Motivation: 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. Results: 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-theart methods. Availability and Implementation: The source code is available for academic use at http://202.118. 75.18:8080/DDI/SCNN-DDI.zip.
Zhao et al. REF utilized word embeddings in a syntax convolutional neural network (SCNN) by changing the input of word2vec to the word sequences on the shortest path in the predicate argument sentence structure to extract DDIs (F1 score=0.78).
Drug drug interaction extraction from biomedical literature using syntax convolutional neural network
Bioinformatics
Bioinformatics
Medicine Computer Science