Efficient Heterogeneous Graph Learning via Random Projection
Abstract
Heterogeneous Graph Neural Networks (HGNNs) are powerful tools for deep learning on heterogeneous graphs. Typical HGNNs require repetitive message passing during training, limiting efficiency for large-scale real-world graphs. Recent pre-computation-based HGNNs use one-time message passing to transform a heterogeneous graph into regular-shaped tensors, enabling efficient mini-batch training. Existing pre-computation-based HGNNs can be mainly categorized into two styles, which differ in how much information loss is allowed and efficiency. We propose a hybrid pre-computation-based HGNN, named Random Projection Heterogeneous Graph Neural Network (RpHGNN), which combines the benefits of one style's efficiency with the low information loss of the other style. To achieve efficiency, the main framework of RpHGNN consists of propagate-then-update iterations, where we introduce a Random Projection Squashing step to ensure that complexity increases only linearly. To achieve low information loss, we introduce a Relation-wise Neighbor Collection component with an Even-odd Propagation Scheme, which aims to collect information from neighbors in a finer-grained way. Experimental results indicate that our approach achieves state-of-the-art results on seven small and large benchmark datasets while also being 230\ Surprisingly, our approach not only surpasses pre-processing-based baselines but also outperforms end-to-end methods..
Benchmark Results
Tested on 5 datasets 21 baseline values reported too low
Tables show presented results in global context (best 3 papers + GCN + MLP).
OGB
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | LMSPS+LP+MS | 0.5784
±0.0022 | |
| 2 | SeHGNN+emb+ms | 0.5719
±0.0012 | |
| 3 | SeHGNN+ms | 0.5671
±0.0014 | |
| 19 | SeHGNN | 0.5399
±0.0018 best reported | best at pub: Simple and Efficient Heterogeneous Graph Neural Network (AAAI 2022) |
| 28 | NARS | 0.5240
±0.0016 best reported | best at pub: Graph Attention MLP with Reliable Label Utilization (2021) best today: SCR: Training Graph Neural Networks with Consistency Regularization (2021) |
| 32 | RpHGNN | 0.5207
±0.0017 | This paper |
| 42 | HGT | 0.5023
±0.0048 best reported | best at pub: Graph Attention MLP with Reliable Label Utilization (2021) |
| 48 | RGCN | 0.4811
±0.0048 | prev best: Heterogeneous Graph Representation Learning with Relation Awareness (2021) Improvement within reported uncertainty; not highlighted. |
| 57 | GraphSAGE | 0.4646
±0.0060 | prev best: Heterogeneous Graph Representation Learning with Relation Awareness (2021) |
| 60 | GCN | 0.4290
±0.0050 | |
| 76 | MLP | 0.3243 |
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 | This paper |
| 5 | SeHGNN | 0.9542
±0.0017 best reported | best at pub: Simple and Efficient Heterogeneous Graph Neural Network (AAAI 2022) best today: Spectral Heterogeneous Graph Convolutions via Positive Noncommutative Polynomials (WWW 2023) Difference within reported uncertainty; not counted as underperformance. |
| 13 | HINormer | 0.9494
±0.0021 | This paper |
| 20 | NARS | 0.9461
±0.0042 | This paper |
| 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 | 0.9448
±0.0022 best reported | best at pub: Heterogeneous Graph Benchmarks (KDD 2021) best today: Graph Neural Networks with a Distribution of Parametrized Graphs (ICML 2023) |
| 24 | Simple-HGN | 0.9448
±0.0038 best reported | best at pub: Heterogeneous Graph Benchmarks (KDD 2021) 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 at pub: Heterogeneous Graph Benchmarks (KDD 2021) 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 | best at pub: Heterogeneous Graph Contrastive Multi-view Learning (2022) |
| 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 | prev best: Gophormer: Ego-Graph Transformer for Node Classification (2021) |
| 66 | RGCN | 0.9207
±0.0050 | This paper |
| 88 | GIN | 0.8720 | |
| 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 | |
| 4 | RpHGNN | 0.9404
±0.0059 | This paper |
| 5 | SeHGNN | 0.9398
±0.0036 best reported | best at pub: Simple and Efficient Heterogeneous Graph Neural Network (AAAI 2022) best today: Spectral Heterogeneous Graph Convolutions via Positive Noncommutative Polynomials (WWW 2023) Difference within reported uncertainty; not counted as underperformance. |
| 7 | HINormer | 0.9383
±0.0045 best reported | best at pub: Long-range Meta-path Search on Large-scale Heterogeneous Graphs (NeurIPS 2023) |
| 11 | Simple-HGN | 0.9335
±0.0045 | This paper |
| 14 | NARS | 0.9331
±0.0033 | 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 at pub: Heterogeneous Graph Benchmarks (KDD 2021) best today: Revisiting Self-Supervised Heterogeneous Graph Learning from Spectral Clustering Perspective (NeurIPS 2024) Difference within reported uncertainty; not counted as underperformance. |
| 43 | HAN | 0.9147
±0.0022 best reported | best at pub: Heterogeneous Graph Benchmarks (KDD 2021) 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 |
| 52 | GraphSAGE | 0.9063
±0.0076 | prev best: Mixed Graph Contrastive Network for Semi-Supervised Node Classification (2022) |
| 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 | Micro-F1 ↑ | Paper |
|---|---|---|---|
| 1 | ELLA | 0.7930
±0.0010 | |
| 2 | MHGCN | 0.7820
±0.0138 | |
| 3 | PSHGCN | 0.7446
±0.0032 | |
| 5 | SeHGNN | 0.7342
±0.0047 best reported | best at pub: Spectral Heterogeneous Graph Convolutions via Positive Noncommutative Polynomials (WWW 2023) |
| 7 | RpHGNN | 0.6977
±0.0066 | This paper |
| 13 | GTN | 0.6827
±0.0065 best reported | best at pub: Spectral Heterogeneous Graph Convolutions via Positive Noncommutative Polynomials (WWW 2023) |
| 14 | GCN | 0.6813
±0.0083 best reported | best at pub: Spectral Heterogeneous Graph Convolutions via Positive Noncommutative Polynomials (WWW 2023) |
| 15 | GAT | 0.6808
±0.0049 best reported | best at pub: Spectral Heterogeneous Graph Convolutions via Positive Noncommutative Polynomials (WWW 2023) |
| 16 | HINormer | 0.6783
±0.0034 | This paper |
| 17 | MAGNN | 0.6782
±0.0154 best reported | best at pub: Spectral Heterogeneous Graph Convolutions via Positive Noncommutative Polynomials (WWW 2023) |
| 18 | HAN | 0.6769
±0.0064 best reported | best at pub: Spectral Heterogeneous Graph Convolutions via Positive Noncommutative Polynomials (WWW 2023) |
| 22 | Simple-HGN | 0.6736
±0.0057 | This paper |
| 24 | HGT | 0.6720
±0.0057 | This paper |
| 26 | RGCN | 0.6651
±0.0028 best reported | best at pub: Spectral Heterogeneous Graph Convolutions via Positive Noncommutative Polynomials (WWW 2023) |
| 28 | NARS | 0.6618
±0.0070 | This paper |
| 35 | RSHN | 0.6422
±0.0103 | This paper |
| 44 | GraphSAGE | 0.6276 best reported | best at pub: Heterogeneous Graph Representation Learning with Relation Awareness (2021) Difference within reported uncertainty; not counted as underperformance. |
| 53 | HetSANN | 0.6069 best reported | best at pub: Heterogeneous Graph Representation Learning with Relation Awareness (2021) |
| 74 | MLP | 0.5514 | |
| 83 | HetGNN | 0.5116
±0.0065 | This paper |
| # | 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 | |
| 20 | RpHGNN | 0.5402
±0.0088 | This paper |
| 22 | HINormer | 0.5218
±0.0039 best reported | best at pub: Long-range Meta-path Search on Large-scale Heterogeneous Graphs (NeurIPS 2023) Difference within reported uncertainty; not counted as underperformance. |
| 23 | SeHGNN | 0.5187
±0.0086 best reported | best at pub: Simple and Efficient Heterogeneous Graph Neural Network (AAAI 2022) Difference within reported uncertainty; not counted as underperformance. |
| 25 | GAT | 0.5109 best reported | |
| 26 | NARS | 0.4998
±0.0177 | This paper |
| 29 | Simple-HGN | 0.4772
±0.0148 | This paper |
| 32 | RGCN | 0.4678
±0.0077 | This paper |
| 34 | GraphSAGE | 0.4417
±0.0114 | This paper |
