RadGraph: Extracting Clinical Entities and Relations from Radiology Reports

Saahil Jain, Ashwin Agrawal, Adriel Saporta, Steven Truong, Du Nguyen Duong, Tan Bui, Pierre Chambon, Yuhao Zhang, Matthew P. Lungren, Andrew Y. Ng, Curtis Langlotz, Pranav Rajpurkar

Keywords: natural language processing, radiology, entity and relation extraction, multi-modal, graph

TL;DR: We present RadGraph, a dataset of entities and relations in radiology reports based on a novel information extraction schema.

Abstract: Extracting structured clinical information from free-text radiology reports can enable the use of radiology report information for a variety of critical healthcare applications. In our work, we present RadGraph, a dataset of entities and relations in full-text chest X-ray radiology reports based on a novel information extraction schema we designed to structure radiology reports. We release a development dataset, which contains board-certified radiologist annotations for 500 radiology reports from the MIMIC-CXR dataset (14,579 entities and 10,889 relations), and a test dataset, which contains two independent sets of board-certified radiologist annotations for 100 radiology reports split equally across the MIMIC-CXR and CheXpert datasets. Using these datasets, we train and test a deep learning model, RadGraph Benchmark, that achieves a micro F1 of 0.82 and 0.73 on relation extraction on the MIMIC-CXR and CheXpert test sets respectively. Additionally, we release an inference dataset, which contains annotations automatically generated by RadGraph Benchmark across 220,763 MIMIC-CXR reports (around 6 million entities and 4 million relations) and 500 CheXpert reports (13,783 entities and 9,908 relations) with mappings to associated chest radiographs. Our freely available dataset can facilitate a wide range of research in medical natural language processing, as well as computer vision and multi-modal learning when linked to chest radiographs.

URL: https://doi.org/10.13026/hm87-5p47