TMLR 2025

Efficient Text-Attributed Graph Learning through Selective Annotation and Graph Alignment

Huanyi Xie, Lijie Hu, Lu Yu, Tianhao Huang, Longfei Li, Meng Li, Jun Zhou, Huan Wang, Di Wang

Main figure for Efficient Text-Attributed Graph Learning through Selective Annotation and Graph Alignment

Abstract

In the realm of Text-attributed Graphs (TAGs), traditional graph neural networks (GNNs) often fall short due to the complex textual information associated with each node. Recent methods have improved node representations by leveraging large language models (LLMs) to enhance node text features, but these approaches typically require extensive annotations or fine-tuning across all nodes, which is both time-consuming and costly. To overcome these challenges, we introduce GAGA, an efficient framework for TAG representation learning. GAGA reduces annotation time and cost by focusing on annotating only representative nodes and edges. It constructs an annotation graph that captures the topological relationships among these annotations. Furthermore, GAGA employs a two-level alignment module to effectively integrate the annotation graph with the TAG, aligning their underlying structures. Experiments show that GAGA achieves classification accuracies on par with or surpassing state-of-the-art methods while requiring only 1\

Proposed method: GAGA

Benchmark Results

Tested on 3 datasets 15 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
11
ENGINE
0.9148 ±0.0010
This paper
14
TAPE
actual #14 vs paper #14
0.9119 ±0.0012
actual #14 vs paper #14
paper 0.9119 ±0.0012
paper 0.9119 ±0.0012 Δ at pub 0.0189
15
InstructGLM
actual #15 vs paper #140 125 places worse
0.9077
best reported
actual #15 vs paper #140 125 places worse
paper 0.8708 ±0.0012
paper 0.8708 ±0.0012 Δ at pub 0.0369
21
GCN
actual #21 vs paper #80 59 places worse
0.9004
best reported
actual #21 vs paper #80 59 places worse
paper 0.8824 ±0.0010
paper 0.8824 ±0.0010 Δ at pub 0.0180
26
GAGA
0.8967 ±0.0012
This paper
39
SAGE
actual #39 vs paper #39
0.8911 ±0.0012
actual #39 vs paper #39
paper 0.8911 ±0.0012
paper 0.8911 ±0.0012 Δ at pub 0.0338
40
RevGAT
0.8911 ±0.0010
This paper
93
SimTEG
0.8804 ±0.0012
This paper
141
GraphSAGE
0.8708 ±0.0085
200
GLEM
actual #200 vs paper #778 578 places worse
0.8560 ±0.0009
best reported
actual #200 vs paper #778 578 places worse
paper 0.7469 ±0.0018
paper 0.7469 ±0.0018 Δ at pub 0.1091
203
GIANT
0.8552 ±0.0018
This paper
456
Graphormer
actual #456 vs paper #636 180 places worse
0.8262 ±0.0012
best reported
actual #456 vs paper #636 180 places worse
paper 0.8041 ±0.0020
724
MLP
actual #724 vs paper #868 144 places worse
0.7768
best reported
actual #724 vs paper #868 144 places worse
paper 0.6388 ±0.0012
paper 0.6388 ±0.0012 Δ at pub 0.1380
#ModelAccuracy ↑Paper
1
LGTL
0.9518 ±0.0011
2
MixHop (LO)
0.9513 ±0.0038
3
GraphSAGE (LO)
0.9511 ±0.0036
10
GAGA
0.9462 ±0.0020
This paper
12
TAPE
0.9431 ±0.0015
This paper
15
InstructGLM
0.9384 ±0.0015
This paper
18
GCN
actual #18 vs paper #418 400 places worse
0.9296 ±0.0015
best reported
actual #18 vs paper #418 400 places worse
paper 0.8031 ±0.0015
19
GLEM
0.9257 ±0.0020
This paper
116
SAGE
actual #116 vs paper #116
0.8881 ±0.0015
actual #116 vs paper #116
paper 0.8881 ±0.0015
paper 0.8881 ±0.0015 Δ at pub 0.1099
125
GraphSAGE
0.8864 ±0.0030
131
RevGAT
0.8850 ±0.0020
This paper
151
Graphormer
0.8824 ±0.0015
This paper
210
MLP
actual #210 vs paper #226 16 places worse
0.8690 ±0.0074
best reported
actual #210 vs paper #226 16 places worse
paper 0.8635 ±0.0020

Difference within reported uncertainty; not counted as underperformance.

paper 0.8635 ±0.0020 Δ at pub 0.0055
310
GIANT
actual #310 vs paper #743 433 places worse
0.8275 ±0.0028
best reported
actual #310 vs paper #743 433 places worse
paper 0.7690 ±0.0020
360
SimTEG
0.8120 ±0.0001
This paper
803
ENGINE
0.7472 ±0.0015
This paper

OGB

#ModelAccuracy ↑Paper
1
Jacobi
0.8968
2
GPR
0.8953
3
LEMP4HG
0.8939
4
SAGE
actual #4 vs paper #342 338 places worse
0.8933
best reported
actual #4 vs paper #342 338 places worse
paper 0.6913 ±0.0020
paper 0.6913 ±0.0020 Δ at pub 0.2020
6
GCN
actual #6 vs paper #332 326 places worse
0.8868
best reported
actual #6 vs paper #332 326 places worse
paper 0.7052 ±0.0012
paper 0.7052 ±0.0012 Δ at pub 0.1816
8
RevGAT
actual #8 vs paper #340 332 places worse
0.8859
best reported
actual #8 vs paper #340 332 places worse
paper 0.6964 ±0.0015
paper 0.6964 ±0.0015 Δ at pub 0.1895
15
GLEM
actual #15 vs paper #305 290 places worse
0.8736 ±0.0007
best reported
actual #15 vs paper #305 290 places worse
paper 0.7377 ±0.0015
paper 0.7377 ±0.0015 Δ at pub 0.1359
39
SimTEG
actual #39 vs paper #286 247 places worse
0.8540 ±0.0028
best reported
actual #39 vs paper #286 247 places worse
paper 0.7451 ±0.0020
paper 0.7451 ±0.0020 Δ at pub 0.1089
83
GraphSAGE
0.8287
90
TAPE
actual #90 vs paper #147 57 places worse
0.8234 ±0.0036
best reported
actual #90 vs paper #147 57 places worse
paper 0.7996 ±0.0020
137
GIANT
actual #137 vs paper #294 157 places worse
0.8049 ±0.0028
best reported
actual #137 vs paper #294 157 places worse
paper 0.7406 ±0.0012
paper 0.7406 ±0.0012 Δ at pub 0.0643
145
ENGINE
0.8005 ±0.0015
This paper
171
Graphormer
actual #171 vs paper #343 172 places worse
0.7934 ±0.0025
best reported
actual #171 vs paper #343 172 places worse
paper 0.6815 ±0.0012
paper 0.6815 ±0.0012 Δ at pub 0.1119
195
GAGA
0.7887 ±0.0018
This paper
351
MLP
actual #351 vs paper #384 33 places worse
0.6605 ±0.0020
best reported
actual #351 vs paper #384 33 places worse
paper 0.5385 ±0.0018
paper 0.5385 ±0.0018 Δ at pub 0.3033 Δ today 0.1220
356
InstructGLM
0.6532 ±0.0002
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