基于Charm算法挖掘基因表达保序子序列  

Mining gene expression order⁃preserving subsequence based on Charm algorithm

作　　者：廖旭红 江华 廖莎 李志杰 Liao Xuhong;Jiang Hua;Liao Sha;Li Zhijie(School of Information Science and Engineering,Hunan Institute of Science and Technology,Yueyang 414006,China)

机构地区：[1]湖南理工学院信息科学与工程学院,岳阳414006

出　　处：《现代计算机》2023年第14期8-13,共6页Modern Computer

基　　金：湖南省自然科学基金(2019JJ40111)。

摘　　要：保序子序列(OPSS)是基因表达数据重要的定性测度双聚类方法,通常将基因实数表达值排序后替换成相应的列标签,OPSS的部分行在部分列下同升同降。提出一种基于Charm算法的保序子序列挖掘方法Charm_Seq,将Charm由频繁闭合项集挖掘改造为频繁闭合序列挖掘,充分利用了Charm高效的Itemset⁃Tidset前缀搜索树数据结构。在人工和实际基因表达数据集上进行实验,实验结果验证了该方法的高效性和有效性。Order‑preserving subsequence(OPSS)is an important biclustering method for gene expression data based on qualitative measures.Usually,the expression value of genes is sorted and replaced with corresponding column labels,and then frequent sequence sets are mined.In this paper,we propose Charm_Seq which is a frequent subsequence mining method based on Charm algorithm.Charm_Seq transformed Charm from frequent closed itemset mining to frequent closed sequence mining,and made full use of Charm’s efficient Itemset‑Tidset prefix search tree data structure.Experiments are carried out on artificial and real gene expression data sets,and the experimental results verify the efficiency and effectiveness of this method.

关 键 词：基因表达数据 双聚类 保序子序列 CHARM 序列挖掘 

分 类 号：Q811.4[生物学—生物工程] TP311.13[自动化与计算机技术—计算机软件与理论]