Mechanistic Interpretability Should Prioritize Feature Consistency in Sparse Autoencoders

Sparse Autoencoders (SAEs) are a prominent tool in mechanistic interpretability (MI) for decomposing neural network activations into interpretable features. However, the aspiration to identify a canonical set of features is challenged by the observed inconsistency of learned SAE features across different training runs, undermining reproducibility and complicating model comparison. We study run-to-run feature consistency in SAEs and argue that it should be reported as a standard evaluation axis alongside reconstruction and sparsity. We propose the Pairwise Dictionary Mean Correlation Coefficient (PW-MCC) as an assignment-based metric to quantify consistency and demonstrate that high levels are achievable (PW-MCC ≈ 0.80 for TopK SAEs on LLM activations) with appropriate architectural choices. Our contributions include: (i) theoretical grounding for strong consistency in the idealized setting of TopK SAEs; (ii) synthetic validation using a model organism, which verifies PW-MCC as a reliable proxy for ground-truth recovery; and (iii) empirical analysis on LLM activations, where PW-MCC correlates with the similarity of automatically generated natural-language feature explanations. We hope these results encourage routine reporting of feature consistency to support more robust cumulative progress in MI. 1