Actions Speak Louder than Prompts: A Large-Scale Study of LLMs for Graph Inference

Abstract

Large language models (LLMs) are increasingly leveraged for text-rich graph machine learning tasks, with node classification standing out due to its high-impact application domains such as fraud detection and recommendation systems. Yet, despite a surge of interest, the field lacks a principled understanding of the capabilities of LLMs in processing graph data. In this work, we conduct a large-scale, controlled evaluation across the key axes of variability: the LLM-graph interaction mode, comparing prompting, tool-use, and code generation; dataset domains, spanning citation, web-link, e-commerce, and social networks; homophilic vs. heterophilic regimes; short- vs. long-text features; LLM sizes and reasoning capabilities. We further analyze dependencies by independently truncating features, deleting edges, and removing labels to quantify reliance on input types. Our findings provide actionable guidance for both research and practice. (1) Code generation mode achieves the strongest overall performance, with especially large gains on long-text or high-degree graphs where prompting quickly exceeds the token budget. (2) All interaction strategies remain effective on heterophilic graphs, challenging the assumption that LLM-based methods collapse under low homophily. (3) Code generation mode is able to flexibly shift its reliance to the most informative input type, whether that be structure, features, or labels. Together, these results establish a clear picture of the strengths and limitations of current LLM–graph interaction modes and point to design principles for future methods.