Biomedical named entity recognition using BERT in the machine reading comprehension framework

نویسندگان

چکیده

Isothermal surfaces within the device • We achieve named entity recognition in machine reading comprehension framework. explore effect of different model components on recognition. use Query to introduce external knowledge and its impact performance. Our method obtains state-of-the-art performance six biomedical datasets. Recognition entities from literature is a challenging research focus, which foundation for extracting large amount existing unstructured texts into structured formats. Using sequence labeling framework implement (BioNER) currently conventional method. This method, however, often cannot take full advantage semantic information dataset, not always satisfactory. In this work, instead treating BioNER task as problem, we formulate it (MRC) problem. formulation can more prior utilizing well-designed queries, no longer need decoding processes such conditional random fields (CRF). conduct experiments datasets, experimental results demonstrate effectiveness our achieves (SOTA) BC4CHEMD, BC5CDR-Chem, BC5CDR-Disease, NCBI-Disease, BC2GM JNLPBA achieving F1-scores 92.92%, 94.19%, 87.83%, 90.04%, 85.48% 78.93%, respectively.

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ژورنال

عنوان ژورنال: Journal of Biomedical Informatics

سال: 2021

ISSN: ['1532-0480', '1532-0464']

DOI: https://doi.org/10.1016/j.jbi.2021.103799