When Trees Are Not Enough: Learning Mixed-Topology Feature Graphs with Adaptive Graph Sparse Autoencoders

Abstract:Sparse autoencoders (SAEs) expose interpretable features in large language model activations, yet existing structured SAEs impose single-parent trees or forests, while post-hoc graphs permit multiple parents but neither guide feature learning nor ensure reliable relation recovery. We introduce the Adaptive Graph Sparse Autoencoder (AG-SAE), a structure-guided training paradigm that treats each feature's complete parent set as an atomic structural hypothesis and lets evidence select zero, one, or multiple parents. By competing complete parent sets against null, subset, and alternative explanations, AG-SAE identifies jointly necessary multi-parent relations while rejecting redundant or spurious alternatives and verifying that each child contributes beyond its parents. The induced topology over SAE features then defines a differentiable structural loss that guides SAE training, while topology-guided refinement mitigates feature absorption and uses persistent reconstruction gaps exposed by the learned structure to initialize new features. The entire graph is then induced again from the revised dictionary by reassessing every feature's complete parent set, closing the dictionary-graph self-consistency cycle. Experiments demonstrate exact mixed-topology recovery in a controlled toy model, greater relational reliability and semantic validity than structured and post-hoc baselines on real LLM activations, and stronger feature-level causal interventions than conventional SAE features. AG-SAE thereby turns recovered mixed-topology feature structure into an unsupervised training signal that improves the dictionary, enables reliable feature organization beyond the topological limitations of trees, and exhibits stronger causal control beyond reconstruction.

Machine Learning (cs.LG); Computation and Language (cs.CL)

arXiv:2609.36294 [cs.LG]

(or arXiv:2609.36294v1 [cs.LG] for this version)

https://doi.org/10.48550/arXiv.2609.36294 Focus to learn more arXiv-issued DOI via DataCite (pending registration)

arXivLabs is a framework that allows collaborators to develop and share new arXiv features directly on our website.

Both individuals and organizations that work with arXivLabs have embraced and accepted our values of openness, community, excellence, and user data privacy. arXiv is committed to these values and only works with partners that adhere to them.

Have an idea for a project that will add value for arXiv's community? Learn more about arXivLabs.