Where Computation Lives Inside TabPFN: Causal Localisation of Attention Head Function

Abstract: We present the first causal mechanistic analysis of a tabular foundation model, investigating how TabPFN 2.5's feature wise attention heads distribute computation across layers. Using activation patching, ablation, and attention entropy across two synthetic regression datasets, we find clear temporal specialisation: one head's causal necessity dominates that of the others by 2 to 5 times at peak layer, with its dominant layer shifting across tasks of different complexity, while the remaining heads exhibit symmetric late layer profiles. Attention entropy and patching provide convergent evidence for the computationally active layers of the dominant head. We additionally investigate inference time steerability via contrastive activation steering, which fails to transfer across samples. We attribute this result to TabPFN's in context learning mechanism, which encodes task structure through context dependent attention rather than the stable parametric directions that make steering tractable in language models.

Atharva Gupta
Dhruv Kumar
Murari Mandal
Saurabh Deshpande


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

Abstract: 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
Daniil Laptev
Vadim Kurochkin
Daniil Gavrilov


Interpretable enzyme function prediction via sparse autoencoder features of ESMC across the microbial protein universe

Abstract: Microbial genomes and metagenomes contain millions of proteins whose enzymatic functions remain unknown, the enzyme dark matter. While deep learning has improved protein function prediction, most methods are black boxes relying on sequence or structural similarity, limiting discovery of novel catalytic activities. The ESMC-6B protein language model and its sparse autoencoder with a 16,384-dimensional codebook of interpretable biological concepts, each annotated by GPT-5, creates a new opportunity: using these features directly as semantic signatures for enzyme function. Here, we show that ESMC-SAE features enable accurate and interpretable enzyme commission (EC) number prediction without task-specific training or GPU-intensive computation. On a balanced benchmark of 4,868 microbial SwissProt enzymes across 161 EC3 subclasses, ESMC-SAE binary features achieve 78.9% top-1 and 88.5% top-5 accuracy, 37.6% higher than 3-mer baselines (57.3%). In leave-one-EC3-class-out evaluation simulating discovery of novel enzyme classes, SAE features recover the EC1 superclass in 47.7% of cases (3.3x random, 14.3%), versus 26.6% for sequence methods. Discriminative features correspond to mechanistically interpretable concepts: catalytic triad geometry for hydrolases, NAD(P)H-binding Rossmann folds for oxidoreductases, phosphate-binding P-loops for transferases. We also survey the ESM Atlas of 7.7 million clusters and identify 169,859 dark enzyme-like candidates across all major microbial phyla. Our results establish a paradigm for enzyme function discovery in microbial dark matter: interpretable by design, scalable without GPU clusters, and applicable to the billions of proteins in the ESM Atlas.

Yue Hu
Wanyu Cheng
Junqing Wang
Yingchao Liu


ICA Lens: Interpreting Language Models Without Training Another Dictionary

Abstract: Finding interpretable directions in language-model representations is critical for understanding and controlling model behavior. Sparse autoencoders (SAEs) have become the standard tool for this purpose, but using them as the default first lens often requires training, storing, and evaluating large overcomplete dictionaries. This bottleneck limits rapid exploration and raises a fundamental question: how much interpretable structure is already visible from activation geometry before training another neural dictionary? Our intuition is simple: many interpretable directions are selective on tokens, and these directions should look less Gaussian than random directions. We therefore revisit independent component analysis (ICA), a classical method for finding non-Gaussian directions, as a compact lens for language-model interpretability. We find that ICA has been underestimated for LLM interpretability, because prior uses often relied on off-the-shelf ICA implementations that are brittle on LLM activations and lacked systematic tools for inspecting and evaluating the recovered directions. To bridge these gaps, we introduce ICALens, the first practical workflow for stable, efficient, and auditable ICA analysis of LLM representations. It combines an optimized GPU-parallel FastICA pipeline with LLM-specific stability recipes and better fitting diagnostics, enabling efficient and reliable layer-wise analysis. Across GPT-2 Small, Gemma 2 2B, and Qwen 3.5 2B Base, ICALens efficiently recovers compact, human-interpretable directions without per-layer gradient-based dictionary training. On SAEBench, ICA is competitive with public SAEs in sparse probing and outperforms them in targeted probe perturbation under small-to-medium budgets. These results suggest that ICA should not be viewed as a weak baseline, but as an efficient and complementary first lens for exploring language-model representations.


XtrAIn: Training-Guided Occlusion for Feature Attribution

Abstract: Occlusion-based attribution methods provide an intuitive way to estimate feature importance by perturbing input features and measuring the resulting change in model output. However, their reliability is strongly affected by how feature removal is implemented: externally selected baselines can introduce bias, out-of-distribution samples, and unstable explanations, while in nonlinear models the occlusion of a set of features can also alter the contribution of non-occluded features. We refer to this effect as attribution shift, as the attribution scores of the non-occluded features drift from their initial values. To challenge these major issues that render explanations unstable, we introduce XtrAIn, a training-guided attribution method that transfers the occlusion operation from the input space to the parameter space. Instead of replacing input values with hand-crafted baselines, XtrAIn follows the model's training trajectory and measures how feature-associated parameter updates affect the output logits. We further introduce Xstep, a lightweight approximation for reducing computational cost, and XtrAIn+, a target-focused variant that emphasizes updates aligned with the target class. Experiments on controlled image datasets and PAM50 breast-cancer subtype classification show that the proposed methods produce cleaner and more interpretable attribution patterns than standard attribution baselines. Overall, XtrAIn provides a training-aware perspective on feature attribution and offers a useful diagnostic tool for studying how feature-level evidence is formed during training.

Thodoris Lymperopoulos
Ioannis Kakogeorgiou
Denia Kanellopoulou


VFUSE: Virulent Feature Understanding with Sparse autoEncoders

Abstract: 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.


Interactions Between Crosscoder Features: A Compact Proofs Perspective

Abstract: 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
Oliver Clive-Griffin
Chun-Hei Yip
Rajashree Agrawal
Jason Gross


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

Abstract: 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
Daniil Gavrilov


Closure-Validated Circuit Discovery in Attention Heads: Co-activation Proposes, Ablation Disposes

Abstract: Interpretability increasingly treats groups of components, not individual units, as the basic object, and proposes to find them by clustering co-activation statistics. We ask whether such a cheap signal actually identifies an attention-head circuit. Adapting a sparse-autoencoder clustering recipe to attention heads -- but validating by causal ablation rather than reconstruction -- we cluster heads and then run a closure test: ablate the discovered community and compare per-example damage to matched-random controls. Across two dense 1B-scale models (Pythia 1B, OLMo 1B) and two input distributions, the communities pass closure. In a Mixture-of-Experts model (OLMoE-1B-7B), route-conditional clustering recovers a statistically real signal that nonetheless does not survive closure -- ablation improves loss, the wrong direction. Extending closure across training, attention-target selectivity and participation ratio decouple from function in both directions. We conclude that a cheap signal is a circuit proposal, not a confirmed circuit; closure is what separates them.


SAEExplainer: Interpreting SAE Features with Activation-Guided Preference Optimization

Abstract: Although Sparse Autoencoders (SAEs) have mitigated the opacity of large language models (LLMs) by decomposing dense representations into sparse features, explaining these features still remains a central challenge. Current explanation methods, however, typically operate within an open-loop paradigm, failing to leverage mechanistic feedback for further refinement. In this paper, we propose SAEExplainer, a training framework utilizes activation scores as an objective reward signal to train the model for self-correction and iterative bootstrapping. By iteratively verifying and correcting foundational explanations through a two-round optimization process, SAEExplainer achieves continuous improvement in its explanatory capabilities. This mechanism significantly reduces explanation hallucinations and reinforces causal triggering patterns. Extensive experiments demonstrate our approach improves upon established baselines across most metrics, especially in causal triggering and discriminative activation.

Jingyi He
Haiyan Zhao
Ruxue Shi
Yanguang Liu
Xin Wang
Fei Sun
Mengnan Du


Ablation-Reversible Heads Don't Transfer: A Stress Test for Mechanistic Role Claims in Transformers

Abstract: In mechanistic interpretability, attention heads are commonly elevated to role claims (e.g., "this head represents addition") when they are necessary for a behavior, encode it linearly, and recover that behavior when restored after ablation. We show this evidence is insufficient: across three 7-8B instruction-tuned models and five computation families, heads passing all three checks routinely fail to transfer the computation when their activations are patched into a different prompt under matched controls. We introduce KID (Knowing / Intent / Doing), a role-assignment lens for attention heads, and pair it with a three-stage pipeline: capability-selective screening (CSS), singular value decomposition (SVD), and activation transduction under matched controls. Our results document a preliminary role taxonomy (including prompt-trajectory stabilizers, answer-side logit-bias heads, and soft computation-pattern carriers) and show that the same-answer control (a transduction target sharing the answer string but not the requested computation) is an underused check that exposes broad state transfer masquerading as semantic specificity.


Pre-Intervention Prediction of Sparse Autoencoder Steering Side Effects

Abstract: 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.


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

Abstract: 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.


When Attribution Patching Lies: Diagnosis and a Second-Order Correction

Abstract: A central goal of mechanistic interpretability is to identify which internal components causally drive a language model's behavior. Because these importance estimates serve as the evidence for identifying circuits, systematic errors can lead to the misidentification of the underlying mechanisms. While activation patching provides a gold-standard causal metric, its computational cost is prohibitive at scale. Practitioners instead rely on attribution patching, a gradient-based, first-order approximation whose reliability remains poorly understood. In this work, we characterize the source of this unreliability, demonstrating that the dominant error stems from the non-linearities in the downstream network rather than local curvature at the patched component. This insight yields three practical tools: (i) a reliability score to detect untrustworthy estimates, (ii) error bounds quantifying potential attribution mis-specifications, and (iii) a Hessian-vector-product (HVP) correction that eliminates the leading-order error with only one additional backward pass. In evaluations across five model families (124M-9B parameters) and both random-token and naturalistic (name-swap) perturbations, HVP is the only second-order correction feasible at larger scale, where standard baselines like Integrated Gradients become computationally prohibitive. In comparative experiments, a multi-step HVP variant matches or exceeds the accuracy of Integrated Gradients at significantly lower compute, outperforming prior second-order baselines. These improvements lead to higher-fidelity circuit recovery on standard benchmarks and support a Screen-Flag-Fix workflow that targets computational effort only toward the components flagged as unreliable.


Interpreting Brain Responses to Language with Sparse Features from Language Models

Abstract: 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


Subspace-Aware Sparse Autoencoders for Effective Mechanistic Interpretability

Abstract: 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.


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

Abstract: 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.


Mechanistic Insights into Functional Sparsity in Multimodal LLMs via CoRe Heads

Abstract: While Multimodal Large Language Models (MLLMs) demonstrate remarkable proficiency on complex vision-language tasks, the mechanisms by which they extract query-relevant visual features from complex, noisy contexts remain opaque. In this paper, we present an in-depth interpretability study that uncovers a profound structural property within MLLMs: functional sparsity in cross-modal retrieval. Leveraging a token-level metric termed Retrieval Attention Mass (RAM), we identify and characterize a highly specialized subset of attention heads, referred to as Context-aware Retrieval (CoRe) heads. Across diverse visual domains and model scales, we observe a clear functional division: CoRe heads act as dedicated information extractors, while most other heads distribute attention over broader contextual regions. Causal interventions further demonstrate the necessity of these specialized heads. Ablating only the top 5% of CoRe heads causes significant degradation in multimodal reasoning performance, whereas ablating lower-ranked heads has minimal effect. Moreover, acceleration experiments validate the utility of CoRe heads, showing that leveraging this localized sparsity significantly accelerates inference while maintaining robust task performance. Our findings reveal a structural principle of functional sparsity within MLLMs, refining the current understanding of mechanistic interpretability and laying a theoretical foundation that can inspire future architecture design and model optimization.

Ruoxi Sun
Quantong Qiu
Juntao Li
Zecheng Tang
Yihang Lou
Min Zhang


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

Abstract: 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.


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

Abstract: 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
Gang Zhou
Ye Gao


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

Abstract: 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
Hyelim Lim
Taeuk Kim


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

Abstract: 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.


Toward Identifiable Sparse Autoencoders

Abstract: 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


Latent Space Disentanglement via Activation Steering for Interpretable Attribute Control in Symbolic Music Generation

Abstract: Transformer-based architectures have significantly advanced the generation of complex symbolic sequences, yet a significant gap remains in achieving fine-grained, interpretable control over discrete signal attributes. This paper investigates the mechanistic interpretability of the Multitrack Music Transformer (MMT) and proposes a framework for deterministic attribute modulation without retraining to bridge this gap via inference-time activation steering. Utilizing the Difference-in-Means (DiffMean) methodology, we isolate latent directions for signal attributes, specifically Pitch and Duration, within the residual stream. We validate the Linear Representation Hypothesis in this domain, achieving high correlation between steering magnitude and attribute shift. To address the inherent feature entanglement in multi-attribute steering, we introduce a Dual Steering framework utilizing Gram-Schmidt Orthogonalization. Experimental results demonstrate that this geometric decoupling reduces conceptual interference and signal degradation compared to naive vector addition, enabling independent deterministic control even against strong autoregressive conditioning.

Ioannis Prokopiou
Pantelis Vikatos
Maximos Kaliakatsos-Papakostas
Theodoros Giannakopoulos
Themos Stafylakis


Scaling Monosemanticity: Extracting Interpretable Features from Claude 3 Sonnet

Abstract: 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
Jack Lindsey
Trenton Bricken
Brian Chen
Adam Pearce
Craig Citro
Emmanuel Ameisen
Andy Jones
Hoagy Cunningham
Nicholas L Turner
Callum McDougall
Monte MacDiarmid
Alex Tamkin
Esin Durmus
Tristan Hume
Francesco Mosconi
C. Daniel Freeman
Theodore R. Sumers
Edward Rees
Joshua Batson
Adam Jermyn
Shan Carter
Chris Olah
Tom Henighan


Discovering a Zeta Map Algorithm on Dyck Paths via Mechanistic Interpretability

Abstract: Machine learning is increasingly used in mathematical discovery, but in mathematics the desired output is often not a prediction itself, but an explicit construction that can be checked independently. We study this setting through the zeta map on Dyck paths, a classical bijection in the combinatorics of the q,t-Catalan numbers. We train a deliberately small one-layer, one-head encoder-decoder transformer on this map and analyze its learned computation using mechanistic interpretability tools, including decoder cross-attention analysis, linear probing, and causal intervention. The analysis reveals a level-based mechanism: encoder representations make path levels linearly accessible, while the decoder selects and traverses input positions in a structured way. Translating these signals into combinatorics leads to the scaffolding map, an explicit peak-centered traversal algorithm for Dyck paths. We prove that this algorithm agrees with the zeta map, modulo a reversal convention in the labeling. This gives a controlled example of AI-assisted mathematical discovery in which mechanistic interpretability turns model behavior into a precise, human-verifiable combinatorial algorithm.


Semantic Optimal Transport for Sparse Autoencoder Feature Matching and Circuit Compression

Abstract: 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.


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

Abstract: 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.


Residualized Temporal Sparse Autoencoders for Interpreting Diffusion Models

Abstract: Text-to-image diffusion models generate images through an iterative denoising process, so internal neural layers produce trajectories of activations rather than single static representations. Sparse autoencoders (SAEs) have recently been used to decompose diffusion activations into interpretable feature directions, but most approaches analyze activations at individual timesteps or condition on time rather than learning directly from full activation trajectories. In this work, we introduce residualized temporal SAEs for diffusion activation trajectories. We collect activations across denoising time, fit linear predictors between neighboring timesteps, and represent each trajectory using an initial activation together with residual components not explained by these linear dynamics. Training an SAE on this residualized representation encourages sparse latents to capture structure beyond what is linearly predictable. The residualized decoder directions can be mapped back into activation space, allowing each latent to be analyzed as a feature trajectory over denoising time. Through reconstruction and ablation studies, spatiotemporal feature analysis, and qualitative steering experiments on Stable Diffusion~1.5, we show that residualized temporal SAEs provide a useful framework for studying temporally structured diffusion activations.

Calvin Yeung
Prathyush Poduval
Ali Zakeri
Zhuowen Zou
Mohsen Imani


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

Abstract: 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
Victor Hugo Jaramillo Velasquez
Wioletta Stobieniecka


SAE-FD: Sparse Autoencoder Feature Distillation for Continual Learning of Large Language Models

Abstract: Continual learning enables large language models to adapt to evolving tasks without retraining from scratch, yet catastrophic forgetting remains a central obstacle. Among continual learning methods, regularization-based approaches are widely used to constrain model updates and reduce forgetting, operating in weight space, gradient space, or output space. However, these dense representation spaces suffer from feature superposition, where multiple concepts are encoded in overlapping dimensions, making it difficult to selectively protect previously learned knowledge without impeding new-task learning. To address this issue, we propose \method (Sparse Autoencoder Feature Distillation), which anchors model representations in the sparse feature space of a pre-trained Sparse Autoencoder, where dense activations are decomposed into a sparse overcomplete basis that reduces representational entanglement, enabling more targeted regularization with less interference to new-task learning. Experiments on two continual learning benchmarks across three model architectures show that \method consistently outperforms existing regularization-based methods, achieving up to 52.70% average accuracy with only -0.46 backward transfer.

Mingxu Zhang
Yuhan Li
Lujundong Li
Dazhong Shen
Hui Xiong
Ying Sun


MechRL: Reinforcement Learning Agents Perform Circuit Discovery for Mechanistic Interpretability

Abstract: Mechanistic interpretability has identified small sets of attention heads that implement specific behaviours in transformer language models, but recovering these circuits typically requires a bespoke analytical pipeline for each new task. We recast circuit discovery as a reinforcement-learning problem. An agent operates over the 144 attention heads of GPT-2 small as a discrete action space; each action triggers a zero-ablation and a contrastive reward that subtracts the ablation's damage to general next-token prediction from its damage to the target task. A single PPO policy, trained on two tasks (induction and IOI) in a vectorised multi-task environment, attains the per-episode oracle on both training tasks and on a held-out third task (docstring completion). Its preferred heads coincide with the canonical heads of established literature on precisely the axes those papers identify as causally non-redundant under single-head ablation; the categories they identify as redundant are correctly de-prioritised by the agent. On the held-out task, best-of-five planning recovers 96\% of the oracle ceiling with no task signal supplied at evaluation. These results indicate that reinforcement learning over causal interventions is a viable, transferable substrate for identifying the single-head bottlenecks of mechanistic circuits, complementary to existing path-patching approaches.


Interpretability Transfer from Language to Vision via Sparse Autoencoders

Abstract: Recent advances in language model interpretability using sparse autoencoders (SAEs) have yet to effectively translate to the visual domain, mainly due to the difficulty and ambiguity of labeling visual concepts. In this paper, we introduce Visual Interpretability via SAE Transfer Alignment (VISTA), a framework that transfers interpretability from language to vision in a LLaVA-style vision-language model by constraining a visual projector to map visual tokens into an LLM's pre-existing, labeled textual SAE space. This approach enables visual interpretability without training dedicated vision SAEs. By regularizing the projector using the LLM's SAE reconstruction loss, VISTA achieves a threefold increase in the matching rate, which measures how accurately the most activating textual concepts in the SAE space correspond to semantic elements in the image. Using this framework, we further analyze spatial localization properties of different vision encoders and show that DINOv2 features have stronger localization abilities than other encoders. Leveraging this precision, we validate VISTA's cross-modal alignment through fine-grained, localized concept interventions, where specific objects are removed or replaced in the model's perception while preserving the surrounding scene. This results in improvements of 35% in object removal and 47% in object replacement tasks over vision-only baselines, providing causal evidence that visual tokens inhabit the text SAE manifold. These contributions are validated across multiple LLM architectures.

Alexey Kravets
Da Li
Chuan Li
Da Chen
Vinay P. Namboodiri


Transformer Field Theory: A Response-Theoretic Approach to Mechanistic Interpretability

Abstract: Mechanistic interpretability often studies Transformer behavior by intervening on internal activations through activation patching, causal tracing, path patching, and steering directions. This paper develops Transformer Field Theory: a response-theoretic framework in which the residual stream of a fixed forward pass is treated as a Transformer field over layer depth and token position. In this formulation, patching becomes a localized source insertion into the Transformer field, first-order sensitivity fields predict patch effects, Green functions describe downstream propagation, and patch selection is posed as an adjoint inverse problem. Empirically, we test the theory's forward response objects in GPT-2-style autoregressive Transformers. Localized Transformer-field interventions exhibit a bounded local linear regime; first-order sensitivities predict patch effects across layer-token sites; localized sources generate structured anisotropic Transformer-field propagation; high-sensitivity sites and sliced Green operators provide reduced response descriptions; and prompt-induced Transformer-field displacements partially transfer answer behavior. These results establish sensitivities, Transformer-field responses, and sliced Green operators as practical objects for organizing patching experiments, while providing the forward mathematical basis for patch-site inference and cross-scale response transfer.

David N. Olivieri
Antonio F. Pérez Rodríguez


Geometry-Adaptive Explainer for Faithful Dictionary-Based Interpretability under Distribution Shift

Abstract: Mechanistic interpretability aims to explain a model's behavior by identifying causally responsible internal structures. Dictionary-based explainers such as sparse autoencoders and transcoders are a primary tool, but their faithfulness under out-of-distribution (OOD) shift has received little systematic attention. We show that distribution shift rotates the subspace that the model actively uses, misaligning the explainer's dictionary trained on in-distribution (ID) activations. We formalize this misalignment as the faithfulness gap, a geometric distance between the ID dictionary and the OOD-active subspace, and show that it controls OOD faithfulness degradation. To reduce this gap, we propose the Geometry-Adaptive Explainer (GAE), which realigns the explainer's dictionary with the OOD-active subspace while preserving the original feature structure. This requires only unlabeled OOD activations and no gradient updates. We prove that GAE improves over the unadapted ID explainer, with excess loss bounded quadratically by the second-moment shift. Empirically, GAE even matches or surpasses all training-based baselines in causal faithfulness across multiple models and OOD settings.

Sungjun Lim
Heedong Kim
Andrew Lee
Kyungwoo Song


The Attribution Contract: Feature Attribution for Generative Language Models

Abstract: Feature attribution methods promise to identify which input features matter for a model output. In generative language models, however, it is often unclear what should count as a feature in the first place. In autoregressive language models, earlier generated tokens are both outputs of the model and inputs to later predictions. In diffusion language models, generation proceeds through iterative denoising or unmasking rather than fixed left-to-right prediction, so local explanation may target a state of diffusion rather than a next token. We argue that this ambiguity is not merely an implementation detail, but a conceptual limitation of carrying classifier-era feature attribution directly into generative language modeling. We introduce the Attribution Contract, a specification for feature-attribution claims that names what output is being explained, which features are eligible to receive attribution, what generative process is assumed, what is held fixed, and what model score is being attributed. The contract clarifies why the same attribution method can answer different questions depending on how it is instantiated. We argue that many disagreements about feature attribution in generative language models are not disagreements about attribution algorithms, but about unstated explanatory contracts. Using autoregressive and diffusion language models as case studies, we show when attribution to earlier generated tokens, intermediate states, or denoising stages is informative, when it is misleading, and why feature-attribution methods in generative language models should be evaluated as method-contract pairs.


Mechanistic origins of catastrophic forgetting: why RL preserves circuits better than SFT?

Abstract: Fine-tuning large language models (LLMs) frequently induces catastrophic forgetting of prior capabilities. Recent work has shown that reinforcement learning (RL) retains prior capabilities more effectively than supervised fine-tuning (SFT), attributing this to policy-gradient updates remaining closer to the base policy \cite{shenfeld2025rl}. We extend this behavioral account to the mechanistic level and ask whether RL's advantage is mirrored by stronger preservation of internal computational circuits. We introduce differential circuit vulnerability, a head-level measure of how much a circuit degrades under fine-tuning, and use it to compare RL and SFT on Qwen2.5-3B-Instruct adapted to scientific question-answering. We find a clear mechanistic trade-off: SFT adapts more rapidly to the target task but produces substantially greater circuit disruption and forgetting of prior capabilities, whereas RL preserves a larger fraction of the base circuit at the cost of slower task adaptation. These findings suggest that circuit preservation may help explain why RL is more robust to catastrophic forgetting. We released our code here: https://github.com/rl-sft-circuit-research/differential-circuit-vulnerability.

Jeanmely Rojas Nunez
Viraj Sawant
Nathan Allen
Nomgondalai Amgalanbaatar
Yannis Zongo
Vasu Sharma
Maheep Chaudhary


Reading Task Failure Off the Activations: A Sparse-Feature Audit of GPT-2 Small on Indirect Object Identification

Abstract: We report a small, reproducible audit of which sparse-autoencoder (SAE) features of GPT-2 small fire differently on failed versus successful trials of the Indirect Object Identification (IOI) task. On 300 prompts, GPT-2 small reaches 79.7% accuracy; 146 of the 24,576 features in the layer-8 residual-stream SAE release of Bloom (2024) clear a Holm-corrected significance threshold and 105 reach a large effect size (|Cohen's d| > 0.8). The strongest single correlate of failure -- feature 17,491, d=+2.93, Neuronpedia label 'cryptographic keys' -- is essentially silent except when the prompt's transferred object is 'the keys,' on which GPT-2 small fails 93.3% of the time vs. 7.5% on the other seven objects (Fisher exact p = 8.79 x 10^-33). We put this correlate through three controls that a mechanistic claim should pass. (i) A causal ablation: zeroing feature 17,491 in the residual stream across all token positions of the 45 keys prompts does not restore accuracy (6.7% -> 4.4%); the feature is a correlate, not a sufficient cause at this layer. (ii) A representation baseline: a logistic regression on the raw 768-dimensional residual stream reaches 5-fold ROC AUC = 0.929, matching the top-100 SAE features (0.927); the SAE basis adds interpretability, not predictive power. (iii) A seed-robustness check: across five random seeds the keys-subset failure rate stays in 75.0--93.3% (the behavioural effect is real), but feature 17,491 is the top-|d| feature in only 1 of 5 runs. The methodological contribution is therefore the audit pipeline (cheap, model-agnostic, surfaces named correlates) rather than any single feature found through it. We release the code, the 300-prompt corpus, the 300x24,576 activation matrix, the ablation and baseline scripts, and the figures. The full pipeline runs on a laptop (Apple M3 Max, no discrete GPU).


SegCompass: Exploring Interpretable Alignment with Sparse Autoencoders for Enhanced Reasoning Segmentation

Abstract: While large language models provide strong compositional reasoning, existing reasoning segmentation pipelines fail to transparently connect this reasoning to visual perception. Current methods, such as latent query alignment, are end-to-end yet opaque "black boxes". Conversely, textual localization readout is merely readable, not truly interpretable, often functioning as an unconstrained post-hoc step. To bridge this interpretability gap, we propose SegCompass, an end-to-end model that leverages a Sparse Autoencoder (SAE) to forge an explicit, interpretable, and differentiable alignment pathway. Given an image-instruction pair, SegCompass first generates a chain-of-thought (CoT) trace. The core of our method is an SAE that maps both the CoT and visual tokens into a shared, high-dimensional sparse concept space. A query codebook selects salient concepts from this space, which are then spatially grounded by a slot mapper into a multi-slot heatmap that guides the final mask decoder. The entire model is trained jointly, unifying reinforcement learning for the reasoning path with standard segmentation supervision. This SAE-driven interface provides a "white-box" connection that is significantly more traceable than latent queries and more coherent than textual readouts. Extensive experiments on five challenging benchmarks demonstrate that SegCompass matches or surpasses state-of-the-art performance. Crucially, our visual and quantitative analyses show a strong correlation between the quality of the learned sparse concepts and final mask accuracy, confirming that SegCompass achieves superior results through its enhanced and inspectable alignment. Code is available at https://github.com/ZhenyuLU-Heliodore/SegCompass.

Zhenyu Lu
Liupeng Li
Jinpeng Wang
Haoqian Kang
Yan Feng
Ke Chen
Yaowei Wang


From Correlation to Cause: A Five-Stage Methodology for Feature Analysis in Transformer Language Models

Abstract: We propose a five-stage methodology for causal feature analysis in transformer language models (probe design, feature extraction, causal validation, robustness testing, and deployment integration) and demonstrate it end-to-end on GPT-2 small performing the Indirect Object Identification (IOI) task. Activation patching recovers the canonical IOI circuit (layer-9 head 9 alone gives recovery +1.02). A sparse autoencoder recovers per-name selective features with effect sizes of 30 to 50 activation units. Causal validation finds these features specifically but only partially causal: ablating fifteen of them leaves the model accurate on 98% of prompts. Two NLA-inspired evaluations strengthen this picture: the fifteen selective features explain only 31% of activation variance versus the SAE's 99.7%, and selectivity ratio anticorrelates with causal force (r = -0.56). Robustness testing under three distribution shifts finds that the circuit transfers cleanly but feature ablation effects degrade substantially, exposing a gap between detection robustness and causal robustness. A cost-based deployment evaluation (assumed $50/FN, $0.42/FP, 2% error rate) finds an optimal monitor configuration yielding $8.96 per 1000 queries against a $1000 baseline, a 99.1% saving. Optimal composition strategy varies with cost ratio and base rate. The conjunction of stages produces findings no single stage would.


Steered Generation via Gradient-Based Optimization on Sparse Query Features

Abstract: Latent steering exploits internal representations of Large Language Models (LLMs) to guide generation, yet interventions on dense states can entangle distinct semantic features. In this paper, we investigate attention query activations as a high-fidelity site for precise control, hypothesizing that manipulating the attention mechanism itself offers sharper steerability than general state interventions. We introduce Prototype-Based Sparse Steering, a framework that applies Sparse Autoencoders (SAEs) specifically to query activations, to decompose them into interpretable features, then apply gradient-based optimization during inference to align the sparse representation with class prototypes of target behaviors. To validate this architectural insight, we first analyze the mechanism in Textualized Gridworld, a controlled environment for verifiable planning constraints. We demonstrate that optimizing sparse query features enables effective navigation of rigid planning requirements (i.e., safe vs. short paths), confirming the method's ability to satisfy objective rules. We then demonstrate the framework's versatility by training SAEs on a high-dimensional educational domain, where the framework steers the cognitive complexity of feedback (i.e., Bloom's Taxonomy). Our experiments establish that sparse query representations provide the necessary disentanglement for unified, interpretable control over both logical planning and stylistic nuance.


From Circuit Evidence to Mechanistic Theory: An Inductive Logic Approach

Abstract: Mechanistic interpretability produces circuit-level causal analyses of neural network behaviour, but discovered circuits often remain isolated experimental artefacts: there is no shared formal representation for what circuits compute, how they relate, or when two findings provide evidence for the same mechanism. This work provides a formal infrastructure for cumulative mechanistic science by treating circuit interpretation as inductive theory construction. Each circuit is characterised at two levels: a Causal Functional Signature (CFS), which grounds component behaviour in causal attribution evidence and token role profiles, and an architectural signature $τ_{\mathrm{arch}}$, learned by inductive logic programming (ILP) from scale-invariant structural predicates. Together, these constitute a formal coherence layer that makes mechanistic claims explicit, comparable via $θ$-subsumption, and portable across model scales. CFS reveals qualitatively distinct computational strategies across task types, including attention-mediated copying versus MLP-mediated binding. ILP signatures achieve substantially better structural separation than graph kernel and feature-vector baselines, and support principled transfer across model scales and architecture families.

Nura Aljaafari
Danilo S. Carvalho
Andre Freitas


Mechanistic Interpretability for Learning Assurance of a Vision-Based Landing System

Abstract: EASA's learning-assurance guidance requires data-driven aviation systems to build and monitor their own situation representation, yet for neural networks the technical means to provide such evidence remain an open problem. We address this gap for a vision-based aircraft landing system: we propose that a minimally assurable model must at least be shown to separate content from style in its own situation representation. Showing that the model's predictions then rely largely on the contentful representation components leads to a concrete assurance path. To demonstrate this assurance path on a concrete model we train a vision transformer model for runway keypoint regression on the LARDv2 dataset. The model, which acts as the subject for our assurance demonstration, produces per-patch embeddings that we decompose into interpretable atoms via K-SVD sparse dictionary learning. A qualitative visualization confirms that contentful atoms track task-relevant runway structure and stylistic atoms track domain-specific appearance, and the regression head is shown to place almost all of its linear weight on contentful atoms. We further build on the content/style separation and define out-of-model-scope (OOMS) detection, a novel runtime assurance approach directly monitoring the model's situation representation. OOMS monitoring is complementary to operational design domain and output-space out-of-distribution monitoring and addresses concrete requirements of the recent EASA guidance. By directly analyzing a model's situation representation both at test time and runtime, this work delivers the first concrete piece of the representation-level evidence that EASA learning-assurance guidance demands, and points to mechanistic interpretability as a practical building block of future aviation safety cases.

Romeo Valentin
Olivia Beyer Bruvik
Marc R. Schlichting
Mykel J. Kochenderfer


Learning fMRI activations dictionaries across individual geometries via optimal transport

Abstract: Dictionary learning is a powerful tool for creating interpretable representations. When applied to functional magnetic resonance imaging (fMRI) data, the resulting patterns of brain activity can be used for various downstream tasks, such as brain state classification or population-level analysis. However, a major challenge is the variability in brain geometry across individuals. This is usually addressed by projecting each individual brain geometry onto a common template, which removes subject-specific information. In this work, we introduce a novel approach to dictionary learning on fMRI data that explicitly accounts for this variability. We use the optimal transport-based Fused Gromov-Wasserstein (FGW) distance to compare graphs with different geometries and features. To address the challenge of computing multiple FGW distances for large graphs such as those arising from fMRI data, we rely on amortized optimization to learn a neural network that predicts an approximation of the optimal transport plans, which substantially reduces the computational cost. Additionally, we learn dictionary atoms that depend on the FGW trade-off parameter, which controls the balance between feature alignment and structural consistency. Numerical experiments on the HCP dataset demonstrate that the proposed approach captures different levels of geometric variability in the data and provides representations that preserve essential information.

Sonia Mazelet
Rémi Flamary
Bertrand Thirion


Spectral Integrated Gradients for Coarse-to-Fine Feature Attribution

Abstract: Integrated Gradients (IG) is a widely adopted feature attribution method that satisfies desirable axiomatic properties. However, the choice of integration path significantly affects the quality of attributions, and the standard straight-line path introduces all input features simultaneously, often accumulating noisy gradients along the way. To address this limitation, we propose Spectral Integrated Gradients, which constructs integration paths based on singular value decomposition (SVD) of the baseline-to-input difference. By progressively activating singular components from largest to smallest, SIG introduces global structure before fine-grained details, naturally following a coarse-to-fine progression. Through extensive evaluation across diverse image classification datasets, we demonstrate that SIG produces cleaner attribution maps with reduced noise and achieves improved quantitative performance compared to existing path-based attribution methods. Our code is available at https://github.com/leekwoon/sig/.

Soyeon Kim
Seongwoo Lim
Kyowoon Lee
Jaesik Choi


Aligned Training: A Parameter-Free Method to Improve Feature Quality and Stability of Sparse Autoencoders (SAE)

Abstract: 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.


Toy Combinatorial Interpretability Models Reveal Lottery Tickets in Early Feature Space

Abstract: The lottery ticket hypothesis posits that dense networks contain sparse subnetworks, ``winning tickets,'' that, when rewound to their initial weights and retrained in isolation, match the performance of the full model. We ask a more mechanistic question: what internal object does a winning ticket preserve? We work in a combinatorial, clause-structured toy setting that admits an interpretable feature-space representation with well-defined combinatorial distances between features. We show that winning tickets in weight space correspond to precursor locations in feature space that are already near, at initialization, to the final feature-channel codes. Dense SGD resolves these locations through structured selection: proximal locations either converge to final codes or are rejected, with rejection concentrated at more crowded neurons, implicating competition under superposition. A winning ticket is thus a family of compatible code locations that jointly balance proximity to final codes with low inter-feature interference. Sparse retraining often re-expresses the same clause/template family on a different row, so the preserved object is family-level rather than microscopic row identity. We validate this account with lightweight probes based on feature-space distance and motion; in our setting, these probes frequently outperform established weight-based ticket discovery methods in both accuracy and exact code recovery. Although these findings are grounded in a toy setting, they suggest that the lottery ticket structure is governed by hidden feature-space geometry rather than weight-space subnetwork identity.


Beyond Linear Superposition: Discovering Climate Features in AI Weather Models with KAN-SAE

Abstract: Deep learning weather prediction models achieve remarkable predictive skill yet remain largely opaque: we know little about how they represent physical climate phenomena internally. Mechanistic interpretability through Sparse Autoencoders (SAEs) offers a principled route to decomposing these representations, but existing SAEs assume strictly linear feature superposition - a constraint ill-suited for the highly nonlinear atmospheric dynamics encoded in modern transformers. We introduce KAN-SAE, a sparse autoencoder whose encoder replaces the standard ReLU with learnable per-feature B-spline activations drawn from Kolmogorov-Arnold Networks (KANs), allowing each latent dimension to develop its own nonlinear gating profile. Applied to Sonny, KAN-SAE discovers 975 alive features (vs. 566 for a linear baseline, a 72% improvement) with 20% lower inter-feature redundancy and comparable reconstruction fidelity. Without any climate supervision, KAN-SAE identifies an interpretable European heatwave feature spatially concentrated over western Europe, and a western Pacific typhoon tracker confirmed by causal steering experiments. Our results demonstrate that nonlinear activations are essential for mechanistic interpretability of deep learning weather prediction models, recovering climate features that remain invisible to linear baselines.


A Distributional View for Visual Mechanistic Interpretability: KL-Minimal Soft-Constraint Principle

Abstract: Most current paradigms in visual mechanistic interpretability (MI) remain confined to interpreting internal units of the vision model via heuristic methods (e.g., top-$K$ activation retrieval or optimization with regularization). In this work, we establish a theoretical distributional view for visual MI, which models the influence of a feature activation on the natural image distribution, thereby formulating a Kullback-Leibler (KL)-minimal optimization problem to model the MI task. Under this framework, statistical biases are identified within previous MI paradigms, which reveal that they may either be perceptually uninterpretable to humans (i.e., deviate from the natural image distribution), or mechanistically unfaithful to the vision models (i.e., unable to activate model features). To resolve the biases under the distributional view, we propose a model with a KL-minimal soft-constraint principle for visual MI that theoretically balances interpretability and faithfulness. We realize this principle via energy-guided diffusion posterior sampling. Extensive experiments validate the theoretical soundness of the proposed distributional view and demonstrate the practical effectiveness of our paradigm on the DINOv3 vision model.

Guancheng Zhou
Yisi Luo
Zhengfu He
Zhenyu Jin
Xuyang Ge
Wentao Shu
Deyu Meng
Xipeng Qiu


Mechanistically Interpretable Neural Encoding Reveals Fine-Grained Functional Selectivity in Human Visual Cortex

Abstract: A central goal in understanding human vision is to uncover the visual features that drive neuronal activity. A growing body of work has used artificial neural networks as encoding models to predict cortical responses to natural images, revealing the visual content that activates category-selective regions. However, existing approaches are largely correlational and treat the encoder as a black box, leaving open which image features drive each voxel's response. We introduce Mechanistically Interpretable Neural Encoding (MINE), a framework that opens this black box by applying mechanistic-interpretability tools to localize the features within natural images that drive millimeter-scale (voxel-level) activity. MINE predicts each voxel's response using language-aligned image representations, and produces semantically interpretable descriptions of the features critical for the voxel's activation. We further generalize these per-image features into per-voxel functional profiles. To validate the per-image descriptions, we show they are sufficient to generate images that elicit voxel responses matching the responses to the original images, more accurately than images generated from random or low-attribution controls. Moreover, counterfactually inserting or removing the predicted features from images shifts activation in the expected direction, providing causal evidence. Counterfactual editing guided by the per-voxel activation profiles produces even stronger activation shifts, indicating that the profiles faithfully capture each voxel's selectivity. Finally, we apply MINE to well-studied category-selective brain regions, showing it recovers their known categorical preferences while revealing fine-grained unique voxel structure within each region. Overall, our results establish mechanistic interpretability as a path to discover and causally validate fine-grained hypotheses about neural function.

Idan Daniel Grosbard
Mor Geva
Galit Yovel


AGOP-IxG: A Gradient Covariance Filter for Local Feature Attribution on Tabular Data, with a Controlled Benchmark

Abstract: Automated machine learning pipelines increasingly produce models whose predictions must be explained to end users, auditors, and downstream decision systems. The most widely used feature attribution methods (SHAP, Integrated Gradients, LIME) are typically chosen by convention rather than measured fidelity, because rigorous evaluation is impeded by the absence of ground-truth attribution on real data. We propose AGOP-IxG, a fast per-sample attribution method for tabular classifiers that pre-multiplies the per-sample gradient by a top-$K$ rank-truncated Average Gradient Outer Product matrix, and evaluate it against four widely-used baselines on a controlled tabular benchmark designed for AutoML practitioners. In Part 1, we construct three synthetic multi-class tabular tasks (linear, sparse nonlinear, interaction-based) where ground-truth attribution per sample is analytically or numerically derivable, and compare five methods: AGOP-IxG, SHAP (DeepExplainer), Integrated Gradients, InputXGradient, and LIME. AGOP-IxG leads on Spearman rank correlation and noise feature mass on all three synthetic datasets, and on top-$k$ precision on the interaction dataset. Across all settings, AGOP-IxG is approximately $350\times$ to $1{,}650\times$ faster than SHAP. In Part 2, we evaluate global faithfulness on Adult Income and Credit Card Default using the ROAR protocol; the methods cluster within $\sim 1.7\%$ relative AUC, consistent with AGOP-IxG being optimized for per-sample local attribution rather than global feature ranking.


Sparse Autoencoders enable Robust and Interpretable Fine-tuning of CLIP models

Abstract: Large-scale pre-trained vision-language models like CLIP demonstrate remarkable zero-shot performance across diverse tasks. However, fine-tuning these models to improve downstream performance often degrades robustness against distribution shifts. Recent approaches have attempted to mitigate this trade-off, but often rely on computationally expensive text-guidance. We propose a novel method for robust fine-tuning, SAE-FT, which operates only on the model's visual representations. SAE-FT regularizes changes to these representations by penalizing the addition and removal of semantically meaningful features identified by a Sparse Autoencoder trained on the pre-trained model. This constraint prevents catastrophic forgetting and makes the fine-tuning process interpretable, enabling direct analysis of semantic changes. SAE-FT is both mechanistically transparent and computationally efficient, matching or exceeding state-of-the-art performance on ImageNet and its associated distribution shift benchmarks. Code is publicly available at: https://github.com/Fabian-Mor/sae-ft.

Fabian Morelli
Arnas Uselis
Ankit Sonthalia
Seong Joon Oh


RoSHAP: A Distributional Framework and Robust Metric for Stable Feature Attribution

Abstract: Feature attribution analysis is critical for interpreting machine learning models and supporting reliable data-driven decisions. However, feature attribution measures often exhibit stochastic variation: different train--test splits, random seeds, or model-fitting procedures can produce substantially different attribution values and feature rankings. This paper proposes a framework for incorporating stochastic nature of feature attribution and a robust attribution metric, RoSHAP, for stable feature ranking based on the SHAP metric. The proposed framework models the distribution of feature attribution scores and estimates it through bootstrap resampling and kernel density estimation. We show that, under mild regularity conditions, the aggregated feature attribution score is asymptotically Gaussian, which greatly reduces the computational cost of distribution estimation. The RoSHAP summarizes the distribution of SHAP into a robust feature-ranking criterion that simultaneously rewards features that are active, strong, and stable. Through simulations and real-data experiments, the proposed framework and RoSHAP outperform standard single-run attribution measures in identifying signal features. In addition, models built using RoSHAP-selected features achieve predictive performance comparable to full-feature models while using substantially fewer predictors. The proposed RoSHAP approach improves the stability and interpretability of machine learning models, enabling reliable and consistent insights for analysis.

Lanxin Xiang
Liang Shi
Youhui Ye
Boyu Jiang
Dawei Zhou
Feng Guo


Exemplar Partitioning for Mechanistic Interpretability

Abstract: We introduce Exemplar Partitioning (EP), an unsupervised method for constructing interpretable feature dictionaries from large language model activations with $\sim 10^3\times$ fewer tokens than comparable sparse autoencoders (SAEs). An EP dictionary is a Voronoi partition of activation space, built by leader-clustering streamed activations within a distance threshold. Each region is anchored by an observed exemplar that serves as both its membership criterion and intervention direction; dictionary size is not prespecified, but determined by the activation geometry at that threshold. Because exemplars are observed rather than learned, dictionaries built from the same data stream are directly comparable across layers, models, and training checkpoints. We characterise EP as an interpretability object via targeted demonstrations of properties newly accessible through this construction, plus one head-to-head benchmark. In Gemma-2-2B, EP dictionary regions are interpretable and support causal interventions: refusal in instruction-tuned Gemma concentrates in a region whose exemplar ablation can collapse held-out refusal. Cross-checkpoint matching between base and instruction-tuned dictionaries separates the directions preserved through finetuning from those introduced by it. EP regions and Gemma Scope SAE features decompose activation space differently but agree on a shared core: $\sim$20% of EP regions match an SAE feature at $F_1 > 0.5$, and EP one-hot probes retain $\sim$97% of raw-activation probe accuracy at $\ell_0 = 1$. Nearest-exemplar distance provides a free out-of-distribution signal at inference. On AxBench latent concept detection at Gemma-2-2B-it L20, EP at $p_1$ reaches mean AUROC 0.881, +0.126 over the canonical GemmaScope SAE leaderboard entry and within 0.030 of SAE-A's 0.911, at $\sim 10^3\times$ less build compute.


From Weight Perturbation to Feature Attribution for Explaining Fully Connected Neural Networks

Abstract: Fully Connected Neural Networks (FCNNs) are often regarded as simple and intuitive architectures, yet they serve as the foundation for more complex models. Nonetheless, the lack of consensus on their interpretability continues to pose challenges, underscoring the enduring relevance of simpler, attribution-based approaches for understanding even the most advanced neural architectures. In this regard, we explore a novel idea for estimating feature attribution, by applying perturbation to the features' attached weights instead of their values. This method offers a fresh perspective aimed at mitigating common limitations in Occlusion techniques, such as Added Bias and Out-of-Distribution data. The application of this rule leads to the formation of a pair of novel attribution methods we call XWP and XWP_c. Founded on simple rules, our methods achieve competitive performance in identifying image signals for simple DNNs, competing with the most established attribution methods on standard baseline metrics. Our work thus contributes to the field of Explainability by introducing a robust framework that paves the way for addressing these long-standing vulnerabilities, and leads to more reliable and interpretable model explanations.

Thodoris Lymperopoulos
Denia Kanellopoulou


Exploring Geographic Relative Space in Large Language Models through Activation Patching

Abstract: The increased use of Large Language Models (LLMs) in geography raises substantial questions about the safety of integrating these tools across a wide range of processes and analyses, given our very limited understanding of their inner workings. In this extended abstract, we examine how LLMs process relative geographic space using activation patching, an emerging tool for mechanistic interpretability.

Stef De Sabbata
Rahul Baiju
Stefano Mizzaro
Kevin Roitero


Descriptive Collision in Sparse Autoencoder Auto-Interpretability: When One Explanation Describes Many Features

Abstract: Sparse autoencoders (SAEs) are now standard tools for decomposing language model activations into interpretable features, and automated interpretability pipelines routinely assign each feature a short natural-language explanation. Existing critiques of this practice focus on polysemanticity -- one feature with many meanings -- or on whether explanations predict activations. We identify a complementary, structurally distinct problem we call descriptive collision: many distinct SAE features admit the same explanation. Reanalyzing the largest publicly-available dataset of human-annotated SAE features (Marks et al., 2025), comprising 722 annotated features across Gemma 2 2B and Pythia 70M, we find that the mean annotation string is reused across 3.07 features; 82.1% of features share their annotation with at least one other feature; and the single most common annotation string ("plural nouns") labels 101 distinct features spanning 18 layers and four model components. Information-theoretically, the average annotation resolves only 70% of feature identity. We formalize a property called discrimination, prove that current detection-style auto-interpretability scoring is invariant to collision, and propose two complementary corrective metrics -- collision-adjusted detection and discrimination scoring -- that explicitly penalize explanations that fail to distinguish a feature from its neighbors. The collision problem is independent of, and additive with, previously identified failure modes of auto-interpretability; ignoring it inflates reported feature interpretability by a quantity equal to roughly one-third of the bits required to identify a feature.


Mechanistic Interpretability of EEG Foundation Models via Sparse Autoencoders

Abstract: EEG foundation models achieve state-of-the-art clinical performance, yet the internal computations driving their predictions remain opaque: a barrier to clinical trust. We apply TopK Sparse Autoencoders (SAEs) across three architecturally distinct EEG transformers: SleepFM, REVE, and LaBraM to extract sparse feature dictionaries from their embeddings. By grounding these features in a clinical taxonomy (abnormality, age, sex, and medication), we benchmark monosemanticity and entanglement across architectures. A single hyperparameter procedure, driven by an intrinsic dictionary health audit, transfers robustly across all three architectures. Via concept steering, we introduce a "target vs. off-target" probe area metric to quantify steering selectivity and reveal three operational regimes: selectively steerable, encoded but entangled, and non-encoded. This framework exposes critical representational failures: "wrecking-ball" interventions that collapse global model performance, and clinical entanglements, such as age-pathology confounding, where it is impossible to suppress one concept without corrupting the other. Finally, a spectral decoder maps these interventions back to the amplitude spectrum, translating latent manipulations into physiologically interpretable frequency signatures, such as pathological slow-wave suppression and $α$-band restoration.

William Lehn-Schiøler
Magnus Ruud Kjær
Rahul Thapa
Magnus Guldberg Pedersen
Anton Mosquera Storgaard
Nick Williams
Radu Gatej
Tue Lehn-Schiøler
Andreas Brink-Kjær
Sadasivan Puthusserypady
Sándor Beniczky
James Zou
Lars Kai Hansen


Deep Learning as Neural Low-Degree Filtering: A Spectral Theory of Hierarchical Feature Learning

Abstract: Understanding how deep neural networks learn useful internal representations from data remains a central open problem in the theory of deep learning. We introduce Neural Low-Degree Filtering (Neural LoFi), a stylized limit of gradient-based training in which hierarchical feature learning becomes an explicit iterative spectral procedure. In this limit, the dynamics at each layer decouple: given the current representation, the next layer selects directions with maximal accessible low-degree correlation to the label. This yields a tractable surrogate mechanism for deep learning, together with a natural kernel-space interpretation. Neural LoFi provides a mathematically explicit framework for studying multi-layer feature learning beyond the lazy regime. It predicts how representations are selected layer by layer, explains how emergence of concepts arises with given sample complexity,and gives a concrete mechanism by which depth progressively constructs new features from old ones through low-degree compositionality. We complement the theory with mechanistic experiments on fully connected and convolutional architectures, showing that Neural LoFi improves over lazy random-feature baselines, recovers meaningful structured filters, and predicts representations aligned with early gradient-descent feature discovery with real datasets.

Yatin Dandi
Matteo Vilucchio
Luca Arnaboldi
Hugo Tabanelli
Florent Krzakala


Feature Visualization Recovers Known Cortical Selectivity from TRIBE v2

Abstract: Brain encoder models predict cortical fMRI responses from the internal activations of pretrained vision and language networks, and are typically evaluated by held-out prediction accuracy. This is a useful signal for training but a poor one for interpretation: it tells us an encoder fits the data without telling us whether it has internalized the functional organization of the brain. We propose feature visualization -- gradient ascent on the encoder's predicted activation for a target region of interest (ROI) -- as a complementary interpretability technique, and apply it to TRIBE v2 composed with V-JEPA 2 (ViT-G, 40 layers), holding both frozen and synthesizing still images for seven regions spanning the ventral and dorsal visual hierarchies. Under identical hyperparameters, the probe recovers a visible progression of increasing spatial scale and feature complexity across V1 to V4, matching the ventral-stream hierarchy. It also produces three distinctive downstream regimes: radial "frozen-motion" streaks for the middle temporal area (MT) despite static-only optimization, face-like features for the fusiform face area (FFA), and consistent rectilinear line patterns for the parahippocampal place area (PPA). Optimized FFA stimuli drive the predicted region ~4x as much as a natural face photograph, consistent with feature visualization producing adversarial super-stimuli rather than canonical exemplars. The probe is simple, differentiable, and applicable to any brain encoder with a differentiable backbone, allowing for qualitative evaluation of brain encoders.


Mechanistic Interpretability of ASR models using Sparse Autoencoders

Abstract: Understanding the internal machinations of deep Transformer-based NLP models is more crucial than ever as these models see widespread use in various domains that affect the public at large, such as industry, academia, finance, health. While these models have advanced rapidly, their internal mechanisms remain largely a mystery. Techniques such as Sparse Autoencoders (SAE) have emerged to understand these mechanisms by projecting dense representations into a sparse vector. While existing research has demonstrated the viability of the SAE in interpreting text-based Large Language Models (LLMs), there are no equivalent studies that demonstrate the application of a SAE to audio processing models like Automatic Speech Recognizers (ASRs). In this work, a SAE is applied to Whisper, a Transformer-based ASR, training a high-dimensional sparse latent space on frame-level embeddings extracted from the Whisper encoder. Our work uncovers diverse monosemantic features across linguistic and non-linguistic boundaries, and demonstrates cross-lingual feature steering. This work establishes the viability of a SAE model and demonstrates that Whisper encodes a rich amount of linguistic information.

Dan Pluth
Zachary Nicholas Houghton
Yu Zhou
Vijay K. Gurbani


Qwen-Scope: Turning Sparse Features into Development Tools for Large Language Models

Abstract: Large language models have achieved remarkable capabilities across diverse tasks, yet their internal decision-making processes remain largely opaque, limiting our ability to inspect, control, and systematically improve them. This opacity motivates a growing body of research in mechanistic interpretability, with sparse autoencoders (SAEs) emerging as one of the most promising tools for decomposing model activations into sparse, interpretable feature representations. We introduce Qwen-Scope, an open-source suite of SAEs built on the Qwen model family, comprising 14 groups of SAEs across 7 model variants from the Qwen3 and Qwen3.5 series, covering both dense and mixture-of-expert architectures. Built on top of these SAEs, we show that SAEs can go beyond post-hoc analysis to serve as practical interfaces for model development along four directions: (i) inference-time steering, where SAE feature directions control language, concepts, and preferences without modifying model weights; (ii) evaluation analysis, where activated SAE features provide a representation-level proxy for benchmark redundancy and capability coverage; (iii) data-centric workflows, where SAE features support multilingual toxicity classification and safety-oriented data synthesis; and (iv) post-training optimization, where SAE-derived signals are incorporated into supervised fine-tuning and reinforcement learning objectives to mitigate undesirable behaviors such as code-switching and repetition. Together, these results demonstrate that SAEs can serve not only as post-hoc analysis tools, but also as reusable representation-level interfaces for diagnosing, controlling, evaluating, and improving large language models. By open-sourcing Qwen-Scope, we aim to support mechanistic research and accelerate practical workflows that connect model internals to downstream behavior.

Boyi Deng
Xu Wang
Yaoning Wang
Yu Wan
Yubo Ma
Baosong Yang
Haoran Wei
Jialong Tang
Huan Lin
Ruize Gao
Tianhao Li
Qian Cao
Xuancheng Ren
Xiaodong Deng
An Yang
Fei Huang
Dayiheng Liu
Jingren Zhou


AGOP as Explanation: From Feature Learning to Per-Sample Attribution in Image Classifiers

Abstract: The Average Gradient Outer Product (AGOP) governs feature learning in neural networks: the Neural Feature Ansatz states that weight Gram matrices at each layer align with the corresponding AGOP matrices computed over the training distribution. We ask a complementary question: can this same quantity serve as a post-hoc attribution method for explaining individual predictions? We introduce AGOP-Weighted: a novel attribution method that multiplies the per-sample gradient by sqrt(diag(M) / max diag(M)), a training-distribution prior that suppresses gradient noise and amplifies consistently important pixels -- a combination not present in any prior attribution method. We formalise two companion variants -- AGOP-Local (per-sample gradient, equivalent to VanillaGrad) and AGOP-Global (diag(M) directly as a zero-cost saliency map) -- and implement an efficient training-time accumulation hook; AGOP-Global then requires zero inference cost (disk lookup) while AGOP-Weighted requires only a single gradient pass. We conduct the first rigorous comparison of AGOP attribution against Integrated Gradients (IG), SmoothGrad, GradCAM, and VanillaGrad across two benchmarks with pixel-level ground truth: (i) the synthetic XAI-TRIS benchmark (four classification scenarios, 8x8 images, CNN8by8) and (ii) the photorealistic CLEVR-XAI benchmark (ResNet-18 fine-tuned from ImageNet). AGOP-Weighted achieves 44% higher mIoU than IG on linear tasks; AGOP-Global achieves 7x higher mIoU than IG on multiplicative tasks (where IG falls below random) at zero inference cost. Both findings generalise to ResNet-18 on CLEVR-XAI (+18% and +37% respectively). We further show that GradCAM fails on small-resolution images due to spatial resolution collapse, and that diag(M) quality improves monotonically throughout training even after classification accuracy has plateaued.