WWW 2023

HetGPT: Harnessing the Power of Prompt Tuning in Pre-Trained Heterogeneous Graph Neural Networks

Yihong Ma, Ning Yan, Jiayu Li, Masood Mortazavi, Nitesh V. Chawla

Main figure for 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

#ModelMicro-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
actual #22 vs paper #70 48 places worse
0.9456
best reported
actual #22 vs paper #70 48 places worse
paper 0.9158 ±0.0048
paper 0.9158 ±0.0048 Δ at pub 0.0298
37
HAN
actual #37 vs paper #70 33 places worse
0.9369
best reported
actual #37 vs paper #70 33 places worse
paper 0.9170 ±0.0042
39
HGT
actual #39 vs paper #74 35 places worse
0.9365
best reported
actual #39 vs paper #74 35 places worse
paper 0.9085 ±0.0567

Difference within reported uncertainty; not counted as underperformance.

paper 0.9085 ±0.0567 Δ at pub 0.0280
41
HGMAE
actual #41 vs paper #64 23 places worse
0.9340 ±0.0060
best reported
actual #41 vs paper #64 23 places worse
paper 0.9213 ±0.0027
paper 0.9213 ±0.0027 Δ today 0.0127
44
DMGI
actual #44 vs paper #93 49 places worse
0.9331
best reported
actual #44 vs paper #93 49 places worse
paper 0.8654 ±0.0095
59
HetGPT + HDMI
0.9246 ±0.0029
This paper
62
HeCo
actual #62 vs paper #68 6 places worse
0.9224 ±0.0048
best reported
actual #62 vs paper #68 6 places worse
paper 0.9183 ±0.0025

Difference within reported uncertainty; not counted as underperformance.

paper 0.9183 ±0.0025 Δ at pub 0.0041
63
HetGPT + HeCo
0.9222 ±0.0016
This paper
64
HDMI
actual #64 vs paper #64
0.9216 ±0.0014
actual #64 vs paper #64
paper 0.9216 ±0.0014
paper 0.9216 ±0.0014 Δ at pub 0.1106
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) .

#ModelMicro-F1 ↑ defaultMi-F1 (Micro-F1) ↑Paper
1
LMSPS
0.9469 ± 0.0036
—
2
PSHGCN
0.9427 ± 0.0023
—
3
SlotGAT
0.9406 ± 0.0022
—
29
GCN
0.9229
—
38
HDMI + HetGPT
0.9194 ± 0.0033
—
Mi-F1 (Micro-F1) —
This paper
41
HGT
0.9160 ±0.0060
best reported
—
Mi-F1 (Micro-F1) —
paper 0.8621 ±0.0368
best at pub: Heterogeneous Graph Benchmarks (KDD 2021)

Difference within reported uncertainty; not counted as underperformance.

paper 0.8621 ±0.0368 Δ at pub 0.0479 Δ today 0.0539
43
HAN
0.9147 ±0.0022
best reported
—
Mi-F1 (Micro-F1) —
paper 0.8624 ±0.0067
best at pub: Heterogeneous Graph Benchmarks (KDD 2021)
paper 0.8624 ±0.0067 Δ at pub 0.0455 Δ today 0.0523
47
HDMI
0.9116 ± 0.0056
—
Mi-F1 (Micro-F1) —
This paper
51
MAGNN
0.9077 ±0.0065
best reported
—
Mi-F1 (Micro-F1) —
paper 0.8639 ±0.0069
best at pub: Heterogeneous Graph Benchmarks (KDD 2021)
paper 0.8639 ±0.0069 Δ at pub 0.0438 Δ today 0.0438
53
HGMAE
0.9060 ±0.0070
best reported
—
Mi-F1 (Micro-F1) —
paper 0.8859 ±0.0071
paper 0.8859 ±0.0071 Δ today 0.0201
62
DMGI+HetGPT
0.9013 ± 0.0043
—
Mi-F1 (Micro-F1) —
This paper
64
DMGI
0.8980 ±0.0010
best reported
—
Mi-F1 (Micro-F1) —
paper 0.8834 ±0.0063
best at pub: Implicit Graph Neural Networks (NeurIPS 2020)
paper 0.8834 ±0.0063 Δ at pub 0.0146 Δ today 0.0146
68
HeCo
0.8897 ±0.0112
best reported
—
Mi-F1 (Micro-F1) —
paper 0.8848 ±0.0094

Difference within reported uncertainty; not counted as underperformance.

paper 0.8848 ±0.0094 Δ at pub 0.0049
70
HeCo + HetGPT
0.8891 ± 0.0062
—
Mi-F1 (Micro-F1) —
This paper
102
GPPT
—
0.8416 ± 0.0045
Mi-F1 (Micro-F1) 0.8416 ± 0.0045
This paper
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) .

#ModelMicro-F1 ↑ defaultMi-F1 (Micro-F1) ↑Paper
1
ELLA
0.7930 ± 0.0010
—
2
MHGCN
0.7820 ± 0.0138
—
3
PSHGCN
0.7446 ± 0.0032
—
14
GCN
0.6813 ± 0.0083
—
17
MAGNN
0.6782 ±0.0154
best reported
—
Mi-F1 (Micro-F1) —
paper 0.4897 ±0.0038
paper 0.4897 ±0.0038 Δ at pub 0.1885
18
HAN
0.6769 ±0.0064
best reported
—
Mi-F1 (Micro-F1) —
paper 0.4951 ±0.0072
paper 0.4951 ±0.0072 Δ at pub 0.1818
24
HGT
0.6720 ±0.0057
best reported
—
Mi-F1 (Micro-F1) —
paper 0.5153 ±0.0106
best at pub: Heterogeneous Graph Benchmarks (KDD 2021)
paper 0.5153 ±0.0106 Δ at pub 0.1567 Δ today 0.1567
29
HDMI
0.6580
best reported
—
Mi-F1 (Micro-F1) —
paper 0.5217 ±0.0167
paper 0.5217 ±0.0167 Δ at pub 0.1363
33
DMGI
0.6480
best reported
—
Mi-F1 (Micro-F1) —
paper 0.5114 ±0.0125
best at pub: Implicit Graph Neural Networks (NeurIPS 2020)
paper 0.5114 ±0.0125 Δ at pub 0.1366 Δ today 0.1366
74
MLP
0.5514
—
78
HDMI + HetGPT
0.5383 ± 0.0136
—
Mi-F1 (Micro-F1) —
This paper
82
HeCo
0.5212 ±0.0072
best reported
—
Mi-F1 (Micro-F1) —
paper 0.4812 ±0.0127
paper 0.4812 ±0.0127 Δ at pub 0.0400
88
DMGI+HetGPT
—
0.4939 ± 0.0098
Mi-F1 (Micro-F1) 0.4939 ± 0.0098
This paper
88
HeCo + HetGPT
0.4919 ± 0.0142
—
Mi-F1 (Micro-F1) —
This paper
93
HGMAE
0.4660 ± 0.0230
—
Mi-F1 (Micro-F1) —
This paper
102
GPPT
—
0.4485 ± 0.0058
Mi-F1 (Micro-F1) 0.4485 ± 0.0058
This paper
SOTA performance (not significantly different from the best) Proposed method (this paper) Baseline / comparison (this paper) Global context (other papers) Best at pub — reported result worse than the best known when published (best reported in green) Best at pub — reported value improved over the best known when published Best today — OK at publication; today's leaderboard best is elsewhere