GNN-surv: Discrete-Time Survival Prediction Using Graph Neural Networks

Abstract

Survival prediction models play a key role in patient prognosis and personalized treatment. However, their accuracy can be improved by incorporating patient similarity networks, which uncover complex data patterns. Our study uses Graph Neural Networks (GNNs) to enhance discrete-time survival predictions (GNN-surv) by leveraging relationships in these networks. We build these networks using cancer patients’ genomic and clinical data and train various GNN models on them, integrating Logistic Hazard and PMF survival models. GNN-surv models exhibit superior performance in survival prediction across two urologic cancer datasets, outperforming traditional MLP models. They maintain robustness and effectiveness under varying graph construction hyperparameter μ values, with performance boosts of up to 14.6% and 7.9% in the time-dependent concordance index and reductions in the integrated brier score of 26.7% and 24.1% in the BLCA and KIRC datasets, respectively. Notably, these models also maintain their effectiveness across three different types of GNN models, suggesting potential adaptability to other cancer datasets. The superior performance of our GNN-surv models underscores their wide applicability in the fields of oncology and personalized medicine, providing clinicians with a more accurate tool for patient prognosis and personalized treatment planning. Future studies can further optimize these models by incorporating other survival models or additional data modalities.