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Pre-trained language models in biomedical domain: A systematic survey
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 …
language processing tasks. This also benefits the biomedical domain: researchers from …
BioRED: a rich biomedical relation extraction dataset
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 …
text mining applications in both research and real-world settings. However, most existing …
Named entity recognition and relation detection for biomedical information extraction
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 …
knowledge in the biomedical, health, and clinical sciences. Since there is currently no …
Information retrieval and text mining technologies for chemistry
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 …
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
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 …
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
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 …
success of the Critical Assessment of protein Structure Prediction (CASP) in bioinformatics …
Broad-coverage biomedical relation extraction with SemRep
Background In the era of information overload, natural language processing (NLP)
techniques are increasingly needed to support advanced biomedical information …
techniques are increasingly needed to support advanced biomedical information …
GNormPlus: an integrative approach for tagging genes, gene families, and protein domains
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 …
biomedical text has been widely studied in recent years, as these tasks play an important …
LINNAEUS: a species name identification system for biomedical literature
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 …
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
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 …
text-mining tools increasingly clear. The identification of named biological entities in text is a …