Uncertain but Useful: Leveraging CNN Variability into Data Augmentation

Abstract

Deep learning (DL) is rapidly advancing neuroimaging by achieving state-of-the-art performance with reduced computation times. Yet the numerical stability of DL models -- particularly during training -- remains underexplored. While inference with DL is relatively stable, training introduces additional variability primarily through iterative stochastic optimization. We investigate this training-time variability using FastSurfer, a CNN-based whole-brain segmentation pipeline. Controlled perturbations are introduced via floating point perturbations and random seeds. We find that: (i) FastSurfer exhibits higher variability compared to that of a traditional neuroimaging pipeline, suggesting that DL inherits and is particularly susceptible to sources of instability present in its predecessors; (ii) ensembles generated with perturbations achieve performance similar to an unperturbed baseline; and (iii) variability effectively produces ensembles of numerical model families that can be repurposed for downstream applications. As a proof of concept, we demonstrate that numerical ensembles can be used as a data augmentation strategy for brain age regression. These findings position training-time variability not only as a reproducibility concern but also as a resource that can be harnessed to improve robustness and enable new applications in neuroimaging.