A survey on deep learning for named entity recognition

J Li, A Sun, J Han, C Li - IEEE transactions on knowledge and …, 2020 - ieeexplore.ieee.org
Named entity recognition (NER) is the task to identify mentions of rigid designators from text
belonging to predefined semantic types such as person, location, organization etc. NER …

[HTML][HTML] 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 …

BioBERT: a pre-trained biomedical language representation model for biomedical text mining

J Lee, W Yoon, S Kim, D Kim, S Kim, CH So… - …, 2020 - academic.oup.com
Motivation Biomedical text mining is becoming increasingly important as the number of
biomedical documents rapidly grows. With the progress in natural language processing …

ScispaCy: fast and robust models for biomedical natural language processing

M Neumann, D King, I Beltagy, W Ammar - arXiv preprint arXiv …, 2019 - arxiv.org
Despite recent advances in natural language processing, many statistical models for
processing text perform extremely poorly under domain shift. Processing biomedical and …

Adaptive methods for nonconvex optimization

M Zaheer, S Reddi, D Sachan… - Advances in neural …, 2018 - proceedings.neurips.cc
Adaptive gradient methods that rely on scaling gradients down by the square root of
exponential moving averages of past squared gradients, such RMSProp, Adam, Adadelta …

A comparative study of pretrained language models for long clinical text

Y Li, RM Wehbe, FS Ahmad, H Wang… - Journal of the American …, 2023 - academic.oup.com
Objective Clinical knowledge-enriched transformer models (eg, ClinicalBERT) have state-of-
the-art results on clinical natural language processing (NLP) tasks. One of the core …

[HTML][HTML] Named entity recognition and relation detection for biomedical information extraction

N Perera, M Dehmer, F Emmert-Streib - Frontiers in cell and …, 2020 - frontiersin.org
The number of scientific publications in the literature is steadily growing, containing our
knowledge in the biomedical, health, and clinical sciences. Since there is currently no …

BERN2: an advanced neural biomedical named entity recognition and normalization tool

M Sung, M Jeong, Y Choi, D Kim, J Lee, J Kang - Bioinformatics, 2022 - academic.oup.com
In biomedical natural language processing, named entity recognition (NER) and named
entity normalization (NEN) are key tasks that enable the automatic extraction of biomedical …

Enriching contextualized language model from knowledge graph for biomedical information extraction

H Fei, Y Ren, Y Zhang, D Ji, X Liang - Briefings in bioinformatics, 2021 - academic.oup.com
Biomedical information extraction (BioIE) is an important task. The aim is to analyze
biomedical texts and extract structured information such as named entities and semantic …

COVID-19 literature knowledge graph construction and drug repurposing report generation

Q Wang, M Li, X Wang, N Parulian, G Han, J Ma… - arXiv preprint arXiv …, 2020 - arxiv.org
To combat COVID-19, both clinicians and scientists need to digest vast amounts of relevant
biomedical knowledge in scientific literature to understand the disease mechanism and …