Sparse Autoencoders

Also known as SAE

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16 papers in the last four weeks, up 100% on the four weeks before. 0.2% of all new papers.

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Latest papers 149

Jun 12, 2026cs.LG

Rational Sparse Autoencoder

Sparse autoencoders (SAEs) are standard tools for mechanistic interpretability, but current SAE families are constrained by fixed encoder nonlinearities such as ReLU, JumpReLU, and TopK. This hard-codes a particular sparsity mechanism into the model and can distort the reconstruction-versus-sparsity trade-off. We introduce the Rational Sparse Autoencoder (RSAE), which replaces the fixed encoder activation with a trainable rational function. Rational activations are flexible enough to uniformly approximate the activation primitives used by existing SAE families on compact domains (for TopK, the thresholded gate obtained after a separating top-k threshold is supplied), while also providing a richer function class for adapting to the observed pre-activation geometry. We realise this idea through a two-stage pipeline: an initialisation procedure that copies the pre-trained baseline SAE weights, plugs in rational coefficients obtained by the relaxed Remez exchange on synthetic data, and calibrates the scale parameters along with the rational coefficients; followed by a fine-tuning step under the standard sparsity-regularised reconstruction objective. Empirically, on residual-stream activations of three open-weight language models and across all three baseline activation families, the RSAE strictly improves on it after the fine-tuning step, both on reconstruction-side metrics and on downstream-behaviour metrics, without sacrificing feature-level interpretability under sparse probing. These gains are consistent across host language models, across baseline activation families, and across the full range of baseline sparsity we tested, while the upgrade itself adds only a handful of scalar parameters per autoencoder and runs in minutes on a single consumer GPU.

Naiyu Yin, Yue Yu

Department of Mathematics · Lehigh University · Bethlehem, PA 18015

Activation Sparsity LLM Interpretability Sparse Autoencoders Sparse Coding

Jun 12, 2026cs.LG

Decompose Sparsely Where You Should, Absorb Densely Where You Should No

Sparse autoencoders (SAEs) are typically trained to reconstruct the \textbf{entire} residual stream through a sparse dictionary, implicitly assuming that all activation content is amenable to sparse, monosemantic decomposition. We question this assumption and hypothesize that activations contain a low-rank, dense component that is computationally important to the model yet inherently unsuitable for sparse representation, which serves as a major source of the persistent dense latents widely observed in trained SAEs. To test this, we add a small rank-

r

linear bottleneck in parallel with standard SAEs (BatchTopK and Matryoshka), allowing dense structure to be absorbed before sparse reconstruction. On Gemma-2-2B layer 12, a rank-24 bottleneck reduces dense latent count by up to 84% while improving sparse probing and targeted probe perturbation on both architectures at matched sparsity. The absorbed component is (i) \textbf{structurally identifiable} as the top principal components and outlier dimensions; (ii) \textbf{causally necessary}, with removing it raising next-token cross-entropy by 7.5

\times

, far exceeding the 2.8

\times

from removing the geometrically near-identical top-24 PCA directions; and (iii) \textbf{redundantly encoded by sparse dictionaries}, with ablating 787 maximally aligned sparse features raising cross-entropy by only 2.9

\times

and ablating 2,048 topic-aligned features leaving MMLU topic classification virtually unchanged, whereas removing the scaffold drops it from 98.7% to chance. Together, our findings identify a compact, semantically informative and causally important component of residual stream activations (which we term a \textbf{computational scaffold}) that standard sparse dictionaries represent inefficiently, suggesting that the scope of sparsity-based interpretability methods warrants careful re-examination.

Ruixuan Deng, Zehao Jin, Zekun Wang +1

School of Psychology Georgia Institute of Technology · College of Computing Georgia Institute of Technology · School of Interactive Computing Georgia Institute of Technology

Transformer Interpretability Representation Learning Activation Sparsity Sparse Autoencoders Sparse Coding

Jun 10, 2026cs.LG

Unstable Features, Reproducible Subspaces: Understanding Seed Dependence in Sparse Autoencoders

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

T-Tech

Representation Identifiability Sparse Autoencoders Mechanistic Interpretability

Jun 8, 2026cs.LG

VFUSE: Virulent Feature Understanding with Sparse autoEncoders

Generative models have shown remarkable progress in a variety of domains such as protein design, but such power enables the opaque generation of hazardous proteins. In this work, we introduce VFUSE (Virulent Feature Understanding with Sparse autoEncoders), a mechanistic interpretability approach that trains SAEs on diffusion-transformer activations to audit protein models for hazard-aware features. We apply VFUSE to RoseTTAFold3 and RFDiffusion3, popular open-weight models for protein folding and synthesis. We find that for certain blocks, linear probes detect hazardous designs significantly better when fit in the SAE latent space over the original model's representations: improving interpretability without sacrificing model performance. Furthermore, we identify monosemantic features from the SAE that fire only on hazardous designs at up to AUROC

0.84

(

q < 10^{-13}

). To our knowledge this is the first SAE trained on an all-atom diffusion model and the first feature-level virulence audit of a protein design model, paving the way towards safe and interpretable protein design.

Michael Yu, Matthew L. Olson

Raft Bioworks · Independent

Sparse Autoencoders Mechanistic Interpretability Protein Design

Jun 8, 2026cs.LG

Interpreting and Steering a Text-to-Speech Language Model with Sparse Autoencoders

Language models increasingly serve as the backbone of text-to-speech (TTS) systems, yet we understand little about the representations they build when text and generated speech tokens share a single residual stream. We train BatchTopK sparse autoencoders on the LM backbone of CosyVoice3 and introduce a modality-aware auto-interp pipeline that labels each feature from where it fires-text-prefix context, 1-second speech clips, or both. The recovered features are interpretable, spanning phonemes, laughter, accent prompts and speaker gender. Steering through the SAE latent space shows these features are causal rather than merely descriptive: targeted interventions raise laughter probability from 0.02 to 0.79, flip perceived speaker gender, and control speech rate while preserving spoken content. SAE features thus serve both as interpretability objects and as control directions for TTS synthesis.

Nikita Koriagin, Georgii Aparin, Nikita Balagansky +1

♣T-Tech · ♦AI Foundation and Algorithm Lab

TTS Synthesis Language Model Steering LLM Interpretability Sparse Autoencoders Controllable Speech Generation Speech Language Models

Jun 8, 2026cs.LG

A Unifying Framework for Concept-Based Representational Similarity

Learned representations across models and modalities often exhibit striking structural similarities, suggesting shared underlying concept decompositions. However, concept alignment remains poorly defined: existing approaches optimize different objectives under the same terminology, obscuring what is actually aligned. We propose a unifying framework that decomposes alignment along two axes: what is aligned (representations vs. concepts) and at what level (instance-wise vs. distributional). This induces four corresponding properties -- instance-wise and distributional variants of translation and concept consistency -- and reveals precisely which of these guarantees existing methods provide. We further introduce \InterVenchA, an intervention-based benchmark that separately measures extraction quality, translation quality, and concept consistency. Through theory and experiments, we show that commonly assumed equivalences between alignment objectives fail in practice: optimizing one property does not reliably recover the others, and purely unsupervised objectives fail to recover meaningful instance-level alignment. We then propose the Coupled Sparse Autoencoder (CoSAE), which jointly enforces complementary alignment objectives. Strong alignment emerges only in this regime. Surprisingly, as little as 0.1% paired data is sufficient to recover instance-level alignment when anchoring distributional objectives. Overall, our results show that concept alignment is fundamentally multi-objective: it must be defined, measured, and optimized as such.

Grégoire Dhimoïla, Victor Boutin, Agustin Martin Picard +2

Brown University · ENS Paris Saclay · CNRS +2

Representational Similarity Analysis Cross-Modal Alignment Sparse Autoencoders

Jun 8, 2026cs.LG

Interactions Between Crosscoder Features: A Compact Proofs Perspective

Dictionary learning methods like Sparse Autoencoders (SAEs) and crosscoders attempt to explain a model by decomposing its activations into independent features. Interactions between features hence induce errors in the reconstruction. We formalize this intuition via compact proofs and make five contributions. First, we show how, \textit{in principle}, a compact proof of model performance can be constructed using a crosscoder. Second, we show that an error term arising in this proof can naturally be interpreted as a measure of interaction between crosscoder features and provide an explicit expression for the interaction term in the Multi-Layer Perceptron (MLP) layers. We then provide three applications of this new interaction measure. In our third contribution we show that the interaction term itself can be used as a differentiable loss penalty. Applying this penalty, we can achieve ``computationally sparse'' crosscoders that retain

60\%

of MLP performance when only keeping a single feature at each datapoint and neuron, compared to

10\%

in standard crosscoders. We then show that clustering according to our interaction measure provides semantically meaningful feature clusters, and finally that sleeper agents have significant interactions. Code is available at https://github.com/chainik1125/crosscoders-feature-interactions/tree/arxiv.

Dmitry Manning-Coe, Thomas Read, Anna Soligo +4

1Anthony J. Leggett Institute for Condensed Matter Theory · 2MATS · 3UK AI Security Institute (AISI) +4

Feature Interaction Modeling Sparse Autoencoders Neural Network Interpretability

Jun 6, 2026cs.LG

Pre-Intervention Prediction of Sparse Autoencoder Steering Side Effects

Sparse autoencoder (SAE) features are increasingly used to steer language models, but feature steering is rarely clean: the same intervention can behave inconsistently across contexts and perturb unrelated features. We introduce a pre-intervention screening framework for forecasting SAE steering side effects from feature statistics computed before steering. We operationalize side effects along two axes of steering modularity, effect stability and collateral spread, and evaluate GPT-2-small, Pythia-70M-deduped, Gemma-2-2B, and Llama-3.1-8B across ReLU, JumpReLU, and TopK SAE dictionaries. Across these settings, decoder geometry, activation statistics, co-activation structure, and direct-logit footprint predict steering modularity better than frequency-only and activation-magnitude baselines. The signal is strongest in GPT-2-small, Pythia-70M, and Llama-3.1-8B, where it survives residualization against magnitude-related confounds, and weaker in Gemma-2-2B. Held-out screening shows that ranking unseen features by predicted cleanliness can select features that steer more cleanly on fresh contexts, but the successful axis varies by setting: GPT-2 improves most cleanly, Pythia improves mainly on stability, Llama mainly on collateral, and Gemma only partially. A controlled Llama Scope width comparison shows that the predictive signal persists under a 32K-to-128K dictionary-width change, although the screening payoff becomes less stable. Overall, SAE steering side effects are predictable in advance, but the useful predictor signature and transferred modularity axis are model- and dictionary-setting dependent.

Evan Duan

Language Model Steering LLM Interpretability Sparse Autoencoders Causal Interventions in Language Models

Jun 5, 2026cs.SD

Whisper Hallucination Detection and Mitigation via Hidden Representation Steering and Sparse AutoEncoders

Whisper, a widely adopted ASR model, is known to suffer from hallucinations - coherent transcriptions generated for non-speech audio entirely disconnected from the input. We investigate whether hallucinations can be detected and mitigated through Whisper's internal representations. We extract audio encoder activations and evaluate two representation spaces: raw Whisper activations and Sparse AutoEncoder (SAE) latents. We show that both spaces encode linearly separable hallucination-related information, with discriminative power concentrated in a sparse feature subset and increasing toward deeper encoder layers. We propose two steering strategies: activation-space steering and SAE latent-space steering. SAE-based steering reduces hallucination rate from 72.63% to 14.11% for Whisper small and from 86.88% to 27.33% for Whisper large-v3 on the full non-speech test set, with small WER degradation on speech data, approaching the performance of fine-tuning-based methods.

Georgii Aparin, Vadim Popov, Tasnima Sadekova +1

AI Foundation and Algorithm Lab · National Research University Higher School of Economics

Audio-Language Model Hallucination Detection Sparse Autoencoders Automatic Speech Recognition Representation Engineering Representation Steering

Jun 5, 2026cs.LG

A Geometric View for Understanding Concept Learning and Neuron Interpretation in Sparse Autoencoders

We propose a unified mathematical framework for a geometric understanding of concept learning and neuron interpretation in sparse autoencoders (SAEs). While SAEs improve interpretability of neural networks by learning sparse feature representations, a principled definition of ''concept'' and ''learning'' remains unclear. We formalize concepts as sets of data points and cast concept learning as a set-alignment problem between human-defined and model-induced concepts. This formulation distinguishes three increasingly strong notions of learning -- detection, separation, and approximation -- and yields geometric conditions, error bounds, and capacity constraints for when concepts can be represented by individual neurons or multi-neuron units. It also provides a set-theoretic account for common SAE phenomena, including feature splitting, feature absorption, feature families, and hierarchical concepts. Finally, we connect concept learning and neuron interpretation through formal concept analysis, showing that the two directions need not agree and that their many-to-many structure can be organized by concept lattices. Experiments on synthetic data with ReLU and Top-

K

SAEs illustrate the theory and reveal the effects of SAE size and sparsity on concept learning.

Chenhao Zhang, Chris Lin, Su-In Lee

Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, USA.

Sparse Autoencoders Neural Network Interpretability Formal Concept Analysis

Jun 5, 2026cs.CL

Interpreting Brain Responses to Language with Sparse Features from Language Models

A central goal of cognitive neuroscience is to characterize the features that are represented by human language cortex. Artificial language models (LMs) have emerged as a powerful tool to address this challenge, but studies relating biological and artificial representations are often criticized as relating one black box to another. The present work introduces Augmented Sparse Encoding Models, an encoding framework that replaces dense LM hidden states with hierarchically-organized sparse autoencoder (SAE) features, while explicitly including surprisal as a predictor. Using this approach, we (i) produce interpretations of neural responses and (ii) test whether model-brain alignment reflects primary or idiosyncratic variation in LM representations. Using a high-field 7T fMRI dataset of eight participants listening to 200 linguistically diverse sentences, we first validate our modeling framework by recovering previous interpretations of voxel populations tuned to processing difficulty and meaning abstractness. We then interpret a previously-uncharacterized (but reliable) voxel population and find that it is tuned to people-related content. Next, we show that the fronto-temporal human language network is predicted by a common set of features across its constituent regions, but find that frontal regions are relatively well-explained by surprisal alone, even in the absence of LM-based features. Finally, we show that brain responses during language processing are not merely predictable from an arbitrary set of LM features. Rather, brain responses are best explained by the features that tend to capture the most general information encoded in LM representations, suggesting a nontrivial correspondence between brain and LM language representation.

Michael A. Lepori, Kendrick Kay, Greta Tuckute

Dept. of Computer Science Brown University · Dept. of Radiology University of Minnesota · Kempner Institute Harvard University

LLM Interpretability Sparse Autoencoders Neural Encoding

Jun 4, 2026cs.CV

Inside the Visual Mind: Neuroscience-Motivated Concept Circuits for Interpreting and Steering Vision Transformers

Despite high accuracy, Vision Transformer (ViT) predictions can be driven by spurious cues, raising the need to understand their inner workings before safe deployment. Sparse autoencoders (SAEs) provide a promising lens for decomposing model representations into human-interpretable concepts, yet adapting SAE-based interpretation to ViTs remains challenging due to limited control over concept coverage and subjective, non-scalable feature interpretation. To fill the gaps, motivated by neuroscience-inspired principles, we propose ViSAE, a mechanistic interpretability toolbox for understanding ViT inner workings through concept circuits. ViSAE consists of three components: (1) A probing suite with 64K images and a 16K visually grounded concept vocabulary, improving concept coverage efficiency by 20x over ImageNet and interpretation accuracy by 28.7% over existing concept sets. (2) Top-down concept reading and Bottom-up circuit tracing algorithms that automatically recover ViT inner workings via concept circuits. (3) Applications for auditing and steering ViT behavior. Through concept editing, ViSAE improves the worst-group accuracy on WaterBirds by 48.2%, outperforming existing methods by 23.8%. Our data and code: https://github.com/deep-real/ViSAE.

Tang Li, Yanlin Chen, Mengmeng Ma +1

Department of Computer & Information Science, University of Delaware, Newark, DE, USA · Department of Computer Science, University of Virginia, Charlottesville, VA, USA

Transformer Interpretability Vision Transformer Sparse Autoencoders Mechanistic Interpretability Concept-Based Explanations

Jun 4, 2026cs.LG

Subspace-Aware Sparse Autoencoders for Effective Mechanistic Interpretability

Sparse Autoencoders (SAEs) are widely used for mechanistic interpretability in large language models, yet their formulation assigns each latent feature a single decoder direction, implicitly assuming features to be one-dimensional. We show that this assumption mismatches with the multi-dimensional structure of model features, provably inducing feature splitting through two distinct mechanisms. Geometrically, reconstructing a feature of intrinsic dimension

d_i \ge 2

to error

\varepsilon

with single-direction decoders forces a number of atoms that is exponential in

d_i

. From an end-to-end optimization perspective, this splitting is not merely possible but actively preferred. We prove that there exists a continuous path from the true

d_i

-dimensional basis to a strictly lower risk of the

\ell_1

-regularized SAE objective, whose descent directions drive any trained dictionary into that exponential regime. A single coherent feature is therefore fragmented across many near-collinear latents, producing spurious multiplicity and obscuring the intrinsic geometry. Motivated by this, we introduce Subspace-Aware Sparse Autoencoders (SASA), which replace single-vector decoders with learned decoder subspaces, enforce block sparsity via Top-

s

group gating, and adapt each group's effective rank with a nuclear-norm regularizer. We then show that once the block size satisfies

r \ge d_i

, a single group not only can represent the entire feature slice but is the global minimizer of the SASA objective. This consolidation yields a sample complexity polynomial in

d_i

rather than exponential -- a decisive advantage given that every training activation costs an LLM forward pass. Empirically, on GPT-2 and Mistral-7B, SASA reduces feature splitting and absorption, improves monosemanticity and interpretability, and matches or exceeds standard SAEs while training on roughly half the token budget.

Seyed Arshan Dalili, Mehrdad Mahdavi

The Pennsylvania State University

Representation Disentanglement Sparse Autoencoders Mechanistic Interpretability Sparse Coding

Jun 2, 2026cs.LG

Perplexity Can Miss SAE Feature Damage Under Quantization

Quantization is a standard path to deploying large language models, and quantized models are typically judged acceptable when perplexity or downstream accuracy remains close to the full-precision original. But behavioral parity need not imply feature fidelity: the sparse-autoencoder (SAE) features used to interpret a full-precision model may change after weight rounding. We test this directly by using a frozen SAE as a fixed measurement basis, encoding full-precision and round-to-nearest (RTN) quantized activations on identical tokens, and measuring per-feature survival by Pearson correlation across bit-widths from INT8 to INT4 on Pythia-70M and Gemma-2-2B. Our central finding is that perplexity can miss feature damage: on Gemma-2-2B, INT7 improves perplexity while degrading 18.7% of active SAE features, and under sliding-window evaluation INT6 also improves perplexity while only 51.3% of active features survive. Feature survival is graded rather than cliff-like, with 62.4% of active Pythia features and 51.3% of active Gemma features surviving at INT6; most non-surviving features are blurred rather than fully damaged. Survival is also predictable from full-precision feature statistics alone, with cross-validated AUC 0.92--0.97 and peak activation as the strongest marginal predictor. Finally, RTN quantization and matched-perplexity magnitude pruning damage strongly overlapping feature sets, with Jaccard overlap 0.79--0.86 and damage-score Spearman correlation 0.98. These results show that behavioral metrics alone are insufficient evidence that full-precision interpretability findings transfer to quantized models, motivating feature-level audits of compression.

Evan Duan

University of Michigan

LLM Quantization LLM Interpretability Sparse Autoencoders Post-Training Quantization

Jun 1, 2026q-bio.NC

How Optimality Structures Sparse Dictionaries: A Theory for Understanding SAE Representations

Sparse Autoencoders (SAEs) have found success parsing neural representations into interpretable concepts, providing a basis for understanding and control. However, what exactly SAEs extract, and, correspondingly, the scientific conclusions we can draw from them, are not obvious. Empirically, the proof is in the pudding: SAEs learn interpretable features. Theoretically, we lack a clear account of what properties a 'concept' must satisfy for an SAE to extract it. There has been extensive identifiability work studying the conditions under which sparse coding recovers ground-truth features; however, these approaches tends to focus on simple data-generating models (e.g. sparse independent features) which poorly approximate the internet-swallowing language-model representations on which SAEs are trained. Here, avoiding data-generating models, we ask simply what properties any dictionary learning optimum must satisfy. Concretely, we extend local optimality analyses (Gribonval & Schnass, 2010) to the nonnegative joint-optimisation problem that vanilla SAEs approximate, and derive constraints relating optimal SAE features to their distributions. We use these constraints to explain a range of observed SAE behaviours - hierarchical splitting & absorption, the structure of residuals, and dense antipodal features - each reflecting how L1+nonnegativity interact with data to structure optimal dictionaries. Finally, we construct a novel large-dictionary convex problem and explore the wide atom-per-datapoint limit. In sum, we hope to tease model assumptions from unexpected observations, letting us learn more from SAEs' successes and provide principles for designing their successors.

William Dorrell

Kempner Institute · Harvard University

Representation Learning Sparse Autoencoders Mechanistic Interpretability Dictionary Learning Sparse Coding

Jun 1, 2026cs.LG

Ablating Archetypes: The Stability of Archetypal SAEs is an Artifact of Initialization and Metric Design

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.

Michał Brzozowski, Neo Christopher Chung

Samsung AI Center, Warsaw, Poland · University of Warsaw, Poland

Sparse Autoencoders Mechanistic Interpretability Dictionary Learning

May 31, 2026cs.CL

Sparse Autoencoders for Interpretable Emotion Control in Text-to-Speech

Integrating large language models (LLMs) into text-to-speech (TTS) systems has improved speech expressiveness, yet interpretable emotional control remains challenging. Existing approaches primarily rely on external conditioning or global activation steering, offering limited insight into the internal representations underlying emotional control. In this work, we analyze emotion-related variation in the semantic hidden states of LLM-based TTS models using sparse autoencoders (SAEs) to identify sparse latent features. Our analysis shows that emotional variation is distributed across multiple sparse latent features, while intervening on a small subset enables interpretable emotion control. Building on this observation, we introduce a feature-level intervention framework for bidirectional emotion induction and suppression without modifying backbone parameters. We further show that distinct latent features are associated with specific acoustic attributes (e.g., pitch), suggesting that emotional expression arises from coordinated latent contributions rather than a single global shift. Empirically, steering these sparse latent features achieves comparable or superior emotion induction and suppression performance relative to global steering and existing TTS baselines.

Hongfei Du, Jiacheng Shi, Sidi Lu +2

Department of Computer Science, William & Mary, USA.

TTS Synthesis Sparse Autoencoders Mechanistic Interpretability Controllable Speech Generation Emotional Speech Synthesis

May 30, 2026cs.LG

Query Lens: Interpreting Sparse Key-Value Features with Indirect Effects

While sparse autoencoders provide features more interpretable than individual neurons, reliably characterizing them remains challenging. We propose Query Lens, which extends Logit Lens to enable more comprehensive and faithful interpretations of sparse features. By jointly considering encoder-side key features and decoder-side value features, we identify both the inputs that activate a feature and the outputs it promotes. We also account for indirect, module-mediated effects that arise when the feature is processed by downstream modules, going beyond the direct effect captured by Logit Lens. In experiments, we find that Query Lens yields coherent token signatures for features that remain uninterpretable under Logit Lens. Finally, we propose the Subspace Channel Hypothesis, suggesting that downstream modules read features through layer-specific subspaces.

Hwiyeong Lee, Ingyu Bang, Uiji Hwang +2

1Hanyang University, Seoul, Republic of Korea.

Representation Learning LLM Interpretability Sparse Autoencoders Mechanistic Interpretability

May 29, 2026cs.CL

How Far Do Auto-Interpretation Labels Generalize: A Controlled Study Across Languages, Scripts, and Rewordings

Sparse autoencoder (SAE) features are increasingly used to interpret language models, with auto-generated natural-language labels serving as the primary interface for understanding what each feature represents. We ask whether these labels generalize: does a feature labeled for a concept actually track that concept across languages and scripts? Using Serbian digraphia as a controlled testbed -- the same language written in both Latin and Cyrillic via deterministic transliteration -- we first find that SAE feature sets activated by the same content in different languages, scripts, and wordings share substantial overlap (mean Jaccard 0.39 vs 0.13 random baseline, peaking at 0.57), suggesting genuine cross-lingual semantic features. We then test whether auto-interpretation labels keep pace. They often do not: features whose labels describe semantic content miss the same meaning in Serbian up to 4

\times

more often than within English, and miss Serbian Cyrillic more than Serbian Latin -- two scripts that are deterministic transliterations of each other. The gap grows with network depth, yet the labels give no indication that they fail. These results suggest that auto-interpretation labels reflect a feature's behavior on the languages and scripts a model has seen most in training, rather than the concept itself.

Sripad Karne

Columbia University

LLM Interpretability Sparse Autoencoders Automated Evaluation

May 29, 2026cs.LG

On the Relationship Between Activation Outliers and Feature Death in Sparse Autoencoders

Sparse autoencoders (SAEs) decompose neural network activations into interpretable features, but many learned features never activate, a problem called feature death that wastes dictionary capacity and can reintroduce superposition. Death rates vary dramatically between models: near-zero on GPT-2, over 70% on AlphaFold3 with identical configurations. We find that dimension-level activation outliers (dimensions whose mean magnitude is large relative to per-token variation) cause this by shifting pre-activations at initialization based on each feature's alignment with the activation mean. Features anti-aligned with the mean receive permanently negative pre-activations and never fire. We formalize outlier severity as

γ= \|μ\|/\|σ\|

; it predicts initial death rates (Spearman

ρ= 0.89

for dead-by-TopK,

0.82

for dead-by-ReLU) across 454 model-layer combinations spanning language, vision, protein, and genomic models. Dead features can revive during training, but recovery requires the SAE bias to learn the activation mean, a process that is prohibitively slow at high

γ

. Mean-centering (subtracting the activation mean) sidesteps this and eliminates outlier-induced death across all tested models, confirming the mechanism and providing a principled basis for when and why this preprocessing step is necessary.

Elana Simon, Etowah Adams, James Zou

1Stanford University · 2Columbia University

Activation Outliers Sparse Autoencoders

May 29, 2026cs.LG

Toward Identifiable Sparse Autoencoders

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

Institute of Science and Technology Austria · 2Pyramidal Inc. · and Achira Inc., USA.

Parameter Identifiability Sparse Autoencoders Dictionary Learning Sparse Coding

May 29, 2026cs.CL

Steering LLMs? Actually, Sparse Autoencoders can outperform simple baselines

Sparse Autoencoders (SAEs) have been seen as a promising avenue for exploring the internals of Large Language Models (LLMs) and for steering model output generation. When AxBench - a model steering benchmark - was introduced in Wu et al. (2025), SAEs did not seem to live up to their original hype due to poor steering performance relative to a set of simple baselines. This work serves as a partial rebuttal for Sparse Autoencoders and suggests that the results of Wu et al. (2025) did not do them full justice. We find that Sparse Autoencoders can, in fact, perform close to on par with the reference LoRA performance on the AxBench benchmark, when features are selected and labelled with our supervised pipeline. We also find that our pipeline selects features that are surprisingly causal of their identified labels when using only its interpretability-based components. Lastly, we present evidence that high sparsity (low l0) may not be crucial for successful steering based on interpretability, which is in contrast to the earlier findings in Wang et al. (2025).

Mikkel Godsk Jørgensen, Lars Kai Hansen

DTU Compute · Technical University of Denmark

Language Model Steering LLM Interpretability Sparse Autoencoders

May 28, 2026cs.AI

BioRefusalAudit: Auditing Biosecurity Refusal Depth Using General and Domain-Fine-Tuned Sparse Autoencoders

Biosecurity evaluations of language models typically ask whether models produce hazardous output. This paper asks a complementary question: when a model refuses, is that refusal structurally sound, or does it disappear under modest changes to prompt framing, formatting, or output length? Across five architectures, no model cleanly discriminated benign from hazard. Gemma 2 2B-IT never genuinely refused across 75 prompts, hedging on every hazard-adjacent query. Gemma 4 E2B-IT refused 65/75 prompts with chat-template formatting and 0/75 without it. Both Gemma models collapsed to 0% under an 80-token cap. Qwen 2.5 1.5B and Phi-3-mini over-refused, flagging 83-87% of benign biology as hazardous. Llama 3.2 1B showed the only meaningful tier gradient (61-point spread). To probe what drives such over-refusal, we tested a panel of Schedule I but biologically non-toxic compounds (notably psilocybin cultivation, with FDA Breakthrough Therapy status). Some models refused these at rates exceeding genuinely hazardous biology, suggesting refusal tracks legality and cultural salience over CBRN hazard. To measure the internal side, we introduce a divergence score D comparing a model's surface response label to its internal sparse autoencoder (SAE) feature activations. Full D was computed on Gemma 2 2B-IT (Gemma Scope 1) and Gemma 4 E2B-IT (author-trained bio SAE). Two fine-tuned Gemma 2 domain SAEs were released. On Gemma 4, comply and refuse responses separated by a 0.647-point gap with zero overlap (n=75), though this is preliminary, with a narrow catalog, within-sample calibration, and Gemma-family-only SAE coverage. Built over one hackathon weekend on consumer hardware (GTX 1650 Ti Max-Q, plus Colab T4 for SAE training), this preliminary evidence suggests activation-level auditing may surface failure modes invisible to behavioral evaluation, with substantial variation across architectures.

Caleb DeLeeuw

Independent researcher

Language Model Safety Evaluation Sparse Autoencoders LLM Refusal Behavior Language Model Robustness Refusal Behavior in Language Models

May 28, 2026cs.AI

Scaling Monosemanticity: Extracting Interpretable Features from Claude 3 Sonnet

We demonstrate that sparse autoencoders can extract interpretable features from Claude 3 Sonnet, a production-scale language model, addressing the open question of whether dictionary learning methods scale beyond small transformers. We trained sparse autoencoders with up to 34 million features on the model's middle layer residual stream, using scaling laws to guide hyperparameter selection. The resulting features are multilingual and multimodal (generalizing to images despite text-only training), respond to both concrete instances and abstract discussions of concepts, and can be used to steer model behavior in ways consistent with their interpretations. We find features corresponding to famous entities and locations, as well as more abstract concepts like sarcasm or errors in code. We also identify features relevant to ways in which language models might cause harm--including features representing deception, power-seeking, sycophancy, and bias--and show that these causally influence model outputs when manipulated. Additionally, we conduct analyses of feature interpretability, geometry, and computational function. However, significant limitations remain: our suite of features is incomplete, and we lack rigorous methods for evaluating whether our features faithfully capture model computations.

Adly Templeton, Tom Conerly, Jonathan Marcus +23

Anthropic

LLM Interpretability Sparse Autoencoders Mechanistic Interpretability Sparse Coding

May 27, 2026cs.LG

Interpretability-Guided Layer Selection over Subspace Projection: SAEs as Stethoscopes, Not Scalpels, for Raw Task Vector Model Editing

LLMs increasingly require surgical model editing to enhance domain-specific capabilities without incurring the computational cost or catastrophic forgetting associated with full fine-tuning. Sparse Autoencoders (SAEs) have emerged as a promising tool in this setting, in principle allowing for feature-level identification of where to intervene. In this work, we rigorously evaluate an SAE-guided editing pipeline for mathematical reasoning on Gemma-3-4B-IT and uncover a fundamental failure mode: the intuitively appealing approach of projecting task vectors onto SAE feature subspaces acts as an information bottleneck that discards approximately 97% of the modification energy, yielding no statistically significant improvements across seven math subjects. We show that this failure stems from a geometric misalignment between activation-space SAE directions and weight-space task vectors. We then propose a shift in perspective: SAE as a Stethoscope, Not a Scalpel, where SAEs are used for layer-level diagnosis rather than intervention-level filtering. By injecting unfiltered raw task vectors only into layers identified by an SAE-derived specificity score, we improve Number Theory accuracy from 29.6% to 39.4% (z=+3.41, p=0.0007) on the Minerva Math benchmark; 5 of 7 math subjects significantly improved and none significantly degraded. Our method is fully deterministic, requires no additional inference cost, and provides a principled framework for interpretability-guided model editing.

Li Lei, Madalina Ciobanu, Qingqing Mao +1

Incept Labs Houston, TX · Incept Labs, Houston, TX · Titan Holdings, San Francisco, CA

Task Vectors LLM Interpretability Sparse Autoencoders Model Editing Language Model Editing

May 27, 2026cs.LG

Semantic Optimal Transport for Sparse Autoencoder Feature Matching and Circuit Compression

Sparse autoencoders (SAEs) have become a central tool for interpreting language models. However, two key SAE analyses that remain difficult to scale are (1) matching semantically similar features across multi-layers and (2) compressing large feature circuits into interpretable supernodes. Although these have been treated as separate problems, we show that both are instances of a more fundamental challenge, which we frame as the estimation of semantic distances between SAE features that lie on different activation manifolds. We introduce a distributional framework for this problem, in which each feature is represented not by a single decoder vector like in the literature, but by an activation-weighted distribution over the hidden states that express it. By projecting these distributions into a shared reference space and comparing them with Wasserstein distance, our method provides a unified semantic metric for cross-layer feature comparison. We prove that our representation is invariant to activation rescaling, stable under perturbations, and recovers true matches under finite-sample margin conditions. Empirically, our method outperforms decoder-vector and LLM-based baselines and captures subtle functional distinctions between related features. Notably, our method compresses large feature circuits into interpretable supernodes automatically.

Tue M. Cao, Nguyen Do, My T. Thai

Department of Computer and Information Science and Engineering, University of Florida

Sparse Autoencoders Mechanistic Interpretability Neural Network Compression Optimal Transport

May 27, 2026cs.LG

Feature Geometry of LoRA Adapters: A Sparse Autoencoder Analysis of Representational Divergence in Fine-Tuned Language Models

Low-Rank Adaptation (LoRA) has emerged as a widely adopted approach for adapting large language models, yet the internal representational changes induced by LoRA fine-tuning remain insufficiently understood. In this work, we investigate the geometry of LoRA-induced representations using Sparse Autoencoders (SAEs). We introduce a delta activation framework that isolates the adapter-specific contribution to the residual stream. Using Gemma-2-9B with LoRA ranks 4, 8, 16, and 32, we train adapter-specific SAEs across multiple transformer layers and compare their learned feature spaces with pretrained SAE dictionaries. We evaluate representational alignment using cosine similarity between decoder directions, principal-angle analysis of feature subspaces, and Centered Kernel Alignment (CKA) between activation representations. Across layers and ranks, we consistently observe comparatively weak geometric alignment between LoRA-induced feature dictionaries and pretrained SAE features. Adapter-specific SAEs also reconstruct delta activations more effectively than pretrained SAEs, suggesting that LoRA updates occupy partially distinct representational structure within the residual stream. Additionally, feature density increases with rank and depth, while geometric divergence remains relatively stable across ranks. These findings provide empirical evidence that LoRA fine-tuning can induce feature structures that are not fully captured by pretrained interpretability dictionaries, with implications for mechanistic interpretability, adaptation analysis, and safety auditing of fine-tuned language models.

Prasanth K K

Independent AI Safety Researcher

LLM Interpretability Sparse Autoencoders Low-Rank Adaptation

May 27, 2026cs.LG

Sign-Aware Gated Sparse Autoencoders: Modeling Anticorrelated Features with Bi-Jump-ReLU Activations

Sparse Autoencoders (SAEs) extract interpretable features from Large Language Models, but standard variants enforce non-negativity, forcing separate latents for diametrically opposed concepts (e.g., "pressure too high" vs. "pressure too low") and wasting dictionary capacity when features are anticorrelated. We propose the Sign-Aware Gated SAE (SA-GSAE): two-sided gated sparsity with signed magnitude and auxiliary supervision. A polarity-sensitive gate selects support on either sign, a signed-magnitude path avoids L1 shrinkage, and an auxiliary reconstruction prevents gate collapse. Bipolar sharing - one latent encoding both signs along a shared direction - is realised via a new Bi-Jump-ReLU activation; parameter accounting shows sign-awareness stays parameter-efficient even when anticorrelated pairs are rare. On real LLM activations across three mid-depth hookpoints on Pythia-1B and SmolLM3-3B (6 cells, 3 seeds), a half-width SA-GSAE at width H strictly Pareto-dominates a full-width Gated SAE at 2H over the entire swept L0 overlap on 3 of 6 cells (both MLP-output hookpoints and resid-mid/Pythia-1B); on the remaining 3 it matches R^2 within 0.025 (max gap -0.008) while cutting dead fraction by 0.35-0.62 absolute. Sweep-geomean dead-fraction reductions are ~100x-500x on MLP-output cells and Pythia-1B resid, ~2x-4x on attention cells and SmolLM3-3B resid. Ablations show the two-sided gate and auxiliary loss are load-bearing (no auxiliary collapses LR to 0.27, 98% dead); tying r_i^+ = r_i^- is indistinguishable (|Delta R^2| = 0.0015), and we recommend this symmetric variant as default. MLP-output gains come from most latents carrying both polarities; on attention, bipolar structure concentrates in a small set of top latents. Full-width SA-GSAE exhibits a reproducible reconstruction collapse at SmolLM3-3B resid that the half-width entirely avoids.

Bartosz Wieciech, Zmnako Awrahman, Marcin Czelej +2

Amazon Web Services

Activation Sparsity LLM Interpretability Sparse Autoencoders Sparse Neural Networks

May 27, 2026cs.LG

ReSAE: Residualized Sparse Autoencoders for Multi-Layer Transformer Interventions

Sparse autoencoders are usually trained one layer at a time, even though transformer residual stream activations are strongly coupled across depth. This creates a practical problem for multi-layer interventions: different layerwise dictionaries can spend capacity representing the same carried-forward information, and replacing several layers at once can produce interactions that are not predicted by single-layer behavior. We introduce Residualized Sparse Autoencoders (ReSAEs), which fit an affine map between selected layers and train each later-layer SAE on the unexplained residual rather than on the full activation. Reconstructions are mapped back into the original activation space through the fitted affine chain, so ReSAEs can be evaluated with the same intervention protocols as ordinary SAEs. On Pythia-1.4B and Gemma-2-9B, residualization reduces decoder redundancy and improves sparse probing and targeted perturbation in most tested settings. Despite reconstructing less of the raw activation variance, ReSAEs recover more transformer cross entropy under multi-layer replacement. This gain is clearest under teacher-forcing and at sufficient sparsity online, indicating that ReSAEs preserve the components of the activation most relevant to the model's downstream computation. These results suggest that removing linearly predictable cross-layer structure is a useful default for multi-layer SAE interventions.

Prathyush Poduval, Calvin Yeung, Neel Desai +1

Department of Computer Science University of California, Irvine Irvine, CA 92697 · Georgia Institute of Technology Atlanta, GA 30332

Transformer Interpretability Activation Sparsity Sparse Autoencoders Causal Interventions in Language Models

May 27, 2026cs.CV

Residualized Temporal Sparse Autoencoders for Interpreting Diffusion Models

Text-to-image diffusion models generate images by iterative denoising, so their internal layers produce trajectories of activations rather than single static representations. Sparse autoencoders (SAEs) have recently been used to decompose diffusion activations into interpretable features, but most approaches analyze individual timesteps or condition on time rather than learning from full trajectories. Training one SAE on whole trajectories would make each feature a single trajectory across timesteps, but adjacent activations are largely linearly predictable from one another, so such an SAE spends its latents on content carried forward from step to step. We introduce residualized temporal SAEs (ReSAE), which fit linear predictors between neighboring timesteps and represent each trajectory by its initial activation and the residuals these dynamics leave unexplained. Training an SAE on this representation is equivalent to training it on raw trajectories under a metric induced by the linear dynamics, and it encourages latents to capture structure beyond what is linearly predictable. Each latent's decoder direction maps back to activation space as a feature trajectory over denoising time. Across Stable Diffusion~1.5 and a Diffusion Transformer, ReSAE features span the whole trajectory while pinpointing when changes enter it, making ReSAE a natural tool for studying how a diffusion model generates an image over time.

Calvin Yeung, Prathyush Poduval, Ali Zakeri +2

Department of Computer Science University of California, Irvine Irvine, CA 92697

Autoencoders Sparse Autoencoders T2I Diffusion Models Diffusion Models