Discrete-time survival analysis in the critically ill: a deep learning approach using heterogeneous data

• Published in: NPJ digital medicine Vol. 5; no. 1; pp. 142 - 10
• Main Authors: Thorsen-Meyer, Hans-Christian, Placido, Davide, Kaas-Hansen, Benjamin Skov, Nielsen, Anna P., Lange, Theis, Nielsen, Annelaura B., Toft, Palle, Schierbeck, Jens, Strøm, Thomas, Chmura, Piotr J., Heimann, Marc, Belling, Kirstine, Perner, Anders, Brunak, Søren
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 14.09.2022; Nature Publishing Group; Nature Portfolio
• Subjects: 692/308/409; 692/700/1750; Biomedicine; Biotechnology; Deep learning; Digital technology; Intensive care; Medical prognosis; Medical technology; Medicine; Medicine & Public Health; Survival analysis; Denmark
• ISSN: 2398-6352; 2398-6352
• DOI: 10.1038/s41746-022-00679-6

Prediction of survival for patients in intensive care units (ICUs) has been subject to intense research. However, no models exist that embrace the multiverse of data in ICUs. It is an open question whether deep learning methods using automated data integration with minimal pre-processing of mixed data domains such as free text, medical history and high-frequency data can provide discrete-time survival estimates for individual ICU patients. We trained a deep learning model on data from patients admitted to ten ICUs in the Capital Region of Denmark and the Region of Southern Denmark between 2011 and 2018. Inspired by natural language processing we mapped the electronic patient record data to an embedded representation and fed the data to a recurrent neural network with a multi-label output layer representing the chance of survival at different follow-up times. We evaluated the performance using the time-dependent concordance index. In addition, we quantified and visualized the drivers of survival predictions using the SHAP methodology. We included 37,355 admissions of 29,417 patients in our study. Our deep learning models outperformed traditional Cox proportional-hazard models with concordance index in the ranges 0.72–0.73, 0.71–0.72, 0.71, and 0.69–0.70, for models applied at baseline 0, 24, 48, and 72 h, respectively. Deep learning models based on a combination of entity embeddings and survival modelling is a feasible approach to obtain individualized survival estimates in data-rich settings such as the ICU. The interpretable nature of the models enables us to understand the impact of the different data domains.