Leveraging unlabelled data for generalizable neural population decoding

Robust and accurate neural decoders are integral to neurotechnologies such as brain-computer interfaces and closed-loop experiments. Recent work has shown that tokenizing neural data at the spike level facilitates multi-session pretraining and delivers state-of-the-art decoding performance. However, current spike-based models are restricted to supervised learning (SL), limiting training to datasets with paired behavioural labels. To address this limitation, we introduce MOJO (Masked autOencoder-based JOint training), a training framework for spike-tokenizing models that jointly leverages self-supervised learning (SSL) via masked autoencoding and SL objectives. We evaluate MOJO on three spiking datasets spanning monkey motor cortex during reaching tasks and multi-regional mouse recordings during vision and decision making tasks, demonstrating superior performance over purely SL-trained models. This improvement is especially pronounced when training with limited labelled data, particularly in few-shot finetuning, where only a small amount of labelled data from a new session is available. Incorporating SSL also yields more interpretable neuronal representations, improving performance on brain region classification and spike-statistics prediction without explicit optimization for these tasks. We further show that MOJO generalizes beyond spiking data to human electrocorticography during speech, where it continues to outperform purely SL-trained models and achieves performance comparable to neuro-foundation models (NFMs) designed specifically for continuous signals. Overall, augmenting spike-tokenizing models with SSL improves performance in label-impoverished settings and enables the use of unlabelled data across various tasks and species, while generalizing to other neural modalities. These results suggest a path towards more flexible and scalable data usage when training NFMs.

Cross-Subject Semantic Decoding with Shared-Space Alignment for Generalized Neural Representation Learning

Generalizing across subjects remains challenging in invasive neural recordings because electrode configurations, anatomical structures, and neural signal patterns vary substantially across individuals. To investigate such inter-subject variability, we propose a cross-subject semantic decoding framework that aligns neural responses to speech perception from multiple subjects into a shared latent space and learns a mapping from the aligned neural representations to contextual embeddings. More specifically, using electrocorticography data collected during natural language comprehension, we estimate the shared space using the shared response model and train a decoder to predict contextual semantic embeddings from projected neural responses. For a held-out subject, we estimate a subject-specific projection into the predefined shared space, and directly apply the pretrained decoder without any retraining. Experimental results demonstrate that the proposed framework consistently outperforms baseline methods across evaluation settings and exhibits a reduced performance drop from source subject to held-out subject testing, indicating improved cross-subject generalization. These results suggest that aligning neural activity into a shared latent space, while decoding in a semantic embedding space, provides an effective strategy for improving cross-subject generalization by reducing subject-specific differences in neural responses while effectively capturing shared stimulus-related representations.