Discovering the Representation Bottleneck of Graph Neural Networks

Fang Wu, Siyuan Li, Lirong Wu, Dragomir R. Radev, Stan Z. Li

Main figure for Discovering the Representation Bottleneck of Graph Neural Networks

Abstract

Graph neural networks (GNNs) rely mainly on the message-passing paradigm to propagate node features and build interactions, and different graph learning problems require different ranges of node interactions. In this work, we explore the capacity of GNNs to capture node interactions under contexts of different complexities. We discover that GNNs usually fail to capture the most informative kinds of interaction styles for diverse graph learning tasks, and thus name this phenomenon GNNs' representation bottleneck. As a response, we demonstrate that the inductive bias introduced by existing graph construction mechanisms can result in this representation bottleneck, i.e., preventing GNNs from learning interactions of the most appropriate complexity. To address that limitation, we propose a novel graph rewiring approach based on interaction patterns learned by GNNs to dynamically adjust each node's receptive fields. Extensive experiments on both real-world and synthetic datasets prove the effectiveness of our algorithm in alleviating the representation bottleneck and its superiority in enhancing the performance of GNNs over state-of-the-art graph rewiring baselines.

Benchmark Results

Tested on 4 datasets 6 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 0.8195 ±0.0062
paper 0.8195 ±0.0062 Δ at pub 0.0522 Δ today 0.0809
39
SAGE
0.8911 ±0.0012
68
NodeFormer
actual #68 vs paper #701 633 places worse
0.8848 ±0.0033
best reported
actual #68 vs paper #701 633 places worse
paper 0.7881 ±0.0121
paper 0.7881 ±0.0121 Δ today 0.0967
301
ISGR
0.8408 ±0.0047
This paper
569
GEN
0.8166 ±0.0091
This paper
724
MLP
0.7768
806
SLAPS
0.7229 ±0.0101
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
actual #44 vs paper #527 483 places worse
0.8033 ±0.0088
best reported
actual #44 vs paper #527 483 places worse
paper 0.7134 ±0.0048
paper 0.7134 ±0.0048 Δ at pub 0.0809 Δ today 0.0899
61
GraphSAGE
0.7923 ±0.0053
76
NodeFormer
actual #76 vs paper #599 523 places worse
0.7856 ±0.0009
best reported
actual #76 vs paper #599 523 places worse
paper 0.7039 ±0.0204
paper 0.7039 ±0.0204 Δ today 0.0817
303
GEN
0.7321 ±0.0062
This paper
315
ISGR
0.7316 ±0.0159
This paper
350
MLP
0.7289 ±0.0010
624
SLAPS
0.7000 ±0.0129
This paper
#ModelAccuracy ↑Paper
1
LGTL
0.9518 ±0.0011
2
MixHop (LO)
0.9513 ±0.0038
3
GraphSAGE (LO)
0.9511 ±0.0036
7
NodeFormer
actual #7 vs paper #652 645 places worse
0.9490 ±0.0019
best reported
actual #7 vs paper #652 645 places worse
paper 0.7838 ±0.0194
18
GCN
actual #18 vs paper #600 582 places worse
0.9296 ±0.0015
best reported
actual #18 vs paper #600 582 places worse
paper 0.7898 ±0.0035
116
SAGE
0.8881 ±0.0015
210
MLP
0.8690 ±0.0074
486
ISGR
0.7963 ±0.0042
This paper
643
GEN
0.7849 ±0.0398
This paper
833
SLAPS
0.7096 ±0.0099
This paper

Heterophilic Graphs

#ModelAccuracy ↑Paper
1
Hetero-S (GAT 8-layer)
0.8693
2
Dir-GNN+CNA
0.8586 ±0.0180
3
GAT
actual #3 vs paper #223 220 places worse
0.8560
best reported
actual #3 vs paper #223 220 places worse
paper 0.4590 ±0.0230
paper 0.4590 ±0.0230 Δ at pub 0.1910 Δ today 0.3970
52
GCN
actual #52 vs paper #237 185 places worse
0.7033
best reported
actual #52 vs paper #237 185 places worse
paper 0.4310 ±0.0270
paper 0.4310 ±0.0270 Δ at pub 0.2450 Δ today 0.2723
108
SAGE
0.6340 ±0.0300
115
GraphSAGE
actual #115 vs paper #209 94 places worse
0.6215 ±0.0042
best reported
actual #115 vs paper #209 94 places worse
paper 0.4770 ±0.0200
paper 0.4770 ±0.0200 Δ at pub 0.1103 Δ today 0.1445
169
MLP
0.5429
183
GraphSAGE + ISGR
0.5200 ±0.0170
This paper
186
GAT + ISGR
0.5170 ±0.0140
This paper
187
GIN + ISGR
0.5160 ±0.0190
This paper
189
GCN + ISGR
0.5140 ±0.0190
This paper
192
GIN + SDRF
0.5040 ±0.0390
This paper
195
GCN + SDRF
0.5030 ±0.0360
This paper
196
GraphSAGE + SDRF
0.5030 ±0.0380
This paper
198
GAT + SDRF
0.5010 ±0.0400
This paper
210
GAT + DIGL
0.4770 ±0.0240
This paper
211
GraphSage+GPL
0.4770 ±0.0240
This paper
216
GIN + FA
0.4650 ±0.0210
This paper
219
GIN
0.4610 ±0.0170
This paper
220
GIN + DIGL
0.4610 ±0.0180
This paper
221
GAT + FA
0.4600 ±0.0200
This paper
222
GraphSAGE +AE
0.4600 ±0.0210
This paper
233
GCN + FA
0.4360 ±0.0210
This paper
239
GCN + DIGL
0.4300 ±0.0300
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 today — OK at publication; today's leaderboard best is elsewhere