Pan-cancer Histopathology WSI Pre-training with Position-aware Masked Autoencoder
This addresses a gap in histopathology image analysis for cancer diagnosis by enabling more effective WSI-level feature learning, though it appears incremental as an adaptation of masked autoencoders to this domain.
The paper tackles the lack of whole-slide image (WSI)-level pre-training models in histopathology by proposing a position-aware masked autoencoder (PAMA) framework, which achieves superior performance on pan-cancer classification tasks across 7 datasets compared to 8 existing methods.
Large-scale pre-training models have promoted the development of histopathology image analysis. However, existing self-supervised methods for histopathology images primarily focus on learning patch features, while there is a notable gap in the availability of pre-training models specifically designed for WSI-level feature learning. In this paper, we propose a novel self-supervised learning framework for pan-cancer WSI-level representation pre-training with the designed position-aware masked autoencoder (PAMA). Meanwhile, we propose the position-aware cross-attention (PACA) module with a kernel reorientation (KRO) strategy and an anchor dropout (AD) mechanism. The KRO strategy can capture the complete semantic structure and eliminate ambiguity in WSIs, and the AD contributes to enhancing the robustness and generalization of the model. We evaluated our method on 7 large-scale datasets from multiple organs for pan-cancer classification tasks. The results have demonstrated the effectiveness and generalization of PAMA in discriminative WSI representation learning and pan-cancer WSI pre-training. The proposed method was also compared with 8 WSI analysis methods. The experimental results have indicated that our proposed PAMA is superior to the state-of-the-art methods. The code and checkpoints are available at https://github.com/WkEEn/PAMA.