LOGIN: A Large Language Model Consulted Graph Neural Network Training Framework
Abstract
Recent prevailing works on graph machine learning typically follow a similar methodology that involves designing advanced variants of graph neural networks (GNNs) to maintain the superior performance of GNNs on different graphs. In this paper, we aim to streamline the GNN design process and leverage the advantages of Large Language Models (LLMs) to improve the performance of GNNs on downstream tasks. We formulate a new paradigm, coined ``LLMs-as-Consultants'', which integrates LLMs with GNNs in an interactive manner. A framework named L [0.8]OG [0.8]IN ([0.8]LM [0.9]c [0.9]nsulted [0.8]NN [0.9]tra [0.9]ing) is instantiated, empowering the interactive utilization of LLMs within the GNN training process. First, we attentively craft concise prompts for spotted nodes, carrying comprehensive semantic and topological information, and serving as input to LLMs. Second, we refine GNNs by devising a complementary coping mechanism that utilizes the responses from LLMs, depending on their correctness. We empirically evaluate the effectiveness of L [0.8]OG [0.8]IN on node classification tasks across both homophilic and heterophilic graphs. The results illustrate that even basic GNN architectures, when employed within the proposed LLMs-as-Consultants paradigm, can achieve comparable performance to advanced GNNs with intricate designs. Our codes are available at.
Benchmark Results
Tested on 5 datasets 10 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 | |
| 20 | SSP | 0.9020
±0.0060 best reported | best today: Revisiting the Necessity of Graph Learning and Common Graph Benchmarks (2024) Difference within reported uncertainty; not counted as underperformance. |
| 21 | GCN | 0.9004 | |
| 45 | GCNII | 0.8893
±0.0137 best reported | best at pub: Language is All a Graph Needs (2023) best today: Large Language Model Meets Graph Neural Network in Knowledge Distillation (AAAI 2024) Difference within reported uncertainty; not counted as underperformance. |
| 51 | H2GCN | 0.8882
±0.0011 best reported | best at pub: Feature Transportation Improves Graph Neural Networks (AAAI 2023) |
| 54 | GCNII+LOGIN | 0.8879
±0.0105 | This paper |
| 108 | APPNP | 0.8787 best reported | best at pub: Orthogonal Graph Neural Networks (AAAI 2021) best today: Feature Transportation Improves Graph Neural Networks (AAAI 2023) Difference within reported uncertainty; not counted as underperformance. |
| 132 | GraphSAGE LO | 0.8727
±0.0219 | This paper |
| 136 | GraphSAGE OR | 0.8720
±0.0216 | This paper |
| 148 | GCN LO | 0.8694
±0.0177 | This paper |
| 154 | GCN FT | 0.8683
±0.0191 | This paper |
| 178 | GCN OR | 0.8630
±0.0219 | This paper |
| 180 | MixHop LO | 0.8624
±0.0253 | This paper |
| 183 | APPNP+LOGIN | 0.8614
±0.0332 | This paper |
| 187 | MixHop OR | 0.8601
±0.0281 | This paper |
| 188 | GraphSAGE FT | 0.8592
±0.0363 | This paper |
| 195 | JK-Net | 0.8579
±0.0001 | prev best: ROD: Reception-aware Online Distillation for Sparse Graphs (KDD 2021) |
| 197 | MixHop FT | 0.8572
±0.0123 | This paper |
| 223 | SGC | 0.8509
±0.0648 | prev best: Node Representation Learning in Graph via Node-to-Neighbourhood Mutual Information Maximization (2022) Improvement within reported uncertainty; not highlighted. |
| 589 | GPT 3.5-turbo-0125 | 0.8123
±0.0254 | This paper |
| 724 | MLP | 0.7768 | |
| 809 | Vicuna-v1.5-13b | 0.7202
±0.0201 | This paper |
| 815 | MLP LO | 0.7063
±0.0201 | This paper |
| 816 | Vicuna-v1.5-7b | 0.7063
±0.0331 | This paper |
| 828 | MLP FT | 0.6897
±0.0102 | This paper |
| 867 | MLP OR | 0.6438
±0.0331 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | LGTL | 0.9518
±0.0011 | |
| 2 | MixHop (LO) | 0.9513
±0.0038 | This paper |
| 3 | GraphSAGE (LO) | 0.9511
±0.0036 | This paper |
| 4 | MLP (LO) | 0.9505
±0.0036 | This paper |
| 13 | GCN (LO) | 0.9396
±0.0030 | This paper |
| 16 | H2GCN | 0.9361
±0.0013 best reported | best at pub: Optimization-Induced Graph Implicit Nonlinear Diffusion (ICML 2022) |
| 17 | APPNP | 0.9355
±0.0060 | prev best: Tackling Over-Smoothing for General Graph Convolutional Networks (2020) |
| 18 | GCN | 0.9296
±0.0015 | |
| 22 | SSP | 0.9178
±0.0116 | This paper |
| 58 | GCNII | 0.9030
±0.0043 best reported | best at pub: Feature Transportation Improves Graph Neural Networks (AAAI 2023) |
| 135 | JK-Net | 0.8841
±0.0001 | prev best: PaSca: a Graph Neural Architecture Search System under the Scalable Paradigm (WWW 2022) |
| 141 | SGC | 0.8832
±0.0055 | |
| 210 | MLP | 0.8690
±0.0074 |
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 | |
| 34 | MLP | 0.9230
±0.0070 | |
| 40 | H2GCN | 0.8667
±0.0022 | prev best: How Curvature Enhance the Adaptation Power of Framelet GCNs (2023) Improvement within reported uncertainty; not highlighted. |
| 46 | APPNP | 0.9131
±0.0197 best reported | best at pub: A Quasi-Wasserstein Loss for Learning Graph Neural Networks (WWW 2023) |
| 53 | GraphSAGE | 0.9000
±0.0365 | |
| 70 | GCNII | 0.8918
±0.0443 best reported | best at pub: Convolutional Neural Networks on Graphs with Chebyshev Approximation, Revisited (NeurIPS 2022) best today: Piecewise Constant Spectral Graph Neural Network (TMLR 2025) |
| 74 | MLP LO | 0.8895
±0.0820 | This paper |
| 206 | MLP FT | 0.8211
±0.0681 | This paper |
| 215 | MixHop LO | 0.8158
±0.0930 | This paper |
| 229 | MLP OR | 0.8105
±0.0730 | This paper |
| 283 | GraphSAGE LO | 0.7737
±0.1311 | This paper |
| 305 | GraphSAGE FT | 0.7579
±0.1123 | This paper |
| 330 | SGC | 0.7440
±0.0600 best reported | best at pub: Restructuring Graphs for Higher Homophily via Adaptive Spectral Clustering (AAAI 2022) |
| 332 | JK-Net | 0.7431
±0.0041 | This paper |
| 335 | MixHop FT | 0.7421
±0.1075 | This paper |
| 460 | SSP | 0.6302
±0.0850 | This paper |
| 543 | GCN LO | 0.5789
±0.0588 | This paper |
| 565 | GCN FT | 0.5526
±0.0832 | This paper |
| 566 | MixHop OR | 0.5526
±0.1500 | This paper |
| 578 | GraphSAGE OR | 0.5053
±0.0776 | This paper |
| 599 | GCN OR | 0.4579
±0.0711 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | P^2GNN | 0.9541
±0.0272 | |
| 2 | ACM-GCN | 0.9480
±0.0380 | |
| 3 | RF-GCN | 0.9429 | |
| 21 | APPNP | 0.9181
±0.0196 best reported | best at pub: LON-GNN: Spectral GNNs with Learnable Orthonormal Basis (2023) |
| 24 | MLP | 0.9136
±0.0070 | |
| 35 | GCNII | 0.8918
±0.0396 best reported | best at pub: Convolutional Neural Networks on Graphs with Chebyshev Approximation, Revisited (NeurIPS 2022) best today: $P^2$GNN: Two Prototype Sets to boost GNN Performance (2026) |
| 68 | H2GCN | 0.8623
±0.0471 best reported | best at pub: Design your own universe: a physics-informed agnostic method for enhancing graph neural networks (2024) best today: $P^2$GNN: Two Prototype Sets to boost GNN Performance (2026) Difference within reported uncertainty; not counted as underperformance. |
| 138 | SAGE | 0.8269 | |
| 172 | MLP LO | 0.8051
±0.0618 | This paper |
| 174 | MLP FT | 0.8049
±0.0602 | This paper |
| 227 | MLP OR | 0.7538
±0.0669 | This paper |
| 252 | SGC | 0.7350
±0.0430 best reported | best at pub: Restructuring Graphs for Higher Homophily via Adaptive Spectral Clustering (AAAI 2022) |
| 270 | GraphSAGE FT | 0.7179
±0.1189 | This paper |
| 271 | MixHop LO | 0.7179
±0.0314 | This paper |
| 290 | SSP | 0.6923
±0.0314 | This paper |
| 293 | GraphSAGE LO | 0.6872
±0.0896 | This paper |
| 308 | MixHop FT | 0.6718
±0.1397 | This paper |
| 339 | JK-Net | 0.6459
±0.0075 | This paper |
| 375 | GraphSAGE OR | 0.6051
±0.0389 | This paper |
| 456 | GCN FT | 0.5282
±0.0644 | This paper |
| 460 | GCN LO | 0.5231
±0.0292 | This paper |
| 492 | MixHop OR | 0.4974
±0.0803 | This paper |
| 541 | GCN OR | 0.4308
±0.0664 | 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 | |
| 22 | H2GCN | 0.8790
±0.0420 best reported | best at pub: Unleashing the Potential of Fractional Calculus in Graph Neural Networks with FROND (ICLR 2024) best today: When Graph Neural Networks Meet Dynamic Mode Decomposition (ICLR 2024) Difference within reported uncertainty; not counted as underperformance. |
| 37 | MLP | 0.8629
±0.0450 | |
| 43 | MLP LO | 0.8528
±0.0588 | This paper |
| 55 | MLP FT | 0.8415
±0.0391 | This paper |
| 63 | GCN | 0.8310
±0.0320 | |
| 71 | MLP OR | 0.8113
±0.0718 | This paper |
| 91 | SGC | 0.7780
±0.0470 best reported | best at pub: Restructuring Graphs for Higher Homophily via Adaptive Spectral Clustering (AAAI 2022) |
| 109 | GraphSAGE LO | 0.7434
±0.0930 | This paper |
| 112 | JK-Net | 0.7431
±0.0041 | This paper |
| 117 | GraphSAGE FT | 0.7211
±0.1324 | This paper |
| 121 | MixHop LO | 0.7094
±0.0738 | This paper |
| 122 | MixHop FT | 0.7092
±0.1035 | This paper |
| 155 | SSP | 0.6302
±0.0850 | This paper |
| 165 | GraphSAGE OR | 0.6113
±0.0662 | This paper |
| 177 | MixHop OR | 0.5736
±0.1183 | This paper |
| 210 | GCN LO | 0.5057
±0.0430 | This paper |
| 217 | GCN FT | 0.4415
±0.1152 | This paper |
| 219 | GCN OR | 0.3736
±0.0672 | This paper |
