VQGraph: Graph Vector-Quantization for Bridging GNNs and MLPs

Graph Neural Networks (GNNs) conduct message passing which aggregates local neighbors to update node representations. Such message passing leads to scalability issues in practical latency-constrained applications. To address this issue, recent methods adopt knowledge distillation (KD) to learn computationally-efficient multi-layer perceptron (MLP) by mimicking the output of GNN. However, the existing GNN representation space may not be expressive enough for representing diverse local structures of the underlying graph, which limits the knowledge transfer from GNN to MLP. Here we present a novel framework VQGraph to learn a powerful graph representation space for bridging GNNs and MLPs. We adopt the encoder of a variant of a vector-quantized variational autoencoder (VQ-VAE) as a structure-aware graph tokenizer, which explicitly represents the nodes of diverse local structures as numerous discrete tokens and constitutes a meaningful codebook. Equipped with the learned codebook, we propose a new token-based distillation objective based on soft token assignments to sufficiently transfer the structural knowledge from GNN to MLP. Extensive experiments and analyses demonstrate the strong performance of VQGraph, where we achieve new state-of-the-art performance on GNN-MLP distillation in both transductive and inductive settings across seven graph datasets. We show that VQGraph with better performance infers faster than GNNs by 828x, and also achieves accuracy improvement over GNNs and stand-alone MLPs by 3.90% and 28.05% on average, respectively. Code: https://github.com/YangLing0818/VQGraph.