From Overfitting to Robustness: Quantity, Quality, and Variety Oriented Negative Sample Selection in Graph Contrastive Learning
Abstract
Graph contrastive learning (GCL) aims to contrast positive-negative counterparts to learn the node embeddings, whereas graph data augmentation methods are employed to generate these positive-negative samples. The variation, quantity, and quality of negative samples compared to positive samples play crucial roles in learning meaningful embeddings for node classification downstream tasks. Less variation, excessive quantity, and low-quality negative samples cause the model to be overfitted for particular nodes, resulting in less robust models. To solve the overfitting problem in the GCL paradigm, this study proposes a novel Cumulative Sample Selection (CSS) algorithm by comprehensively considering the quality, variations, and quantity of negative samples. Initially, three negative sample pools are constructed: easy, medium, and hard negative samples, which contain 25\ Then, 10\ After that, a decision agent module evaluates model training results and decides whether to explore more negative samples from three negative sample pools by increasing the ratio or keep exploiting the current sampling ratio. The proposed algorithm is integrated into a proposed graph contrastive learning framework named NegAmplify. NegAmplify is compared with the SOTA methods on nine graph node classification datasets, with seven achieving better node classification accuracy with up to 2.86\ NegAmplify is available at:.
Benchmark Results
Tested on 4 datasets 5 baseline values reported too low Non-standard metric on 1 dataset
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 | |
| 92 | LG2AR | 0.9410
±0.0040 | This paper |
| 97 | NegAmplify_r | 0.9409
±0.0039 | This paper |
| 113 | ProGCL | 0.9381
±0.0048 best reported | best at pub: Architecture Matters: Uncovering Implicit Mechanisms in Graph Contrastive Learning (NeurIPS 2023) Difference within reported uncertainty; not counted as underperformance. |
| 121 | NegAmplify_c | 0.9373
±0.0021 | This paper |
| 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. |
| 149 | ABGML | 0.9350
±0.0040 best reported | best today: CORE: Contrastive Masked Feature Reconstruction on Graphs (2025) 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) |
| 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) Difference within reported uncertainty; not counted as underperformance. |
| 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 | |
| 263 | COSTA | 0.9267
±0.0016 best reported | best at pub: Graph Soft-Contrastive Learning via Neighborhood Ranking (2022) best today: Noise-Resilient Unsupervised Graph Representation Learning via Multi-Hop Feature Quality Estimation (2024) Difference within reported uncertainty; not counted as underperformance. |
| 284 | AF-GCL | 0.9249
±0.0031 | This paper |
| 390 | MLP | 0.9128
±0.0063 | |
| 420 | AdaS | 0.9063
±0.0113 | This paper |
| 447 | DW+F | 0.9005
±0.0008 | This paper |
| 465 | DW | 0.8944
±0.0011 | This paper |
| 540 | rf | 0.7853 | This paper |
| # | 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 | |
| 63 | NegAmplify_r | 0.8204
±0.1000 | This paper |
| 67 | NegAmplify_c | 0.8169
±0.1000 | This paper |
| 94 | GRACE | 0.8014
±0.4800 | This paper |
| 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. |
| 129 | COSTA | 0.7912
±0.0200 | This paper |
| 133 | AF-GCL | 0.7901
±0.5100 | 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) Difference within reported uncertainty; not counted as underperformance. |
| 149 | ABGML | 0.7870
±0.5600 | This paper |
| 150 | ProGCL | 0.7868
±0.1200 | This paper |
| 151 | DGI | 0.7865
±0.0690 best reported | best at pub: Learning Graph Augmentations to Learn Graph Representations (2022) best today: Quantizing Text-attributed Graphs for Semantic-Structural Integration (KDD 2025) Difference within reported uncertainty; not counted as underperformance. |
| 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. |
| 184 | LG2AR | 0.7780
±0.5000 | This paper |
| 190 | MVGRL | 0.7757
±0.0046 best reported | best at pub: Graph Barlow Twins: A self-supervised representation learning framework for graphs (2021) best today: Negative-Free Self-Supervised Gaussian Embedding of Graphs (2024) Difference within reported uncertainty; not counted as underperformance. |
| 201 | DW+F | 0.7721
±0.0300 | This paper |
| 237 | MLP | 0.7469
±0.0085 | |
| 241 | DW | 0.7435
±0.0600 | This paper |
| 257 | rf | 0.7198 | This paper |
Heterophilic Graphs
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | DiGGR | 0.4535
±0.0353 | |
| 2 | TRIGON | 0.4402
±0.0028 | |
| 3 | DoG | 0.4320
±0.0120 | |
| 42 | MLP | 0.4026
±0.0108 | |
| 68 | GraphSAGE | 0.3899
±0.0085 | |
| 251 | GRACE | 0.3450
±0.0110 best reported | best at pub: Graph Contrastive Learning under Heterophily via Graph Filters (2023) |
| 323 | NegAmplify_c | 0.3114
±0.0066 | This paper |
| 338 | NegAmplify_r | 0.3047
±0.0009 | This paper |
| 356 | BGRL | 0.2986 best reported | best at pub: Beyond Smoothing: Unsupervised Graph Representation Learning with Edge Heterophily Discriminating (AAAI 2022) |
Heterogeneous Graph Benchmarks
DBLP
Global leaderboard →Sorted by Accuracy. Highlighted rows are from other papers.
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | HG-SCM | 0.9490
±0.0015 | |
| 2 | SeHGNN | 0.9489
±0.0018 | |
| 3 | AdvSynGNN | 0.9486
±0.0012 | |
| 34 | DGI | 0.8800
±0.0020 best reported | best at pub: I'm Me, We're Us, and I'm Us: Tri-directional Contrastive Learning on Hypergraphs (AAAI 2022) |
| 36 | GCN | 0.8758
±0.0020 | |
| 43 | NegAmplify_r | 0.8587
±0.0005 | This paper |
| 45 | NegAmplify_c | 0.8540
±0.0004 | This paper |
| 50 | GRAM | 0.8470
±0.0010 | This paper |
| 51 | COSTA | 0.8450
±0.0010 | This paper |
| 54 | GRACE | 0.8420
±0.0010 | This paper |
| 55 | BGRL | 0.8407
±0.0023 | This paper |
| 65 | MLP | 0.8118
±0.0020 |
