基于机器学习方法的丙型肝炎病毒聚合酶NS5B非核苷抑制剂的定量构效关系研究

对89 个苯并异噻唑和苯并噻嗪类丙型肝炎病毒(HCV) NS5B聚合酶非核苷抑制剂进行了定量构效关系(QSAR)研究. 采用遗传算法组合偏最小二乘(GA-PLS)和线性逐步回归分析(LSRA)两种特征选择方法选择最优描述符子集, 然后建立多元线性回归和偏最小二乘线性回归模型. 并首次尝试使用遗传算法耦合支持向量机方法(GA-SVM)对两种特征选择方法所选的描述符子集分别建立非线性支持向量机回归模型. 三种机器学习方法所建模型均得到比较满意的预测效果. 采用LSRA所选的6 个描述符建立的三个QSAR模型对于测试集的相关系数为0.958-0.962, GA-SVM法给出最好的预测精度(0.962). 采用GA-PLS所选的7个描述符建立的三个QSAR模型对于测试集的相关系数为0.918-0.960, 偏最小二乘回归模型的结果最好(0.960). 本工作提供了一种有效的方法来预测丙型肝炎病毒抑制剂的生物活性, 该方法也可以扩展到其他类似的定量构效关系研究领域.     

Beyond linear least squares regression

Regression is a collection of statistical methods that are used to study relationships among predictor and response variables. In addition to the most popular linear model, solved by least squares, several other techniques have found an application in analytical chemistry. Biased methods such as stepwise regression, ridge regression, principal components regression, and partial least squares regression are especially useful in cases of poorly or underdetermined systems with collinearity. When structural and/or distributional assumptions associated with linear least squares are violated, nonlinear regression, robust regression or generalized least squares estimators may offer potential remedies.     

New approach by Kriging models to problems in QSAR

Most models in quantitative structure and activity relationship (QSAR) research, proposed by various techniques such as ordinary least squares regression, principal components regression, partial least squares regression, and multivariate adaptive regression splines, involve a linear parametric part and a random error part. The random errors in those models are assumed to be independently identical distributed. However, the independence assumption is not reasonable in many cases. Some dependence among errors should be considered just like Kriging. It has been successfully used in computer experiments for modeling. The aim of this paper is to apply Kriging models to QSAR. Our experiments show that the Kriging models can significantly improve the performances of the models obtained by many existing methods.