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
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | GraphTARIF | 0.9703
±0.0019 | |
| 2 | GAT | 0.9669
±0.0014 best reported | |
| 3 | GAT+T | 0.9660
±0.0007 | |
| 7 | SAGE | 0.9643
±0.0027 | |
| 8 | GCN | 0.9632
±0.0008 best reported | |
| 56 | GraphSAGE | 0.9508
±0.0026 best reported | best at pub: A Quasi-Wasserstein Loss for Learning Graph Neural Networks (WWW 2023) |
| 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 |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | GraphTARIF | 0.9461
±0.0017 | |
| 2 | GCN | 0.9412
±0.0008 best reported | best at pub: Diss-l-ECT: Dissecting Graph Data with local Euler Characteristic Transforms (ICML 2024) |
| 3 | GAT | 0.9398
±0.0022 best reported | best at pub: Diss-l-ECT: Dissecting Graph Data with local Euler Characteristic Transforms (ICML 2024) |
| 8 | SAGE | 0.9351
±0.0006 | |
| 13 | TabPFN-GN | 0.9271
±0.0003 | This paper |
| 34 | GraphGPS | 0.9179
±0.0063 best reported | best at pub: Polynormer: Polynomial-Expressive Graph Transformer in Linear Time (ICLR 2024) best today: Graph Transductive Sharpening: Leveraging Unlabeled Predictions in Node Classification (2026) Difference within reported uncertainty; not counted as underperformance. |
| 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 |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | GCN | 0.9302
±0.0011 best reported | best at pub: Augmentation-Free Graph Contrastive Learning with Performance Guarantee (2022) |
| 2 | RSE + RGCN (70b) | 0.8852
±0.0019 | |
| 3 | LEMP+T | 0.8825 | |
| 9 | SAGE | 0.8771 | |
| 31 | GAT | 0.8533 best reported | |
| 69 | GraphSAGE | 0.8146
±0.0010 best reported | |
| 116 | TabPFN-GN | 0.7940
±0.0077 | This paper |
| 120 | GraphGPS | 0.7926
±0.0057 best reported | best at pub: GrokFormer: Graph Fourier Kolmogorov-Arnold Transformers (ICML 2024) Difference within reported uncertainty; not counted as underperformance. |
| 233 | GraphAny | 0.7495
±0.0061 best reported | best at pub: Fully-inductive Node Classification on Arbitrary Graphs (ICLR 2024) best today: Can TabPFN Compete with GNNs for Node Classification via Graph Tabularization? (LoG 2025) Difference within reported uncertainty; not counted as underperformance. |
| 237 | MLP | 0.7469
±0.0085 | |
| 251 | TabPFN | 0.7208
±0.0059 | This paper |
Heterophilic Graphs
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | P^2GNN | 0.9672
±0.0147 | |
| 2 | DoG | 0.9660
±0.0210 | |
| 3 | GPF-plus | 0.9583
±0.0419 | |
| 28 | GPRGNN | 0.9295
±0.0131 best reported | best at pub: GrokFormer: Graph Fourier Kolmogorov-Arnold Transformers (ICML 2024) |
| 34 | MLP | 0.9230
±0.0070 | |
| 40 | H2GCN | 0.9189
±0.0393 best reported | best at pub: GrokFormer: Graph Fourier Kolmogorov-Arnold Transformers (ICML 2024) |
| 53 | GraphSAGE | 0.9000
±0.0365 best reported | best at pub: A Quasi-Wasserstein Loss for Learning Graph Neural Networks (WWW 2023) best today: Graph Neural Networks Need Cluster-Normalize-Activate Modules (NeurIPS 2024) |
| 189 | SAGE | 0.8269 | |
| 211 | GAT | 0.8162
±0.0645 best reported | best at pub: Equivariance Everywhere All At Once: A Recipe for Graph Foundation Models (2025) |
| 231 | TabPFN-GN | 0.8081
±0.0475 | This paper |
| 257 | GCN | 0.7933
±0.0447 best reported | best at pub: Graph Wave Networks (WWW 2025) |
| 260 | TabPFN | 0.7919
±0.0383 | This paper |
| 354 | GraphAny | 0.7297
±0.0271 | Improvement within reported uncertainty; not highlighted. |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | P^2GNN | 0.9541
±0.0272 | |
| 2 | ACM-GCN | 0.9480
±0.0380 | |
| 3 | RF-GCN | 0.9429 | |
| 22 | GPRGNN | 0.9157
±0.0196 best reported | best at pub: Simplified PCNet with Robustness (2024) Difference within reported uncertainty; not counted as underperformance. |
| 24 | MLP | 0.9136
±0.0070 | |
| 68 | H2GCN | 0.8623
±0.0471 best reported | best at pub: Heterophily-informed Message Passing (TMLR 2025) best today: $P^2$GNN: Two Prototype Sets to boost GNN Performance (2026) |
| 138 | SAGE | 0.8269 | |
| 157 | GraphSAGE | 0.8196
±0.0739 best reported | best at pub: Heterophily-Aware Graph Attention Network (2023) Difference within reported uncertainty; not counted as underperformance. |
| 158 | GAT | 0.8190
±0.0540 best reported | best at pub: Restructuring Graphs for Higher Homophily via Adaptive Spectral Clustering (AAAI 2022) |
| 170 | GCN | 0.8082
±0.0360 best reported | best at pub: Bayesian Neighborhood Adaptation for Graph Neural Networks (TMLR 2025) |
| 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 |
| # | Model | Accuracy ↑ | 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 | 0.3992
±0.0067 best reported | best at pub: LON-GNN: Spectral GNNs with Learnable Orthonormal Basis (2023) best today: GrokFormer: Graph Fourier Kolmogorov-Arnold Transformers (ICML 2024) |
| 68 | GraphSAGE | 0.3899
±0.0085 best reported | best at pub: A Quasi-Wasserstein Loss for Learning Graph Neural Networks (WWW 2023) |
| 71 | H2GCN | 0.3885
±0.0117 best reported | best at pub: ES-GNN: Generalizing Graph Neural Networks Beyond Homophily with Edge Splitting (2022) best today: $P^2$GNN: Two Prototype Sets to boost GNN Performance (2026) |
| 123 | TabPFN-GN | 0.3722
±0.0108 | This paper |
| 135 | GCN | 0.3690 best reported | best at pub: Beyond Low-frequency Information in Graph Convolutional Networks (AAAI 2021) |
| 169 | TabPFN | 0.3637
±0.0131 | This paper |
| 182 | GAT | 0.3605
±0.0035 best reported | best at pub: Hierarchical Graph Transformer with Adaptive Node Sampling (NeurIPS 2022) |
| 266 | GIN | 0.3410
±0.0030 | |
| 384 | GraphAny | 0.2860
±0.0021 |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | Hetero-S (GAT 8-layer) | 0.8693 | |
| 2 | Dir-GNN+CNA | 0.8586
±0.0180 | |
| 3 | GAT* | 0.8560 best reported | best at pub: The Heterophilic Snowflake Hypothesis: Training and Empowering GNNs for Heterophilic Graphs (KDD 2024) |
| 52 | GCN* | 0.7033 best reported | best at pub: Understanding Heterophily for Graph Neural Networks (ICML 2024) |
| 72 | GPRGNN | 0.6748
±0.0040 best reported | best at pub: LON-GNN: Spectral GNNs with Learnable Orthonormal Basis (2023) best today: $P^2$GNN: Two Prototype Sets to boost GNN Performance (2026) |
| 85 | GraphAny | 0.6540
±0.0163 best reported | best at pub: Equivariance Everywhere All At Once: A Recipe for Graph Foundation Models (2025) |
| 108 | SAGE | 0.6340
±0.0300 | |
| 115 | GraphSAGE* | 0.6215
±0.0042 best reported | best at pub: Hierarchical Graph Transformer with Adaptive Node Sampling (NeurIPS 2022) |
| 133 | H2GCN | 0.6030
±0.0231 best reported | best at pub: Optimization-Induced Graph Implicit Nonlinear Diffusion (ICML 2022) |
| 169 | MLP | 0.5429 | |
| 203 | TabPFN-GN | 0.4911
±0.0434 | This paper |
| 226 | TabPFN | 0.4516
±0.0432 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | IBG-NN | 0.7763
±0.0179 | |
| 2 | Dir-GNN+CNA | 0.7747
±0.0128 | |
| 3 | DHGNN | 0.7684
±0.0161 | |
| 39 | H2GCN | 0.6190
±0.0140 best reported | best at pub: Efficient Learning on Large Graphs using a Densifying Regularity Lemma (2025) |
| 46 | GCN | 0.6067 | |
| 76 | GPRGNN | 0.5435
±0.0087 best reported | best at pub: Directed Homophily-Aware Graph Neural Network (2025) |
| 93 | GraphAny | 0.4974
±0.0047 best reported | best at pub: Equivariance Everywhere All At Once: A Recipe for Graph Foundation Models (2025) |
| 103 | TabPFN-GN | 0.4666
±0.0143 | This paper |
| 172 | MLP | 0.3930
±0.0079 | |
| 194 | TabPFN | 0.3751
±0.0127 | This paper |
