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Traditional Chinese medicine entity relation extraction based on CNN with segment attention

  • S.I: Cognitive-inspired Computing and Applications
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Abstract

Extracting medical entity relations from Traditional Chinese Medicine (TCM) related article is crucial to connect domain knowledge between TCM with modern medicine. Herb accounts for the majority of Traditional Chinese Medicine, so our work mainly focuses on herb. The problem would be effectively solved by extracting herb-related entity relations from PubMed literature. In order to realize the entity relation mining, we propose a novel deep-learning model with improved layers without manual feature engineering. We design a new segment attention mechanism based on Convolutional Neural Network, which enables extracting local semantic features through word embedding. Then we classify the relations by connecting different embedding features. We first test this method on the Chemical-Induced Disease task and the experiment show better result comparing to other state-of-the-art deep learning methods. Further, we apply this method to a herbal-related data set (Herbal-Disease and Herbal Chemistry, HD-HC) constructed from PubMed to explore entity relation classification. The experiment shows superior results than other baseline methods.

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Funding

This work is supported by the Development Project of Jilin Province of China (Nos.20200801033GH, YDZJ202101ZYTS128), Jilin Provincial Key Laboratory of Big Data Intelligent Computing (No.20180622002JC), The Fundamental Research Funds for the Central University, JLU.

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Authors and Affiliations

  1. College of Computer Science and Technology, Jilin University, Changchun, 130012, China

    Tian Bai, Haotian Guan, Ye Wang & Lan Huang

  2. College of Software, Jilin University, Changchun, 130012, China

    Shang Wang

  3. Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, 130012, China

    Tian Bai, Haotian Guan, Shang Wang, Ye Wang & Lan Huang

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  1. Tian Bai
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  2. Haotian Guan
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  3. Shang Wang
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  4. Ye Wang
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  5. Lan Huang
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Correspondence to Lan Huang.

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Bai, T., Guan, H., Wang, S. et al. Traditional Chinese medicine entity relation extraction based on CNN with segment attention. Neural Comput & Applic 34, 2739–2748 (2022). https://doi.org/10.1007/s00521-021-05897-9

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