Graph Neural Network Training Systems: A Performance Comparison of Full-Graph and Mini-Batch

Graph Neural Networks (GNNs) have gained significant attention in recent years due to their ability to learn representations of graph-structured data. Two common methods for training GNNs are mini-batch training and full-graph training. Since these two methods require different training pipelines and systems optimizations, two separate classes of GNN training systems emerged, each tailored for one method. Works that introduce systems belonging to a particular category predominantly compare them with other systems within the same category, offering limited or no comparison with systems from the other category. Some prior work also justifies its focus on one specific training method by arguing that it achieves higher accuracy than the alternative. The literature, however, has incomplete and contradictory evidence in this regard. In this paper, we provide a comprehensive empirical comparison of representative full-graph and mini-batch GNN training systems. We find that the mini-batch training systems consistently converge faster than the full-graph training ones across multiple datasets, GNN models, and system configurations. We also find that minibatch training techniques converge to similar to or often higher accuracy values than full-graph training ones, showing that minibatch sampling is not necessarily detrimental to accuracy. Our work highlights the importance of comparing systems across different classes, using time-to-accuracy rather than epoch time for performance comparison, and selecting appropriate hyperparameters for each training method separately.