有机污染物的生物富集因子与拓扑指数的数学模型

依据价连接性指数(xi)、电性拓扑态指数(ej)及电性距离矢量(mk)构建239种有机污染物生物富集因子(FBC)的6参数QSFR(定量结构-生物富集因子相关性)模型, 不仅相关程度高, 而且所用自变量数少. 该模型的传统相关系数(R2)为0.821, LOO(levae-one-out)交互验证系数(Q2)为0.809, 证明具有良好的稳健性及预测能力. 根据进入该模型的6个参数可知, 影响有机污染物FBC的主要结构基团是: —C—、>C—、—O—、—X、—NH2以及分子的柔韧性、折叠程度等空间因素. 可以认为在生物富集过程中,“诱导契合机理”也发挥一定作用. 对自变量集进行正交变换, 既不影响模型的相关性, 又能降低其自相关性.     

Using support vector machine to predict beta- and gamma-turns in proteins

By using the composite vector with increment of diversity, position conservation scoring function, and predictive secondary structures to express the information of sequence, a support vector machine (SVM) algorithm for predicting beta- and gamma-turns in the proteins is proposed. The 426 and 320 nonhomologous protein chains described by Guruprasad and Rajkumar (Guruprasad and Rajkumar J. Biosci 2000, 25,143) are used for training and testing the predictive model of the beta- and gamma-turns, respectively. The overall prediction accuracy and the Matthews correlation coefficient in 7-fold cross-validation are 79.8% and 0.47, respectively, for the beta-turns. The overall prediction accuracy in 5-fold cross-validation is 61.0% for the gamma-turns. These results are significantly higher than the other algorithms in the prediction of beta- and gamma-turns using the same datasets. In addition, the 547 and 823 nonhomologous protein chains described by Fuchs and Alix (Fuchs and Alix Proteins: Struct Funct Bioinform 2005, 59, 828) are used for training and testing the predictive model of the beta- and gamma-turns, and better results are obtained. This algorithm may be helpful to improve the performance of protein turns' prediction. To ensure the ability of the SVM method to correctly classify beta-turn and non-beta-turn (gamma-turn and non-gamma-turn), the receiver operating characteristic threshold independent measure curves are provided.     

A new type SVM-projected SVM

Support vector machine (SVM), developed by Vapnik et al., is a new and promising technique for classification and regression and has been proved to be competitive with the best available learning machines in many applications. However, the classification speed of SVM is substantially slower than that of other techniques with similar generalization ability. A new type SVM named projected SVM (PSVM), which is a combination of feature vector selection (FVS) method and linear SVM (LSVM), is proposed in present paper. In PSVM, the FVS method is first used to select a relevant subset (feature vectors, FVs) from the training data, and then both the training data and the test data are projected into the subspace constructed by FVs, and finally linear SVM(LSVM) is applied to classify the projected data. The time required by PSVM to calculate the class of new samples is proportional to the count of FVs. In most cases, the count of FVs is smaller than that of support vectors (SVs), and therefore PSVM is faster than SVM in running. Compared with other speeding-up techniques of SVM, PSVM is proved to possess not only speeding-up ability but also de-noising ability for high-noised data, and is found to be of potential use in mechanical fault pattern recognition.     

Using support vector machines for prediction of protein structural classes based on discrete wavelet transform

The prediction of secondary structure is a fundamental and important component in the analytical study of protein structure and functions. How to improve the predictive accuracy of protein structural classification by effectively incorporating the sequence‐order effects is an important and challenging problem. In this study, a new method, in which the support vector machine combines with discrete wavelet transform, is developed to predict the protein structural classes. Its performance is assessed by cross‐validation tests. The predicted results show that the proposed approach can remarkably improve the success rates, and might become a useful tool for predicting the other attributes of proteins as well. © 2008 Wiley Periodicals, Inc. J Comput Chem 2009     

基于支持向量机的高维特征非线性快速筛选与肽QSAR建模

以氨基酸的531个物理化学性质参数直接表征肽的结构, 基于支持向量回归发展了一种新的高维特征非线性快速筛选方法, 将其应用于苦味二肽和血管紧张素转化酶抑制剂2个肽体系的定量序效关系(QSAR)建模, 各筛选获得10个意义明确的保留描述子. 以保留描述子建立支持向量回归模型, 其拟合精度、留一法交叉测试精度和外部预测精度较文献报道结果均有较大幅度提升, 优势明显; 对所建模型进行了非线性回归显著性测验、单因子相对重要性显著性测验和单因子效应分析, 增强了模型的可解释性. 新方法在肽、蛋白质QSAR建模等高维数据回归预测领域有广泛应用前景.     

高效液相色谱中用于梯度洗脱的有机溶剂的纯度测试

在反相高效液相色谱中,空白梯度基线的漂移和杂质峰,可能由含水溶剂和有机溶剂中杂质所引起的。当含水溶剂通过预柱在线净化后,根据空白梯度色谱图可测试有机溶剂的纯度。按照此法,对国产不同等级的乙腈和甲醇进行了测试,指明这些试剂用于梯度洗脱的可能性。     

Improving protein structural class prediction using novel combined sequence information and predicted secondary structural features

Protein structural class prediction solely from protein sequences is a challenging problem in bioinformatics. Numerous efficient methods have been proposed for protein structural class prediction, but challenges remain. Using novel combined sequence information coupled with predicted secondary structural features (PSSF), we proposed a novel scheme to improve prediction of protein structural classes. Given an amino acid sequence, we first transformed it into a reduced amino acid sequence and calculated its word frequencies and word position features to combine novel sequence information. Then we added the PSSF to the combine sequence information to predict protein structural classes. The proposed method was tested on four benchmark datasets in low homology and achieved the overall prediction accuracies of 83.1%, 87.0%, 94.5%, and 85.2%, respectively. The comparison with existing methods demonstrates that the overall improvements range from 2.3% to 27.5%, which indicates that the proposed method is more efficient, especially for low-homology amino acid sequences.     

拉曼光谱结合背景扣除化学计量学方法用于汽油中MTBE含量的快速测定研究

应用便携式拉曼光谱仪测量了汽油样本的拉曼光谱,以自适应迭代惩罚最小二乘方法(airPLS)对光谱进行了背景扣除和平滑处理,并选取特征峰区间利用偏最小二乘方法(PLS)建立了预测甲基叔丁基醚(MT-BE)的校正模型。以训练集相关系数和拟合误差及测试集相关系数和预测误差作为判定依据,确定了最佳建模条件。最终训练集相关系数为0.996 0,拟合误差为0.316 1,测试集相关系数为0.996 6,预测误差为0.490 1。结果表明采用便携式拉曼光谱结合化学计量学方法处理,可以满足对汽油中MTBE含量快速检测的要求。     

A combination of modified particle swarm optimization algorithm and support vector machine for gene selection and tumor classification

In the analysis of gene expression profiles, the number of tissue samples with genes expression levels available is usually small compared with the number of genes. This can lead either to possible overfitting or even to a complete failure in analysis of microarray data. The selection of genes that are really indicative of the tissue classification concerned is becoming one of the key steps in microarray studies. In the present paper, we have combined the modified discrete particle swarm optimization (PSO) and support vector machines (SVM) for tumor classification. The modified discrete PSO is applied to select genes, while SVM is used as the classifier or the evaluator. The proposed approach is used to the microarray data of 22 normal and 40 colon tumor tissues and showed good prediction performance. It has been demonstrated that the modified PSO is a useful tool for gene selection and mining high dimension data.