The development of an explainable machine learning system for predicting brain atrophies from electronic health records

Abstract

AbstractBackgroundThe number of elderly living with dementia is projected to dramatically increase, especially in low‐income and middle‐income countries (LMICs). While obtaining brain scans to detect atrophies and significant radiology findings related to dementia might be costly, the use of electronic health record (EHR) for elderly patients could facilitate identifying patients at a high risk based on routinely collected data. This works, evaluates the use of an interpretable machine learning‐based system that predicts brain atrophies and small vessel disease based on EHR data.MethodWe develop a machine learning predictive system to predict atrophies or small vessel disease from retrospective anonymized EHR data recorded for patients above the age of 50 years from a multispecialty outpatient medical center from Ramallah, Palestine. The patient labelling involved using natural language processing to identify cases in unstructured radiology reports for structural brain Magnetic Resonance Imaging (MRI). For input features, we extracted and preprocessed 30 features for the most commonly collected clinical features such as demographics and laboratory results. The dataset was split into training and test sets, where data preprocessing and augmentation, and hyperparameter tuning were applied before training multiple models including Xgboost, Support Vector Machines, Random Forest, and Logistic Regression. To better understand the relative impact each feature had on the model’s prediction, shapely feature importance analysis was conducted for the top performing model.ResultThe top preforming model was Random Forest, with a performance of Area Under the Precision‐Recall Curve (AUPRC) of 0.989, and 0.842 for Area Under Receiving Operating Curve (AUROC). The feature importance analysis revealed that age, sex, Vitamin D, Vitamin B12 and red blood cell distribution width were the features with highest impact on the model’s predictionConclusionPredicting atrophies from EHRs for elderly visiting outpatient clinics could assist in case‐finding for dementia patients and ultimately help identify patients that would benefit from an MRI. In future works, we aim to further investigate building low‐cost diagnostic tools based on a smaller feature set, which could be valuable for facilities from LMICs.