SeeGera: Self-supervised Semi-implicit Graph Variational Auto-encoders with Masking
Abstract
Generative graph self-supervised learning (SSL) aims to learn node representations by reconstructing the input graph data. However, most existing methods focus on unsupervised learning tasks only and very few work has shown its superiority over the state-of-the-art graph contrastive learning (GCL) models, especially on the classification task. While a very recent model has been proposed to bridge the gap, its performance on unsupervised learning tasks is still unknown. In this paper, to comprehensively enhance the performance of generative graph SSL against other GCL models on both unsupervised and supervised learning tasks, we propose the SeeGera\ model, which is based on the family of self-supervised variational graph auto-encoder (VGAE). Specifically, SeeGera\ adopts the semi-implicit variational inference framework, a hierarchical variational framework, and mainly focuses on feature reconstruction and structure/feature masking. On the one hand, SeeGera\ co-embeds both nodes and features in the encoder and reconstructs both links and features in the decoder. Since feature embeddings contain rich semantic information on features, they can be combined with node embeddings to provide fine-grained knowledge for feature reconstruction. On the other hand, SeeGera\ adds an additional layer for structure/feature masking to the hierarchical variational framework, which boosts the model generalizability. We conduct extensive experiments comparing SeeGera\ with 9 other state-of-the-art competitors. Our results show that SeeGera\ can compare favorably against other state-of-the-art GCL methods in a variety of unsupervised and supervised learning tasks.
Benchmark Results
Tested on 3 datasets 3 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 | |
| 3 | GAT+T | 0.9660
±0.0007 | |
| 7 | SAGE | 0.9643
±0.0027 | |
| 164 | GraphMAE | 0.9341
±0.0010 best reported | best at pub: HAT-GAE: Self-Supervised Graph Auto-encoders with Hierarchical Adaptive Masking and Trainable Corruption (2023) best today: Rethinking and Simplifying Bootstrapped Graph Latents (2023) 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. |
| 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: 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) |
| 237 | SeeGera-v3 | 0.9281
±0.0045 | This paper |
| 257 | SeeGera-v2 | 0.9270
±0.0042 | This paper |
| 279 | SeeGera-v1 | 0.9253
±0.0041 | This paper |
| 390 | MLP | 0.9128
±0.0063 |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | GraphTARIF | 0.9461
±0.0017 | |
| 2 | GCN | 0.9412
±0.0008 | |
| 3 | GAT | 0.9398
±0.0022 | |
| 8 | SAGE | 0.9351
±0.0006 | |
| 100 | GraphMAE | 0.8834
±0.0027 | prev best: HAT-GAE: Self-Supervised Graph Auto-encoders with Hierarchical Adaptive Masking and Trainable Corruption (2023) best today: Discrepancy-Aware Graph Mask Auto-Encoder (KDD 2025) Improvement within reported uncertainty; not highlighted. |
| 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) |
| 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. |
| 179 | MVGRL | 0.8861
±0.0064 best reported | best at pub: Graph Contrastive Learning with Adaptive Augmentation (WWW 2020) |
| 187 | SeeGera-v1 | 0.8844
±0.0024 | This paper |
| 190 | SeeGera-v2 | 0.8839
±0.0026 | This paper |
| 191 | SeeGera-v3 | 0.8839
±0.0026 | 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) |
| 320 | MLP | 0.8463 |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | GrokFormer | 0.9831
±0.0018 | |
| 2 | PolyFormer | 0.9808
±0.0027 | |
| 3 | SGFormer | 0.9796
±0.0081 | |
| 9 | GCN | 0.9774
±0.0035 | |
| 58 | MLP | 0.9597
±0.0007 | |
| 77 | GRACE | 0.9574
±0.0006 best reported | best at pub: Beyond Smoothing: Unsupervised Graph Representation Learning with Edge Heterophily Discriminating (AAAI 2022) best today: Learn Beneficial Noise as Graph Augmentation (ICML 2025) |
| 106 | CCA-SSG | 0.9559
±0.0007 best reported | best at pub: Wiener Graph Deconvolutional Network Improves Graph Self-Supervised Learning (AAAI 2022) |
| 117 | GraphMAE | 0.9550
±0.0010 best reported | |
| 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. |
| 130 | SeeGera-v1 | 0.9540
±0.0010 | This paper |
| 132 | SeeGera-v2 | 0.9539
±0.0008 | This paper |
| 133 | SeeGera-v3 | 0.9539
±0.0008 | 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. |
