Bundle Neural Networks for message diffusion on graphs

Jacob Bamberger, Federico Barbero, Xiaowen Dong, Michael M. Bronstein

Main figure for Bundle Neural Networks for message diffusion on graphs

Abstract

The dominant paradigm for learning on graph-structured data is message passing. Despite being a strong inductive bias, the local message passing mechanism suffers from pathological issues such as over-smoothing, over-squashing, and limited node-level expressivity. To address these limitations we propose Bundle Neural Networks (BuNN), a new type of GNN that operates via message diffusion over flat vector bundles - structures analogous to connections on Riemannian manifolds that augment the graph by assigning to each node a vector space and an orthogonal map. A BuNN layer evolves the features according to a diffusion-type partial differential equation. When discretized, BuNNs are a special case of Sheaf Neural Networks (SNNs), a recently proposed MPNN capable of mitigating over-smoothing. The continuous nature of message diffusion enables BuNNs to operate on larger scales of the graph and, therefore, to mitigate over-squashing. Finally, we prove that BuNN can approximate any feature transformation over nodes on any (potentially infinite) family of graphs given injective positional encodings, resulting in universal node-level expressivity. We support our theory via synthetic experiments and showcase the strong empirical performance of BuNNs over a range of real-world tasks, achieving state-of-the-art results on several standard benchmarks in transductive and inductive settings.

Proposed method: BuNN

Benchmark Results

Tested on 8 datasets

Tables show presented results in global context (best 3 papers + GCN + MLP).

LRGB

#ModelMAE ↓Paper
1
GCN
actual #1 vs paper #31 30 places worse
0.2421 ±0.0016
best reported
actual #1 vs paper #31 30 places worse
paper 0.2460 ±0.0007
paper 0.2460 ±0.0007 Δ today 0.0039
2
IPR-MPNN
0.2422 ±0.0007
3
TANGO-GPS
0.2422 ±0.0014
5
GIN
0.2429 ±0.0019
7
GatedGCN
actual #7 vs paper #57 50 places worse
0.2431 ±0.0020
best reported
actual #7 vs paper #57 50 places worse
paper 0.2477 ±0.0009
paper 0.2477 ±0.0009 Δ today 0.0046
21
GAPH ViT
0.2449 ±0.0016
This paper
36
BuNN
0.2463 ±0.0012
This paper
49
GINE
0.2473 ±0.0017
This paper
66
Exphormer
0.2481 ±0.0007
This paper
85
GPS
actual #85 vs paper #96 11 places worse
0.2500 ±0.0005
best reported
actual #85 vs paper #96 11 places worse
paper 0.2509 ±0.0014

Difference within reported uncertainty; not counted as underperformance.

paper 0.2509 ±0.0014 Δ at pub 0.0009 Δ today 0.0009
115
DRew
0.2536 ±0.0015
This paper
124
SAN
0.2545 ±0.0012
This paper
201
MLP
0.4351 ±0.0008
#ModelAP ↑Paper
1
S^2GCN
0.7311 ±0.0066
2
S4G
0.7293 ±0.0004
3
BuNN
0.7276 ±0.0065
This paper
4
GCN
actual #4 vs paper #49 45 places worse
0.7261 ±0.0011
best reported
actual #4 vs paper #49 45 places worse
paper 0.6860 ±0.0050
paper 0.6860 ±0.0050 Δ today 0.0401
13
DRew
actual #13 vs paper #13
0.7150 ±0.0044
actual #13 vs paper #13
paper 0.7150 ±0.0044
paper 0.7150 ±0.0044 Δ at pub 0.0154
26
GIN
0.7059 ±0.0089
34
GatedGCN
actual #34 vs paper #58 24 places worse
0.7006 ±0.0033
best reported
actual #34 vs paper #58 24 places worse
paper 0.6765 ±0.0047
paper 0.6765 ±0.0047 Δ today 0.0241
45
GAPH ViT
0.6942 ±0.0075
This paper
78
GINE
0.6621 ±0.0067
This paper
87
GPS
actual #87 vs paper #94 7 places worse
0.6562 ±0.0115
best reported
actual #87 vs paper #94 7 places worse
paper 0.6534 ±0.0091

Difference within reported uncertainty; not counted as underperformance.

paper 0.6534 ±0.0091 Δ at pub 0.0028
95
Exphormer
0.6527 ±0.0043
This paper
112
SAN
0.6439 ±0.0075
This paper
181
MLP
0.4060 ±0.0021
#ModelF1 ↑Paper
1
NeuralWalker
0.4912 ±0.0042
2
PPGT
0.4641 ±0.0033
3
CRaWl
0.4588 ±0.0079
14
GPS
0.4440 ±0.0065
This paper
19
Exphormer
actual #19 vs paper #32 13 places worse
0.4242 ±0.0044
best reported
actual #19 vs paper #32 13 places worse
paper 0.3975 ±0.0037
paper 0.3975 ±0.0037 Δ today 0.0267
31
BuNN
0.4049 ±0.0046
This paper
41
GatedGCN
0.3880 ±0.0040
This paper
42
Gated-GCN
0.3880 ±0.0040
65
DRew
0.3314 ±0.0024
This paper
66
SAN
0.3230 ±0.0039
This paper
75
GINE
0.2718 ±0.0054
This paper
81
GCN
actual #81 vs paper #83 2 places worse
0.2380 ±0.0160
best reported
actual #81 vs paper #83 2 places worse
paper 0.2078 ±0.0031
paper 0.2078 ±0.0031 Δ today 0.0302
93
MLP
0.1140 ±0.0230

Heterophily Benchmark

#ModelAccuracy ↑Paper
1
Dir-Poly
0.9451 ±0.0022
2
D-CDE
0.9387 ±0.0041
3
LargeScaleNet
0.9358 ±0.0024
15
BuNN
0.9175 ±0.0039
This paper
26
GraphSAGE
0.9106 ±0.0027
40
GAT-sep
0.8875 ±0.0041
This paper
54
GT-sep
0.8732 ±0.0039
This paper
59
GT
0.8651 ±0.0073
This paper
64
SAGE
0.8574 ±0.0067
This paper
77
GCN
actual #77 vs paper #113 36 places worse
0.8272 ±0.0082
best reported
actual #77 vs paper #113 36 places worse
paper 0.7369 ±0.0074
83
GAT
actual #83 vs paper #84 1 place worse
0.8145 ±0.0009
best reported
actual #83 vs paper #84 1 place worse
paper 0.8087 ±0.0030
paper 0.8087 ±0.0030 Δ today 0.0058
88
NSD
0.8041 ±0.0072
This paper
135
MLP
0.6665 ±0.0047
#ModelAccuracy ↑Paper
1
UniGAP
0.6375 ±0.0110
2
H2GCN + HalfHop
0.5961 ±0.0100
3
GraphSAGE + HalfHop
0.5897 ±0.0150
12
SAGE
actual #12 vs paper #30 18 places worse
0.5569 ±0.0023
best reported
actual #12 vs paper #30 18 places worse
paper 0.5363 ±0.0039
14
GAT
actual #14 vs paper #105 91 places worse
0.5559 ±0.0027
best reported
actual #14 vs paper #105 91 places worse
paper 0.4909 ±0.0063
15
GraphSAGE
0.5540 ±0.0020
24
GCN
actual #24 vs paper #111 87 places worse
0.5411 ±0.0034
best reported
actual #24 vs paper #111 87 places worse
paper 0.4870 ±0.0063
28
BuNN
0.5374 ±0.0051
This paper
52
GAT-sep
0.5270 ±0.0062
This paper
62
GT-sep
0.5218 ±0.0080
This paper
72
GT
0.5117 ±0.0066
This paper
84
MLP
0.5058
170
NSD
0.4276 ±0.0054
This paper
#ModelROC-AUC ↑Paper
1
BuNN
0.9899 ±0.0016
This paper
2
DC-GNN
0.9850 ±0.0021
3
Tango -GPS
0.9839 ±0.0054
36
GAT
actual #36 vs paper #60 24 places worse
0.9391 ±0.0035
best reported
actual #36 vs paper #60 24 places worse
paper 0.9201 ±0.0068
paper 0.9201 ±0.0068 Δ today 0.0190
37
GAT-sep
0.9391 ±0.0035
This paper
42
GraphSAGE
0.9358 ±0.0005
46
SAGE
0.9351 ±0.0057
This paper
57
GT-sep
0.9229 ±0.0047
This paper
60
NSD
0.9215 ±0.0084
This paper
63
GT
0.9185 ±0.0076
This paper
68
GCN
actual #68 vs paper #88 20 places worse
0.9150 ±0.0006
best reported
actual #68 vs paper #88 20 places worse
paper 0.8975 ±0.0052
paper 0.8975 ±0.0052 Δ today 0.0175
156
MLP
0.5099 ±0.0147
#ModelROC-AUC ↑Paper
1
Polynormer-r
0.8591 ±0.0074
2
DC-GNN
0.8588 ±0.0081
3
TANGO-GPS
0.8566 ±0.0101
21
BuNN
0.8478 ±0.0080
This paper
28
GAT
actual #28 vs paper #47 19 places worse
0.8443 ±0.0100
best reported
actual #28 vs paper #47 19 places worse
paper 0.8370 ±0.0047

Difference within reported uncertainty; not counted as underperformance.

paper 0.8370 ±0.0047 Δ today 0.0073
41
GAT-sep
0.8378 ±0.0043
This paper
50
GCN
0.8364 ±0.0067
This paper
61
GT
actual #61 vs paper #61
0.8323 ±0.0064
actual #61 vs paper #61
paper 0.8323 ±0.0064
paper 0.8323 ±0.0064 Δ at pub 0.0399
73
GT-sep
0.8252 ±0.0092
This paper
76
SAGE
0.8243 ±0.0044
This paper
77
GraphSAGE
0.8243 ±0.0044
103
NSD
0.7883 ±0.0076
This paper
139
MLP
0.7362 ±0.0020
#ModelROC-AUC ↑Paper
1
NID_GAT
0.9703 ±0.0002
2
NID_GCN
0.9685 ±0.0010
3
UniGAP
0.8421 ±0.0080
16
GCN
actual #16 vs paper #62 46 places worse
0.7902 ±0.0060
best reported
actual #16 vs paper #62 46 places worse
paper 0.7609 ±0.0127
22
BuNN
0.7875 ±0.0109
This paper
26
GAT
actual #26 vs paper #38 12 places worse
0.7743 ±0.0120
actual #26 vs paper #38 12 places worse
paper 0.7743 ±0.0120
paper 0.7743 ±0.0120 Δ at pub 0.0710
29
GT-sep
0.7805 ±0.0093
This paper
30
GT
actual #30 vs paper #30
0.7795 ±0.0068
actual #30 vs paper #30
paper 0.7795 ±0.0068
paper 0.7795 ±0.0068 Δ at pub 0.0712
46
GraphSAGE
0.7721 ±0.0130
54
GAT-sep
0.7679 ±0.0071
This paper
58
SAGE
0.7644 ±0.0062
This paper
96
MLP
0.7082 ±0.0010
109
NSD
0.6969 ±0.0146
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 value improved over the best known when published Best today — OK at publication; today's leaderboard best is elsewhere