Interpretable deep learning for improving cancer patient survival based on personal transcriptomes

Precision medicine chooses the optimal drug for a patient by considering individual differences. With the tremendous amount of data accumulated for cancers, we develop an interpretable neural network to predict cancer patient survival based on drug prescriptions and personal transcriptomes (CancerIDP). The deep learning model achieves 96% classification accuracy in distinguishing short-lived from long-lived patients. The Pearson correlation between predicted and actual months-to-death values is as high as 0.937. About 27.4% of patients may survive longer with an alternative medicine chosen by our deep learning model. The median survival time of all patients can increase by 3.9 months. Our interpretable neural network model reveals the most discriminating pathways in the decision-making process, which will further facilitate mechanistic studies of drug development for cancers.