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A LSTM-Based Method with Attention Mechanism for Adverse Drug Reaction Sentences Detection

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Advanced Intelligent Systems for Sustainable Development (AI2SD’2019) (AI2SD 2019)

Abstract

Adverse drug reactions (ADRs) are among the top causes of morbidity, mortality and substantial healthcare costs and thus should be detected early to reduce consequences on health outcomes. Many conventional machine learning based methods have been presented to automatically detect adverse drug effect (ADE) mentions from biomedical texts. However, owing to the complexity of natural language text in the biomedical domain, some ADE mentions might not be detected. In this paper, we propose a Long Short-Term Memory with Attention (LSTMA) which incorporates attention mechanism and LSTM network to address the problem of automatic detection of ADR assertive text segments from biomedical texts. Experimental results on standard ADE dataset show that the proposed method outperforms significantly the state-of-the art methods for ADR class with an F-scores of 0.89.

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Notes

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References

  1. Ji, Y., Ying, H., Dews, P., Mansour, A., Tran, J., Miller, R.E., Massanari, R.M.: A potential causal association mining algorithm for screening adverse drug reactions in postmarketing surveillance. IEEE Trans. Inf. Technol. Biomed. 15(3), 428–437 (2011). https://doi.org/10.1109/titb.2011.2131669

    Article  Google Scholar 

  2. Harpaz, R., Callahan, A., Tamang, S., Low, Y., Odgers, D., Finlayson, S., Jung, K., LePendu, P., Shah, N.H.: Text mining for adverse drug events: the promise, challenges, and state of the art. Drug Saf. 37(10), 777–790 (2014). https://doi.org/10.1007/s40264-014-0218-z

    Article  Google Scholar 

  3. Segura-Bedmar, I., Martínez, P.: Pharmacovigilance through the development of text mining and natural language processing techniques. J. Biomed. Inf. 58, 288–291 (2015). https://doi.org/10.1016/j.jbi.2015.11.001

    Article  Google Scholar 

  4. Demner-Fushman, D., Shooshan, S.E., Rodriguez, L., Aronson, A.R., Lang, F., Rogers, W., Roberts, K., Tonning, J.: A dataset of 200 structured product labels annotated for adverse drug reactions. Sci. Data 5(180), 001 (2018). https://doi.org/10.1038/sdata.2018.1

    Article  Google Scholar 

  5. Gurulingappa, H., Rajput, A.M., Roberts, A., Fluck, J., Hofmann-Apitius, M., Toldo, L.: Development of a benchmark corpus to support the automatic extraction of drug-related adverse effects from medical case reports. J. Biomed. Inf. 45, 885–892 (2012). https://doi.org/10.1016/j.jbi.2012.04.008

    Article  Google Scholar 

  6. Stanovsky, G., Gruhl, D., Mendes, P.: Recognizing mentions of adverse drug reaction in social media using knowledge-infused recurrent models. In: Proceedings of the 15th Conference of the European Chapter of the Association for Computational Linguistics, vol. 1, Long Papers. Association for Computational Linguistics (2017). https://doi.org/10.18653/v1/e17-1014

  7. El-allaly, E., Sarrouti, M., En-Nahnahi, N., Alaoui, S.O.E.: Adverse drug reaction mentions extraction from drug labels: an experimental study. In: Advanced Intelligent Systems for Sustainable Development (AI2SD 2018), vol. 4: Advanced Intelligent Systems Applied to Health, vol. 914, pp. 216–231. Springer International Publishing (2019). https://doi.org/10.1007/978-3-030-11884-6_21

    Google Scholar 

  8. Gurulingappa, H., Mateen-Rajput, A., Toldo, L.: Extraction of potential adverse drug events from medical case reports. J. Biomed. Semant. 3, 15 (2012). https://doi.org/10.1186/2041-1480-3-15

    Article  Google Scholar 

  9. Sarrouti, M., Ouatik El Alaoui, S.: A passage retrieval method based on probabilistic information retrieval and UMLS concepts in biomedical question answering. J. Biomed. Inf. 68, 96–103 (2017). https://doi.org/10.1016/j.jbi.2017.03.001

    Article  Google Scholar 

  10. Sarrouti, M., Alaoui, S.O.E.: A machine learning-based method for question type classification in biomedical question answering. Meth. Inf. Med. 56(03), 209–216 (2017). https://doi.org/10.3414/ME16-01-0116

    Article  Google Scholar 

  11. Sarrouti, M., Alaoui, S.O.E.: A yes/no answer generator based on sentiment-word scores in biomedical question answering. Int. J. Healthc. Inf. Syst. Inf. (IJHISI) 13(3), 12 (2017). https://doi.org/10.4018/IJHISI.2017070104

    Article  Google Scholar 

  12. Sarrouti, M., Alaoui, S.O.E.: A biomedical question answering system in BioASQ 2017. In: BioNLP 2017. Association for Computational Linguistics (2017). https://doi.org/10.18653/v1/w17-2337

  13. Sarrouti, M., Alaoui S.O.E.: A generic document retrieval framework based on UMLS similarity for biomedical question answering system. In: Intelligent Decision Technologies 2016. Springer International Publishing, pp. 207–216 (2016). https://doi.org/10.1007/978-3-319-39627-9_18

    Chapter  Google Scholar 

  14. Gurulingappa, H., Fluck, J., Hofmann-Apitius, M., Toldo, L.: Identication of adverse drug event assertive sentences in medical case reports. In: 1st International Workshop on Knowledge Discovery and Health Care Management (KD-HCM) Co-located at the European Conference on Machine Learning and Principles and Practice of Knowledge Discovery In Databases (ECML PKDD), pp. 16–27 (2011)

    Google Scholar 

  15. Sarker, A., Gonzalez, G.: Portable automatic text classification for adverse drug reaction detection via multi-corpus training. J. Biomed. Inf. 53, 196–207 (2015). https://doi.org/10.1016/j.jbi.2014.11.002

    Article  Google Scholar 

  16. Rastegar-Mojarad, M., Elayavilli, R.K., Yu, Y., Liu, H.: Detecting signals in noisy data-can ensemble classifiers help identify adverse drug reaction in tweets? In: Proceedings of the Social Media Mining Shared Task Workshop at the Pacific Symposium on Bio-computing (2015)

    Google Scholar 

  17. Zhang, Z., Nie, J.-Y.: An ensemble method for binary classification of adverse drug reactions from social media (2015)

    Google Scholar 

  18. Jonnagaddala, J., Jue, T.R., Dai, H.-J.: Binary classification of twitter posts for adverse drug reactions (2015)

    Google Scholar 

  19. Huynh, T., He, Y., Willis, A., Rüger, S.: Adverse drug reaction classification with deep neural networks. In: Proceedings of COLING 2016: Technical Papers, COLING, pp. 877–887 (2016)

    Google Scholar 

  20. Miranda, D.S.: Automated detection of adverse drug reactions in the biomedical literature using convolutional neural networks and biomedical word embeddings (2018). CoRR abs/1804.09148

    Google Scholar 

  21. Pyysalo, S., Ginter, F., Moen, H., Salakoski, T., Ananiadou, S.: Distributional semantics resources for biomedical text processing. Proc. LBM 2013, 39–44 (2013)

    Google Scholar 

  22. Elman, J.L.: Finding structure in time. Cogn. Sci. 14(2), 179–211 (1990). https://doi.org/10.1207/s15516709cog1402_1

    Article  Google Scholar 

  23. Yang, Z., Yang, D., Dyer, C., He, X., Smola, A., Hovy, E.: Hierarchical attention networks for document classification. In: Proceedings of the 2016 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies. Association for Computational Linguistics (2016). https://doi.org/10.18653/v1/n16-1174

  24. Zheng, W., Lin, H., Luo, L., Zhao, Z., Li, Z., Zhang, Y., Yang, Z., Wang, J.: An attention-based effective neural model for drug-drug interactions extraction. BMC Bioinf. 18(1), 445 (2017). https://doi.org/10.1186/s12859-017-1855-x

    Article  Google Scholar 

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Correspondence to Ed-drissiya El-allaly .

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El-allaly, Ed., Sarrouti, M., En-Nahnahi, N., Alaoui, S.O.E. (2020). A LSTM-Based Method with Attention Mechanism for Adverse Drug Reaction Sentences Detection. In: Ezziyyani, M. (eds) Advanced Intelligent Systems for Sustainable Development (AI2SD’2019). AI2SD 2019. Advances in Intelligent Systems and Computing, vol 1103. Springer, Cham. https://doi.org/10.1007/978-3-030-36664-3_3

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