# Tree SAE: Learning Hierarchical Feature Structures in Sparse Autoencoders

arXiv: https://arxiv.org/abs/2605.07922 · HTML: https://mlsanity.com/paper/2605.07922/

## Key facts

- Cited by 4 papers in the map (data through 14 Oct 2026).
- Placed in SAE features and their applications, one of 13 directions in Mechanistic interpretability.
- Builds on 21 of its 33 references that are in the map.
- First posted on arXiv 8 May 2026.

## Placed in

- Mechanistic interpretability / [SAE features and their applications](https://mlsanity.com/mechinterp/sae-features-and-their-applications/)

## Builds on (most cited first, 21 of 21)

- [The Pile: An 800GB Dataset of Diverse Text for Language Modeling](https://mlsanity.com/paper/2101.00027/) (2020)
- [Sparse Autoencoders Find Highly Interpretable Features in Language Models](https://mlsanity.com/paper/2309.08600/) (2023)
- [The Linear Representation Hypothesis and the Geometry of Large Language Models](https://mlsanity.com/paper/2311.03658/) (2023)
- [Scaling and evaluating sparse autoencoders](https://mlsanity.com/paper/2406.04093/) (2024)
- [Sparse Feature Circuits: Discovering and Editing Interpretable Causal Graphs in Language Models](https://mlsanity.com/paper/2403.19647/) (2024)
- [Gemma Scope: Open Sparse Autoencoders Everywhere All At Once on Gemma 2](https://mlsanity.com/paper/2408.05147/) (2024)
- [Finding Neurons in a Haystack: Case Studies with Sparse Probing](https://mlsanity.com/paper/2305.01610/) (2023)
- [Jumping Ahead: Improving Reconstruction Fidelity with JumpReLU Sparse Autoencoders](https://mlsanity.com/paper/2407.14435/) (2024)
- [Matryoshka Representation Learning](https://mlsanity.com/paper/2205.13147/) (2022)
- [Not All Language Model Features Are One-Dimensionally Linear](https://mlsanity.com/paper/2405.14860/) (2024)
- [Transcoders Find Interpretable LLM Feature Circuits](https://mlsanity.com/paper/2406.11944/) (2024)
- [A is for Absorption: Studying Feature Splitting and Absorption in Sparse Autoencoders](https://mlsanity.com/paper/2409.14507/) (2024)
- [The Geometry of Categorical and Hierarchical Concepts in Large Language Models](https://mlsanity.com/paper/2406.01506/) (2024)
- [Learning Multi-Level Features with Matryoshka Sparse Autoencoders](https://mlsanity.com/paper/2503.17547/) (2025)
- [BatchTopK Sparse Autoencoders](https://mlsanity.com/paper/2412.06410/) (2024)
- [SAEBench: A Comprehensive Benchmark for Sparse Autoencoders in Language Model Interpretability](https://mlsanity.com/paper/2503.09532/) (2025)
- [Automatically Interpreting Millions of Features in Large Language Models](https://mlsanity.com/paper/2410.13928/) (2024)
- [Sparse Autoencoders Do Not Find Canonical Units of Analysis](https://mlsanity.com/paper/2502.04878/) (2025)
- [From Flat to Hierarchical: Extracting Sparse Representations with Matching Pursuit](https://mlsanity.com/paper/2506.03093/) (2025)
- [Interpretability as Compression: Reconsidering SAE Explanations of Neural Activations with MDL-SAEs](https://mlsanity.com/paper/2410.11179/) (2024)
- [Dense SAE Latents Are Features, Not Bugs](https://mlsanity.com/paper/2506.15679/) (2025)

## Built on by (most cited first, 4 of 4)

- [A Dominant Diffuse Phase in the Sparse Autoencoder Phase Diagram](https://mlsanity.com/paper/2609.10299/) (2026)
- [When Trees Are Not Enough: Learning Mixed-Topology Feature Graphs with Adaptive Graph Sparse Autoencoders](https://mlsanity.com/paper/2609.36294/) (2026)
- [Weights Read and Write Features: Scalable Parameter Decomposition Grounded in Activation Space](https://mlsanity.com/paper/2609.37731/) (2026)
- [A Testable Theory of Atomic Features](https://mlsanity.com/paper/2610.05794/) (2026)

## Abstract (arXiv)

Learning hierarchical features in Sparse Autoencoders (SAEs) is essential for capturing the structured nature of real-world data and mitigating issues like feature absorption or splitting. Existing works attempt to identify hierarchical relationships within independent feature sets by relying on activation coverage, the assumption that child feature should only activate when its parent feature activates. However, we demonstrate that this condition alone is insufficient; that is, it often produces false positives where parent and child concepts are semantically unrelated. To address this, we introduce a novel reconstruction condition that enforces a deeper functional link between hierarchical levels. By combining both activation and reconstruction constraints, we propose the Tree SAE, a model designed to learn hierarchical structures directly from within the feature set. Our results demonstrate that Tree SAEs significantly surpass the existing SAEs at learning hierarchical pairs while maintaining competitive performance to the state-of-the-art on several key benchmarks. Finally, we demonstrate the practical utility of our Tree SAE in mapping the geometry of child feature subspaces and uncovering the complex hierarchical concept structures encoded within large language models.