Self-Supervised Representation Learning via Latent Graph Prediction
Abstract
Self-supervised learning (SSL) of graph neural networks is emerging as a promising way of leveraging unlabeled data. Currently, most methods are based on contrastive learning adapted from the image domain, which requires view generation and a sufficient number of negative samples. In contrast, existing predictive models do not require negative sampling, but lack theoretical guidance on the design of pretext training tasks. In this work, we propose the LaGraph, a theoretically grounded predictive SSL framework based on latent graph prediction. Learning objectives of LaGraph are derived as self-supervised upper bounds to objectives for predicting unobserved latent graphs. In addition to its improved performance, LaGraph provides explanations for recent successes of predictive models that include invariance-based objectives. We provide theoretical analysis comparing LaGraph to related methods in different domains. Our experimental results demonstrate the superiority of LaGraph in performance and the robustness to decreasing of training sample size on both graph-level and node-level tasks.
Benchmark Results
Tested on 6 datasets 9 baseline values reported too low
Tables show presented results in global context (best 3 papers + GCN + MLP).
Classic
Default metric is F1. The paper reports 3 values on F1 and 1 value on F1-micro .
| # | Model | F1 ↑ default | F1-micro ↑ | Paper |
|---|---|---|---|---|
| 1 | EnGCN | 0.9714
±
0.0003 | — | |
| 2 | SAGN+SLE | 0.9710
±
0.0000 | — | |
| 3 | GAMLP(JK) | 0.9704
±
0.0001 | — | F1-micro
— |
| 14 | GraphSAGE | 0.9660 best reported | — | F1-micro
— best at pub: Accelerating Large Scale Real-Time GNN Inference using Channel Pruning (2021) |
| 58 | GCN | 0.9530
±
0.0010 | — | |
| 61 | LaGraph | —
| 0.9520
±
0.0000 | F1-micro
0.9520
±
0.0000 |
| 103 | Super-GCN | 0.9330
±
0.0010 | — | F1-micro
— |
| 133 | Raw Feat. | 0.5850
±
0.0010 | — | F1-micro
— |
PPI
Global leaderboard →Default metric is F1. The paper reports 8 values on F1 and 1 value on F1-micro .
| # | Model | F1 ↑ default | F1-micro ↑ | Paper |
|---|---|---|---|---|
| 1 | GAMLP(JK) | 0.9982
±
0.0001 | — | F1-micro
— |
| 2 | GraphCON-GCN | 0.9960 | — | F1-micro
— |
| 3 | GCNII | 0.9953
±
0.0001 | — | |
| 21 | GCN | 0.9850 | — | F1-micro
— |
| 59 | Super-GAT | 0.9730
±
0.0020 | — | F1-micro
— |
| 101 | GraphSAGE | 0.7860 best reported | — | F1-micro
— best at pub: Graph Neural Networks With Convolutional ARMA Filters (2019) best today: Optimization-Induced Graph Implicit Nonlinear Diffusion (ICML 2022) |
| 108 | VGAE | 0.7580
±
0.0000 | — | F1-micro
— |
| 109 | GAE | 0.7570
±
0.0000 | — | F1-micro
— |
| 113 | LaGraph | —
| 0.7460
±
0.0000 | F1-micro
0.7460
±
0.0000 |
| 123 | BGRL-GAT | 0.7050
±
0.0010 | — | F1-micro
— |
| 129 | BGRL-GCN | 0.6960
±
0.0020 | — | F1-micro
— |
| 165 | Super-GCN | 0.5150
±
0.0060 | — | F1-micro
— |
| 173 | MLP | 0.4620 | — | F1-micro
— |
| 177 | Raw Feat. | 0.4250
±
0.0030 | — | F1-micro
— |
TU Dortmund
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | MSH-GNN | 0.9910
±0.0030 | |
| 2 | ID-GNN+BEC | 0.9830
±0.0360 | |
| 3 | SupCosine | 0.9830
±0.0250 | |
| 39 | GIN | 0.9330
±0.0290 | |
| 159 | WL | 0.9040
±0.0570 best reported | best at pub: Understanding Isomorphism Bias in Graph Data Sets (2019) best today: How Powerful are $K$-hop Message Passing Graph Neural Networks (NeurIPS 2022) |
| 180 | LaGraph | 0.9020
±0.0110 | This paper |
| 199 | MVGRL | 0.8993
±0.0616 best reported | best at pub: Graph Self-Supervised Learning: A Survey (2021) best today: Improving Expressivity of GNNs with Subgraph-specific Factor Embedded Normalization (KDD 2023) Difference within reported uncertainty; not counted as underperformance. |
| 228 | GAE | 0.8950
±0.0150 best reported | best today: Revisiting Graph Autoencoders as Implicit Contrastive Learners (KDD 2024) |
| 257 | InfoGraph | 0.8930
±0.0514 best reported | best at pub: Graph Contrastive Learning Automated (ICML 2021) best today: Improving Expressivity of GNNs with Subgraph-specific Factor Embedded Normalization (KDD 2023) Difference within reported uncertainty; not counted as underperformance. |
| 354 | GraphCL | 0.8766
±0.0103 best reported | best at pub: Graph Contrastive Learning Automated (ICML 2021) best today: Graph Masked Autoencoders with Transformers (2022) Difference within reported uncertainty; not counted as underperformance. |
| 365 | DGK | 0.8744
±0.0272 best reported | best at pub: Provably Powerful Graph Networks (NeurIPS 2019) best today: Model-Driven Graph Contrastive Learning (2025) Difference within reported uncertainty; not counted as underperformance. |
| 403 | MLP | 0.8660
±0.0495 | |
| 407 | graph2vec | 0.8644
±0.0125 best reported | best at pub: CogDL: A Comprehensive Library for Graph Deep Learning (WWW 2021) best today: Graph Masked Autoencoders with Transformers (2022) Difference within reported uncertainty; not counted as underperformance. |
| 444 | GL | 0.8520
±0.0090 best reported | best at pub: On Valid Optimal Assignment Kernels and Applications to Graph Classification (NeurIPS 2016) |
| 472 | Sub2Vec | 0.8447
±0.0037 best reported | best at pub: Learning Graph Representation by Aggregating Subgraphs via Mutual Information Maximization (2021) best today: Graph Masked Autoencoders with Transformers (2022) Difference within reported uncertainty; not counted as underperformance. |
| 475 | VGAE | 0.8440
±0.0060 | This paper |
| 746 | Node2Vec | 0.7263
±0.1020 best reported | best at pub: Graph Contrastive Learning Automated (ICML 2021) best today: Model-Driven Graph Contrastive Learning (2025) Difference within reported uncertainty; not counted as underperformance. |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | WL-MLP | 0.9954 | |
| 2 | GIN | 0.9934 | |
| 3 | GCN | 0.9727 | |
| 12 | WL | 0.8590
±0.0010 best reported | best at pub: Propagation Kernels (2014) |
| 104 | GraphCL | 0.8250
±0.0013 best reported | best at pub: Augmentations in Graph Contrastive Learning: Current Methodological Flaws & Towards Better Practices (WWW 2021) best today: Label-invariant Augmentation for Semi-Supervised Graph Classification (NeurIPS 2022) |
| 131 | GraphSAGE | 0.8200
±0.0100 | |
| 210 | DGK | 0.8031
±0.0046 best reported | best at pub: Graph Capsule Convolutional Neural Networks (ICML 2018) best today: Model-Driven Graph Contrastive Learning (2025) Difference within reported uncertainty; not counted as underperformance. |
| 227 | LaGraph | 0.7990
±0.0050 | This paper |
| 236 | GAE | 0.7978
±0.0017 best reported | best today: Label-invariant Augmentation for Semi-Supervised Graph Classification (NeurIPS 2022) |
| 338 | InfoGraph | 0.7750
±0.0074 best reported | best at pub: CogDL: A Comprehensive Library for Graph Deep Learning (WWW 2021) best today: Graph Masked Autoencoders with Transformers (2022) Difference within reported uncertainty; not counted as underperformance. |
| 356 | MVGRL | 0.7700
±0.0080 best reported | best at pub: InfoGCL: Information-Aware Graph Contrastive Learning (NeurIPS 2021) best today: Graph Self-Supervised Learning with Learnable Structural and Positional Encodings (WWW 2025) |
| 406 | graph2vec | 0.7540
±0.0120 best reported | best at pub: InfoGCL: Information-Aware Graph Contrastive Learning (NeurIPS 2021) Difference within reported uncertainty; not counted as underperformance. |
| 441 | VGAE | 0.7370
±0.0030 | This paper |
| 557 | Sub2Vec | 0.5976
±0.0035 best reported | best at pub: Graph Contrastive Learning Automated (ICML 2021) best today: Graph Masked Autoencoders with Transformers (2022) |
| 571 | Node2Vec | 0.5490
±0.0160 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | WL-MLP | 0.9792 | |
| 2 | MSH-GNN | 0.9640
±0.0070 | |
| 3 | CoCN | 0.8722
±0.0013 | |
| 6 | graph2vec | 0.8558 best reported | best at pub: CogDL: A Comprehensive Library for Graph Deep Learning (WWW 2021) |
| 23 | GCN | 0.8260
±0.0220 | |
| 80 | GraphCL | 0.8108
±0.0017 best reported | best at pub: Prototypical Graph Contrastive Learning (2021) best today: Label-invariant Augmentation for Semi-Supervised Graph Classification (NeurIPS 2022) |
| 91 | GAE | 0.8078
±0.0012 best reported | best today: Label-invariant Augmentation for Semi-Supervised Graph Classification (NeurIPS 2022) |
| 146 | InfoGraph | 0.7940 best reported | best at pub: CogDL: A Comprehensive Library for Graph Deep Learning (WWW 2021) |
| 151 | MLP | 0.7920
±0.0240 | |
| 189 | LaGraph | 0.7760
±0.0020 | This paper |
| 325 | Sub2Vec | 0.6210
±0.0140 | This paper |
| 339 | VGAE | 0.5630 | This paper |
| 341 | Node2Vec | 0.5610
±0.0020 best reported | best at pub: InfoGCL: Information-Aware Graph Contrastive Learning (NeurIPS 2021) |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | OEPG | 0.9630
±0.0090 | |
| 2 | MSH-GNN | 0.9580
±0.0090 | |
| 3 | GNN-AK+ | 0.9480
±0.0080 | |
| 13 | GIN | 0.9240
±0.0250 | |
| 23 | GraphCL | 0.9169
±0.0070 best reported | best at pub: Graph Contrastive Learning Automated (ICML 2021) best today: Graph Contrastive Learning with Cohesive Subgraph Awareness (WWW 2024) |
| 33 | LaGraph | 0.9040
±0.0080 | This paper |
| 46 | InfoGraph | 0.8939
±0.0181 best reported | best at pub: Graph Self-Supervised Learning: A Survey (2021) best today: Graph Contrastive Learning with Cohesive Subgraph Awareness (WWW 2024) |
| 55 | GAE | 0.8769
±0.0040 best reported | best today: Graph Contrastive Learning with Personalized Augmentation (2022) |
| 65 | MVGRL | 0.8450
±0.0060 | This paper |
| 73 | DGK | 0.7804
±0.0039 best reported | best at pub: Graph Contrastive Learning Automated (ICML 2021) best today: Model-Driven Graph Contrastive Learning (2025) Difference within reported uncertainty; not counted as underperformance. |
| 75 | GL | 0.7734
±0.0018 best reported | best at pub: Graph Contrastive Learning Automated (ICML 2021) best today: Model-Driven Graph Contrastive Learning (2025) Difference within reported uncertainty; not counted as underperformance. |
| 80 | graph2vec | 0.7580
±0.0100 | This paper |
| 81 | VGAE | 0.7480
±0.0020 | This paper |
| 82 | Node2Vec | 0.7380
±0.0050 | This paper |
| 83 | Sub2Vec | 0.7150
±0.0040 | prev best: Graph Contrastive Learning Automated (ICML 2021) Improvement within reported uncertainty; not highlighted. |
| 85 | WL | 0.6882
±0.0041 best reported | best at pub: Graph Contrastive Learning Automated (ICML 2021) best today: Model-Driven Graph Contrastive Learning (2025) Difference within reported uncertainty; not counted as underperformance. |
