AI In Medicine Clinical Imaging Classification Save

This is the code for "AI in Medicine " By Siraj Raval on Youtube

Project README

EyeNet

Overview

This is the code for this video on Youtube by Siraj Raval on medical classification.

Detecting Diabetic Retinopathy With Deep Learning

Objective

Diabetic retinopathy is the leading cause of blindness in the working-age population of the developed world. The condition is estimated to affect over 93 million people.

The need for a comprehensive and automated method of diabetic retinopathy screening has long been recognized, and previous efforts have made good progress using image classification, pattern recognition, and machine learning. With photos of eyes as input, the goal of this capstone is to create a new model, ideally resulting in realistic clinical potential.

The motivations for this project are twofold:

  • Image classification has been a personal interest for years, in addition to classification on a large scale data set.

  • Time is lost between patients getting their eyes scanned (shown below), having their images analyzed by doctors, and scheduling a follow-up appointment. By processing images in real-time, EyeNet would allow people to seek & schedule treatment the same day.

Retinopathy GIF

Table of Contents

  1. Data
  2. Exploratory Data Analysis
  3. Preprocessing
  4. CNN Architecture
  5. Results
  6. Next Steps
  7. References

Data

The data originates from a 2015 Kaggle competition. However, is an atypical Kaggle dataset. In most Kaggle competitions, the data has already been cleaned, giving the data scientist very little to preprocess. With this dataset, this isn't the case.

All images are taken of different people, using different cameras, and of different sizes. Pertaining to the preprocessing section, this data is extremely noisy, and requires multiple preprocessing steps to get all images to a useable format for training a model.

The training data is comprised of 35,126 images, which are augmented during preprocessing.

Exploratory Data Analysis

The very first item analyzed was the training labels. While there are five categories to predict against, the plot below shows the severe class imbalance in the original dataset.

EDA - Class Imbalance

Of the original training data, 25,810 images are classified as not having retinopathy, while 9,316 are classified as having retinopathy.

Due to the class imbalance, steps taken during preprocessing in order to rectify the imbalance, and when training the model.

Furthermore, the variance between images of the eyes is extremely high. The first two rows of images show class 0 (no retinopathy); the second two rows show class 4 (proliferative retinopathy).

No DR 1 No DR 2
Proliferative DR 1 Proliferative DR 2

Preprocessing

The preprocessing pipeline is the following:

  1. Download all images to EC2 using the download script.
  2. Crop & resize all images using the resizing script and the preprocessing script.
  3. Rotate & mirror all images using the rotation script.
  4. Convert all images to array of NumPy arrays, using the conversion script.

Download All Images to EC2

The images were downloaded using the Kaggle CLI. Running this on an EC2 instance allows you to download the images in about 30 minutes. All images are then placed in their respective folders, and expanded from their compressed files. In total, the original dataset totals 35 gigabytes.

Crop and Resize All Images

All images were scaled down to 256 by 256. Despite taking longer to train, the detail present in photos of this size is much greater then at 128 by 128.

Additionally, 403 images were dropped from the training set. Scikit-Image raised multiple warnings during resizing, due to these images having no color space. Because of this, any images that were completely black were removed from the training data.

Rotate and Mirror All Images

All images were rotated and mirrored.Images without retinopathy were mirrored; images that had retinopathy were mirrored, and rotated 90, 120, 180, and 270 degrees.

The first images show two pairs of eyes, along with the black borders. Notice in the cropping and rotations how the majority of noise is removed.

Unscaled Images Rotated Images

After rotations and mirroring, the class imbalance is rectified, with a few thousand more images having retinopathy. In total, there are 106,386 images being processed by the neural network.

EDA - Corrected Class Imbalance

Neural Network Architecture

The model is built using Keras, utilizing TensorFlow as the backend. TensorFlow was chosen as the backend due to better performance over Theano, and the ability to visualize the neural network using TensorBoard.

For predicting two categories, EyeNet utilizes three convolutional layers, each having a depth of 32. A Max Pooling layer is applied after all three convolutional layers with size (2,2).

After pooling, the data is fed through a single dense layer of size 128, and finally to the output layer, consisting of 2 softmax nodes.

TensorBoard CNN

Results

The EyeNet classifier was created to determine if a patient has retinopathy. The current model returns the following scores.

Metric Value
Accuracy (Train) 82%
Accuracy (Test) 80%
Precision 88%
Recall 77%

So, why does the neural network perform this way? Besides the class imbalance, the cropping is definitely helping in the network's performance. By not having extra black parts in the images, the network is able to process only the eye itself.

Next Steps

  1. Program the neural network to retrain with new photos. This is a common practice, and only serves to optimize the model. Checks would be put in place to validate the images before being added to the classifier, in order to prevent low quality images from altering the classifier too drastically.

  2. Port the Keras model to CoreML, and deploy to an EyeNet iOS application. CoreML is a framework designed by Apple for adding machine learning to iOS devices. This allows the ability of Python developers to export their models, convert the file to a .mlmodel file, and add the file to the iOS development cycle.

Furthermore, the model is able to perform classification on the local device. There is no need for an internet connection for the application to work. Because of this, the ability to use EyeNet in remote areas is further justified, and that much easier.

References

  1. What is Diabetic Retinopathy?

  2. Diabetic Retinopathy Winners' Interview: 4th place, Julian & Daniel

  3. TensorFlow: Machine Learning For Everyone

Tech Stack

tech_stack_banner

Credits

The credits for this code go to gregwchase. I've merely created a wrapper to get people started.

Open Source Agenda is not affiliated with "AI In Medicine Clinical Imaging Classification" Project. README Source: llSourcell/AI_in_Medicine_Clinical_Imaging_Classification
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Last Commit
5 years ago
License
MIT

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