Bootstrap Latents of Nodes and Neighbors for Graph Self-Supervised Learning
Abstract
Contrastive learning is a significant paradigm in graph self-supervised learning. However, it requires negative samples to prevent model collapse and learn discriminative representations. These negative samples inevitably lead to heavy computation, memory overhead and class collision, compromising the representation learning. Recent studies present that methods obviating negative samples can attain competitive performance and scalability enhancements, exemplified by bootstrapped graph latents (BGRL). However, BGRL neglects the inherent graph homophily, which provides valuable insights into underlying positive pairs. Our motivation arises from the observation that subtly introducing a few ground-truth positive pairs significantly improves BGRL. Although we can't obtain ground-truth positive pairs without labels under the self-supervised setting, edges in the graph can reflect noisy positive pairs, i.e., neighboring nodes often share the same label. Therefore, we propose to expand the positive pair set with node-neighbor pairs. Subsequently, we introduce a cross-attention module to predict the supportiveness score of a neighbor with respect to the anchor node. This score quantifies the positive support from each neighboring node, and is encoded into the training objective. Consequently, our method mitigates class collision from negative and noisy positive samples, concurrently enhancing intra-class compactness. Extensive experiments are conducted on five benchmark datasets and three downstream task node classification, node clustering, and node similarity search. The results demonstrate that our method generates node representations with enhanced intra-class compactness and achieves state-of-the-art performance. Our implementation code is available at.
Benchmark Results
Tested on 4 datasets 18 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 best reported | |
| 3 | GAT+T | 0.9660
±0.0007 | |
| 7 | SAGE | 0.9643
±0.0027 | |
| 8 | GCN | 0.9632
±0.0008 best reported | |
| 113 | ProGCL | 0.9381
±0.0048 best reported | best at pub: Architecture Matters: Uncovering Implicit Mechanisms in Graph Contrastive Learning (NeurIPS 2023) |
| 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. |
| 144 | BLNN | 0.9354
±0.0023 | This paper |
| 164 | GraphMAE | 0.9341
±0.0010 best reported | best at pub: Rethinking and Simplifying Bootstrapped Graph Latents (2023) 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. |
| 186 | CCA-SSG | 0.9325
±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) |
| 198 | gCooL | 0.9318
±0.0012 | This paper |
| 203 | GRACE | 0.9313
±0.0017 best reported | best at pub: Learning Graph Augmentations to Learn Graph Representations (2022) best today: Learn Beneficial Noise as Graph Augmentation (ICML 2025) |
| 206 | MVGRL | 0.9310
±0.0040 best reported | best at pub: Decoupling Weighing and Selecting for Integrating Multiple Graph Pre-training Tasks (ICLR 2024) Difference within reported uncertainty; not counted as underperformance. |
| 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. |
| 228 | FastGCL | 0.9291
±0.0007 | This paper |
| 263 | COSTA | 0.9267
±0.0016 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. |
| 267 | G-BT | 0.9263
±0.0044 best reported | best at pub: Barlow Graph Auto-Encoder for Unsupervised Network Embedding (2021) best today: Rethinking Graph Contrastive Learning through Relative Similarity Preservation (IJCAI 2025) Difference within reported uncertainty; not counted as underperformance. |
| 284 | AF-GCL | 0.9249
±0.0031 | This paper |
| 297 | CGKS | 0.9240
±0.0010 | This paper |
| 390 | MLP | 0.9128
±0.0063 best reported | best at pub: Clarify Confused Nodes via Separated Learning (2023) |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | GraphTARIF | 0.9461
±0.0017 | |
| 2 | GCN | 0.9412
±0.0008 best reported | best at pub: Clarify Confused Nodes via Separated Learning (2023) |
| 3 | GAT | 0.9398
±0.0022 best reported | |
| 8 | SAGE | 0.9351
±0.0006 | |
| 53 | BLNN | 0.9102
±0.0023 | This paper |
| 79 | BGRL | 0.9034
±0.0019 | This paper |
| 100 | GraphMAE | 0.9002
±0.0024 best reported | best at pub: Rethinking and Simplifying Bootstrapped Graph Latents (2023) best today: Discrepancy-Aware Graph Mask Auto-Encoder (KDD 2025) Difference within reported uncertainty; not counted as underperformance. |
| 112 | AFGRL | 0.8988
±0.0033 | This paper |
| 127 | AF-GCL | 0.8968
±0.0019 | This paper |
| 135 | ProGCL | 0.8928
±0.0015 | prev best: HomoGCL: Rethinking Homophily in Graph Contrastive Learning (KDD 2023) best today: Adaptive Negative Scheduling for Graph Contrastive Learning (2026) |
| 139 | GRACE | 0.8953
±0.0035 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) |
| 145 | FastGCL | 0.8935
±0.0009 | This paper |
| 159 | CCA-SSG | 0.8896
±0.0013 best reported | best at pub: Graph Soft-Contrastive Learning via Neighborhood Ranking (2022) best today: Str-GCL: Structural Commonsense Driven Graph Contrastive Learning (WWW 2025) Difference within reported uncertainty; not counted as underperformance. |
| 160 | GCA | 0.8894
±0.0015 best reported | best at pub: Barlow Graph Auto-Encoder for Unsupervised Network Embedding (2021) best today: Adaptive Negative Scheduling for Graph Contrastive Learning (2026) |
| 166 | gCooL | 0.8885
±0.0014 | This paper |
| 179 | MVGRL | 0.8861
±0.0064 best reported | best at pub: Training MLPs on Graphs without Supervision (2024) best today: Balancing Graph Embedding Smoothness in Self-Supervised Learning via Information-Theoretic Decomposition (WWW 2025) Difference within reported uncertainty; not counted as underperformance. |
| 185 | CGKS | 0.8850
±0.0020 | This paper |
| 192 | COSTA | 0.8837
±0.0022 best reported | best at pub: HomoGCL: Rethinking Homophily in Graph Contrastive Learning (KDD 2023) Difference within reported uncertainty; not counted as underperformance. |
| 202 | G-BT | 0.8814
±0.0033 best reported | best at pub: Barlow Graph Auto-Encoder for Unsupervised Network Embedding (2021) best today: Rethinking Graph Contrastive Learning through Relative Similarity Preservation (IJCAI 2025) Difference within reported uncertainty; not counted as underperformance. |
| 210 | DGI | 0.8798
±0.0081 | prev best: Decoupling Weighing and Selecting for Integrating Multiple Graph Pre-training Tasks (ICLR 2024) Improvement within reported uncertainty; not highlighted. |
| 320 | MLP | 0.8463 best reported |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | GrokFormer | 0.9831
±0.0018 | |
| 2 | PolyFormer | 0.9808
±0.0027 | |
| 3 | SGFormer | 0.9796
±0.0081 | |
| 6 | GAT | 0.9782
±0.0028 best reported | best at pub: Clarify Confused Nodes via Separated Learning (2023) best today: GrokFormer: Graph Fourier Kolmogorov-Arnold Transformers (ICML 2024) |
| 9 | GCN | 0.9774
±0.0035 best reported | best at pub: SelfGNN: Self-supervised Graph Neural Networks without explicit negative sampling (WWW 2021) best today: GrokFormer: Graph Fourier Kolmogorov-Arnold Transformers (ICML 2024) |
| 17 | SAGE | 0.9739
±0.0018 | |
| 58 | MLP | 0.9597
±0.0007 best reported | best at pub: Clarify Confused Nodes via Separated Learning (2023) |
| 63 | GCA | 0.9590
±0.0020 best reported | best at pub: Unifying Graph Contrastive Learning with Flexible Contextual Scopes (2022) Difference within reported uncertainty; not counted as underperformance. |
| 65 | BLNN | 0.9586
±0.0010 | This paper |
| 69 | BGRL | 0.9580
±0.0040 best reported | best at pub: Unifying Graph Contrastive Learning with Flexible Contextual Scopes (2022) Difference within reported uncertainty; not counted as underperformance. |
| 77 | GRACE | 0.9574
±0.0006 best reported | best at pub: Building Shortcuts between Distant Nodes with Biaffine Mapping for Graph Convolutional Networks (2023) best today: Learn Beneficial Noise as Graph Augmentation (ICML 2025) |
| 78 | AFGRL | 0.9574
±0.0010 best reported | best at pub: Wiener Graph Deconvolutional Network Improves Graph Self-Supervised Learning (AAAI 2022) Difference within reported uncertainty; not counted as underperformance. |
| 100 | COSTA | 0.9560
±0.0002 | This paper |
| 106 | CCA-SSG | 0.9559
±0.0007 best reported | best at pub: Wiener Graph Deconvolutional Network Improves Graph Self-Supervised Learning (AAAI 2022) |
| 111 | FastGCL | 0.9553
±0.0002 | This paper |
| 117 | GraphMAE | 0.9550
±0.0010 best reported | best at pub: Rethinking and Simplifying Bootstrapped Graph Latents (2023) best today: CORE: Contrastive Masked Feature Reconstruction on Graphs (2025) Difference within reported uncertainty; not counted as underperformance. |
| 125 | MVGRL | 0.9544
±0.0027 best reported | best at pub: HAT-GAE: Self-Supervised Graph Auto-encoders with Hierarchical Adaptive Masking and Trainable Corruption (2023) Difference within reported uncertainty; not counted as underperformance. |
| 141 | G-BT | 0.9525
±0.0013 | prev best: Barlow Graph Auto-Encoder for Unsupervised Network Embedding (2021) Improvement within reported uncertainty; not highlighted. |
| 154 | AF-GCL | 0.9512
±0.0015 | This paper |
| 167 | DGI | 0.9489
±0.0009 best reported | best at pub: Beyond Smoothing: Unsupervised Graph Representation Learning with Edge Heterophily Discriminating (AAAI 2022) best today: Balancing Graph Embedding Smoothness in Self-Supervised Learning via Information-Theoretic Decomposition (WWW 2025) Difference within reported uncertainty; not counted as underperformance. |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | GCN | 0.9302
±0.0011 best reported | best at pub: Augmentation-Free Graph Contrastive Learning with Performance Guarantee (2022) |
| 2 | RSE + RGCN (70b) | 0.8852
±0.0019 | |
| 3 | LEMP+T | 0.8825 | |
| 9 | SAGE | 0.8771 | |
| 31 | GAT | 0.8533 best reported | |
| 84 | GraphMAE | 0.8052
±0.0032 best reported | best at pub: Rethinking and Simplifying Bootstrapped Graph Latents (2023) best today: Discrepancy-Aware Graph Mask Auto-Encoder (KDD 2025) |
| 86 | BLNN | 0.8048
±0.0052 | This paper |
| 94 | GRACE | 0.8014
±0.0048 best reported | best at pub: Large-Scale Representation Learning on Graphs via Bootstrapping (ICLR 2021) best today: Adaptive Negative Scheduling for Graph Contrastive Learning (2026) |
| 100 | BGRL | 0.8000
±0.0010 best reported | best at pub: Learning Graph Augmentations to Learn Graph Representations (2022) best today: PyG-SSL: A Graph Self-Supervised Learning Toolkit (2024) Difference within reported uncertainty; not counted as underperformance. |
| 125 | FastGCL | 0.7920
±0.0007 | This paper |
| 126 | CGKS | 0.7920
±0.0010 | This paper |
| 129 | COSTA | 0.7912
±0.0002 | This paper |
| 130 | CCA-SSG | 0.7908
±0.0053 | This paper |
| 133 | AF-GCL | 0.7901
±0.0051 | This paper |
| 143 | AFGRL | 0.7890
±0.0060 best reported | best at pub: Augmentation-Free Self-Supervised Learning on Graphs (AAAI 2021) best today: PyG-SSL: A Graph Self-Supervised Learning Toolkit (2024) |
| 147 | gCooL | 0.7874
±0.0004 | This paper |
| 150 | ProGCL | 0.7868
±0.0012 | This paper |
| 151 | DGI | 0.7825
±0.0056 | prev best: Learning Graph Augmentations to Learn Graph Representations (2022) |
| 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. |
| 190 | MVGRL | 0.7757
±0.0046 | prev best: Graph Barlow Twins: A self-supervised representation learning framework for graphs (2021) Improvement within reported uncertainty; not highlighted. |
| 211 | G-BT | 0.7683
±0.0073 | prev best: Graph Barlow Twins: A self-supervised representation learning framework for graphs (2021) Improvement within reported uncertainty; not highlighted. |
| 237 | MLP | 0.7469
±0.0085 best reported | best at pub: Fully-inductive Node Classification on Arbitrary Graphs (ICLR 2024) best today: View Space: Learning Representation across Arbitrary Graphs (ICML 2025) |
