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

Abstract

Abstract Background 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. Methods 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. Results 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. Conclusions 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.

Keywords

• Biomedical event extraction
• Distributed representation
• Deep learning
• Convolutional neural network