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.

Conformal prediction has emerged as a widely used framework for constructing valid prediction sets in classification and regression tasks. In this work, we extend the split conformal prediction framework to hierarchical classification, where prediction sets are commonly restricted to internal nodes of a predefined hierarchy, and propose two computationally efficient inference algorithms. The first algorithm returns internal nodes as prediction sets, while the second relaxes this restriction, using the notion of representation complexity, yielding a more general and combinatorial inference problem, but smaller set sizes. Empirical evaluations on several benchmark datasets demonstrate the effectiveness of the proposed algorithms in achieving nominal coverage.

To generate accurate and reliable predictions, modern AI systems need to combine data from multiple modalities, such as text, images, audio, spreadsheets, and time series. Multi-modal data introduces new opportunities and challenges for disentangling uncertainty: it is commonly assumed in the machine learning community that epistemic uncertainty can be reduced by collecting more data, while aleatoric uncertainty is irreducible. However, this assumption is challenged in modern AI systems when information is obtained from different modalities. This paper introduces an innovative data acquisition framework where uncertainty disentanglement leads to actionable decisions, allowing sampling in two directions: sample size and data modality. The main hypothesis is that aleatoric uncertainty decreases as the number of modalities increases, while epistemic uncertainty decreases by collecting more observations. We provide proof-of-concept implementations on two multi-modal datasets to showcase our data acquisition framework, which combines ideas from active learning, active feature acquisition and uncertainty quantification.

Recently, machine learning (ML) has gained popularity in the early stages of drug discovery. This trend is unsurprising given the increasing volume of relevant experimental data and the continuous improvement of ML algorithms. However, conventional models, which rely on the principle of molecular similarity, often fail to capture the complexities of chemical interactions, particularly those involving activity cliffs (ACs) - compounds that are structurally similar but exhibit evidently different activity behaviors. In this work, we address two distinct yet related tasks: (1) activity cliff (AC) prediction and (2) drug-target interaction (DTI) prediction. Leveraging insights gained from the AC prediction task, we aim to improve the performance of DTI prediction through transfer learning. A universal model was developed for AC prediction, capable of identifying activity cliffs across diverse targets. Insights from this model were then incorporated into DTI prediction, enabling better handling of challenging cases involving ACs while maintaining similar overall performance. This approach establishes a strong foundation for integrating AC awareness into predictive models for drug discovery. Scientific Contribution This study presents a novel approach that applies transfer learning from AC prediction to enhance DTI prediction, addressing limitations of traditional similarity-based models. By introducing AC-awareness, we improve DTI model performance in structurally complex regions, demonstrating the benefits of integrating compound-specific and protein-contextual information. Unlike previous studies, which treat AC and DTI predictions as separate problems, this work establishes a unified framework to address both data scarcity and prediction challenges in drug discovery.

Scientific Machine Learning is a new class of approaches that integrate physical knowledge and mechanistic models with data-driven techniques for uncovering governing equations of complex processes. Among the available approaches, Universal Differential Equations (UDEs) are used to combine prior knowledge in the form of mechanistic formulations with universal function approximators, like neural networks. Integral to the efficacy of UDEs is the joint estimation of parameters within mechanistic formulations and the universal function approximators using empirical data. The robustness and applicability of resultant models, however, hinge upon the rigorous quantification of uncertainties associated with these parameters, as well as the predictive capabilities of the overall model or its constituent components. With this work, we provide a formalisation of uncertainty quantification (UQ) for UDEs and investigate important frequentist and Bayesian methods. By analysing three synthetic examples of varying complexity, we evaluate the validity and efficiency of ensembles, variational inference and Markov chain Monte Carlo sampling as epistemic UQ methods for UDEs.

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.

Conformal prediction, and split conformal prediction as a specific implementation, offer a distribution-free approach to estimating prediction intervals with statistical guarantees. Recent work has shown that split conformal prediction can produce state-of-the-art prediction intervals when focusing on marginal coverage, i.e., on a calibration dataset the method produces on average prediction intervals that contain the ground truth with a predefined coverage level. However, such intervals are often not adaptive, which can be problematic for regression problems with heteroskedastic noise. This paper tries to shed new light on how adaptive prediction intervals can be constructed using methods such as normalized and Mondrian conformal prediction. We present theoretical and experimental results in which these methods are investigated in a systematic way.

Multi-class classification methods that produce sets of probabilistic classifiers, such as ensemble learning methods, are able to model aleatoric and epistemic uncertainty. Aleatoric uncertainty is then typically quantified via the Bayes error, and epistemic uncertainty via the size of the set. In this paper, we extend the notion of calibration, which is commonly used to evaluate the validity of the aleatoric uncertainty representation of a single probabilistic classifier, to assess the validity of an epistemic uncertainty representation obtained by sets of probabilistic classifiers. Broadly speaking, we call a set of probabilistic classifiers calibrated if one can find a calibrated convex combination of these classifiers. To evaluate this notion of calibration, we propose a novel nonparametric calibration test that generalizes an existing test for single probabilistic classifiers to the case of sets of probabilistic classifiers. Making use of this test, we empirically show that ensembles of deep neural networks are often not well calibrated.

Out-of-sample prediction is the acid test of predictive models, yet an independent test dataset is often not available for assessment of the prediction error. For this reason, out-of-sample performance is commonly estimated using data splitting algorithms such as cross-validation or the bootstrap. For quantitative outcomes, the ratio of variance explained to total variance can be summarized by the coefficient of determination or in-sample $R^2$, which is easy to interpret and to compare across different outcome variables. As opposed to the in-sample $R^2$, the out-of-sample $R^2$ has not been well defined and the variability on the out-of-sample $\hat{R}^2$ has been largely ignored. Usually only its point estimate is reported, hampering formal comparison of predictability of different outcome variables. Here we explicitly define the out-of-sample $R^2$ as a comparison of two predictive models, provide an unbiased estimator and exploit recent theoretical advances on uncertainty of data splitting estimates to provide a standard error for the $\hat{R}^2$. The performance of the estimators for the $R^2$ and its standard error are investigated in a simulation study. We demonstrate our new method by constructing confidence intervals and comparing models for prediction of quantitative $\text{Brassica napus}$ and $\text{Zea mays}$ phenotypes based on gene expression data.

It is well known that accurate probabilistic predictors can be trained through empirical risk minimisation with proper scoring rules as loss functions. While such learners capture so-called aleatoric uncertainty of predictions, various machine learning methods have recently been developed with the goal to let the learner also represent its epistemic uncertainty, i.e., the uncertainty caused by a lack of knowledge and data. An emerging branch of the literature proposes the use of a second-order learner that provides predictions in terms of distributions on probability distributions. However, recent work has revealed serious theoretical shortcomings for second-order predictors based on loss minimisation. In this paper, we generalise these findings and prove a more fundamental result: There seems to be no loss function that provides an incentive for a second-order learner to faithfully represent its epistemic uncertainty in the same manner as proper scoring rules do for standard (first-order) learners. As a main mathematical tool to prove this result, we introduce the generalised notion of second-order scoring rules.