Extracting Social Determinants of Health from Pediatric Patient Notes Using Large Language Models: Novel Corpus and Methods

Social determinants of health (SDoH) play a critical role in shaping health outcomes, particularly in pediatric populations where interventions can have long-term implications. SDoH are frequently studied in the Electronic Health Record (EHR), which provides a rich repository for diverse patient data. In this work, we present a novel annotated corpus, the Pediatric Social History Annotation Corpus (PedSHAC), and evaluate the automatic extraction of detailed SDoH representations using fine-tuned and in-context learning methods with Large Language Models (LLMs). PedSHAC comprises annotated social history sections from 1,260 clinical notes obtained from pediatric patients within the University of Washington (UW) hospital system. Employing an event-based annotation scheme, PedSHAC captures ten distinct health determinants to encompass living and economic stability, prior trauma, education access, substance use history, and mental health with an overall annotator agreement of 81.9 F1. Our proposed fine-tuning LLM-based extractors achieve high performance at 78.4 F1 for event arguments. In-context learning approaches with GPT-4 demonstrate promise for reliable SDoH extraction with limited annotated examples, with extraction performance at 82.3 F1 for event triggers.

A Novel Corpus of Annotated Medical Imaging Reports and Information Extraction Results Using BERT-based Language Models

Medical imaging is critical to the diagnosis, surveillance, and treatment of many health conditions, including oncological, neurological, cardiovascular, and musculoskeletal disorders, among others. Radiologists interpret these complex, unstructured images and articulate their assessments through narrative reports that remain largely unstructured. This unstructured narrative must be converted into a structured semantic representation to facilitate secondary applications such as retrospective analyses or clinical decision support. Here, we introduce the Corpus of Annotated Medical Imaging Reports (CAMIR), which includes 609 annotated radiology reports from three imaging modality types: Computed Tomography, Magnetic Resonance Imaging, and Positron Emission Tomography-Computed Tomography. Reports were annotated using an event-based schema that captures clinical indications, lesions, and medical problems. Each event consists of a trigger and multiple arguments, and a majority of the argument types, including anatomy, normalize the spans to pre-defined concepts to facilitate secondary use. CAMIR uniquely combines a granular event structure and concept normalization. To extract CAMIR events, we explored two BERT (Bi-directional Encoder Representation from Transformers)-based architectures, including an existing architecture (mSpERT) that jointly extracts all event information and a multi-step approach (PL-Marker++) that we augmented for the CAMIR schema.