Journal of Software:2017.28(8):2175-2195

(西北工业大学 计算机学院, 陕西 西安 710072)
Constrained Query of Order-Preserving Submatrix Based on Signature and Trie
JIANG Tao,LI Zhan-Huai,SHANG Xue-Qun,CHEN Bo-Lin,LI Wei-Bang,YIN Zhi-Lei
(School of Computer Science, Northwestern Polytechnical University, Xi'an 710072, China)
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Received:January 20, 2016    Revised:May 20, 2016
> 中文摘要: 目前,基因芯片技术飞速发展,促使生物学家积累了大量的不同实验条件下的基因表达数据.事实证明,基因芯片数据分析在理解基因功能、基因调控和分子生命过程中发挥着重要作用.保序子矩阵(order-preserving submatrix,简称OPSM)是基因芯片数据分析技术中的一种有效模型,其可以发现在部分基因和不同实验条件下具有相同表达趋势的聚类.在分析基因表达机理的过程中,OPSM的检索无疑节省了生物学家的时间与精力.目前,OPSM的查询主要是基于关键词的检索方法,但是分析者对结果具有微弱的控制力.通常,分析者所能决定的临时的参数设置往往偏离其领域知识,致使检索结果与真实想要的结果相去甚远.为了解决上述问题,提出两类基于数字签名与Trie的OPSM索引与约束查询方法.在真实数据上进行了大量的实验,实验结果表明,所提出的方法具有良好的有效性与可扩展性.
Abstract:The advances of microarray technology have made large amount of gene expression data available from a variety of different experimental conditions. Analyzing the microarray data plays a key role in understanding gene functions, gene regulation and cellular process. Order-Preserving Submatrix (OPSM) is an important model in microarray data analysis, which captures the identical tendency of gene expressions across a subset of conditions. In the process of analyzing mechanism of gene expression, OPSM search undoubtedly saves the time and effort of biologists. However, OPSM retrieval mainly depends on keyword search, resulting a weak control on the obtained clusters. Typically, the analyst can determine the ad-hoc parameters which are far from the declarative specification of desired properties on operation and concept. Motivated by obtaining much more accurate query relevancy, this paper proposes two types of OPSM indexing and constrained query methods based on signature and Trie. Extensive experiments conducted on real datasets demonstrate the proposed methods have better behaviors than the state-of-the-art methods on efficiency and effectiveness.
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基金项目:国家重点基础研究发展计划(973)(2012CB316203);国家自然科学基金(61033007,61272121,61332014,61572367,61472321,61502390);国家高技术研究发展计划(863)(2015AA015307);中央高校基本科研业务费专项资金(3102015JSJ0011);西北工业大学研究生创业种子基金(Z2012128) 国家重点基础研究发展计划(973)(2012CB316203);国家自然科学基金(61033007,61272121,61332014,61572367,61472321,61502390);国家高技术研究发展计划(863)(2015AA015307);中央高校基本科研业务费专项资金(3102015JSJ0011);西北工业大学研究生创业种子基金(Z2012128)
Foundation items:National Program on Key Basic Research Project of China (973) (2012CB316203); National Natural Science Foundation of China (61033007, 61272121, 61332014, 61572367, 61472321, 61502390); National High-Tech R&D Program of China (863) (2015AA015307); Fundamental Research Funds for the Central Universities (3102015JSJ0011); Graduate Starting Seed Fund of the Northwestern Polytechnical University (Z2012128)
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JIANG Tao,LI Zhan-Huai,SHANG Xue-Qun,CHEN Bo-Lin,LI Wei-Bang,YIN Zhi-Lei.Constrained Query of Order-Preserving Submatrix Based on Signature and Trie.Journal of Software,2017,28(8):2175-2195