# Interpreting Latent Protein Language Model Features with Geometric Annotations

arXiv: https://arxiv.org/abs/2608.26419 · HTML: https://mlsanity.com/paper/2608.26419/

## 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 12 of its 42 references that are in the map.
- First posted on arXiv 26 Aug 2026.

## Placed in

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

## Builds on (most cited first, 12 of 12)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [Scaling and evaluating sparse autoencoders](https://mlsanity.com/paper/2406.04093/) (2024)
- [Learning Multi-Level Features with Matryoshka Sparse Autoencoders](https://mlsanity.com/paper/2503.17547/) (2025)
- [Automatically Interpreting Millions of Features in Large Language Models](https://mlsanity.com/paper/2410.13928/) (2024)
- [The geometry of hidden representations of large transformer models](https://mlsanity.com/paper/2302.00294/) (2023)
- [BERTology Meets Biology: Interpreting Attention in Protein Language Models](https://mlsanity.com/paper/2006.15222/) (2020)
- [InterPLM: Discovering Interpretable Features in Protein Language Models via Sparse Autoencoders](https://mlsanity.com/paper/2412.12101/) (2024)
- [Interpreting and Steering Protein Language Models through Sparse Autoencoders](https://mlsanity.com/paper/2502.09135/) (2025)
- [Concept Bottleneck Language Models For protein design](https://mlsanity.com/paper/2411.06090/) (2024)
- [Towards Interpretable Protein Structure Prediction with Sparse Autoencoders](https://mlsanity.com/paper/2503.08764/) (2025)
- [ProtSAE: Disentangling and Interpreting Protein Language Models via Semantically-Guided Sparse Autoencoders](https://mlsanity.com/paper/2509.05309/) (2025)

## Abstract (arXiv)

Protein language models (pLMs) encode information about protein sequences which enable downstream tasks such as structure prediction, but their internal representations are not well understood. Sparse autoencoders (SAEs) provide a promising tool to disentangle latent pLM representations into interpretable features, but existing annotation pipelines largely rely on protein-level annotations derived from database labels and LLM annotations of top activating sequences. Such annotations can overlook the localized residue-level and geometric patterns encoded by sparse features. We introduce an automated and scalable method for interpreting SAE features in ESM-2 by using geometrically inspired features of the protein Cα backbone. Across ESM-2 8M layers, an FDR-controlled discovery analysis shows that local geometry is significantly associated with many SAE features, with varying levels of predictive strength, expanding coverage beyond database and sequence-based methods. In particular, geometry can distinguish SAE features sharing the same database annotation, revealing substructure within known biological labels. A significant portion of SAE features activate on unannotated metagenomic protein sequences enabling us to use our SAE annotations to better understand these sequences. In addition, ablation experiments at the level of contact prediction show that removing found geometric features shifts ESM-2's predicted contact maps in the direction of the descriptor. This provides a robust method of annotating proteins activated within SAE neurons at a residue level, providing a bridge between mechanistic interpretability and structural biology.