Dynamic survival prediction in intensive care units from heterogeneous time series without the need for variable selection or pre-processing

We present a machine learning pipeline and model that uses the entire uncurated EHR for prediction of in-hospital mortality at arbitrary time intervals, using all available chart, lab and output events, without the need for pre-processing or feature engineering. Data for more than 45,000 American ICU patients from the MIMIC-III database were used to develop an ICU mortality prediction model. All chart, lab and output events were treated by the model in the same manner inspired by NLP. Patient events were discretized by percentile and mapped to learnt embeddings before being passed to a Recurrent Neural Network (RNN) to provide early prediction of in-patient mortality risk. We compared mortality predictions with the Simplified Acute Physiology Score II (SAPS II) and the Oxford Acute Severity of Illness Score (OASIS). Data were split into an independent test set (10%) and a ten-fold cross-validation was carried out during training to avoid overfitting. 13,233 distinct variables with heterogeneous data types were included without manual selection or pre-processing. Recordings in the first few hours of a patient's stay were found to be strongly predictive of mortality, outperforming models using SAPS II and OASIS scores within just 2 hours and achieving a state of the art Area Under the Receiver Operating Characteristic (AUROC) value of 0.80 (95% CI 0.79-0.80) at 12 hours vs 0.70 and 0.66 for SAPS II and OASIS at 24 hours respectively. Our model achieves a very strong performance of AUROC 0.86 (95% CI 0.85-0.86) for in-patient mortality prediction after 48 hours on the MIMIC-III dataset. Predictive performance increases over the first 48 hours of the ICU stay, but suffers from diminishing returns, providing rationale for time-limited trials of critical care and suggesting that the timing of decision making can be optimised and individualised.