# Transcoder-based Circuit Analysis for Interpretable Single-Cell Foundation Models

arXiv: https://arxiv.org/abs/2509.14723 · HTML: https://mlsanity.com/paper/2509.14723/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Placed in Interpreting biomedical and science models, one of 13 directions in Mechanistic interpretability.
- Builds on 5 of its 16 references that are in the map.
- First posted on arXiv 18 Sep 2025.

## Placed in

- Mechanistic interpretability / [Interpreting biomedical and science models](https://mlsanity.com/mechinterp/interpreting-biomedical-and-science-models/)

## Builds on (most cited first, 5 of 5)

- [Pythia: A Suite for Analyzing Large Language Models Across Training and Scaling](https://mlsanity.com/paper/2304.01373/) (2023)
- [Sparse Autoencoders Find Highly Interpretable Features in Language Models](https://mlsanity.com/paper/2309.08600/) (2023)
- [Toy Models of Superposition](https://mlsanity.com/paper/2209.10652/) (2022)
- [Transcoders Find Interpretable LLM Feature Circuits](https://mlsanity.com/paper/2406.11944/) (2024)
- [Can sparse autoencoders make sense of gene expression latent variable models?](https://mlsanity.com/paper/2410.11468/) (2024)

## Abstract (arXiv)

Single-cell foundation models (scFMs) have demonstrated state-of-the-art performance on various tasks, such as cell-type annotation and perturbation response prediction, by learning gene regulatory networks from large-scale transcriptome data. However, a significant challenge remains: the decision-making processes of these models are less interpretable compared to traditional methods like differential gene expression analysis. Recently, transcoders have emerged as a promising approach for extracting interpretable decision circuits from large language models (LLMs). In this work, we train a transcoder on the cell2sentence (C2S) model, a state-of-the-art scFM. By leveraging the trained transcoder, we extract internal decision-making circuits from the C2S model. We demonstrate that the discovered circuits correspond to real-world biological mechanisms, confirming the potential of transcoders to uncover biologically plausible pathways within complex single-cell models.