LoG 2025

Can TabPFN Compete with GNNs for Node Classification via Graph Tabularization?

Jeongwhan Choi, Woosung Kang, Minseo Kim, Jongwook Kim, Noseong Park

Main figure for Can TabPFN Compete with GNNs for Node Classification via Graph Tabularization?

Abstract

Foundation models pretrained on large data have demonstrated remarkable zero-shot generalization capabilities across domains. Building on the success of TabPFN for tabular data and its recent extension to time series, we investigate whether graph node classification can be effectively reformulated as a tabular learning problem. We introduce TabPFN-GN, which transforms graph data into tabular features by extracting node attributes, structural properties, positional encodings, and optionally smoothed neighborhood features. This enables TabPFN to perform direct node classification without any graph-specific training or language model dependencies. Our experiments on 12 benchmark datasets reveal that TabPFN-GN achieves competitive performance with GNNs on homophilous graphs and consistently outperforms them on heterophilous graphs. These results demonstrate that principled feature engineering can bridge the gap between tabular and graph domains, providing a practical alternative to task-specific GNN training and LLM-dependent graph foundation models.

Benchmark Results

Tested on 8 datasets 28 baseline values reported too low

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

Classic

#ModelAccuracy ↑Paper
1
GraphTARIF
0.9703 ±0.0019
2
GAT
actual #2 vs paper #111 109 places worse
0.9669 ±0.0014
best reported
actual #2 vs paper #111 109 places worse
paper 0.9387 ±0.0011
3
GAT+T
0.9660 ±0.0007
7
SAGE
0.9643 ±0.0027
8
GCN
actual #8 vs paper #254 246 places worse
0.9632 ±0.0008
best reported
actual #8 vs paper #254 246 places worse
paper 0.9270 ±0.0020
56
GraphSAGE
actual #56 vs paper #72 16 places worse
0.9508 ±0.0026
best reported
actual #56 vs paper #72 16 places worse
paper 0.9459 ±0.0014
paper 0.9459 ±0.0014 Δ at pub 0.0049
57
GraphGPS
0.9506 ±0.0013
This paper
142
TabPFN-GN
0.9355 ±0.0005
This paper
185
TabPFN
0.9327
This paper
390
MLP
0.9128 ±0.0063
423
GraphAny
0.9060 ±0.0082
This paper
#ModelAccuracy ↑Paper
1
GraphTARIF
0.9461 ±0.0017
2
GCN
actual #2 vs paper #128 126 places worse
0.9412 ±0.0008
best reported
actual #2 vs paper #128 126 places worse
paper 0.8965 ±0.0052
3
GAT
actual #3 vs paper #60 57 places worse
0.9398 ±0.0022
best reported
actual #3 vs paper #60 57 places worse
paper 0.9078 ±0.0013
8
SAGE
0.9351 ±0.0006
13
TabPFN-GN
0.9271 ±0.0003
This paper
34
GraphGPS
actual #34 vs paper #46 12 places worse
0.9179 ±0.0063
best reported
actual #34 vs paper #46 12 places worse
paper 0.9119 ±0.0054

Difference within reported uncertainty; not counted as underperformance.

paper 0.9119 ±0.0054 Δ today 0.0060
46
GraphSAGE
0.9120 ±0.0029
This paper
320
MLP
0.8463
382
GraphAny
0.8304 ±0.0124
This paper
445
TabPFN
0.7670
This paper
#ModelAccuracy ↑Paper
1
GCN
actual #1 vs paper #193 192 places worse
0.9302 ±0.0011
best reported
actual #1 vs paper #193 192 places worse
paper 0.7747 ±0.0085
paper 0.7747 ±0.0085 Δ at pub 0.1555
2
RSE + RGCN (70b)
0.8852 ±0.0019
3
LEMP+T
0.8825
9
SAGE
0.8771
31
GAT
actual #31 vs paper #209 178 places worse
0.8533
best reported
actual #31 vs paper #209 178 places worse
paper 0.7691 ±0.0082
paper 0.7691 ±0.0082 Δ at pub 0.0842
69
GraphSAGE
actual #69 vs paper #235 166 places worse
0.8146 ±0.0010
best reported
actual #69 vs paper #235 166 places worse
paper 0.7477 ±0.0095
116
TabPFN-GN
0.7940 ±0.0077
This paper
120
GraphGPS
actual #120 vs paper #150 30 places worse
0.7926 ±0.0057
best reported
actual #120 vs paper #150 30 places worse
paper 0.7866 ±0.0049

Difference within reported uncertainty; not counted as underperformance.

paper 0.7866 ±0.0049 Δ at pub 0.0060
233
GraphAny
actual #233 vs paper #233
0.7495 ±0.0061
best reported
actual #233 vs paper #233
paper 0.7495 ±0.0061

Difference within reported uncertainty; not counted as underperformance.

paper 0.7495 ±0.0061 Δ at pub 0.0006
237
MLP
0.7469 ±0.0085
251
TabPFN
0.7208 ±0.0059
This paper

Heterophilic Graphs

#ModelAccuracy ↑Paper
1
P^2GNN
0.9672 ±0.0147
2
DoG
0.9660 ±0.0210
3
GPF-plus
0.9583 ±0.0419
28
GPRGNN
actual #28 vs paper #269 241 places worse
0.9295 ±0.0131
best reported
actual #28 vs paper #269 241 places worse
paper 0.7838 ±0.0436
paper 0.7838 ±0.0436 Δ at pub 0.1457
34
MLP
0.9230 ±0.0070
40
H2GCN
actual #40 vs paper #246 206 places worse
0.9189 ±0.0393
best reported
actual #40 vs paper #246 206 places worse
paper 0.7973 ±0.0325
paper 0.7973 ±0.0325 Δ at pub 0.1216
53
GraphSAGE
actual #53 vs paper #499 446 places worse
0.9000 ±0.0365
best reported
actual #53 vs paper #499 446 places worse
paper 0.6020 ±0.0721
paper 0.6020 ±0.0721 Δ at pub 0.2980 Δ today 0.2980
189
SAGE
0.8269
211
GAT
actual #211 vs paper #496 285 places worse
0.8162 ±0.0645
best reported
actual #211 vs paper #496 285 places worse
paper 0.6054 ±0.0622
paper 0.6054 ±0.0622 Δ at pub 0.2108
231
TabPFN-GN
0.8081 ±0.0475
This paper
257
GCN
actual #257 vs paper #508 251 places worse
0.7933 ±0.0447
best reported
actual #257 vs paper #508 251 places worse
paper 0.5973 ±0.0970
best at pub: Graph Wave Networks (WWW 2025)
paper 0.5973 ±0.0970 Δ at pub 0.1960
260
TabPFN
0.7919 ±0.0383
This paper
354
GraphAny
actual #354 vs paper #354
0.7297 ±0.0271
actual #354 vs paper #354
paper 0.7297 ±0.0271

Improvement within reported uncertainty; not highlighted.

paper 0.7297 ±0.0271 Δ at pub 0.0162
#ModelAccuracy ↑Paper
1
P^2GNN
0.9541 ±0.0272
2
ACM-GCN
0.9480 ±0.0380
3
RF-GCN
0.9429
22
GPRGNN
actual #22 vs paper #177 155 places worse
0.9157 ±0.0196
best reported
actual #22 vs paper #177 155 places worse
paper 0.8027 ±0.0811

Difference within reported uncertainty; not counted as underperformance.

paper 0.8027 ±0.0811 Δ at pub 0.1130
24
MLP
0.9136 ±0.0070
68
H2GCN
actual #68 vs paper #271 203 places worse
0.8623 ±0.0471
best reported
actual #68 vs paper #271 203 places worse
paper 0.7162 ±0.0557
best at pub: Heterophily-informed Message Passing (TMLR 2025)
paper 0.7162 ±0.0557 Δ at pub 0.1458 Δ today 0.1461
138
SAGE
0.8269
157
GraphSAGE
actual #157 vs paper #278 121 places worse
0.8196 ±0.0739
best reported
actual #157 vs paper #278 121 places worse
paper 0.7073 ±0.0659

Difference within reported uncertainty; not counted as underperformance.

paper 0.7073 ±0.0659 Δ at pub 0.1123
158
GAT
actual #158 vs paper #430 272 places worse
0.8190 ±0.0540
best reported
actual #158 vs paper #430 272 places worse
paper 0.5460 ±0.0790
paper 0.5460 ±0.0790 Δ at pub 0.2730
170
GCN
actual #170 vs paper #537 367 places worse
0.8082 ±0.0360
best reported
actual #170 vs paper #537 367 places worse
paper 0.4378 ±0.0315
paper 0.4378 ±0.0315 Δ at pub 0.3704
249
TabPFN-GN
0.7405 ±0.0696
This paper
259
TabPFN
0.7270 ±0.0633
This paper
321
GraphAny
0.6594 ±0.0148
This paper
#ModelAccuracy ↑Paper
1
DiGGR
0.4535 ±0.0353
2
TRIGON
0.4402 ±0.0028
3
DoG
0.4320 ±0.0120
42
MLP
0.4026 ±0.0108
52
GPRGNN
actual #52 vs paper #223 171 places worse
0.3992 ±0.0067
best reported
actual #52 vs paper #223 171 places worse
paper 0.3530 ±0.0080
paper 0.3530 ±0.0080 Δ at pub 0.0462 Δ today 0.0462
68
GraphSAGE
actual #68 vs paper #319 251 places worse
0.3899 ±0.0085
best reported
actual #68 vs paper #319 251 places worse
paper 0.3124 ±0.0171
paper 0.3124 ±0.0171 Δ at pub 0.0775
71
H2GCN
actual #71 vs paper #177 106 places worse
0.3885 ±0.0117
best reported
actual #71 vs paper #177 106 places worse
paper 0.3618 ±0.0045
paper 0.3618 ±0.0045 Δ at pub 0.0222 Δ today 0.0267
123
TabPFN-GN
0.3722 ±0.0108
This paper
135
GCN
actual #135 vs paper #420 285 places worse
0.3690
best reported
actual #135 vs paper #420 285 places worse
paper 0.2587 ±0.0121
paper 0.2587 ±0.0121 Δ at pub 0.1103
169
TabPFN
0.3637 ±0.0131
This paper
182
GAT
actual #182 vs paper #398 216 places worse
0.3605 ±0.0035
best reported
actual #182 vs paper #398 216 places worse
paper 0.2782 ±0.0028
paper 0.2782 ±0.0028 Δ at pub 0.0823
266
GIN
0.3410 ±0.0030
384
GraphAny
actual #384 vs paper #384
0.2860 ±0.0021
actual #384 vs paper #384
paper 0.2860 ±0.0021
paper 0.2860 ±0.0021 Δ at pub 0.0106
#ModelAccuracy ↑Paper
1
Hetero-S (GAT 8-layer)
0.8693
2
Dir-GNN+CNA
0.8586 ±0.0180
3
GAT*
actual #3 vs paper #229 226 places worse
0.8560
best reported
actual #3 vs paper #229 226 places worse
paper 0.4413 ±0.0417
paper 0.4413 ±0.0417 Δ at pub 0.4147
52
GCN*
actual #52 vs paper #216 164 places worse
0.7033
best reported
actual #52 vs paper #216 164 places worse
paper 0.4629 ±0.0340
paper 0.4629 ±0.0340 Δ at pub 0.2404
72
GPRGNN
actual #72 vs paper #254 182 places worse
0.6748 ±0.0040
best reported
actual #72 vs paper #254 182 places worse
paper 0.3993 ±0.0330
paper 0.3993 ±0.0330 Δ at pub 0.2735 Δ today 0.2755
85
GraphAny
actual #85 vs paper #254 169 places worse
0.6540 ±0.0163
best reported
actual #85 vs paper #254 169 places worse
paper 0.3998 ±0.0312
paper 0.3998 ±0.0312 Δ at pub 0.2542
108
SAGE
0.6340 ±0.0300
115
GraphSAGE*
actual #115 vs paper #227 112 places worse
0.6215 ±0.0042
best reported
actual #115 vs paper #227 112 places worse
paper 0.4481 ±0.0704
paper 0.4481 ±0.0704 Δ at pub 0.1734
133
H2GCN
actual #133 vs paper #279 146 places worse
0.6030 ±0.0231
best reported
actual #133 vs paper #279 146 places worse
paper 0.2675 ±0.0364
paper 0.2675 ±0.0364 Δ at pub 0.3355
169
MLP
0.5429
203
TabPFN-GN
0.4911 ±0.0434
This paper
226
TabPFN
0.4516 ±0.0432
This paper
#ModelAccuracy ↑Paper
1
IBG-NN
0.7763 ±0.0179
2
Dir-GNN+CNA
0.7747 ±0.0128
3
DHGNN
0.7684 ±0.0161
39
H2GCN
actual #39 vs paper #217 178 places worse
0.6190 ±0.0140
best reported
actual #39 vs paper #217 178 places worse
paper 0.3510 ±0.0115
paper 0.3510 ±0.0115 Δ at pub 0.2680
46
GCN
0.6067
76
GPRGNN
actual #76 vs paper #173 97 places worse
0.5435 ±0.0087
best reported
actual #76 vs paper #173 97 places worse
paper 0.3895 ±0.0199
paper 0.3895 ±0.0199 Δ at pub 0.1540
93
GraphAny
actual #93 vs paper #177 84 places worse
0.4974 ±0.0047
best reported
actual #93 vs paper #177 84 places worse
paper 0.3874 ±0.0201
paper 0.3874 ±0.0201 Δ at pub 0.1100
103
TabPFN-GN
0.4666 ±0.0143
This paper
172
MLP
0.3930 ±0.0079
194
TabPFN
0.3751 ±0.0127
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 at pub — reported value improved over the best known when published Best today — OK at publication; today's leaderboard best is elsewhere