Link Prediction with Untrained Message Passing Layers
Abstract
In this work, we explore the use of untrained message passing layers in graph neural networks for link prediction. The untrained message passing layers we consider are derived from widely used graph neural network architectures by removing trainable parameters and nonlinearities in their respective message passing layers. Experimentally, we find that untrained message passing layers can lead to competitive and even superior link prediction performance compared to fully trained message passing layers while being more efficient, especially in the presence of high-dimensional features. We also provide a theoretical analysis of untrained message passing layers in the context of link prediction and show that the inner product of features produced by untrained message passing layers relate to common neighbour and path-based topological measures which are widely used for link prediction. As such, untrained message passing layers offer a more efficient alternative to trained message passing layers in link prediction tasks, with clearer theoretical links to classical path-based heuristics.
Benchmark Results
Tested on 4 datasets 26 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: Node Identifiers: Compact, Discrete Representations for Efficient Graph Learning (ICLR 2024) best today: On the Impact of Feature Heterophily on Link Prediction with Graph Neural Networks (NeurIPS 2024) |
| 10 | Neo-GNN | 0.6613
±0.0061 best reported | best at pub: Neo-GNNs: Neighborhood Overlap-aware Graph Neural Networks for Link Prediction (NeurIPS 2022) best today: PROXI: Challenging the GNNs for Link Prediction (TMLR 2024) |
| 14 | BUDDY | 0.6594
±0.0058 best reported | best at pub: Efficient Link Prediction via GNN Layers Induced by Negative Sampling (2023) best today: Node Identifiers: Compact, Discrete Representations for Efficient Graph Learning (ICLR 2024) |
| 15 | NCNC (GIN) | 0.6587
±0.0074 | This paper |
| 17 | SNCNC (SGCN) | 0.6540
±0.0046 | This paper |
| 19 | NCN | 0.6476
±0.0087 best reported | best at pub: Node Identifiers: Compact, Discrete Representations for Efficient Graph Learning (ICLR 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) |
| 23 | AA | 0.6435 best reported | best at pub: Efficient Link Prediction via GNN Layers Induced by Negative Sampling (2023) best today: On the Impact of Feature Heterophily on Link Prediction with Graph Neural Networks (NeurIPS 2024) |
| 26 | RA | 0.6400 best reported | best at pub: Efficient Link Prediction via GNN Layers Induced by Negative Sampling (2023) best today: On the Impact of Feature Heterophily on Link Prediction with Graph Neural Networks (NeurIPS 2024) |
| 27 | CN | 0.6137 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) |
| 28 | SAGE | 0.5944
±0.0137 best reported | best at pub: Pairwise Learning for Neural Link Prediction (2021) best today: PROXI: Challenging the GNNs for Link Prediction (TMLR 2024) Difference within reported uncertainty; not counted as underperformance. |
| 34 | GAT | 0.5643
±0.0086 best reported | best at pub: Asymmetric Learning for Graph Neural Network based Link Prediction (2023) |
| 41 | GraphSAGE | 0.5463
±0.0112 | |
| 45 | SGCN | 0.5413
±0.0097 | This paper |
| 63 | SSAGE | 0.4992
±0.0152 | This paper |
| 68 | Node2Vec | 0.4929
±0.0064 best reported | best at pub: Asymmetric Learning for Graph Neural Network based Link Prediction (2023) |
| 94 | MLP | 0.4438
±0.0347 best reported | best at pub: GNNBenchmark (JMLR 2023) best today: Weak Models Can be Good Teachers: A Case Study on Link Prediction with MLPs (2025) |
| 98 | MF | 0.4181
±0.0167 best reported | best at pub: Formatting Instructions for ICLR 2021 Conference Submissions (2020) best today: PROXI: Challenging the GNNs for Link Prediction (TMLR 2024) |
| 111 | NCNC + SAGE | 0.1517
±0.0215 | This paper |
| 112 | NCNC + GCN | 0.1399
±0.0144 | This paper |
| 113 | NCNC + GIN | 0.1128
±0.0256 | This paper |
| 115 | NCNC + SGCN | 0.0672
±0.0085 | This paper |
| 116 | Katz | 0.0631 | This paper |
| 118 | PEG | 0.0483
±0.0021 | This paper |
| 119 | Shortest Path | 0.0266 | This paper |
| 120 | NTGCN + GAE | 0.0066 | This paper |
| 122 | NTSAGE + GAE | 0.0000 | This paper |
| 123 | NTGIN + GAE | 0.0000 | This paper |
| # | Model | Hits@20 ↑ | Paper |
|---|---|---|---|
| 1 | ELGNN | 0.9777
±0.0037 | |
| 2 | GIDN | 0.9542 | |
| 3 | AGDN | 0.9538
±0.0094 | |
| 14 | NCN | 0.8232
±0.0610 best reported | best today: PageRank Bandits for Link Prediction (NeurIPS 2024) |
| 16 | BUDDY | 0.7851
±0.0136 best reported | best at pub: Graph Neural Networks for Link Prediction with Subgraph Sketching (ICLR 2022) best today: Using Random Noise Equivariantly to Boost Graph Neural Networks Universally (2025) |
| 20 | SAGE | 0.6719
±0.0118 | prev best: Pairwise Learning for Neural Link Prediction (2021) |
| 21 | GAT | 0.6683
±0.0223 | prev best: Neo-GNNs: Neighborhood Overlap-aware Graph Neural Networks for Link Prediction (NeurIPS 2022) |
| 24 | GCN | 0.6476
±0.0145 | prev best: Revisiting Link Prediction: a data perspective (ICLR 2023) |
| 25 | Node2Vec | 0.6363
±0.0205 | prev best: Formatting Instructions for ICLR 2021 Conference Submissions (2020) |
| 26 | Neo-GNN | 0.6357
±0.0352 best reported | best at pub: Neo-GNNs: Neighborhood Overlap-aware Graph Neural Networks for Link Prediction (NeurIPS 2022) best today: Using Random Noise Equivariantly to Boost Graph Neural Networks Universally (2025) Difference within reported uncertainty; not counted as underperformance. |
| 31 | MF | 0.5950
±0.0168 | prev best: Formatting Instructions for ICLR 2021 Conference Submissions (2020) |
| 34 | GraphConv + GAE | 0.5636
±0.0045 | This paper |
| 36 | SNCNC (SGIN) | 0.5453
±0.1102 | This paper |
| 37 | GIN + GAE | 0.5421
±0.0095 | This paper |
| 38 | GraphSAGE | 0.5390
±0.0474 | |
| 42 | PEG | 0.5012
±0.0655 | This paper |
| 43 | SEAL | 0.4974
±0.0239 | prev best: Labeling Trick: A Theory of Using Graph Neural Networks for Multi-Node Representation Learning (NeurIPS 2020) |
| 46 | NCNC (GCN) | 0.4653
±0.2924 | This paper |
| 47 | RA | 0.4401 | prev best: Graph Neural Networks for Link Prediction with Subgraph Sketching (ICLR 2022) |
| 50 | AA | 0.3975 | prev best: Labeling Trick: A Theory of Using Graph Neural Networks for Multi-Node Representation Learning (NeurIPS 2020) |
| 51 | CN | 0.3869 | prev best: Labeling Trick: A Theory of Using Graph Neural Networks for Multi-Node Representation Learning (NeurIPS 2020) |
| 52 | Katz | 0.3869 | prev best: Revisiting Link Prediction: a data perspective (ICLR 2023) |
| 54 | GAE | 0.3707
±0.0507 best reported | |
| 56 | GCN + GAE | 0.3448
±0.0152 | This paper |
| 57 | NTGCN + GAE | 0.3323 | This paper |
| 61 | SAGE + GAE | 0.2930
±0.0144 | This paper |
| 72 | SGCN | 0.2214
±0.0338 | This paper |
| 75 | SSAGE | 0.1944
±0.1084 | This paper |
| 77 | SGCN + GAE | 0.1821
±0.1038 | This paper |
| 85 | SSAGE + GAE | 0.1098
±0.0076 | This paper |
| 98 | Shortest Path | 0.0000 | This paper |
| 99 | SGIN + GAE | 0.0000 | This paper |
| 100 | NTSAGE + GAE | 0.0000 | This paper |
| 101 | NTGIN + GAE | 0.0000 | 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 | |
| 6 | NCNC (GIN) | 0.5947
±0.0160 | This paper |
| 14 | SAGE | 0.5013
±0.0055 best reported | best at pub: Asymmetric Learning for Graph Neural Network based Link Prediction (2023) |
| 22 | SNCNC (SGCN) | 0.4602
±0.0119 | This paper |
| 23 | MLP | 0.4600 | |
| 45 | GCN | 0.3084
±0.0178 | prev best: Revisiting Link Prediction: a data perspective (ICLR 2023) Improvement within reported uncertainty; not highlighted. |
| 63 | GraphSAGE | 0.1655
±0.0240 | |
| 66 | SGCN | 0.1234
±0.0195 | This paper |
| 69 | SSAGE | 0.0886
±0.0080 | This paper |
