Graph Convolutional Neural Networks with Node Transition Probability-based Message Passing and DropNode Regularization

Tien Huu Do, Duc Minh Nguyen, Giannis Bekoulis, Adrian Munteanu, Nikos Deligiannis

Main figure for Graph Convolutional Neural Networks with Node Transition Probability-based Message Passing and DropNode Regularization

Abstract

Graph convolutional neural networks (GCNNs) have received much attention recently, owing to their capability in handling graph-structured data. Among the existing GCNNs, many methods can be viewed as instances of a neural message passing motif; features of nodes are passed around their neighbors, aggregated and transformed to produce better nodes' representations. Nevertheless, these methods seldom use node transition probabilities, a measure that has been found useful in exploring graphs. Furthermore, when the transition probabilities are used, their transition direction is often improperly considered in the feature aggregation step, resulting in an inefficient weighting scheme. In addition, although a great number of GCNN models with increasing level of complexity have been introduced, the GCNNs often suffer from over-fitting when being trained on small graphs. Another issue of the GCNNs is over-smoothing, which tends to make nodes' representations indistinguishable. This work presents a new method to improve the message passing process based on node transition probabilities by properly considering the transition direction, leading to a better weighting scheme in nodes' features aggregation compared to the existing counterpart. Moreover, we propose a novel regularization method termed DropNode to address the over-fitting and over-smoothing issues simultaneously. DropNode randomly discards part of a graph, thus it creates multiple deformed versions of the graph, leading to data augmentation regularization effect. Additionally, DropNode lessens the connectivity of the graph, mitigating the effect of over-smoothing in deep GCNNs. Extensive experiments on eight benchmark datasets for node and graph classification tasks demonstrate the effectiveness of the proposed methods in comparison with the state of the art.

Proposed method: GPCONV

Benchmark Results

Tested on 4 datasets 5 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
actual #21 vs paper #536 515 places worse
0.9004
best reported
actual #21 vs paper #536 515 places worse
paper 0.8190 ±0.0070
paper 0.8190 ±0.0070 Δ at pub 0.0527 Δ today 0.0814
39
SAGE
0.8911 ±0.0012
44
GAT
actual #44 vs paper #424 380 places worse
0.8897 ±0.0014
best reported
actual #44 vs paper #424 380 places worse
paper 0.8300 ±0.0070
177
DGI
actual #177 vs paper #486 309 places worse
0.8630 ±0.0020
best reported
actual #177 vs paper #486 309 places worse
paper 0.8230 ±0.0060
paper 0.8230 ±0.0060 Δ today 0.0400
192
PGCN + DropNode (RW-dropping)
0.8590 ±0.0040
This paper
249
GCN + DropNode
0.8460 ±0.0100
This paper
262
Graph U-Net
0.8440 ±0.0060
This paper
327
GMNN
0.8370
This paper
441
GCN + DropEdge
0.8280
This paper
561
GPCONV
0.8170 ±0.0050
This paper
579
DGCNN
0.8140 ±0.0050
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
35
GAT
actual #35 vs paper #388 353 places worse
0.8080 ±0.0026
best reported
actual #35 vs paper #388 353 places worse
paper 0.7250 ±0.0070
paper 0.7250 ±0.0070 Δ at pub 0.0610 Δ today 0.0830
44
GCN
actual #44 vs paper #588 544 places worse
0.8033 ±0.0088
best reported
actual #44 vs paper #588 544 places worse
paper 0.7050 ±0.0080
61
GraphSAGE
0.7923 ±0.0053
66
DGI
actual #66 vs paper #474 408 places worse
0.7890 ±0.0020
best reported
actual #66 vs paper #474 408 places worse
paper 0.7180 ±0.0070
paper 0.7180 ±0.0070 Δ today 0.0710
183
PGCN_n + DropNode (RW-dropping)
0.7490 ±0.0050
This paper
210
GCN_n + DropNode
0.7430 ±0.0050
This paper
304
Graph U-Net
0.7320 ±0.0050
This paper
339
GMNN
0.7290
This paper
350
MLP
0.7289 ±0.0010
429
GCN + DropEdge
0.7230
This paper
586
PGCN_n
0.7060 ±0.0070
This paper
631
DGCNN
0.6980 ±0.0070
This paper

TU Dortmund

#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
57
Graph U-Net
0.7768
This paper
69
PGCN_g+DropNode
0.7721
This paper
106
GCN_g+DropNode
0.7658
This paper
126
CapsGNN
actual #126 vs paper #130 4 places worse
0.7630 ±0.0360
best reported
actual #126 vs paper #130 4 places worse
paper 0.7628

Difference within reported uncertainty; not counted as underperformance.

paper 0.7628 Δ at pub 0.0002
132
DGCNN
actual #132 vs paper #190 58 places worse
0.7554
actual #132 vs paper #190 58 places worse
paper 0.7554
best today: Orthogonal Graph Neural Networks (AAAI 2021)
paper 0.7554 Δ at pub 0.0234 Δ today 0.0072
133
Diff-Pool (Soft Assign)
0.7625
This paper
149
MLP
0.7600 ±0.0320
232
PGCN_g+2FC
0.7513
This paper
267
GCN + 2FC
0.7486
This paper
278
FCN
0.7468
This paper
417
SAGPool_h
0.7186
This paper
459
SAGPool_g
0.7004
This paper
#ModelAccuracy ↑Paper
1
GMN
0.7866
2
MemGNN
0.7550
3
TFGW SP
0.7510 ±0.0500
14
PGCN_g+DropNode
0.7050
This paper
17
GatedGCN
0.7000 ±0.0494
19
GCN_g+DropNode
0.6900
This paper
26
GraphSAGE
0.6817 ±0.0545
37
GCN + 2FC
0.6645
This paper
39
FCN (2FC)
0.6617
This paper
40
PGCN_g+2FC
0.6617
This paper
69
Diff-Pool (Soft Assign)
0.6253
This paper
119
DGCNN
actual #119 vs paper #167 48 places worse
0.5712
best reported
actual #119 vs paper #167 48 places worse
paper 0.4633
124
MLP
0.5583 ±0.0352
127
CapsGNN
actual #127 vs paper #136 9 places worse
0.5531 ±0.0423
best reported
actual #127 vs paper #136 9 places worse
paper 0.5467

Difference within reported uncertainty; not counted as underperformance.

paper 0.5467 Δ at pub 0.0003 Δ today 0.0064
161
Graph U-Net
0.4833
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) Improved at pub — later paper surpassed this result Best today — OK at publication; today's leaderboard best is elsewhere