Heterogeneous Graph Benchmarks
Abstract
Heterogeneous graph neural networks (HGNNs) have been blossoming in recent years, but the unique data processing and evaluation setups used by each work obstruct a full understanding of their advancements. In this work, we present a systematical reproduction of 12 recent HGNNs by using their official codes, datasets, settings, and hyperparameters, revealing surprising findings about the progress of HGNNs. We find that the simple homogeneous GNNs, e.g., GCN and GAT, are largely underestimated due to improper settings. GAT with proper inputs can generally match or outperform all existing HGNNs across various scenarios. To facilitate robust and reproducible HGNN research, we construct the Heterogeneous Graph Benchmark (HGB), and the HGB leaderboard is at linkcolor., consisting of 11 diverse datasets with three tasks. HGB standardizes the process of heterogeneous graph data splits, feature processing, and performance evaluation. Finally, we introduce a simple but very strong baseline Simple-HGN ---which significantly outperforms all previous models on HGB---to accelerate the advancement of HGNNs in the future.
Benchmark Results
Tested on 5 datasets 13 baseline values reported too low
Tables show presented results in global context (best 3 papers + GCN + MLP).
TU Dortmund
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | MSH-GNN | 0.9910
±0.0030 | |
| 2 | ID-GNN+BEC | 0.9830
±0.0360 | |
| 3 | SupCosine | 0.9830
±0.0250 | |
| 39 | GIN | 0.9330
±0.0290 | |
| 63 | GCN | 0.9220
±0.0440 best reported | best at pub: Breaking the Limits of Message Passing Graph Neural Networks (ICML 2021) best today: Depth-Adaptive Graph Neural Networks via Learnable Bakry-Émery Curvature (KDD 2025) |
| 183 | GAT | 0.9010
±0.0580 best reported | best at pub: Breaking the Limits of Message Passing Graph Neural Networks (ICML 2021) best today: The Expressive Power of Graph Neural Networks: A Survey (2023) |
| 403 | MLP | 0.8660
±0.0495 | |
| 557 | HAN | 0.8235 | This paper |
| 558 | GTN | 0.8235 | This paper |
| 559 | RSHN | 0.8235 | This paper |
Heterogeneous Graph Benchmarks
| # | Model | Micro-F1 ↑ | Paper |
|---|---|---|---|
| 1 | LMSPS | 0.9566
±0.0020 | |
| 2 | PSHGCN | 0.9561
±0.0012 | |
| 3 | RpHGNN | 0.9555
±0.0029 | |
| 21 | GCN | 0.9460
±0.0031 best reported | best at pub: Leveraging Meta-path Contexts for Classification in Heterogeneous Information Networks (2020) best today: Graph Neural Networks with a Distribution of Parametrized Graphs (ICML 2023) |
| 22 | MAGNN | 0.9456 best reported | |
| 23 | GAT | 0.9339
±0.0030 | prev best: Leveraging Meta-path Contexts for Classification in Heterogeneous Information Networks (2020) best today: Graph Neural Networks with a Distribution of Parametrized Graphs (ICML 2023) |
| 24 | Simple-HGN | 0.9448
±0.0038 best reported | best today: Graph Neural Networks with a Distribution of Parametrized Graphs (ICML 2023) Difference within reported uncertainty; not counted as underperformance. |
| 32 | GTN | 0.9417
±0.0026 best reported | best today: Graph Neural Networks with a Distribution of Parametrized Graphs (ICML 2023) Difference within reported uncertainty; not counted as underperformance. |
| 35 | RSHN | 0.9381
±0.0055 | This paper |
| 37 | HAN | 0.9369 best reported | |
| 39 | HGT | 0.9365 best reported | best at pub: Leveraging Meta-path Contexts for Classification in Heterogeneous Information Networks (2020) Difference within reported uncertainty; not counted as underperformance. |
| 43 | HetGNN | 0.9336 best reported | |
| 46 | GraphSAGE | 0.9306
±0.0047 | |
| 66 | RGCN | 0.9207
±0.0050 | This paper |
| 132 | HetSANN | 0.8056
±0.0150 | This paper |
| 176 | MLP | 0.6447
±0.0136 |
| # | Model | Micro-F1 ↑ | Paper |
|---|---|---|---|
| 1 | LMSPS | 0.9469
±0.0036 | |
| 2 | PSHGCN | 0.9427
±0.0023 | |
| 3 | SlotGAT | 0.9406
±0.0022 | |
| 11 | Simple-HGN | 0.9335
±0.0045 | This paper |
| 19 | GAT | 0.9273 best reported | best at pub: Self-supervised Auxiliary Learning with Meta-paths for Heterogeneous Graphs (NeurIPS 2020) Difference within reported uncertainty; not counted as underperformance. |
| 22 | GTN | 0.9258 best reported | best at pub: Self-supervised Auxiliary Learning with Meta-paths for Heterogeneous Graphs (NeurIPS 2020) |
| 29 | GCN | 0.9229 best reported | best at pub: Self-supervised Auxiliary Learning with Meta-paths for Heterogeneous Graphs (NeurIPS 2020) Difference within reported uncertainty; not counted as underperformance. |
| 41 | HGT | 0.9160
±0.0060 best reported | best today: Revisiting Self-Supervised Heterogeneous Graph Learning from Spectral Clustering Perspective (NeurIPS 2024) Difference within reported uncertainty; not counted as underperformance. |
| 43 | HAN | 0.9079
±0.0043 | prev best: Implicit Graph Neural Networks (NeurIPS 2020) best today: Beyond Redundancy: Information-aware Unsupervised Multiplex Graph Structure Learning (NeurIPS 2024) |
| 44 | RGCN | 0.9141
±0.0075 | This paper |
| 49 | GIN | 0.9092 | |
| 51 | MAGNN | 0.9077
±0.0065 | This paper |
| 60 | RSHN | 0.9032
±0.0154 | This paper |
| 63 | HetSANN | 0.8991
±0.0037 | This paper |
| 92 | HetGNN | 0.8605
±0.0025 | This paper |
| 109 | MLP | 0.7102
±0.0221 |
| # | Model | Macro-F1 ↑ | Paper |
|---|---|---|---|
| 1 | ConCH | 0.6475 | |
| 2 | HetGNN | 0.6292 | |
| 3 | GC-HGNN | 0.6247
±0.0042 | |
| 5 | HGT | 0.6176 best reported | |
| 7 | GCN | 0.6090 best reported | |
| 10 | HAN | 0.6011 best reported | |
| 25 | GAT | 0.5109 best reported | |
| 29 | Simple-HGN | 0.4772
±0.0148 | This paper |
| 32 | RGCN | 0.4678
±0.0077 | This paper |
| 34 | GraphSAGE | 0.4417
±0.0114 |
