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Life sciences · Preprint
arXiv · October 5, 2026
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Graph neural networks (GNNs) are the standard tool for node representation learning and are increasingly used in high-stakes settings. Their message-passing backbone, however, can amplify topological bias, raising fairness concerns. We study group fairness at the level of downstream predictions for node classification, link prediction, and node regression, and bound the demographic parity gap for an arbitrary number of sensitive groups. Our node classification bound is provably no looser than the closest prior result. For link prediction, ours is the first bound on the parity gap of the deployed sigmoid-activated prediction rather than a pre-activation proxy, and for node regression we provide the first such bound. Across all three tasks, the analysis identifies two distinct sources of bias: the separation between group means and the within-group covariance of the final representations. Building on this insight, we embed fairness into propagation itself by augmenting the convex smoothing problem underlying APPNP with a convex group-mean constraint and a within-group covariance regularizer. Unfolding projected gradient descent on this problem yields FairProp, whose layers pair a propagation step with a closed-form projection and which provably converges linearly to the unique fair optimum. Experiments on three tasks show that FairProp, even with exact group-mean equalization alone, provides a strong inductive bias that achieves excellent fairness-utility trade-offs against strong baselines.