HunFlair2 in a cross-corpus evaluation of biomedical named entity recognition and normalization tools

M Sänger, S Garda, XD Wang, L Weber-Genzel… - …, 2024 - academic.oup.com
Motivation With the exponential growth of the life sciences literature, biomedical text mining
(BTM) has become an essential technology for accelerating the extraction of insights from …

Chemical–protein relation extraction with ensembles of carefully tuned pretrained language models

L Weber, M Sänger, S Garda, F Barth, C Alt, U Leser - Database, 2022 - academic.oup.com
The identification of chemical–protein interactions described in the literature is an important
task with applications in drug design, precision medicine and biotechnology. Manual …

WETM: A word embedding-based topic model with modified collapsed Gibbs sampling for short text

J Rashid, J Kim, A Hussain, U Naseem - Pattern Recognition Letters, 2023 - Elsevier
Short texts are a common source of knowledge, and the extraction of such valuable
information is beneficial for several purposes. Traditional topic models are incapable of …

Large language model based framework for automated extraction of genetic interactions from unstructured data

JK Gill, M Chetty, S Lim, J Hallinan - Plos one, 2024 - journals.plos.org
Extracting biological interactions from published literature helps us understand complex
biological systems, accelerate research, and support decision-making in drug or treatment …

HunFlair2 in a cross-corpus evaluation of named entity recognition and normalization tools

M Sänger, S Garda, XD Wang, L Weber-Genzel… - arXiv preprint arXiv …, 2024 - arxiv.org
With the exponential growth of the life science literature, biomedical text mining (BTM) has
become an essential technology for accelerating the extraction of insights from publications …

Extraction of gene-disease association from literature using BioBERT

C Deng, J Zou, J Deng, M Bai - The 2nd international conference on …, 2021 - dl.acm.org
With the rapid growth of biomedical literatures, there are a large amount of bio-text data to
be exploited. A wealth of knowledge concerning diseases associated with genes is present …

[HTML][HTML] YTLR: Extracting yeast transcription factor-gene associations from the literature using automated literature readers

TH Yang, CY Wang, HC Tsai, YC Yang… - Computational and …, 2022 - Elsevier
Cells adapt to environmental stresses mainly via transcription reprogramming. Correct
transcription control is mediated by the interactions between transcription factors (TF) and …

Ontology-aware biomedical relation extraction

A Aghaebrahimian, M Anisimova, M Gil - International Conference on Text …, 2022 - Springer
Automatically extracting relationships from biomedical texts among multiple sorts of entities
is an essential task in biomedical natural language processing with numerous applications …

Hierarchical network analysis of co-occurring bioentities in literature

H Yang, N Lee, B Park, J Park, J Lee, HS Jang… - Scientific Reports, 2022 - nature.com
Biomedical databases grow by more than a thousand new publications every day. The large
volume of biomedical literature that is being published at an unprecedented rate hinders the …

[PDF][PDF] Open Information Extraction Methodology for a New Curated Biomedical Literature Dataset

NAA Hassan, RAAAA Seoud… - International Journal of …, 2023 - pdfs.semanticscholar.org
The research articles contain a wealth of information about the interactions between
biomedical entities. However, manual relation extraction processing from the literature by …