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As Artificial Intelligence models grow in complexity, interpretability has become an indispensable tool for understanding, debugging, and controlling their computations. However, interpretability lacks general theories to deductively design interpretable methods. This gap between theories and methods results in a fragmented literature and inconsistent evaluation protocols. To fill this gap, we introduce the Standard Interpretable Model (SIM), a general theory grounded in Lagrangian mechanics that enables the deductive design of interpretable methods. Specifically, the SIM summarises, in a set of premises, what interpretability is for a target user. From these premises, the SIM systematically derives interpretability symmetries and corresponding constraints, which shape the landscape of a Lagrangian whose minima correspond to optimal interpretable models. To reach the minima, one can either update the parameter values of an opaque model to make it more interpretable or compile constraints into an interpretable architecture. We empirically show that the SIM identifies and solves limitations of existing methods (including traditional, concept-based, and mechanistic interpretability), highlights underexplored research directions, and informs the design of core programming interfaces. Beyond being a research method, the deductive nature of the SIM offers pedagogical grounding for interpretability curricula and may shift the scientific community's perspective of a discipline that has long been fragmented.

Hybrid interpretable models combine a transparent component with a black-box model by assigning some examples to the former and deferring the rest to the latter. While this design enables flexible tradeoffs between accuracy and interpretability, it also raises a distinct procedural fairness concern: some demographic groups may systematically receive interpretable decisions, while others are disproportionately routed to a black box. We formalize this issue as Interpretability Coverage Disparity (ICD), a demographic-parity-style measure applied to the routing decision of hybrid interpretable models. Using tools from predictive multiplicity, we study ICD across four hybrid interpretable learning methods, three standard fairness benchmark datasets, and multiple sensitive attributes. Our experiments reveal substantial ICD in intermediate transparency regimes, where both the interpretable and black-box components are actively used. We further show that simple coverage-disparity constraints can significantly reduce ICD in exact hybrid learning methods, with marginal impact on accuracy and sparsity. In several settings, ICD mitigation also improves standard algorithmic fairness metrics. These results show that hybrid interpretable models should be audited not only for predictive fairness, but also for how they allocate interpretability across individuals and groups.

We observe that existing model interpretation methods generally ignore the baseline, and such neglect often results in imprecise or even incorrect interpretation. In this paper, we reformulate the task of model interpretation and the interpretation principles for model interpretation results to demonstrate the importance of the baseline. For the first time, we unify gradient-based methods, Integrated Gradients (IG), and Taylor expansion, clarify the relationships among the three, and explicitly identify the corresponding baseline for each method. This may have a significant impact on the further performance improvement of some gradient-based schemes. On this basis, we analyze the flaws and errors in related model interpretation methods (IG, LayerCAM, ODAM, Difference Map). We advocate evaluating the quality of model interpretation results precisely through the attribution error between the attribution result and the attribution target, rather than adopting flawed evaluation methods, such as those based on marginal-effect or the assumption of perfect model performance. We revise IG and develope a model interpretation method with a clear and reasonable baseline, achieving better results. Our method supports model interpretation based on features from any layer. Interpretation based on features from different layers are all reasonable, and the differences among these results reflect varying degrees of feature extraction at different feature extraction stages.

High-consequence subsurface decisions often rely on sparse data that permit competing geological interpretations. Determining consistency of these interpretations with the available observations remains challenging. We present a workflow that addresses this challenge by translating competing geologic interpretations into alternative priors and ranking them according to their consistency with hydraulic-head observations. A key step in this workflow is exploiting the broad knowledge of image-generation foundation models to transform nuanced geologic interpretations into data ready for computer modeling. For each interpretation, a text-to-image foundation model generates an ensemble of geologic images, and a separately trained variational autoencoder learns an interpretation-specific latent representation. A supervised inverse network maps head observations into this latent space, and the frozen decoder reconstructs an image that is mapped to a log-conductivity field. Steady-state flow simulations predict heads, and the aggregate normalized head error determines the ranking. We evaluate the framework using a synthetic benchmark based on the Johansen Formation with three interpretations of decreasing consistency with the reference geology. Across 595 test cases, the Precise & Accurate interpretation produces lower normalized errors than Accurate in 58.5% of cases and Mismatched in 82.5% of cases. Accurate outperforms Mismatched in 65.5% of cases. We then compare spatial representations of two published conceptual models of the Culebra Dolomite Member at the Waste Isolation Pilot Plant. The revised representation yields an aggregate normalized error of 7.598, compared with 8.595 for the original, consistent with the documented conceptual-model revision. The framework enables quantitative comparison of competing geological interpretations using available hydraulic observations.

How interpretable are the features of leading vision models? The question is increasingly pressing as these models move from research benchmarks into high-stakes deployments, yet existing methods cannot answer it reliably. We close this gap with a framework for measuring and comparing the human interpretability of vision models, built around two complementary psychophysics protocols: (1) localizability -- can an observer predict where a feature fires on a novel image? -- and (2) nameability -- can an observer accurately describe what the feature represents? Features are recovered via sparse autoencoders, and a chance-anchored scoring function places every model on a common scale. Applying the framework to six vision transformers -- two supervised ViTs and four foundation models (DINOv2, DINOv3, CLIP, SigLIP) -- we collected more than $15{,}000$ behavioral responses, analyzing the $13{,}400$ responses from the $377$ participants who passed our pre-specified quality checks. Foundation models are consistently less interpretable than their supervised counterparts, and the gap is not a capability tradeoff: interpretability does not correlate with downstream task performance on any benchmark we examine. What does correlate is the locality of a feature's activations and coarse-grained semantic alignment with humans -- models with focal activations and representations that reflect the world's broad categorical structure produce more interpretable features, whereas fine-grained perceptual alignment does not. The two protocols yield strongly correlated rankings and share the same predictors, establishing interpretability as an independent, measurable dimension of representation quality -- and, surprisingly, one on which every foundation model we tested falls below the supervised baselines that came before. Capability alone cannot close that gap; locality and coarse-grained alignment can.

We present a method for diagnosing interpretation in neural networks by identifying an input subspace where a proposed interpretation is highly faithful. Our method is particularly useful for causal-abstraction-style interpretability, where a high-level causal hypothesis is evaluated by interchange interventions. Rather than treating interchange intervention accuracy as a single global summary, we refine this framework by partitioning the input space into well-interpreted and under-interpreted regions according to pairwise interchange-intervention behavior. This turns causal abstraction from a purely global evaluation into a more diagnostic tool: it not only measures whether an interpretation works, but also reveals where it works, where it fails, and what distinguishes the two cases. This diagnostic view also provides practical heuristics for improving interpretations. By analyzing the structure of the well-interpreted and under-interpreted regions, we can identify missing distinctions in a high-level hypothesis, discover previously unmodeled intermediate variables, and combine complementary partial interpretations into a stronger one. We instantiate this idea as a simple four-step recipe and show that it yields informative error analyses across multiple causal abstraction settings. In a toy logic task, recursively applying the recipe recovers a high-level hypothesis from scratch. More broadly, our results suggest that partitioning the input space is a useful step toward more precise, constructive, and scalable mechanistic interpretability.

Machine Learning (ML) Engineering is a growing field that necessitates an increase in the rigor of ML development. It draws many ideas from software engineering and more specifically, from requirements engineering. Existing literature on ML Engineering defines quality models and Non-Functional Requirements (NFRs) specific to ML, in particular interpretability being one such NFR. However, a major challenge occurs in verifying ML NFRs, including interpretability. Although existing literature defines interpretability in terms of ML, it remains an immeasurable requirement, making it impossible to definitively confirm whether a model meets its interpretability requirement. This paper shows how ML provenance can be used to verify ML interpretability requirements. This work provides an approach for how ML engineers can save various types of model and data provenance to make the model's behavior transparent and interpretable. Saving this data forms the basis of quantifiable Functional Requirements (FRs) whose verification in turn verifies the interpretability NFR. Ultimately, this paper contributes a method to verify interpretability NFRs for ML models.

Harmful online communication often contains slang, coded terms, abbreviations, and community-specific expressions, which make messages difficult to interpret. This paper presents an exploratory study of interpretation difficulty in Discord chats related to cybercrime. We construct reference interpretations of purposefully selected difficult messages, which were reviewed by an expert. We then use them to evaluate human and large language model (LLM) interpretations under different context conditions. The results show that local context alone is often insufficient for humans, while external knowledge and extended conversational context substantially improve human interpretation. For LLMs, local context also improves interpretation, and the larger model performs better. We further conduct a qualitative error analysis and propose a preliminary classification of factors that make harmful chats difficult to interpret. These findings suggest that harmful-content analysis should treat interpretation as an evidence-integration problem, rather than as message-level classification alone.

We develop a framework for interpreting AI systems as agents, drawing on the philosophical tradition of radical interpretation and the tools of mechanistic interpretability. The core question is: given the computational facts about a system, how do we solve for its beliefs, desires, and meanings? This matters increasingly for safety. We want to be able to trust the systems we deploy, whether by understanding their goals or, more modestly, by reliably detecting deception. Interpretability researchers are building tools to read beliefs and desires off a model's internals, but there is no settled account of when such a tool has succeeded. This book supplies one. We propose criteria on both representationalist and interpretationist approaches, and tie each to tests current interpretability methods can carry out. A central lesson is that these attributions cannot be made piecemeal. Beliefs, desires, and the propositional structure they presuppose are jointly constrained, and a method that fixes one while measuring the others inherits whatever distortions that introduces. This holism becomes pressing for AI systems, which may not share the interpreter's concepts. However, it also provides leverage: a system's attitudes constrain its propositional structure, that structure constrains which attitudes can be attributed, and mechanistic interpretability can help us measure both.

Interpreting machine-learning models has attracted increasing attention, particularly in the physical sciences, where one often seeks to understand the underlying mechanisms rather than merely make predictions. Multiple linear regression is often regarded as an interpretable alternative to more complex models, such as deep neural networks, because its predictions are expressed as explicit weighted sums of input features. However, when input features are strongly correlated, namely in the presence of multicollinearity, the learned weights can exhibit large dataset-to-dataset fluctuations and oscillatory behavior across physically similar features, making their interpretation difficult or even impossible. Although the instability of the weights under multicollinearity is well known in statistics, its consequences for physical interpretation, in particular its connection to oscillatory weights across physically similar features, have not been systematically clarified. Here, we theoretically discuss the mechanism behind this loss of interpretability by analyzing the eigenmodes of the feature correlation matrix. We show that small-eigenvalue modes associated with multicollinearity amplify fluctuations in the weights and generate oscillatory patterns that do not necessarily reflect meaningful contributions. We test this theoretical picture numerically on physics datasets and show that Ridge regularization suppresses these unstable modes, although the resulting weights must still be interpreted with caution. We further confirm the generality of our findings beyond physics by analyzing a diverse collection of publicly available datasets. Our results clarify why, in the presence of multicollinearity, physical interpretation can remain difficult even for linear regression models.

Interpretability aims to explain the behavior of deep neural networks. Despite rapid growth, there is mounting concern that much of this work has not translated into practical impact, raising questions about its relevance and utility. This position paper argues that the central missing ingredient is not new methods, but evaluation criteria: interpretability should be evaluated by actionability--the extent to which insights enable concrete decisions and interventions beyond interpretability research itself. We define actionable interpretability along two dimensions--concreteness and validation--and analyze the barriers currently preventing real-world impact. To address these barriers, we identify five domains where interpretability offers unique leverage and present a framework for actionable interpretability with evaluation criteria aligned with practical outcomes. Our goal is not to downplay exploratory research, but to establish actionability as a core objective of interpretability research.

Agentic data science (ADS) systems are rapidly improving their capability to autonomously analyze, fit, and interpret data, potentially moving towards a future where agents conduct the vast majority of data-science work. However, current ADS systems use statistical tools designed to be interpretable by humans, rather than interpretable by agents. To address this, we introduce Agentic-imodels, an agentic autoresearch loop that evolves data-science tools designed to be interpretable by agents. Specifically, it develops a library of scikit-learn-compatible regressors for tabular data that are optimized for both predictive performance and a novel LLM-based interpretability metric. The metric measures a suite of LLM-graded tests that probe whether a fitted model's string representation is "simulatable" by an LLM, i.e. whether the LLM can answer questions about the model's behavior by reading its string output alone. We find that the evolved models jointly improve predictive performance and agent-facing interpretability, generalizing to new datasets and new interpretability tests. Furthermore, these evolved models improve downstream end-to-end ADS, increasing performance for Copilot CLI, Claude Code, and Codex on the BLADE benchmark by up to 73%

Recent text-guided image editing (TIE) models have achieved remarkable progress, however, many edited results still suffer from artifacts, unintended modifications, and suboptimal aesthetics. Although several benchmarks and evaluation methods have been proposed, most existing approaches rely on scalar scores and lack interpretability. This limitation largely stems from the absence of high-quality interpretation datasets for TIE and effective reward models to train interpretable evaluators. To address these challenges, we introduce ReasonEdit-22K, the first dataset that combines 22K edited images with 113K Chain-of-Thought (CoT) samples, along with 1.3M human judgments assessing these interpretations in terms of logicality, accuracy, and usefulness. Building upon this dataset, we propose RE-Reward, a multimodal large language model (MLLM)-based reward model designed to provide human-aligned feedback for evaluating interpretable reasoning in image editing. Furthermore, we develop ReasonEdit, which is trained using reward signals derived from RE-Reward and the Group Relative Policy Optimization (GRPO) algorithm to learn an interpretable evaluation model. Extensive experiments demonstrate that ReasonEdit achieves superior alignment with human preferences and exhibits strong generalization across public benchmarks. In addition, it is capable of generating high-quality interpretable evaluation text, enabling more transparent and trustworthy assessment for image editing. The code is available at https://github.com/IntMeGroup/ReasonEdit.

Heterogeneity across Collaborative Perception (CP) agents is a major challenge for emerging CP frameworks due to domain gaps from differing sensors, architectures, and training data. Prior works mitigate this challenge by aligning features in a unified space via model retraining or per-agent-type interpreters. These strategies (a) require access to neighbor configurations, (b) do not fully address real-time CP deployment, and (c) generalize poorly to unseen agents joining at run time. To overcome these challenges, we present PEARL, a Prompt-Embedding framework for Anonymous and Real-time Lightweight heterogeneous CP. PEARL supports multiple CP interpreters and selects one for a new-joining agent in real time using two lightweight, multi-scale interpreters trained in parallel: a sparse-detection (LWSD) interpreter that aligns salient regions for cooperative detection, and a dense, domain-invariant (LWDDI) interpreter that produces agent-invariant features for fast interpreter selection. Both interpreters use low-rank visual prompts to reduce computation, storage, and model complexity. Extensive experiments on simulated (OPV2V, V2XSet) and real (DAIR-V2X) datasets show that PEARL generalizes across simulated and real-world cooperative driving scenarios. Its real-time model-selection strategy yields an 8.2% Average Precision (AP) gain over a random-selection baseline while running in 1.67 ms on average. Although primarily designed for real-time CP, PEARL also outperforms state-of-the-art heterogeneous CP frameworks under traditional offline training by 5.6% AP on average while reducing communication cost by up to 34.7 times. Equally important, PEARL does not require sharing agents' configurations or model settings, thereby protecting information that may be proprietary or private. These results establish PEARL as a scalable and practical framework for heterogeneous collaborative perception.

In recent years, large-scale vision-language models have been driving a paradigm shift in intelligent remote sensing image interpretation. By incorporating textual semantic information, the cognitive expression, semantic understanding, and human-computer interaction capabilities of interpretation models have been significantly improved, achieving initial progress in the field of Synthetic Aperture Radar (SAR) image interpretation. However, SAR images are affected by factors such as coherent imaging mechanisms, complex scattering characteristics, speckle noise interference, and target-background coupling, resulting in complex and variable image features with significant uncertainties and specializations. Existing SAR vision-language models do not yet possess the step-by-step analysis, logical judgment, and self-correction capabilities of human experts, making it difficult to support reliable intelligent interpretation in complex scenarios. To address this issue, this paper proposes a large-scale reasoning model, FUSAR-R1, for intelligent interpretation of SAR images. The model first constructs explicit chain-of-thought reasoning data by simulating the interpretation process of human experts and uses this data to guide instruction learning, thereby endowing the model with basic reasoning capabilities. Subsequently, a reinforcement learning strategy is introduced to optimize the model's outputs based on inference results, enabling self-correction and more reliable reasoning. Experimental results demonstrate that FUSAR-R1 consistently outperforms existing multimodal large-scale models across various SAR interpretation tasks, including target detection, target counting and classification, and land-cover category recognition.

Existing feature-interpretation pipelines typically operate on uniformly sampled units or exhaustive feature sets, incurring massive costs on units irrelevant to target behaviors. To address this, we introduce the first CLT-native end-to-end pruning framework, PIE, which pioneers the paradigm of pruning first and interpreting later. PIE connects Pruning, automatic Interpretation, and interpretation Evaluation, establishing a comprehensive benchmarking environment to systematically measure behavioral fidelity and downstream interpretability under pruning. Within this framework, we adapt strong relevance baselines and propose Feature Attribution Patching (FAP), a patch-grounded attribution method that scores CLT features by aggregating gradient-weighted write contributions. Furthermore, we introduce FAP-Synergy, a systematic synergy-aware reranking procedure. We evaluate pruning using KL-divergence behavior retention and assess interpretation quality with FADE-style metrics across IOI and Doc-String datasets. Across budget constraints of K in {50, 100, 200, 400, 800}, our rigorous benchmarking reveals distinct operational regimes: while base FAP and adapted baselines perform robustly at relaxed budgets, FAP-Synergy excels in highly constrained, strict-budget regimes. Crucially, we demonstrate a practical "Effective Budget" advantage: on the IOI task for both Llama-3.2-1B and Gemma-2-2B, FAP-Synergy at K=50 functionally matches the behavioral fidelity of baseline circuits at K=75. Because downstream evaluation costs scale linearly per feature, Synergy effectively grants the pipeline 25 "free" features, achieving K=75 fidelity while reducing interpretation costs by 33%.

Image quality scoring and interpreting are two fundamental components of Image Quality Assessment (IQA). The former quantifies image quality, while the latter enables descriptive question answering about image quality. Traditionally, these two tasks have been addressed independently. However, image-quality-specific psychophysical studies suggest that these two tasks are conceptually interconnected: interpreting explicitly represents perceived quality attributes whereas scoring summarizes such evidence into an overall quality judgment. Thus, unifying these capabilities within a single model is both intuitive and logically coherent. In this paper, we propose Q-SiT (Quality Scoring and Interpreting joint Teaching), a unified framework that enables large multimodal models (LMMs) to learn both image quality scoring and interpreting simultaneously. We achieve this by transforming conventional IQA datasets into learnable question-answering datasets and incorporating human-annotated quality interpreting data for training. Furthermore, we introduce an efficient scoring & interpreting balance strategy, which first determines the optimal data mix ratio on lightweight LMMs and then maps this ratio to primary LMMs for fine-tuning adjustment. This strategy not only mitigates task interference and enhances cross-task knowledge transfer but also significantly reduces computational costs compared to direct optimization on full-scale LMMs. With this joint learning framework and corresponding training strategy, we develop Q-SiT, the first model capable of simultaneously performing image quality scoring and interpreting tasks, along with its lightweight variant, Q-SiT-mini. Experimental results demonstrate that Q-SiT achieves strong performance in both tasks with superior generalization IQA abilities, while Q-SiT-mini significantly reduces computational overhead while maintaining competitive performance.

We review the concepts of interpretability and explainability as they apply to machine learning in physics. We define interpretability as concerning the structural transparency of a model (the ability to understand or approximate its inner workings) and explainability as concerning the scientific content of a model (the ability to map it onto domain knowledge). We discuss the trade-offs each entails (interpretability vs. expressivity; explainability vs. adaptability), the contexts in which each is needed, and the intrinsic and post-hoc tools available for achieving them. Throughout, we emphasize that machine-learned models are subject to the same scientific questions as classical models, differing only in scale, and that interpretability and explainability are best understood as deliberate modeling choices rather than inherent properties. We also emphasize the importance of task specification and intervention plans as a core aspect of model design.

Wearable sensors continuously capture fine-grained multivariate time-series data, providing opportunities to model behavioural patterns associated with health outcomes. However, existing deep learning methods prioritise predictive accuracy over interpretability, limiting their application in health research. In this study, we present HealthCAT, a flexible framework that integrates an Encoder-only Transformer with an Attentive Class Activation Token (AttentiveCAT) to generate class-specific, time-step-level interpretations. These interpretations can be mapped back onto behavioural cycles that are relevant to the domain (e.g., time-of-day), supporting individual-level analysis of wearable sensor data. We evaluated HealthCAT using two real-world wearable sensor datasets (306 participants in total). HealthCAT outperformed deep learning baselines by up to 17% in F1-score and 12% in accuracy on both datasets ($p<0.05$). In masking experiments, the time steps identified by HealthCAT carried significantly more predictive value than random selection across all masking conditions ($p<0.05$), indicating that the identified time steps are predictively informative. By coupling predictive performance with validated time-step-level interpretability, HealthCAT moves wearable sensor analysis beyond aggregated metrics towards temporal patterns that support health monitoring, behavioural pattern analysis, and intervention design in health research. The significance of this work is that it enables accurate prediction of health indicators from wearable sensor data while providing insights into when and how physical activity patterns occur, rather than relying solely on aggregated summary measures.

Machine interpreting (MI), the live, real-time application of speech translation, has achieved remarkable progress on standard benchmarks, with some systems approaching human parity on textual fidelity. Yet the user experience remains far inferior to interpreter-mediated communication, revealing what we term the accuracy illusion: systems that appear accurate on paper but fail in practice to support smooth, goal-oriented interaction. This paper defines MI as a distinct subfield of speech translation, with its own characteristics and the need for evaluation methods grounded in communicative effectiveness rather than isolated fidelity metrics. Drawing on insights from interpreting studies, we identify critical dimensions of professional interpreting practice that are overlooked by current systems, and consolidate them into three interdependent design priorities for future MI: agency (context-sensitive initiative and repair), grounding (multimodal and discourse-level situational awareness), and experience (adaptive improvement through real interaction). Together, these priorities chart a path toward closing the usability gap and enabling systems that can sustain authentic multilingual communication in real time.

Large language models are usually interpreted through concepts that humans already possess: truthfulness, refusal, deception, personality, harmfulness, and related categories. This paper asks whether models may also represent and use distinctions for which no adequate human concept exists. We call such internal structures xeno-representations, and their study xeno-interpretability. We distinguish the human-interpretable semantic space from the xeno-semantic space: the region of model-native representations for which no adequate human conceptual counterpart is available. We show that the space of possible internal distinctions in an LLM is substantially larger than the space available through finite human descriptions. We then separate experimental identification from semantic interpretation: an internal representation may be reproducibly located, geometrically characterized, causally manipulated, and linked to downstream behaviour even when its semantic content cannot be adequately expressed in human terms. On this basis, we sketch an empirical programme to identify xeno-representations. We finally examine the implications for AI safety and multi-agent systems, where model-native representations may propagate and stabilize across interacting agents while remaining only partially visible through human-readable communication. Xeno-interpretability therefore shifts the aim of interpretability from finding human concepts inside models toward discovering and characterizing the representational structures that are native to the models themselves and might affect their behaviour in unpredictable ways.

Mechanistic interpretability has become the dominant lens for understanding frontier language models, as their inner workings are complex and inherently black boxes. To gain insights into these models, interpretable replacement networks (IRNs) are trained at all layers, exposing interpretable features through sparsely activated neurons. However, the faithfulness of an IRN is usually evaluated only empirically on clean data, and we show that even semantically minor input perturbations flip the dominant IRN features-and thus the human-understandable interpretation-across five open-weight model families (GPT-2 small, Gemma 2 2B, Gemma 3 1B, Llama 3.2 1B, R1-Distill-Qwen 1.5B). We propose the first formal verification framework for the faithfulness of an IRN, where reachability analysis certifies a sound upper bound of the faithfulness gap in adversarial scenarios. Moreover, we show that verification-aware training of IRNs substantially tightens this certified bound, restoring a feature-level interpretation that safety auditors can act on. Together, these results give, to the best of our knowledge, the first formal guarantees for mechanistic interpretability of large language models.

Existing benchmarks for electrocardiogram foundation models primarily evaluate downstream predictive performance, providing limited insight into whether their internal representations can be faithfully decomposed, clinically interpreted, or reproduced across independent analyses. We introduce ECG-InterpBench, a benchmark designed to systematically evaluate the interpretability of ECG foundation-model representations. ECG-InterpBench uses sparse autoencoders as standardized measurement instruments and matches their capacity across models to enable controlled comparisons. We evaluate six frozen ECG foundation models across five standardized encoder depths, five matched dictionary widths, and three random seeds, producing a 450-cell interpretability atlas comprising 75 exactly matched six-model comparison blocks. The benchmark evaluates complementary dimensions of representation interpretability, including sparse reconstruction fidelity, single-feature accessibility and coverage of 49 clinically meaningful ECG measurements, and cross-seed feature reproducibility. The evaluation further quantifies patient-sampling uncertainty, depth- and seed-dependent variation, and sensitivity to the sparsity parameterization. The benchmark reveals that ECG foundation models exhibit distinct interpretability profiles. A matched replication on MIMIC-IV-ECG confirms that reconstruction fidelity and clinical accessibility identify different leading models. The benchmark is accompanied by executable evaluation code, standardized manifests, cell-level metrics, and reproducibility audits. ECG-InterpBench complements performance-centered ECG benchmarks by providing a capacity-controlled and reproducible framework for comparing ECG foundation models across distinct dimensions of representation interpretability.

Model organisms (MOs) - language models trained to exhibit undesired or unnatural behaviours - are frequently used as testbeds for evaluating white-box interpretability techniques. Current MOs are typically constructed via post-hoc supervised fine-tuning (SFT) on behavioural transcripts or synthetic documents. Prior research has shown that interpretability methods can easily identify hidden behaviours in these MOs. However, recent work suggests that such post-hoc training methods may make interpretability unrealistically easy. We investigate this claim by constructing a suite of 54 $\verb|OLMo2-1B|$- and $\verb|gemma-3-1b-it|$-based MOs trained with seven different techniques, including standard post-hoc SFT, post-hoc DPO, and more realistic integration of MO data into the OLMo post-training DPO phase. We use these MO variants to benchmark activation oracles, activation steering, logit lens, and sparse autoencoders. Our findings show that (i) MO interpretability depends strongly on training objective, target behaviour, model architecture, and training data generation pipeline; (ii) substantial variance remains even after controlling for differences in the strength of target behaviour expression; and (iii) our more realistic $\textit{integrated training}$ often yields less interpretable MOs than standard post-hoc methods. Our results cast substantial doubt on the validity of current MOs as interpretability proxies.

Interpretable Mesomorphic Neural Networks (IMNs) offer a promising framework that combines the predictive power of deep neural networks with the interpretability of linear models. However, the original formulation lacks safeguards to ensure that the learned interpretations are in fact reliable. In particular, the network is free to concentrate all explanatory variance into a single weight of the linear output layer, achieving strong predictive performance while producing interpretations that are largely meaningless. Paradoxically, the L1 penalty proposed to encourage sparse solutions exacerbates this problem by further incentivizing such degenerate configurations. To address this vulnerability, we introduce Local Fidelity Regularization (LFR), a novel penalty term that prevents degenerate weight collapse by aligning the linear output weights with local data variations. This structural constraint guarantees faithful explanations and substantially improves the reliability of model interpretations. Furthermore, empirical evaluations across the OpenML benchmark suite demonstrate that LFR does not compromise accuracy for explainability; rather, it achieved improved AUROC over the unregularized IMN. By yielding results highly competitive with state-of-the-art black-box models, LFR provides the dual benefit of reliable interpretability and superior predictive performance. Source code and usage instructions are available at https://github.com/hugohammer/LFR-IMN.git.

Nucleotide sequence analysis is central to problems spanning regulatory genomics, evolutionary biology, and phenotype prediction. Classical bioinformatics methods extract interpretable sequence properties such as motifs and k-mer composition, but their flexibility is limited. In contrast, modern deep learning models can learn powerful predictive representations directly from raw sequences, yet their internal representations and decision mechanisms are difficult to inspect. Interpretable machine learning methods (e.g., sparse linear models and decision trees) provide human-understandable representations of predictive relationships but are not designed to operate directly on nucleotide sequences. Here, we introduce SeqMaestro, a machine learning framework that proposes biological hypotheses from nucleotide sequences using interpretable models. Our solution is centered around a two-layer interface that connects nucleotide sequences with the broader ecosystem of interpretable machine learning. SeqMaestro uses this interface to fit diverse combinations of interpretable models, feature representations, and extraction strategies, leveraging variability across transparent models to identify robust biological signals and richer predictive relationships than feature importance alone can provide. The system also supports data transformation and cleaning, model fitting, hyperparameter tuning, reliability analysis, and synthesis of results into a contextualized written report. By providing these capabilities through a no-code workflow, SeqMaestro is designed to make interpretable sequence analysis accessible to researchers without requiring extensive programming or machine learning expertise. SeqMaestro thereby provides an accessible route from nucleotide sequences to biological hypotheses.

T cell receptor (TCR)-epitope binding prediction is essential for understanding adaptive immunity and developing immunotherapies. Existing sequence- and structure-based models often generalize poorly to unseen epitopes and provide limited interpretability. Furthermore, the impact of generated structures on model learning remains unclear. We present TCR-SRIM, a structure-regularized interpretable-by-design model that combines protein language model embeddings with interpretable contact prototypes to capture residue-level TCR-epitope interactions. TCR-SRIM achieves state-of-the-art predictive performance and improved interpretation quality on the TCR-XAI benchmark. Using its inherent interpretability, we further evaluate the effect of generated structures on model learning. While structures predicted by AlphaFold3, TCRModel2, and tFold-TCR yield competitive performance, they lead to less accurate interaction patterns and reduced binding-site diversity than experimentally-resolved structures. Our results highlight limitations of current structure prediction models for TCR-epitope learning and demonstrate the value of interpretable-by-design models for studying generated biological structures.

Text-to-image person re-identification (TI-ReID) relies on natural-language text descriptions to retrieve top matching individuals from a gallery of reference images. While recent large vision-language models (VLMs) achieve strong retrieval performance, their decisions remain largely uninterpretable. Existing interpretability approaches in TI-ReID rely solely on slot-attention to highlight attended regions, but fail to reliably bind visual regions to semantically meaningful concepts, limiting interpretation to qualitative visualizations over a restricted vocabulary. This paper introduces InterPartAbility, an interpretable TI-ReID method that performs explicit part-wise matching and enables phrase-region grounding. Unlike parameter-heavy slot-attention methods that yield only qualitative interpretability, our open-vocabulary patch-phrase interaction module (PPIM) guides a standard TI-ReID model with concept-level phrases. Concept-based part phrases provide evidence that encourages the model to attend to the corresponding local image regions. InterPartAbility further leverages CLIP ViT self-attention to produce spatially concentrated patch activations aligned with each part-level phrase, yielding grounded explanation maps. Finally, a quantitative interpretability protocol for TI-ReID is introduced that extends current perturbation-based evaluation metrics into the TI-Reid domain. This includes a counterfactual region removal that measures retrieval degradation when top-ranked explanatory regions are removed. Empirical results on three challenging benchmarks show that InterPartAbility can achieve SOTA interpretability performance under these metrics, while sustaining competitive retrieval accuracy.

Background: Neurosymbolic (NeSy) artificial intelligence describes the combination of logic or rule-based techniques with neural networks. Compared to neural approaches, NeSy methods often possess enhanced interpretability, which is particularly promising for biomedical applications like drug discovery. However, no clear guidelines exist to assess the biological plausibility of model interpretations. Methods: To assess interpretability in the context of drug discovery, we devise a novel prediction task, called drug mechanism-of-action (MoA) deconvolution, with an associated, tailored knowledge graph (KG), MoA-net. We then develop the MoA Retrieval System (MARS), a NeSy approach for drug discovery which leverages logical rules with learned rule weights. Results: Using MARS' interpretable features alongside domain knowledge, we find that MARS and other NeSy approaches on KGs are susceptible to reasoning shortcuts, in which the prediction of true labels is driven by ``degree-bias'' rather than the domain-based rules. Subsequently, we demonstrate ways to identify and mitigate this. Thereafter, MARS achieves performance on par with current state-of-the-art models while producing model interpretations aligned with known MoAs. Conclusion: Through MARS, we showcase the novel task of computational MoA deconvolution. Our results emphasize the importance of using interpretable models, like NeSy ones, for applications in drug discovery. Specifically, by identifying and mitigating reasoning shortcuts, MARS MoA predictions which are biologically meaningful and, therefore, more reliable for downstream drug discovery research.

We observe a phenomenon that current algorithmic research in the field of explainable artificial intelligence primarily pursues better performance on several proxy metrics. On the one hand, these proxy metrics themselves are more or less flawed and cannot properly measure the quality of methods. On the other hand, metric-oriented research approaches often lead to the neglect of the rationality and interpretability of the methods themselves. Explainable artificial intelligence is abbreviated as XAI. The metric-driven research paradigm has resulted in a lack of interpretability of the relevant XAI methods themselves. Accordingly, there is a need for interpretability research on XAI methods, which can be playfully referred to as XXAI. This paper is one of our works on XXAI. This paper takes Generic Attention-model Explainability (GAE), a widely influential model interpretation method , or rather, XAI method that represents an important technical route, as the research object, and explores the real working mechanism and flaws of this method as well as the technical route it represents. Based on the conclusions of this study, it may be necessary to re-examine or verify GAE-related methods and their domain applications. We argue that GAE is an interpretation method that focuses on the attention process. After pointing out the working mechanism and flaws of GAE, we propose Cumulative Asset Holdings (CAH), a more reasonable Transformer interpretation method integrating both process-based and feature-based ideas from an economic zero-sum games perspective. In addition, it is worth noting that our method is applicable to models with special tokens, where existing methods may suffer from limitations. The model simplification research method and the analysis of additive operations adopted in this study may provide inspiration for other research works in XAI.