AGCN: Attention-based graph convolutional networks for drug-drug interaction extraction

Chanhee Park, Jinuk Park, Sanghyun Park

Research output: Contribution to journalArticlepeer-review

35 Citations (Scopus)


Extracting drug-drug interaction (DDI) relations is one of the most typical tasks in the field of biomedical relation extraction. Automatic DDI extraction from the biomedical corpus is central to the mining of knowledge hidden in the biomedical literature. Existing approaches for DDI extraction primarily focus on either the contextual or the structural information of the sentence, despite their complementary role. Also, previous studies do not even exploit the entire knowledge of the input sentence, which could lead to a loss of crucial clues. In this paper, we propose an Attention-based Graph Convolutional Networks (AGCN) to address these issues. In contrast to the existing DDI extraction methods, the AGCN is designed to leverage contextual and structural knowledge together, where GCN is employed in combination with encoders based on recurrent networks. Additionally, we apply a novel attention-based pruning strategy to optimally use syntactic information while ignoring irrelevant information, in contrast to previous rule-based pruning methods. Therefore, AGCN can take advantage of the context and structure of the input sentence as efficiently as possible. We evaluate our model using a dominant DDI extraction corpus. The experimental results demonstrate the effectiveness of our model, which outperforms existing approaches.

Original languageEnglish
Article number113538
JournalExpert Systems with Applications
Publication statusPublished - 2020 Nov 30

Bibliographical note

Funding Information:
This research was supported by the Next Generation Information Computing Development Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Science, ICT (NRF 2015M3C4A7065522).

Publisher Copyright:
© 2020 Elsevier Ltd

All Science Journal Classification (ASJC) codes

  • Engineering(all)
  • Computer Science Applications
  • Artificial Intelligence


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