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- ---
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- license: apache-2.0
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- ---
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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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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+
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+ # SAIL — Pretrained SAE Weights
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+
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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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+
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+ Two checkpoints are provided, one for each foundation model (FM) embedding space:
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+
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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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+
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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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+
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+ ## Usage
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+
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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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+
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+ ```bash
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+ bash pretrained/download_weights.sh
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+ ```
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+
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+ ## Citation
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+
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+ If you find this work useful, please cite our paper:
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+
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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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+ ```