Do Deep Ensembles Actually Capture Uncertainty in Graph Neural Networks?

ArXi:2605.22593v1 Announce Type: new 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.