Automated Recognition of Visual Acuity Measurements in Ophthalmology Clinical Notes Using Deep Learning

Abstract

Visual acuity (VA) is a critical component of the eye examination but is often only documented in electronic health records (EHRs) as unstructured free-text notes, making it challenging to use in research. This study aimed to improve on existing rule-based algorithms by developing and evaluating deep learning models to perform named entity recognition of different types of VA measurements and their lateralities from free-text ophthalmology notes: VA for each of the right and left eyes, with and without glasses correction, and with and without pinhole. Cross-sectional study. A total of 319 756 clinical notes with documented VA measurements from approximately 90 000 patients were included. The notes were split into train, validation, and test sets. Bidirectional Encoder Representations from Transformers (BERT) models were fine-tuned to identify VA measurements from the progress notes and included BERT models pretrained on biomedical literature (BioBERT), critical care EHR notes (ClinicalBERT), both (BlueBERT), and a lighter version of BERT with 40% fewer parameters (DistilBERT). A baseline rule-based algorithm was created to recognize the same VA entities to compare against BERT models. Model performance was evaluated on a held-out test set using microaveraged precision, recall, and F1 score for all entities. On the human-annotated subset, BlueBERT achieved the best microaveraged F1 score (F1= 0.92), followed by ClinicalBERT (F1= 0.91), DistilBERT (F1= 0.90), BioBERT (F1= 0.84), and the baseline model (F1= 0.83). Common errors included labeling VA in sections outside of the examination portion of the note, difficulties labeling current VA alongside a series of past VAs, and missing nonnumeric VAs. This study demonstrates that deep learning models are capable of identifying VA measurements from free-text ophthalmology notes with high precision and recall, achieving significant performance improvements over a rule-based algorithm. The ability to recognize VA from free-text notes would enable a more detailed characterization of ophthalmology patient cohorts and enhance the development of models to predict ophthalmology outcomes. Proprietary or commercial disclosure may be found in the Footnotes and Disclosures at the end of this article.