Drug drug interaction extraction from the literature using a recursive neural network

Sangrak Lim, Kyubum Lee, Jaewoo Kang

Research output: Contribution to journalArticlepeer-review

63 Citations (Scopus)


Detecting drug-drug interactions (DDI) is important because information on DDIs can help prevent adverse effects from drug combinations. Since there are many new DDI-related papers published in the biomedical domain, manually extracting DDI information from the literature is a laborious task. However, text mining can be used to find DDIs in the biomedical literature. Among the recently developed neural networks, we use a Recursive Neural Network to improve the performance of DDI extraction. Our recursive neural network model uses a position feature, a subtree containment feature, and an ensemble method to improve the performance of DDI extraction. Compared with the state-of-the-art models, the DDI detection and type classifiers of our model performed 4.4% and 2.8% better, respectively, on the DDIExtraction Challenge’13 test data. We also validated our model on the PK DDI corpus that consists of two types of DDIs data: in vivo DDI and in vitro DDI. Compared with the existing model, our detection classifier performed 2.3% and 6.7% better on in vivo and in vitro data respectively. The results of our validation demonstrate that our model can automatically extract DDIs better than existing models.

Original languageEnglish
Article numbere0190926
JournalPloS one
Issue number1
Publication statusPublished - 2018 Jan

Bibliographical note

Funding Information:
Funding: This research was supported by the National Research Foundation of Korea (http:// www.nrf.re.kr/) grants (NRF-2016M3A9A7916996, 2015M3A9D7031070, 2014M3C9A3063543 to JK). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Publisher Copyright:
Copyright: © 2018 Lim et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

ASJC Scopus subject areas

  • General


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