Drug-drug interaction extraction from biomedical texts using long short-term memory network

Journal of Biomedical Informatics
Sunil Kumar Sahu, Ashish Anand

Abstract

The simultaneous administration of multiple drugs increases the probability of interaction among them, as one drug may affect the activities of others. This interaction among drugs may have a positive or negative impact on the therapeutic outcomes. Thus, identification of unknown drug-drug interactions (DDIs) is of significant concern for improving the safety and efficacy of drug consumption. Although multiple DDI resources exist, it is becoming infeasible to maintain these up-to-date manually with the number of biomedical texts growing at a fast pace. Most existing methods model DDI extraction as a classification problem and rely mainly on handcrafted features, and certain features further depend on domain-specific tools. Recently, neural network models using latent features have been demonstrated to yield similar or superior performance compared to existing models. In this study, we present three long short-term memory (LSTM) network models, namely B-LSTM, AB-LSTM, and Joint AB-LSTM. All three models use word and position embedding as latent features; thus, they do not rely on explicit feature engineering. Furthermore, the use of a bidirectional LSTM (Bi-LSTM) network allows for extraction of implicit features from an entire ...Continue Reading

Citations

Sep 20, 2019·BMC Bioinformatics·Tongxuan ZhangYijia Zhang
Mar 2, 2019·BMC Medical Informatics and Decision Making·Merijn BeeksmaStef Groenewoud
Apr 30, 2020·Briefings in Bioinformatics·Chun Yen Lee, Yi-Ping Phoebe Chen
Sep 25, 2019·Journal of the American Medical Informatics Association : JAMIA·Xue ShiHua Xu
Sep 18, 2020·BMC Bioinformatics·Jian WangYiJia Zhang
Sep 29, 2020·Frontiers in Cell and Developmental Biology·Nadeesha PereraFrank Emmert-Streib
May 28, 2019·Database : the Journal of Biological Databases and Curation·Yijia ZhangYuanyuan Sun
Jan 30, 2020·BMC Bioinformatics·Jin-Woo ChungJong C Park
Dec 18, 2020·Computer Methods and Programs in Biomedicine·Sara SantisoArantza Casillas
Feb 12, 2021·Journal of Biomedical Informatics·Mohsen Fatehifar, Hossein Karshenas
Mar 19, 2021·Frontiers in Artificial Intelligence·Frank Emmert-StreibMatthias Dehmer
Apr 27, 2020·Journal of Biomedical Informatics·Hong WuJun Liao
May 27, 2020·Journal of Biomedical Informatics·Yu ZhuXueyang Qin
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Aug 24, 2021·Computational and Mathematical Methods in Medicine·Sajid HussainMir Yasir Umair
Oct 6, 2021·BMC Bioinformatics·Rogia KpanouJacques Corbeil
Nov 7, 2020·Journal of Biomedical Informatics·Chen ZhanJiuyong Li

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