Graph Positional and Structural Encoder

Positional and structural encodings (PSE) enable better identifiability of nodes within a graph, as in general graphs lack a canonical node ordering. This renders PSEs essential tools for empowering modern GNNs, and in particular graph Transformers. However, designing PSEs that work optimally for a variety of graph prediction tasks is a challenging and unsolved problem. Here, we present the graph positional and structural encoder (GPSE), a first-ever attempt to train a graph encoder that captures rich PSE representations for augmenting any GNN. GPSE can effectively learn a common latent representation for multiple PSEs, and is highly transferable. The encoder trained on a particular graph dataset can be used effectively on datasets drawn from significantly different distributions and even modalities. We show that across a wide range of benchmarks, GPSE-enhanced models can significantly improve the performance in certain tasks, while performing on par with those that employ explicitly computed PSEs in other cases. Our results pave the way for the development of large pre-trained models for extracting graph positional and structural information and highlight their potential as a viable alternative to explicitly computed PSEs as well as to existing self-supervised pre-training approaches.