NeurIPS 2024

Text-space Graph Foundation Models: Comprehensive Benchmarks and New Insights

Zhikai Chen, Haitao Mao, Jingzhe Liu, Yu Song, Bingheng Li, Wei-dong Jin, Bahare Fatemi, Anton Tsitsulin, Bryan Perozzi, Hui Liu, Jiliang Tang

Main figure for Text-space Graph Foundation Models: Comprehensive Benchmarks and New Insights

Abstract

Given the ubiquity of graph data and its applications in diverse domains, building a Graph Foundation Model (GFM) that can work well across different graphs and tasks with a unified backbone has recently garnered significant interests. A major obstacle to achieving this goal stems from the fact that graphs from different domains often exhibit diverse node features. Inspired by multi-modal models that align different modalities with natural language, the text has recently been adopted to provide a unified feature space for diverse graphs. Despite the great potential of these text-space GFMs, current research in this field is hampered by two problems. First, the absence of a comprehensive benchmark with unified problem settings hinders a clear understanding of the comparative effectiveness and practical value of different text-space GFMs. Second, there is a lack of sufficient datasets to thoroughly explore the methods' full potential and verify their effectiveness across diverse settings. To address these issues, we conduct a comprehensive benchmark providing novel text-space datasets and comprehensive evaluation under unified problem settings. Empirical results provide new insights and inspire future research directions. Our code and data are publicly available from.

Benchmark Results

Tested on 11 datasets 4 baseline values reported too low

Tables show presented results in global context (best 3 papers + GCN + MLP).

Classic

#ModelAccuracy ↑Paper
1
GraphSAGE+CNA
0.9418 ±0.0033
2
GCN+CNA
0.9366 ±0.0048
3
TransformerConv
0.9350 ±0.0058
21
GCN
0.9004
124
LLaGA
actual #124 vs paper #586 462 places worse
0.8745
best reported
actual #124 vs paper #586 462 places worse
paper 0.8125
177
DGI
actual #177 vs paper #550 373 places worse
0.8630 ±0.0020
best reported
actual #177 vs paper #550 373 places worse
paper 0.8180
paper 0.8180 Δ at pub 0.0450
280
GraphMAE
actual #280 vs paper #606 326 places worse
0.8420 ±0.0040
best reported
actual #280 vs paper #606 326 places worse
paper 0.8100
paper 0.8100 Δ today 0.0320
680
OFA
0.7941
This paper
724
MLP
0.7768
788
mpnet
0.7403
This paper
842
minilm
0.6755
This paper
#ModelAccuracy ↑Paper
1
CNA
0.9575 ±0.0058
2
IS-GIB
0.9390 ±0.0187
3
EERM
0.9112 ±0.0145
44
GCN
0.8033 ±0.0088
209
GraphMAE
actual #209 vs paper #209
0.7436
actual #209 vs paper #209
paper 0.7436
350
MLP
0.7289 ±0.0010
659
LLaGA
0.6880
This paper
#ModelAccuracy ↑Paper
1
LGTL
0.9518 ±0.0011
2
MixHop (LO)
0.9513 ±0.0038
3
GraphSAGE (LO)
0.9511 ±0.0036
18
GCN
0.9296 ±0.0015
210
MLP
0.8690 ±0.0074
760
mpnet
0.7637
This paper
820
minilm
0.7259
This paper
#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
8
GCN
actual #8 vs paper #524 516 places worse
0.9632 ±0.0008
best reported
actual #8 vs paper #524 516 places worse
paper 0.8242
213
DGI
actual #213 vs paper #522 309 places worse
0.9309 ±0.0008
best reported
actual #213 vs paper #522 309 places worse
paper 0.8338
390
MLP
0.9128 ±0.0063
511
mpnet
0.8453
This paper
512
minilm
0.8450
This paper
514
Single
0.8446
This paper
#ModelAccuracy ↑Paper
1
GraphTARIF
0.9461 ±0.0017
2
GCN
actual #2 vs paper #238 236 places worse
0.9412 ±0.0008
best reported
actual #2 vs paper #238 236 places worse
paper 0.8743
3
GAT
0.9398 ±0.0022
8
SAGE
0.9351 ±0.0006
223
LLaGA
0.8775
This paper
265
mpnet
0.8663
This paper
272
Single
0.8648
This paper
276
minilm
0.8632
This paper
320
MLP
0.8463
#ModelAccuracy ↑Paper
1
GCN
0.9302 ±0.0011
2
RSE + RGCN (70b)
0.8852 ±0.0019
3
LEMP+T
0.8825
9
SAGE
0.8771
225
mpnet
0.7547
This paper
237
MLP
0.7469 ±0.0085
250
minilm
0.7216
This paper

OGB

#ModelAccuracy ↑Paper
1
Jacobi
0.8968
2
GPR
0.8953
3
LEMP4HG
0.8939
4
SAGE
0.8933
17
Single
0.8735
This paper
19
Co-train
0.8684
This paper
35
mpnet
0.8560
This paper
36
minilm
0.8558
This paper
351
MLP
0.6605 ±0.0020

MoleculeNet

#ModelROC-AUC ↑Paper
1
HIMP
0.8740 ±0.0050
2
GINE w/ VN
0.8720 ±0.0030
3
NaiveGINe+ K=3 w/ VN
0.8700 ±0.0040
14
GCN
0.8400 ±0.0040
28
OFA
0.8250
This paper
244
Single (Atom)
0.7460
This paper
#ModelROC-AUC ↑Paper
1
ProtoMol
0.9140 ±0.0030
2
MMSG
0.9080 ±0.0050
3
MemGNN
0.9070
43
GIN
0.8646 ±0.0081
220
OFA
actual #220 vs paper #226 6 places worse
0.7788 ±0.0108
best reported
actual #220 vs paper #226 6 places worse
paper 0.7732

Difference within reported uncertainty; not counted as underperformance.

paper 0.7732 Δ today 0.0056
264
Single (Atom)
0.7240
This paper
#ModelROC-AUC ↑Paper
1
MAGPrompt+
0.9432 ±0.0238
2
CamS-LLaMA
0.9420
3
SE(3)-I MPPH
0.9400 ±0.0210
34
GIN
0.8875 ±0.0049
153
OFA
0.6997
This paper
212
Single (Text)
0.6771
This paper
#ModelROC-AUC ↑Paper
1
GeomGCL
0.7630
2
LiGhT DeepGPT
0.7570 ±0.0110
3
CoMPT
0.7550
14
GCN
0.7350 ±0.0020
54
OFA
0.6839
This paper
187
Single (Atom)
0.6150
This paper
SOTA performance (not significantly different from the best) 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