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