MGNN: Graph Neural Networks Inspired by Distance Geometry Problem

Graph Neural Networks (GNNs) have emerged as a prominent research topic in the field of machine learning. Existing GNN models are commonly categorized into two types: spectral GNNs, which are designed based on polynomial graph filters, and spatial GNNs, which utilize a message-passing scheme as the foundation of the model. For the expressive power and universality of spectral GNNs, a natural approach is to improve the design of basis functions for better approximation ability. As for spatial GNNs, models like Graph Isomorphism Networks (GIN) analyze their expressive power based on Graph Isomorphism Tests. Recently, there have been attempts to establish connections between spatial GNNs and geometric concepts like curvature and cellular sheaves, as well as physical phenomena like oscillators. However, despite the recent progress, there is still a lack of comprehensive analysis regarding the universality of spatial GNNs from the perspectives of geometry and physics. In this paper, we propose MetricGNN (MGNN), a spatial GNN model inspired by the congruent-insensitivity property of classifiers in the classification phase of GNNs. We demonstrate that a GNN model is universal in the spatial domain if it can generate embedding matrices that are congruent to any given embedding matrix. This property is closely related to the Distance Geometry Problem (DGP). Since DGP is an NP-Hard combinatorial optimization problem, we propose optimizing an energy function derived from spring networks and the Multi-Dimensional Scaling (MDS) problem. This approach also allows our model to handle both homophilic and heterophilic graphs. Finally, we propose employing the iteration method to optimize our energy function. We extensively evaluate the effectiveness of our model through experiments conducted on both synthetic and real-world datasets. Our code is available at: https://github.com/GuanyuCui/MGNN.