An Interpretable Deep Learning Framework for Biomarker Discovery in Complex Disease Survival Outcomes

Identification of important biomarkers associated with complex disease survival outcomes is fundamental for gaining an in-depth understanding of disease mechanisms and advancing precision medicine in conditions such as cancer and cardiovascular disorders. However, these tasks are complicated by the unique nature of time-to-event data, which captures both the occurrence and timing of clinical events. Notably, complex associations such as the non-linear and non-additive biomarker interactions and the high-dimensionality challenge conventional survival data modeling approaches. To address these difficulties, we propose SurvDNN, an enhanced deep neural network framework specifically designed for survival outcomes modeling. SurvDNN incorporates a bootstrapping-based regularization strategy to mitigate overfitting and a novel stability-driven filtering algorithm to improve model robustness. To enable interpretable biomarker discovery, we extend the Permutation-based Feature Importance Test (PermFIT) to survival settings, allowing rigorous quantification of individual biomarker contributions under complex biomarker-outcome associations. Through extensive simulations and applications to real-world datasets, SurvDNN consistently outperforms existing machine learning approaches in both biomarker identification and predictive accuracy. Our results demonstrate the potential of SurvDNN coupled with PermFIT as an interpretable, robust, and powerful tool for biomarker-driven survival modeling in complex diseases. An open-source R package implementing SurvDNN is publicly available on GitHub (https://github.com/BZou-lab/SurvDNN).