Group-level Brain Decoding with Deep Learning

Richard Csaky, Mats W.J. Van Es, Oiwi Parker Jones, Mark Woolrich

Keywords: deep learning, transfer learning, decoding, neuroimaging, MEG, permutation feature importance

TL;DR: We propose a neuroscientifically interpretable deep learning model capable of jointly decoding multiple subjects in neuroimaging data aided by subject embeddings.

Abstract: Decoding experimental variables from brain imaging data is gaining popularity, with applications in brain-computer interfaces and the study of neural representations. Decoding is typically subject-specific and does not generalise well over subjects. Here, we propose a method that uses subject embedding, analogous to word embedding in Natural Language Processing, to learn and exploit the structure in between subject variability as part of a decoding model, our adaptation of the WaveNet architecture for classification. We apply this to magnetoencephalography data, where 15 subjects viewed 118 different images, with 30 examples per image; to classify images using the entire 1s window following image presentation. We show that the combination of deep learning and subject embedding is crucial to closing the performance gap between subject- and group-level decoding models. Importantly, group models outperform subject models on low-accuracy subjects (but impair high-accuracy subjects) and can be helpful for initialising subject models. The potential of such group modelling is even higher with bigger datasets. To better enable physiological interpretation at the group level we demonstrate the use of permutation feature importance developing insights into the spatio-temporal and spectral information encoded in the models. All code is available on GitHub.

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