ENGAGE: Explanation Guided Data Augmentation for Graph Representation Learning
Abstract
The recent contrastive learning methods, due to their effectiveness in representation learning, have been widely applied to modeling graph data. Random perturbation is widely used to build contrastive views for graph data, which however, could accidentally break graph structures and lead to suboptimal performance. In addition, graph data is usually highly abstract, so it is hard to extract intuitive meanings and design more informed augmentation schemes. Effective representations should preserve key characteristics in data and abandon superfluous information. In this paper, we propose ENGAGE (ExplaNation Guided data AuGmEntation), where explanation guides the contrastive augmentation process to preserve the key parts in graphs and explore removing superfluous information. Specifically, we design an efficient unsupervised explanation method called smoothed activation map as the indicator of node importance in representation learning. Then, we design two data augmentation schemes on graphs for perturbing structural and feature information, respectively. We also provide justification for the proposed method in the framework of information theories. Experiments of both graph-level and node-level tasks, on various model architectures and on different real-world graphs, are conducted to demonstrate the effectiveness and flexibility of ENGAGE. The code of ENGAGE can be found here [1]..
Benchmark Results
Tested on 8 datasets 40 baseline values reported too low
Tables show presented results in global context (best 3 papers + GCN + MLP).
Classic
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | GraphSAGE+CNA | 0.9418
±0.0033 | |
| 2 | GCN+CNA | 0.9366
±0.0048 | |
| 3 | TransformerConv | 0.9350
±0.0058 | |
| 21 | GCN | 0.9004 best reported | best at pub: SplineCNN: Fast Geometric Deep Learning with Continuous B-Spline Kernels (2017) best today: Understanding Heterophily for Graph Neural Networks (ICML 2024) |
| 39 | SAGE | 0.8911
±0.0012 | |
| 44 | GAT | 0.8897
±0.0014 best reported | best at pub: Learned Low Precision Graph Neural Networks (2020) |
| 156 | MVGRL | 0.8680
±0.0050 | |
| 177 | DGI | 0.8630
±0.0020 best reported | best at pub: Oversmoothing: A Nightmare for Graph Contrastive Learning? (2023) |
| 302 | EG-SimCLR(GCN) | 0.8407
±0.0018 | This paper |
| 359 | GRACE(GAT) | 0.8357
±0.0055 | This paper |
| 379 | EG-Simsiam(GCN) | 0.8346
±0.0056 | This paper |
| 435 | DeepWalk | 0.8290 best reported | best at pub: Graph Representation Learning: A Survey (2019) |
| 454 | RD-Simsiam(GCN) | 0.8265
±0.0062 | This paper |
| 654 | GAE | 0.8011
±0.0022 best reported | best at pub: Graph Masked Autoencoders with Transformers (2022) |
| 724 | MLP | 0.7768 |
| # | 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: Feature Expansion for Graph Neural Networks (ICML 2023) |
| 44 | GCN | 0.8033
±0.0088 best reported | best at pub: Gophormer: Ego-Graph Transformer for Node Classification (2021) |
| 61 | GraphSAGE | 0.7923
±0.0053 | |
| 66 | DGI | 0.7890
±0.0020 best reported | best at pub: Oversmoothing: A Nightmare for Graph Contrastive Learning? (2023) |
| 87 | MVGRL | 0.7808
±0.0006 best reported | |
| 350 | MLP | 0.7289
±0.0010 | |
| 417 | EG-SimCLR(GCN) | 0.7240
±0.0046 | This paper |
| 488 | GRACE(GAT) | 0.7170
±0.0055 | This paper |
| 514 | EG-Simsiam(GCN) | 0.7149
±0.0031 | This paper |
| 577 | RD-Simsiam(GCN) | 0.7072
±0.0064 | This paper |
| 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) Difference within reported uncertainty; not counted as underperformance. |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | GraphTARIF | 0.9703
±0.0019 | |
| 2 | GAT | 0.9669
±0.0014 best reported | best at pub: Clarify Confused Nodes via Separated Learning (2023) |
| 3 | GAT+T | 0.9660
±0.0007 | |
| 7 | SAGE | 0.9643
±0.0027 | |
| 8 | GCN | 0.9632
±0.0008 best reported | best at pub: Clarify Confused Nodes via Separated Learning (2023) |
| 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) |
| 206 | MVGRL | 0.9310
±0.0040 best reported | best at pub: Beyond Smoothing: Unsupervised Graph Representation Learning with Edge Heterophily Discriminating (AAAI 2022) 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) |
| 223 | EG-SimCLR(GAT) | 0.9297
±0.0007 | This paper |
| 247 | EG-Simsiam(GCN) | 0.9277
±0.0014 | This paper |
| 251 | GRACE(GAT) | 0.9274
±0.0020 | This paper |
| 268 | RD-Simsiam(GAT) | 0.9263
±0.0012 | This paper |
| 352 | GAE | 0.9185
±0.0006 best reported | best at pub: Graph Masked Autoencoders with Transformers (2022) |
| 390 | MLP | 0.9128
±0.0063 | |
| 444 | DeepWalk | 0.9005
±0.0008 | This paper |
| # | 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 | best at pub: Clarify Confused Nodes via Separated Learning (2023) |
| 8 | SAGE | 0.9351
±0.0006 | |
| 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) |
| 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) |
| 177 | EG-Simsiam(GCN) | 0.8866
±0.0019 | This paper |
| 179 | MVGRL | 0.8861
±0.0064 best reported | best at pub: Graph Contrastive Learning with Adaptive Augmentation (WWW 2020) |
| 182 | EG-SimCLR(GAT) | 0.8856
±0.0017 | This paper |
| 210 | DGI | 0.8798
±0.0081 best reported | best at pub: Unifying Graph Contrastive Learning with Flexible Contextual Scopes (2022) best today: Bootstrap Latents of Nodes and Neighbors for Graph Self-Supervised Learning (2024) |
| 212 | RD-Simsiam(GAT) | 0.8796
±0.0027 | This paper |
| 264 | GAE | 0.8666
±0.0007 best reported | best at pub: Graph Masked Autoencoders with Transformers (2022) |
| 278 | DeepWalk | 0.8628
±0.0007 | This paper |
| 320 | MLP | 0.8463 |
TU Dortmund
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | WL-MLP | 0.9954 | |
| 2 | GIN | 0.9934 | |
| 3 | GCN | 0.9727 | |
| 12 | WL | 0.8590
±0.0010 best reported | best at pub: Propagation Kernels (2014) |
| 77 | EG-SimCLR | 0.8297
±0.0020 | This paper |
| 104 | GraphCL | 0.8250
±0.0013 best reported | best at pub: Label-invariant Augmentation for Semi-Supervised Graph Classification (NeurIPS 2022) |
| 131 | GraphSAGE | 0.8200
±0.0100 | |
| 141 | SimGRACE | 0.8180
±0.0015 best reported | best at pub: Label-invariant Augmentation for Semi-Supervised Graph Classification (NeurIPS 2022) |
| 146 | JOAOv2 | 0.8170
±0.0026 best reported | best at pub: Label-invariant Augmentation for Semi-Supervised Graph Classification (NeurIPS 2022) |
| 153 | EG-Simsiam | 0.8149
±0.0019 | This paper |
| 187 | HG-Simsiam | 0.8070
±0.0064 | This paper |
| 198 | HG-SimCLR | 0.8048
±0.0044 | This paper |
| 210 | DGK | 0.8031
±0.0046 | This paper |
| 241 | RD-Simsiam | 0.7962
±0.0059 | This paper |
| 262 | RD-SimCLR | 0.7902
±0.0052 | This paper |
| 301 | JOAO | 0.7840
±0.0050 best reported | best at pub: Omni-Granular Ego-Semantic Propagation for Self-Supervised Graph Representation Learning (ICML 2022) Difference within reported uncertainty; not counted as underperformance. |
| 338 | InfoGraph | 0.7750
±0.0074 best reported | best at pub: Graph Masked Autoencoders with Transformers (2022) Difference within reported uncertainty; not counted as underperformance. |
| 356 | MVGRL | 0.7700
±0.0080 | This paper |
| 406 | graph2vec | 0.7540
±0.0120 best reported | best at pub: InfoGCL: Information-Aware Graph Contrastive Learning (NeurIPS 2021) Difference within reported uncertainty; not counted as underperformance. |
| 557 | Sub2Vec | 0.5976
±0.0035 best reported | best at pub: Graph Masked Autoencoders with Transformers (2022) |
| 571 | Node2Vec | 0.5490
±0.0160 best reported | best at pub: InfoGCL: Information-Aware Graph Contrastive Learning (NeurIPS 2021) best today: GPS: graph contrastive learning via multi-scale augmented views from adversarial pooling (2024) Difference within reported uncertainty; not counted as underperformance. |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | MSH-GNN | 0.9410
±0.0330 | |
| 2 | GRDL | 0.8260
±0.0120 | |
| 3 | GMN | 0.8225 | |
| 32 | GIN | 0.7880
±0.0410 | |
| 145 | EG-Simsiam | 0.7606
±0.0051 | 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) |
| 197 | HG-Simsiam | 0.7545
±0.0072 | This paper |
| 200 | EG-SimCLR | 0.7544
±0.0065 | This paper |
| 202 | RD-Simsiam | 0.7542
±0.0050 | This paper |
| 209 | SimGRACE | 0.7535
±0.0009 | This paper |
| 256 | HG-SimCLR | 0.7493
±0.0062 | This paper |
| 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. |
| 282 | RD-SimCLR | 0.7461
±0.0056 | This paper |
| 283 | JOAO | 0.7460
±0.0040 best reported | best at pub: Adversarial Graph Augmentation to Improve Graph Contrastive Learning (NeurIPS 2021) best today: Balancing Graph Embedding Smoothness in Self-Supervised Learning via Information-Theoretic Decomposition (WWW 2025) Difference within reported uncertainty; not counted as underperformance. |
| 294 | InfoGraph | 0.7444
±0.0031 | This paper |
| 309 | JOAOv2 | 0.7407
±0.0110 | This paper |
| 350 | graph2vec | 0.7330
±0.0205 | This paper |
| 474 | Sub2Vec | 0.6731
±0.0050 best reported | best at pub: Graph Masked Autoencoders with Transformers (2022) |
| 514 | Node2Vec | 0.5750
±0.0360 best reported | best today: GPS: graph contrastive learning via multi-scale augmented views from adversarial pooling (2024) Difference within reported uncertainty; not counted as underperformance. |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | WL-MLP | 0.9792 | |
| 2 | MSH-GNN | 0.9640
±0.0070 | |
| 3 | CoCN | 0.8722
±0.0013 | |
| 6 | graph2vec | 0.8558 best reported | best at pub: CogDL: A Comprehensive Library for Graph Deep Learning (WWW 2021) |
| 23 | GCN | 0.8260
±0.0220 | |
| 32 | JOAOv2 | 0.8216
±0.0017 best reported | best at pub: Label-invariant Augmentation for Semi-Supervised Graph Classification (NeurIPS 2022) |
| 37 | SimGRACE | 0.8188
±0.0023 best reported | best at pub: Label-invariant Augmentation for Semi-Supervised Graph Classification (NeurIPS 2022) |
| 80 | GraphCL | 0.8108
±0.0017 best reported | best at pub: Label-invariant Augmentation for Semi-Supervised Graph Classification (NeurIPS 2022) |
| 104 | MVGRL | 0.8048
±0.0029 best reported | best at pub: Label-invariant Augmentation for Semi-Supervised Graph Classification (NeurIPS 2022) best today: Graph Contrastive Learning with Cohesive Subgraph Awareness (WWW 2024) |
| 146 | InfoGraph | 0.7940 best reported | best at pub: CogDL: A Comprehensive Library for Graph Deep Learning (WWW 2021) |
| 151 | MLP | 0.7920
±0.0240 | |
| 153 | WL | 0.7910
±0.0010 best reported | best at pub: On Valid Optimal Assignment Kernels and Applications to Graph Classification (NeurIPS 2016) |
| 217 | EG-SimCLR | 0.7660
±0.0126 | This paper |
| 248 | JOAO | 0.7535
±0.0093 best reported | best at pub: Spectral Augmentation for Self-Supervised Learning on Graphs (ICLR 2022) |
| 255 | EG-Simsiam | 0.7473
±0.0079 | This paper |
| 274 | DGK | 0.7310
±0.0030 best reported | best at pub: Wasserstein Embedding for Graph Learning (ICLR 2020) best today: InfoGCL: Information-Aware Graph Contrastive Learning (NeurIPS 2021) |
| 278 | HG-Simsiam | 0.7284
±0.0091 | This paper |
| 282 | HG-SimCLR | 0.7253
±0.0097 | This paper |
| 306 | RD-SimCLR | 0.6932
±0.0154 | This paper |
| 315 | RD-Simsiam | 0.6650
±0.0231 | This paper |
| 325 | Sub2Vec | 0.6210
±0.0140 best reported | best at pub: Self-Supervised Representation Learning via Latent Graph Prediction (ICML 2022) |
| 341 | Node2Vec | 0.5610
±0.0020 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | OEPG | 0.9630
±0.0090 | |
| 2 | MSH-GNN | 0.9580
±0.0090 | |
| 3 | GNN-AK+ | 0.9480
±0.0080 | |
| 13 | GIN | 0.9240
±0.0250 | |
| 23 | GraphCL | 0.9169
±0.0070 best reported | best at pub: Graph Contrastive Learning Automated (ICML 2021) best today: Graph Contrastive Learning with Cohesive Subgraph Awareness (WWW 2024) |
| 24 | JOAO | 0.9166
±0.0059 best reported | best at pub: Graph Contrastive Learning with Personalized Augmentation (2022) best today: Graph Contrastive Learning with Cohesive Subgraph Awareness (WWW 2024) |
| 32 | EG-SimCLR | 0.9070
±0.0046 | This paper |
| 40 | HG-SimCLR | 0.8992
±0.0053 | This paper |
| 43 | HG-Simsiam | 0.8963
±0.0055 | This paper |
| 44 | SimGRACE | 0.8951
±0.0089 | This paper |
| 46 | InfoGraph | 0.8939
±0.0181 best reported | best at pub: Graph Contrastive Learning with Personalized Augmentation (2022) best today: Graph Contrastive Learning with Cohesive Subgraph Awareness (WWW 2024) |
| 48 | EG-Simsiam | 0.8917
±0.0043 | This paper |
| 49 | JOAOv2 | 0.8879
±0.0065 best reported | best at pub: Graph Contrastive Learning with Personalized Augmentation (2022) |
| 61 | RD-Simsiam | 0.8612
±0.0180 | This paper |
| 62 | RD-SimCLR | 0.8567
±0.0540 | This paper |
| 65 | MVGRL | 0.8450
±0.0060 | This paper |
| 73 | DGK | 0.7804
±0.0039 | This paper |
| 80 | graph2vec | 0.7580
±0.0100 best reported | best at pub: Prototypical Graph Contrastive Learning (2021) best today: Self-Supervised Representation Learning via Latent Graph Prediction (ICML 2022) Difference within reported uncertainty; not counted as underperformance. |
| 83 | Sub2Vec | 0.7150
±0.0040 best reported | best at pub: Self-Supervised Representation Learning via Latent Graph Prediction (ICML 2022) Difference within reported uncertainty; not counted as underperformance. |
| 85 | WL | 0.6882
±0.0041 | This paper |
