When Do LLMs Help With Node Classification? A Comprehensive Analysis

Xixi Wu, Yifei Shen, Fangzhou Ge, Caihua Shan, Yizhu Jiao, Xiangguo Sun, Hong Cheng
Proceedings of the 42nd International Conference on Machine Learning, PMLR 267:67623-67649, 2025.

Abstract

Node classification is a fundamental task in graph analysis, with broad applications across various fields. Recent breakthroughs in Large Language Models (LLMs) have enabled LLM-based approaches for this task. Although many studies demonstrate the impressive performance of LLM-based methods, the lack of clear design guidelines may hinder their practical application. In this work, we aim to establish such guidelines through a fair and systematic comparison of these algorithms. As a first step, we developed LLMNodeBed, a comprehensive codebase and testbed for node classification using LLMs. It includes 10 homophilic datasets, 4 heterophilic datasets, 8 LLM-based algorithms, 8 classic baselines, and 3 learning paradigms. Subsequently, we conducted extensive experiments, training and evaluating over 2,700 models, to determine the key settings (e.g., learning paradigms and homophily) and components (e.g., model size and prompt) that affect performance. Our findings uncover 8 insights, e.g., (1) LLM-based methods can significantly outperform traditional methods in a semi-supervised setting, while the advantage is marginal in a supervised setting; (2) Graph Foundation Models can beat open-source LLMs but still fall short of strong LLMs like GPT-4o in a zero-shot setting. We hope that the release of LLMNodeBed, along with our insights, will facilitate reproducible research and inspire future studies in this field. Codes and datasets are released at https://llmnodebed.github.io/.

Cite this Paper

BibTeX
@InProceedings{pmlr-v267-wu25y, title = {When Do {LLM}s Help With Node Classification? {A} Comprehensive Analysis}, author = {Wu, Xixi and Shen, Yifei and Ge, Fangzhou and Shan, Caihua and Jiao, Yizhu and Sun, Xiangguo and Cheng, Hong}, booktitle = {Proceedings of the 42nd International Conference on Machine Learning}, pages = {67623--67649}, year = {2025}, editor = {Singh, Aarti and Fazel, Maryam and Hsu, Daniel and Lacoste-Julien, Simon and Berkenkamp, Felix and Maharaj, Tegan and Wagstaff, Kiri and Zhu, Jerry}, volume = {267}, series = {Proceedings of Machine Learning Research}, month = {13--19 Jul}, publisher = {PMLR}, pdf = {https://raw.githubusercontent.com/mlresearch/v267/main/assets/wu25y/wu25y.pdf}, url = {https://proceedings.mlr.press/v267/wu25y.html}, abstract = {Node classification is a fundamental task in graph analysis, with broad applications across various fields. Recent breakthroughs in Large Language Models (LLMs) have enabled LLM-based approaches for this task. Although many studies demonstrate the impressive performance of LLM-based methods, the lack of clear design guidelines may hinder their practical application. In this work, we aim to establish such guidelines through a fair and systematic comparison of these algorithms. As a first step, we developed LLMNodeBed, a comprehensive codebase and testbed for node classification using LLMs. It includes 10 homophilic datasets, 4 heterophilic datasets, 8 LLM-based algorithms, 8 classic baselines, and 3 learning paradigms. Subsequently, we conducted extensive experiments, training and evaluating over 2,700 models, to determine the key settings (e.g., learning paradigms and homophily) and components (e.g., model size and prompt) that affect performance. Our findings uncover 8 insights, e.g., (1) LLM-based methods can significantly outperform traditional methods in a semi-supervised setting, while the advantage is marginal in a supervised setting; (2) Graph Foundation Models can beat open-source LLMs but still fall short of strong LLMs like GPT-4o in a zero-shot setting. We hope that the release of LLMNodeBed, along with our insights, will facilitate reproducible research and inspire future studies in this field. Codes and datasets are released at https://llmnodebed.github.io/.} }
Endnote
%0 Conference Paper %T When Do LLMs Help With Node Classification? A Comprehensive Analysis %A Xixi Wu %A Yifei Shen %A Fangzhou Ge %A Caihua Shan %A Yizhu Jiao %A Xiangguo Sun %A Hong Cheng %B Proceedings of the 42nd International Conference on Machine Learning %C Proceedings of Machine Learning Research %D 2025 %E Aarti Singh %E Maryam Fazel %E Daniel Hsu %E Simon Lacoste-Julien %E Felix Berkenkamp %E Tegan Maharaj %E Kiri Wagstaff %E Jerry Zhu %F pmlr-v267-wu25y %I PMLR %P 67623--67649 %U https://proceedings.mlr.press/v267/wu25y.html %V 267 %X Node classification is a fundamental task in graph analysis, with broad applications across various fields. Recent breakthroughs in Large Language Models (LLMs) have enabled LLM-based approaches for this task. Although many studies demonstrate the impressive performance of LLM-based methods, the lack of clear design guidelines may hinder their practical application. In this work, we aim to establish such guidelines through a fair and systematic comparison of these algorithms. As a first step, we developed LLMNodeBed, a comprehensive codebase and testbed for node classification using LLMs. It includes 10 homophilic datasets, 4 heterophilic datasets, 8 LLM-based algorithms, 8 classic baselines, and 3 learning paradigms. Subsequently, we conducted extensive experiments, training and evaluating over 2,700 models, to determine the key settings (e.g., learning paradigms and homophily) and components (e.g., model size and prompt) that affect performance. Our findings uncover 8 insights, e.g., (1) LLM-based methods can significantly outperform traditional methods in a semi-supervised setting, while the advantage is marginal in a supervised setting; (2) Graph Foundation Models can beat open-source LLMs but still fall short of strong LLMs like GPT-4o in a zero-shot setting. We hope that the release of LLMNodeBed, along with our insights, will facilitate reproducible research and inspire future studies in this field. Codes and datasets are released at https://llmnodebed.github.io/.
APA
Wu, X., Shen, Y., Ge, F., Shan, C., Jiao, Y., Sun, X. & Cheng, H.. (2025). When Do LLMs Help With Node Classification? A Comprehensive Analysis. Proceedings of the 42nd International Conference on Machine Learning, in Proceedings of Machine Learning Research 267:67623-67649 Available from https://proceedings.mlr.press/v267/wu25y.html.

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