A Machine Learning Approach for Identifying People with Neuroinfectious Diseases in Electronic Health Records: Original Research Article (Preprint)

BACKGROUND Identifying NID cases using manual chart review is time-consuming, and billing codes are imprecise. EHR-based ML models for NID identification have yet to be investigated. OBJECTIVE To develop and validate a machine learning (ML) model to identify neuroinfectious diseases (NID) from unstructured patient notes. METHODS Clinical notes from patients who had undergone lumbar puncture were obtained using the EHR of an academic hospital network (Mass General Brigham, MGB), with half associated with NID-related diagnostic codes. Ground-truth was established by chart review with six NID-expert physicians. NID keywords were generated with regular expressions, and extracted texts were converted into bag-of-words representations using n-grams (n=1, 2, 3). Notes were randomly split into training (80%) and hold-out testing (20%) sets. Feature selection was performed using logistic regression with L1 regularization. An extreme gradient boosting (XGBoost) model classified NID cases, and performance was evaluated using the Area Under the Receiver Operating Curve (AUROC) and the Precision-Recall Curve (AUPRC). The model was validated in an external dataset from an independent hospital (Beth Israel Deaconess Medical Center, BIDMC). RESULTS This study included 3,000 patient notes from MGB from January 22, 2010, to September 21, 2023. Of the initial 1,284 n-gram features, 342 were selected, with the most significant features being ‘meningitis,’ ‘ventriculitis,’ and ‘meningoencephalitis.’ The XGBoost model demonstrated an AUROC of 0.977 (0.964 - 0.988) and AUPRC of 0.894 (0.831 - 0.943) on the MGB hold-out test set. On 600 notes from BIDMC, the model performance based on AUROC and AUPRC was 0.976 (0.961 - 0.989) and 0.779 (0.655 - 0.885), respectively. CONCLUSIONS Our ML model identifies NID cases using clinical notes tested on two independent hospitals, thereby enhancing efficiency in future large-scale NID research and cohort generation. Future studies incorporating patient notes from different regions are needed to ensure generalizability.