SMART-Net - Official Pytorch Implementation

This is not complete....!

We proposed a supervised multi-task aiding representation transfer learning network called SMART-Net. This repository provides the official implementation of training SMART-Net as well as the usage of the pre-trained SMART-Net.

💡 Highlights

• Develop a robust feature extractor of brain hemorrhage in head & neck NCCT through three kinds of multi-task representation learning.
• Propose the consistency loss to alleviate the disparity of two pretext tasks' heads, resulting in improved transferability and representation. Connect the feature extractor with the target-specific 3D operator via transfer learning to expand volume-level tasks.
• Explore relationships of the proposed multi-pretext task combinations and perform ablation studies on optimal 3D operators for volume-level ICH tasks.
• Validate the model on multiple datasets with previous methods and ablation studies for the robustness and practicality of our method.

Paper

Title: Improved performance and robustness of multi-task representation learning with consistency loss between pretexts for intracranial hemorrhage identification in head CT
Authors: Sunggu Kyung¹, Keewon Shin, Hyunsu Jeong, Ki Duk Kim, Jooyoung Park, Kyungjin Cho, Jeong Hyun Lee, Gil-Sun Hong, and Namkug Kim
LAB: MI2RL LAB
Journal: Medical Image Analysis (MedIA)

Requirements

• Linux
• Python 3.8.5
• PyTorch 1.8.0

📦 SMART-Net Framework

1. Clone the repository and install dependencies

$ git clone https://github.com/babbu3682/SMART-Net.git
$ cd SMART-Net/
$ pip install -r requirements.txt

2. Preparing data

For your convenience, we have provided few 3D nii samples from Physionet publish dataset as well as their mask labels.

Note: We do not use this data as a train, it is just for code publishing examples.

You can use your own data using the dicom2nifti for converting from dicom to nii.

• The processed hemorrhage directory structure

  datasets/samples/
  train
      |--  sample1_hemo_img.nii.gz
      |--  sample1_hemo_mask.nii
      |--  sample2_normal_img.nii.gz
      |--  sample2_normal_mask.nii        
              .
              .
              .
  valid
      |--  sample9_hemo_img.nii.gz
      |--  sample9_hemo_mask.nii
      |--  sample10_normal_img.nii.gz
      |--  sample10_normal_mask.nii
              .
              .
              .
  test
      |--  sample20_hemo_img.nii.gz
      |--  sample20_hemo_mask.nii
      |--  sample21_normal_img.nii.gz
      |--  sample21_normal_mask.nii
              .
              .
              .   

Excuse

For personal information security reasons of medical data in Korea, our datasets cannot be disclosed.

📝 Citation

If you use this code for your research, please cite our papers:

@article{
  title={Improved performance and robustness of multi-task representation learning with consistency loss between pretexts for intracranial hemorrhage identification in head CT},
  author={Sunggu Kyung, Keewon Shin, Hyunsu Jeong, Ki Duk Kim, Jooyoung Park, Kyungjin Cho, Jeong Hyun Lee, Gil-Sun Hong, Namkug Kim},
  journal={Medical Image Analysis},
  year={2022}
}

🤝 Acknowledgement

We build SMART-Net framework by referring to the released code at qubvel/segmentation_models.pytorch and Project-MONAI/MONAI. This is a patent-pending technology.

🛡️ License

Project is distributed under MIT License