CONCLUSIONS: MaskHGL shows a great improvement, brought by considering the intrinsic non-pairwise relationships within WSI, in multiple downstream WSI classification tasks. In particular, the designed masked hypergraph reconstruction module promisingly alleviates the data scarcity and greatly enhances the robustness and classification ability of our MaskHGL. Notably, it has shown great potential in cancer subtyping and fine-grained lung cancer gene mutation prediction from hematoxylin and …