uncertainty-estimation-DiabeticRetinopathy

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uncertainty-estimation-DiabeticRetinopathy

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Estimating uncertainty of neural networks for automated screening of Diabetic Retinopathy using the PyTorch framework. Generated visual explanation of the deep learning system to convey the pixels in the image that influences its decision Integrated Gradient method.

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# Uncertainty Estimation of Neural Network for Detection of Diabetic Retinopathy
This project aims at disease detection from medical images using Computer Vision, specifically, automated screening of Diabetic Retinopathy (DR), using the **PyTorch Framework**. Inspite of the thrust on computer vision for medical applications, it is not widely adapted in real-life. Our aim is to build trust on the deep learning system, and deploy such a system in the following ways:   
- Apart from achieving high accuracy in predicting the class of DR using Convolutional Neural Networks, we estimate the uncertainty of neural networks in making its prediction. The deep learning system should give high confidence predictions when the predictions are likely to be correct and low confidence when the system is unsure.   
- We also generate visual explanation of the deep learning system to convey the pixels in the image that influences its decision. For a visual explanation to enhance trust, it has to be specific and relevant. It should only highlight the parts of image that is most relevant to how human justify its decision.  
- Create an end-to-end application which enables an end-user (such as a clinician) to obtain all the results on a dashboard to interpret model predictions. Deep-learning systems could thus, aid physicians by offering second opinions and flagging concerning areas in images.

Together, these reveal the deep learning system’s competency and limits to the human, and in turn the human can know when to trust the deep learning system.

## Environment
- Python 3.7  
- PyTorch >= 1.0.0  
- CUDA 9.0

**Note:** It is recommended to use Anaconda distribution of Python.

### Dependencies
 The dependencies are available in [requirements.txt](https://github.com/asmitapoddar/uncertainty-estimation-DR/blob/master/requirements.txt)
 
 ## Dataset
 The dataset used to train the network are Diabetic Retinopathy images from the Singapore national DR screening Program (SiDRP).
 There are 5 classes:   
 0 - No DR,   
 1 - Mild,   
 2 - Moderate,   
 3 - Severe   
 4 - Proliferative DR
 
 ## Pipeline
 - Training ([train.py](https://github.com/asmitapoddar/uncertainty-estimation-DR/blob/master/train.py)): We load the data into PyTorch using ```torch.utils.data.DataLoader``` after composing various transforms and normalizations. We train a Convolutional Neural Network with ResNet-18 architecture using our dataset of the DR images.
 - Prediction ([prediction.py](https://github.com/asmitapoddar/uncertainty-estimation-DR/blob/master/prediction.py)): We predict the class of the test DR image. We use an ensemble of classifiers, so we get multpile predictions for the test image. We use the average of the softmax layer values over each class to get the predicted class for an image. The predicted logits and probabilities are stored in the file 'res_norotate'.
 - Feature attribution ([visualization_attribution.py](https://github.com/asmitapoddar/uncertainty-estimation-DR/blob/master/visualization_attribution.py)): We attribute the prediction of a neural network network to its input features using two methods - Gradient-weighted Class Activation Mapping (Grad-CAM) and Integrated Gradient method. These methods use the gradients of the target, flowing into the final convolutional layer to produce a coarse localization map highlighting the important regions in the image for the used by the neural network for its predictions. The gradienst are stored in the .npy format.
 - Visualization ([display_image.py](https://github.com/asmitapoddar/uncertainty-estimation-DR/blob/master/display_image.py)): The attributions produced in the .npy files are visualized as a .jpg image. The blue channel signifies positive attribution while the red channel signifies negative attribution of the pixels.
 - Uncertainty Estimation ([uncertainty.py](https://github.com/asmitapoddar/uncertainty-estimation-DR/blob/master/uncertainty.py)): Uncertainty of the neural network is estimated using measures like standard deviation and entropy of the predictions over multiple runs of the transformed image through the neural network. The effect of uncertain predictions on accuracy of the network is visualized through graphs.
 
 ## Usage
### Preprocessing
[preprocessing.py](https://github.com/asmitapoddar/uncertainty-estimation-DR/blob/master/preprocessing.py) shows the preprocessing done on the input image. The preprocessed results are stored as the two .jpeg images in the folder ```preprocessing_results```.
### Models  
[train.py](https://github.com/asmitapoddar/uncertainty-estimation-DR/blob/master/train.py) trains the neural network using the ResNet-18 architecture. The trained model, ```resnet-18_trained.t7``` is stored in the folders ```models``` and ```networks```. Though we cannot release the data used for training our neural network or the trained model, the script [train.py](https://github.com/asmitapoddar/uncertainty-estimation-DR/blob/master/train.py) can be used for training with Kaggle, Messidor data or DR images from other sources.
### Application
I have created an interactive Flask application ([app.py](https://github.com/asmitapoddar/uncertainty-estimation-DR/blob/master/app.py)) which runs through the above workflow to give the results. This contains the whole pipeline of the project, such that it can be used by an end-user like a medical professional to upload a Diabetic Retinopathy image and get the required results.   
To run:
- ```python app.py```  
  This launches a simple built-in server.
- Run local host (http://127.0.0.1:5000/) on the browser.  
- Select an image from your computer and upload to the application.

Thus, we automate the whole machine learning and disease detection pipeline, which not only decreases the cost and time required for diagnosis of Diabetic Retinopathy by assisting doctors, but also increases trust of humans in the deep learning system.

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