Learning Graph Quantized Tokenizers

Transformers serve as the backbone architectures of Foundational Models, where domain-specific tokenizers allow them to adapt to various domains. Graph Transformers (GTs) have recently emerged as leading models in geometric deep learning, outperforming Graph Neural Networks (GNNs) in various graph learning tasks. However, the development of tokenizers for graphs has lagged behind other modalities, with existing approaches relying on heuristics or GNNs co-trained with Transformers. To address this, we introduce GQT (\textbf{G}raph \textbf{Q}uantized \textbf{T}okenizer), which decouples tokenizer training from Transformer training by leveraging multi-task graph self-supervised learning, yielding robust and generalizable graph tokens. Furthermore, the GQT utilizes Residual Vector Quantization (RVQ) to learn hierarchical discrete tokens, resulting in significantly reduced memory requirements and improved generalization capabilities. By combining the GQT with token modulation, a Transformer encoder achieves state-of-the-art performance on 20 out of 22 benchmarks, including large-scale homophilic and heterophilic datasets. The implementation is publicly available at \href{https://github.com/limei0307/GQT}{https://github.com/limei0307/GQT}.