Deep neural model with enhanced embeddings for pharmaceutical and chemical entities recognition in Spanish clinical text

Renzo Rivera, Paloma Martínez


Abstract
In this work, we introduce a Deep Learning architecture for pharmaceutical and chemical Named Entity Recognition in Spanish clinical cases texts. We propose a hybrid model approach based on two Bidirectional Long Short-Term Memory (Bi-LSTM) network and Conditional Random Field (CRF) network using character, word, concept and sense embeddings to deal with the extraction of semantic, syntactic and morphological features. The approach was evaluated on the PharmaCoNER Corpus obtaining an F-measure of 85.24% for subtask 1 and 49.36% for subtask2. These results prove that deep learning methods with specific domain embedding representations can outperform the state-of-the-art approaches.
Anthology ID:
D19-5707
Volume:
Proceedings of the 5th Workshop on BioNLP Open Shared Tasks
Month:
November
Year:
2019
Address:
Hong Kong, China
Editors:
Kim Jin-Dong, Nédellec Claire, Bossy Robert, Deléger Louise
Venue:
BioNLP
SIG:
Publisher:
Association for Computational Linguistics
Note:
Pages:
38–46
Language:
URL:
https://aclanthology.org/D19-5707
DOI:
10.18653/v1/D19-5707
Bibkey:
Cite (ACL):
Renzo Rivera and Paloma Martínez. 2019. Deep neural model with enhanced embeddings for pharmaceutical and chemical entities recognition in Spanish clinical text. In Proceedings of the 5th Workshop on BioNLP Open Shared Tasks, pages 38–46, Hong Kong, China. Association for Computational Linguistics.
Cite (Informal):
Deep neural model with enhanced embeddings for pharmaceutical and chemical entities recognition in Spanish clinical text (Rivera & Martínez, BioNLP 2019)
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PDF:
https://aclanthology.org/D19-5707.pdf