High Throughput Phenotyping of Physician Notes with Large Language and Hybrid NLP Models

Deep phenotyping is the detailed description of patient signs and symptoms using concepts from an ontology. The deep phenotyping of the numerous physician notes in electronic health records requires high throughput methods. Over the past 30 years, progress toward making high-throughput phenotyping feasible. In this study, we demonstrate that a large language model and a hybrid NLP model (combining word vectors with a machine learning classifier) can perform high throughput phenotyping on physician notes with high accuracy. Large language models will likely emerge as the preferred method for high throughput deep phenotyping physician notes.Clinical relevance: Large language models will likely emerge as the dominant method for the high throughput phenotyping of signs and symptoms in physician notes.