Pre-trained language models in biomedical domain: A systematic survey

B Wang, Q **e, J Pei, Z Chen, P Tiwari, Z Li… - ACM Computing …, 2023‏ - dl.acm.org
Pre-trained language models (PLMs) have been the de facto paradigm for most natural
language processing tasks. This also benefits the biomedical domain: researchers from …

BioRED: a rich biomedical relation extraction dataset

L Luo, PT Lai, CH Wei, CN Arighi… - Briefings in …, 2022‏ - academic.oup.com
Automated relation extraction (RE) from biomedical literature is critical for many downstream
text mining applications in both research and real-world settings. However, most existing …

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 …

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 …

PubMed and beyond: a survey of web tools for searching biomedical literature

Z Lu - Database, 2011‏ - academic.oup.com
The past decade has witnessed the modern advances of high-throughput technology and
rapid growth of research capacity in producing large-scale biological data, both of which …

Community challenges in biomedical text mining over 10 years: success, failure and the future

CC Huang, Z Lu - Briefings in bioinformatics, 2016‏ - academic.oup.com
One effective way to improve the state of the art is through competitions. Following the
success of the Critical Assessment of protein Structure Prediction (CASP) in bioinformatics …

Broad-coverage biomedical relation extraction with SemRep

H Kilicoglu, G Rosemblat, M Fiszman, D Shin - BMC bioinformatics, 2020‏ - Springer
Background In the era of information overload, natural language processing (NLP)
techniques are increasingly needed to support advanced biomedical information …

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 …

LINNAEUS: a species name identification system for biomedical literature

M Gerner, G Nenadic, CM Bergman - BMC bioinformatics, 2010‏ - Springer
Background The task of recognizing and identifying species names in biomedical literature
has recently been regarded as critical for a number of applications in text and data mining …

The SPECIES and ORGANISMS resources for fast and accurate identification of taxonomic names in text

E Pafilis, SP Frankild, L Fanini, S Faulwetter… - PloS one, 2013‏ - journals.plos.org
The exponential growth of the biomedical literature is making the need for efficient, accurate
text-mining tools increasingly clear. The identification of named biological entities in text is a …