Existing question answering (QA) datasets derived from electronic health records (EHR) are artificially generated and consequently fail to capture realistic physician information needs. We present Discharge Summary Clinical Questions (DiSCQ), a newly curated question dataset composed of 2,000+ questions paired with the snippets of text (triggers) that prompted each question. The questions are generated by medical experts from 100+ MIMIC-III discharge summaries. We analyze this dataset to characterize the types of information sought by medical experts. We also train baseline models for trigger detection and question generation (QG), paired with unsupervised answer retrieval over EHRs. Our baseline model is able to generate high quality questions in over 62% of cases when prompted with human selected triggers. We release this dataset (and all code to reproduce baseline model results) to facilitate further research into realistic clinical QA and QG: https://github.com/elehman16/discq.

While much data within a patient’s electronic health record (EHR) is coded, crucial information concerning the patient’s care and management remain buried in unstructured clinical notes, making it difficult and time-consuming for physicians to review during their usual clinical workflow. In this paper, we present our clinical note processing pipeline, which extends beyond basic medical natural language processing (NLP) with concept recognition and relation detection to also include components specific to EHR data, such as structured data associated with the encounter, sentence-level clinical aspects, and structures of the clinical notes. We report on the use of this pipeline in a disease-specific extractive text summarization task on clinical notes, focusing primarily on progress notes by physicians and nurse practitioners. We show how the addition of EHR-specific components to the pipeline resulted in an improvement in our overall system performance and discuss the potential impact of EHR-specific components on other higher-level clinical NLP tasks.

We propose a novel methodology to generate domain-specific large-scale question answering (QA) datasets by re-purposing existing annotations for other NLP tasks. We demonstrate an instance of this methodology in generating a large-scale QA dataset for electronic medical records by leveraging existing expert annotations on clinical notes for various NLP tasks from the community shared i2b2 datasets. The resulting corpus (emrQA) has 1 million questions-logical form and 400,000+ question-answer evidence pairs. We characterize the dataset and explore its learning potential by training baseline models for question to logical form and question to answer mapping.