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BioMed Research International
Volume 2016 (2016), Article ID 1850404, 10 pages
http://dx.doi.org/10.1155/2016/1850404
Research Article

Multichannel Convolutional Neural Network for Biological Relation Extraction

1Graduate School of System Informatics, Kobe University, Kobe, Japan
2Department of Computer and Information Science, Hefei University of Technology, Hefei, China

Received 22 June 2016; Accepted 9 November 2016

Academic Editor: Oliver Ray

Copyright © 2016 Chanqin Quan et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

The plethora of biomedical relations which are embedded in medical logs (records) demands researchers’ attention. Previous theoretical and practical focuses were restricted on traditional machine learning techniques. However, these methods are susceptible to the issues of “vocabulary gap” and data sparseness and the unattainable automation process in feature extraction. To address aforementioned issues, in this work, we propose a multichannel convolutional neural network (MCCNN) for automated biomedical relation extraction. The proposed model has the following two contributions: it enables the fusion of multiple (e.g., five) versions in word embeddings; the need for manual feature engineering can be obviated by automated feature learning with convolutional neural network (CNN). We evaluated our model on two biomedical relation extraction tasks: drug-drug interaction (DDI) extraction and protein-protein interaction (PPI) extraction. For DDI task, our system achieved an overall -score of 70.2% compared to the standard linear SVM based system (e.g., 67.0%) on DDIExtraction 2013 challenge dataset. And for PPI task, we evaluated our system on Aimed and BioInfer PPI corpus; our system exceeded the state-of-art ensemble SVM system by 2.7% and 5.6% on -scores.