WWW 2023

SeeGera: Self-supervised Semi-implicit Graph Variational Auto-encoders with Masking

Xiang Li, Tiandi Ye, Caihua Shan, Dongsheng Li, Ming Gao

Main figure for 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

#ModelAccuracy ↑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
actual #164 vs paper #222 58 places worse
0.9341 ±0.0010
best reported
actual #164 vs paper #222 58 places worse
paper 0.9298 ±0.0035

Difference within reported uncertainty; not counted as underperformance.

paper 0.9298 ±0.0035 Δ at pub 0.0003 Δ today 0.0043
186
CCA-SSG
actual #186 vs paper #201 15 places worse
0.9325 ±0.0021
best reported
actual #186 vs paper #201 15 places worse
paper 0.9314 ±0.0014

Difference within reported uncertainty; not counted as underperformance.

paper 0.9314 ±0.0014 Δ at pub 0.0011
203
GRACE
actual #203 vs paper #324 121 places worse
0.9313 ±0.0017
best reported
actual #203 vs paper #324 121 places worse
paper 0.9215 ±0.0024
paper 0.9215 ±0.0024 Δ at pub 0.0065 Δ today 0.0098
206
MVGRL
actual #206 vs paper #359 153 places worse
0.9310 ±0.0040
best reported
actual #206 vs paper #359 153 places worse
paper 0.9174 ±0.0007
213
DGI
actual #213 vs paper #366 153 places worse
0.9309 ±0.0008
best reported
actual #213 vs paper #366 153 places worse
paper 0.9161 ±0.0022
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
#ModelAccuracy ↑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
actual #100 vs paper #193 93 places worse
0.8834 ±0.0027
actual #100 vs paper #193 93 places worse
paper 0.8834 ±0.0027

Improvement within reported uncertainty; not highlighted.

paper 0.8834 ±0.0027 Δ at pub 0.0002 Δ today 0.0168
139
GRACE
actual #139 vs paper #282 143 places worse
0.8953 ±0.0035
best reported
actual #139 vs paper #282 143 places worse
paper 0.8625 ±0.0025
paper 0.8625 ±0.0025 Δ at pub 0.0328 Δ today 0.0328
159
CCA-SSG
actual #159 vs paper #171 12 places worse
0.8896 ±0.0013
best reported
actual #159 vs paper #171 12 places worse
paper 0.8874 ±0.0028

Difference within reported uncertainty; not counted as underperformance.

paper 0.8874 ±0.0028 Δ today 0.0022
179
MVGRL
actual #179 vs paper #235 56 places worse
0.8861 ±0.0064
best reported
actual #179 vs paper #235 56 places worse
paper 0.8752 ±0.0011
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
actual #210 vs paper #354 144 places worse
0.8798 ±0.0081
best reported
actual #210 vs paper #354 144 places worse
paper 0.8395 ±0.0047
320
MLP
0.8463
#ModelAccuracy ↑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
actual #77 vs paper #140 63 places worse
0.9574 ±0.0006
best reported
actual #77 vs paper #140 63 places worse
paper 0.9526 ±0.0002
paper 0.9526 ±0.0002 Δ at pub 0.0013 Δ today 0.0048
106
CCA-SSG
actual #106 vs paper #133 27 places worse
0.9559 ±0.0007
best reported
actual #106 vs paper #133 27 places worse
paper 0.9538 ±0.0006
paper 0.9538 ±0.0006 Δ at pub 0.0021
117
GraphMAE
actual #117 vs paper #136 19 places worse
0.9550 ±0.0010
best reported
actual #117 vs paper #136 19 places worse
paper 0.9530 ±0.0012
125
MVGRL
actual #125 vs paper #134 9 places worse
0.9544 ±0.0027
best reported
actual #125 vs paper #134 9 places worse
paper 0.9533 ±0.0003

Difference within reported uncertainty; not counted as underperformance.

paper 0.9533 ±0.0003 Δ at pub 0.0011
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
actual #167 vs paper #174 7 places worse
0.9489 ±0.0009
best reported
actual #167 vs paper #174 7 places worse
paper 0.9451 ±0.0052

Difference within reported uncertainty; not counted as underperformance.

paper 0.9451 ±0.0052 Δ at pub 0.0006 Δ today 0.0038
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 today — OK at publication; today's leaderboard best is elsewhere