In Silico Mapping of Visual Categorical Selectivity Across the Whole Brain

VI icon Visual Inference Lab
1Zuckerman Mind Brain Behavior Institute, Columbia University
2University of Hong Kong
NeurIPS 2025
teaser

TL;DR: We train a cutting-edge transformer model to make fMRI predictions for the whole brain. We apply the model to select optimal stimuli from huge image datasets (BrainDIVE, ImageNet), which we evaluate in silico using statistical tests on a held-out dataset. Our pipeline using brain encoders can test concepts that were not explicitly shown to the subject in the scanner, effectively enriching the diversity and size of the fMRI training set. These hypotheses can be tested in targeted future fMRI experiments by showing only the sets of optimal stimuli, accelerating data collection and experiment iteration, and lowering the cost of data acquisition.


Key Contributions

  1. Massive scale: applying in silico mapping on millions of images (ImageNet, BrainDIVE) with a transformer-based brain encoder, enabling discovery of parcel selectivity for concepts never shown in training. To the best of our knowledge, no other study has been done on this scale.
  2. Mapping of the whole brain: expanding beyond visual cortex and revealing human-specific semantic selectivity.We introduce a large-scale evaluation benchmark that captures both compositional and contextual reasoning.
  3. In silico verification: our pipeline verifies selectivity hypotheses in silico with rigorous tests that evaluate how well a label can predict ground-truth activation on a held-out set within and across subjects.
  4. New fMRI experimental paradigm: as datasets grow and encoding models improve, our pipeline offers a way to leverage these advances to accelerate and improve the accuracy of whole-brain mapping.

Abstract

A fine-grained understanding of functional selectivity in human cortex is fundamental for elucidating how visual information is processed and represented in the brain. Classical work utilizing designed experiments has uncovered a number of category-selective regions. However, this approach of cognitive neuroscience requires preconceived hypotheses about the categories. More data-driven approaches that employ rich sets of natural stimuli and simple encoding models have so far lacked the capacity to capture the complexity of neural responses under naturalistic conditions. We propose a novel in silico approach for data-driven discovery of novel category-selectivity hypotheses. We use an encoder-decoder transformer that leverages a brain-region to image-feature cross-attention mechanism, designed to non-linearly align high-dimensional deep network features with cortical responses. Unlike earlier encoding models that apply linear regression to deep-network activations, our architecture learns to flexibly map stimulus features to semantic patterns of fMRI activity in an end-to-end manner. We introduce a method that leverages diffusion-based image generative models and large image datasets to synthesize and select images that maximally activate different cortical parcels. Our method reveals regions with complex compositional selectivity involving diverse semantic concepts. In silico mapping of categorical selectivity provides a data-driven approach for generating novel visual-selectivity hypotheses about the human brain---to be confirmed in future fMRI studies.

Poster

BibTeX

@article{Hwang2025,
  title={In Silico Mapping of Visual Categorical Selectivity Across the Whole Brain},
  author={Hwang, Ethan and Adeli, Hossein and Guo, Wenxuan and Luo, Andrew and Kriegeskorte, Nikolaus},
  journal={Advances in Neural Information Processing Systems (NeurIPS)},
  year={2025},
  url={https://kriegeskorte-lab.github.io/in-silico-mapping-web/}
}