AIMC Topic: Natural Language Processing

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Does BERT need domain adaptation for clinical negation detection?

Journal of the American Medical Informatics Association : JAMIA
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.

Can artificial intelligence replace manual search for systematic literature? Review on cutaneous manifestations in primary Sjögren's syndrome.

Rheumatology (Oxford, England)
OBJECTIVES: Manual systematic literature reviews are becoming increasingly challenging due to the sharp rise in publications. The primary objective of this literature review was to compare manual and computer software using artificial intelligence re...

medExtractR: A targeted, customizable approach to medication extraction from electronic health records.

Journal of the American Medical Informatics Association : JAMIA
OBJECTIVE: We developed medExtractR, a natural language processing system to extract medication information from clinical notes. Using a targeted approach, medExtractR focuses on individual drugs to facilitate creation of medication-specific research...

Deep learning in clinical natural language processing: a methodical review.

Journal of the American Medical Informatics Association : JAMIA
OBJECTIVE: This article methodically reviews the literature on deep learning (DL) for natural language processing (NLP) in the clinical domain, providing quantitative analysis to answer 3 research questions concerning methods, scope, and context of c...

Cross-lingual semantic annotation of biomedical literature: experiments in Spanish and English.

Bioinformatics (Oxford, England)
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...

Applying citizen science to gene, drug and disease relationship extraction from biomedical abstracts.

Bioinformatics (Oxford, England)
MOTIVATION: Biomedical literature is growing at a rate that outpaces our ability to harness the knowledge contained therein. To mine valuable inferences from the large volume of literature, many researchers use information extraction algorithms to ha...

BioBERT: a pre-trained biomedical language representation model for biomedical text mining.

Bioinformatics (Oxford, England)
MOTIVATION: Biomedical text mining is becoming increasingly important as the number of biomedical documents rapidly grows. With the progress in natural language processing (NLP), extracting valuable information from biomedical literature has gained p...

Expert artificial intelligence-based natural language processing characterises childhood asthma.

BMJ open respiratory research
INTRODUCTION: The lack of effective, consistent, reproducible and efficient asthma ascertainment methods results in inconsistent asthma cohorts and study results for clinical trials or other studies. We aimed to assess whether application of expert a...

Natural language processing for structuring clinical text data on depression using UK-CRIS.

Evidence-based mental health
BACKGROUND: Utilisation of routinely collected electronic health records from secondary care offers unprecedented possibilities for medical science research but can also present difficulties. One key issue is that medical information is presented as ...

Considerations for advancing nephrology research and practice through natural language processing.

Kidney international
Much of medical data is buried in the free text of clinical notes and not captured by structured data, such as administrative codes. Natural language processing (NLP) can locate and use information that resides in unstructured free text. Chan et al. ...