Papers › Dimensionality Reduction Meets Message Passing for Graph Node Embeddings
Dimensionality Reduction Meets Message Passing for Graph Node Embeddings
Krzysztof Sadowski, Michał Szarmach, Eddie Mattia
Graph Neural Networks (GNNs) have become a popular approach for various applications, ranging from social network analysis to modeling chemical properties of molecules. While GNNs often show remarkable performance on public datasets, they can struggle to learn long-range dependencies in the data due to over-smoothing and over-squashing tendencies. To alleviate this challenge, we propose PCAPass, a method which combines Principal Component Analysis (PCA) and message passing for generating node embeddings in an unsupervised manner and leverages gradient boosted decision trees for classification tasks. We show empirically that this approach provides competitive performance compared to popular GNNs on node classification benchmarks, while gathering information from longer distance neighborhoods. Our research demonstrates that applying dimensionality reduction with message passing and skip connections is a promising mechanism for aggregating long-range dependencies in graph structured data.
Code
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Tasks
Results from the paper archive 2025-07-28
| Task | Dataset | Model | Metric | Value | Rank at snapshot | Leaderboard | Report |
|---|---|---|---|---|---|---|---|
| Node Classification | PCAPass + XGBoost | Accuracy | 96.26 ± 0.02% | #10 of 16 | Archive leaderboard | report | |
| Node Property Prediction | ogbn-arxiv | PCAPass + XGBoost | Ext. data | No | #75 of 86 | Archive leaderboard | report |
| Node Property Prediction | ogbn-arxiv | PCAPass + XGBoost | Number of params | 0 | #75 of 86 | Archive leaderboard | report |
| Node Property Prediction | ogbn-arxiv | PCAPass + XGBoost | Test Accuracy | 0.7187 ± 0.0003 | #75 of 86 | Archive leaderboard | report |
| Node Property Prediction | ogbn-arxiv | PCAPass + XGBoost | Validation Accuracy | 0.7325 ± 0.0005 | #75 of 86 | Archive leaderboard | report |
| Node Property Prediction | ogbn-papers100M | PCAPass + LightGBM | Ext. data | No | #16 of 20 | Archive leaderboard | report |
| Node Property Prediction | ogbn-papers100M | PCAPass + LightGBM | Number of params | 0 | #16 of 20 | Archive leaderboard | report |
| Node Property Prediction | ogbn-papers100M | PCAPass + LightGBM | Test Accuracy | 0.6591 ± 0.0003 | #16 of 20 | Archive leaderboard | report |
| Node Property Prediction | ogbn-papers100M | PCAPass + LightGBM | Validation Accuracy | 0.6982 ± 0.0002 | #16 of 20 | Archive leaderboard | report |
| Node Property Prediction | ogbn-products | PCAPass + XGBoost | Ext. data | No | #39 of 64 | Archive leaderboard | report |
| Node Property Prediction | ogbn-products | PCAPass + XGBoost | Number of params | 0 | #39 of 64 | Archive leaderboard | report |
| Node Property Prediction | ogbn-products | PCAPass + XGBoost | Test Accuracy | 0.8115 ± 0.0002 | #39 of 64 | Archive leaderboard | report |
| Node Property Prediction | ogbn-products | PCAPass + XGBoost | Validation Accuracy | 0.9200 ± 0.0005 | #39 of 64 | 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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