Journal of the American Medical Informatics Association : JAMIA
Apr 29, 2015
OBJECTIVE: Analysis of narrative (text) data from electronic health records (EHRs) can improve population-scale phenotyping for clinical and genetic research. Currently, selection of text features for phenotyping algorithms is slow and laborious, req...
BACKGROUND: Controlled vocabularies such as the Unified Medical Language System (UMLS) and Medical Subject Headings (MeSH) are widely used for biomedical natural language processing (NLP) tasks. However, the standard terminology in such collections s...
INTRODUCTION: The ambiguity of biomedical abbreviations is one of the challenges in biomedical text mining systems. In particular, the handling of term variants and abbreviations without nearby definitions is a critical issue. In this study, we adopt...
INTRODUCTION: This article explores how measures of semantic similarity and relatedness are impacted by the semantic groups to which the concepts they are measuring belong. Our goal is to determine if there are distinctions between homogeneous compar...
Journal of the American Medical Informatics Association : JAMIA
Aug 21, 2014
OBJECTIVE: The ShARe/CLEF eHealth 2013 Evaluation Lab Task 1 was organized to evaluate the state of the art on the clinical text in (i) disorder mention identification/recognition based on Unified Medical Language System (UMLS) definition (Task 1a) a...
Studies in health technology and informatics
Sep 3, 2025
INTRODUCTION: Medical entity linking is an important task in biomedical natural language processing, aiming to align textual mentions of medical concepts with standardized concepts in ontologies. Most existing approaches rely on supervised models or ...
Studies in health technology and informatics
Sep 3, 2025
INTRODUCTION: Whole Exome Sequencing (WES) promises to open a new range of personalized treatments due to breaking the limits of former panel-based methods of molecular analysis. While the methodology is well established and already included in clini...
Studies in health technology and informatics
Aug 7, 2025
Understanding health concepts in free text is an important task in biomedical NLP. Being able to map the extracted concepts to unique concept identifiers can facilitate integration of and interoperability across biomedical informatics applications. A...
Studies in health technology and informatics
Aug 7, 2025
Antonyms are words that have opposite or contrasting meanings in a specific domain. For example, "increase" is the opposite of "decrease" in the domain of "quantity". Antonyms play an important role in NLP applications to improve performance. This pa...
OBJECTIVE: The full fine-tuning paradigm becomes impractical when applying pre-trained models to downstream tasks due to significant computational and storage costs. Parameter-efficient fine-tuning (PEFT) methods can alleviate the issue. However, sol...
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