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RETFound - A foundation model for retinal image
- Host: GitHub
- URL: https://github.com/rmaphoh/RETFound_MAE
- Owner: rmaphoh
- License: other
- Created: 2023-01-30T23:38:40.000Z (almost 2 years ago)
- Default Branch: main
- Last Pushed: 2024-06-03T10:18:43.000Z (6 months ago)
- Last Synced: 2024-08-01T02:26:49.306Z (4 months ago)
- Language: Jupyter Notebook
- Size: 392 KB
- Stars: 325
- Watchers: 16
- Forks: 69
- Open Issues: 8
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
## RETFound - A foundation model for retinal imaging
Official repo for [RETFound: a foundation model for generalizable disease detection from retinal images](https://www.nature.com/articles/s41586-023-06555-x), which is based on [MAE](https://github.com/facebookresearch/mae):
Please contact **[email protected]** or **[email protected]** if you have questions.
Keras version implemented by Yuka Kihara can be found [here](https://github.com/uw-biomedical-ml/RETFound_MAE)
### 📝Key features
- RETFound is pre-trained on 1.6 million retinal images with self-supervised learning
- RETFound has been validated in multiple disease detection tasks
- RETFound can be efficiently adapted to customised tasks
### 🎉News
- 🐉2024/01: [Feature vector notebook](https://github.com/rmaphoh/RETFound_MAE/blob/main/RETFound_Feature.ipynb) are now online!
- 🐉2024/01: [Data split and model checkpoints](BENCHMARK.md) for public datasets are now online!
- 🎄2023/12: [Colab notebook](https://colab.research.google.com/drive/1_X19zdMegmAlqPAEY0Ao659fzzzlx2IZ?usp=sharing) is now online - free GPU & simple operation!
- 2023/09: a [visualisation demo](https://github.com/rmaphoh/RETFound_MAE/blob/main/RETFound_visualize.ipynb) is added
- 2023/10: change the hyperparameter of [input_size](https://github.com/rmaphoh/RETFound_MAE#:~:text=finetune%20./RETFound_cfp_weights.pth%20%5C-,%2D%2Dinput_size%20224,-For%20evaluation%20only) for any image size
### 🔧Install environment
1. Create environment with conda:
```
conda create -n retfound python=3.7.5 -y
conda activate retfound
```
2. Install dependencies
```
git clone https://github.com/rmaphoh/RETFound_MAE/
cd RETFound_MAE
pip install -r requirement.txt
```
### 🌱Fine-tuning with RETFound weights
To fine tune RETFound on your own data, follow these steps:
1. Download the RETFound pre-trained weights
ViT-Large
Colour fundus image
download
OCT
download
2. Organise your data into this directory structure (Public datasets used in this study can be [downloaded here](BENCHMARK.md))
```
├── data folder
├──train
├──class_a
├──class_b
├──class_c
├──val
├──class_a
├──class_b
├──class_c
├──test
├──class_a
├──class_b
├──class_c
```
3. Start fine-tuning (use IDRiD as example). A fine-tuned checkpoint will be saved during training. Evaluation will be run after training.
```
python -m torch.distributed.launch --nproc_per_node=1 --master_port=48798 main_finetune.py \
--batch_size 16 \
--world_size 1 \
--model vit_large_patch16 \
--epochs 50 \
--blr 5e-3 --layer_decay 0.65 \
--weight_decay 0.05 --drop_path 0.2 \
--nb_classes 5 \
--data_path ./IDRiD_data/ \
--task ./finetune_IDRiD/ \
--finetune ./RETFound_cfp_weights.pth \
--input_size 224
```
4. For evaluation only (download data and model checkpoints [here](BENCHMARK.md); change the path below)
```
python -m torch.distributed.launch --nproc_per_node=1 --master_port=48798 main_finetune.py \
--eval --batch_size 16 \
--world_size 1 \
--model vit_large_patch16 \
--epochs 50 \
--blr 5e-3 --layer_decay 0.65 \
--weight_decay 0.05 --drop_path 0.2 \
--nb_classes 5 \
--data_path ./IDRiD_data/ \
--task ./internal_IDRiD/ \
--resume ./finetune_IDRiD/checkpoint-best.pth \
--input_size 224
```
### Load the model and weights (if you want to call the model in your code)
```python
import torch
import models_vit
from util.pos_embed import interpolate_pos_embed
from timm.models.layers import trunc_normal_
# call the model
model = models_vit.__dict__['vit_large_patch16'](
num_classes=2,
drop_path_rate=0.2,
global_pool=True,
)
# load RETFound weights
checkpoint = torch.load('RETFound_cfp_weights.pth', map_location='cpu')
checkpoint_model = checkpoint['model']
state_dict = model.state_dict()
for k in ['head.weight', 'head.bias']:
if k in checkpoint_model and checkpoint_model[k].shape != state_dict[k].shape:
print(f"Removing key {k} from pretrained checkpoint")
del checkpoint_model[k]
# interpolate position embedding
interpolate_pos_embed(model, checkpoint_model)
# load pre-trained model
msg = model.load_state_dict(checkpoint_model, strict=False)
assert set(msg.missing_keys) == {'head.weight', 'head.bias', 'fc_norm.weight', 'fc_norm.bias'}
# manually initialize fc layer
trunc_normal_(model.head.weight, std=2e-5)
print("Model = %s" % str(model))
```
### 📃Citation
If you find this repository useful, please consider citing this paper:
```
@article{zhou2023foundation,
title={A foundation model for generalizable disease detection from retinal images},
author={Zhou, Yukun and Chia, Mark A and Wagner, Siegfried K and Ayhan, Murat S and Williamson, Dominic J and Struyven, Robbert R and Liu, Timing and Xu, Moucheng and Lozano, Mateo G and Woodward-Court, Peter and others},
journal={Nature},
volume={622},
number={7981},
pages={156--163},
year={2023},
publisher={Nature Publishing Group UK London}
}
```