Tumor gene expression data classification via sample expansion-based deep learning

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Abstract

// Jian Liu 1, * , Xuesong Wang 1, * , Yuhu Cheng 1 and Lin Zhang 1 1 School of Information and Control Engineering, China University of Mining and Technology, Xuzhou 221116, China * Joint First Authors Correspondence to: Xuesong Wang, email: wangxuesongcumt@163.com Yuhu Cheng, email: chengyuhu@163.com Keywords: gene expression data; classification; sample expansion; deep learning; 1-dimensional convolutional neural network Received: August 31, 2017     Accepted: October 29, 2017     Published: November 30, 2017 ABSTRACT Since tumor is seriously harmful to human health, effective diagnosis measures are in urgent need for tumor therapy. Early detection of tumor is particularly important for better treatment of patients. A notable issue is how to effectively discriminate tumor samples from normal ones. Many classification methods, such as Support Vector Machines (SVMs), have been proposed for tumor classification. Recently, deep learning has achieved satisfactory performance in the classification task of many areas. However, the application of deep learning is rare in tumor classification due to insufficient training samples of gene expression data. In this paper, a Sample Expansion method is proposed to address the problem. Inspired by the idea of Denoising Autoencoder (DAE), a large number of samples are obtained by randomly cleaning partially corrupted input many times. The expanded samples can not only maintain the merits of corrupted data in DAE but also deal with the problem of insufficient training samples of gene expression data to a certain extent. Since Stacked Autoencoder (SAE) and Convolutional Neural Network (CNN) models show excellent performance in classification task, the applicability of SAE and 1-dimensional CNN (1DCNN) on gene expression data is analyzed. Finally, two deep learning models, Sample Expansion-Based SAE (SESAE) and Sample Expansion-Based 1DCNN (SE1DCNN), are designed to carry out tumor gene expression data classification by using the expanded samples. Experimental studies indicate that SESAE and SE1DCNN are very effective in tumor classification.

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