Autoencoder-based prediction of ICU clinical codes

Availability of diagnostic codes in Electronic Health Records (EHRs) is crucial for patient care as well as reimbursement purposes. However, entering them in the EHR is tedious, and some clinical codes may be overlooked. Given an incomplete list of clinical codes, we investigate the performance of ML methods on predicting the complete ones, and assess the added predictive value of including other clinical patient data in this task. We used the MIMIC-III dataset and frame the task of completing the clinical codes as a recommendation problem. We consider various autoencoder approaches plus two strong baselines; item co-occurrence and Singular Value Decomposition (SVD). Inputs are 1) a record’s known clinical codes, 2) the codes plus variables. The co-occurrence-based approach performed slightly better (F1 score = 0.26, Mean Average Precision [MAP] = 0.19) than the SVD (F1 = 0.24, MAP = 0.18). However, the adversarial autoencoder achieved the best performance when using the codes plus variables (F1 = 0.32, MAP = 0.25). Adversarial autoencoders performed best in terms of F1 and were equal to vanilla and denoising autoencoders in term of MAP. Using clinical variables in addition to the incomplete codes list, improves the predictive performance of the models.