arXiv Machine Learning By Pedro C. Vieira, Viacheslav Borovitskiy, Pedro Ribeiro

Do Deep Ensembles Actually Capture Uncertainty in Graph Neural Networks?

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The paper examines whether deep ensembles effectively capture uncertainty in message‑passing graph neural networks. Across eight diverse datasets, ensembles only marginally outperform single models, mainly by reducing optimization noise rather than improving uncertainty estimates. The authors identify an epistemic collapse—independently trained networks converge to similar predictions—due to the smoothing bias of message passing, and provide a theoretical bound linking this collapse to graph topology and Dirichlet energy.

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