COVID-19 Literature Knowledge Graph Construction and Drug Repurposing Report Generation

To combat COVID-19, both clinicians and scientists need to digest the vast amount of relevant biomedical knowledge in literature to understand the disease mechanism and the related biological functions. We have developed a novel and comprehensive knowledge discovery framework, \textbf{COVID-KG} to extract fine-grained multimedia knowledge elements (entities, relations and events) from scientific literature. We then exploit the constructed multimedia knowledge graphs (KGs) for question answering and report generation, using drug repurposing as a case study. Our framework also provides detailed contextual sentences, subfigures and knowledge subgraphs as evidence. All of the data, KGs, reports, resources and shared services are publicly available.Comment: 11 pages, submitted to ACL 2020 Workshop on Natural Language Processing for COVID-19 (NLP-COVID), for resources see http://blender.cs.illinois.edu/covid19/, for video see http://159.89.180.81/demo/covid/Covid-KG_DemoVideo.mp

Neural Natural Language Processing for Unstructured Data in Electronic Health Records: a Review

Electronic health records (EHRs), digital collections of patient healthcare events and observations, are ubiquitous in medicine and critical to healthcare delivery, operations, and research. Despite this central role, EHRs are notoriously difficult to process automatically. Well over half of the information stored within EHRs is in the form of unstructured text (e.g. provider notes, operation reports) and remains largely untapped for secondary use. Recently, however, newer neural network and deep learning approaches to Natural Language Processing (NLP) have made considerable advances, outperforming traditional statistical and rule-based systems on a variety of tasks. In this survey paper, we summarize current neural NLP methods for EHR applications. We focus on a broad scope of tasks, namely, classification and prediction, word embeddings, extraction, generation, and other topics such as question answering, phenotyping, knowledge graphs, medical dialogue, multilinguality, interpretability, etc.Comment: 33 pages, 11 figure