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Brain Decodes Deep Nets
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Maps pre-trained vision transformers onto fMRI brain voxels via a factorized, topology-smooth brain encoding model (FactorTopy) to visualize deep-network layers, scales and channels against brain ROIs.
Problem
How to explicitly map deep vision network features (space, layer, scale, channel) to brain regions so that the internal computation of pre-trained models can be visualized and compared with the visual brain hierarchy.
Approach
Use a brain encoding model with factorized soft selectors over space, layer, and scale plus a topology-based smoothness constraint across voxels, then read the learned layer selectors as a brain-to-network map, and use brain hierarchy knowledge to analyze networks (training objective, scaling, fine-tuning).
Key results
- CLIP shows the best layer-to-brain hierarchical alignment; its hierarchy slope rises with scale (0.32 for base to 0.50 for large, 0.52 for XL) while other models' slopes decrease when scaled.
- After fine-tuning on small datasets, CLIP and MAE keep brain score closer to original (CLIP 0.131 to 0.115 on ISIC) than SAM (0.111 to 0.086) and DiNOv2 (0.128 to 0.085).
- Channel clustering of brain voxels with 20 clusters aligns with known ROIs; V1 features capture edge information and FFA features are face-selective.
Measured effects reported in the paper
| What was changed | Where | Measured | Effect |
|---|---|---|---|
| Fine-tune CLIP on ISIC | CLIP · NSD test | brain score R2: 0.131 -> 0.115 | Hurt |
| Fine-tune CLIP on EuroSAT | CLIP · NSD test | brain score R2: 0.131 -> 0.112 | Hurt |
| Fine-tune MAE on ISIC | MAE · NSD test | brain score R2: 0.128 -> 0.117 | Hurt |
| Fine-tune MAE on EuroSAT | MAE · NSD test | brain score R2: 0.128 -> 0.113 | Hurt |
| Fine-tune SAM on ISIC | SAM · NSD test | brain score R2: 0.111 -> 0.086 | Hurt |
| Fine-tune SAM on EuroSAT | SAM · NSD test | brain score R2: 0.111 -> 0.087 | Hurt |
| Fine-tune DiNOv2 on ISIC | DiNOv2 · NSD test | brain score R2: 0.128 -> 0.085 | Hurt |
| Fine-tune DiNOv2 on EuroSAT | DiNOv2 · NSD test | brain score R2: 0.128 -> 0.082 | Hurt |
| Fine-tune the model on small downstream datasets | CLIP, MAE, SAM, and DiNOv2 · ISIC and EuroSAT | hierarchical organization after fine-tuning | Mixed |
| Scale up model size and training data | CLIP · NSD | hierarchy slope: 0.32 for M, 0.50 for L, 0.52 for XL | Helped |
| Scale up model size | ImageNet, SAM, MoCov3, and DiNOv2 · NSD | hierarchy slope | Hurt |
Surprising findings
- Supervised ImageNet and SAM final layers align with mid-level brain regions rather than high-level ones.
- DiNOv2 and SAM lose hierarchical structure rapidly when fine-tuned on small datasets.
Limitations
- Relies on NSD, the only publicly available large paired image-fMRI dataset.
- Brain-network comparison is less informative if networks compute in non-brain-like ways.
- Analysis of hierarchy uses only coarse ROIs and ignores feedback computation.
Experimental setup
Datasets: Natural Scenes Dataset (NSD) ISIC EuroSAT
Benchmarks: Natural Scenes Dataset (NSD) brain encoding
Metrics: R2 brain score hierarchy slope b0 b1 root sum squared difference
Baselines: Layer-specific spatial feature selection (state-of-the-art brain encoding [1]) Per-voxel independent encoding
Builds on: Memory Encoding Model (Algonauts 2023 winner) Natural Scenes Dataset
Closest papers by meaning
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- See Through Their Minds: Learning Transferable Brain Decoding Models from Cross-Subject fMRI (AAAI 2025 · similarity 0.86)
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- Transformer brain encoders explain human high-level visual responses (NeurIPS 2025 · similarity 0.86)
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