Efficient Tuning and Inference for Large Language Models on Textual Graphs
Abstract
Rich textual and topological information of textual graphs need to be modeled in real-world applications such as webpages, e-commerce, and academic articles. Practitioners have been long following the path of adopting a shallow text encoder and a subsequent graph neural network (GNN) to solve this problem. In light of recent advancements in large language models (LLMs), it is apparent that integrating LLMs for enhanced textual encoding can substantially improve the performance of textual graphs. Nevertheless, the efficiency of these methods poses a significant challenge. In this paper, we propose ENGINE, a parameter- and memory-efficient fine-tuning method for textual graphs with an LLM encoder. The key insight is to combine the LLMs and GNNs through a tunable side structure, which significantly reduces the training complexity without impairing the joint model's capacity. Extensive experiments on textual graphs demonstrate our method's effectiveness by achieving the best model performance, meanwhile having the lowest training cost compared to previous methods. Moreover, we introduce two variants with caching and dynamic early exit to further enhance training and inference speed. Specifically, caching accelerates ENGINE's training by 12x, and dynamic early exit achieves up to 5x faster inference with a negligible performance drop (at maximum 1.17\
Benchmark Results
Tested on 4 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 | |
| 11 | ENGINE | 0.9148
±0.0032 | This paper |
| 14 | TAPE | 0.9119
±0.0012 best reported | best at pub: Graph Agent: Explicit Reasoning Agent for Graphs (2023) best today: Efficient Text-Attributed Graph Learning through Selective Annotation and Graph Alignment (TMLR 2025) |
| 21 | GCN | 0.9004 best reported | best at pub: Understanding Heterophily for Graph Neural Networks (ICML 2024) |
| 39 | SAGE | 0.8573
±0.0065 | |
| 44 | GAT | 0.8897
±0.0014 best reported | best at pub: Learned Low Precision Graph Neural Networks (2020) |
| 68 | NodeFormer | 0.8848
±0.0033 | prev best: Discovering Data Geometry: Energy-Driven Neural Diffusion (ICLR 2023) |
| 93 | SimTEG | 0.8804
±0.0136 | This paper |
| 141 | GraphSAGE | 0.8708
±0.0085 | |
| 200 | GLEM | 0.8560
±0.0009 | This paper |
| 203 | GIANT | 0.8552
±0.0074 | This paper |
| 635 | GraphFormers | 0.8044
±0.0189 | This paper |
| 653 | BERT | 0.8015
±0.0167 | This paper |
| 660 | LoRA | 0.7995
±0.0044 | This paper |
| 701 | SentenceBert | 0.7882
±0.0139 | This paper |
| 721 | DeBERTa | 0.7779
±0.0226 | This paper |
| 724 | MLP | 0.7768 best reported | best at pub: Understanding Heterophily for Graph Neural Networks (ICML 2024) Difference within reported uncertainty; not counted as underperformance. |
| 727 | LST | 0.7760
±0.0076 | This paper |
| 752 | IA3 | 0.7643
±0.0129 | This paper |
| 791 | Prompt Tuning | 0.7373
±0.0205 | 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: Gophormer: Ego-Graph Transformer for Node Classification (2021) |
| 61 | GraphSAGE | 0.7923
±0.0053 | |
| 76 | NodeFormer | 0.7574
±0.0054 | prev best: Discovering Data Geometry: Energy-Driven Neural Diffusion (ICLR 2023) |
| 81 | ENGINE | 0.7846
±0.0049 | This paper |
| 106 | SimTEG | 0.7722
±0.0143 | This paper |
| 143 | GLEM | 0.7589
±0.0053 | This paper |
| 179 | LST | 0.7505
±0.0136 | This paper |
| 259 | SAGE | 0.7361
±0.0190 | prev best: Extract the Knowledge of Graph Neural Networks and Go Beyond it: An Effective Knowledge Distillation Framework (WWW 2021) Improvement within reported uncertainty; not highlighted. |
| 260 | LoRA | 0.7361
±0.0189 | This paper |
| 313 | BERT | 0.7317
±0.0175 | This paper |
| 316 | DeBERTa | 0.7313
±0.0194 | This paper |
| 350 | MLP | 0.7289
±0.0010 best reported | best at pub: On the Equivalence of Graph Convolution and Mixup (TMLR 2023) best today: Gumbel-MPNN: Graph Rewiring with Gumbel-Softmax (2025) |
| 358 | SentenceBert | 0.7279
±0.0171 | This paper |
| 423 | GIANT | 0.7238
±0.0083 | This paper |
| 535 | GraphFormers | 0.7128
±0.0117 | This paper |
| 555 | IA3 | 0.7107
±0.0124 | This paper |
| 634 | Prompt Tuning | 0.6962
±0.0214 | 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 best reported | |
| 31 | GAT | 0.7821
±0.0066 | prev best: Learning Graph Augmentations to Learn Graph Representations (2022) best today: Language Models as Messengers: Enhancing Message Passing in Heterophilic Graph Learning (2025) Improvement within reported uncertainty; not highlighted. |
| 54 | GIN | 0.8303
±0.0021 | |
| 68 | ENGINE | 0.8156
±0.0097 | This paper |
| 74 | NodeFormer | 0.8103
±0.0094 best reported | best today: GrokFormer: Graph Fourier Kolmogorov-Arnold Transformers (ICML 2024) |
| 131 | SimTEG | 0.7907
±0.0065 | This paper |
| 141 | GLEM | 0.7892
±0.0019 | This paper |
| 142 | LoRA | 0.7891
±0.0126 | This paper |
| 165 | BERT | 0.7833
±0.0043 | This paper |
| 177 | SentenceBert | 0.7792
±0.0007 | This paper |
| 189 | LST | 0.7759
±0.0070 | This paper |
| 220 | GIANT | 0.7581
±0.0026 | This paper |
| 231 | DeBERTa | 0.7511
±0.0197 | This paper |
| 237 | MLP | 0.7469
±0.0085 best reported | best at pub: Augmentation-Free Graph Contrastive Learning with Performance Guarantee (2022) best today: View Space: Learning Representation across Arbitrary Graphs (ICML 2025) |
| 252 | GraphFormers | 0.7207
±0.0031 | This paper |
| 266 | IA3 | 0.7008
±0.0126 | This paper |
| 283 | Prompt Tuning | 0.6714
±0.0150 | This paper |
OGB
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | Jacobi | 0.8968 | |
| 2 | GPR | 0.8953 | |
| 3 | LEMP4HG | 0.8939 | |
| 4 | SAGE | 0.8933 best reported | best at pub: Learning on Large-scale Text-attributed Graphs via Variational Inference (ICLR 2022) |
| 6 | GCN | 0.8868 best reported | best at pub: PaSca: a Graph Neural Architecture Search System under the Scalable Paradigm (WWW 2022) |
| 9 | GAT | 0.8829 best reported | best at pub: PaSca: a Graph Neural Architecture Search System under the Scalable Paradigm (WWW 2022) |
| 15 | GLEM | 0.8736
±0.0007 best reported | best at pub: SimTeG: A Frustratingly ple Approach Improves xtual raph Learning (2023) |
| 39 | SimTEG | 0.8540
±0.0028 best reported | best at pub: SimTeG: A Frustratingly ple Approach Improves xtual raph Learning (2023) |
| 66 | NodeFormer | 0.8372 best reported | best today: Clustering as Reasoning: A $k$-Means Interpretation of Chain-of-Thought Graph Learning (ICML 2026) |
| 83 | GraphSAGE | 0.8287 | |
| 90 | TAPE | 0.8234
±0.0036 best reported | |
| 137 | GIANT | 0.8049
±0.0028 best reported | best at pub: Train Your Own GNN Teacher: Graph-Aware Distillation on Textual Graphs (2023) |
| 145 | ENGINE | 0.8005
±0.0045 | This paper |
| 223 | BERT | 0.7764
±0.0008 best reported | best at pub: Train Your Own GNN Teacher: Graph-Aware Distillation on Textual Graphs (2023) |
| 242 | LST | 0.7610
±0.0079 | This paper |
| 246 | IA3 | 0.7582
±0.0010 | This paper |
| 253 | DeBERTa | 0.7561
±0.0028 | This paper |
| 259 | LoRA | 0.7550
±0.0005 | This paper |
| 267 | SentenceBert | 0.7507
±0.0013 | This paper |
| 287 | Prompt Tuning | 0.7450
±0.0099 | This paper |
| 344 | GraphFormers | 0.6815
±0.0076 | This paper |
| 351 | MLP | 0.6605
±0.0020 best reported | best at pub: SCR: Training Graph Neural Networks with Consistency Regularization (2021) best today: Latent Graph Inference using Product Manifolds (ICLR 2022) |
