Journal of the American Medical Informatics Association : JAMIA
Oct 1, 2020
OBJECTIVE: The 2019 National Natural language processing (NLP) Clinical Challenges (n2c2)/Open Health NLP (OHNLP) shared task track 3, focused on medical concept normalization (MCN) in clinical records. This track aimed to assess the state of the art...
AIMS: Natural Language Processing (NLP) offers an automated method to extract data from unstructured free text fields for arthroplasty registry participation. Our objective was to investigate how accurately NLP can be used to extract structured clini...
Studies in health technology and informatics
Jun 26, 2020
Having precise information about health IT evaluation studies is important for evidence-based decisions in medical informatics. In a former feasibility study, we used a faceted search based on ontological modeling of key elements of studies to retrie...
Studies in health technology and informatics
Jun 26, 2020
The automated detection of adverse events in medical records might be a cost-effective solution for patient safety management or pharmacovigilance. Our group proposed an information extraction algorithm (IEA) for detecting adverse events in neurosurg...
Studies in health technology and informatics
Jun 16, 2020
Recent studies in the biomedical domain suggest that learning statistical word representations (static or contextualized word embeddings) on large corpora of specialized data improve the results on downstream natural language processing (NLP) tasks. ...
Studies in health technology and informatics
Jun 16, 2020
In this paper, we present and discuss two new measures of inter- and intra-rater agreement to assess the reliability of the raters, and hence of their labeling, in multi-rater setings, which are common in the production of ground truth for machine le...
Studies in health technology and informatics
Jun 16, 2020
This paper presents five document retrieval systems for a small (few thousands) and domain specific corpora (weekly peer-reviewed medical journals published in French) as well as an evaluation methodology to quantify the models performance. The propo...
SUMMARY: Glycoinformatics plays a major role in glycobiology research, and the development of a comprehensive glycoinformatics knowledgebase is critical. This application note describes the GlyGen data model, processing workflow and the data access i...
Journal of the American Medical Informatics Association : JAMIA
Apr 1, 2020
INTRODUCTION: Classifying whether concepts in an unstructured clinical text are negated is an important unsolved task. New domain adaptation and transfer learning methods can potentially address this issue.
MOTIVATION: Biomedical literature is one of the most relevant sources of information for knowledge mining in the field of Bioinformatics. In spite of English being the most widely addressed language in the field; in recent years, there has been a gro...