GraphMix: Improved Training of GNNs for Semi-Supervised Learning

Vikas Verma, Meng Qu, Alex Lamb, Yoshua Bengio, Juho Kannala, Jian Tang

Main figure for GraphMix: Improved Training of GNNs for Semi-Supervised Learning

Abstract

We present GraphMix, a regularization method for Graph Neural Network based semi-supervised object classification, whereby we propose to train a fully-connected network jointly with the graph neural network via parameter sharing and interpolation-based regularization. Further, we provide a theoretical analysis of how GraphMix improves the generalization bounds of the underlying graph neural network, without making any assumptions about the "aggregation" layer or the depth of the graph neural networks. We experimentally validate this analysis by applying GraphMix to various architectures such as Graph Convolutional Networks, Graph Attention Networks and Graph-U-Net. Despite its simplicity, we demonstrate that GraphMix can consistently improve or closely match state-of-the-art performance using even simpler architectures such as Graph Convolutional Networks, across three established graph benchmarks: Cora, Citeseer and Pubmed citation network datasets, as well as three newly proposed datasets: Cora-Full, Co-author-CS and Co-author-Physics.

Benchmark Results

Tested on 5 datasets 3 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
43
DropEdge*
actual #43 vs paper #439 396 places worse
0.8900
best reported
actual #43 vs paper #439 396 places worse
paper 0.8280
paper 0.8280 Δ today 0.0620
307
GraphMix
0.8394 ±0.0057
This paper
342
BVAT*
0.8360 ±0.0050
This paper
426
GraphSGAN*
0.8300 ±0.0130
This paper
434
GAT (self-training)
0.8295 ±0.0023
This paper
460
GraphVAT*
0.8260
This paper
466
GraphAT*
0.8250
This paper
528
GCN (self-training)
0.8203 ±0.0043
This paper
530
Graph-U-Net (self-training)
0.8201 ±0.0091
This paper
724
MLP
0.7768
#ModelAccuracy ↑Paper
1
CNA
0.9575 ±0.0058
2
IS-GIB
0.9390 ±0.0187
3
EERM
0.9112 ±0.0145
24
DropEdge
actual #24 vs paper #426 402 places worse
0.8130
best reported
actual #24 vs paper #426 402 places worse
paper 0.7230
paper 0.7230 Δ today 0.0900
44
GCN
0.8033 ±0.0088
230
BVAT
0.7400 ±0.0060
This paper
251
GraphVAT
0.7370
This paper
267
DisenGCN
actual #267 vs paper #279 12 places worse
0.7360 ±0.0080
best reported
actual #267 vs paper #279 12 places worse
paper 0.7340

Difference within reported uncertainty; not counted as underperformance.

paper 0.7340 Δ today 0.0020
279
GraphAT
actual #279 vs paper #279
0.7349 ±0.0038
best reported
actual #279 vs paper #279
paper 0.7340

Difference within reported uncertainty; not counted as underperformance.

paper 0.7340 Δ today 0.0009
290
GCN (self-training)
0.7338 ±0.0035
This paper
304
Graph U-Net
0.7320
This paper
317
GraphSGAN
0.7310 ±0.0180
This paper
322
GraphScan
0.7310 ±0.0180
This paper
350
MLP
actual #350 vs paper #872 522 places worse
0.7289 ±0.0010
best reported
actual #350 vs paper #872 522 places worse
paper 0.4650
paper 0.4650 Δ at pub 0.0860 Δ today 0.2639
351
GAT (self-training)
0.7287 ±0.0051
This paper
513
FCN (self-training)
0.7150 ±0.0080
This paper
617
Chebyshev
actual #617 vs paper #630 13 places worse
0.7010 ±0.0080
best reported
actual #617 vs paper #630 13 places worse
paper 0.6980

Difference within reported uncertainty; not counted as underperformance.

paper 0.6980 Δ at pub 0.0030
649
ICA
0.6910
This paper
681
SemiEmb
actual #681 vs paper #833 152 places worse
0.6810 ±0.0010
best reported
actual #681 vs paper #833 152 places worse
paper 0.5960
paper 0.5960 Δ at pub 0.0850
692
DeepWalk
actual #692 vs paper #883 191 places worse
0.6785 ±0.0079
best reported
actual #692 vs paper #883 191 places worse
paper 0.4320
697
ManiReg
actual #697 vs paper #831 134 places worse
0.6770 ±0.0160
best reported
actual #697 vs paper #831 134 places worse
paper 0.6010
paper 0.6010 Δ at pub 0.0760
782
Planetoid
0.6470
This paper
877
LP
0.4530
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
actual #18 vs paper #585 567 places worse
0.9296 ±0.0015
best reported
actual #18 vs paper #585 567 places worse
paper 0.7900 ±0.0030
20
GAT
actual #20 vs paper #585 565 places worse
0.9233 ±0.0018
best reported
actual #20 vs paper #585 565 places worse
paper 0.7900 ±0.0030
116
SAGE
0.8881 ±0.0015
210
MLP
0.8690 ±0.0074
367
GraphMix
0.8110 ±0.0078
This paper
406
DisenGCN
0.8050
This paper
462
BVAT
0.7990 ±0.0040
This paper
490
Graph U-Net
0.7960
This paper
727
Planetoid
0.7720
This paper
#ModelAccuracy ↑Paper
1
GrokFormer
0.9831 ±0.0018
2
PolyFormer
0.9808 ±0.0027
3
SGFormer
0.9796 ±0.0081
6
GAT
actual #6 vs paper #252 246 places worse
0.9782 ±0.0028
best reported
actual #6 vs paper #252 246 places worse
paper 0.9250 ±0.0090
paper 0.9250 ±0.0090 Δ today 0.0532
9
GCN
actual #9 vs paper #245 236 places worse
0.9774 ±0.0035
best reported
actual #9 vs paper #245 236 places worse
paper 0.9290 ±0.0092
paper 0.9290 ±0.0092 Δ today 0.0484
17
SAGE
0.9739 ±0.0018
58
MLP
0.9597 ±0.0007
177
GraphMix
0.9449 ±0.0084
This paper
241
GS-mean
0.9300 ±0.0080
This paper
252
Graph-U-Net
0.9257 ±0.0081
This paper
253
MoNet
0.9250 ±0.0090
This paper
#ModelAccuracy ↑Paper
1
DoG
0.9690 ±0.0030
2
GWN-fa
0.9667 ±0.0026
3
GWN-sym
0.9666 ±0.0026
6
GraphSAGE
0.9593 ±0.0025
12
GCN
actual #12 vs paper #147 135 places worse
0.9514 ±0.0025
best reported
actual #12 vs paper #147 135 places worse
paper 0.9127 ±0.0056
best today: Graph Wave Networks (WWW 2025)
paper 0.9127 ±0.0056 Δ today 0.0387
21
GAT
actual #21 vs paper #156 135 places worse
0.9437 ±0.0028
best reported
actual #21 vs paper #156 135 places worse
paper 0.9050 ±0.0060
best today: Graph Wave Networks (WWW 2025)
paper 0.9050 ±0.0060 Δ today 0.0387
88
MLP
0.9280 ±0.0020
131
GraphMix
0.9183 ±0.0051
This paper
141
GS-mean
0.9130 ±0.0280
This paper
154
Graph-U-Net
0.9089 ±0.0043
This paper
155
MoNet
actual #155 vs paper #155
0.9082 ±0.0160
best reported
actual #155 vs paper #155
paper 0.9080 ±0.0060

Difference within reported uncertainty; not counted as underperformance.

paper 0.9080 ±0.0060 Δ today 0.0002
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