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bioRxiv · 10.1101/2021.03.18.436005

RENET2: High-Performance Full-text Gene-Disease Relation Extraction with Iterative Training Data Expansion

Su, J.·Wu, Y.·Ting, H.-F.·Lam, T.-W.·Luo, R.
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Abstract

BackgroundRelation extraction is a fundamental task for extracting gene-disease associations from biomedical text. Existing tools have limited capacity, as they can extract gene-disease associations only from single sentences or abstract texts. ResultsIn this work, we propose RENET2, a deep learning-based relation extraction method, which implements section filtering and ambiguous relations modeling to extract gene-disease associations from full-text articles. We designed a novel iterative training data expansion strategy to build an annotated full-text dataset to resolve the scarcity of labels on full-text articles. In our experiments, RENET2 achieved an F1-score of 72.13% for extracting gene-disease associations from an annotated full-text dataset, which was 27.22%, 30.30% and 29.24% higher than the best existing tools BeFree, DTMiner and BioBERT, respectively. We applied RENET2 to (1) ~1.89M full-text articles from PMC and found ~3.72M gene-disease associations; and (2) the LitCovid articles set and ranked the top 15 proteins associated with COVID-19, supported by recent articles. ConclusionRENET2 is an efficient and accurate method for full-text gene-disease association extraction. The source-code, manually curated abstract/full-text training data, and results of RENET2 are available at https://github.com/sujunhao/RENET2.

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Su, J., Wu, Y., Ting, H.-F., Lam, T.-W., Luo, R.. 2021-03-19. RENET2: High-Performance Full-text Gene-Disease Relation Extraction with Iterative Training Data Expansion. https://doi.org/10.1101/2021.03.18.436005

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