faizan1234567 / recognition-and-gradient-based-localization-of-chest-radiographs

Disease diagnoses in chest radiographs with different neural network architectures, and models activations localization using grad-cam. The whole implementation is in Pytorch.

Recognition and Gradient-based Localization of Chest Radiographs

COVID-19 infection	VGG-16	ResNet-18	DenseNet-121

Figure 1: Localization of model high confidence areas using Grad-CAM

Contents

• Introduction
• Overview
• Project Pipeline
• Results
• Installation
• Usage
• Todo
• Conclusion
• Acknowlegdments

Introduction

Chest diseases such as COVID-19, Pneumonia, and other abnormalities are among ubiquities medical conditions in the world. They are usually done using pathological photographs of a patient’s lungs. There are a lot of details and essential clues, but manual evaluation may not be as fast and accurate. Therefore, it’s important to use effective and efficient diagnoses with minimal cost, time, and high accuracy. [1] Furthermore, diagnoses become even harder if there is a change on chest x-ray images related to Pneumonia manifestation or other patient’s medical history. Moreover, patients might have other pre-existing conditions such as bleeding, pulmonary edema, lung cancer, atelectasis, or surgical reasons. The goal of using AI to highlight specific regions where pneumonia or a disease area exists. [2] This project aims to train state-of-the-art deep neural networks on large scale chest x-ray database to improve the quality of diagnosis of three diseases categories such as COVID-19, Pneumonia, and lung opacity. In addition, we use normal class to differentiate between patients and normal people. Initially, we are training on ResNet18 [3], VGG16 [4], and DenseNet121 [5]. However, later we will design a state-of-the-art model based on observations and experiments using attention models such vision transformers. [6]

Overview

This repository uses chest radiograph dataset from Kaggle [7], [8]. It has a total of 21165 examples of chest x-ray categorized under COVID-19, Pneumonia, Lung Opacity, and Normal. Furthermore, some preprocessing transforms have been defined. To get the insight from the data, we used image understanding models such as ResNet18 [3], DenseNet121 [5], and VGG16 [4] trained on ImageNet [9] Dataset, however, we fine-tunned it on the chest radiographs dataset. The results will be presented in a section later. Finally, by using Gradient weighted class activation maps (Grad-CAM) [10], models high confidence regions have been localized.

Project Pipeline

1. Dataset Exploration
2. Dataset Information

   Type	COVID-19	Lung Opacity	Normal	Viral Pneumonia	Total
   Train	3496	5892	10072	1225	20685
   Val	60	60	60	60	240
   Test	60	60	60	60	240

3. Fine-tune ResNet, VGG16, and DenseNet121
4. Dataset Transformations
5. Handling imbalanced dataset
6. Loading prepretrained models
7. Hyperparameters used

   • Hyper-parameters
     Learning rate	3e-5
     Batch Size	64
     Number of Epochs	10

   • Loss Function	Optimizer
     Categorical Cross Entropy	Adam

8. Loading dataset
9. Training
10. Inference
11. Gradient-based Localization

Results

1. Plotting running losses and accuracies

• Model	Loss and Accuracy Plots
  VGG-16
  ResNet-18
  DenseNet-121

confusion matrices and other quantitative results

	VGG-16	ResNet-18	DenseNet-121
Pathology COVID-19 Lung Opacity Normal Viral Pneumonia	Accuracy Precision Recall F1-Score 0.978 0.983 0.936 0.959 0.953 0.85 0.962 0.902 0.953 0.933 0.888 0.910 0.995 1.0 0.983 0.991	Accuracy Precision Recall F1-Score 0.9871 0.9667 0.9830 0.9748 0.9664 0.8667 1.0000 0.9286 0.9664 1.0000 0.8823 0.9375 0.9957 1.0000 0.9836 0.9917	Accuracy Precision Recall F1-Score 0.9871 0.9500 1.0000 0.9743 0.9665 0.9333 0.9333 0.9333 0.9746 0.9666 0.9354 0.9508 0.9956 1.0000 0.9836 0.9917
Confusion Matrices

• Qualitative results: Localization of model activations on radiographs

COVID-19 infection	VGG-16	ResNet-18	DenseNet-121

Installation

git clone https://github.com/faizan1234567/Recognition-and-gradient-based-localization-of-chest-radiographs.git
cd Recognition-and-gradient-based-localization-of-chest-radiographs

Create and activate Anaconda Environment

conda create -n chest-xray python=3.9.0
conda activate chest-xray

Now install all the required dependencies

pip install --upgrade pip
pip install -r requirements.txt

Installation done !

Usage

To get play with data loading, run the following script

python dataset/data.py 

To train on your dataset

python train.py -h
python train.py --epochs 100 --learning_rate 3e-5 --batch 32 --save runs/ --workers 8 --model 'resnet18' 

To run inference on test dataset

python test.py -h
python test.py --batch 32 --weights <path> --model 'resnet18' --classes 4 --kind 'test'
--subset

To run Grad-CAM for localizating activations

python draw_cam.py -h
python draw_cam.py --model 'resnet18' --output <path> --connfig configs/configs.yaml --save <path>

If you face any issue in installation and usage, please create an issue. If you have any ideas for improvments kindly create a PR.

TODO

• Automatic hyperparameters optimization
• Multi-GPU training support
• Other Gradient based localization techniques integration
• Other state-of-the-art models architectures design
• Adding Hydra configurations
• Adding Data Version Control

Conclusion

In this repository, three image understanding models namely DenseNet121, ResNet18, and VGG16 have fine-tuned on the x-ray dataset. Since the dataset is pretty unbalanced, oversampling stretegy helped with imbalanced dataset. In addition to that, Grad-CAM localization have increased model's interpretablility and chances for improvments. The models have been trained on 10 epochs which are not enough. Based on the results obtained, more data augmentation, better hyperparameters optimization, and model architecutre should be designed for good accuracy.

This repository used some features from the great work [11], we are continously updating and adding new features, models, and large database ,so we can build a robust recognizer. If you find the repository useful, please star the repository.

Acknowledgements

[1]. H. Su et al., “Multilevel threshold image segmentation for COVID-19 chest radiography: A framework using horizontal and vertical multiverse optimization,” Comput. Biol. Med., vol. 146, no. May, p. 105618, 2022, doi: 10.1016/j.compbiomed.2022.105618.

[2] I. Sirazitdinov, M. Kholiavchenko, T. Mustafaev, Y. Yixuan, R. Kuleev, and B. Ibragimov, “Deep neural network ensemble for pneumonia localization from a large-scale chest x-ray database,” Comput. Electr. Eng., vol. 78, pp. 388–399, 2019, doi: 10.1016/j.compeleceng.2019.08.004.

[3] K. He, X. Zhang, S. Ren, and J. Sun, “Deep Residual Learning for Image Recognition,” Dec. 2015, [Online]. Available: http://arxiv.org/abs/1512.03385

[4] “ K. Simonyan and A. Zisserman. Very deep convolutional networks for large-scale image recognition. In ICLR, 2015.”.

[5] G. Huang, Z. Liu, L. Van Der Maaten, and K. Q. Weinberger, “Densely connected convolutional networks,” Proc. - 30th IEEE Conf. Comput. Vis. Pattern Recognition, CVPR 2017, vol. 2017-January, pp. 2261–2269, 2017, doi: 10.1109/CVPR.2017.243.

[6] A. Vaswani, “Attention Is All You Need,” no. Nips, 2017.

[7] M. E. H. Chowdhury et al., “Can AI Help in Screening Viral and COVID-19 Pneumonia?,” IEEE Access, vol. 8, pp. 132665–132676, 2020, doi: 10.1109/ACCESS.2020.3010287.

[8] T. Rahman et al., “Exploring the effect of image enhancement techniques on COVID-19 detection using chest X-ray images,” Comput. Biol. Med., vol. 132, no. March, p. 104319, 2021, doi: 10.1016/j.compbiomed.2021.104319.

[9] J. Deng, W. Dong, R. Socher, L.-J. Li, K. Li, and L. Fei-Fei, “ImageNet: A large-scale hierarchical image database,” in 2009 IEEE Conference on Computer Vision and Pattern Recognition, 2009, pp. 248–255. doi: 10.1109/CVPR.2009.5206848.

[10] R. R. Selvaraju, M. Cogswell, A. Das, R. Vedantam, D. Parikh, and D. Batra, “Grad-CAM: Visual Explanations from Deep Networks via Gradient-Based Localization,” Int. J. Comput. Vis., vol. 128, no. 2, pp. 336–359, 2020, doi: 10.1007/s11263-019-01228-7.

[11] https://github.com/priyavrat-misra/xrays-and-gradcam

[12]. Wikipedia deep leanring