Neo-GNNs: Neighborhood Overlap-aware Graph Neural Networks for Link Prediction
Abstract
Graph Neural Networks (GNNs) have been widely applied to various fields for learning over graph-structured data. They have shown significant improvements over traditional heuristic methods in various tasks such as node classification and graph classification. However, since GNNs heavily rely on smoothed node features rather than graph structure, they often show poor performance than simple heuristic methods in link prediction where the structural information, e.g., overlapped neighborhoods, degrees, and shortest paths, is crucial. To address this limitation, we propose Neighborhood Overlap-aware Graph Neural Networks (Neo-GNNs) that learn useful structural features from an adjacency matrix and estimate overlapped neighborhoods for link prediction. Our Neo-GNNs generalize neighborhood overlap-based heuristic methods and handle overlapped multi-hop neighborhoods. Our extensive experiments on Open Graph Benchmark datasets (OGB) demonstrate that Neo-GNNs consistently achieve state-of-the-art performance in link prediction. Our code is publicly available at.
Benchmark Results
Tested on 4 datasets 9 baseline values reported too low
Tables show presented results in global context (best 3 papers + GCN + MLP).
OGB
| # | Model | Hits@50 ↑ | Paper |
|---|---|---|---|
| 1 | PROXI | 0.7650
±0.0027 | |
| 2 | OGB Leader | 0.7129
±0.0018 | |
| 3 | GIDN | 0.7096
±0.0055 | |
| 9 | GCN | 0.6621
±0.0033 best reported | best at pub: OGB (NeurIPS 2020) best today: On the Impact of Feature Heterophily on Link Prediction with Graph Neural Networks (NeurIPS 2024) |
| 20 | SEAL | 0.6474
±0.0043 best reported | best at pub: Labeling Trick: A Theory of Using Graph Neural Networks for Multi-Node Representation Learning (NeurIPS 2020) best today: Node Identifiers: Compact, Discrete Representations for Efficient Graph Learning (ICLR 2024) |
| 28 | SAGE | 0.5944
±0.0137 | |
| 33 | Neo-GNN (w/ GCN) | 0.5752
±0.0037 | This paper |
| 34 | GAT | 0.5643
±0.0086 best reported | best today: Asymmetric Learning for Graph Neural Network based Link Prediction (2023) |
| 41 | GraphSAGE | 0.5463
±0.0112 best reported | best at pub: OGB (NeurIPS 2020) |
| 49 | Adamic Adar | 0.5300 | This paper |
| 50 | Resource Allocation | 0.5289 | This paper |
| 62 | Common Neighbors | 0.5006 | This paper |
| 68 | Node2Vec | 0.4929
±0.0064 best reported | best at pub: Formatting Instructions for ICLR 2021 Conference Submissions (2020) best today: Asymmetric Learning for Graph Neural Network based Link Prediction (2023) |
| 77 | JK-Net | 0.4884
±0.0083 | This paper |
| 94 | MLP | 0.1998
±0.0096 | prev best: OGB (NeurIPS 2020) best today: Weak Models Can be Good Teachers: A Case Study on Link Prediction with MLPs (2025) Improvement within reported uncertainty; not highlighted. |
| 103 | Matrix Factorization | 0.3874
±0.0030 | This paper |
| # | Model | Hits@20 ↑ | Paper |
|---|---|---|---|
| 1 | ELGNN | 0.9777
±0.0037 | |
| 2 | GIDN | 0.9542 | |
| 3 | AGDN | 0.9538
±0.0094 | |
| 20 | SAGE | 0.6719
±0.0118 | |
| 21 | GAT | 0.6683
±0.0223 best reported | best today: Link Prediction with Untrained Message Passing Layers (2024) |
| 24 | GCN | 0.4460
±0.0887 | prev best: Equivariant and Stable Positional Encoding for More Powerful Graph Neural Networks (ICLR 2022) best today: Link Prediction with Untrained Message Passing Layers (2024) |
| 25 | Node2Vec | 0.6363
±0.0205 best reported | best at pub: Formatting Instructions for ICLR 2021 Conference Submissions (2020) best today: Link Prediction with Untrained Message Passing Layers (2024) |
| 26 | Neo-GNN | 0.6357
±0.0352 | This paper |
| 32 | JK-Net | 0.5798
±0.0688 | This paper |
| 38 | GraphSAGE | 0.5390
±0.0474 best reported | best at pub: OGB (NeurIPS 2020) best today: Ensemble Learning for Graph Neural Networks (2023) Difference within reported uncertainty; not counted as underperformance. |
| 43 | SEAL | 0.4974
±0.0239 best reported | best at pub: Labeling Trick: A Theory of Using Graph Neural Networks for Multi-Node Representation Learning (NeurIPS 2020) best today: Link Prediction with Untrained Message Passing Layers (2024) |
| 76 | Adamic Adar | 0.1861 | This paper |
| 78 | Matrix Factorization | 0.1792
±0.0357 | prev best: Adaptive Graph Diffusion Networks (2020) Improvement within reported uncertainty; not highlighted. |
| 79 | Common Neighbors | 0.1773 | This paper |
| 92 | Resource Allocation | 0.0623 | This paper |
| # | Model | Hits@100 ↑ | Paper |
|---|---|---|---|
| 1 | OGB Leader | 0.6524
±0.0150 | |
| 2 | PRB | 0.6347
±0.0175 | |
| 3 | LPFormer | 0.6332
±0.0063 | |
| 14 | SAGE | 0.5013
±0.0055 | |
| 17 | Resource Allocation | 0.4933 | This paper |
| 18 | Neo-GNN | 0.4913
±0.0060 | This paper |
| 19 | SEAL | 0.4880
±0.0316 best reported | best at pub: Labeling Trick: A Theory of Using Graph Neural Networks for Multi-Node Representation Learning (NeurIPS 2020) best today: Using Random Noise Equivariantly to Boost Graph Neural Networks Universally (2025) Difference within reported uncertainty; not counted as underperformance. |
| 23 | MLP | 0.4600 best reported | best at pub: OGB (NeurIPS 2020) best today: Efficient Link Prediction via GNN Layers Induced by Negative Sampling (2023) |
| 40 | Adamic Adar | 0.3245 | This paper |
| 43 | Matrix Factorization | 0.3229
±0.0094 best reported | best at pub: Adaptive Graph Diffusion Networks (2020) |
| 45 | GCN | 0.3084
±0.0178 best reported | best at pub: Formatting Instructions for ICLR 2021 Conference Submissions (2020) best today: Link Prediction with Untrained Message Passing Layers (2024) |
| 52 | Common Neighbors | 0.2765 | This paper |
| 57 | Node2Vec | 0.2230
±0.0080 best reported | best at pub: Formatting Instructions for ICLR 2021 Conference Submissions (2020) |
| 63 | GraphSAGE | 0.1655
±0.0240 best reported | best at pub: OGB (NeurIPS 2020) best today: Simplifying Subgraph Representation Learning for Scalable Link Prediction (2023) |
| 67 | JK-Net | 0.1140
±0.0204 | This paper |
| # | Model | MRR ↑ | Paper |
|---|---|---|---|
| 1 | CFG | 0.8997
±0.0015 | |
| 2 | SIEG | 0.8987
±0.0018 | |
| 3 | LPFormer | 0.8981
±0.0013 | |
| 8 | SEAL | 0.8767
±0.0032 best reported | best at pub: Labeling Trick: A Theory of Using Graph Neural Networks for Multi-Node Representation Learning (NeurIPS 2020) best today: Efficient Link Prediction via GNN Layers Induced by Negative Sampling (2023) |
| 11 | Neo-GNN | 0.8726
±0.0084 | This paper |
| 12 | GCN | 0.8479
±0.0024 | prev best: OGB (NeurIPS 2020) best today: On the Impact of Feature Heterophily on Link Prediction with Graph Neural Networks (NeurIPS 2024) Improvement within reported uncertainty; not highlighted. |
| 30 | SAGE | 0.8292
±0.0022 | |
| 32 | GraphSAGE | 0.8264
±0.0001 | prev best: OGB (NeurIPS 2020) Improvement within reported uncertainty; not highlighted. |
| 48 | Common Neighbors | 0.7620 | This paper |
| 49 | Resource Allocation | 0.7620 | prev best: Adaptive Graph Diffusion Networks (2020) |
| 50 | Adamic Adar | 0.7612 | prev best: Adaptive Graph Diffusion Networks (2020) |
| 59 | Node2Vec | 0.6141
±0.0011 best reported | best at pub: OGB (NeurIPS 2020) best today: Efficient Link Prediction via GNN Layers Induced by Negative Sampling (2023) |
| 61 | Matrix Factorization | 0.5308
±0.0419 | prev best: Adaptive Graph Diffusion Networks (2020) Improvement within reported uncertainty; not highlighted. |
| 71 | MLP | 0.3917
±0.0044 best reported | best at pub: Labeling Trick: A Theory of Using Graph Neural Networks for Multi-Node Representation Learning (NeurIPS 2020) best today: Weak Models Can be Good Teachers: A Case Study on Link Prediction with MLPs (2025) |
