Clinical Utility of the Automatic Phenotype Annotation in Unstructured Clinical Notes: ICU Use Cases

Clinical notes contain information not present elsewhere, including drug response and symptoms, all of which are highly important when predicting key outcomes in acute care patients. We propose the automatic annotation of phenotypes from clinical notes as a method to capture essential information to predict outcomes in the Intensive Care Unit (ICU). This information is complementary to typically used vital signs and laboratory test results. We demonstrate and validate our approach conducting experiments on the prediction of in-hospital mortality, physiological decompensation and length of stay in the ICU setting for over 24,000 patients. The prediction models incorporating phenotypic information consistently outperform the baseline models leveraging only vital signs and laboratory test results. Moreover, we conduct a thorough interpretability study, showing that phenotypes provide valuable insights at the patient and cohort levels. Our approach illustrates the viability of using phenotypes to determine outcomes in the ICU.