基于基因表达谱的肿瘤预测模型研究

 本文从肿瘤基因表达谱分析入手,研究并选取胃癌相关标志基因集合,以此集合为基础抽取甄别肿瘤与正常组织的基因分类规则集,进而建立起肿瘤预测模型.首先,以支持向量机为分类器用特征基因集合的样本识别率为适应度函数,采用遗传算法对特征基因进行筛选.然后用决策树抽取特征基因的规则集,结合肿瘤分子生物学文献和生物实验建立肿瘤预测模型.最后通过对胃癌基因表达谱数据的分析,建立了胃癌预测模型,结果表明该模型对胃癌分子生物学实验和临床诊断具有一定的指导意义和参考价值.     

量子神经网络的多发性骨髓瘤预测建模

为了提高多发性骨髓瘤的预测精度,对于多发性骨髓瘤基因表达数据库,采用BP神经网络创建多发性骨髓瘤预测模型,但其算法存在收敛速度慢、网络泛化能力差等缺点,影响预测精度。鉴于此,文中提出采用量子神经网络模型进行多发性骨髓瘤预测建模。结果表明,该预测方法较BP神经网络方法而言,其预测精度提高了8%,达到了很好的预测效果。结论与传统BP神经网络相比,其收敛精度、收敛速度有了显著提高,同时能避免陷入局部极小的缺点。     

基于对称不确定性和Lasso的基因数据特征选择算法

基于目前肿瘤基因表达谱数据在医学相关结合行业的广泛普及,运用特征选择算法对其处理成了如今大量学者们的重点研究方向.基于此,提出了一种FCBF-Lasso结合算法.首先,采用FCBF算法对各基因数据集进行特征选择,通过删除冗余的和不相关的特征,得到特征子集;然后,再利用Lasso方法对得到特征子集进行特征选择,进一步地删...     

基于基因表达谱的肿瘤亚型识别与分类特征基因选取研究

利用肿瘤基因表达谱建立有效的"预测性"分类模型,对肿瘤的不同亚型进行准确判别并找出决定样本类别的一组特征基因是当前生物信息学研究的重要课题.本文在分析肿瘤基因表达谱特征的基础上,以急性白血病的基因表达谱为例,研究了肿瘤亚型识别与分类特征基因选取问题.在类别可分离性判据的问题上,修正了已有的"信噪比"指标,据此进行无关基因的剔除,并以支持向量机作为分类器进行肿瘤亚型的识别.在特征基因选取问题上,本文从生物学分析出发,首先剔除无关基因和具有较强相关性的冗余基因,然后采用顺序浮动搜索算法进行分类特征基因的选取.实验结果表明了上述方法的可行性和有效性.     

基于粒计算的基因挖掘

有关基因挖掘及其功能分析的研究已有很多。近年来,研究者已进行了基因表达数据分析中的特征基因提取、基于粗糙集的基因表达数据分类研究、粒计算在基因微阵列数据特征选择中的应用等研究。应用粒计算约简理论对基因表达数据进行分析,有助于发现具有不同效用的基因;在粒计算的基础上对特征基因进行挖掘,是当今生物学与信息技术学相互联系进行研究的重点和热点。     

一种新型多类别生物芯片cDNA基因表达数据标准化方法

cDNA生物芯片表达数据广泛用于生物医学研究,利用计算机对其进行处理还有很多挑战性课题。该文提出了一种新的基于不变基因的多类生物芯片监督型集合cDNA表达数据标准化方法。在达到标准化的同时,该方法也可直接用于基因表达数据的特征选择,实验证明效果较好。     

基于云平台的互信息最大化特征提取方法研究

随着大规模基因芯片的应用,针对高维度的基因表达数据存在大量无关和冗余特征可能降低分类器性能的问题,提出了一种基于云平台的互信息最大化特征提取（CMI-Selection）方法。Hadoop云计算平台对基因表达数据划分后进行并行计算,同时结合互信息最大化方法对特征进行提取,实现了云计算平台上的特征过滤模型。实验结果表明,基于云平台的互信息最大化特征提取方法能够在保证较高分类精度的情况下,快速提取特征,节省大量时间资源,是一种高效的基因特征提取系统。     

基于跨视角相似度顺序保持的基因特征提取方法

基因表达数据通常具有维数高、样本少、类别分布不均等特点,如何提取基因表达数据的有效特征是基因分类研究的关键问题。该文借助相关分析理论,构建鉴别敏感的视角内相似度顺序保持散布并且约束鉴别敏感的视角间相似度相关,从而形成了一种新的基因特征提取方法,即相似度顺序保持跨视角相关分析(SOPACA)。该文方法在保持不同视角间特征类内聚集性和相似度顺序的同时具有较大的类间离散性。在癌症基因表达数据集上的良好实验结果显示了该文方法的有效性。     

基于主曲线的脱机手写数字识别

该文提出了一种基于主曲线的脱机手写数字识别方法.该方法将主曲线及知识约简算法运用于识别模型中.主曲线是主成份分析的非线性推广,它是通过数据分布"中间"并满足"自相合"的光滑曲线.它较好地反映了数据分布的结构特征.粗糙集理论的知识约简是从决策表中获取决策(分类)规则的有效工具.本文将主曲线用于训练数据的特征提取,根据主曲线的特征生成决策表;利用我们提出的知识约简算法对决策表进行处理,自动获得分类规则.这种方法既符合人的识别习惯,又克服了利用统计特征识别所带来的不足.实验结果表明了该方法能有效提高手写数字的识别率,为脱机手写数字识别的研究提供了一条新途径.     

基于MST的基因数据社团挖掘算法

使用机器学习方法来分析生物信息学中一些复杂的基因表达数据是目前重要的研究领域之一.使用社团挖掘的方法对基因表达数据进行分类,社团内由类似的基因数据组成,研究和分析每个社团的结构和功能以及社团之间的关系,这对深刻认识诸多生物过程的本质有重要意义.将最小生成树的概念引入生物信息学中基因表达数据的社团挖掘分析中,设计了最小生成树来表示基因表达数据和基于此的社团挖掘算法,针对该算法提出一些目标函数,来判别基因表达数据社团挖掘算法的性能.最后,通过实验验证了该算法对于一些目标函数能够产生最优的社团划分,并且社团挖掘算法的性能良好.     

Dynamic-Model-Based Method for Selecting Significantly Expressed Genes From Time-Course Expression Profiles

This paper proposes a dynamic-model-based method for selecting significantly expressed (SE) genes from their time-course expression profiles. A gene is considered to be SE if its time-course expression profile is more likely time-dependent than random. The proposed method describes a time-dependent gene expression profile by a nonzero-order autoregressive (AR) model, and a time-independent gene expression profile by a zero-order AR model. Akaike information criterion (AIC) is used to compare the models and subsequently determine whether a time-course gene expression profile is time-independent or time-dependent. The performance of the proposed method is investigated on both a synthetic dataset and a real-life biological dataset in terms of the false discovery rate (FDR) and the false nondiscovery rate (FNR). The results show that the proposed method is valid for selecting SE genes from their time-course expression profiles.      

An evolutionary approach for gene expression patterns

This study presents an evolutionary algorithm, called a heterogeneous selection genetic algorithm (HeSGA), for analyzing the patterns of gene expression on microarray data. Microarray technologies have provided the means to monitor the expression levels of a large number of genes simultaneously. Gene clustering and gene ordering are important in analyzing a large body of microarray expression data. The proposed method simultaneously solves gene clustering and gene-ordering problems by integrating global and local search mechanisms. Clustering and ordering information is used to identify functionally related genes and to infer genetic networks from immense microarray expression data. HeSGA was tested on eight test microarray datasets, ranging in size from 147 to 6221 genes. The experimental clustering and visual results indicate that HeSGA not only ordered genes smoothly but also grouped genes with similar gene expressions. Visualized results and a new scoring function that references predefined functional categories were employed to confirm the biological interpretations of results yielded using HeSGA and other methods. These results indicate that HeSGA has potential in analyzing gene expression patterns.     

基于稀疏类别保留投影的基因表达数据降维方法

针对基因表达数据高维小样本特性所带来的维数灾难问题,结合回归和类别保留投影方法,提出一种新的基因表达数据降维方法,叫稀疏类别保留投影.相比类别保留投影,能有效避免类别保留投影在基因表达数据降维上存在的矩阵奇异和过拟合问题.通过对真实基因表达数据进行数据可视化和分类识别,验证了方法的有效性.     

Cluster analysis of gene expression data based on self-splitting and merging competitive learning

Cluster analysis of gene expression data from a cDNA microarray is useful for identifying biologically relevant groups of genes. However, finding the natural clusters in the data and estimating the correct number of clusters are still two largely unsolved problems. In this paper, we propose a new clustering framework that is able to address both these problems. By using the one-prototype-take-one-cluster (OPTOC) competitive learning paradigm, the proposed algorithm can find natural clusters in the input data, and the clustering solution is not sensitive to initialization. In order to estimate the number of distinct clusters in the data, we propose a cluster splitting and merging strategy. We have applied the new algorithm to simulated gene expression data for which the correct distribution of genes over clusters is known a priori. The results show that the proposed algorithm can find natural clusters and give the correct number of clusters. The algorithm has also been tested on real gene expression changes during yeast cell cycle, for which the fundamental patterns of gene expression and assignment of genes to clusters are well understood from numerous previous studies. Comparative studies with several clustering algorithms illustrate the effectiveness of our method.     

An original genetic approach to the fully automatic gridding of microarray images

Gridding microarray images remains, at present, a major bottleneck. It requires human intervention which causes variations of the gene expression results. In this paper, an original and fully automatic approach for accurately locating a distorted grid structure in a microarray image is presented. The gridding process is expressed as an optimization problem which is solved by using a genetic algorithm (GA). The GA determines the line-segments constituting the grid structure. The proposed method has been compared with existing software tools as well as with a recently published technique. For this purpose, several real and artificial microarray images containing more than one million spots have been used. The outcome has shown that the accuracy of the proposed method achieves the high value of 94% and it outperforms the existing approaches. It is also noise-resistant and yields excellent results even under adverse conditions such as arbitrary grid rotations, and the appearance of various spot sizes.     

Identification of Shared Components and Sparse Networks in Gene Expression Time-Course Data

High-throughput gene expression technologies such as microarrays have been utilized in a variety of scientific applications. In this article, we develop multivariate techniques for visualizing gene regulatory networks using independent components analysis (ICA) techniques. A desirable feature of the ICA method is that it approximates a biological model for the gene expression. The methods are outlined and illustrated with application to yeast gene expression data.     

Construction of Gene Networks With Hybrid Approach From Expression Profile and Gene Ontology

Gene regulatory networks have been long studied in model organisms as a means of identifying functional relationships among genes or their corresponding products. Despite many existing methods for genome-wide construction of such networks, solutions to the gene regulatory networks problem are however not trivial. Here, we present, a hybrid approach with gene expression profiles and gene ontology (HAEO). HAEO makes use of multimethods (overlapping clustering and reverse engineering methods) to effectively and efficiently construct gene regulatory networks from multisources (gene expression profiles and gene ontology). Application to yeast cell cycle dataset demonstrates HAEO’s ability to construct validated gene regulatory networks, such as some potential gene regulatory pairs, which cannot be discovered by general inferring methods and identifying cycles (i.e., feedback loops) between genes. We also experimentally study the efficiency of building networks and show that the proposed method, HAEO is much faster than Bayesian networks method.      

A modified binary particle swarm optimization for selecting the small subset of informative genes from gene expression data

Gene expression data are expected to be of significant help in the development of efficient cancer diagnoses and classification platforms. In order to select a small subset of informative genes from the data for cancer classification, recently, many researchers are analyzing gene expression data using various computational intelligence methods. However, due to the small number of samples compared to the huge number of genes (high dimension), irrelevant genes, and noisy genes, many of the computational methods face difficulties to select the small subset. Thus, we propose an improved (modified) binary particle swarm optimization to select the small subset of informative genes that is relevant for the cancer classification. In this proposed method, we introduce particles' speed for giving the rate at which a particle changes its position, and we propose a rule for updating particle's positions. By performing experiments on ten different gene expression datasets, we have found that the performance of the proposed method is superior to other previous related works, including the conventional version of binary particle swarm optimization (BPSO) in terms of classification accuracy and the number of selected genes. The proposed method also produces lower running times compared to BPSO.