CIN++: Enhancing Topological Message Passing

Lorenzo Giusti, Teodora Reu, Francesco Ceccarelli, Cristian Bodnar, Pietro Lio'

Main figure for CIN++: Enhancing Topological Message Passing

Abstract

Graph Neural Networks (GNNs) have demonstrated remarkable success in learning from graph-structured data. However, they face significant limitations in expressive power, struggling with long-range interactions and lacking a principled approach to modeling higher-order structures and group interactions. Cellular Isomorphism Networks (CINs) recently addressed most of these challenges with a message passing scheme based on cell complexes. Despite their advantages, CINs make use only of boundary and upper messages which do not consider a direct interaction between the rings present in the underlying complex. Accounting for these interactions might be crucial for learning representations of many real-world complex phenomena such as the dynamics of supramolecular assemblies, neural activity within the brain, and gene regulation processes. In this work, we propose CIN++, an enhancement of the topological message passing scheme introduced in CINs. Our message passing scheme accounts for the aforementioned limitations by letting the cells to receive also lower messages within each layer. By providing a more comprehensive representation of higher-order and long-range interactions, our enhanced topological message passing scheme achieves state-of-the-art results on large-scale and long-range chemistry benchmarks.

Proposed method: CIN

Benchmark Results

Tested on 6 datasets 12 baseline values reported too low

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

Classic

#ModelMAE ↓Paper
1
TIGT
0.0140 ±0.0010
2
FloydNet
0.0160
3
GSSC
0.0190 ±0.0010
7
CIN
actual #7 vs paper #7
0.0210 ±0.0010
actual #7 vs paper #7
paper 0.0210 ±0.0010

Improvement within reported uncertainty; not highlighted.

paper 0.0210 ±0.0010 Δ at pub 0.0010
53
CIN++-small
0.0440 ±0.0040
This paper
69
GIN
0.0880 ±0.0020

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
26
CIN
actual #26 vs paper #26
0.9440 ±0.0370
actual #26 vs paper #26
paper 0.9440 ±0.0370

Improvement within reported uncertainty; not highlighted.

paper 0.9440 ±0.0370 Δ at pub 0.0170
29
CAN
0.9410 ±0.0480
This paper
39
GIN
actual #39 vs paper #237 198 places worse
0.9330 ±0.0290
best reported
actual #39 vs paper #237 198 places worse
paper 0.8940 ±0.0560

Difference within reported uncertainty; not counted as underperformance.

paper 0.8940 ±0.0560 Δ at pub 0.0390
64
GSN
0.9220 ±0.0750
This paper
63
GCN
0.9220 ±0.0440
139
PPGNs
0.9060 ±0.0870
This paper
164
WL kernel
0.9040 ±0.0570
This paper
244
Natural GN
0.8940 ±0.0160
This paper
403
MLP
0.8660 ±0.0495
425
DGCNN
actual #425 vs paper #425
0.8583 ±0.0116
best reported
actual #425 vs paper #425
paper 0.8580 ±0.0180

Difference within reported uncertainty; not counted as underperformance.

paper 0.8580 ±0.0180 Δ at pub 0.0003 Δ today 0.0003
467
PK
actual #467 vs paper #695 228 places worse
0.8450 ±0.0060
best reported
actual #467 vs paper #695 228 places worse
paper 0.7600 ±0.0270
best at pub: Propagation Kernels (2014)
paper 0.7600 ±0.0270 Δ at pub 0.0850
492
IGN
0.8390 ±0.1300
This paper
584
GK (k=3)
0.8140 ±0.0170
This paper
643
RWK
0.7920 ±0.0210
This paper
#ModelAccuracy ↑Paper
1
WL-MLP
0.9954
2
GIN
actual #2 vs paper #91 89 places worse
0.9934
best reported
actual #2 vs paper #91 89 places worse
paper 0.8270 ±0.0170
paper 0.8270 ±0.0170 Δ at pub 0.1664
3
GCN
0.9727
10
WL kernel
0.8600 ±0.0180
This paper
19
CIN
actual #19 vs paper #19
0.8530 ±0.0120
actual #19 vs paper #19
paper 0.8530 ±0.0120

Improvement within reported uncertainty; not highlighted.

paper 0.8530 ±0.0120 Δ at pub 0.0170
28
PK
actual #28 vs paper #103 75 places worse
0.8450 ±0.0010
best reported
actual #28 vs paper #103 75 places worse
paper 0.8250 ±0.0050
best at pub: Propagation Kernels (2014)
paper 0.8250 ±0.0050 Δ at pub 0.0200
29
CAN
0.8450 ±0.0160
This paper
50
GSN
0.8350 ±0.0200
This paper
64
PPGNs
0.8320 ±0.0110
This paper
82
SIN
actual #82 vs paper #91 9 places worse
0.8280 ±0.0220
best reported
actual #82 vs paper #91 9 places worse
paper 0.8270 ±0.0210

Difference within reported uncertainty; not counted as underperformance.

paper 0.8270 ±0.0210 Δ at pub 0.0010
109
Natural GN
0.8240 ±0.0130
This paper
131
GraphSAGE
0.8200 ±0.0100
373
DGCNN
actual #373 vs paper #424 51 places worse
0.7650 ±0.0190
best reported
actual #373 vs paper #424 51 places worse
paper 0.7440 ±0.0050

Difference within reported uncertainty; not counted as underperformance.

paper 0.7440 ±0.0050 Δ at pub 0.0210
428
IGN
actual #428 vs paper #430 2 places worse
0.7433 ±0.0271
best reported
actual #428 vs paper #430 2 places worse
paper 0.7430 ±0.0270

Difference within reported uncertainty; not counted as underperformance.

paper 0.7430 ±0.0270 Δ at pub 0.0003
540
DCNN
actual #540 vs paper #566 26 places worse
0.6261
best reported
actual #540 vs paper #566 26 places worse
paper 0.5660 ±0.0100
541
GK (k=3)
0.6250 ±0.0030
This paper
#ModelAccuracy ↑Paper
1
MSH-GNN
0.9410 ±0.0330
2
GRDL
0.8260 ±0.0120
3
GMN
0.8225
12
CIN
actual #12 vs paper #12
0.8050 ±0.0390
actual #12 vs paper #12
paper 0.8050 ±0.0390

Improvement within reported uncertainty; not highlighted.

paper 0.8050 ±0.0390 Δ at pub 0.0350
32
GIN
actual #32 vs paper #135 103 places worse
0.7880 ±0.0410
best reported
actual #32 vs paper #135 103 places worse
paper 0.7620 ±0.0280

Difference within reported uncertainty; not counted as underperformance.

paper 0.7620 ±0.0280 Δ at pub 0.0080 Δ today 0.0260
44
CAN
0.7820 ±0.0200
This paper
67
SAGE
0.7726 ±0.0228
74
PPGNs
0.7720 ±0.0470
This paper
100
IGN
actual #100 vs paper #100
0.7660 ±0.0550
actual #100 vs paper #100
paper 0.7660 ±0.0550

Improvement within reported uncertainty; not highlighted.

paper 0.7660 ±0.0550 Δ at pub 0.0002
102
GSN
actual #102 vs paper #102
0.7660 ±0.0500
actual #102 vs paper #102
paper 0.7660 ±0.0500

Improvement within reported uncertainty; not highlighted.

paper 0.7660 ±0.0500 Δ at pub 0.0200
118
SIN
0.7640 ±0.0330
This paper
132
DGCNN
actual #132 vs paper #190 58 places worse
0.7626
best reported
actual #132 vs paper #190 58 places worse
paper 0.7550 ±0.0090
best at pub: Orthogonal Graph Neural Networks (AAAI 2021)

Difference within reported uncertainty; not counted as underperformance.

paper 0.7550 ±0.0090 Δ at pub 0.0076
149
MLP
0.7600 ±0.0320
252
WL kernel
0.7500 ±0.0310
This paper
328
PK
0.7370 ±0.0070
This paper
421
Natural GN
0.7170 ±0.0100
This paper
430
GK (k=3)
0.7140 ±0.0030
This paper
501
DCNN
actual #501 vs paper #501
0.6130 ±0.0160
actual #501 vs paper #501
paper 0.6130 ±0.0160

Improvement within reported uncertainty; not highlighted.

paper 0.6130 ±0.0160 Δ at pub 0.0001
510
RWK
0.5960 ±0.0010
This paper

LRGB

#ModelMAE ↓Paper
1
GCN
actual #1 vs paper #183 182 places worse
0.2421 ±0.0016
best reported
actual #1 vs paper #183 182 places worse
paper 0.3496 ±0.0013
paper 0.3496 ±0.0013 Δ at pub 0.1008 Δ today 0.1075
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 #182 175 places worse
0.2431 ±0.0020
best reported
actual #7 vs paper #182 175 places worse
paper 0.3420 ±0.0013
paper 0.3420 ±0.0013 Δ at pub 0.0897 Δ today 0.0989
49
GINE
actual #49 vs paper #184 135 places worse
0.2473 ±0.0017
best reported
actual #49 vs paper #184 135 places worse
paper 0.3547 ±0.0045
paper 0.3547 ±0.0045 Δ at pub 0.0963 Δ today 0.1074
69
GatedGCN+RWSE
actual #69 vs paper #179 110 places worse
0.2485 ±0.0022
best reported
actual #69 vs paper #179 110 places worse
paper 0.3357 ±0.0006
paper 0.3357 ±0.0006 Δ at pub 0.0828 Δ today 0.0872
110
CIN
0.2523 ±0.0013
This paper
113
Transformer+LapPE
0.2529 ±0.0016
This paper
123
SAN+RWSE
0.2545 ±0.0012
This paper
155
SAN+LapPE
actual #155 vs paper #155
0.2680 ±0.0040
best reported
actual #155 vs paper #155
paper 0.2683 ±0.0043
best at pub: LRGB (NeurIPS 2022)

Difference within reported uncertainty; not counted as underperformance.

paper 0.2683 ±0.0043 Δ today 0.0003
183
GCNII
0.3471 ±0.0010
This paper
201
MLP
0.4351 ±0.0008
This paper
#ModelAP ↑Paper
1
S^2GCN
0.7311 ±0.0066
2
S4G
0.7293 ±0.0004
3
BuNN
0.7276 ±0.0065
4
GCN
actual #4 vs paper #142 138 places worse
0.7261 ±0.0011
best reported
actual #4 vs paper #142 138 places worse
paper 0.5930 ±0.0023
paper 0.5930 ±0.0023 Δ at pub 0.0693 Δ today 0.1331
26
GIN
0.7059 ±0.0089
34
GatedGCN
actual #34 vs paper #149 115 places worse
0.7006 ±0.0033
best reported
actual #34 vs paper #149 115 places worse
paper 0.5864 ±0.0077
paper 0.5864 ±0.0077 Δ at pub 0.0771 Δ today 0.1142
35
GCNII
actual #35 vs paper #159 124 places worse
0.6990 ±0.0030
best reported
actual #35 vs paper #159 124 places worse
paper 0.5543 ±0.0078
best at pub: LRGB (NeurIPS 2022)
paper 0.5543 ±0.0078 Δ today 0.1447
73
GatedGCN+RWSE
actual #73 vs paper #134 61 places worse
0.6685 ±0.0062
best reported
actual #73 vs paper #134 61 places worse
paper 0.6069 ±0.0035
paper 0.6069 ±0.0035 Δ at pub 0.0616
78
GINE
actual #78 vs paper #162 84 places worse
0.6621 ±0.0067
best reported
actual #78 vs paper #162 84 places worse
paper 0.5498 ±0.0079
paper 0.5498 ±0.0079 Δ at pub 0.0848 Δ today 0.1123
86
CIN
0.6569 ±0.0117
This paper
89
SAN+RWSE
actual #89 vs paper #111 22 places worse
0.6562 ±0.0075
best reported
actual #89 vs paper #111 22 places worse
paper 0.6439 ±0.0075

Difference within reported uncertainty; not counted as underperformance.

paper 0.6439 ±0.0075 Δ at pub 0.0123
116
SAN+LapPE
0.6384 ±0.0121
This paper
118
Transformer+LapPE
0.6326 ±0.0126
This paper
181
MLP
0.4060 ±0.0021
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