A Multi-attribute Controllable Generative Model for Histopathology Image Synthesis

This is the pytorch implementation for our MICCAI 2021 paper.

A Multi-attribute Controllable Generative Model for Histopathology Image Synthesis
Jiarong Ye, Yuan Xue, Peter Liu, Richard Zaino, Keith C. Cheng, Xiaolei Huang
paper (MICCAI 2021 Poster) video

Abstract: Generative models have been applied in the medical imaging domain for various image recognition and synthesis tasks. However, a more controllable and interpretable image synthesis model is still lacking yet necessary for important applications such as assisting in medical training. In this work, we leverage the efficient self-attention and contrastive learning modules and build upon state-of-the-art generative adversarial networks (GANs) to achieve an attribute-aware image synthesis model, termed AttributeGAN, which can generate high-quality histopathology images based on multi-attribute inputs. In comparison to existing single-attribute conditional generative models, our proposed model better reflects input attributes and enables smoother interpolation among attribute values. We conduct experiments on a histopathology dataset containing stained H&E images of urothelial carcinoma and demonstrate the effectiveness of our proposed model via comprehensive quantitative and qualitative comparisons with state-of-the-art models as well as different variants of our model.

Keywords: Histopathology image synthesis, Attribute-aware conditional generative model, Conditional contrastive learning

Architecture

Usage

Environment

• Python >= 3.6
• Pytorch 1.9.1
• CUDA 10.2

Dependencies:

Install the dependencies:

pip install -r requirements.txt

Datasets

Dataset download link: nmi-wsi-diagnosis

Training

python run.py

Visualization

Tensorboard monitoring

tensorboard --logdir saved_models/histology --port 
   

   

Generate images

Download the pre-trained model to the pretrain_model directory: Google Drive Link

python generate.py

Acknowledgment

• Dataset credit:

@article{zhang2019pathologist,
  title={Pathologist-level interpretable whole-slide cancer diagnosis with deep learning},
  author={Zhang, Zizhao and Chen, Pingjun and McGough, Mason and Xing, Fuyong and Wang, Chunbao and Bui, Marilyn and Xie, Yuanpu and Sapkota, Manish and Cui, Lei and Dhillon, Jasreman and others},
  journal={Nature Machine Intelligence},
  volume={1},
  number={5},
  pages={236--245},
  year={2019},
  publisher={Nature Publishing Group}
}

• This repo borrows code from light-weight GAN

@inproceedings{liu2020towards,
  title={Towards Faster and Stabilized GAN Training for High-fidelity Few-shot Image Synthesis},
  author={Liu, Bingchen and Zhu, Yizhe and Song, Kunpeng and Elgammal, Ahmed},
  booktitle={International Conference on Learning Representations},
  year={2020}
}

Citation

If you find our work useful in your research, please cite our paper:

@inproceedings{Ye2021AMC,
  title={A Multi-attribute Controllable Generative Model for Histopathology Image Synthesis},
  author={Jiarong Ye and Yuan Xue and Peter Xiaoping Liu and Richard J. Zaino and Keith C. Cheng and Xiaolei Huang},
  booktitle={MICCAI},
  year={2021}
}