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LiteMedSAM

A lightweight version of MedSAM for fast training and inference. The model was trained with the following two states:

• Stage 1. Distill a lightweight image encoder TinyViT from the MedSAM image encoder ViT by imposing the image embedding outputs to be the same
• State 2. Replace the MedSAM image encoder ViT with TinyViT and fine-tune the whole pipeline

Obtained training test results

• The best model can be downloaded. Or you can download it from the release section.

Sanity test

• Run the following command for a sanity test.

python CVPR24_LiteMedSAM_infer_v2.py -i test_demo/imgs/ -o test_demo/segs

We have improved the original code to save the process of model transformation and shorten the test time.

Installation

The official recommendation is tested with: Ubuntu 20.04 | Python 3.10 | CUDA 11.8 | Pytorch 2.1.2 Also, we have tested with: CentOS 7.9 | Python 3.10.13 | CUDA 12.2 | Pytorch 2.1.2

1. Create a virtual environment conda create -n medsam python=3.10 -y and activate it conda activate medsam
2. Install Pytorch 2.0
3. git clone -b LiteMedSAM https://github.com/bowang-lab/MedSAM/
4. Enter the MedSAM folder cd MedSAM and run pip install -e .

Model Training

Data preprocessing

1. Download the Lite-MedSAM checkpoint and put it under the current directory.
2. The data set is divided into the training set and the test set according to the ratio of 4:1.
3. The ability to convert training data from 'npz' to 'npy' format was added to the training file: train_one_gpu.py

Loss function

1. ShapeDistLossis newly introduced.
2. AutomaticWeightedLoss is added to adjust the weight of each loss function by means of adaptation.

The definitions of ShapeDistLoss and AutomaticWeightedLoss can be viewed at loss_op.py

Single GPU

We trained Lite-MedSAM on a single GPU, run:

python train_one_gpu.py \
    -data_root data/MedSAM_train \
    -pretrained_checkpoint lite_medsam.pth \
    -work_dir work_dir \
    -num_workers 4 \
    -batch_size 4 \
    -num_epochs 10

To resume interrupted training from a checkpoint, run:

python train_one_gpu.py \
    -data_root data/MedSAM_train \
    -resume work_dir/medsam_lite_latest.pth \
    -work_dir work_dir \
    -num_workers 4 \
    -batch_size 4 \
    -num_epochs 10

For additional command line arguments, see python train_one_gpu.py -h.

Acknowledgements

We thank the authors of MobileSAM and TinyViT for making their source code publicly available.