Extracting Drug-Drug Interactions with Attention CNNs

BioNLP 2017 - SIGBioMed Workshop on Biomedical Natural Language Processing, Proceedings of the 16th BioNLP Workshop

Volumn , Issue , 2017, Pages 9-18

  Asada, Masaki ^a   Miwa, Makoto ^a   Sasaki, Yutaka ^a  

^a TOYOTA TECHNOLOGICAL INSTITUTE   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

CLASSIFICATION (OF INFORMATION); COMPUTATIONAL LINGUISTICS; EXTRACTION; NATURAL LANGUAGE PROCESSING SYSTEMS; NEURAL NETWORKS;

ATTENTION MECHANISMS; CLASSIFICATION TASKS; CONVOLUTIONAL NEURAL NETWORK; DRUG-DRUG INTERACTIONS; EXTRACTION MODELING; INTERACTION EXTRACTION; INTERACTION MODELING; NETWORK-BASED; PERFORMANCE; RELATION CLASSIFICATIONS;

DRUG INTERACTIONS;

EID: 85052493437     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (22)

1. Jari Björne, Suwisa Kaewphan, and Tapio Salakoski. 2013. UTurku: drug named entity recognition and drug-drug interaction extraction using SVM classification and domain knowledge. In Second Joint Conference on Lexical and Computational Semantics (* SEM). volume 2, pages 651–659.
2. Y-Lan Boureau, Jean Ponce, and Yann LeCun. 2010. A theoretical analysis of feature pooling in visual recognition. In Proceedings of the 27th international conference on machine learning (ICML-10). pages 111–118.
3. Md Faisal Mahbub Chowdhury and Alberto Lavelli. 2013. FBK-irst: A multi-phase kernel based approach for drug-drug interaction detection and classification that exploits linguistic information. Atlanta, Georgia, USA 351:53.
4. Cicero Nogueira dos Santos, Bing Xiang, and Bowen Zhou. 2015. Classifying relations by ranking with convolutional neural networks. In Proceedings of the 53rd Annual Meeting of the Association for Computational Linguistics. Association for Computational Linguistics. volume 1, pages 626–634.
5. Iris Hendrickx, Su Nam Kim, Zornitsa Kozareva, Preslav Nakov, Diarmuid Ó Séaghdha, Sebastian Padó, Marco Pennacchiotti, Lorenza Romano, and Stan Szpakowicz. 2009. SemEval-2010 Task 8: Multi-way classification of semantic relations between pairs of nominals. In Proceedings of the Workshop on Semantic Evaluations: Recent Achievements and Future Directions. Association for Computational Linguistics, pages 94–99.
6. María Herrero-Zazo, Isabel Segura-Bedmar, Paloma Martínez, and Thierry Declerck. 2013. The DDI corpus: An annotated corpus with pharmacological substances and drug–drug interactions. Journal of biomedical informatics 46(5):914–920.
7. Sun Kim, Haibin Liu, Lana Yeganova, and W John Wilbur. 2015. Extracting drug–drug interactions from literature using a rich feature-based linear kernel approach. Journal of biomedical informatics 55:23–30.
8. Yoon Kim. 2014. Convolutional neural networks for sentence classification. In Proceedings of the 2014 Conference on Empirical Methods in Natural Language Processing, EMNLP 2014, October 25-29, 2014, Doha, Qatar, A meeting of SIGDAT, a Special Interest Group of the ACL. pages 1746–1751.
9. Diederik Kingma and Jimmy Ba. 2015. Adam: A method for stochastic optimization. In The International Conference on Learning Representations (ICLR), San Diego, 2015.
10. Vivian Law, Craig Knox, Yannick Djoumbou, Tim Jewison, An Chi Guo, Yifeng Liu, Adam Maciejewski, David Arndt, Michael Wilson, Vanessa Neveu, et al. 2014. DrugBank 4.0: shedding new light on drug metabolism. Nucleic acids research 42(D1):D1091–D1097.
11. Shengyu Liu, Buzhou Tang, Qingcai Chen, and Xiao-long Wang. 2016. Drug-drug interaction extraction via convolutional neural networks. Computational and mathematical methods in medicine 2016.
12. Tomas Mikolov, Ilya Sutskever, Kai Chen, Greg S Corrado, and Jeff Dean. 2013. Distributed representations of words and phrases and their compositionality. In Advances in neural information processing systems. pages 3111–3119.
13. Chanqin Quan, Lei Hua, Xiao Sun, and Wenjun Bai. 2016. Multichannel convolutional neural network for biological relation extraction. BioMed Research International 2016.
14. Sunil Kumar Sahu and Ashish Anand. 2017. Drug-drug interaction extraction from biomedical text using long short term memory network. arXiv preprint arXiv:1701.08303 .
15. Isabel Segura Bedmar, Paloma Martínez, and María Herrero Zazo. 2013. SemEval-2013 Task 9: Extraction of drug-drug interactions from biomedical texts (DDIExtraction 2013). In Proceedings of the 7th International Workshop on Semantic Evaluations. Association for Computational Linguistics, pages 341–350.
16. Philippe Thomas, Mariana Neves, Tim Rocktäschel, and Ulf Leser. 2013. WBI-DDI: drug-drug interaction extraction using majority voting. In Second Joint Conference on Lexical and Computational Semantics (* SEM). volume 2, pages 628–635.
17. Caroline F Thorn, Teri E Klein, and Russ B Altman. 2013. PharmGKB: the pharmacogenomics knowledge base. Pharmacogenomics: Methods and Protocols pages 311–320.
18. Yoshimasa Tsuruoka, Yuka Tateishi, Jin-Dong Kim, Tomoko Ohta, John McNaught, Sophia Ananiadou, and Junichi Tsujii. 2005. Developing a robust part-of-speech tagger for biomedical text. In Panhellenic Conference on Informatics. Springer, pages 382–392.
19. Linlin Wang, Zhu Cao, Gerard de Melo, and Zhiyuan Liu. 2016. Relation classification via multi-level attention CNNs. In Proceedings of the 54th Annual Meeting of the Association for Computational Linguistics. Association for Computational Linguistics. pages 1298–1307.
20. Hong Yang, Chu Qin, Ying Hong Li, Lin Tao, Jin Zhou, Chun Yan Yu, Feng Xu, Zhe Chen, Feng Zhu, and Yu Zong Chen. 2016. Therapeutic target database update 2016: enriched resource for bench to clinical drug target and targeted pathway information. Nucleic acids research 44(D1):D1069–D1074.
21. Daojian Zeng, Kang Liu, Siwei Lai, Guangyou Zhou, Jun Zhao, et al. 2014. Relation classification via convolutional deep neural network. In COLING. pages 2335–2344.
22. Zhehuan Zhao, Zhihao Yang, Ling Luo, Hongfei Lin, and Jian Wang. 2016. Drug drug interaction extraction from biomedical literature using syntax convolutional neural network. Bioinformatics 32(22):3444–3453.