Deep Recurrent Encoder: an end-to-end network to model magnetoencephalography at scale

Understanding how the brain responds to sensory inputs from non-invasive brain recordings like magnetoencephalography (MEG) can be particularly challenging: (i) the high-dimensional dynamics of mass neuronal activity are notoriously difficult to model, (ii) signals can greatly vary across subjects and trials and (iii) the relationship between these brain responses and the stimulus features is non-trivial. These challenges have led the community to develop a variety of preprocessing and analytical (almost exclusively linear) methods, each designed to tackle one of these issues. Instead, we propose to address these challenges through a specific end-to-end deep learning architecture, trained to predict the MEG responses of multiple subjects at once. We successfully test this approach on a large cohort of MEG recordings acquired during a one-hour reading task. Our Deep Recurrent Encoder (DRE) reliably predicts MEG responses to words with a three-fold improvement over classic linear methods. We further describe a simple variable importance analysis to investigate the MEG representations learnt by our model and recover the expected evoked responses to word length and word frequency. Last, we show that, contrary to linear encoders, our model captures modulations of the brain response in relation to baseline fluctuations in the alpha frequency band. The quantitative improvement of the present deep learning approach paves the way to a better characterization of the complex dynamics of brain activity from large MEG datasets.