PyG-SSL: A Graph Self-Supervised Learning Toolkit
Abstract
Graph Self-Supervised Learning (SSL) has emerged as a pivotal area of research in recent years. By engaging in pretext tasks to learn the intricate topological structures and properties of graphs using unlabeled data, these graph SSL models achieve enhanced performance, improved generalization, and heightened robustness. Despite the remarkable achievements of these graph SSL methods, their current implementation poses significant challenges for beginners and practitioners due to the complex nature of graph structures, inconsistent evaluation metrics, and concerns regarding reproducibility hinder further progress in this field. Recognizing the growing interest within the research community, there is an urgent need for a comprehensive, beginner-friendly, and accessible toolkit consisting of the most representative graph SSL algorithms. To address these challenges, we present a Graph SSL toolkit named PyG-SSL, which is built upon PyTorch and is compatible with various deep learning and scientific computing backends. Within the toolkit, we offer a unified framework encompassing dataset loading, hyper-parameter configuration, model training, and comprehensive performance evaluation for diverse downstream tasks. Moreover, we provide beginner-friendly tutorials and the best hyper-parameters of each graph SSL algorithm on different graph datasets, facilitating the reproduction of results. The GitHub repository of the library is.
Benchmark Results
Tested on 4 datasets 6 baseline values reported too low
Tables show presented results in global context (best 3 papers + GCN + MLP).
Classic
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | GraphTARIF | 0.9703
±0.0019 | |
| 2 | GAT | 0.9669
±0.0014 | |
| 3 | GAT+T | 0.9660
±0.0007 | |
| 7 | SAGE | 0.9643
±0.0027 | |
| 130 | AFGRL | 0.9361
±0.0020 best reported | best at pub: Wiener Graph Deconvolutional Network Improves Graph Self-Supervised Learning (AAAI 2022) Difference within reported uncertainty; not counted as underperformance. |
| 172 | BGRL | 0.9337
±0.0021 best reported | best at pub: Wiener Graph Deconvolutional Network Improves Graph Self-Supervised Learning (AAAI 2022) Difference within reported uncertainty; not counted as underperformance. |
| 191 | GCA | 0.9320
±0.0060 best reported | best at pub: Unifying Graph Contrastive Learning with Flexible Contextual Scopes (2022) best today: Decoupling Weighing and Selecting for Integrating Multiple Graph Pre-training Tasks (ICLR 2024) |
| 194 | SUGRL | 0.9320
±0.0020 | This paper |
| 206 | MVGRL | 0.9310
±0.0040 best reported | best at pub: Decoupling Weighing and Selecting for Integrating Multiple Graph Pre-training Tasks (ICLR 2024) |
| 213 | DGI | 0.9309
±0.0008 best reported | best at pub: Noise-Resilient Unsupervised Graph Representation Learning via Multi-Hop Feature Quality Estimation (2024) Difference within reported uncertainty; not counted as underperformance. |
| 272 | ReGCL | 0.9260
±0.0030 | This paper |
| 320 | GraphCL | 0.8170
±0.0090 | prev best: Rethinking and Scaling Up Graph Contrastive Learning: An Extremely Efficient Approach with Group Discrimination (NeurIPS 2022) best today: Model-Driven Graph Contrastive Learning (2025) |
| 390 | MLP | 0.9128
±0.0063 |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | GCN | 0.9302
±0.0011 | |
| 2 | RSE + RGCN (70b) | 0.8852
±0.0019 | |
| 3 | LEMP+T | 0.8825 | |
| 9 | SAGE | 0.8771 | |
| 100 | BGRL | 0.8000
±0.0010 | This paper |
| 138 | SUGRL | 0.7897
±0.0022 best reported | best at pub: Graph Soft-Contrastive Learning via Neighborhood Ranking (2022) best today: Rethinking Graph Contrastive Learning through Relative Similarity Preservation (IJCAI 2025) |
| 143 | AFGRL | 0.7890
±0.0060 | prev best: Augmentation-Free Self-Supervised Learning on Graphs (AAAI 2021) |
| 148 | ReGCL | 0.7870
±0.0070 | This paper |
| 151 | DGI | 0.7865
±0.0690 best reported | best at pub: Bootstrap Latents of Nodes and Neighbors for Graph Self-Supervised Learning (2024) best today: Quantizing Text-attributed Graphs for Semantic-Structural Integration (KDD 2025) |
| 162 | GCA | 0.7840
±0.0013 best reported | best at pub: Learning Graph Augmentations to Learn Graph Representations (2022) best today: Augmentation-Free Graph Contrastive Learning with Performance Guarantee (2022) Difference within reported uncertainty; not counted as underperformance. |
| 163 | GraphCL | 0.7837
±0.0077 best reported | best today: Toward General Digraph Contrastive Learning: A Dual Spatial Perspective (2025) Difference within reported uncertainty; not counted as underperformance. |
| 190 | MVGRL | 0.7757
±0.0046 best reported | best at pub: Bootstrap Latents of Nodes and Neighbors for Graph Self-Supervised Learning (2024) best today: Negative-Free Self-Supervised Gaussian Embedding of Graphs (2024) |
| 237 | MLP | 0.7469
±0.0085 |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | DoG | 0.9690
±0.0030 | |
| 2 | GWN-fa | 0.9667
±0.0026 | |
| 3 | GWN-sym | 0.9666
±0.0026 | |
| 6 | GraphSAGE | 0.9593
±0.0025 | |
| 33 | ReGCL | 0.9370
±0.0030 | This paper |
| 43 | DGI | 0.9350
±0.0030 | |
| 51 | GCA | 0.9332
±0.0012 best reported | best at pub: Beyond Smoothing: Unsupervised Graph Representation Learning with Edge Heterophily Discriminating (AAAI 2022) |
| 53 | BGRL | 0.9331
±0.0013 best reported | best at pub: Spectral Augmentation for Self-Supervised Learning on Graphs (ICLR 2022) best today: Adaptive Negative Scheduling for Graph Contrastive Learning (2026) Difference within reported uncertainty; not counted as underperformance. |
| 56 | AFGRL | 0.9330
±0.0020 | prev best: Rethinking and Simplifying Bootstrapped Graph Latents (2023) Improvement within reported uncertainty; not highlighted. |
| 83 | SUGRL | 0.9290
±0.0010 | |
| 88 | MLP | 0.9280
±0.0020 | |
| 116 | MVGRL | 0.9211
±0.0012 best reported | best at pub: Graph Contrastive Learning with Adaptive Augmentation (WWW 2020) best today: Adaptive Negative Scheduling for Graph Contrastive Learning (2026) |
| 190 | GraphCL | 0.8400
±0.0060 | This paper |
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 | |
| 257 | InfoGraph | 0.8930
±0.0514 best reported | best at pub: Improving Expressivity of GNNs with Subgraph-specific Factor Embedded Normalization (KDD 2023) Difference within reported uncertainty; not counted as underperformance. |
| 258 | GraphMAE | 0.8930
±0.0110 best reported | best at pub: Revisiting Graph Autoencoders as Implicit Contrastive Learners (KDD 2024) Difference within reported uncertainty; not counted as underperformance. |
| 354 | GraphCL | 0.8766
±0.0103 best reported | best at pub: Graph Masked Autoencoders with Transformers (2022) Difference within reported uncertainty; not counted as underperformance. |
| 403 | MLP | 0.8660
±0.0495 |
