Information retrieval and text mining technologies for chemistry

M Krallinger, O Rabal, A Lourenco, J Oyarzabal… - Chemical …, 2017 - ACS Publications
Efficient access to chemical information contained in scientific literature, patents, technical
reports, or the web is a pressing need shared by researchers and patent attorneys from …

Deep learning with word embeddings improves biomedical named entity recognition

M Habibi, L Weber, M Neves, DL Wiegandt… - …, 2017 - academic.oup.com
Motivation Text mining has become an important tool for biomedical research. The most
fundamental text-mining task is the recognition of biomedical named entities (NER), such as …

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 …

HunFlair: an easy-to-use tool for state-of-the-art biomedical named entity recognition

L Weber, M Sänger, J Münchmeyer, M Habibi… - …, 2021 - academic.oup.com
Named entity recognition (NER) is an important step in biomedical information extraction
pipelines. Tools for NER should be easy to use, cover multiple entity types, be highly …

Transfer learning for biomedical named entity recognition with neural networks

JM Giorgi, GD Bader - Bioinformatics, 2018 - academic.oup.com
Motivation The explosive increase of biomedical literature has made information extraction
an increasingly important tool for biomedical research. A fundamental task is the recognition …

Text mining patents for biomedical knowledge

R Rodriguez-Esteban, M Bundschus - Drug discovery today, 2016 - Elsevier
Highlights•Text mining techniques can unlock the information stored in biomedical
patents.•Most research in mining such patents is limited to identifying terms.•Future …

AIONER: all-in-one scheme-based biomedical named entity recognition using deep learning

L Luo, CH Wei, PT Lai, R Leaman, Q Chen… - Bioinformatics, 2023 - academic.oup.com
Motivation Biomedical named entity recognition (BioNER) seeks to automatically recognize
biomedical entities in natural language text, serving as a necessary foundation for …

Chemu 2020: Natural language processing methods are effective for information extraction from chemical patents

J He, DQ Nguyen, SA Akhondi… - Frontiers in Research …, 2021 - frontiersin.org
Chemical patents represent a valuable source of information about new chemical
compounds, which is critical to the drug discovery process. Automated information extraction …

HUNER: improving biomedical NER with pretraining

L Weber, J Münchmeyer, T Rocktäschel… - …, 2020 - academic.oup.com
Motivation Several recent studies showed that the application of deep neural networks
advanced the state-of-the-art in named entity recognition (NER), including biomedical NER …

Overview of bioasq 2021: The ninth bioasq challenge on large-scale biomedical semantic indexing and question answering

A Nentidis, G Katsimpras, E Vandorou… - Experimental IR Meets …, 2021 - Springer
Advancing the state-of-the-art in large-scale biomedical semantic indexing and question
answering is the main focus of the BioASQ challenge. BioASQ organizes respective tasks …