基于一级序列预测蛋白质亚细胞定位的超级学习机方法.docVIP

Hans Journal of Data Mining数据挖掘, 2013, 3, 6-11 /10.12677/hjdm.2013.31002 Published Online January 2013 (/journal/hjdm.html) Extreme Learning Machine for Protein Subcellular Localization from Primary Sequence* Feng Shi, Hong Chen, Huijuan Xiong # College of Science, Huazhong Agricultural University, Wuhan # Email: xiongdou1231@ Received: Sep. 28 , 2012; revised: Oct. 26 , 2012; accepted: Nov. 4 , 2012 th th th Abstract: Predicting protein subcellular localization from primary sequence is crucial to genome annotation, protein function prediction, drug discovery and etc. Extreme learning machine is an attractive learning method in recent years. This paper explores the potential of extreme learning machine for protein subcellular localization prediction. For this, a new feature selection strategy is established first. By utilizing the feature selection strategy, each primary sequence can be expressed as a 25-dimensional numerical vector. Furthermore, some numerical comparisons of Support Vector Ma- chine with new features, Extreme Learning Machine with new features and another existing Support Vector Machine method with Pseudo amino acid composition features are given on 852 mycobcterial proteins data. The data arises from Swiss-Prot 48 database and belongs to four different classes. Results of five cross-validation for 852 protein sequences show that ELM with new features achieves the best accuracy. It achieves 97.2% accuracy, SVM with new features ob- tains 96.4% accuracy and SVM with Pseudo amino acid composition features displays 95.2% accuracy. Keywords: Protein Subcellular Localization; Extreme Learning Machine; Homologous Protein 基于一级序列预测蛋白质亚细胞定位的超级学习机方法* 石 峰，陈 洪，熊慧娟# 华中农业大学理学院，武汉 Email: xiongdou1231@ # 收稿日期：2012年 9月 28日；修回日期：2012年 10月 26日；录用日期：2012年 11月 4日 摘 要：蛋白质一级序列的亚细胞定位在基因组注释、蛋白质功能预测、药物发