mlr3mbo: Bayesian Optimization in R

We present mlr3mbo, a comprehensive and modular toolbox for Bayesian optimization in R. mlr3mbo supports single- and multi-objective optimization, multi-point proposals, batch and asynchronous parallelization, input and output transformations, and robust error handling. While it can be used for many standard Bayesian optimization variants in applied settings, researchers can also construct custom BO algorithms from its flexible building blocks. In addition to an introduction to the software, its design principles, and its building blocks, the paper presents two extensive empirical evaluations of the software on the surrogate-based benchmark suite YAHPO Gym. To identify robust default configurations for both numeric and mixed-hierarchical optimization regimes, and to gain further insights into the respective impacts of individual settings, we run a coordinate descent search over the mlr3mbo configuration space and analyze its results. Furthermore, we demonstrate that mlr3mbo achieves state-of-the-art performance by benchmarking it against a wide range of optimizers, including HEBO, SMAC3, Ax, and Optuna.

Analyzing Error Sources in Global Feature Effect Estimation

Global feature effects such as partial dependence (PD) and accumulated local effects (ALE) plots are widely used to interpret black-box models. However, they are only estimates of true underlying effects, and their reliability depends on multiple sources of error. Despite the popularity of global feature effects, these error sources are largely unexplored. In particular, the practically relevant question of whether to use training or holdout data to estimate feature effects remains unanswered. We address this gap by providing a systematic, estimator-level analysis that disentangles sources of bias and variance for PD and ALE. To this end, we derive a mean-squared-error decomposition that separates model bias, estimation bias, model variance, and estimation variance, and analyze their dependence on model characteristics, data selection, and sample size. We validate our theoretical findings through an extensive simulation study across multiple data-generating processes, learners, estimation strategies (training data, validation data, and cross-validation), and sample sizes. Our results reveal that, while using holdout data is theoretically the cleanest, potential biases arising from the training data are empirically negligible and dominated by the impact of the usually higher sample size. The estimation variance depends on both the presence of interactions and the sample size, with ALE being particularly sensitive to the latter. Cross-validation-based estimation is a promising approach that reduces the model variance component, particularly for overfitting models. Our analysis provides a principled explanation of the sources of error in feature effect estimates and offers concrete guidance on choosing estimation strategies when interpreting machine learning models.

CASHomon Sets: Efficient Rashomon Sets Across Multiple Model Classes and their Hyperparameters

Rashomon sets are model sets within one model class that perform nearly as well as a reference model from the same model class. They reveal the existence of alternative well-performing models, which may support different interpretations. This enables selecting models that match domain knowledge, hidden constraints, or user preferences. However, efficient construction methods currently exist for only a few model classes. Applied machine learning usually searches many model classes, and the best class is unknown beforehand. We therefore study Rashomon sets in the combined algorithm selection and hyperparameter optimization (CASH) setting and call them CASHomon sets. We propose TruVaRImp, a model-based active learning algorithm for level set estimation with an implicit threshold, and provide convergence guarantees. On synthetic and real-world datasets, TruVaRImp reliably identifies CASHomon sets members and matches or outperforms naive sampling, Bayesian optimization, classical and implicit level set estimation methods, and other baselines. Our analyses of predictive multiplicity and feature-importance variability across model classes question the common practice of interpreting data through a single model class.

xplainfi: Feature Importance and Statistical Inference for Machine Learning in R

We introduce xplainfi, an R package built on top of the mlr3 ecosystem for global, loss-based feature importance methods for machine learning models. Various feature importance methods exist in R, but significant gaps remain, particularly regarding conditional importance methods and associated statistical inference procedures. The package implements permutation feature importance, conditional feature importance, relative feature importance, leave-one-covariate-out, and generalizations thereof, and both marginal and conditional Shapley additive global importance methods. It provides a modular conditional sampling architecture based on Gaussian distributions, adversarial random forests, conditional inference trees, and knockoff-based samplers, which enable conditional importance analysis for continuous and mixed data. Statistical inference is available through multiple approaches, including variance-corrected confidence intervals and the conditional predictive impact framework. We demonstrate that xplainfi produces importance scores consistent with existing implementations across multiple simulation settings and learner types, while offering competitive runtime performance. The package is available on CRAN and provides researchers and practitioners with a comprehensive toolkit for feature importance analysis and model interpretation in R.

Structured Credal Learning

Real-world learning tasks often encounter uncertainty due to covariate shift and noisy or inconsistent labels. However, existing robust learning methods merge these effects into a single distributional uncertainty set. In this work, we introduce a novel structured credal learning framework that explicitly separates these two sources. Specifically, we derive geometric bounds on the total variation diameter of structured credal sets and demonstrate how this quantity decomposes into contributions from covariate shift and expected label disagreement. This decomposition reveals a gating effect: covariate modulates how much label disagreement contributes to the joint uncertainty, such that seemingly benign covariate shifts can substantially increase the effective uncertainty. We also establish finite-sample concentration bounds in a fixed covariate regime and demonstrate that this quantity can be efficiently estimated. Lastly, we show that robust optimization over these structured credal sets reduces to a tractable discrete min-max problem, avoiding ad-hoc robustness parameters. Overall, our approach provides a principled and practical foundation for robust learning under combined covariate and label mechanism ambiguity.

Optimal Transport Group Counterfactual Explanations

Group counterfactual explanations find a set of counterfactual instances to explain a group of input instances contrastively. However, existing methods either (i) optimize counterfactuals only for a fixed group and do not generalize to new group members, (ii) strictly rely on strong model assumptions (e.g., linearity) for tractability or/and (iii) poorly control the counterfactual group geometry distortion. We instead learn an explicit optimal transport map that sends any group instance to its counterfactual without re-optimization, minimizing the group's total transport cost. This enables generalization with fewer parameters, making it easier to interpret the common actionable recourse. For linear classifiers, we prove that functions representing group counterfactuals are derived via mathematical optimization, identifying the underlying convex optimization type (QP, QCQP, ...). Experiments show that they accurately generalize, preserve group geometry and incur only negligible additional transport cost compared to baseline methods. If model linearity cannot be exploited, our approach also significantly outperforms the baselines.

Revisiting Active Learning under (Human) Label Variation

Access to high-quality labeled data remains a limiting factor in applied supervised learning. While label variation (LV), i.e., differing labels for the same instance, is common, especially in natural language processing, annotation frameworks often still rest on the assumption of a single ground truth. This overlooks human label variation (HLV), the occurrence of plausible differences in annotations, as an informative signal. Similarly, active learning (AL), a popular approach to optimizing the use of limited annotation budgets in training ML models, often relies on at least one of several simplifying assumptions, which rarely hold in practice when acknowledging HLV. In this paper, we examine foundational assumptions about truth and label nature, highlighting the need to decompose observed LV into signal (e.g., HLV) and noise (e.g., annotation error). We survey how the AL and (H)LV communities have addressed -- or neglected -- these distinctions and propose a conceptual framework for incorporating HLV throughout the AL loop, including instance selection, annotator choice, and label representation. We further discuss the integration of large language models (LLM) as annotators. Our work aims to lay a conceptual foundation for HLV-aware active learning, better reflecting the complexities of real-world annotation.

Overtuning in Hyperparameter Optimization

Hyperparameter optimization (HPO) aims to identify an optimal hyperparameter configuration (HPC) such that the resulting model generalizes well to unseen data. As the expected generalization error cannot be optimized directly, it is estimated with a resampling strategy, such as holdout or cross-validation. This approach implicitly assumes that minimizing the validation error leads to improved generalization. However, since validation error estimates are inherently stochastic and depend on the resampling strategy, a natural question arises: Can excessive optimization of the validation error lead to overfitting at the HPO level, akin to overfitting in model training based on empirical risk minimization? In this paper, we investigate this phenomenon, which we term overtuning, a form of overfitting specific to HPO. Despite its practical relevance, overtuning has received limited attention in the HPO and AutoML literature. We provide a formal definition of overtuning and distinguish it from related concepts such as meta-overfitting. We then conduct a large-scale reanalysis of HPO benchmark data to assess the prevalence and severity of overtuning. Our results show that overtuning is more common than previously assumed, typically mild but occasionally severe. In approximately 10% of cases, overtuning leads to the selection of a seemingly optimal HPC with worse generalization error than the default or first configuration tried. We further analyze how factors such as performance metric, resampling strategy, dataset size, learning algorithm, and HPO method affect overtuning and discuss mitigation strategies. Our results highlight the need to raise awareness of overtuning, particularly in the small-data regime, indicating that further mitigation strategies should be studied.

Semi-Implicit Variational Inference via Kernelized Path Gradient Descent

Semi-implicit variational inference (SIVI) is a powerful framework for approximating complex posterior distributions, but training with the Kullback-Leibler (KL) divergence can be challenging due to high variance and bias in high-dimensional settings. While current state-of-the-art semi-implicit variational inference methods, particularly Kernel Semi-Implicit Variational Inference (KSIVI), have been shown to work in high dimensions, training remains moderately expensive. In this work, we propose a kernelized KL divergence estimator that stabilizes training through nonparametric smoothing. To further reduce the bias, we introduce an importance sampling correction. We provide a theoretical connection to the amortized version of the Stein variational gradient descent, which estimates the score gradient via Stein's identity, showing that both methods minimize the same objective, but our semi-implicit approach achieves lower gradient variance. In addition, our method's bias in function space is benign, leading to more stable and efficient optimization. Empirical results demonstrate that our method outperforms or matches state-of-the-art SIVI methods in both performance and training efficiency.

Revisiting Unbiased Implicit Variational Inference

Recent years have witnessed growing interest in semi-implicit variational inference (SIVI) methods due to their ability to rapidly generate samples from complex distributions. However, since the likelihood of these samples is non-trivial to estimate in high dimensions, current research focuses on finding effective SIVI training routines. Although unbiased implicit variational inference (UIVI) has largely been dismissed as imprecise and computationally prohibitive because of its inner MCMC loop, we revisit this method and show that UIVI's MCMC loop can be effectively replaced via importance sampling and the optimal proposal distribution can be learned stably by minimizing an expected forward Kullback-Leibler divergence without bias. Our refined approach demonstrates superior performance or parity with state-of-the-art methods on established SIVI benchmarks.