Whole slide images are 2d point clouds: Context-aware survival prediction using patch-based graph convolutional networks

RJ Chen, MY Lu, M Shaban, C Chen, TY Chen… - … Image Computing and …, 2021 - Springer
Medical Image Computing and Computer Assisted Intervention–MICCAI 2021: 24th …, 2021Springer
Cancer prognostication is a challenging task in computational pathology that requires
context-aware representations of histology features to adequately infer patient survival.
Despite the advancements made in weakly-supervised deep learning, many approaches
are not context-aware and are unable to model important morphological feature interactions
between cell identities and tissue types that are prognostic for patient survival. In this work,
we present Patch-GCN, a context-aware, spatially-resolved patch-based graph …
Abstract
Cancer prognostication is a challenging task in computational pathology that requires context-aware representations of histology features to adequately infer patient survival. Despite the advancements made in weakly-supervised deep learning, many approaches are not context-aware and are unable to model important morphological feature interactions between cell identities and tissue types that are prognostic for patient survival. In this work, we present Patch-GCN, a context-aware, spatially-resolved patch-based graph convolutional network that hierarchically aggregates instance-level histology features to model local- and global-level topological structures in the tumor microenvironment. We validate Patch-GCN with 4,370 gigapixel WSIs across five different cancer types from the Cancer Genome Atlas (TCGA), and demonstrate that Patch-GCN outperforms all prior weakly-supervised approaches by 3.58–9.46%. Our code and corresponding models are publicly available at https://github.com/mahmoodlab/Patch-GCN .
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