Concept-based explanation of gene expression prediction from H&E images

Recent advances in pathology foundation models have enabled accurate prediction of spatial transcriptomics (ST) from routine H&E images. However, existing explainability methods for vision transformer (ViT)-based models are largely limited to local heatmaps and do not reveal how morphological concepts contribute to ST predictions. Here, we introduce an explainable framework that combines relevance propagation and concept discovery to link transcriptional programs to tissue morphology. We developed a ViT-based framework for virtual ST from H&E images that combines ViT-aware layer-wise relevance propagation with relaxed archetypal TopK sparse autoencoder-based concept discovery. This approach provides both local explanations and global insights into the morphological patterns associated with transcriptional programs. We applied the framework to colorectal cancer ST data from the HEST-1k cohort and evaluated its generalizability in TCGA COAD. Our architecture accurately predicts clinically relevant ST signatures and accompanying molecular phenotypes. Measured and predicted gene expression profiles reveal substantial spatial heterogeneity of the colorectal cancer subtypes iCMS2 and iCMS3 across a large number of samples. Spatially resolved and aggregated iCMS classification achieve weighted F1 scores of 0.872 and 0.819 (0.770 in TCGA COAD), respectively, and both stratify patient outcome. Beyond prediction, our framework establishes a relevance-based concept atlas linking molecular phenotypes to histopathological representations. Comparison of activation- with relevance-derived concepts demonstrates that relevances provide a more direct link between tissue morphology and downstream predictions. We establish a general strategy for concept-based explanation of spatial prediction, and our framework is readily applicable to a broad range of ViT-based pathology models.

Predicting Future Behaviors in Reasoning Models Enables Better Steering

Deployed large reasoning models (LRMs) often behave unexpectedly. Test-time steering controls LRM outputs by intervening on their hidden representations, but it can degrade output quality. We argue that prior steering work implicitly relies on internal features that detect behavior in already generated text. We show that these detection features are poor predictors of future behavioral outcomes, and thus not the natural intervention target. Instead, we train activation probes to predict future behavior likelihoods from intermediate reasoning steps. These probes predict the most likely behavior with 64%-91% accuracy, revealing a separate type of internal prediction features. Building on these prediction features, we introduce a text-level steering method, Future Probe Controlled Generation. FPCG samples multiple candidate sentences and chooses the best one according to a probe predicting the future behavior likelihood. This enables steering with almost no output quality degradation. FPCG also enables steering in several evaluations where activation steering fails. These results show that distinguishing detection and prediction features enables a more nuanced approach to controlling LRM behaviors.

Fast & Faithful Function Vectors

Function vectors (FVs) are task representations elicited during in-context learning that can be used to steer Large Language Models (LLMs). However, design choices in their formulation remain underexplored. In this work, we study the impact of varying FV definitions for instructions along two degrees of freedom: attention head selection and steering. For head selection, using gradient-based attributions with Layer-wise Relevance Propagation (LRP) substantially improves efficiency as well as accuracy. For FV steering, applying it in a distributed manner yields a higher accuracy compared to simple aggregation. Our code is publicly available.

Playing the network backward: A Game Theoretic Attribution Framework

Attribution methods explain which input features drive a model's prediction, making them central to model debugging and mechanistic interpretability. Yet backward attribution methods, including gradients, LRP, and transformer-specific rules, lack a shared framework in which to compare the underlying backward calculations. We introduce such a framework by recasting backward attribution as a two-player game on an extended network graph, building on Gaubert and Vlassopoulos' ReLU Net Game. Gradients and the full alpha-beta-LRP family arise as integrals over game trajectories under specific equilibria, so attribution maps become projections of trajectory distributions rather than the primary object. Desired explanation properties, such as localisation focus, robustness to input noise, or stable attention routing, can be specified as game-theoretic concepts, including policy regularization, risk aversion, and extended action sets, and translate directly into novel adaptations of the well-known backward rules. On ViT-B/16, one such selected adaptation of alpha-beta-LRP outperforms prior transformer-specific backward methods across all considered localisation metrics.

Contrastive Semantic Projection: Faithful Neuron Labeling with Contrastive Examples

Neuron labeling assigns textual descriptions to internal units of deep networks. Existing approaches typically rely on highly activating examples, often yielding broad or misleading labels by focusing on dominant but incidental visual factors. Prior work such as FALCON introduced contrastive examples -- inputs that are semantically similar to activating examples but elicit low activations -- to sharpen explanations, but it primarily addresses subspace-level interpretability rather than scalable neuron-level labeling. We revisit contrastive explanations for neuron-level labeling in two stages: (1) candidate label generation with vision language models (VLMs) and (2) label assignment with CLIP-like encoders. First, we show that providing contrastive image sets to VLMs yields candidate labels that are more specific and more faithful. Second, we introduce Contrastive Semantic Projection (CSP), an extension of SemanticLens that incorporates contrastive examples directly into its CLIP-based scoring and selection pipeline. Across extensive experiments and a case study on melanoma detection, contrastive labeling improves both faithfulness and semantic granularity over state-of-the-art baselines. Our results demonstrate that contrastive examples are a simple yet powerful and currently underutilized component of neuron labeling and analysis pipelines.

From Weights to Activations: Is Steering the Next Frontier of Adaptation?

Post-training adaptation of language models is commonly achieved through parameter updates or input-based methods such as fine-tuning, parameter-efficient adaptation, and prompting. In parallel, a growing body of work modifies internal activations at inference time to influence model behavior, an approach known as steering. Despite increasing use, steering is rarely analyzed within the same conceptual framework as established adaptation methods. In this work, we argue that steering should be regarded as a form of model adaptation. We introduce a set of functional criteria for adaptation methods and use them to compare steering approaches with classical alternatives. This analysis positions steering as a distinct adaptation paradigm based on targeted interventions in activation space, enabling local and reversible behavioral change without parameter updates. The resulting framing clarifies how steering relates to existing methods, motivating a unified taxonomy for model adaptation.

From Attribution to Action: A Human-Centered Application of Activation Steering

Explainable AI (XAI) methods reveal which features influence model predictions, yet provide limited means for practitioners to act on these explanations. Activation steering of components identified via XAI offers a path toward actionable explanations, although its practical utility remains understudied. We introduce an interactive workflow combining SAE-based attribution with activation steering for instance-level analysis of concept usage in vision models, implemented as a web-based tool. Based on this workflow, we conduct semi-structured expert interviews (N=8) with debugging tasks on CLIP to investigate how practitioners reason about, trust, and apply activation steering. We find that steering enables a shift from inspection to intervention-based hypothesis testing (8/8 participants), with most grounding trust in observed model responses rather than explanation plausibility alone (6/8). Participants adopted systematic debugging strategies dominated by component suppression (7/8) and highlighted risks including ripple effects and limited generalization of instance-level corrections. Overall, activation steering renders interpretability more actionable while raising important considerations for safe and effective use.

Structural Compactness as a Complementary Criterion for Explanation Quality

In the evaluation of attribution quality, the quantitative assessment of explanation legibility is particularly difficult, as it is influenced by varying shapes and internal organization of attributions not captured by simple statistics. To address this issue, we introduce Minimum Spanning Tree Compactness (MST-C), a graph-based structural metric that captures higher-order geometric properties of attributions, such as spread and cohesion. These components are combined into a single score that evaluates compactness, favoring attributions with salient points spread across a small area and spatially organized into few but cohesive clusters. We show that MST-C reliably distinguishes between explanation methods, exposes fundamental structural differences between models, and provides a robust, self-contained diagnostic for explanation compactness that complements existing notions of attribution complexity.

Concept-based explanations of Segmentation and Detection models in Natural Disaster Management

Deep learning models for flood and wildfire segmentation and object detection enable precise, real-time disaster localization when deployed on embedded drone platforms. However, in natural disaster management, the lack of transparency in their decision-making process hinders human trust required for emergency response. To address this, we present an explainability framework for understanding flood segmentation and car detection predictions on the widely used PIDNet and YOLO architectures. More specifically, we introduce a novel redistribution strategy that extends Layer-wise Relevance Propagation (LRP) explanations for sigmoid-gated element-wise fusion layers. This extension allows LRP relevances to flow through the fusion modules of PIDNet, covering the entire computation graph back to the input image. Furthermore, we apply Prototypical Concept-based Explanations (PCX) to provide both local and global explanations at the concept level, revealing which learned features drive the segmentation and detection of specific disaster semantic classes. Experiments on a publicly available flood dataset show that our framework provides reliable and interpretable explanations while maintaining near real-time inference capabilities, rendering it suitable for deployment on resource-constrained platforms, such as Unmanned Aerial Vehicles (UAVs).

Building Trust in PINNs: Error Estimation through Finite Difference Methods

Physics-informed neural networks (PINNs) constitute a flexible deep learning approach for solving partial differential equations (PDEs), which model phenomena ranging from heat conduction to quantum mechanical systems. Despite their flexibility, PINNs offer limited insight into how their predictions deviate from the true solution, hindering trust in their prediction quality. We propose a lightweight post-hoc method that addresses this gap by producing pointwise error estimates for PINN predictions, which offer a natural form of explanation for such models, identifying not just whether a prediction is wrong, but where and by how much. For linear partial differential equations, the error between a PINN approximation and the true solution satisfies the same differential operator as the original problem, but driven by the PINN's PDE residual as its source term. We solve this error equation numerically using finite difference methods requiring no knowledge of the true solution. Evaluated on several benchmark PDEs, our method yields accurate error maps at low computational cost, enabling targeted and interpretable validation of PINNs.