title: Drug drug interaction extraction from biomedical literature using syntax convolutional neural network.
abstract: Detecting drug-drug interaction (DDI) has become a vital part of public health safety. Therefore, using text mining techniques to extract DDIs from biomedical literature has received great attentions. However, this research is still at an early stage and its performance has much room to improve.
  
  
  
  In this article, we present a syntax convolutional neural network (SCNN) based DDI extraction method. In this method, a novel word embedding, syntax word embedding, is proposed to employ the syntactic information of a sentence. Then the position and part of speech features are introduced to extend the embedding of each word. Later, auto-encoder is introduced to encode the traditional bag-of-words feature (sparse 0-1 vector) as the dense real value vector. Finally, a combination of embedding-based convolutional features and traditional features are fed to the softmax classifier to extract DDIs from biomedical literature. Experimental results on the DDIExtraction 2013 corpus show that SCNN obtains a better performance (an F-score of 0.686) than other state-of-the-art methods.
  
  
  
  The source code is available for academic use at http://202.118.75.18:8080/DDI/SCNN-DDI.zip CONTACT: yangzh@dlut.edu.cnSupplementary information: Supplementary data are available at Bioinformatics online.
authors.affiliation: College of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China.
authors.forename: Zhehuan
authors.initials: Z
authors.lastname: Zhao
authors.affiliation: College of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China.
authors.forename: Zhihao
authors.initials: Z
authors.lastname: Yang
authors.affiliation: College of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China.
authors.forename: Ling
authors.initials: L
authors.lastname: Luo
authors.affiliation: College of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China.
authors.forename: Hongfei
authors.initials: H
authors.lastname: Lin
authors.affiliation: College of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China.
authors.forename: Jian
authors.initials: J
authors.lastname: Wang
mesh_terms: D057225:Data Mining; D004347:Drug Interactions; D006801:Humans; D016571:Neural Networks, Computer; D011381:Programming Languages; D011642:Publications