Learning Pseudo-Riemannian Manifolds for Heterophilic Graphs via Graph Signature

Graph Neural Networks (GNNs) operate under the implicit assumption that the underlying data manifold is Riemannian, where the metric tensor is strictly positive-definite. While effective for homophilic graphs, this inductive bias creates a fundamental geometric mismatch for heterophilic graphs, where edges often signify dissimilarity or structural repulsion. In this work, we propose a paradigm shift from learning on fixed manifolds to learning the manifold itself. We postulate that heterophilic graphs are naturally embedded in pseudo Riemannian manifolds endowed with an indefinite metric, allowing for negative squared distances to model repulsive interactions. To formalize this, we introduce the Graph Signature Index, a spectral invariant that diagnoses the geometric nature of a graph. This index enables our proposed Pseudo-Riemannian Attention Network (PRAT) to dynamically learn an indefinite metric tensor, effectively capturing both attractive and repulsive interactions. By unifying these opposing forces within a single framework, PRAT demonstrates how a subtle shift in the metric signature yields substantial performance gains on heterophilic benchmarks. Our analysis reveals that PRAT’s learned geometry emergently aligns with the spectral signature of the graph, validating our geometric hypothesis.