An overview of biomedical entity linking throughout the years

E French, BT McInnes - Journal of biomedical informatics, 2023 - Elsevier
Abstract Biomedical Entity Linking (BEL) is the task of map** of spans of text within
biomedical documents to normalized, unique identifiers within an ontology. This is an …

HunFlair2 in a cross-corpus evaluation of biomedical named entity recognition and normalization tools

M Sänger, S Garda, XD Wang, L Weber-Genzel… - …, 2024 - academic.oup.com
Motivation With the exponential growth of the life sciences literature, biomedical text mining
(BTM) has become an essential technology for accelerating the extraction of insights from …

[HTML][HTML] NILINKER: attention-based approach to NIL entity linking

P Ruas, FM Couto - Journal of Biomedical Informatics, 2022 - Elsevier
The existence of unlinkable (NIL) entities is a major hurdle affecting the performance of
Named Entity Linking approaches, and, consequently, the performance of downstream …

An automatic generation of heterogeneous knowledge graph for global disease support: A demonstration of a cancer use case

N Maghawry, S Ghoniemy, E Shaaban… - Big Data and Cognitive …, 2023 - mdpi.com
Semantic data integration provides the ability to interrelate and analyze information from
multiple heterogeneous resources. With the growing complexity of medical ontologies and …

HunFlair2 in a cross-corpus evaluation of named entity recognition and normalization tools

M Sänger, S Garda, XD Wang, L Weber-Genzel… - arxiv preprint arxiv …, 2024 - arxiv.org
With the exponential growth of the life science literature, biomedical text mining (BTM) has
become an essential technology for accelerating the extraction of insights from publications …

Chemical entity normalization for successful translational development of Alzheimer's disease and dementia therapeutics

S Mullin, R McDougal, KH Cheung, H Kilicoglu… - Journal of Biomedical …, 2024 - Springer
Background Identifying chemical mentions within the Alzheimer's and dementia literature
can provide a powerful tool to further therapeutic research. Leveraging the Chemical Entities …

Hybrid semantic recommender system for chemical compounds in large-scale datasets

M Barros, A Moitinho, FM Couto - Journal of cheminformatics, 2021 - Springer
The large, and increasing, number of chemical compounds poses challenges to the
exploration of such datasets. In this work, we propose the usage of recommender systems to …

Hybrid X-Linker: Automated Data Generation and Extreme Multi-label Ranking for Biomedical Entity Linking

P Ruas, F Gallego, FJ Veredas, FM Couto - arxiv preprint arxiv …, 2024 - arxiv.org
State-of-the-art deep learning entity linking methods rely on extensive human-labelled data,
which is costly to acquire. Current datasets are limited in size, leading to inadequate …

Multilingual bi‐encoder models for biomedical entity linking

ZA Guven, A Lamurias - Expert Systems, 2023 - Wiley Online Library
Natural language processing (NLP) is a field of study that focuses on data analysis on texts
with certain methods. NLP includes tasks such as sentiment analysis, spam detection, entity …

Creating Recommender Systems Datasets in Scientific Fields

M Barros, FM Couto, M Pato, P Ruas - Proceedings of the 27th ACM …, 2021 - dl.acm.org
Recommender systems (RS) have been successfully explored in a vast number of domains,
eg movies and tv shows, music, or e-commerce. In these domains we have a large number …