HetGPT: Harnessing the Power of Prompt Tuning in Pre-Trained Heterogeneous Graph Neural Networks
Abstract
Graphs have emerged as a natural choice to represent and analyze the intricate patterns and rich information of the Web, enabling applications such as online page classification and social recommendation. The prevailing ``pre-train, fine-tune'' paradigm has been widely adopted in graph machine learning tasks, particularly in scenarios with limited labeled nodes. However, this approach often exhibits a misalignment between the training objectives of pretext tasks and those of downstream tasks. This gap can result in the ``negative transfer'' problem, wherein the knowledge gained from pre-training adversely affects performance in the downstream tasks. The surge in prompt-based learning within Natural Language Processing (NLP) suggests the potential of adapting a ``pre-train, prompt" paradigm to graphs as an alternative. However, existing graph prompting techniques are tailored to homogeneous graphs, neglecting the inherent heterogeneity of Web graphs. To bridge this gap, we propose HetGPT, a general post-training prompting framework to improve the predictive performance of pre-trained heterogeneous graph neural networks (HGNNs). The key is the design of a novel prompting function that integrates a virtual class prompt and a heterogeneous feature prompt, with the aim to reformulate downstream tasks to mirror pretext tasks. Moreover, HetGPT introduces a multi-view neighborhood aggregation mechanism, capturing the complex neighborhood structure in heterogeneous graphs. Extensive experiments on three benchmark datasets demonstrate HetGPT's capability to enhance the performance of state-of-the-art HGNNs on semi-supervised node classification.
Benchmark Results
Tested on 3 datasets 12 baseline values reported too low
Tables show presented results in global context (best 3 papers + GCN + MLP).
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 | |
| 22 | MAGNN | 0.9456 best reported | |
| 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. |
| 41 | HGMAE | 0.9340
±0.0060 best reported | best today: Revisiting Self-Supervised Heterogeneous Graph Learning from Spectral Clustering Perspective (NeurIPS 2024) |
| 44 | DMGI | 0.9331 best reported | best at pub: Heterogeneous Graph Contrastive Multi-view Learning (2022) |
| 59 | HetGPT + HDMI | 0.9246
±0.0029 | This paper |
| 62 | HeCo | 0.9224
±0.0048 best reported | best at pub: Heterogeneous Graph Contrastive Multi-view Learning (2022) Difference within reported uncertainty; not counted as underperformance. |
| 63 | HetGPT + HeCo | 0.9222
±0.0016 | This paper |
| 64 | HDMI | 0.9216
±0.0014 | prev best: Relational Self-Supervised Learning on Graphs (2022) |
| 118 | DMGI + HetGPT | 0.8283
±0.0163 | This paper |
| 156 | GPPT | 0.7456
±0.0064 | This paper |
| 176 | MLP | 0.6447
±0.0136 |
ACM
Global leaderboard →Default metric is Micro-F1. The paper reports 10 values on Micro-F1 and 1 value on Mi-F1 (Micro-F1) .
| # | Model | Micro-F1 ↑ default | Mi-F1 (Micro-F1) ↑ | Paper |
|---|---|---|---|---|
| 1 | LMSPS | 0.9469
±
0.0036 | — | Mi-F1 (Micro-F1)
— |
| 2 | PSHGCN | 0.9427
±
0.0023 | — | |
| 3 | SlotGAT | 0.9406
±
0.0022 | — | Mi-F1 (Micro-F1)
— |
| 29 | GCN | 0.9229 | — | |
| 38 | HDMI + HetGPT | 0.9194
±
0.0033 | — | Mi-F1 (Micro-F1)
— |
| 41 | HGT | 0.9160
±0.0060 best reported | — | Mi-F1 (Micro-F1)
— 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 | — | Mi-F1 (Micro-F1)
— best at pub: Heterogeneous Graph Benchmarks (KDD 2021) best today: Beyond Redundancy: Information-aware Unsupervised Multiplex Graph Structure Learning (NeurIPS 2024) |
| 47 | HDMI | 0.9116
±
0.0056 | — | Mi-F1 (Micro-F1)
— |
| 51 | MAGNN | 0.9077
±0.0065 best reported | — | Mi-F1 (Micro-F1)
— best at pub: Heterogeneous Graph Benchmarks (KDD 2021) best today: SlotGAT: Slot-based Message Passing for Heterogeneous Graphs (ICML 2024) |
| 53 | HGMAE | 0.9060
±0.0070 best reported | — | Mi-F1 (Micro-F1)
— best today: Revisiting Self-Supervised Heterogeneous Graph Learning from Spectral Clustering Perspective (NeurIPS 2024) |
| 62 | DMGI+HetGPT | 0.9013
±
0.0043 | — | Mi-F1 (Micro-F1)
— |
| 64 | DMGI | 0.8980
±0.0010 best reported | — | Mi-F1 (Micro-F1)
— best at pub: Implicit Graph Neural Networks (NeurIPS 2020) best today: Revisiting Self-Supervised Heterogeneous Graph Learning from Spectral Clustering Perspective (NeurIPS 2024) |
| 68 | HeCo | 0.8897
±0.0112 best reported | — | Mi-F1 (Micro-F1)
— best at pub: Heterogeneous Graph Contrastive Multi-view Learning (2022) Difference within reported uncertainty; not counted as underperformance. |
| 70 | HeCo + HetGPT | 0.8891
±
0.0062 | — | Mi-F1 (Micro-F1)
— |
| 102 | GPPT | —
| 0.8416
±
0.0045 | Mi-F1 (Micro-F1)
0.8416
±
0.0045 |
| 109 | MLP | 0.7102
±
0.0221 | — |
IMDB
Global leaderboard →Default metric is Micro-F1. The paper reports 9 values on Micro-F1 and 2 values on Mi-F1 (Micro-F1) .
| # | Model | Micro-F1 ↑ default | Mi-F1 (Micro-F1) ↑ | Paper |
|---|---|---|---|---|
| 1 | ELLA | 0.7930
±
0.0010 | — | Mi-F1 (Micro-F1)
— |
| 2 | MHGCN | 0.7820
±
0.0138 | — | Mi-F1 (Micro-F1)
— |
| 3 | PSHGCN | 0.7446
±
0.0032 | — | |
| 14 | GCN | 0.6813
±
0.0083 | — | |
| 17 | MAGNN | 0.6782
±0.0154 best reported | — | Mi-F1 (Micro-F1)
— best at pub: Spectral Heterogeneous Graph Convolutions via Positive Noncommutative Polynomials (WWW 2023) |
| 18 | HAN | 0.6769
±0.0064 best reported | — | Mi-F1 (Micro-F1)
— best at pub: Spectral Heterogeneous Graph Convolutions via Positive Noncommutative Polynomials (WWW 2023) |
| 24 | HGT | 0.6720
±0.0057 best reported | — | Mi-F1 (Micro-F1)
— best at pub: Heterogeneous Graph Benchmarks (KDD 2021) best today: SlotGAT: Slot-based Message Passing for Heterogeneous Graphs (ICML 2024) |
| 29 | HDMI | 0.6580 best reported | — | Mi-F1 (Micro-F1)
— best at pub: Relational Self-Supervised Learning on Graphs (2022) |
| 33 | DMGI | 0.6480 best reported | — | Mi-F1 (Micro-F1)
— best at pub: Implicit Graph Neural Networks (NeurIPS 2020) best today: Relational Self-Supervised Learning on Graphs (2022) |
| 74 | MLP | 0.5514 | — | Mi-F1 (Micro-F1)
— |
| 78 | HDMI + HetGPT | 0.5383
±
0.0136 | — | Mi-F1 (Micro-F1)
— |
| 82 | HeCo | 0.5212
±0.0072 best reported | — | Mi-F1 (Micro-F1)
— best at pub: Heterogeneous Graph Contrastive Multi-view Learning (2022) |
| 88 | DMGI+HetGPT | —
| 0.4939
±
0.0098 | Mi-F1 (Micro-F1)
0.4939
±
0.0098 |
| 88 | HeCo + HetGPT | 0.4919
±
0.0142 | — | Mi-F1 (Micro-F1)
— |
| 93 | HGMAE | 0.4660
±
0.0230 | — | Mi-F1 (Micro-F1)
— |
| 102 | GPPT | —
| 0.4485
±
0.0058 | Mi-F1 (Micro-F1)
0.4485
±
0.0058 |
