Abstract
Purpose: Uncertainty Quantification (UQ) has gained traction in an attempt to improve the interpretability and robustness of machine learning predictions. Specifically (medical) biosignals such as electroencephalography (EEG), electrocardiography (ECG), electrooculography (EOG), and electromyography (EMG) could benefit from good UQ, since these suffer from a poor signal-to-noise ratio, and good human interpretability is pivotal for medical applications. To determine how uncertainty estimation can be used for biosignal tasks, we investigate current methods, use cases, applications, evaluations, and uncertainty measures. Methods: In this paper, we systematically review the state of the art of applying Uncertainty Quantification to Machine Learning tasks in the biosignal domain. All works from Web of Science, Scopus, IEEE XPlore and PsycINFO that discuss uncertainty in Machine Learning on one of the aforementioned biosignals is included. Results: We present various methods, shortcomings, uncertainty measures and theoretical frameworks that currently exist in this application domain based on the 53 reviewed papers and related literature. We address misconceptions in the field, provide recommendations for future work, and discuss gaps in the literature in relation to diagnostic implementations as well as control for prostheses or brain-computer interfaces. Conclusion: Overall it can be concluded that promising UQ methods are available, but that research is needed on how people and systems may interact with an uncertainty-model in a (clinical) environment.
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Jul 22, 2026cs.LG
This Good Practice Guide presents work done in the QUMPHY project (Uncertainty quantification for machine learning models applied to photoplethysmography signals) that considered both machine learning and uncertainty quantification for problems which used photoplethysmography (PPG) signals from wearable devices as input. It provides high-level guidance on what types of machine learning model might be used and how different models compare when applied to both regression and classification tasks. It provides guidance on the implementation of different methods for uncertainty quantification, covering both model-dependent and model-independent techniques, and on the validation of the results provided by those methods. It also describes six benchmark problems together with pointers to different benchmark datasets for each problem. Software is described that can assist practitioners in implementing the methods described herein and there is a brief consideration of ethical issues. It concludes with a summary and recommendations.
P. Harris, C. Bench, M. Rinkevičius +6
Jun 17, 2026cs.LG
Uncertainty quantification (UQ) is essential for reliable decision-making in safety-critical applications in probabilistic machine learning. For regression problems, dominant scalar UQ approaches - notably, those based on proper scoring rules - measure uncertainty via pointwise predictive risk. This can lead to counterintuitive results when the target statistic is not the conditional expectation. We propose an alternative framework, in which uncertainty is characterised by the volume of the most probable subset of a distribution's support. QUEST (Quantifying Uncertainty via highest dEnSiTy regions) is a novel approach to UQ based on the concentration of Lebesgue measure at a distribution's peak(s), evaluated at one or more values of a robustness parameter
α. We establish connections between our measures and classical statistics from information theory and economics. We show that, unlike popular alternatives based on proper scoring rules, QUEST measures of epistemic and aleatoric uncertainty satisfy a set of axioms adapted from the UQ literature, including monotonicity under distributional spread and invariance to location shifts. Selective prediction benchmarks confirm that QUEST performs favourably against standard measures such as variance and differential entropy.
Sam Goring, Tom Kuipers, Nicola Paoletti +1
Aug 11, 2026cs.LG
Deep learning models have emerged as the standard computational tool for a wide range of applications in genomics. Yet, uncertainty quantification (UQ) -- and more specifically, the reliability of different uncertainty estimates in this domain -- has received little systematic attention. This work presents an empirical analysis of UQ in deep learning models, focusing on genomics applications. In a series of experiments, we contrast Deep Ensembles, Bayesian Neural Networks, and Monte Carlo-dropout methods. We assess their ability to quantify uncertainty in different scenarios, accounting for common dataset characteristics in two genomic application areas and modalities: sequence-to-activity models, and single-cell expression analysis. Our systematic comparison framework provides guidelines for the applicability and reliability of UQ methods in genomics, highlighting their strengths and limitations in different scenarios. We show that Bayesian Neural Networks are better at capturing uncertainty caused by strong class imbalance and out-of-distribution data in genomics, despite their computational disadvantages. Moreover, we show how uncertainty scores can be used to select high-quality predictions in protein-RNA interactions.
Sepideh Saran, Mahsa Ghanbari, Uwe Ohler