Understanding spatial language in radiology: Representation framework, annotation, and spatial relation extraction from chest X-ray reports using deep learning.

Authors

Surabhi Datta, University of Texas Health Science Center at Houston, School of Health Information Sciences, Houston TX, USA
Yuqi Si
Laritza Rodriguez
Sonya E Shooshan
Dina Demner-Fushman
Kirk Roberts

Publication Date

8-1-2020

Journal

Journal of Biomedical Informatics

Abstract

Radiology reports contain a radiologist's interpretations of images, and these images frequently describe spatial relations. Important radiographic findings are mostly described in reference to an anatomical location through spatial prepositions. Such spatial relationships are also linked to various differential diagnoses and often described through uncertainty phrases. Structured representation of this clinically significant spatial information has the potential to be used in a variety of downstream clinical informatics applications. Our focus is to extract these spatial representations from the reports. For this, we first define a representation framework based on the Spatial Role Labeling (SpRL) scheme, which we refer to as Rad-SpRL. In Rad-SpRL, common radiological entities tied to spatial relations are encoded through four spatial roles: Trajector, Landmark, Diagnosis, and Hedge, all identified in relation to a spatial preposition (or Spatial Indicator). We annotated a total of 2,000 chest X-ray reports following Rad-SpRL. We then propose a deep learning-based natural language processing (NLP) method involving word and character-level encodings to first extract the Spatial Indicators followed by identifying the corresponding spatial roles. Specifically, we use a bidirectional long short-term memory (Bi-LSTM) conditional random field (CRF) neural network as the baseline model. Additionally, we incorporate contextualized word representations from pre-trained language models (BERT and XLNet) for extracting the spatial information. We evaluate both gold and predicted Spatial Indicators to extract the four types of spatial roles. The results are promising, with the highest average F1 measure for Spatial Indicator extraction being 91.29 (XLNet); the highest average overall F1 measure considering all the four spatial roles being 92.9 using gold Indicators (XLNet); and 85.6 using predicted Indicators (BERT pre-trained on MIMIC notes). The corpus is available in Mendeley at http://dx.doi.org/10.17632/yhb26hfz8n.1 and https://github.com/krobertslab/datasets/blob/master/Rad-SpRL.xml.

Keywords

Deep Learning, Language, Natural Language Processing, Radiology, X-Rays