Learning Pseudo-Riemannian Manifolds for Heterophilic Graphs via Graph Signature

Abstract

Several widely used families of Graph Neural Networks carry a positive-definite geometric prior. Graph convolution read as heat diffusion needs a positive semi-definite operator, hyperbolic models place features on positive-definite Riemannian manifolds, and dot-product and GAT-style attention scores use positive-definite inner products. On heterophilic graphs, where edges often signify dissimilarity or structural repulsion, that prior is a mismatch: no positive-definite form can assign a negative squared distance to a direction the labels separate. To measure the mismatch, we introduce the Graph Signature Index ($s_{\mathcal{G}}$), the inertia of a class-compatibility matrix built from label topology alone, and we prove that no value of the edge or node homophily index in $(0,1)$ rules out a negative eigenvalue. We then propose the Pseudo-Riemannian Attention Network (PRAT), whose attention logit is a signed squared pseudo-distance under a learnable diagonal metric initialized from $s_{\mathcal{G}}$. The design is diagnose-then-learn: the signature supplies a sign structure that unconstrained training keeps outside near-zero directions, and the projection learns the rest of the metric around it. Across fifteen node-classification benchmarks PRAT outperforms or matches the strongest heterophily-adapted models. A controlled ablation ties that performance to the sign structure itself: with architecture and protocol fixed, forbidding the metric to be indefinite costs accuracy on the graphs $s_{\mathcal{G}}$ marks as indefinite and leaves the others unchanged.