From Anchors to Answers: A Novel Node Tokenizer for Integrating Graph Structure into Large Language Models

Enabling large language models (LLMs) to effectively process and reason with graph-structured data remains a significant challenge despite their remarkable success in natural language tasks. Current approaches either convert graph structures into verbose textual descriptions, consuming substantial computational resources, or employ complex graph neural networks as tokenizers, which introduce significant training overhead. To bridge this gap, we present NT-LLM, a novel framework with an anchor-based positional encoding scheme for graph representation. Our approach strategically selects reference nodes as anchors and encodes each node's position relative to these anchors, capturing essential topological information without the computational burden of existing methods. Notably, we identify and address a fundamental issue: the inherent misalignment between discrete hop-based distances in graphs and continuous distances in embedding spaces. By implementing a rank-preserving objective for positional encoding pretraining, NT-LLM achieves superior performance across diverse graph tasks ranging from basic structural analysis to complex reasoning scenarios. Our comprehensive evaluation demonstrates that this lightweight yet powerful approach effectively enhances LLMs' ability to understand and reason with graph-structured information, offering an efficient solution for graph-based applications of language models.