Extracting Biomedical Events with Parallel Multi-Pooling Convolutional Neural Networks

Biomedical event extraction is important for medical research and disease prevention, which has attracted much attention in recent years. Traditionally, most of the state-of-the-art systems have been based on shallow machine learning methods, which require many complex, hand-designed features. In addition, the words encoded by one-hot are unable to represent semantic information. Therefore, we utilize dependency-based embeddings to represent words semantically and syntactically. Then, we propose a parallel multi-pooling convolutional neural network (PMCNN) model to capture the compositional semantic features of sentences. Furthermore, we employ a rectified linear unit, which creates sparse representations with true zeros, and which is adapted to the biomedical event extraction, as a nonlinear function in PMCNN architecture. The experimental results from MLEE dataset show that our approach achieves an $F1$ score of 80.27 percent in trigger identification and an $F1$ score of 59.65 percent in biomedical event extraction, which performs better than other state-of-the-art methods.