Prototypes of the Mind: A Unified Framework for Probing the Visual Brain

Deep learning has driven substantial progress in modeling fMRI responses, yet most existing approaches are optimized for a single objective—such as neural encoding, stimulus decoding, or post hoc interpretation—making it difficult to obtain a coherent account of neural representations. We introduce a unified framework that connects vision foundation models to brain activity while supporting neural analysis from multiple complementary perspectives. Our approach replaces black-box features with a sparse, interpretable representation composed of visual prototypes, and links these prototypes to voxel responses through a linear readout. This design makes the model transparent at both levels: prototype activations expose the visual concepts present in the stimulus, while the learned linear weights characterize each voxel's selectivity. Using this interface, we identify which visual concepts drive neural responses and where they appear in the image, reveal cortical organization through voxel tuning in prototype space, and perform controlled stimulus synthesis to probe cortical selectivity through targeted interventions. Together, these results establish prototype-based representations as a unified and interpretable foundation for studying visual representations in the human brain.