Beyond Smoothing: Unsupervised Graph Representation Learning with Edge Heterophily Discriminating
Abstract
Unsupervised graph representation learning (UGRL) has drawn increasing research attention and achieved promising results in several graph analytic tasks. Relying on the homophily assumption, existing UGRL methods tend to smooth the learned node representations along all edges, ignoring the existence of heterophilic edges that connect nodes with distinct attributes. As a result, current methods are hard to generalize to heterophilic graphs where dissimilar nodes are widely connected, and also vulnerable to adversarial attacks. To address this issue, we propose a novel unsupervised raph epresentation learning method with dge h terophily discrimina ing (GREET) which learns representations by discriminating and leveraging homophilic edges and heterophilic edges. To distinguish two types of edges, we build an edge discriminator that infers edge homophily/heterophily from feature and structure information. We train the edge discriminator in an unsupervised way through minimizing the crafted pivot-anchored ranking loss, with randomly sampled node pairs acting as pivots. Node representations are learned through contrasting the dual-channel encodings obtained from the discriminated homophilic and heterophilic edges. With an effective interplaying scheme, edge discriminating and representation learning can mutually boost each other during the training phase. We conducted extensive experiments on 14 benchmark datasets and multiple learning scenarios to demonstrate the superiority of GREET.
Benchmark Results
Tested on 12 datasets 81 baseline values reported too low
Tables show presented results in global context (best 3 papers + GCN + MLP).
Classic
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | CNA | 0.9575
±0.0058 | |
| 2 | IS-GIB | 0.9390
±0.0187 | |
| 3 | EERM | 0.9112
±0.0145 | |
| 35 | GAT | 0.8080
±0.0026 best reported | best at pub: Gophormer: Ego-Graph Transformer for Node Classification (2021) best today: Feature Expansion for Graph Neural Networks (ICML 2023) |
| 44 | GCN | 0.8033
±0.0088 | |
| 66 | DGI | 0.7890
±0.0020 best reported | best at pub: Node Representation Learning in Graph via Node-to-Neighbourhood Mutual Information Maximization (2022) best today: Oversmoothing: A Nightmare for Graph Contrastive Learning? (2023) |
| 73 | GMI | 0.7869
±0.0016 best reported | |
| 87 | MVGRL | 0.7808
±0.0006 best reported | |
| 136 | BGRL | 0.7600
±0.0020 best reported | best at pub: Augmentation-Free Graph Contrastive Learning with Performance Guarantee (2022) best today: Oversmoothing: A Nightmare for Graph Contrastive Learning? (2023) |
| 201 | GRACE | 0.7450
±0.0010 best reported | best at pub: Enhancing Graph Contrastive Learning with Node Similarity (2022) best today: Oversmoothing: A Nightmare for Graph Contrastive Learning? (2023) |
| 302 | GREET | 0.7322
±0.0064 best reported | best today: Discrepancy-Aware Graph Mask Auto-Encoder (KDD 2025) Difference within reported uncertainty; not counted as underperformance. |
| 350 | MLP | 0.7289
±0.0010 best reported | best at pub: Block Modeling-Guided Graph Convolutional Neural Networks (AAAI 2021) best today: Gumbel-MPNN: Graph Rewiring with Gumbel-Softmax (2025) |
| 505 | GCA | 0.7150
±0.0030 best reported | best at pub: Augmentation-Free Graph Contrastive Learning with Performance Guarantee (2022) Difference within reported uncertainty; not counted as underperformance. |
| 625 | VGAE | 0.6990
±0.0057 best reported | best at pub: Decoupled Self-supervised Learning for Non-Homophilou Graphs (2022) |
| 692 | DeepWalk | 0.6785
±0.0079 best reported | best at pub: Decoupled Self-supervised Learning for Non-Homophilou Graphs (2022) |
| 739 | GAE | 0.6639
±0.0024 best reported | best at pub: Decoupled Self-supervised Learning for Non-Homophilou Graphs (2022) |
| 766 | Node2Vec | 0.6552
±0.0018 best reported |
| # | 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 | |
| 20 | GAT | 0.9233
±0.0018 best reported | best at pub: Tackling Over-Smoothing for General Graph Convolutional Networks (2020) |
| 144 | BGRL | 0.8830
±0.0010 best reported | best at pub: Decoupled Self-supervised Learning for Non-Homophilou Graphs (2022) best today: Oversmoothing: A Nightmare for Graph Contrastive Learning? (2023) |
| 194 | GRACE | 0.8730
±0.0010 best reported | best at pub: Enhancing Graph Contrastive Learning with Node Similarity (2022) best today: Oversmoothing: A Nightmare for Graph Contrastive Learning? (2023) |
| 195 | GMI | 0.8726
±0.0016 best reported | |
| 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: Block Modeling-Guided Graph Convolutional Neural Networks (AAAI 2021) best today: On the Equivalence of Graph Convolution and Mixup (TMLR 2023) |
| 223 | DeepWalk | 0.8652
±0.0012 best reported | |
| 251 | Node2Vec | 0.8520
±0.0002 best reported | |
| 255 | GCA | 0.8512
±0.0023 best reported | best at pub: Graph Masked Autoencoders with Transformers (2022) |
| 299 | VGAE | 0.8307
±0.0029 best reported | best at pub: Decoupled Self-supervised Learning for Non-Homophilou Graphs (2022) |
| 304 | GAE | 0.8294
±0.0031 best reported | best at pub: Decoupled Self-supervised Learning for Non-Homophilou Graphs (2022) |
| 426 | GREET | 0.8029
±0.0100 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | GraphTARIF | 0.9703
±0.0019 | |
| 2 | GAT | 0.9264
±0.0042 | prev best: Learning Graph Augmentations to Learn Graph Representations (2022) best today: Graph Transductive Sharpening: Leveraging Unlabeled Predictions in Node Classification (2026) Improvement within reported uncertainty; not highlighted. |
| 3 | GAT+T | 0.9660
±0.0007 | |
| 7 | SAGE | 0.9643
±0.0027 | |
| 8 | GCN | 0.9632
±0.0008 best reported | best at pub: Graph Contrastive Learning with Adaptive Augmentation (WWW 2020) |
| 132 | GREET | 0.9361
±0.0035 best reported | best today: Learn Beneficial Noise as Graph Augmentation (ICML 2025) |
| 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) Difference within reported uncertainty; not counted as underperformance. |
| 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 | 0.9201
±0.0013 | prev best: Graph Contrastive Learning with Adaptive Augmentation (WWW 2020) best today: Decoupling Weighing and Selecting for Integrating Multiple Graph Pre-training Tasks (ICLR 2024) |
| 213 | DGI | 0.9309
±0.0008 best reported | best at pub: Graph Contrastive Learning with Adaptive Augmentation (WWW 2020) |
| 317 | VGAE | 0.9224 best reported | best at pub: Barlow Graph Auto-Encoder for Unsupervised Network Embedding (2021) Difference within reported uncertainty; not counted as underperformance. |
| 352 | GAE | 0.9185
±0.0006 best reported | best at pub: Graph Masked Autoencoders with Transformers (2022) |
| 390 | MLP | 0.7854
±0.0005 | prev best: Eliciting Structural and Semantic Global Knowledge in Unsupervised Graph Contrastive Learning (AAAI 2022) best today: Clarify Confused Nodes via Separated Learning (2023) Improvement within reported uncertainty; not highlighted. |
| 408 | GMI | 0.9072
±0.0033 | prev best: Learning Graph Augmentations to Learn Graph Representations (2022) Improvement within reported uncertainty; not highlighted. |
| 444 | DeepWalk | 0.9005
±0.0008 best reported | best at pub: Barlow Graph Auto-Encoder for Unsupervised Network Embedding (2021) |
| 457 | Node2Vec | 0.8970
±0.0010 best reported | best at pub: Learning Graph Augmentations to Learn Graph Representations (2022) best today: Multiplex Graph Contrastive Learning with Soft Negatives (2024) Difference within reported uncertainty; not counted as underperformance. |
| # | 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: SelfGNN: Self-supervised Graph Neural Networks without explicit negative sampling (WWW 2021) 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 | |
| 52 | GREET | 0.9613
±0.0012 | This paper |
| 58 | MLP | 0.9354
±0.0005 | prev best: Unifying Graph Contrastive Learning with Flexible Contextual Scopes (2022) best today: Graph Transductive Sharpening: Leveraging Unlabeled Predictions in Node Classification (2026) Improvement within reported uncertainty; not highlighted. |
| 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. |
| 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 | 0.9539
±0.0032 | prev best: Wiener Graph Deconvolutional Network Improves Graph Self-Supervised Learning (AAAI 2022) Improvement within reported uncertainty; not highlighted. |
| 114 | MVRL | 0.9553
±0.0010 | prev best: Omni-Granular Ego-Semantic Propagation for Self-Supervised Graph Representation Learning (ICML 2022) |
| 146 | GAE | 0.9520
±0.0010 best reported | best at pub: Graph Contrastive Learning with Adaptive Augmentation (WWW 2020) best today: Revisiting Graph Autoencoders as Implicit Contrastive Learners (KDD 2024) |
| 163 | DeepWalk | 0.9490 best reported | best at pub: Barlow Graph Auto-Encoder for Unsupervised Network Embedding (2021) |
| 167 | DGI | 0.9457
±0.0038 | prev best: Graph Contrastive Learning with Adaptive Augmentation (WWW 2020) Improvement within reported uncertainty; not highlighted. |
| 174 | VGAE | 0.9452 | This paper |
| 268 | Node2Vec | 0.9120
±0.0010 best reported | best at pub: Learning Graph Augmentations to Learn Graph Representations (2022) best today: Unifying Graph Contrastive Learning with Flexible Contextual Scopes (2022) Difference within reported uncertainty; not counted as underperformance. |
| # | 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 | |
| 12 | GCN | 0.9514
±0.0025 best reported | best at pub: Unifying Graph Convolutional Neural Networks and Label Propagation (2020) best today: Graph Wave Networks (WWW 2025) |
| 19 | GREET | 0.9465
±0.0018 | This paper |
| 21 | GAT | 0.9437
±0.0028 best reported | best at pub: Unifying Graph Convolutional Neural Networks and Label Propagation (2020) best today: Graph Wave Networks (WWW 2025) |
| 43 | DGI | 0.9350
±0.0030 best reported | best at pub: Towards Graph Self-Supervised Learning with Contrastive Adjusted Zooming (2021) best today: PyG-SSL: A Graph Self-Supervised Learning Toolkit (2024) |
| 51 | GCA | 0.9332
±0.0012 | prev best: Learning Graph Augmentations to Learn Graph Representations (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. |
| 69 | GRACE | 0.9301
±0.0003 best reported | best at pub: Towards Graph Self-Supervised Learning with Contrastive Adjusted Zooming (2021) best today: A Fused Gromov-Wasserstein Approach to Subgraph Contrastive Learning (TMLR 2025) Difference within reported uncertainty; not counted as underperformance. |
| 88 | MLP | 0.9280
±0.0020 best reported | best at pub: Unifying Graph Convolutional Neural Networks and Label Propagation (2020) best today: Revisiting the Necessity of Graph Learning and Common Graph Benchmarks (2024) |
| 117 | VGAE | 0.9211
±0.0009 | This paper |
| 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) Difference within reported uncertainty; not counted as underperformance. |
| 163 | GAE | 0.9005
±0.0035 best reported | best at pub: Graph Contrastive Learning with Adaptive Augmentation (WWW 2020) best today: HAT-GAE: Self-Supervised Graph Auto-encoders with Hierarchical Adaptive Masking and Trainable Corruption (2023) Difference within reported uncertainty; not counted as underperformance. |
| 184 | Node2Vec | 0.8510 best reported | best at pub: Learning Graph Augmentations to Learn Graph Representations (2022) Difference within reported uncertainty; not counted as underperformance. |
| 188 | DeepWalk | 0.8461
±0.0022 | This paper |
Heterophilic Graphs
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | P^2GNN | 0.9672
±0.0147 | |
| 2 | DoG | 0.9660
±0.0210 | |
| 3 | GPF-plus | 0.9583
±0.0419 | |
| 30 | GPR-GNN | 0.9291
±0.0132 best reported | best at pub: Convolutional Neural Networks on Graphs with Chebyshev Approximation, Revisited (NeurIPS 2022) |
| 34 | MLP | 0.9230
±0.0070 best reported | best at pub: Convolutional Neural Networks on Graphs with Chebyshev Approximation, Revisited (NeurIPS 2022) |
| 40 | H2GCN | 0.9189
±0.0393 best reported | best at pub: Graph-Coupled Oscillator Networks (ICML 2022) best today: GrokFormer: Graph Fourier Kolmogorov-Arnold Transformers (ICML 2024) Difference within reported uncertainty; not counted as underperformance. |
| 53 | GraphSAGE | 0.9000
±0.0365 | |
| 61 | FAGCN | 0.8432 | prev best: A Piece-wise Polynomial Filtering Approach for Graph Neural Networks (2021) best today: Node-oriented Spectral Filtering for Graph Neural Networks (2022) Improvement within reported uncertainty; not highlighted. |
| 101 | GREET | 0.8703 | This paper |
| 211 | GAT | 0.8162
±0.0645 best reported | best at pub: Restructuring Graphs for Higher Homophily via Adaptive Spectral Clustering (AAAI 2022) best today: Equivariance Everywhere All At Once: A Recipe for Graph Foundation Models (2025) |
| 257 | GCN | 0.7933
±0.0447 best reported | best at pub: Restructuring Graphs for Higher Homophily via Adaptive Spectral Clustering (AAAI 2022) best today: Graph Wave Networks (WWW 2025) |
| 304 | DGI | 0.6059 | prev best: Decoupled Self-supervised Learning for Non-Homophilou Graphs (2022) best today: Adaptive Graph Mixture of Residual Experts: Unsupervised Learning on Diverse Graphs with Heterogeneous Specialization (2025) Improvement within reported uncertainty; not highlighted. |
| 351 | MVGRL | 0.6238 | prev best: Graph Auto-Encoder Via Neighborhood Wasserstein Reconstruction (ICLR 2022) best today: Adaptive Graph Mixture of Residual Experts: Unsupervised Learning on Diverse Graphs with Heterogeneous Specialization (2025) Improvement within reported uncertainty; not highlighted. |
| 369 | GRACE | 0.7215
±0.0453 best reported | |
| 409 | BGRL | 0.5919 | |
| 451 | GRACE-FA | 0.6405 | This paper |
| 515 | GCA | 0.5946 | This paper |
| 523 | VGAE | 0.5920 | prev best: Decoupled Self-supervised Learning for Non-Homophilou Graphs (2022) |
| 526 | GAE | 0.5909
±0.1626 best reported | best at pub: Graph Auto-Encoder Via Neighborhood Wasserstein Reconstruction (ICLR 2022) best today: Multi-View Graph Representation Learning Beyond Homophily (2023) Difference within reported uncertainty; not counted as underperformance. |
| 579 | GMI | 0.5049 | This paper |
| 590 | Node2Vec | 0.4864
±0.0292 best reported | best at pub: Graph Auto-Encoder Via Neighborhood Wasserstein Reconstruction (ICLR 2022) |
| 595 | DeepWalk | 0.4649 | prev best: Decoupled Self-supervised Learning for Non-Homophilou Graphs (2022) |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | P^2GNN | 0.9541
±0.0272 | |
| 2 | ACM-GCN | 0.9480
±0.0380 | |
| 3 | RF-GCN | 0.9429 | |
| 11 | GPR-GNN | 0.9279
±0.0312 best reported | best at pub: Convolutional Neural Networks on Graphs with Chebyshev Approximation, Revisited (NeurIPS 2022) best today: Heterophily-Aware Graph Attention Network (2023) |
| 24 | MLP | 0.9136
±0.0070 best reported | best at pub: Is Homophily a Necessity for Graph Neural Networks? (ICLR 2021) best today: Node-oriented Spectral Filtering for Graph Neural Networks (2022) |
| 38 | FAGCN | 0.8135 | best today: Node-oriented Spectral Filtering for Graph Neural Networks (2022) |
| 68 | H2GCN | 0.8623
±0.0471 best reported | best at pub: Graph-Coupled Oscillator Networks (ICML 2022) best today: $P^2$GNN: Two Prototype Sets to boost GNN Performance (2026) Difference within reported uncertainty; not counted as underperformance. |
| 88 | GREET | 0.8514 | This paper |
| 138 | SAGE | 0.8269 | |
| 158 | GAT | 0.8190
±0.0540 best reported | best at pub: Restructuring Graphs for Higher Homophily via Adaptive Spectral Clustering (AAAI 2022) |
| 170 | GCN | 0.8082
±0.0360 best reported | best at pub: Restructuring Graphs for Higher Homophily via Adaptive Spectral Clustering (AAAI 2022) best today: Bayesian Neighborhood Adaptation for Graph Neural Networks (TMLR 2025) |
| 306 | GRACE-FA | 0.6757 | This paper |
| 340 | MVGRL | 0.6430 | prev best: Graph Auto-Encoder Via Neighborhood Wasserstein Reconstruction (ICLR 2022) |
| 350 | DGI | 0.6335 | prev best: Graph Auto-Encoder Via Neighborhood Wasserstein Reconstruction (ICLR 2022) |
| 354 | GAE | 0.5885 | prev best: Graph Auto-Encoder Via Neighborhood Wasserstein Reconstruction (ICLR 2022) Improvement within reported uncertainty; not highlighted. |
| 386 | VGAE | 0.5919 | prev best: Graph Auto-Encoder Via Neighborhood Wasserstein Reconstruction (ICLR 2022) Improvement within reported uncertainty; not highlighted. |
| 415 | BGRL | 0.5730 | prev best: Decoupled Self-supervised Learning for Non-Homophilou Graphs (2022) |
| 423 | GRACE | 0.5640
±0.0210 best reported | best today: Aggregation-aware MLP: An Unsupervised Approach for Graph Message-passing (2025) Difference within reported uncertainty; not counted as underperformance. |
| 427 | GCA | 0.5541 | This paper |
| 429 | GMI | 0.5476 | This paper |
| 500 | DeepWalk | 0.4867
±0.2784 best reported | best at pub: Decoupled Self-supervised Learning for Non-Homophilou Graphs (2022) best today: Multi-View Graph Representation Learning Beyond Homophily (2023) Difference within reported uncertainty; not counted as underperformance. |
| 542 | Node2Vec | 0.4294 | prev best: Graph Auto-Encoder Via Neighborhood Wasserstein Reconstruction (ICLR 2022) Improvement within reported uncertainty; not highlighted. |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | DMD++ | 0.9190
±0.0260 | |
| 2 | F-GREAD-BS | 0.9059
±0.0380 | |
| 3 | APPNP | 0.9010
±0.0350 | |
| 22 | H2GCN | 0.8667
±0.0469 | prev best: Optimization-Induced Graph Implicit Nonlinear Diffusion (ICML 2022) Improvement within reported uncertainty; not highlighted. |
| 37 | MLP | 0.8629
±0.0450 best reported | best at pub: Is Homophily a Necessity for Graph Neural Networks? (ICLR 2021) Difference within reported uncertainty; not counted as underperformance. |
| 45 | GREET | 0.8490 | This paper |
| 53 | GAT | 0.8430
±0.0370 best reported | best at pub: Restructuring Graphs for Higher Homophily via Adaptive Spectral Clustering (AAAI 2022) |
| 56 | GPR-GNN | 0.8412 | prev best: Is Homophily a Necessity for Graph Neural Networks? (ICLR 2021) Improvement within reported uncertainty; not highlighted. |
| 60 | FAGCN | 0.8333 | prev best: From Node Interaction to Hop Interaction: New Effective and Scalable Graph Learning Paradigm (2022) Improvement within reported uncertainty; not highlighted. |
| 63 | GCN | 0.8310
±0.0320 best reported | best at pub: Restructuring Graphs for Higher Homophily via Adaptive Spectral Clustering (AAAI 2022) |
| 69 | GraphSAGE | 0.8118
±0.0556 | |
| 153 | GRACE-FA | 0.6373 | This paper |
| 161 | MVGRL | 0.6237 | This paper |
| 180 | VGAE | 0.5667 | This paper |
| 186 | DGI | 0.5541 | This paper |
| 197 | GAE | 0.5255 | This paper |
| 201 | BGRL | 0.5235 | This paper |
| 208 | GCA | 0.5078 | This paper |
| 211 | GRACE | 0.5000 | This paper |
| 216 | GMI | 0.4598 | This paper |
| 218 | Node2Vec | 0.3745 | This paper |
| 220 | DeepWalk | 0.3353 | This paper |
