Latent Prediction Yields Cross-Subject Alignable Representations in Sensory-Evoked fMRI

Abstract

Decoding sensory-evoked functional magnetic resonance imaging (fMRI) data is a central analytical tool in cognitive neuroscience. Here we ask whether self-supervised learning (SSL), which has been scarcely explored in this domain, can yield representations that support strong downstream performance. To do so, we adapt a joint embedding predictive architecture (JEPA) to train participant-specific encoders on brain data alone. The encoders never see the stimulus images or any representation derived from them. Applied to the Natural Scenes Dataset (NSD), we evaluate our learned brain embeddings on the downstream tasks of brain captioning and image reconstruction, as well as cross-participant generalization. Our self-supervised approach achieves competitive performance with parameter-rich supervised pipelines that are trained end-to-end with access to image and language data. We further find that encoders trained independently for different participants can be aligned fully unsupervised, using neither images nor stimuli shared between them. After alignment, a neural decoding head trained on one participant can be applied to another without fine-tuning and retains most of its within-subject performance on image reconstruction and brain captioning. By removing the need for images and shared stimuli, our approach is a step towards pooling fMRI data across participants and, eventually, across datasets.