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SciNER: Extracting Named Entities from Scientific Literature
The automated extraction of claims from scientific papers via computer is difficult due to the ambiguity and variability inherent in natural language. Even apparently simple tasks, such as isolating reported values for physical quantities (e.g., “the melting point of X is Y”) can be complicated by s...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7302801/ http://dx.doi.org/10.1007/978-3-030-50417-5_23 |
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author | Hong, Zhi Tchoua, Roselyne Chard, Kyle Foster, Ian |
author_facet | Hong, Zhi Tchoua, Roselyne Chard, Kyle Foster, Ian |
author_sort | Hong, Zhi |
collection | PubMed |
description | The automated extraction of claims from scientific papers via computer is difficult due to the ambiguity and variability inherent in natural language. Even apparently simple tasks, such as isolating reported values for physical quantities (e.g., “the melting point of X is Y”) can be complicated by such factors as domain-specific conventions about how named entities (the X in the example) are referenced. Although there are domain-specific toolkits that can handle such complications in certain areas, a generalizable, adaptable model for scientific texts is still lacking. As a first step towards automating this process, we present a generalizable neural network model, SciNER, for recognizing scientific entities in free text. Based on bidirectional LSTM networks, our model combines word embeddings, subword embeddings, and external knowledge (from DBpedia) to boost its accuracy. Experiments show that our model outperforms a leading domain-specific extraction toolkit by up to 50%, as measured by F1 score, while also being easily adapted to new domains. |
format | Online Article Text |
id | pubmed-7302801 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
record_format | MEDLINE/PubMed |
spelling | pubmed-73028012020-06-19 SciNER: Extracting Named Entities from Scientific Literature Hong, Zhi Tchoua, Roselyne Chard, Kyle Foster, Ian Computational Science – ICCS 2020 Article The automated extraction of claims from scientific papers via computer is difficult due to the ambiguity and variability inherent in natural language. Even apparently simple tasks, such as isolating reported values for physical quantities (e.g., “the melting point of X is Y”) can be complicated by such factors as domain-specific conventions about how named entities (the X in the example) are referenced. Although there are domain-specific toolkits that can handle such complications in certain areas, a generalizable, adaptable model for scientific texts is still lacking. As a first step towards automating this process, we present a generalizable neural network model, SciNER, for recognizing scientific entities in free text. Based on bidirectional LSTM networks, our model combines word embeddings, subword embeddings, and external knowledge (from DBpedia) to boost its accuracy. Experiments show that our model outperforms a leading domain-specific extraction toolkit by up to 50%, as measured by F1 score, while also being easily adapted to new domains. 2020-06-15 /pmc/articles/PMC7302801/ http://dx.doi.org/10.1007/978-3-030-50417-5_23 Text en © Springer Nature Switzerland AG 2020 This article is made available via the PMC Open Access Subset for unrestricted research re-use and secondary analysis in any form or by any means with acknowledgement of the original source. These permissions are granted for the duration of the World Health Organization (WHO) declaration of COVID-19 as a global pandemic. |
spellingShingle | Article Hong, Zhi Tchoua, Roselyne Chard, Kyle Foster, Ian SciNER: Extracting Named Entities from Scientific Literature |
title | SciNER: Extracting Named Entities from Scientific Literature |
title_full | SciNER: Extracting Named Entities from Scientific Literature |
title_fullStr | SciNER: Extracting Named Entities from Scientific Literature |
title_full_unstemmed | SciNER: Extracting Named Entities from Scientific Literature |
title_short | SciNER: Extracting Named Entities from Scientific Literature |
title_sort | sciner: extracting named entities from scientific literature |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7302801/ http://dx.doi.org/10.1007/978-3-030-50417-5_23 |
work_keys_str_mv | AT hongzhi scinerextractingnamedentitiesfromscientificliterature AT tchouaroselyne scinerextractingnamedentitiesfromscientificliterature AT chardkyle scinerextractingnamedentitiesfromscientificliterature AT fosterian scinerextractingnamedentitiesfromscientificliterature |