Mini-Batch Class Composition Bias in Link Prediction

arXiv:2604.25978v1 Announce Type: cross Abstract: Prior work on node classification has shown that Graph Neural Networks (GNNs) can learn representations that transfer across graphs, when underlying graph properties are shared. For a fixed graph, one would then expect GNNs trained for link prediction to learn a representation consistent with that learnt for node classification. We show this intuition does not hold in the general case. Instead, we find popular link prediction models can learn a trivial mini-batch dependent heuristic, enabled by batch-normalisation layers, to solve the edge classification task. When correcting for this, we observe increased alignment of the network representation with node-class relevant features, suggesting the network has learnt a graph representation that better aligns with the underlying graph's properties. Our findings suggest that standard link prediction training may be leading us to overestimate link predictors' ability to learn a generalised representation of a graph that is consistent across tasks.