Abstract
Dictionary learning with sparse autoencoders (SAEs) produces overcomplete bases from neural network activations that are often interpretable and reduces polysemanticity. However, features from SAEs vary substantially across random seeds -- a problem known as instability. Archetypal SAEs (Fel et al., 2025) were proposed as a general dictionary-learning intervention for more reliable concept extraction, and report more stable dictionaries at the end of training. We demonstrate that the stability claimed by archetypal SAEs is a result of setting identical initialization across multiple runs. Through our analyses, we attempt to clarify two distinct notions in mechanistic interpretability that may be ambiguously used: stability is agreement between two independently trained models, whereas stabilization is the convergence of independently initialized runs toward a common solution. This distinction is critical for mechanistic interpretability of natural language processing (NLP), where feature stability is increasingly used as evidence that SAE features are reusable units of analysis. Experiments from archetypal SAEs share a deterministic k-means decoder initialization, setting inter-run dictionary distance to zero before training begins. When this initialization is removed, the archetypal constraint provides no stabilization advantage in our setting. We further identify a preprocessing-dependent cosine geometry issue that complicates interpretation of endpoint stability metrics. Overall, our study supports the value of studying SAEs within the larger dictionary-learning tradition while showing that stability claims require trajectory diagnostics and initialization ablations.
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May 29, 2026cs.LG
Recently, sparse autoencoders (SAEs) have emerged as an attractive tool for interpreting and interacting with representations in practical neural networks. While it is common empirical folklore, we also show theoretically that SAEs are highly unstable: different training runs are likely to produce different concept dictionaries and sparse codes. We characterize the model properties that hinder the stability of real-world SAEs, and address each of these problems through minimal changes to the architecture and training procedure. Together, these changes yield two versions of an \textbf{i}dentifiable SAE (iSAE), a variant of the standard TopK SAE with lower reconstruction error and improved stability. We explain this improvement theoretically by connecting SAEs with traditional dictionary learning approaches, and show that the dictionaries learned in practice satisfy an approximate restricted isometry condition, rendering the corresponding sparse codes in those models near-identifiable.
Walter Nelson, Theofanis Karaletsos, Francesco Locatello
Jun 10, 2026cs.LG
Sparse autoencoders (SAEs) are widely used to interpret neural network representations, but their utility depends on whether the learned features are reproducible across training runs. We study this question through \emph{feature stability}: for each SAE feature, we estimate the probability that a similar feature reappears in an independently trained SAE. This yields a scalable per-feature signal that separates stable from unstable features. In a large-scale study across seeds, models, layers, dictionary sizes, and SAE variants, we find a pronounced functional asymmetry: stable features carry most of the reconstruction- and prediction-relevant signal, while unstable features have weak marginal impact and are dominated by low-frequency surface-form triggers in both activation statistics and automatic explanations. Geometrically, unstable features are individually non-reproducible but concentrate in reproducible lower-rank subspaces, suggesting that seed dependence often reflects basis ambiguity within a shared region of activation space rather than pure noise. A controlled synthetic model makes this mechanism explicit, showing that low-rank ground-truth features can be recovered at the subspace level while remaining non-identifiable as individual SAE latents across seeds. Finally, by pooling unique cross-seed features, we construct more stable SAEs while preserving explained variance in this setting. Together, these results show that unstable features are not merely failed or noisy latents: they have weak individual functional impact, but reflect reproducible low-dimensional structure that standard SAEs resolve differently across seeds.
Gleb Gerasimov, Timofei Rusalev, Nikita Balagansky +3
May 18, 2026cs.LG
Sparse autoencoders (SAEs) are one of the main methods to interpret the inner workings of deep neural networks (DNNs), decomposing activations into higher-dimensional features. However, they exhibit critical shortcomings where a large fraction of features are never activated and are unstable. Despite variants of SAEs that attempt to mitigate these issues, they require additional data, resampling, or training. We propose the \textbf{aligned training}, a parameter-free reparameterization of SAEs that simultaneously improves reconstruction quality, eliminates dead features, and significantly enhances stability across training seeds. Our approach is motivated by an overlooked observation that SAE feature quality, measured by the inner product between encoder and decoder directions (which we call the \textbf{alignment score}), follows a bimodal distribution across all modern architectures. The proposed aligned training enforces a geometric constraint between the encoder and decoder such that their inner product equals one for every feature, which removes a source of degeneracy in the SAE training without adding any hyperparameters. Across multiple models, dictionary sizes, and sparsity levels, the aligned training shows Pareto improvements on the SAEBench benchmarks. Beyond improving dead features, stability and reconstruction, our method readily integrates with techniques in mechanical interpretability such as Top/BatchTop-K architectures and p-Annealing. Overall, the aligned training substantially improves feature quality and stability of SAE without computational complexity or cost.
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