Identifying Protein-protein Interactions in Biomedical Literature using Recurrent Neural Networks with Long Short-Term Memory

Yu Lun Hsieh, Yung-Chun Chang, Nai Wen Chang, Wen Lian Hsu

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

Accurate identification of protein-protein interaction (PPI) helps biomedical researchers to quickly capture crucial information in literatures. This work proposes a recurrent neural network (RNN) model to identify PPIs. Experiments on two largest public benchmark datasets, AIMed and BioInfer, demonstrate that RNN outperforms state-of-the-art methods with relative improvements of 10% and 18%, respectively. Cross-corpus evaluation also indicates that RNN is robust even when trained on data from different domains. These results suggest that RNN effectively captures semantic relationships among proteins without any feature engineering.
Original languageEnglish
Title of host publicationProceedings of the Eighth International Joint Conference on Natural Language Processing
PublisherAsian Federation of Natural Language Processing
Pages240-245
Publication statusPublished - 2017

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Recurrent neural networks
Proteins
Semantics
Long short-term memory
Experiments

Cite this

Hsieh, Y. L., Chang, Y-C., Chang, N. W., & Hsu, W. L. (2017). Identifying Protein-protein Interactions in Biomedical Literature using Recurrent Neural Networks with Long Short-Term Memory. In Proceedings of the Eighth International Joint Conference on Natural Language Processing (pp. 240-245). Asian Federation of Natural Language Processing.

Identifying Protein-protein Interactions in Biomedical Literature using Recurrent Neural Networks with Long Short-Term Memory. / Hsieh, Yu Lun; Chang, Yung-Chun; Chang, Nai Wen; Hsu, Wen Lian.

Proceedings of the Eighth International Joint Conference on Natural Language Processing. Asian Federation of Natural Language Processing, 2017. p. 240-245.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Hsieh, YL, Chang, Y-C, Chang, NW & Hsu, WL 2017, Identifying Protein-protein Interactions in Biomedical Literature using Recurrent Neural Networks with Long Short-Term Memory. in Proceedings of the Eighth International Joint Conference on Natural Language Processing. Asian Federation of Natural Language Processing, pp. 240-245.
Hsieh YL, Chang Y-C, Chang NW, Hsu WL. Identifying Protein-protein Interactions in Biomedical Literature using Recurrent Neural Networks with Long Short-Term Memory. In Proceedings of the Eighth International Joint Conference on Natural Language Processing. Asian Federation of Natural Language Processing. 2017. p. 240-245
Hsieh, Yu Lun ; Chang, Yung-Chun ; Chang, Nai Wen ; Hsu, Wen Lian. / Identifying Protein-protein Interactions in Biomedical Literature using Recurrent Neural Networks with Long Short-Term Memory. Proceedings of the Eighth International Joint Conference on Natural Language Processing. Asian Federation of Natural Language Processing, 2017. pp. 240-245
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