Convolutional Neural Networks for Classification of Alzheimer's Disease: Overview and Reproducible Evaluation

In the past two years, over 30 papers have proposed to use convolutional neural network (CNN) for AD classification. However, the classification performances across studies are difficult to compare. Moreover, these studies are hardly reproducible because their frameworks are not publicly accessible. Lastly, some of these papers may reported biased performances due to inadequate or unclear validation procedure and also it is unclear how the model architecture and parameters were chosen. In the present work, we aim to address these limitations through three main contributions. First, we performed a systematic literature review of studies using CNN for AD classification from anatomical MRI. We identified four main types of approaches: 2D slice-level, 3D patch-level, ROI-based and 3D subject-level CNN. Moreover, we found that more than half of the surveyed papers may have suffered from data leakage and thus reported biased performances. Our second contribution is an open-source framework for classification of AD. Thirdly, we used this framework to rigorously compare different CNN architectures, which are representative of the existing literature, and to study the influence of key components on classification performances. On the validation set, the ROI-based (hippocampus) CNN achieved highest balanced accuracy (0.86 for AD vs CN and 0.80 for sMCI vs pMCI) compared to other approaches. Transfer learning with autoencoder pre-training did not improve the average accuracy but reduced the variance. Training using longitudinal data resulted in similar or higher performance, depending on the approach, compared to training with only baseline data. Sophisticated image preprocessing did not improve the results. Lastly, CNN performed similarly to standard SVM for task AD vs CN but outperformed SVM for task sMCI vs pMCI, demonstrating the potential of deep learning for challenging diagnostic tasks.

Reproducible evaluation of diffusion MRI features for automatic classification of patients with Alzheimers disease

Diffusion MRI is the modality of choice to study alterations of white matter. In the past years, various works have used diffusion MRI for automatic classification of Alzheimers disease. However, the performances obtained with different approaches are difficult to compare because of variations in components such as input data, participant selection, image preprocessing, feature extraction, feature selection (FS) and cross-validation (CV) procedure. Moreover, these studies are also difficult to reproduce because these different components are not readily available. In a previous work (Samper-Gonzalez et al. 2018), we proposed an open-source framework for the reproducible evaluation of AD classification from T1-weighted (T1w) MRI and PET data. In the present paper, we extend this framework to diffusion MRI data. The framework comprises: tools to automatically convert ADNI data into the BIDS standard, pipelines for image preprocessing and feature extraction, baseline classifiers and a rigorous CV procedure. We demonstrate the use of the framework through assessing the influence of diffusion tensor imaging (DTI) metrics (fractional anisotropy - FA, mean diffusivity - MD), feature types, imaging modalities (diffusion MRI or T1w MRI), data imbalance and FS bias. First, voxel-wise features generally gave better performances than regional features. Secondly, FA and MD provided comparable results for voxel-wise features. Thirdly, T1w MRI performed better than diffusion MRI. Fourthly, we demonstrated that using non-nested validation of FS leads to unreliable and over-optimistic results. All the code is publicly available: general-purpose tools have been integrated into the Clinica software (www.clinica.run) and the paper-specific code is available at: https://gitlab.icm-institute.org/aramislab/AD-ML.