Related papers: Knowledge-Rich Self-Supervision for Biomedical Ent…

Off-the-shelf biomedical embeddings obtained from the recently released various pre-trained language models (such as BERT, XLNET) have demonstrated state-of-the-art results (in terms of accuracy) for the various natural language…

Entity summarization is the problem of computing an optimal compact summary for an entity by selecting a size-constrained subset of triples from RDF data. Entity summarization supports a multiplicity of applications and has led to fruitful…

PubMed is an essential resource for the medical domain, but useful concepts are either difficult to extract or are ambiguated, which has significantly hindered knowledge discovery. To address this issue, we constructed a PubMed knowledge…

We present SynCABEL (Synthetic Contextualized Augmentation for Biomedical Entity Linking), a framework that addresses a central bottleneck in supervised biomedical entity linking (BEL): the scarcity of expert-annotated training data.…

Multimodal Entity Linking (MEL) is a fundamental task in data management that maps ambiguous mentions with diverse modalities to the multimodal entities in a knowledge base. However, most existing MEL approaches primarily focus on…

Biomedical named entities often play important roles in many biomedical text mining tools. However, due to the incompleteness of provided synonyms and numerous variations in their surface forms, normalization of biomedical entities is very…

Literature analysis facilitates researchers to acquire a good understanding of the development of science and technology. The traditional literature analysis focuses largely on the literature metadata such as topics, authors, abstracts,…

Cross-lingual Entity Linking (XEL), the problem of grounding mentions of entities in a foreign language text into an English knowledge base such as Wikipedia, has seen a lot of research in recent years, with a range of promising techniques.…

The injection of domain-specific knowledge is crucial for adapting language models (LMs) to specialized fields such as biomedicine. While most current approaches rely on unstructured text corpora, this study explores two complementary…

Automatic summarization generates concise summaries that contain key ideas of source documents. As the most mainstream datasets for the news sub-domain, CNN/DailyMail and BBC XSum have been widely used for performance benchmarking. However,…

Ultrasound (US) imaging is clinically invaluable due to its noninvasive and safe nature. However, interpreting US images is challenging, requires significant expertise, and time, and is often prone to errors. Deep learning offers assistive…

Entity linking is the task of aligning mentions to corresponding entities in a given knowledge base. Previous studies have highlighted the necessity for entity linking systems to capture the global coherence. However, there are two common…

Developing high-performance entity normalization algorithms that can alleviate the term variation problem is of great interest to the biomedical community. Although deep learning-based methods have been successfully applied to biomedical…

Biomedical entity linking aims to map nonstandard entities to standard entities in a knowledge base. Traditional supervised methods perform well but require extensive annotated data to transfer, limiting their usage in low-resource…

As part of the large number of scientific articles being published every year, the publication rate of biomedical literature has been increasing. Consequently, there has been considerable effort to harness and summarize the massive amount…

Named entity recognition on the in-domain supervised and few-shot settings have been extensively discussed in the NLP community and made significant progress. However, cross-domain NER, a more common task in practical scenarios, still poses…

We explore the suitability of unsupervised representation learning methods on biomedical text -- BioBERT, SciBERT, and BioSentVec -- for biomedical question answering. To further improve unsupervised representations for biomedical QA, we…

Knowledge bases such as Wikidata amass vast amounts of named entity information, such as multilingual labels, which can be extremely useful for various multilingual and cross-lingual applications. However, such labels are not guaranteed to…

This paper introduces a new model that uses named entity recognition, coreference resolution, and entity linking techniques, to approach the task of linking people entities on Wikipedia people pages to their corresponding Wikipedia pages if…

Objective: Develop a cost-effective, large language model (LLM)-based pipeline for automatically extracting Review of Systems (ROS) entities from clinical notes. Materials and Methods: The pipeline extracts ROS section from the clinical…