Infection control and hospital epidemiology
May 29, 2015
BACKGROUND: Incidence of catheter-associated urinary tract infection (CAUTI) is a quality benchmark. To streamline conventional detection methods, an electronic surveillance system augmented with natural language processing (NLP), which gathers data ...
UNLABELLED: Nationwide Children's Hospital established an i2b2 (Informatics for Integrating Biology & the Bedside) application for sleep disorder cohort identification. Discrete data were gleaned from semistructured sleep study reports. The system sh...
Many text mining applications in the biomedical domain benefit from automatic clustering of relational phrases into synonymous groups, since it alleviates the problem of spurious mismatches caused by the diversity of natural language expressions. Mos...
The 2014 i2b2/UTHealth natural language processing shared task featured a track focused on identifying risk factors for heart disease (specifically, Cardiac Artery Disease) in clinical narratives. For this track, we used a "light" annotation paradigm...
Clinical documents are rich free-text data sources containing valuable medication and symptom information, which have a great potential to improve health care. In this paper, we build an integrating system for extracting medication names and symptom ...
BMC medical informatics and decision making
May 20, 2015
BACKGROUND: The Entity Linking (EL) task links entity mentions from an unstructured document to entities in a knowledge base. Although this problem is well-studied in news and social media, this problem has not received much attention in the life sci...
BMC medical informatics and decision making
May 20, 2015
BACKGROUND: Parsing, which generates a syntactic structure of a sentence (a parse tree), is a critical component of natural language processing (NLP) research in any domain including medicine. Although parsers developed in the general English domain,...
Journal of the American Medical Informatics Association : JAMIA
May 14, 2015
OBJECTIVE: Many tasks in natural language processing utilize lexical pattern-matching techniques, including information extraction (IE), negation identification, and syntactic parsing. However, it is generally difficult to derive patterns that achiev...
BACKGROUND: Biomedical knowledge bases (KB's) have become important assets in life sciences. Prior work on KB construction has three major limitations. First, most biomedical KBs are manually built and curated, and cannot keep up with the rate at whi...
Journal of the American Medical Informatics Association : JAMIA
May 13, 2015
OBJECTIVE: Literature-based discovery (LBD) aims to identify "hidden knowledge" in the medical literature by: (1) analyzing documents to identify pairs of explicitly related concepts (terms), then (2) hypothesizing novel relations between pairs of un...
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