Automatic Fully-Contextualized Recommendation Extraction from Radiology Reports

Recommendations are a key component of radiology reports. Automatic extraction of recommendations would facilitate tasks such as recommendation tracking, quality improvement, and large-scale descriptive studies. Existing report-parsing systems are frequently limited to recommendations for follow-up imaging studies, operate at the sentence or document level rather than the individual recommendation level, and do not extract important contextualizing information. We present a neural network architecture capable of extracting fully contextualized recommendations from any type of radiology report. We identified six major "questions" necessary to capture the majority of context associated with a recommendation: recommendation, time period, reason, conditionality, strength, and negation. We developed a unified task representation by allowing questions to refer to answers to other questions. Our representation allows for a single system to perform named entity recognition (NER) and classification tasks. We annotated 2272 radiology reports from all specialties, imaging modalities, and multiple hospitals across our institution. We evaluated the performance of a long short-term memory (LSTM) architecture on the six-question task. The single-task LSTM model achieves a token-level performance of 89.2% at recommendation extraction, and token-level performances between 85 and 95% F1 on extracting modifying features. Our model extracts all types of recommendations, including follow-up imaging, tissue biopsies, and clinical correlation, and can operate in real time. It is feasible to extract complete contextualized recommendations of all types from arbitrary radiology reports. The approach is likely generalizable to other clinical entities referenced in radiology reports, such as radiologic findings or diagnoses.