NTFormer: A Composite Node Tokenized Graph Transformer for Node Classification
Abstract
Recently, the emerging graph Transformers have made significant advancements for node classification on graphs. In most graph Transformers, a crucial step involves transforming the input graph into token sequences as the model input, enabling Transformer to effectively learn the node representations. However, we observe that existing methods only express partial graph information of nodes through single-type token generation. Consequently, they require tailored strategies to encode additional graph-specific features into the Transformer to ensure the quality of node representation learning, limiting the model flexibility to handle diverse graphs. To this end, we propose a new graph Transformer called NTFormer to address this issue. NTFormer introduces a novel token generator called Node2Par, which constructs various token sequences using different token elements for each node. This flexibility allows Node2Par to generate valuable token sequences from different perspectives, ensuring comprehensive expression of rich graph features. Benefiting from the merits of Node2Par, NTFormer only leverages a Transformer-based backbone without graph-specific modifications to learn node representations, eliminating the need for graph-specific modifications. Extensive experiments conducted on various benchmark datasets containing homophily and heterophily graphs with different scales demonstrate the superiority of NTFormer over representative graph Transformers and graph neural networks for node classification.
Benchmark Results
Tested on 7 datasets 16 baseline values reported too low Non-standard metric on 1 dataset
Tables show presented results in global context (best 3 papers + GCN + MLP).
Classic
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | CNA | 0.9575
±0.0058 | |
| 2 | IS-GIB | 0.9390
±0.0187 | |
| 3 | EERM | 0.9112
±0.0145 | |
| 18 | NTFormer | 0.8161
±0.0075 | This paper |
| 20 | APPNP | 0.8142
±0.0026 best reported | best at pub: Feature Expansion for Graph Neural Networks (ICML 2023) Difference within reported uncertainty; not counted as underperformance. |
| 31 | STAGNN | 0.8105
±0.0082 | This paper |
| 32 | GPRGNN | 0.8102
±0.0071 | prev best: Feature Expansion for Graph Neural Networks (ICML 2023) |
| 40 | NAGphormer | 0.8057
±0.0072 | This paper |
| 44 | GCN | 0.8033
±0.0088 | prev best: Gophormer: Ego-Graph Transformer for Node Classification (2021) Improvement within reported uncertainty; not highlighted. |
| 57 | Specformer | 0.7938
±0.0096 | This paper |
| 60 | FAGCN | 0.7928
±0.0170 | This paper |
| 61 | GraphSAGE | 0.7923
±0.0053 | |
| 76 | NodeFormer | 0.7856
±0.0009 | prev best: Efficient Tuning and Inference for Large Language Models on Textual Graphs (IJCAI 2024) |
| 89 | SGFormer | 0.7798
±0.0091 | This paper |
| 96 | SGC | 0.7765
±0.0012 best reported | |
| 101 | ANS-GT | 0.7760
±0.0051 | prev best: Hierarchical Transformer for Scalable Graph Learning (IJCAI 2023) |
| 350 | MLP | 0.7289
±0.0010 |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | LGTL | 0.9518
±0.0011 | |
| 2 | MixHop (LO) | 0.9513
±0.0038 | |
| 3 | GraphSAGE (LO) | 0.9511
±0.0036 | |
| 7 | NodeFormer | 0.8827
±0.0004 | prev best: Discovering Data Geometry: Energy-Driven Neural Diffusion (ICLR 2023) |
| 17 | APPNP | 0.9355
±0.0060 best reported | best at pub: LOGIN: A Large Language Model Consulted Graph Neural Network Training Framework (2024) |
| 18 | GCN | 0.9296
±0.0015 best reported | best at pub: Node Identifiers: Compact, Discrete Representations for Efficient Graph Learning (ICLR 2024) |
| 56 | SGFormer | 0.9037
±0.0020 best reported | best today: VecFormer: Towards Efficient and Generalizable Graph Transformer with Graph Token Attention (WWW 2026) |
| 64 | STAGNN | 0.9018
±0.0026 | This paper |
| 73 | FAGCN | 0.8998
±0.0054 best reported | best at pub: Language is All a Graph Needs (2023) |
| 79 | NTFormer | 0.8978
±0.0021 | This paper |
| 89 | Specformer | 0.8947
±0.0048 | |
| 91 | NAGphormer | 0.8939
±0.0013 | This paper |
| 100 | ANS-GT | 0.8914
±0.0026 | prev best: Hierarchical Transformer for Scalable Graph Learning (IJCAI 2023) |
| 101 | GPRGNN | 0.8911
±0.0008 best reported | best at pub: Feature Expansion for Graph Neural Networks (ICML 2023) |
| 116 | SAGE | 0.8881
±0.0015 | |
| 141 | SGC | 0.8832
±0.0055 best reported | best at pub: LOGIN: A Large Language Model Consulted Graph Neural Network Training Framework (2024) |
| 210 | MLP | 0.8690
±0.0074 |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | GraphTARIF | 0.9703
±0.0019 | |
| 2 | GAT | 0.9669
±0.0014 | |
| 3 | GAT+T | 0.9660
±0.0007 | |
| 7 | SAGE | 0.9643
±0.0027 | |
| 8 | GCN | 0.9632
±0.0008 best reported | |
| 10 | NTFormer | 0.9617
±0.0029 | This paper |
| 11 | NAGphormer | 0.9594
±0.0045 | prev best: Polynormer: Polynomial-Expressive Graph Transformer in Linear Time (ICLR 2024) Improvement within reported uncertainty; not highlighted. |
| 18 | Specformer | 0.9580
±0.0026 | |
| 21 | APPNP | 0.9573
±0.0012 | prev best: Polynormer: Polynomial-Expressive Graph Transformer in Linear Time (ICLR 2024) |
| 29 | SGFormer | 0.9558
±0.0036 best reported | |
| 33 | GPRGNN | 0.9549
±0.0014 best reported | best at pub: SignGT: Signed Attention-based Graph Transformer for Graph Representation Learning (2023) Difference within reported uncertainty; not counted as underperformance. |
| 44 | NodeFormer | 0.9527
±0.0022 best reported | best at pub: SignGT: Signed Attention-based Graph Transformer for Graph Representation Learning (2023) best today: GrokFormer: Graph Fourier Kolmogorov-Arnold Transformers (ICML 2024) |
| 50 | SGC | 0.9511
±0.0009 best reported | |
| 60 | ANS-GT | 0.9498
±0.0043 | prev best: Hierarchical Transformer for Scalable Graph Learning (IJCAI 2023) |
| 66 | FAGCN | 0.9489
±0.0048 best reported | best at pub: Clarify Confused Nodes via Separated Learning (2023) Difference within reported uncertainty; not counted as underperformance. |
| 78 | STAGNN | 0.9447
±0.0073 | This paper |
| 390 | MLP | 0.9128
±0.0063 |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | GraphTARIF | 0.9461
±0.0017 | |
| 2 | GCN | 0.9412
±0.0008 best reported | best at pub: Clarify Confused Nodes via Separated Learning (2023) |
| 3 | GAT | 0.9398
±0.0022 | |
| 8 | SAGE | 0.9351
±0.0006 | |
| 18 | SGFormer | 0.9242
±0.0066 best reported | |
| 39 | NTFormer | 0.9169
±0.0032 | This paper |
| 38 | NAGphormer | 0.9169
±0.0030 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. |
| 48 | NodeFormer | 0.9112
±0.0043 best reported | |
| 49 | Specformer | 0.9109
±0.0027 | prev best: SignGT: Signed Attention-based Graph Transformer for Graph Representation Learning (2023) Improvement within reported uncertainty; not highlighted. |
| 58 | APPNP | 0.9093
±0.0018 | prev best: Polynormer: Polynomial-Expressive Graph Transformer in Linear Time (ICLR 2024) |
| 72 | GPRGNN | 0.9050
±0.0091 | prev best: SignGT: Signed Attention-based Graph Transformer for Graph Representation Learning (2023) Improvement within reported uncertainty; not highlighted. |
| 82 | SGC | 0.9022
±0.0021 best reported | |
| 87 | ANS-GT | 0.9017
±0.0044 | This paper |
| 126 | FAGCN | 0.8968
±0.0097 best reported | best at pub: Node-oriented Spectral Filtering for Graph Neural Networks (2022) |
| 193 | STAGNN | 0.8837
±0.0178 | This paper |
| 320 | MLP | 0.8463 |
Sorted by Accuracy. Highlighted rows are from other papers.
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | GAP-EDP | 0.9870
±0.0003 | |
| 2 | NE-ASGCN | 0.9758
±0.0027 | |
| 3 | HSGT | 0.9730
±0.0024 | |
| 21 | GraphSAGE | 0.9653
±0.0011 | |
| 56 | ANS-GT | 0.9530
±0.0081 best reported | best at pub: Hierarchical Transformer for Scalable Graph Learning (IJCAI 2023) |
| 83 | NTFormer | 0.9375
±0.0026 | This paper |
| 84 | NAGphormer | 0.9374
±0.0006 best reported | |
| 126 | SGFormer | 0.8963
±0.0026 | This paper |
| 132 | NodeFormer | 0.8897
±0.0032 | This paper |
| 147 | MLP | 0.8240
±0.0010 |
Heterophily Benchmark
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | Dir-Poly | 0.9451
±0.0022 | |
| 2 | D-CDE | 0.9387
±0.0041 | |
| 3 | LargeScaleNet | 0.9358
±0.0024 | |
| 26 | GraphSAGE | 0.9106
±0.0027 | |
| 77 | GCN | 0.8272
±0.0082 best reported | best at pub: Graph Neural Networks for Graphs with Heterophily: A Survey (2022) best today: HyperAggregation: Aggregating over Graph Edges with Hypernetworks (2024) |
| 90 | SGFormer | 0.8001
±0.0044 best reported | |
| 100 | NTFormer | 0.7839
±0.0111 | This paper |
| 106 | STAGNN | 0.7671
±0.0033 | This paper |
| 108 | FAGCN | 0.7571
±0.0139 | prev best: Unleashing the Potential of Fractional Calculus in Graph Neural Networks with FROND (ICLR 2024) |
| 109 | NodeFormer | 0.7483
±0.0081 best reported | best at pub: Polynormer: Polynomial-Expressive Graph Transformer in Linear Time (ICLR 2024) |
| 112 | NAGphormer | 0.7434
±0.0077 best reported | best at pub: Polynormer: Polynomial-Expressive Graph Transformer in Linear Time (ICLR 2024) best today: TANGO: Graph Neural Dynamics via Learned Energy and Tangential Flows (2025) Difference within reported uncertainty; not counted as underperformance. |
| 125 | ANS-GT | 0.6964
±0.0116 | This paper |
| 133 | GPRGNN | 0.6704
±0.0092 | This paper |
| 135 | MLP | 0.6665
±0.0047 | |
| 159 | Specformer | 0.6273
±0.0196 | This paper |
| 188 | APPNP | 0.5184
±0.0018 | This paper |
| 200 | SGC | 0.4033
±0.0034 | This paper |
Other Graph Benchmarks
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | MA-GCL | 0.8883
±0.0030 | |
| 2 | CCA-SSG | 0.8842
±0.0030 | |
| 3 | ARIEL | 0.8827
±0.0020 | |
| 10 | GCN | 0.8651
±0.0050 | |
| 16 | NTFormer | 0.7803
±0.0044 | This paper |
| 17 | NAGphormer | 0.7798
±0.0016 best reported | |
| 19 | ANS-GT | 0.7632
±0.0038 | This paper |
| 22 | SGFormer | 0.7422
±0.0036 | This paper |
| 24 | NodeFormer | 0.7156
±0.0042 | This paper |
