Assessment of Uncertainty Quantification in Universal Differential Equations

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.

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.

Heteroskedastic conformal regression

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.

The out-of-sample $R^2$: estimation and inference

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.

On Second-Order Scoring Rules for Epistemic Uncertainty Quantification

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.

Hyperparameter optimization in deep multi-target prediction

As a result of the ever increasing complexity of configuring and fine-tuning machine learning models, the field of automated machine learning (AutoML) has emerged over the past decade. However, software implementations like Auto-WEKA and Auto-sklearn typically focus on classical machine learning (ML) tasks such as classification and regression. Our work can be seen as the first attempt at offering a single AutoML framework for most problem settings that fall under the umbrella of multi-target prediction, which includes popular ML settings such as multi-label classification, multivariate regression, multi-task learning, dyadic prediction, matrix completion, and zero-shot learning. Automated problem selection and model configuration are achieved by extending DeepMTP, a general deep learning framework for MTP problem settings, with popular hyperparameter optimization (HPO) methods. Our extensive benchmarking across different datasets and MTP problem settings identifies cases where specific HPO methods outperform others.

On Calibration of Ensemble-Based Credal Predictors

In recent years, several classification methods that intend to quantify epistemic uncertainty have been proposed, either by producing predictions in the form of second-order distributions or sets of probability distributions. In this work, we focus on the latter, also called credal predictors, and address the question of how to evaluate them: What does it mean that a credal predictor represents epistemic uncertainty in a faithful manner? To answer this question, we refer to the notion of calibration of probabilistic predictors and extend it to credal predictors. Broadly speaking, we call a credal predictor calibrated if it returns sets that cover the true conditional probability distribution. To verify this property for the important case of ensemble-based credal predictors, we propose a novel nonparametric calibration test that generalizes an existing test for probabilistic predictors to the case of credal predictors. Making use of this test, we empirically show that credal predictors based on deep neural networks are often not well calibrated.

Set-valued prediction in hierarchical classification with constrained representation complexity

Set-valued prediction is a well-known concept in multi-class classification. When a classifier is uncertain about the class label for a test instance, it can predict a set of classes instead of a single class. In this paper, we focus on hierarchical multi-class classification problems, where valid sets (typically) correspond to internal nodes of the hierarchy. We argue that this is a very strong restriction, and we propose a relaxation by introducing the notion of representation complexity for a predicted set. In combination with probabilistic classifiers, this leads to a challenging inference problem for which specific combinatorial optimization algorithms are needed. We propose three methods and evaluate them on benchmark datasets: a na\"ive approach that is based on matrix-vector multiplication, a reformulation as a knapsack problem with conflict graph, and a recursive tree search method. Experimental results demonstrate that the last method is computationally more efficient than the other two approaches, due to a hierarchical factorization of the conditional class distribution.

On the Difficulty of Epistemic Uncertainty Quantification in Machine Learning: The Case of Direct Uncertainty Estimation through Loss Minimisation

Uncertainty quantification has received increasing attention in machine learning in the recent past. In particular, a distinction between aleatoric and epistemic uncertainty has been found useful in this regard. The latter refers to the learner's (lack of) knowledge and appears to be especially difficult to measure and quantify. In this paper, we analyse a recent proposal based on the idea of a second-order learner, which yields predictions in the form of distributions over probability distributions. While standard (first-order) learners can be trained to predict accurate probabilities, namely by minimising suitable loss functions on sample data, we show that loss minimisation does not work for second-order predictors: The loss functions proposed for inducing such predictors do not incentivise the learner to represent its epistemic uncertainty in a faithful way.

Well-calibrated prediction intervals for regression problems

Over the last few decades, various methods have been proposed for estimating prediction intervals in regression settings, including Bayesian methods, ensemble methods, direct interval estimation methods and conformal prediction methods. An important issue is the calibration of these methods: the generated prediction intervals should have a predefined coverage level, without being overly conservative. In this work, we review the above four classes of methods from a conceptual and experimental point of view. Results on benchmark data sets from various domains highlight large fluctuations in performance from one data set to another. These observations can be attributed to the violation of certain assumptions that are inherent to some classes of methods. We illustrate how conformal prediction can be used as a general calibration procedure for methods that deliver poor results without a calibration step.