GCoT: Chain-of-Thought Prompt Learning for Graphs
Abstract
Chain-of-thought (CoT) prompting has achieved remarkable success in natural language processing (NLP). However, its vast potential remains largely unexplored for graphs. This raises an interesting question: How can we design CoT prompting for graphs to guide graph models to learn step by step? On one hand, unlike natural languages, graphs are non-linear and characterized by complex topological structures. On the other hand, many graphs lack textual data, making it difficult to formulate language-based CoT prompting. In this work, we propose the first CoT prompt learning framework for text-free graphs,. Specifically, we decompose the adaptation process for each downstream task into a series of inference steps, with each step consisting of prompt-based inference, ``thought'' generation, and thought-conditioned prompt learning. While the steps mimic CoT prompting in NLP, the exact mechanism differs significantly. Specifically, at each step, an input graph, along with a prompt, is first fed into a pre-trained graph encoder for prompt-based inference. We then aggregate the hidden layers of the encoder to construct a ``thought'', which captures the working state of each node in the current step. Conditioned on this thought, we learn a prompt specific to each node based on the current state. These prompts are fed into the next inference step, repeating the cycle. To evaluate and analyze the effectiveness of, we conduct comprehensive experiments on eight public datasets, which demonstrate the advantage of our approach.
Benchmark Results
Tested on 8 datasets 14 baseline values reported too low
Tables show presented results in global context (best 3 papers + GCN + MLP).
Classic
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | GraphSAGE+CNA | 0.9418
±0.0033 | |
| 2 | GCN+CNA | 0.9366
±0.0048 | |
| 3 | TransformerConv | 0.9350
±0.0058 | |
| 21 | GCN | 0.9004 best reported | best at pub: Understanding Heterophily for Graph Neural Networks (ICML 2024) |
| 39 | SAGE | 0.8911
±0.0012 | |
| 44 | GAT | 0.8897
±0.0014 best reported | best at pub: Learned Low Precision Graph Neural Networks (2020) |
| 278 | GraphCL | 0.8428
±0.0091 best reported | best at pub: Decoupled Self-supervised Learning for Non-Homophilou Graphs (2022) |
| 724 | MLP | 0.7768 | |
| 877 | GCoT | 0.5967
±0.1551 | This paper |
| 884 | GPF | 0.5760
±0.1388 | prev best: ProG: A Graph Prompt Learning Benchmark (NeurIPS 2024) Improvement within reported uncertainty; not highlighted. |
| 892 | GraphPrompt | 0.5425
±0.0938 | This paper |
| 893 | DGI/InfoGraph | 0.5411
±0.0960 | This paper |
| 899 | ProG | 0.5059
±0.1464 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | CNA | 0.9575
±0.0058 | |
| 2 | IS-GIB | 0.9390
±0.0187 | |
| 3 | EERM | 0.9112
±0.0145 | |
| 35 | GAT | 0.8080
±0.0026 best reported | best at pub: Feature Expansion for Graph Neural Networks (ICML 2023) |
| 44 | GCN | 0.8033
±0.0088 best reported | best at pub: NTFormer: A Composite Node Tokenized Graph Transformer for Node Classification (2024) |
| 61 | GraphSAGE | 0.7923
±0.0053 | |
| 350 | MLP | 0.7289
±0.0010 | |
| 395 | GraphCL | 0.7250
±0.0070 best reported | best at pub: Generative Subgraph Contrast for Self-Supervised Graph Representation Learning (2022) |
| 869 | GPF | 0.4328
±0.0882 | prev best: ProG: A Graph Prompt Learning Benchmark (NeurIPS 2024) Improvement within reported uncertainty; not highlighted. |
| 871 | GraphPrompt | 0.4707
±0.0309 best reported | best today: MAGPrompt: Message-Adaptive Graph Prompt Tuning for Graph Neural Networks (2026) Difference within reported uncertainty; not counted as underperformance. |
| 873 | GCoT | 0.4621
±0.0878 | This paper |
| 878 | DGI/InfoGraph | 0.4500
±0.0919 | This paper |
| 884 | ProG | 0.4317
±0.0849 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | LGTL | 0.9518
±0.0011 | |
| 2 | MixHop (LO) | 0.9513
±0.0038 | |
| 3 | GraphSAGE (LO) | 0.9511
±0.0036 | |
| 18 | GCN | 0.9296
±0.0015 best reported | best at pub: Node Identifiers: Compact, Discrete Representations for Efficient Graph Learning (ICLR 2024) |
| 20 | GAT | 0.9233
±0.0018 best reported | best at pub: Tackling Over-Smoothing for General Graph Convolutional Networks (2020) |
| 116 | SAGE | 0.8881
±0.0015 | |
| 210 | MLP | 0.8690
±0.0074 | |
| 331 | GraphCL | 0.8196
±0.0073 best reported | best at pub: Decoupled Self-supervised Learning for Non-Homophilou Graphs (2022) |
| 863 | GCoT | 0.6443
±0.0996 | This paper |
| 865 | GraphPrompt | 0.6311
±0.1001 | This paper |
| 866 | ProG | 0.6307
±0.1196 | This paper |
| 870 | GPF | 0.5716
±0.1099 | prev best: OpenGraph: Towards Open Graph Foundation Models (2024) Improvement within reported uncertainty; not highlighted. |
| 873 | DGI/InfoGraph | 0.4746
±0.1219 | This paper |
| # | 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 | |
| 390 | MLP | 0.9128
±0.0063 | |
| 563 | DGI/InfoGraph | 0.5889
±0.1097 | This paper |
TU Dortmund
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | MSH-GNN | 0.9410
±0.0330 | |
| 2 | GRDL | 0.8260
±0.0120 | |
| 3 | GMN | 0.8225 | |
| 32 | GIN | 0.7880
±0.0410 | |
| 49 | GAT | 0.7800
±0.0300 best reported | |
| 148 | GCN | 0.7600
±0.0320 best reported | |
| 149 | MLP | 0.7600
±0.0320 | |
| 265 | GraphCL | 0.7489
±0.0065 best reported | best at pub: Graph Masked Autoencoders with Transformers (2022) |
| 491 | GPF | 0.6391
±0.0326 best reported | best at pub: ProG: A Graph Prompt Learning Benchmark (NeurIPS 2024) Difference within reported uncertainty; not counted as underperformance. |
| 516 | GCoT | 0.5624
±0.0860 | This paper |
| 517 | GraphPrompt | 0.5380
±0.0793 | This paper |
| 519 | ProG | 0.5273
±0.0657 | This paper |
| 520 | DGI/InfoGraph | 0.5251
±0.1029 | This paper |
Heterophilic Graphs
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | Hetero-S (GAT 8-layer) | 0.8693 | |
| 2 | Dir-GNN+CNA | 0.8586
±0.0180 | |
| 3 | GAT | 0.8560 | |
| 52 | GCN | 0.7033 | |
| 134 | DGI | 0.6027
±0.0070 best reported | best at pub: Augmentation-Free Graph Contrastive Learning with Performance Guarantee (2022) best today: Discrepancy-Aware Graph Mask Auto-Encoder (KDD 2025) |
| 169 | MLP | 0.5429 | |
| 276 | GraphPrompt | 0.2828
±0.0438 best reported | best today: One Prompt Fits All: Universal Graph Adaptation for Pretrained Models (NeurIPS 2025) Difference within reported uncertainty; not counted as underperformance. |
| 277 | GCoT | 0.2796
±0.0389 | This paper |
| 278 | GraphCL | 0.2716
±0.0431 | This paper |
| 282 | GPF | 0.2612
±0.0375 | This paper |
| 283 | ProG | 0.2590
±0.0395 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | DMD++ | 0.9190
±0.0260 | |
| 2 | F-GREAD-BS | 0.9059
±0.0380 | |
| 3 | APPNP | 0.9010
±0.0350 | |
| 37 | MLP | 0.8629
±0.0450 | |
| 63 | GCN | 0.8310
±0.0320 | |
| 186 | DGI | 0.5541 best reported | best at pub: Beyond Smoothing: Unsupervised Graph Representation Learning with Edge Heterophily Discriminating (AAAI 2022) |
| 221 | GCoT | 0.3280
±0.1159 | This paper |
| 222 | GPF | 0.3218
±0.1136 | This paper |
| 223 | GraphPrompt | 0.3148
±0.0518 | This paper |
| 224 | GraphCL | 0.2985
±0.0846 | This paper |
| 225 | ProG | 0.2899
±0.1114 | This paper |
GNNBenchmark
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | GRPE-Small | 0.8159
±0.0019 | |
| 2 | TANGO-GPS | 0.8011
±0.0014 | |
| 3 | GRIT | 0.8003
±0.0028 | |
| 54 | GatedGCN | 0.7608
±0.0020 | |
| 70 | GCN | 0.6903
±0.0137 | |
| 106 | GCoT | 0.2754 | This paper |
| 109 | GPF | 0.2427 | This paper |
| 110 | GraphCL | 0.2382 | This paper |
| 111 | GraphPrompt | 0.2218 | This paper |
| 113 | DGI | 0.2127 | This paper |
| 114 | MLP | 0.2097
±0.0000 |
