Incorporating intratumoral heterogeneity into weakly-supervised deep learning models via variance pooling

Abstract: Supervised learning tasks such as cancer survival prediction from gigapixel whole slide images (WSIs) are a critical challenge in computational pathology that requires modeling complex features of the tumor microenvironment. These learning tasks are often solved with deep multi-instance learning (MIL) models that do not explicitly capture intratumoral heterogeneity. We develop a novel variance pooling architecture that enables a MIL model to incorporate intratumoral heterogeneity into its predictions. Two interpretability tools based on representative patches are illustrated to probe the biological signals captured by these models. An empirical study with 4,479 gigapixel WSIs from the Cancer Genome Atlas shows that adding variance pooling onto MIL frameworks improves survival prediction performance for five cancer types.