VSP at PharmaCoNER 2019: Recognition of Pharmacological Substances, Compounds and Proteins with Recurrent Neural Networks in Spanish Clinical Cases

Víctor Suárez-Paniagua

Abstract
This paper presents the participation of the VSP team for the PharmaCoNER Tracks from the BioNLP Open Shared Task 2019. The system consists of a neural model for the Named Entity Recognition of drugs, medications and chemical entities in Spanish and the use of the Spanish Edition of SNOMED CT term search engine for the concept normalization of the recognized mentions. The neural network is implemented with two bidirectional Recurrent Neural Networks with LSTM cells that creates a feature vector for each word of the sentences in order to classify the entities. The first layer uses the characters of each word and the resulting vector is aggregated to the second layer together with its word embedding in order to create the feature vector of the word. Besides, a Conditional Random Field layer classifies the vector representation of each word in one of the mention types. The system obtains a performance of 76.29%, and 60.34% in F1 for the classification of the Named Entity Recognition task and the Concept indexing task, respectively. This method presents good results with a basic approach without using pretrained word embeddings or any hand-crafted features.
Anthology ID:
D19-5703
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:
16–20
Language:
URL:
https://preview.aclanthology.org/build-pipeline-with-new-library/D19-5703/
DOI:
10.18653/v1/D19-5703
Bibkey:
Cite (ACL):
Víctor Suárez-Paniagua. 2019. VSP at PharmaCoNER 2019: Recognition of Pharmacological Substances, Compounds and Proteins with Recurrent Neural Networks in Spanish Clinical Cases. In Proceedings of the 5th Workshop on BioNLP Open Shared Tasks, pages 16–20, Hong Kong, China. Association for Computational Linguistics.
Cite (Informal):
VSP at PharmaCoNER 2019: Recognition of Pharmacological Substances, Compounds and Proteins with Recurrent Neural Networks in Spanish Clinical Cases (Suárez-Paniagua, BioNLP 2019)
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PDF:
https://preview.aclanthology.org/build-pipeline-with-new-library/D19-5703.pdf
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