A Hybrid Deep Learning Model for Protein-Protein Interactions Extraction from Biomedical Literature

• 全, 昌勤

• 羅, 志偉

• Wang, Song

抄録

The exponentially increasing size of biomedical literature and the limited ability of manual curators to discover protein-protein interactions (PPIs) in text has led to delays in keeping PPI databases updated with the current findings. The state-of-the-art text mining methods for PPI extraction are primarily based on deep learning (DL) models, and the performance of a DL-based method is mainly affected by the architecture of DL models and the feature embedding methods. In this study, we compared different architectures of DL models, including convolutional neural networks (CNN), long short-term memory (LSTM), and hybrid models, and proposed a hybrid architecture of a bidirectional LSTM+CNN model for PPI extraction. Pretrained word embedding and shortest dependency path (SDP) embedding are fed into a two-embedding channel model, such that the model is able to model long-distance contextual information and can capture the local features and structure information effectively. The experimental results showed that the proposed model is superior to the non-hybrid DL models, and the hybrid CNN+Bidirectional LSTM model works well for PPI extraction. The visualization and comparison of the hidden features learned by different DL models further confirmed the effectiveness of the proposed model.

収録刊行物

• Applied Sciences

  Applied Sciences 10 (8), 2690-2690, 2020-04

  MDPI

キーワード

• protein-protein interactions
• deep learning (DL)
• convolutional neural networks (CNN)
• bidirectional long short-term memory (bidirectional LSTM)

詳細情報

• CRID: 1050294045369002752
• NII論文ID: 120006863581
• ISSN: 20763417
• HANDLE: 20.500.14094/90007153
• 本文言語コード: en
• 資料種別: journal article
• データソース種別:
  • IRDB
  • CiNii Articles