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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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
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
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
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
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
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
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
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
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
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
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
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
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
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)
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
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)
Zhang, Z., Nie, J.-Y.: An ensemble method for binary classification of adverse drug reactions from social media (2015)
Jonnagaddala, J., Jue, T.R., Dai, H.-J.: Binary classification of twitter posts for adverse drug reactions (2015)
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)
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
Pyysalo, S., Ginter, F., Moen, H., Salakoski, T., Ananiadou, S.: Distributional semantics resources for biomedical text processing. Proc. LBM 2013, 39–44 (2013)
Elman, J.L.: Finding structure in time. Cogn. Sci. 14(2), 179–211 (1990). https://doi.org/10.1207/s15516709cog1402_1
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
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
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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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