TMLR 2026

Poisoning the Inner Prediction Logic of Graph Neural Networks for Clean-Label Backdoor Attacks

Yuxiang Zhang, Bin Ma, Enyan Dai

Main figure for Poisoning the Inner Prediction Logic of Graph Neural Networks for Clean-Label Backdoor Attacks

Abstract

Graph Neural Networks (GNNs) have achieved remarkable results in various tasks. Recent studies reveal that graph backdoor attacks can poison the GNN model to predict test nodes with triggers attached as the target class. However, apart from injecting triggers to training nodes, these graph backdoor attacks generally require altering the labels of trigger-attached training nodes into the target class, which is impractical in real-world scenarios. In this work, we focus on the clean-label graph backdoor attack, a realistic but understudied topic where training labels are not modifiable. According to our preliminary analysis, existing graph backdoor attacks generally fail under the clean-label setting. Our further analysis identifies that the core failure of existing methods lies in their inability to poison the prediction logic of GNN models, leading to the triggers being deemed unimportant for prediction. Therefore, we study a novel problem of effective clean-label graph backdoor attacks by poisoning the inner prediction logic of GNN models. We propose Ba-Logic to solve the problem by coordinating a poisoned node selector and a logic-poisoning trigger generator. Extensive experiments on real-world datasets demonstrate that our method effectively enhances the attack success rate and surpasses state-of-the-art graph backdoor attack competitors under clean-label settings. Our code is available at https://anonymous.4open.science/r/BA-Logic.

Proposed method: Ba-Logic (GraphSAGE surrogate)

Benchmark Results

Tested on 5 datasets

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
358
Ba-Logic (GraphSAGE surrogate)
0.8359
This paper
622
ERBA
0.8077
This paper
634
GTA-C
0.8045
This paper
659
UGBA-C
0.7997
This paper
666
DPGBA-C
0.7988
This paper
678
ECGBA
0.7948
This paper
724
MLP
0.7768
787
EBA-C
0.7417
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
228
GTA-C
0.8617
This paper
230
Ba-Logic (GraphSAGE surrogate)
0.8603
This paper
234
ECGBA
0.8586
This paper
241
EBA-C
0.8560
This paper
242
ERBA
0.8558
This paper
245
UGBA-C
0.8541
This paper
248
DPGBA-C
0.8531
This paper

TU Dortmund

#ModelAccuracy ↑Paper
1
MSH-GNN
0.9910 ±0.0030
2
ID-GNN+BEC
0.9830 ±0.0360
3
SupCosine
0.9830 ±0.0250
39
GIN
0.9330 ±0.0290
403
MLP
0.8660 ±0.0495
782
GCLBA
0.6281
This paper
783
SCLBA
0.6277
This paper
784
TRAP
0.6144
This paper
785
Ba-Logic (GraphSAGE surrogate)
0.6132
This paper
#ModelAccuracy ↑Paper
1
WL-MLP
0.9954
2
GIN
0.9934
3
GCN
0.9727
131
GraphSAGE
0.8200 ±0.0100
208
Ba-Logic (GraphSAGE surrogate)
0.8039
This paper
545
TRAP
0.6151
This paper
546
SCLBA
0.6143
This paper
548
GCLBA
0.6097
This paper
#ModelAccuracy ↑Paper
1
MSH-GNN
0.9410 ±0.0330
2
GRDL
0.8260 ±0.0120
3
GMN
0.8225
32
GIN
0.7880 ±0.0410
149
MLP
0.7600 ±0.0320
431
GCLBA
0.7133
This paper
435
SCLBA
0.7125
This paper
499
TRAP
0.6144
This paper
SOTA performance (not significantly different from the best) Proposed method (this paper) Baseline / comparison (this paper) Global context (other papers)