The U.S. Food and Drug Administration (FDA) collects real-world adverse events, including device-associated deaths, injuries, and malfunctions, through passive reporting to the agency’s Manufacturer and User Facility Device Experience (MAUDE) database. However, this system’s full potential remains untapped given the extensive use of unstructured text in medical device adverse event reports and lack of FDA resources and expertise to properly analyze all available data. In this work, we focus on addressing this limitation through the development of an annotated benchmark corpus to support the design and development of state-of-the-art NLP approaches towards automatic extraction of device-related adverse event information from FDA Medical Device Adverse Event Reports. We develop a dataset of labeled medical device reports from a diverse set of high-risk device types, that can be used for supervised machine learning. We develop annotation guidelines and manually annotate for nine entity types. The resulting dataset contains 935 annotated adverse event reports, containing 12252 annotated spans across the nine entity types. The dataset developed in this work will be made publicly available upon publication.

An adverse drug event (ADE) is an injury resulting from medical intervention related to a drug. Automatic ADE detection from text is either fine-grained (ADE entity recognition) or coarse-grained (ADE assertive sentence classification), with limited efforts leveraging inter-dependencies among the two granularities. We instead propose a multi-grained joint deep network to concurrently learn the ADE entity recognition and ADE sentence classification tasks. Our joint approach takes advantage of their symbiotic relationship, with a transfer of knowledge between the two levels of granularity. Our dual-attention mechanism constructs multiple distinct representations of a sentence that capture both task-specific and semantic information in the sentence, providing stronger emphasis on the key elements essential for sentence classification. Our model improves state-of- art F1-score for both tasks: (i) entity recognition of ADE words (12.5% increase) and (ii) ADE sentence classification (13.6% increase) on MADE 1.0 benchmark of EHR notes.