Tree SAE: Learning Hierarchical Feature Structures in Sparse Autoencoders
Authors: Tue M. Cao, Hoang X. Nhat, Raed Alharbi, Phi Le Nguyen, My T. Thai
Abstract
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.
Sparse autoencoders (SAEs) have become an important tool for unsupervised concept discovery in large models. To make the resulting feature spaces more interpretable and manageable, recent approaches have begun imposing hierarchical structure, either explicitly or as an implicit effect of training constraints, yet rigorous comparison remains difficult. There are no agreed-upon requirements for what a meaningful feature hierarchy should satisfy, and evaluation has largely relied on qualitative illustrations with fragmented quantitative protocols. To address this, we derive a set of key requirements for generalization/specialization hierarchies in unsupervised concept discovery, drawing on semantic net and taxonomy research alongside recent SAE work, and use them to derive a concrete evaluation protocol. Applying this protocol to current SAE approaches trained on visual data, we find that while feature spaces generally provide a basis for sensible hierarchies, establishing good hierarchical structure remains challenging. In particular, feature absorption, both in its well-known hard form and in a continuous, soft form, systematically compromises hierarchy quality, pointing to a fundamental tension that future approaches will need to navigate.
Nils Grandien, David Steinmann, Felix Friedrich +1
Sparse Autoencoders (SAEs) extract features from LLM internal activations, meant to correspond to interpretable concepts. A core SAE training hyperparameter is L0: how many SAE features should fire per token on average. Existing work compares SAE algorithms using sparsity-reconstruction tradeoff plots, implying L0 is a free parameter with no inherently correct value aside from its effect on reconstruction. In this work we study the effect of L0 on SAEs, and show that if L0 is not set correctly, the SAE fails to disentangle the underlying features of the LLM. If L0 is too low, the SAE will mix correlated features to improve reconstruction. If L0 is too high, the SAE finds degenerate solutions that also mix features. Further, we present a proxy metric that can help guide the search for the correct L0 for an SAE on a given training distribution. We show that our method finds the correct L0 in toy models and coincides with peak sparse probing performance in LLM SAEs. We find that most commonly used SAEs have an L0 that is too low. Our work shows that practitioners must set L0 correctly to train SAEs with monosemantic features.
Sparse Autoencoders (SAEs) have become an important tool in mechanistic interpretability, helping to analyze internal representations in both Large Language Models (LLMs) and Vision Transformers (ViTs). By decomposing polysemantic activations into sparse sets of monosemantic features, SAEs aim to translate neural network computations into human-understandable concepts. However, common architectures such as TopK SAEs rely on a fixed sparsity level. They enforce the same number of active features (K) across all inputs, ignoring the varying complexity of real-world data. Natural data often lies on manifolds with varying local intrinsic dimensionality, meaning the number of relevant factors can change significantly across samples. This suggests that a fixed sparsity level is not optimal. Simple inputs may require only a few features, while more complex ones need more expressive representations. Using a constant K can therefore introduce noise in simple cases or miss important structure in more complex ones. To address this issue, we propose SoftSAE, a sparse autoencoder with a Dynamic Top-K selection mechanism. Our method uses a differentiable Soft Top-K operator to learn an input-dependent sparsity level k. This allows the model to adjust the number of active features based on the complexity of each input. As a result, the representation better matches the structure of the data, and the explanation length reflects the amount of information in the input. Experimental results confirm that SoftSAE not only finds meaningful features, but also selects the right number of features for each concept. The source code is available at: https://github.com/St0pien/SoftSAE.