AI-based language models powering drug discovery and development

Z Liu, RA Roberts, M Lal-Nag, X Chen, R Huang… - Drug Discovery …, 2021 - Elsevier
The discovery and development of new medicines is expensive, time-consuming, and often
inefficient, with many failures along the way. Powered by artificial intelligence (AI), language …

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 mapping of spans of text within
biomedical documents to normalized, unique identifiers within an ontology. This is an …

PubTator central: automated concept annotation for biomedical full text articles

CH Wei, A Allot, R Leaman, Z Lu - Nucleic acids research, 2019 - academic.oup.com
Abstract PubTator Central (https://www. ncbi. nlm. nih. gov/research/pubtator/) is a web
service for viewing and retrieving bioconcept annotations in full text biomedical articles …

TaggerOne: joint named entity recognition and normalization with semi-Markov Models

R Leaman, Z Lu - Bioinformatics, 2016 - academic.oup.com
Motivation: Text mining is increasingly used to manage the accelerating pace of the
biomedical literature. Many text mining applications depend on accurate named entity …

DNorm: disease name normalization with pairwise learning to rank

R Leaman, R Islamaj Doğan, Z Lu - Bioinformatics, 2013 - academic.oup.com
Motivation: Despite the central role of diseases in biomedical research, there have been
much fewer attempts to automatically determine which diseases are mentioned in a text …

[HTML][HTML] Bert-based ranking for biomedical entity normalization

Z Ji, Q Wei, H Xu - AMIA Summits on Translational Science …, 2020 - ncbi.nlm.nih.gov
Developing high-performance entity normalization algorithms that can alleviate the term
variation problem is of great interest to the biomedical community. Although deep learning …

Biomedical entity representations with synonym marginalization

M Sung, H Jeon, J Lee, J Kang - arXiv preprint arXiv:2005.00239, 2020 - arxiv.org
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 …

tmChem: a high performance approach for chemical named entity recognition and normalization

R Leaman, CH Wei, Z Lu - Journal of cheminformatics, 2015 - Springer
Chemical compounds and drugs are an important class of entities in biomedical research
with great potential in a wide range of applications, including clinical medicine. Locating …

GNormPlus: an integrative approach for tagging genes, gene families, and protein domains

CH Wei, HY Kao, Z Lu - BioMed research international, 2015 - Wiley Online Library
The automatic recognition of gene names and their associated database identifiers from
biomedical text has been widely studied in recent years, as these tasks play an important …

A neural named entity recognition and multi-type normalization tool for biomedical text mining

D Kim, J Lee, CH So, H Jeon, M Jeong, Y Choi… - IEEE …, 2019 - ieeexplore.ieee.org
The amount of biomedical literature is vast and growing quickly, and accurate text mining
techniques could help researchers to efficiently extract useful information from the literature …