Nuclei classification is a critical step in computer-aided diagnosis with histopathology images. In the past, various methods have employed graph neural networks (GNN) to analyze cell graphs that model inter-cell relationships by considering nuclei as vertices. However, they are limited by the GNN mechanism that only passes messages among local nodes via fixed edges. To address the issue, we develop a cell graph transformer (CGT) that treats nodes and edges as input tokens to enable learnable adjacency and information exchange among all nodes. Nevertheless, training the transformer with a cell graph presents another challenge. Poorly initialized features can lead to noisy self-attention scores and inferior convergence, particularly when processing the cell graphs with numerous connections. Thus, we further propose a novel topology-aware pretraining method that leverages a graph convolutional network (GCN) to learn a feature extractor. The pre-trained features may suppress unreasonable correlations and hence ease the finetuning of CGT. Experimental results suggest that the proposed cell graph transformer with topology-aware pretraining significantly improves the nuclei classification results, and achieves the state-of-the-art performance. Code and models are available at https://github.com/lhaof/CGT

核分类是计算机辅助诊断中的关键步骤，本文提出了一种基于细胞图变换器的新方法，通过在细胞图中处理节点和边缘作为输入标记，实现了可学习的邻接和信息交换，结合拓扑感知的预训练方法，显著提高了核分类结果并达到了最先进的性能。

细胞图变换器用于细胞核分类