肿瘤信息基因启发式宽度优先搜索算法研究

基于基因表达谱的肿瘤检测方法有望成为临床医学上一种快速而有效的肿瘤分子诊断方法,但由于基因表达谱数据存在维数过高、样本量很小以及噪音很大等特点,使得肿瘤信息基因选择成为一件有挑战性的工作.根据肿瘤基因表达谱样本集的特点,提出了一种以支持向量机分类性能为评估准则的寻找信息基因的启发式宽度优先搜索算法,其优点是能够同时搜索到基因数量尽可能少而分类能力尽可能强的多个信息基因子集.实验采用了3种肿瘤样本集以验证新算法的可行性和有效性,对于急性白血病、难以分类的结肠癌和多肿瘤亚型的小圆蓝细胞瘤样本集,分别只需2,4和4个信息基因就能获得100%的4-折交叉验证识别准确率.与其它优秀的肿瘤分类方法相比,实验结果在信息基因数量及其分类性能方面具有明显的优越性.为避免样本集的不同划分对分类性能的影响,提出了一种能够更加客观地反映信息基因子集分类性能的全折交叉验证评估方法.

Heuristic Breadth-First Search Algorithm for Informative Gene Selection Based on Gene Expression Profiles

The tumor diagnosis method based on gene expression profiles will be developed into the fast and effective method in clinical domain in the near future. Although DNA microarray experiments provide us with huge amount of gene expression data, only a few of genes are related to tumor in gene expression profiles. Moreover, it is difficult to select informative genes related to tumor from gene expression profiles because of its characteristics such as high dimensionality, small sample set and many noises in gene expression profiles. According to its characteristic, a novel heuristic breadth-first search algorithm based on support vector machines is proposed, which can simultaneously find as many informative gene subsets as possible in which the number of informative genes is almost least but its classification performance is almost highest in spite of its time-consuming characteristic. Three tumor sample sets are examined by the novel approach and experiments show that the novel approach is feasible and effective in tumor classification. Experiment results show that 100% of 4-fold cross-validation accuracy has been achieved by only two, four and four genes for leukemia, colon tumor and SRBCT (Small Round Blue Cells Tumor) datasets, respectively, which is superior to the results of other tumor classification methods. To avoid the affect of different partition of sample set, the full-fold cross-validated method that can more objectively evaluate the classification performance of informative gene subset is proposed.