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In this paper, we propose a new method to perform data augmentation in a reliable way in the High Dimensional Low Sample Size (HDLSS) setting using a geometry-based variational autoencoder (VAE). Our approach combines the proposal of 1) a new VAE model, the latent space of which is modeled as a Riemannian manifold and which combines both Riemannian metric learning and normalizing flows and 2) a new generation scheme which produces more meaningful samples especially in the context of small data sets. The method is tested through a wide experimental study where its robustness to data sets, classifiers and training samples size is stressed. It is also validated on a medical imaging classification task on the challenging ADNI database where a small number of 3D brain magnetic resonance images (MRIs) are considered and augmented using the proposed VAE framework. In each case, the proposed method allows for a significant and reliable gain in the classification metrics. For instance, balanced accuracy jumps from 66.3&#x0025; to 74.3&#x0025; for a  state-of-the-art  convolutional neural network classifier trained with 50 MRIs of cognitively normal (CN) and 50 Alzheimer disease (AD) patients and from 77.7&#x0025; to 86.3&#x0025; when trained with 243 CN and 210 AD while improving greatly sensitivity and specificity metrics.

Data Augmentation in High Dimensional Low Sample Size Setting Using a Geometry-Based Variational Autoencoder