Graph Learning with Distributional Edge Layouts

Xinjian Zhao, Chaolong Ying, Tianshu Yu

Main figure for Graph Learning with Distributional Edge Layouts

Abstract

Graph Neural Networks (GNNs) learn from graph-structured data by passing local messages between neighboring nodes along edges on certain topological layouts. Typically, these topological layouts in modern GNNs are deterministically computed (e.g., attention-based GNNs) or locally sampled (e.g., GraphSage) under heuristic assumptions. In this paper, we for the first time pose that these layouts can be globally sampled via Langevin dynamics following Boltzmann distribution equipped with explicit physical energy, leading to higher feasibility in the physical world. We argue that such a collection of sampled/optimized layouts can capture the wide energy distribution and bring extra expressivity on top of WL-test, therefore easing downstream tasks. As such, we propose Distributional Edge Layouts (DELs) to serve as a complement to a variety of GNNs. DEL is a pre-processing strategy independent of subsequent GNN variants, thus being highly flexible. Experimental results demonstrate that DELs consistently and substantially improve a series of GNN baselines, achieving state-of-the-art performance on multiple datasets.

Benchmark Results

Tested on 7 datasets 8 baseline values reported too low

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

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
38
DEL-F
0.9334 ±0.0068
This paper
39
GIN
actual #39 vs paper #62 23 places worse
0.9330 ±0.0290
best reported
actual #39 vs paper #62 23 places worse
paper 0.9231 ±0.0087

Difference within reported uncertainty; not counted as underperformance.

paper 0.9231 ±0.0087 Δ at pub 0.0099
63
GCN
0.9220 ±0.0440
75
GPS(RWSE)
0.9194 ±0.0150
This paper
159
WL
actual #159 vs paper #563 404 places worse
0.9040 ±0.0570
best reported
actual #159 vs paper #563 404 places worse
paper 0.8205 ±0.0036

Difference within reported uncertainty; not counted as underperformance.

paper 0.8205 ±0.0036 Δ at pub 0.0835
183
GAT
actual #183 vs paper #429 246 places worse
0.9010 ±0.0580
best reported
actual #183 vs paper #429 246 places worse
paper 0.8569 ±0.0106
paper 0.8569 ±0.0106 Δ at pub 0.0441 Δ today 0.0441
202
GMT
actual #202 vs paper #511 309 places worse
0.8990 ±0.0420
best reported
actual #202 vs paper #511 309 places worse
paper 0.8344 ±0.0133
paper 0.8344 ±0.0133 Δ today 0.0646
258
GraphMAE
actual #258 vs paper #326 68 places worse
0.8930 ±0.0110
best reported
actual #258 vs paper #326 68 places worse
paper 0.8819 ±0.0126

Difference within reported uncertainty; not counted as underperformance.

paper 0.8819 ±0.0126 Δ today 0.0111
350
Graph Transformer + DEL-K
0.8777 ±0.0012
This paper
403
MLP
0.8660 ±0.0495
404
GAT + DEL-K
0.8652 ±0.0042
This paper
437
SEP-G
0.8556 ±0.0109
This paper
479
GAT + MPNN
0.8430 ±0.0121
This paper
484
Graphtransformer
0.8402 ±0.0100
This paper
499
Graph Transformer + MPNN
0.8375 ±0.0120
This paper
631
Graph Transformer + Random distance
0.7972 ±0.0082
This paper
644
GAT + Random distance
0.7916 ±0.0177
This paper
#ModelAccuracy ↑Paper
1
WL-MLP
0.9954
2
GIN
actual #2 vs paper #213 211 places worse
0.9934
best reported
actual #2 vs paper #213 211 places worse
paper 0.8026 ±0.0032
paper 0.8026 ±0.0032 Δ at pub 0.1908
3
GCN
0.9727
4
GAT
actual #4 vs paper #323 319 places worse
0.9623
best reported
actual #4 vs paper #323 319 places worse
paper 0.7798 ±0.0024
paper 0.7798 ±0.0024 Δ at pub 0.1825
12
WL
actual #12 vs paper #122 110 places worse
0.8590 ±0.0010
best reported
actual #12 vs paper #122 110 places worse
paper 0.8219 ±0.0018
best at pub: Propagation Kernels (2014)
paper 0.8219 ±0.0018 Δ at pub 0.0371
34
GPS(DEL-F)
0.8436 ±0.0015
This paper
131
GraphSAGE
0.8200 ±0.0100
188
Graph Transformer +DEL-F
0.8062 ±0.0036
This paper
200
GraphMAE
actual #200 vs paper #202 2 places worse
0.8042 ±0.0035
best reported
actual #200 vs paper #202 2 places worse
paper 0.8040 ±0.0030

Difference within reported uncertainty; not counted as underperformance.

paper 0.8040 ±0.0030 Δ today 0.0002
226
GMT
actual #226 vs paper #381 155 places worse
0.7990 ±0.0040
best reported
actual #226 vs paper #381 155 places worse
paper 0.7635 ±0.0262

Difference within reported uncertainty; not counted as underperformance.

paper 0.7635 ±0.0262 Δ today 0.0355
281
GAT +DEL-F
0.7868 ±0.0028
This paper
282
Graph Transformer + DEL-K
0.7867 ±0.0032
This paper
286
Graph Transformer + MPNN
0.7862 ±0.0023
This paper
304
SEP-G
0.7835 ±0.0033
This paper
314
Graphtransformer
0.7816 ±0.0038
This paper
349
GAT + MPNN
0.7728 ±0.0027
This paper
350
GAT + DEL-K
0.7722 ±0.0015
This paper
466
GAT + Random distance
0.7146 ±0.0076
This paper
489
Graph Transformer + Random distance
0.6971 ±0.0012
This paper
#ModelAccuracy ↑Paper
1
MSH-GNN
0.9410 ±0.0330
2
GRDL
0.8260 ±0.0120
3
GMN
0.8225
32
GIN
actual #32 vs paper #161 129 places worse
0.7880 ±0.0410
best reported
actual #32 vs paper #161 129 places worse
paper 0.7587 ±0.0035

Difference within reported uncertainty; not counted as underperformance.

paper 0.7587 ±0.0035 Δ at pub 0.0293
35
Graph Transformer +DEL-F
0.7876 ±0.0040
This paper
36
Graph Transformer + DEL-K
0.7862 ±0.0068
This paper
40
GPS(DEL-K)
0.7842 ±0.0059
This paper
45
GAT +DEL-F
0.7819 ±0.0058
This paper
49
GAT
actual #49 vs paper #89 40 places worse
0.7800 ±0.0300
best reported
actual #49 vs paper #89 40 places worse
paper 0.7689 ±0.0037

Difference within reported uncertainty; not counted as underperformance.

paper 0.7689 ±0.0037 Δ at pub 0.0111
64
GAT + DEL-K
0.7734 ±0.0035
This paper
66
Graph Transformer + MPNN
0.7729 ±0.0068
This paper
67
SAGE
0.7726 ±0.0228
76
GAT + MPNN
0.7718 ±0.0041
This paper
83
Graphtransformer
0.7704 ±0.0024
This paper
114
SEP-G
0.7642 ±0.0039
This paper
116
GAT + Random distance
0.7641 ±0.0054
This paper
149
MLP
0.7600 ±0.0320
190
WL
actual #190 vs paper #277 87 places worse
0.7560 ±0.0040
best reported
actual #190 vs paper #277 87 places worse
paper 0.7468 ±0.0049
paper 0.7468 ±0.0049 Δ at pub 0.0092
213
GraphMAE
0.7530 ±0.0039
This paper
221
Graph Transformer + Random distance
0.7527 ±0.0013
This paper
236
GMT
actual #236 vs paper #239 3 places worse
0.7510 ±0.0060
best reported
actual #236 vs paper #239 3 places worse
paper 0.7509 ±0.0059

Difference within reported uncertainty; not counted as underperformance.

paper 0.7509 ±0.0059 Δ today 0.0001
#ModelAccuracy ↑Paper
1
GC-GNN (GCN)
0.9210 ±0.0810
2
SUGAR
0.8403 ±0.0133
3
Ortho-g-U-Nets
0.8387
11
GPS(DEL-F) [Final]
0.8140 ±0.0046
This paper
12
GPS(RWSE, DEL-K)
0.8121 ±0.0078
This paper
15
SAGE
0.8088 ±0.0233
25
WL
0.7978 ±0.0036
This paper
33
Graph Transformer +DEL-F
0.7950 ±0.0015
This paper
36
GraphMAE
0.7942 ±0.0042
This paper
39
Graph Transformer + DEL-K
0.7925 ±0.0011
This paper
48
GAT +DEL-F
0.7889 ±0.0034
This paper
53
GAT + DEL-K
0.7878 ±0.0035
This paper
55
GMT
0.7872 ±0.0059
This paper
74
GIN
actual #74 vs paper #122 48 places worse
0.7805 ±0.0189
best reported
actual #74 vs paper #122 48 places worse
paper 0.7583 ±0.0065

Difference within reported uncertainty; not counted as underperformance.

paper 0.7583 ±0.0065 Δ at pub 0.0222
77
SEP-G
0.7798 ±0.0057
This paper
#ModelAccuracy ↑Paper
1
ID-GNN+BEC
0.8150 ±0.0240
2
GIN+BEC
0.8080 ±0.0330
3
GCN+BEC
0.7990 ±0.0340
4
GCN
0.7980 ±0.0230
8
GAT +DEL-F
0.7863 ±0.0054
This paper
13
Graph Transformer +DEL-F
0.7828 ±0.0027
This paper
14
GIN
actual #14 vs paper #20 6 places worse
0.7641 ±0.0093
actual #14 vs paper #20 6 places worse
paper 0.7641 ±0.0093
prev best: Graph Homomorphism Convolution (ICML 2020)

Improvement within reported uncertainty; not highlighted.

paper 0.7641 ±0.0093 Δ at pub 0.0131
15
Graph Transformer + DEL-K
0.7765 ±0.0049
This paper
16
GPS(DEL-F)
0.7750 ±0.0065
This paper
18
GAT + DEL-K
0.7686 ±0.0058
This paper
20
Graph Transformer + MPNN
0.7651 ±0.0039
This paper
24
GAT + Random distance
0.7608 ±0.0048
This paper
26
GAT + MPNN
0.7585 ±0.0048
This paper
31
GraphMAE
0.7552 ±0.0066
This paper
33
Graph Transformer + Random distance
0.7527 ±0.0065
This paper
55
SEP-G
0.7412 ±0.0056
This paper
70
GMT
0.7348 ±0.0076
This paper
72
WL
actual #72 vs paper #72
0.7340 ±0.0463
actual #72 vs paper #72
paper 0.7340 ±0.0463

Improvement within reported uncertainty; not highlighted.

paper 0.7340 ±0.0463 Δ at pub 0.0110
#ModelAccuracy ↑Paper
1
GraphSNN
0.7790 ±0.0360
2
SIN
0.7560 ±0.0320
3
CIN
0.7560 ±0.0370
5
GIN
actual #5 vs paper #28 23 places worse
0.7510 ±0.0510
best reported
actual #5 vs paper #28 23 places worse
paper 0.5270 ±0.0076
paper 0.5270 ±0.0076 Δ at pub 0.2240
20
Graph Transformer + DEL-K
0.5354 ±0.0027
This paper
21
Graph Transformer +DEL-F
0.5339 ±0.0033
This paper
22
GAT +DEL-F
0.5327 ±0.0099
This paper
23
GPS(DEL-F)
0.5295 ±0.0064
This paper
24
GAT + DEL-K
0.5286 ±0.0033
This paper
25
GAT + MPNN
0.5286 ±0.0029
This paper
27
Graph Transformer + MPNN
0.5281 ±0.0025
This paper
29
GAT + Random distance
0.5260 ±0.0058
This paper
31
Graph Transformer + Random distance
0.5231 ±0.0045
This paper
38
GCN
0.5190
39
GraphMAE
0.5163 ±0.0052
This paper
41
SEP-G
0.5153 ±0.0065
This paper
50
GMT
0.5066 ±0.0082
This paper
72
WL
actual #72 vs paper #72
0.4933 ±0.0475
actual #72 vs paper #72
paper 0.4933 ±0.0475

Improvement within reported uncertainty; not highlighted.

paper 0.4933 ±0.0475 Δ at pub 0.0233

OGB

#ModelROC-AUC ↑Paper
1
Multi-RF Fusion with Multi-GNN Blending
0.8476 ±0.0002
2
HyperFusion
0.8475 ±0.0003
3
PAS+FPs
0.8420 ±0.0015
9
GatedGCN
0.8090 ±0.0160
69
GPS
actual #69 vs paper #167 98 places worse
0.7880 ±0.0101
best reported
actual #69 vs paper #167 98 places worse
paper 0.7671 ±0.0112
paper 0.7671 ±0.0112 Δ at pub 0.0209 Δ today 0.0209
109
GIN
0.7780 ±0.0182
111
GPS + DEL-K
0.7773 ±0.0161
This paper
132
GPS + DEL-F
0.7735 ±0.0097
This paper
140
GAT
actual #140 vs paper #248 108 places worse
0.7717 ±0.0137
best reported
actual #140 vs paper #248 108 places worse
paper 0.7445 ±0.0153
paper 0.7445 ±0.0153 Δ at pub 0.0272
143
GT + DEL-K
0.7713 ±0.0141
This paper
156
GT + DEL-F
0.7702 ±0.0075
This paper
174
GT
0.7651 ±0.0093
This paper
226
GAT +DEL-F
0.7547 ±0.0105
This paper
233
GAT + DEL-K
0.7524 ±0.0124
This paper
SOTA performance (not significantly different from the best) 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