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01.12.2017 | Research | Sonderheft 3/2017 Open Access

BMC Medical Informatics and Decision Making 3/2017

A multiple distributed representation method based on neural network for biomedical event extraction

BMC Medical Informatics and Decision Making > Sonderheft 3/2017
Anran Wang, Jian Wang, Hongfei Lin, Jianhai Zhang, Zhihao Yang, Kan Xu



Biomedical event extraction is one of the most frontier domains in biomedical research. The two main subtasks of biomedical event extraction are trigger identification and arguments detection which can both be considered as classification problems. However, traditional state-of-the-art methods are based on support vector machine (SVM) with massive manually designed one-hot represented features, which require enormous work but lack semantic relation among words.


In this paper, we propose a multiple distributed representation method for biomedical event extraction. The method combines context consisting of dependency-based word embedding, and task-based features represented in a distributed way as the input of deep learning models to train deep learning models. Finally, we used softmax classifier to label the example candidates.


The experimental results on Multi-Level Event Extraction (MLEE) corpus show higher F-scores of 77.97% in trigger identification and 58.31% in overall compared to the state-of-the-art SVM method.


Our distributed representation method for biomedical event extraction avoids the problems of semantic gap and dimension disaster from traditional one-hot representation methods. The promising results demonstrate that our proposed method is effective for biomedical event extraction.
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