Despite strong average-case performance, deep learning models often exhibit systematic errors on specific population groups, known as error slices. Identifying these groups and the root causes of their failures is critical for model debugging and bias mitigation. However, existing error Slice Discovery Methods (SDMs) typically generate explanations disconnected from the model's inference process, thus only approximating the underlying error source and may be inaccurate. We address this limitation by leveraging Concept Bottleneck Models (CBMs), whose predictions are directly dependent on human-understandable semantic concepts. Since downstream task failures in CBMs commonly arise from concept mispredictions, concept representations provide a strong candidate for error slice identification, offering fine-grained explanations directly linked to the error source. Building on this insight, we introduce CB-SLICE, a concept-based SDM that groups samples with shared concept prediction failures and identifies the keyword concepts most responsible for each slice's failure mode. Across multiple benchmarks, we show that CB-SLICE outperforms state-of-the-art methods in uncovering well-known biases while providing richer and more faithful explanations of model errors.

Understanding the effects of interventions is central to scientific progress, with randomized controlled trials (RCTs) regarded as the gold standard for causal inference in many applied fields. However, RCTs are costly, time-consuming, and often constrained by ethical or practical limitations, motivating the need for causal methods able to draw conclusions from observational data. While such data is collected at ever larger scale, making its use for causal inference is often hindered by the fact that not all variables affecting treatment allocation and the outcome are observed - an issue known as unobserved confounding. In this paper, we introduce a new study design called confounder detection via treatment intent. The idea is to query a human expert who makes treatment decisions, and ask them to compare pairs of units proposed by a principled matching strategy, with the goal of eliciting unobserved variables that explain why treatment decisions differ. We provide a theoretical basis for such a procedure, ascertaining conditions under which such a study design may elicit unobserved confounders. Building on this newly established foundations, we study treatment effects of interventions in the intensive care unit (ICU). First, we show empirical evidence strongly indicating that electronic health records (EHRs) collected in ICUs are subject to unobserved confounding. By using clinical text notes as a proxy for physicians' knowledge and leveraging natural language processing, we provide a proof of concept for our methodology in a semi-synthetic environment with a known ground truth.

Protein-protein interactions (PPIs) govern nearly all cellular processes, yet computational methods for identifying binding partners typically produce ranked predictions without mechanistic justification. This creates a fundamental barrier to adoption because biologists cannot assess whether predictions reflect genuine biochemical insight or spurious correlations. We present \textbf{Protein Thoughts}, a framework that reformulates PPI discovery as an interpretable search problem with explicit reasoning. The system decomposes binding evidence into four biologically meaningful signals: sequence similarity reflecting evolutionary relationships, structural complementarity capturing geometric fit, interface balance, and chemical compatibility encoding residue-level interactions. Rather than collapsing these signals into an opaque score, we preserve their individual contributions through a transparent value function that enables both ranking and auditing. To navigate large candidate spaces efficiently, we introduce hypothesis-guided entropy-regularized Tree-of-Thoughts search. A fine-tuned language model generates search directives from embedding-derived features, classifying candidates as high-priority, exploratory, or skippable. These directives condition a Boltzmann policy that balances exploitation with entropy-driven exploration, while hypothesis-aware pruning prevents premature abandonment of promising candidates. For candidates exhibiting score disagreement, hypothesis-conditioned embedding-space flow matching transports protein embeddings toward the binder manifold. On the SHS148k benchmark, Protein Thoughts achieves mean best-binder rank of 11.2 versus 47.7 for an entropic tree search baseline, a 76% improvement, and for binding prediction the trained value function achieves $91.08 \pm 0.19$ Micro-F1, outperforming existing PPI methods on the same dataset.

The main XAI attribution methods for deep neural networks -- GradCAM, SHAP, LIME, Integrated Gradients -- operate on separate theoretical foundations and are not formally comparable. We present GRALIS (Gradient-Riesz Averaged Locally-Integrated Shapley), a mathematical framework establishing a representation theory for attributions: every additive, linear, and continuous attribution functional on L^2(Q,mu) admits a unique canonical representation (Q, w, Delta), proved necessary by the Riesz Representation Theorem. This class encompasses SHAP, IG, LIME and linearized GradCAM, but excludes nonlinear functionals such as standard GradCAM or attention maps. Seven formal theorems provide simultaneous guarantees absent in any individual method: (T1) necessary canonical form; (T2) exact completeness; (T3) Monte Carlo convergence O(1/sqrt(m))+O(1/k); (T4) exact Shapley Interaction Values; (T5) Hoeffding ANOVA decomposition; (T6) Sobol sensitivity generalization; (T7) multi-scale extension (MS-GRALIS) with minimum-variance weights. An algebraic appendix justifies the GRALIS-SIV correspondence via the Mobius transform without circularity. GRALIS satisfies 13.5/14 axiomatic properties vs. 2.5-6/14 for individual methods, including completeness, sensitivity, locality, order-k interactions and optimal multi-scale aggregation simultaneously. Preliminary validation on BreaKHis (1,187 histology images, DenseNet-121) reports deletion faithfulness AUC +0.015 (malignant), 96% class-conditional consistency, SAL = 0.762+/-0.109 and sparsity index 0.39. Extended comparison with baseline XAI methods is planned for a companion paper.

The functional ANOVA, or Hoeffding decomposition, provides a principled framework for interpretability by decomposing a model prediction into main effects and higher-order interactions. For independent inputs, this classical decomposition is explicit. It is closely connected to SHAP values, generalized additive models, and orthogonal polynomial expansions, and therefore constitutes a fundamental tool for additive explainability. In the more general and realistic dependent setting, however, obtaining a tractable representation and estimating the decomposition from data remain challenging. In this work, we address this problem for continuous inputs. By combining Hilbert space methods with the generalized functional ANOVA, we build an explicit decomposition Riesz Basis allowing to easily compute the decomposition. Our formulation recovers the classical independent case and its associated orthogonal decomposition. Building on this representation, we propose a simple but mighty algorithm to estimate the decomposition from a data sample in a model-agnostic setting and we compare it empirically with several state-of-the-art explanation methods, demonstrating the power of the approach.

Machine learning systems increasingly make life-changing decisions about individuals, such as loan approvals, hiring, and cheating detection, raising a pressing question: how can individuals respond to negative decisions made by these opaque systems? While explainable artificial intelligence (XAI) has largely focused on algorithmic recourse -- helping individuals change their features to obtain a desired outcome -- the parallel problem of algorithmic contestability -- helping individuals review and correct erroneous algorithmic decisions -- has received far less attention, despite its central ethical and legal importance. We trace this neglect to the absence of clear formal definitions and a systematic operationalization of contestability as an algorithmic problem. To address it, we propose an operational definition of contestability as a natural complement to recourse: contestability starts from the presumption that a decision may be incorrect and focuses on identifying evidence to challenge and potentially overturn it, whereas recourse assumes the decision is valid and instead provides pathways for changing it. We show that standard XAI explanations, such as counterfactuals, LIME, or Anchors, even when combined with human intuitions about decision continuity or monotonicity, reveal only errors in the neighborhood of the individual, but provide insufficient grounds for overturning the decision at hand. Going thus beyond traditional XAI, we identify three types of evidence warranting reversal according to the decision maker's own ethical standards: predictive multiplicity, incorrect feature values, and neglected overruling evidence. We argue that these render decisions normatively indefensible and thus successfully contestable. Finally, we analyze how existing EU legislation connects to our framework and argue that individuals already hold some legal rights to these forms of evidence.

We introduce the metagame, a conceptual framework for quantifying second-order interaction effects of model explanations. For any first-order attribution $ϕ(f)$ explaining a model $f$, we measure the directional influence of feature $j$ on the attribution of feature $i$, denoted as meta-attribution $φ_{j \to i}(f)$, by treating the attribution method itself as a cooperative game and computing its Shapley value. Theoretically, we prove that attributions hierarchically decompose into meta-attributions, and establish these as directional extensions of existing interaction indices. Empirically, we demonstrate that the metagame delivers insights across diverse interpretability applications: (i) quantifying token interactions in instruction-tuned language models, (ii) explaining cross-modal similarity in vision-language encoders, and (iii) interpreting text-to-image concepts in multimodal diffusion transformers.

Deep learning models for 12-lead electrocardiogram (ECG) analysis achieve high diagnostic performance but lack the intuitive interpretability required for clinical integration. Standard feature attribution methods are limited by the inherent difficulty in mapping abstract waveform fluctuations to physical anatomical pathologies. To resolve this, we propose a cross-modal method that projects feature attributions from high-performance 12-lead ECG models onto the CineECG 3D anatomical space. Our study reveals that while models trained directly on CineECG signals suffer from reduced accuracy and incoherent attributions, the proposed mapping mechanism effectively recovers clinically relevant feature rankings. Validated against a ground-truth dataset of 20 cases annotated by domain experts, the mapped explanations yield a Dice score of 0.56, significantly outperforming the 0.47 baseline of standard 12-lead attributions. These findings indicate that cross-modal averaging mapping effectively filters attribution instability and improves the localization of pathological features, combining the diagnostic expressiveness of standard ECG with the intuitive clarity of anatomical visualization.

Existing benchmarks for multi-hop question answering (QA) primarily evaluate models based on their ability to reason about entities and the relationships between them. However, there's a lack of insight into how these models perform in terms of both events and entities. In this paper, we introduce a novel semi-automatic question generation strategy by composing event structures from information extraction (IE) datasets and present the first Multi-hop Event-centric Question Answering (MEQA) benchmark. It contains (1) 2,243 challenging questions that require a diverse range of complex reasoning over entity-entity, entity-event, and event-event relations; (2) corresponding multi-step QA-format event reasoning chain (explanation) which leads to the answer for each question. We also introduce two metrics for evaluating explanations: completeness and logical consistency. We conduct comprehensive benchmarking and analysis, which shows that MEQA is challenging for the latest state-of-the-art models encompassing large language models (LLMs); and how they fall short of providing faithful explanations of the event-centric reasoning process.

The widespread deployment of Graph Neural Networks (GNNs) sparks significant interest in their explainability, which plays a vital role in model auditing and ensuring trustworthy graph learning. The objective of GNN explainability is to discern the underlying graph structures that have the most significant impact on model predictions. Ensuring that explanations generated are reliable necessitates consideration of the in-distribution property, particularly due to the vulnerability of GNNs to out-of-distribution data. Unfortunately, prevailing explainability methods tend to constrain the generated explanations to the structure of the original graph, thereby downplaying the significance of the in-distribution property and resulting in explanations that lack reliability. To address these challenges, we propose D4Explainer, a novel approach that provides in-distribution GNN explanations for both counterfactual and model-level explanation scenarios. The proposed D4Explainer incorporates generative graph distribution learning into the optimization objective, which accomplishes two goals: 1) generate a collection of diverse counterfactual graphs that conform to the in-distribution property for a given instance, and 2) identify the most discriminative graph patterns that contribute to a specific class prediction, thus serving as model-level explanations. It is worth mentioning that D4Explainer is the first unified framework that combines both counterfactual and model-level explanations. Empirical evaluations conducted on synthetic and real-world datasets provide compelling evidence of the state-ofthe-art performance achieved by D4Explainer in terms of explanation accuracy, faithfulness, diversity, and robustness. 1