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README.md
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license: apache-2.0
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---
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license: apache-2.0
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language:
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- en
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tags:
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- sparse-autoencoder
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- matryoshka
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- ct
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- mri
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---
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# SAIL — Pretrained SAE Weights
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Pretrained Matryoshka Sparse Autoencoder (SAE) weights for the [SAIL](https://github.com/pwesp/sail) repository. See the project page for the full pipeline and usage instructions.
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Two checkpoints are provided, one for each foundation model (FM) embedding space:
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| File | Foundation model | Input dim | Dictionary sizes | k values |
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|------|-----------------|-----------|-----------------|----------|
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| `biomedparse_sae.ckpt` | BiomedParse | 1536 | 128, 512, 2048, 8192 | 20, 40, 80, 160 |
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| `dinov3_sae.ckpt` | DINOv3 | 1024 | 128, 512, 2048, 8192 | 5, 10, 20, 40 |
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Both SAEs were trained on CT and MRI embeddings from the [TotalSegmentator](https://github.com/wasserth/TotalSegmentator) dataset.
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## Usage
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To download these weights and place them in the expected directory structure, run from the repo root:
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```bash
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bash pretrained/download_weights.sh
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```
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## Citation
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If you find this work useful, please cite our paper:
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```bibtex
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@misc{sail2026,
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title = {Sparse Autoencoders for Interpretable Medical Image Representation Learning},
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author = {Wesp, Philipp and Holland, Robbie and Sideri-Lampretsa, Vasiliki and Gatidis, Sergios},
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year = 2026,
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journal = {arXiv.org},
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howpublished = {https://arxiv.org/abs/2603.23794v1}
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}
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```
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