Papers › Graph Neural Networks with Learnable Structural and Positional Representations
Graph Neural Networks with Learnable Structural and Positional Representations
Vijay Prakash Dwivedi, Anh Tuan Luu, Thomas Laurent, Yoshua Bengio, Xavier Bresson
Graph neural networks (GNNs) have become the standard learning architectures for graphs. GNNs have been applied to numerous domains ranging from quantum chemistry, recommender systems to knowledge graphs and natural language processing. A major issue with arbitrary graphs is the absence of canonical positional information of nodes, which decreases the representation power of GNNs to distinguish e.g. isomorphic nodes and other graph symmetries. An approach to tackle this issue is to introduce Positional Encoding (PE) of nodes, and inject it into the input layer, like in Transformers. Possible graph PE are Laplacian eigenvectors. In this work, we propose to decouple structural and positional representations to make easy for the network to learn these two essential properties. We introduce a novel generic architecture which we call LSPE (Learnable Structural and Positional Encodings). We investigate several sparse and fully-connected (Transformer-like) GNNs, and observe a performance increase for molecular datasets, from 1.79% up to 64.14% when considering learnable PE for both GNN classes.
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Tasks
Results from the paper archive 2025-07-28
| Task | Dataset | Model | Metric | Value | Rank at snapshot | Leaderboard | Report |
|---|---|---|---|---|---|---|---|
| Graph Regression | ZINC-500k | GatedGCN-LSPE | MAE | 0.090 | #18 of 36 | Archive leaderboard | report |
| Graph Regression | ZINC-500k | PNA-LSPE | MAE | 0.095 | #20 of 36 | Archive leaderboard | report |
| Graph Regression | ZINC-500k | SAN-LSPE | MAE | 0.104 | #23 of 36 | Archive leaderboard | report |
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.
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