Skip to main content

Drug-Drug Interaction Extraction via Recurrent Neural Network with Multiple Attention Layers

  • Conference paper
  • First Online:
Advanced Data Mining and Applications (ADMA 2017)

Part of the book series: Lecture Notes in Computer Science ((LNAI,volume 10604))

Included in the following conference series:

Abstract

Drug-drug interaction (DDI) is a vital information when physicians and pharmacists intend to co-administer two or more drugs. Thus, several DDI databases are constructed to avoid mistakenly drug combined use. In recent years, automatically extracting DDIs from biomedical text has drawn researchers’ attention. However, the existing work utilize either complex feature engineering or NLP tools, both of which are insufficient for sentence comprehension. Inspired by the deep learning approaches in natural language processing, we propose a recurrent neural network model with multiple attention layers for DDI classification. We evaluate our model on 2013 SemEval DDIExtraction dataset. The experiments show that our model classifies most of the drug pairs into correct DDI categories, which outperforms the existing NLP or deep learning methods.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Notes

  1. 1.

    https://www.nlm.nih.gov/bsd/medline_lang_distr.html, accessed May 22nd, 2017.

  2. 2.

    https://www.cs.york.ac.uk/semeval-2013/task9.html.

  3. 3.

    http://scikit-learn.org/stable/modules/generated/sklearn.manifold.TSNE.html.

References

  1. Abadi, M., Agarwal, A., Barham, P., Brevdo, E., Chen, Z., Citro, C., Corrado, G.S., Davis, A., Dean, J., Devin, M., et al.: Tensorflow: large-scale machine learning on heterogeneous distributed systems. arXiv preprint arXiv:1603.04467 (2016)

  2. Böttiger, Y., Laine, K., Andersson, M.L., Korhonen, T., Molin, B., Ovesjö, M.L., Tirkkonen, T., Rane, A., Gustafsson, L.L., Eiermann, B.: Sfinx: a drug-drug interaction database designed for clinical decision support systems. Eur. J. Clin. Pharmacol. 65(6), 627–633 (2009)

    Article  Google Scholar 

  3. Chowdhury, M.F.M., Lavelli, A.: Exploiting the scope of negations and heterogeneous features for relation extraction: a case study for drug-drug interaction extraction. In: HLT-NAACL, pp. 765–771 (2013)

    Google Scholar 

  4. Chowdhury, M.F.M., Lavelli, A.: FBK-irst: a multi-phase kernel based approach for drug-drug interaction detection and classification that exploits linguistic information. Atlanta, Georgia, USA 351, 53 (2013)

    Google Scholar 

  5. Der Maaten, L.V., Hinton, G.E.: Visualizing data using t-SNE. J. Mach. Learn. Res. 9, 2579–2605 (2008)

    MATH  Google Scholar 

  6. Herrero-Zazo, M., Segura-Bedmar, I., Martinez, P., Declerck, T.: The DDI corpus: an annotated corpus with pharmacological substances and drug-drug interactions. J. Biomed. Inform. 46(5), 914 (2013)

    Article  Google Scholar 

  7. Kingma, D., Ba, J.: Adam: a method for stochastic optimization. arXiv preprint arXiv:1412.6980 (2014)

  8. Lazarou, J., Pomeranz, B.H., Corey, P.N.: Incidence of adverse drug reactions in hospitalized patients: a meta-analysis of prospective studies. JAMA 279(15), 1200–1205 (1998)

    Article  Google Scholar 

  9. Lin, Y., Shen, S., Liu, Z., Luan, H., Sun, M.: Neural relation extraction with selective attention over instances. In: Meeting of the Association for Computational Linguistics, pp. 2124–2133 (2016)

    Google Scholar 

  10. Liu, S., Tang, B., Chen, Q., Wang, X.: Drug-drug interaction extraction via convolutional neural networks. Comput. Math. Methods Med. 2016, 1–8 (2016)

    Google Scholar 

  11. Liu, S., Chen, K., Chen, Q., Tang, B.: Dependency-based convolutional neural network for drug-drug interaction extraction. In: IEEE International Conference on Bioinformatics and Biomedicine, pp. 1074–1080 (2016)

    Google Scholar 

  12. Melnikov, M.P., Vorobkalov, P.N.: Retrieval of drug-drug interactions information from biomedical texts: use of TF-IDF for classification. In: Kravets, A., Shcherbakov, M., Kultsova, M., Iijima, T. (eds.) JCKBSE 2014. CCIS, vol. 466, pp. 593–602. Springer, Cham (2014). doi:10.1007/978-3-319-11854-3_52

    Google Scholar 

  13. Pedregosa, F., Varoquaux, G., Gramfort, A., Michel, V., Thirion, B., Grisel, O., Blondel, M., Prettenhofer, P., Weiss, R., Dubourg, V., Vanderplas, J., Passos, A., Cournapeau, D., Brucher, M., Perrot, M., Duchesnay, E.: Scikit-learn: machine learning in Python. J. Mach. Learn. Res. 12, 2825–2830 (2011)

    MathSciNet  MATH  Google Scholar 

  14. Pennington, J., Socher, R., Manning, C.: Glove: global vectors for word representation. In: Conference on Empirical Methods in Natural Language Processing, pp. 1532–1543 (2014)

    Google Scholar 

  15. Sahu, S.K., Anand, A.: Drug-drug interaction extraction from biomedical text using long short term memory network. arXiv preprint arXiv:1701.08303 (2017)

  16. Sklar, S.J., Wagner, J.C.: Enhanced theophylline clearance secondary to phenytoin therapy. Ann. Pharmacother. 19(1), 34 (1985)

    Google Scholar 

  17. Takarabe, M., Shigemizu, D., Kotera, M., Goto, S., Kanehisa, M.: Network-based analysis and characterization of adverse drug-drug interactions. J. Chem. Inf. Model. 51(11), 2977–2985 (2011)

    Article  Google Scholar 

  18. Tari, L., Anwar, S., Liang, S., Cai, J., Baral, C.: Discovering drug-drug interactions: a text-mining and reasoning approach based on properties of drug metabolism. Bioinformatics 26(18), 547–53 (2010)

    Article  Google Scholar 

  19. Thomas, P., Neves, M., Rocktschel, T., Leser, U.: WBI-DDI: drug-drug interaction extraction using majority voting. In: DDI Challenge at Semeval (2013)

    Google Scholar 

  20. Zhao, Z., Yang, Z., Luo, L., Lin, H., Wang, J.: Drug drug interaction extraction from biomedical literature using syntax convolutional neural network. Bioinformatics 32(22), 3444–3453 (2016)

    Google Scholar 

  21. Zhou, P., Shi, W., Tian, J., Qi, Z., Li, B., Hao, H., Xu, B.: Attention-based bidirectional long short-term memory networks for relation classification. In: Meeting of the Association for Computational Linguistics, pp. 207–212 (2016)

    Google Scholar 

Download references

Acknowledgments

This work is supported by the NSFC under Grant 61303190.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Zibo Yi .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2017 Springer International Publishing AG

About this paper

Cite this paper

Yi, Z. et al. (2017). Drug-Drug Interaction Extraction via Recurrent Neural Network with Multiple Attention Layers. In: Cong, G., Peng, WC., Zhang, W., Li, C., Sun, A. (eds) Advanced Data Mining and Applications. ADMA 2017. Lecture Notes in Computer Science(), vol 10604. Springer, Cham. https://doi.org/10.1007/978-3-319-69179-4_39

Download citation

  • DOI: https://doi.org/10.1007/978-3-319-69179-4_39

  • Published:

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-69178-7

  • Online ISBN: 978-3-319-69179-4

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics