Beyond Boundary Noise: Aggregated Aleatoric Uncertainty Fails to Capture Presence Ambiguity in 3D Lung Nodule Segmentation

Uncertainty estimation is critical for the safe clinical deployment of deep learning in medical image segmentation, with aleatoric uncertainty theoretically designed to capture irreducible data ambiguity. However, whether entropy-based measures reflect clinically meaningful ambiguity, i.e. case-level disagreement about whether a pathology is present at all, remains poorly understood. Contrary to most prior work, which focused on pixel-wise boundary disagreement, we systematically evaluate how well aleatoric uncertainty captures presence ambiguity. Our evaluation spans 3D lung nodule segmentation across four architectures with Monte Carlo dropout and deep ensembles, on LIDC-IDRI and an external validation cohort (LNDb). We find that entropy-based uncertainty maps align with boundary noise and minor drawing variation but carry insufficient discriminative signal for presence ambiguity. In contrast, a lightweight supervised ambiguity head trained on frozen segmentation features substantially outperforms all entropy-aggregation-based baselines across architectures, metrics, and both cohorts, and matches or exceeds methods that explicitly model ambiguity under disagreement supervision (Probabilistic U-Net, Annotator-Confusion 3D-UNet). A qualitative feature-space analysis shows that presence ambiguity is already encoded in the frozen encoder features of pixel-wise-trained networks, only to be discarded by the segmentation output and its entropy aggregation. Our findings expose a fundamental mismatch between the theoretical promise of aleatoric uncertainty and its practical behavior, and suggest that practitioners should not rely on entropy-based uncertainty as a proxy for clinical ambiguity in safety-critical applications.

Tracing sources of epistemic uncertainty in deep learning predictions: homo- and hetero-scedastic linearized estimators

We adapt two classical statistical estimators for quantifying uncertainty to modern deep learning, in order to provide clearer insights into uncertainty attributable to two sources : aleatoric uncertainty, or locally scarce data. Our approach leverages recent advances in approximate Fisher Information Matrices, to enable scaling to actual architectures. Experimental results demonstrate how each test points is differentially impacted by both sources, highlighting the practical utility of our estimators in improving the robustness of real-world applications.

A Unified Risk View of Uncertainty: Posterior Risk for Disentanglement and Evaluation Beyond Proxies

Reliable uncertainty estimates are critical in safety-sensitive applications, where understanding the sources of predictive uncertainty is essential. This often requires disentangling epistemic uncertainty from aleatoric uncertainty, yet these uncertainty types are not defined consistently across the literature, making it difficult to assess whether a method produces accurate uncertainty estimates. Evaluation is further complicated by the fact that ground-truth epistemic uncertainty is typically unavailable. Existing benchmarks therefore mostly rely on proxy tasks such as out-of-distribution detection, which do not provide complete ground-truth uncertainty targets and offer limited insight into the structure and quality of uncertainty estimates. We propose a unified definition of uncertainty as pointwise posterior risk, the expected loss of a predictor under the distribution of plausible ground-truth functions given the data. This view combines Bayesian uncertainty over functions with estimator-dependent deviations from the posterior mean, capturing effects such as misspecification and optimization error. This formulation constitutes the foundation of a theory-backed benchmark that enables direct computation of oracle epistemic and aleatoric uncertainty using semi-synthetic datasets with real covariates and known generative processes. By avoiding proxy evaluations, the benchmark enables fine-grained analysis of uncertainty estimates. Empirically, we find that accurate prediction does not guarantee reliable uncertainty disentanglement. The benchmark reveals practically useful differences between methods, identifying approaches with meaningful alignment to oracle uncertainty targets while exposing sensitivity to datasets and modeling choices.

Subjective Risk Decomposition: A New View for Uncertainty Quantification

We present a novel viewpoint for uncertainty quantification. Uncertainty measures are not primitives, in need of axioms and argumentation, but instead consequences, of higher-level modelling decisions. We show how epistemic and aleatoric uncertainty measures can be derived via decomposition of a subjective risk, based on a strictly proper loss. Reverse cross-entropy provides a prominent example, where decomposition recovers the classic information-theoretic uncertainty terms. The same approach recovers numerous measures previously proposed across the UQ literature, providing them a common theoretical foundation. From a practical point of view, this suggests a new approach to UQ: given a modelling scenario and strictly proper loss, the corresponding epistemic and aleatoric terms are induced by the subjective-risk decomposition. We then extend our view to learning theory: we introduce and analyse subjective risk analogues of excess risk, approximation error, and estimation error, and identify the connections to UQ. We consider this a first step towards a full learning-theoretic framework for uncertainty quantification.

Interpretable Uncertainty Routing Separating Emotion Ambiguity from Distribution Shift in Facial Expression Recognition

Facial expression recognition (FER) is inherently ambiguous: human annotators frequently disagree, and models deployed in real environments face distribution shift. Crucially, these two conditions demand different downstream actions, as ambiguous in-distribution faces should be reported with their ambiguity whereas out-of-distribution inputs should be rejected. However, a single uncertainty score conflates the two. In this study, uncertainty decomposition into aleatoric and epistemic components for FER is investigated, and Uncertainty-Aware Routing (UAR), an inference-time routing mechanism that exploits the separation, is introduced. Specifically, aleatoric and epistemic uncertainties are obtained from a Deep Ensemble of fully fine-tuned DINOv2 models and are each validated against an independent external signal: aleatoric against human annotator disagreement, and epistemic against distribution shift induced by image corruptions. The proposed dual-validation protocol reveals that aleatoric recovers annotator disagreement with Spearman correlation 0.66 (95% CI: 0.64-0.68), and epistemic detects corruption-induced shifts, achieving average AUROC of 0.699 at the highest corruption severity. UAR retains approximately 1.8 times more ambiguous in-distribution faces than single-uncertainty routing at a matched out-of-distribution rejection rate. A strong label-distribution-learning baseline achieves comparable disagreement recovery but cannot separate ambiguity from shift and therefore cannot route, establishing that the value of decomposition lies in the separation enabling interpretable and differentiated action selection.

What Uncertainties Do We Need for Dynamical Systems?

The distinction between aleatoric and epistemic uncertainty has received considerable attention in machine learning research, mainly in the context of supervised learning but also in other settings such as generative modeling. In this paper, we offer a machine learning perspective on uncertainty modeling for dynamical systems, which has been studied much less so far. In particular, we ask: what uncertainties do we need for dynamical systems? We discuss sources of uncertainty, clarify their nature (aleatoric or epistemic), and consider how the objectives of representing and quantifying uncertainty vary across different tasks.

Credal Concept Bottleneck Models for Epistemic-Aleatoric Uncertainty Decomposition

Concept Bottleneck Models (CBMs) predict through human-interpretable concepts, but they typically output point concept probabilities that conflate epistemic uncertainty (reducible model underspecification) with aleatoric uncertainty (irreducible input ambiguity). This makes concept-level uncertainty hard to interpret and, more importantly, hard to act upon. We introduce CREDENCE (Credal Ensemble Concept Estimation), a CBM framework that decomposes concept uncertainty by construction. CREDENCE represents each concept as a credal prediction (a probability interval), derives epistemic uncertainty from disagreement across diverse concept heads, and estimates aleatoric uncertainty via a dedicated ambiguity output trained to match annotator disagreement when available. The resulting signals support prescriptive decisions: automate low-uncertainty cases, prioritize data collection for high-epistemic cases, route high-aleatoric cases to human review, and abstain when both are high. Across several tasks, we show that epistemic uncertainty is positively associated with prediction errors, whereas aleatoric uncertainty closely tracks annotator disagreement, providing guidance beyond error correlation. Our implementation is available at the following link: https://github.com/Tankiit/Credal_Sets/tree/ensemble-credal-cbm