Improving Chemical Named Entity Recognition in Patents with Contextualized Word Embeddings

Zenan Zhai, Dat Quoc Nguyen, Saber Akhondi, Camilo Thorne, Christian Druckenbrodt, Trevor Cohn, Michelle Gregory, Karin Verspoor

Abstract
Chemical patents are an important resource for chemical information. However, few chemical Named Entity Recognition (NER) systems have been evaluated on patent documents, due in part to their structural and linguistic complexity. In this paper, we explore the NER performance of a BiLSTM-CRF model utilising pre-trained word embeddings, character-level word representations and contextualized ELMo word representations for chemical patents. We compare word embeddings pre-trained on biomedical and chemical patent corpora. The effect of tokenizers optimized for the chemical domain on NER performance in chemical patents is also explored. The results on two patent corpora show that contextualized word representations generated from ELMo substantially improve chemical NER performance w.r.t. the current state-of-the-art. We also show that domain-specific resources such as word embeddings trained on chemical patents and chemical-specific tokenizers, have a positive impact on NER performance.
Anthology ID:
W19-5035
Volume:
Proceedings of the 18th BioNLP Workshop and Shared Task
Month:
August
Year:
2019
Address:
Florence, Italy
Editors:
Dina Demner-Fushman, Kevin Bretonnel Cohen, Sophia Ananiadou, Junichi Tsujii
Venue:
BioNLP
SIG:
SIGBIOMED
Publisher:
Association for Computational Linguistics
Note:
Pages:
328–338
Language:
URL:
https://aclanthology.org/W19-5035
DOI:
10.18653/v1/W19-5035
Bibkey:
Cite (ACL):
Zenan Zhai, Dat Quoc Nguyen, Saber Akhondi, Camilo Thorne, Christian Druckenbrodt, Trevor Cohn, Michelle Gregory, and Karin Verspoor. 2019. Improving Chemical Named Entity Recognition in Patents with Contextualized Word Embeddings. In Proceedings of the 18th BioNLP Workshop and Shared Task, pages 328–338, Florence, Italy. Association for Computational Linguistics.
Cite (Informal):
Improving Chemical Named Entity Recognition in Patents with Contextualized Word Embeddings (Zhai et al., BioNLP 2019)
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PDF:
https://preview.aclanthology.org/add_acl24_videos/W19-5035.pdf
Code
 zenanz/ChemPatentEmbeddings
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