基于机器学习的microRNA预测方法研究进展

doi:10.11896/j.issn.1002-137X.2015.02.002

摘要/Abstract

摘要： 传统的克隆方法受组织和环境影响显著,且实验成本高,而计算方法中的比较方法对进化距离远的microRNA敏感性低,无法预测无同源的microRNA,机器学习方法解决了比较方法依赖同源基因的问题。首先总结了基于机器学习预测microRNA的相关生物学知识；其次,给出基于机器学习的microRNA预测方法的大体流程,列举了基于机器学习的microRNA预测方法的最新研究算法及软件；再次,从数据集选取、特征集选取、分类器设计、特征子集选择、类不平衡问题解决和评价标准等环节出发,归纳总结了各环节中采用的方法及技术,并详细阐述了它们的最新研究进展,部分环节对采用的方法及技术进行了对比分析,总结了各自的优势和不足；最后,总结和展望了基于机器学习的microRNA预测方法的研究工作。

关键词: microRNA,机器学习,分类器,特征选取,类不平衡,生物信息学

Abstract: Traditional cloning experimental approaches are affected by the organizational and environmental impact,and the cost is high.The comparative method that belongs to the computational method is low sensitivity to the far evolutionary distance genes,and can’t predict the no homologous microRNAs.The machine learning method can resolve the restraints that comparative method dependents on the homologous gene.Firstly,this paper summarized the microRNA relevant biological knowledge which the machine learning is related to.Secondly,it outlined the general process and the latest research software and algorithms of machine learning based on microRNA prediction.Thirdly,starting from data selection,feature selection,classifier design,feature subset selection,class imbalance problem,performance evaluation and other aspects in terms of the essential elements of microRNA prediction based on the machine learning,it summarized the method and technology in each process,described their latest research progress.The approaches were contrasted and analyzed respectively in some process,and their respective advantages,disadvantages were summarized.Finally,summary and prospect of the research work on microRNA prediction based on machine learning were given.

Key words: microRNA,Machine learning,Classifier,Feature extraction,Class imbalance,Bioinformatics

王颖,李金,王磊,徐成振,才忠喜. 基于机器学习的microRNA预测方法研究进展[J]. 计算机科学, 2015, 42(2): 7-13. https://doi.org/10.11896/j.issn.1002-137X.2015.02.002

WANG Ying, LI Jin, WANG Lei, XU Cheng-zhen and CAI Zhong-xi. Research and Progress of microRNA Prediction Methods Based on Machine Learning[J]. Computer Science, 2015, 42(2): 7-13. https://doi.org/10.11896/j.issn.1002-137X.2015.02.002

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