Compact set-valued deep ensembling in multi-class classification

We introduce an efficient Bayesian deep ensemble method for predictive regression designed to enhance interpretability while maintaining competitive predictive performance and computational efficiency. Our method combines the statistical rigor of Bayesian inference with the scalability of deep ensembles, providing calibrated uncertainty estimates that enable its use not only for standalone prediction but also as a component within broader learning systems. To achieve these goals, our work relies on three key design components: (i) low-dimensional ensemble representation: predictions are expressed as a combination of a small number of trained neural predictors, enabling scalable inference whose cost depends on ensemble size rather than dataset size; (ii) closed-form Bayesian aggregation: ensemble predictions are combined using Bayesian linear regression, yielding interpretable posterior weights and calibrated uncertainty without approximate inference; and (iii) Independent ensemble training: multiple neural networks are trained separately, producing diverse predictive representations that improve robustness and uncertainty calibration. Empirical results on standard regression benchmarks demonstrate that the proposed approach achieves competitive predictive performance while maintaining reliable uncertainty estimates across settings.

While deep ensembles are widely considered to be the default method for uncertainty quantification in deep learning, their effectiveness for graph-structured data is often simply assumed based on successes in domains like computer vision. We investigate standard deep ensembles specifically for message-passing graph neural networks. Benchmarking across seven datasets representing varied tasks and complexities, we reveal that ensembles provide surprisingly little improvement over a single model. Instead, the observed marginal gains stem primarily from stabilizing optimization noise in point predictions rather than yielding meaningfully better uncertainty estimates. Through an aleatoric-epistemic decomposition, we identify epistemic collapse: independently trained networks consistently converge to overly similar predictions. Because disagreement is the fundamental mechanism through which ensembles capture epistemic uncertainty, this lack of diversity neutralizes their key advantage. Analyzing this phenomenon further, we suggest this collapse is driven by functional rather than weight-space convexity, where distinct parameter solutions induce almost identical behavior. Our results suggest that deep ensemble success does not seamlessly transfer to graph machine learning.

Parallel ensemble methods were compared on $56$ small-to-medium tabular classification tasks drawn from OpenML CC18. A set of ``best practice'' recommendations on the use of ensemble methods was derived from these observations. It was later validated on 28 additional tasks using TabArena's precomputed data, where the recommendation set significantly outperformed Single Best and matched or exceeded individual ensemble methods. Two key observations were made. First, Blending and Stacking are inconsistent, but their inconsistencies are independent and happen on different tasks. Second, while Hard Voting's probabilistic classification is rather weak, a consequence of using vote proportions as posterior estimates, Robust Soft Voting's probabilistic classification is particularly successful, especially in the multiclass case.