Visual Transformers for 3D Medical Images Classification: Use-Case Neurodegenerative Disorders

A Neurodegenerative Disease (ND) is progressive damage to brain neurons, which the human body cannot repair or replace. The well-known examples of such conditions are Dementia and Alzheimer’s Disease (AD), which affect millions of lives each year. Although conducting numerous researches, there are no effective treatments for the mentioned diseases today. However, early diagnosis is crucial in disease management. Diagnosing NDs is challenging for neurologists and requires years of training and experience. So, there has been a trend to harness the power of deep learning, including state-of-the-art Convolutional Neural Network (CNN), to assist doctors in diagnosing such conditions using brain scans. The CNN models lead to promising results comparable to experienced neurologists in their diagnosis. But, the advent of transformers in the Natural Language Processing (NLP) domain and their outstanding performance persuaded Computer Vision (CV) researchers to adapt them to solve various CV tasks in multiple areas, including the medical field. This research aims to develop Vision Transformer (ViT) models using Alzheimer’s Disease Neuroimaging Initiative (ADNI) dataset to classify NDs. More specifically, the models can classify three categories (Cognitively Normal (CN), Mild Cognitive Impairment (MCI), Alzheimer’s Disease (AD)) using brain Fluorodeoxyglucose (18F-FDG) Positron Emission Tomography (PET) scans. Also, we take advantage of Automated Anatomical Labeling (AAL) brain atlas and attention maps to develop explainable models. We propose three ViTs, the best of which obtains an accuracy of 82% on the test dataset with the help of transfer learning. Also, we encode the AAL brain atlas information into the best performing ViT, so the model outputs the predicted label, the most critical region in its prediction, and overlaid attention map on the input scan with the crucial areas highlighted. Furthermore, we develop two CNN models with 2D and 3D convolutional kernels as baselines to classify NDs, which achieve accuracy of 77% and 73%, respectively, on the test dataset. We also conduct a study to find out the importance of brain regions and their combinations in classifying NDs using ViTs and the AAL brain atlas.This thesis was awarded a prize of 50,000 SEK by Getinge Sterilization for projects within Health Innovation.