Whole slide image (WSI) refers to a type of high-resolution scanned tissue image, which is extensively employed in computer-assisted diagnosis (CAD). The extremely high resolution and limited availability of region-level annotations make it challenging to employ deep learning methods for WSI-based digital diagnosis. Multiple instance learning (MIL) is a powerful tool to address the weak annotation problem, while Transformer has shown great success in the field of visual tasks. The combination of both should provide new insights for deep learning based image diagnosis. However, due to the limitations of single-level MIL and the attention mechanism's constraints on sequence length, directly applying Transformer to WSI-based MIL tasks is not practical. To tackle this issue, we propose a Multi-level MIL with Transformer (MMIL-Transformer) approach. By introducing a hierarchical structure to MIL, this approach enables efficient handling of MIL tasks that involve a large number of instances. To validate its effectiveness, we conducted a set of experiments on WSIs classification task, where MMIL-Transformer demonstrate superior performance compared to existing state-of-the-art methods. Our proposed approach achieves test AUC 94.74% and test accuracy 93.41% on CAMELYON16 dataset, test AUC 99.04% and test accuracy 94.37% on TCGA-NSCLC dataset, respectively. All code and pre-trained models are available at: https://github.com/hustvl/MMIL-Transformer

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