Leveraging unlabelled data for generalizable neural population decoding

Robust and accurate neural decoders are integral to the development of neurotechnological applications such as brain-computer interfaces and closed-loop experiments. Recent work has shown that tokenizing neural data at the resolution of individual spikes facilitates multi-session pretraining and delivers state-of-the-art decoding performance. However, these spike-based models are currently restricted to supervised learning (SL) regimes, limiting both pretraining and finetuning to datasets with paired behavioural labels. To address this, we introduce MOJO ($\textbf{M}$asked aut$\textbf{O}$encoder-based $\textbf{JO}$int training), a training framework designed for spike-tokenizing models that jointly leverages self-supervised learning (SSL) via masked autoencoding and SL objectives for better decoding performance and interpretability. We evaluate MOJO on three intracortical spiking datasets—monkey motor cortex across various reaching tasks, multi-regional mouse recordings during vision and cognitive decision making tasks—demonstrating superior performance to purely SL-trained models. This improvement is especially notable when training with limited labelled data, specifically in the few-shot finetuning regime where only a small amount of labelled data is available to adapt a model to a new recording session. The incorporation of SSL also yields more interpretable neuronal representations, improving performance on analyses such as brain region classification and spike-statistics prediction despite the lack of explicit optimization for these tasks. We then show that MOJO generalizes beyond spiking data using human electrocorticography (ECoG) during speech articulation. We show that MOJO continues to outperform purely SL-trained models and achieves performance comparable to neuro-foundation models (NFMs) built specifically for continuous signals. Overall, augmenting spike-tokenizing models with SSL improves their performance in label-impoverished settings and enables the use of unlabelled data across various tasks and species, and while generalizing to other neural modalities. These results suggest a path towards more flexible and scalable data usage when training NFMs.