arXiv subjects

Mira Jürgens

Publications and source records attributed to Mira Jürgens.

4 recordsLinked to original sources

arXiv2026

When should we trust the annotation? Selective prediction for molecular structure retrieval from mass spectra

Machine learning methods for identifying molecular structures from tandem mass spectra (MS/MS) have advanced rapidly, yet current approaches still exhibit significant error rates. In high-stakes applications such as clinical metabolomics and environmental screening, incorrect annotations can have serious consequences, making it essential to determine when a prediction can be trusted. In this work, we introduce a selective prediction framework for molecular structure retrieval from MS/MS spectra, separating low-risk predictions automatically from lower-confidence predictions. We formulate the problem within the risk-coverage tradeoff framework and systematically evaluate uncertainty quantification strategies at three levels: input-level distance in the learned representation, fingerprint-level uncertainty over predicted molecular fingerprint bits, and retrieval-level uncertainty over candidate rankings. We compare scoring functions including first-order confidence measures, aleatoric and epistemic uncertainty estimates from second-order distributions, as well as distance-based measures in the latent space. All experiments are conducted on the MassSpecGym benchmark. Our analysis reveals that while fingerprint-level uncertainty scores are poor proxies for retrieval success, retrieval-level total uncertainty provides the overall strongest rejection criterion, and first-order confidence measures are computationally inexpensive, strong baselines. We demonstrate that by applying distribution-free risk control via generalisation bounds, practitioners can specify a tolerable error rate and obtain a subset of annotations satisfying that constraint with high probability.

cs.LG↗

arXiv2026

Position: Epistemic uncertainty estimation methods are fundamentally incomplete

Identifying and disentangling sources of predictive uncertainty is essential for trustworthy supervised learning. We argue that widely used second-order methods that disentangle aleatoric and epistemic uncertainty are fundamentally incomplete. First, we show that unaccounted bias contaminates uncertainty estimates by overestimating aleatoric (data-related) uncertainty and underestimating the epistemic (model-related) counterpart, leading to incorrect uncertainty quantification. Second, we demonstrate that existing methods capture only partial contributions to the variance-driven part of epistemic uncertainty; different approaches account for different variance sources, yielding estimates that are incomplete and difficult to interpret. Together, these results highlight that current epistemic uncertainty estimates can only be used in safety-critical and high-stakes decision-making when limitations are fully understood by end users and acknowledged by AI developers.

cs.LG↗

arXiv2025

A calibration test for evaluating set-based epistemic uncertainty representations

The accurate representation of epistemic uncertainty is a challenging yet essential task in machine learning. A widely used representation corresponds to convex sets of probabilistic predictors, also known as credal sets. One popular way of constructing these credal sets is via ensembling or specialized supervised learning methods, where the epistemic uncertainty can be quantified through measures such as the set size or the disagreement among members. In principle, these sets should contain the true data-generating distribution. As a necessary condition for this validity, we adopt the strongest notion of calibration as a proxy. Concretely, we propose a novel statistical test to determine whether there is a convex combination of the set's predictions that is calibrated in distribution. In contrast to previous methods, our framework allows the convex combination to be instance dependent, recognizing that different ensemble members may be better calibrated in different regions of the input space. Moreover, we learn this combination via proper scoring rules, which inherently optimize for calibration. Building on differentiable, kernel-based estimators of calibration errors, we introduce a nonparametric testing procedure and demonstrate the benefits of capturing instance-level variability on of synthetic and real-world experiments.

cs.LG↗

arXiv2024

Is Epistemic Uncertainty Faithfully Represented by Evidential Deep Learning Methods?

Trustworthy ML systems should not only return accurate predictions, but also a reliable representation of their uncertainty. Bayesian methods are commonly used to quantify both aleatoric and epistemic uncertainty, but alternative approaches, such as evidential deep learning methods, have become popular in recent years. The latter group of methods in essence extends empirical risk minimization (ERM) for predicting second-order probability distributions over outcomes, from which measures of epistemic (and aleatoric) uncertainty can be extracted. This paper presents novel theoretical insights of evidential deep learning, highlighting the difficulties in optimizing second-order loss functions and interpreting the resulting epistemic uncertainty measures. With a systematic setup that covers a wide range of approaches for classification, regression and counts, it provides novel insights into issues of identifiability and convergence in second-order loss minimization, and the relative (rather than absolute) nature of epistemic uncertainty measures.

cs.AI↗