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The Classification of Short Scientific Texts Using Pretrained BERT Model.

Studies in health technology and informatics
Automated text classification is a natural language processing (NLP) technology that could significantly facilitate scientific literature selection. A specific topical dataset of 630 article abstracts was obtained from the PubMed database. We propose...

Text mining for modeling of protein complexes enhanced by machine learning.

Bioinformatics (Oxford, England)
MOTIVATION: Procedures for structural modeling of protein-protein complexes (protein docking) produce a number of models which need to be further analyzed and scored. Scoring can be based on independently determined constraints on the structure of th...

Large-scale entity representation learning for biomedical relationship extraction.

Bioinformatics (Oxford, England)
MOTIVATION: The automatic extraction of published relationships between molecular entities has important applications in many biomedical fields, ranging from Systems Biology to Personalized Medicine. Existing works focused on extracting relationships...

Health informatics publication trends in Saudi Arabia: a bibliometric analysis over the last twenty-four years.

Journal of the Medical Library Association : JMLA
OBJECTIVE: Understanding health informatics (HI) publication trends in Saudi Arabia may serve as a framework for future research efforts and contribute toward meeting national "e-Health" goals. The authors' intention was to understand the state of th...

Biomedical named entity recognition and linking datasets: survey and our recent development.

Briefings in bioinformatics
Natural language processing (NLP) is widely applied in biological domains to retrieve information from publications. Systems to address numerous applications exist, such as biomedical named entity recognition (BNER), named entity normalization (NEN) ...

Forty-two Million Ways to Describe Pain: Topic Modeling of 200,000 PubMed Pain-Related Abstracts Using Natural Language Processing and Deep Learning-Based Text Generation.

Pain medicine (Malden, Mass.)
OBJECTIVE: Recent efforts to update the definitions and taxonomic structure of concepts related to pain have revealed opportunities to better quantify topics of existing pain research subject areas.

Leveraging PubMed to Create a Specialty-Based Sense Inventory for Spanish Acronym Resolution.

Studies in health technology and informatics
Acronyms frequently occur in clinical text, which makes their identification, disambiguation and resolution an important task in clinical natural language processing. This paper contributes to acronym resolution in Spanish through the creation of a s...

Advancing PICO element detection in biomedical text via deep neural networks.

Bioinformatics (Oxford, England)
MOTIVATION: In evidence-based medicine, defining a clinical question in terms of the specific patient problem aids the physicians to efficiently identify appropriate resources and search for the best available evidence for medical treatment. In order...

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...

Pretraining to Recognize PICO Elements from Randomized Controlled Trial Literature.

Studies in health technology and informatics
PICO (Population/problem, Intervention, Comparison, and Outcome) is widely adopted for formulating clinical questions to retrieve evidence from the literature. It plays a crucial role in Evidence-Based Medicine (EBM). This paper contributes a scalabl...