Is Distance Matrix Enough for Geometric Deep Learning?

Graph Neural Networks (GNNs) are often used for tasks involving the 3D geometry of a given graph, such as molecular dynamics simulation. While incorporating Euclidean distance into Message Passing Neural Networks (referred to as Vanilla DisGNN) is a straightforward way to learn the geometry, it has been demonstrated that Vanilla DisGNN is geometrically incomplete. In this work, we first construct families of novel and symmetric geometric graphs that Vanilla DisGNN cannot distinguish even when considering all-pair distances, which greatly expands the existing counterexample families. Our counterexamples show the inherent limitation of Vanilla DisGNN to capture symmetric geometric structures. We then propose k -DisGNNs, which can effectively exploit the rich geometry contained in the distance matrix.