Papers › Learning Efficient Positional Encodings with Graph Neural Networks

Learning Efficient Positional Encodings with Graph Neural Networks

3 Feb 2025archive 2025-07-28

Charilaos I. Kanatsoulis, Evelyn Choi, Stephanie Jegelka, Jure Leskovec, Alejandro Ribeiro

Positional encodings (PEs) are essential for effective graph representation learning because they provide position awareness in inherently position-agnostic transformer architectures and increase the expressive capacity of Graph Neural Networks (GNNs). However, designing powerful and efficient PEs for graphs poses significant challenges due to the absence of canonical node ordering and the scale of the graph. In this work, we identify four key properties that graph PEs should satisfy: stability, expressive power, scalability, and genericness. We find that existing eigenvector-based PE methods often fall short of jointly satisfying these criteria. To address this gap, we introduce PEARL, a novel framework of learnable PEs for graphs. Our primary insight is that message-passing GNNs function as nonlinear mappings of eigenvectors, enabling the design of GNN architectures for generating powerful and efficient PEs. A crucial challenge lies in initializing node features in a manner that is both expressive and permutation equivariant. We tackle this by initializing GNNs with random node inputs or standard basis vectors, thereby unlocking the expressive power of message-passing operations, while employing statistical pooling functions to maintain permutation equivariance. Our analysis demonstrates that PEARL approximates equivariant functions of eigenvectors with linear complexity, while rigorously establishing its stability and high expressive power. Experimental evaluations show that PEARL outperforms lightweight versions of eigenvector-based PEs and achieves comparable performance to full eigenvector-based PEs, but with one or two orders of magnitude lower complexity.

Code

Repository list and official/mentioned flags are the archive's, frozen 2025-07-28. Reachability, where shown, is from one Syntology probe window (2026-09-16 to 2026-09-18); repositories not probed show nothing. GitHub stars are not tracked.

Code Syntology ran Syntology

Not run by Syntology. Nothing on this page verifies that the listed code works.

Tasks

1 archive task tag without a task page not shown.

Results from the paper archive 2025-07-28

Ranks are positions in the archive's leaderboards as they stood at the 2025-07-28 snapshot. Results published since then are not among these rows, so a rank here is not a current standing.

Report a problem or propose a change · a person checks every report against the paper or source before anything changes; decisions are listed on /corrections