Balancing Graph Embedding Smoothness in Self-Supervised Learning via Information-Theoretic Decomposition
Abstract
Self-supervised learning (SSL) in graphs has garnered significant attention, particularly in employing Graph Neural Networks (GNNs) with pretext tasks initially designed for other domains, such as contrastive learning and feature reconstruction. However, it remains uncertain whether these methods effectively reflect essential graph properties, precisely representation similarity with its neighbors. We observe that existing methods position opposite ends of a spectrum driven by the graph embedding smoothness, with each end corresponding to outperformance on specific downstream tasks. Decomposing the SSL objective into three terms via an information-theoretic framework with a neighbor representation variable reveals that this polarization stems from an imbalance among the terms, which existing methods may not effectively maintain. Further insights suggest that balancing between the extremes can lead to improved performance across a wider range of downstream tasks. A framework, BSG (Balancing Smoothness in Graph SSL), introduces novel loss functions designed to supplement the representation quality in graph-based SSL by balancing the derived three terms: neighbor loss, minimal loss, and divergence loss. We present a theoretical analysis of the effects of these loss functions, highlighting their significance from both the SSL and graph smoothness perspectives. Extensive experiments on multiple real-world datasets across node classification and link prediction consistently demonstrate that BSG achieves state-of-the-art performance, outperforming existing methods. Our implementation code is available at.
Benchmark Results
Tested on 5 datasets 39 baseline values reported too low
Tables show presented results in global context (best 3 papers + GCN + MLP).
Classic
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | LGTL | 0.9518
±0.0011 | |
| 2 | MixHop (LO) | 0.9513
±0.0038 | |
| 3 | GraphSAGE (LO) | 0.9511
±0.0036 | |
| 18 | GCN | 0.9296
±0.0015 best reported | best at pub: Node Identifiers: Compact, Discrete Representations for Efficient Graph Learning (ICLR 2024) |
| 20 | GAT | 0.9233
±0.0018 best reported | best at pub: Tackling Over-Smoothing for General Graph Convolutional Networks (2020) |
| 116 | SAGE | 0.8881
±0.0015 | |
| 136 | CCA-SSG | 0.8840
±0.0060 best reported | best at pub: Oversmoothing: A Nightmare for Graph Contrastive Learning? (2023) |
| 187 | MaskGAE | 0.8748
±0.0020 best reported | |
| 194 | GRACE | 0.8730
±0.0010 best reported | best at pub: Oversmoothing: A Nightmare for Graph Contrastive Learning? (2023) |
| 196 | MVGRL | 0.8725
±0.0012 best reported | |
| 204 | DGI | 0.8708
±0.0017 best reported | |
| 210 | MLP | 0.8690
±0.0074 best reported | best at pub: On the Equivalence of Graph Convolution and Mixup (TMLR 2023) |
| 276 | SSL | 0.8413
±0.0023 | This paper |
| 290 | Bandana | 0.8353
±0.0051 best reported | best at pub: Disentangled Generative Graph Representation Learning (2024) best today: Discrepancy-Aware Graph Mask Auto-Encoder (KDD 2025) Difference within reported uncertainty; not counted as underperformance. |
| 299 | VGAE | 0.8307
±0.0029 best reported | best at pub: LAC: Graph Contrastive Learning with Learnable Augmentation in Continuous Space (2024) |
| 304 | GAE | 0.8294
±0.0031 best reported | best at pub: LAC: Graph Contrastive Learning with Learnable Augmentation in Continuous Space (2024) |
| 344 | ARVGA | 0.8151
±0.0100 | This paper |
| 350 | GraphMAE2 | 0.8140
±0.0050 best reported | best at pub: Disentangled Generative Graph Representation Learning (2024) Difference within reported uncertainty; not counted as underperformance. |
| 364 | AUG-MAE | 0.8112
±0.0053 | This paper |
| 402 | GiGaMAE | 0.8055
±0.0075 | This paper |
| 410 | ARGA | 0.8044
±0.0074 | This paper |
| # | 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 | |
| 150 | GiGaMAE | 0.9350
±0.0050 best reported | best at pub: Revisiting Graph Autoencoders as Implicit Contrastive Learners (KDD 2024) Difference within reported uncertainty; not counted as underperformance. |
| 156 | BSG | 0.9348
±0.0016 | This paper |
| 158 | Bandana | 0.9344
±0.0011 best reported | best today: Discrepancy-Aware Graph Mask Auto-Encoder (KDD 2025) Difference within reported uncertainty; not counted as underperformance. |
| 161 | MaskGAE | 0.9342
±0.0026 best reported | |
| 165 | AUG-MAE | 0.9340
±0.0080 best reported | best at pub: Revisiting Graph Autoencoders as Implicit Contrastive Learners (KDD 2024) 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. |
| 192 | GraphMAE2 | 0.9320
±0.0030 best reported | best at pub: Revisiting Graph Autoencoders as Implicit Contrastive Learners (KDD 2024) best today: CORE: Contrastive Masked Feature Reconstruction on Graphs (2025) |
| 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 | |
| 262 | ARGA | 0.9268 best reported | best at pub: Barlow Graph Auto-Encoder for Unsupervised Network Embedding (2021) |
| 285 | ARVGA | 0.9249 best reported | best at pub: Barlow Graph Auto-Encoder for Unsupervised Network Embedding (2021) |
| 317 | VGAE | 0.9224 best reported | best at pub: Barlow Graph Auto-Encoder for Unsupervised Network Embedding (2021) |
| 352 | GAE | 0.9185
±0.0006 best reported | best at pub: Graph Masked Autoencoders with Transformers (2022) |
| 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: Diss-l-ECT: Dissecting Graph Data with local Euler Characteristic Transforms (ICML 2024) |
| 3 | GAT | 0.9398
±0.0022 best reported | best at pub: Diss-l-ECT: Dissecting Graph Data with local Euler Characteristic Transforms (ICML 2024) |
| 8 | SAGE | 0.9351
±0.0006 | |
| 85 | GiGaMAE | 0.9020
±0.0045 | prev best: Revisiting Graph Autoencoders as Implicit Contrastive Learners (KDD 2024) Improvement within reported uncertainty; not highlighted. |
| 98 | AUG-MAE | 0.9008
±0.0012 best reported | best at pub: Revisiting Graph Autoencoders as Implicit Contrastive Learners (KDD 2024) best today: Discrepancy-Aware Graph Mask Auto-Encoder (KDD 2025) |
| 102 | BSG | 0.8999
±0.0008 | This paper |
| 111 | GraphMAE2 | 0.8990
±0.0030 best reported | best at pub: Revisiting Graph Autoencoders as Implicit Contrastive Learners (KDD 2024) best today: CORE: Contrastive Masked Feature Reconstruction on Graphs (2025) |
| 130 | Bandana | 0.8962
±0.0009 best reported | best today: Discrepancy-Aware Graph Mask Auto-Encoder (KDD 2025) |
| 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) |
| 140 | MaskGAE | 0.8950
±0.0010 best reported | best at pub: Revisiting Graph Autoencoders as Implicit Contrastive Learners (KDD 2024) Difference within reported uncertainty; not counted as underperformance. |
| 159 | CCA-SSG | 0.8876
±0.0036 | prev best: Graph Soft-Contrastive Learning via Neighborhood Ranking (2022) Improvement within reported uncertainty; not highlighted. |
| 179 | MVGRL | 0.8861
±0.0064 | prev best: Training MLPs on Graphs without Supervision (2024) Improvement within reported uncertainty; not highlighted. |
| 210 | DGI | 0.8798
±0.0081 best reported | best at pub: Bootstrap Latents of Nodes and Neighbors for Graph Self-Supervised Learning (2024) Difference within reported uncertainty; not counted as underperformance. |
| 246 | VGAE | 0.8721
±0.0026 best reported | best at pub: HC-GAE: The Hierarchical Cluster-based Graph Auto-Encoder for Graph Representation Learning (NeurIPS 2024) |
| 264 | GAE | 0.8666
±0.0007 best reported | best at pub: Graph Masked Autoencoders with Transformers (2022) Difference within reported uncertainty; not counted as underperformance. |
| 288 | ARVGA | 0.8602
±0.0011 | prev best: Barlow Graph Auto-Encoder for Unsupervised Network Embedding (2021) |
| 293 | ARGA | 0.8586
±0.0011 | prev best: Barlow Graph Auto-Encoder for Unsupervised Network Embedding (2021) |
| 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: GrokFormer: Graph Fourier Kolmogorov-Arnold Transformers (ICML 2024) |
| 9 | GCN | 0.9774
±0.0035 best reported | best at pub: 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) |
| 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) |
| 92 | BSG | 0.9565
±0.0003 | This paper |
| 98 | AUG-MAE | 0.9562
±0.0012 | This paper |
| 101 | MaskGAE | 0.9560
±0.0020 best reported | best at pub: Revisiting Graph Autoencoders as Implicit Contrastive Learners (KDD 2024) |
| 106 | CCA-SSG | 0.9559
±0.0007 best reported | best at pub: Wiener Graph Deconvolutional Network Improves Graph Self-Supervised Learning (AAAI 2022) |
| 108 | Bandana | 0.9557
±0.0003 | This paper |
| 112 | GiGaMAE | 0.9553
±0.0003 | This paper |
| 118 | GraphMAE2 | 0.9525
±0.0005 | prev best: Revisiting Graph Autoencoders as Implicit Contrastive Learners (KDD 2024) |
| 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. |
| 146 | GAE | 0.9520
±0.0010 best reported | best at pub: Revisiting Graph Autoencoders as Implicit Contrastive Learners (KDD 2024) |
| 167 | DGI | 0.9489
±0.0009 | prev best: Revisiting Graph Autoencoders as Implicit Contrastive Learners (KDD 2024) Improvement within reported uncertainty; not highlighted. |
| 174 | VGAE | 0.9452 best reported | best at pub: Graph Contrastive Learning with Adaptive Augmentation (WWW 2020) |
| 181 | ARGA | 0.9432
±0.0004 | prev best: Barlow Graph Auto-Encoder for Unsupervised Network Embedding (2021) |
| 183 | ARVGA | 0.9430 best reported | best at pub: Barlow Graph Auto-Encoder for Unsupervised Network Embedding (2021) |
TU Dortmund
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | MSH-GNN | 0.9410
±0.0330 | |
| 2 | GRDL | 0.8260
±0.0120 | |
| 3 | GMN | 0.8225 | |
| 7 | DiffPool | 0.8161
±0.0232 best reported | |
| 32 | GIN | 0.7880
±0.0410 best reported | best at pub: Permutation-Invariant graph partitioning: How graph neural networks capture structural interactions? (2023) Difference within reported uncertainty; not counted as underperformance. |
| 67 | SAGE | 0.7726
±0.0228 | |
| 135 | BSG | 0.7621
±0.0040 | This paper |
| 149 | MLP | 0.7600
±0.0320 | |
| 178 | DGK | 0.7568
±0.0054 best reported | best at pub: Graph Capsule Convolutional Neural Networks (ICML 2018) best today: Hierarchical Graph Capsule Network (AAAI 2020) |
| 190 | WL | 0.7560
±0.0040 best reported | best at pub: On Valid Optimal Assignment Kernels and Applications to Graph Classification (NeurIPS 2016) |
| 194 | AUG-MAE | 0.7549
±0.0040 | This paper |
| 213 | GraphMAE | 0.7530
±0.0050 | This paper |
| 251 | MVGRL | 0.7500
±0.0290 | prev best: Community-Invariant Graph Contrastive Learning (ICML 2024) Improvement within reported uncertainty; not highlighted. |
| 265 | GraphCL | 0.7489
±0.0065 best reported | best at pub: Graph Masked Autoencoders with Transformers (2022) Difference within reported uncertainty; not counted as underperformance. |
| 283 | JOAO | 0.7460
±0.0040 | This paper |
| 294 | InfoGraph | 0.7444
±0.0040 best reported | best at pub: Adversarial Graph Augmentation to Improve Graph Contrastive Learning (NeurIPS 2021) best today: Adaptive Multi-view Graph Contrastive Learning via Fractional-order Neural Diffusion Networks (2025) Difference within reported uncertainty; not counted as underperformance. |
| 350 | graph2vec | 0.7330
±0.0210 | This paper |
| 368 | InfoGCL | 0.7296
±0.0300 | This paper |
