LigDockCSA: protein-ligand docking using conformational space annealing

Protein–ligand docking techniques are one of the essential tools for structure‐based drug design. Two major components of a successful docking program are an efficient search method and an accurate scoring function. In this work, a new docking method called LigDockCSA is developed by using a powerful global optimization technique, conformational space annealing (CSA), and a scoring function that combines the AutoDock energy and the piecewise linear potential (PLP) torsion energy. It is shown that the CSA search method can find lower energy binding poses than the Lamarckian genetic algorithm of AutoDock. However, lower‐energy solutions CSA produced with the AutoDock energy were often less native‐like. The loophole in the AutoDock energy was fixed by adding a torsional energy term, and the CSA search on the refined energy function is shown to improve the docking performance. The performance of LigDockCSA was tested on the Astex diverse set which consists of 85 protein–ligand complexes. LigDockCSA finds the best scoring poses within 2 Å root‐mean‐square deviation (RMSD) from the native structures for 84.7% of the test cases, compared to 81.7% for AutoDock and 80.5% for GOLD. The results improve further to 89.4% by incorporating the conformational entropy. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011     

Can we trust docking results? Evaluation of seven commonly used programs on PDBbind database

Docking is one of the most commonly used techniques in drug design. It is used for both identifying correct poses of a ligand in the binding site of a protein as well as for the estimation of the strength of protein–ligand interaction. Because millions of compounds must be screened, before a suitable target for biological testing can be identified, all calculations should be done in a reasonable time frame. Thus, all programs currently in use exploit empirically based algorithms, avoiding systematic search of the conformational space. Similarly, the scoring is done using simple equations, which makes it possible to speed up the entire process. Therefore, docking results have to be verified by subsequent in vitro studies. The purpose of our work was to evaluate seven popular docking programs (Surflex, LigandFit, Glide, GOLD, FlexX, eHiTS, and AutoDock) on the extensive dataset composed of 1300 protein–ligands complexes from PDBbind 2007 database, where experimentally measured binding affinity values were also available. We compared independently the ability of proper posing [according to Root mean square deviation (or Root mean square distance) of predicted conformations versus the corresponding native one] and scoring (by calculating the correlation between docking score and ligand binding strength). To our knowledge, it is the first large‐scale docking evaluation that covers both aspects of docking programs, that is, predicting ligand conformation and calculating the strength of its binding. More than 1000 protein–ligand pairs cover a wide range of different protein families and inhibitor classes. Our results clearly showed that the ligand binding conformation could be identified in most cases by using the existing software, yet we still observed the lack of universal scoring function for all types of molecules and protein families. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011     

A bi‐level neural‐based fuzzy classification approach for credit scoring problems

The credit scoring is a risk evaluation task considered as a critical decision for financial institutions in order to avoid wrong decision that may result in huge amount of losses. Classification models are one of the most widely used groups of data mining approaches that greatly help decision makers and managers to reduce their credit risk of granting credits to customers instead of intuitive experience or portfolio management. Accuracy is one of the most important criteria in order to choose a credit‐scoring model; and hence, the researches directed at improving upon the effectiveness of credit scoring models have never been stopped. In this article, a hybrid binary classification model, namely FMLP, is proposed for credit scoring, based on the basic concepts of fuzzy logic and artificial neural networks (ANNs). In the proposed model, instead of crisp weights and biases, used in traditional multilayer perceptrons (MLPs), fuzzy numbers are used in order to better model of the uncertainties and complexities in financial data sets. Empirical results of three well‐known benchmark credit data sets indicate that hybrid proposed model outperforms its component and also other those classification models such as support vector machines (SVMs), K‐nearest neighbor (KNN), quadratic discriminant analysis (QDA), and linear discriminant analysis (LDA). Therefore, it can be concluded that the proposed model can be an appropriate alternative tool for financial binary classification problems, especially in high uncertainty conditions. © 2013 Wiley Periodicals, Inc. Complexity 18: 46–57, 2013     

认知诊断中Q矩阵和Q矩阵理论

Q矩阵和Q矩阵理论是认知诊断中一对容易混淆的概念,一方面需要强调它们的差异,另一方面对Q矩阵理论做一些补充,比如在一定条件下,多级评分的认知诊断中测验蓝图的设计原理.根据实测数据对测验蓝图Q矩阵修正的设想,以及认知诊断模型和多维项目反应模型的联系.     

An intelligent-agent-based fuzzy group decision making model for financial multicriteria decision support: The case of credit scoring

Credit risk analysis is an active research area in financial risk management and credit scoring is one of the key analytical techniques in credit risk evaluation. In this study, a novel intelligent-agent-based fuzzy group decision making (GDM) model is proposed as an effective multicriteria decision analysis (MCDA) tool for credit risk evaluation. In this proposed model, some artificial intelligent techniques, which are used as intelligent agents, are first used to analyze and evaluate the risk levels of credit applicants over a set of pre-defined criteria. Then these evaluation results, generated by different intelligent agents, are fuzzified into some fuzzy opinions on credit risk level of applicants. Finally, these fuzzification opinions are aggregated into a group consensus and meantime the fuzzy aggregated consensus is defuzzified into a crisp aggregated value to support final decision for decision-makers of credit-granting institutions. For illustration and verification purposes, a simple numerical example and three real-world credit application approval datasets are presented.     

基于位置关联性打分方程的人类转录因子结合位点的预测(英文)

转录因子结合位点的识别是阐明基因转录调控机制的重要环节,准确的转录因子结合位点的预测算法将有助于人们识别转录因子的目标基因,进而研究转录因子结合位点在上游调控区中的位置对转录调控的影响.然而,目前存在的预测转录因子结合位点的算法所得结果的特异性普遍较低,因此有必要提出一种新的有效的预测转录因子结合位点的算法.本文利用JASPAR数据库上的数据,在深入分析转录因子结合位点生物学特征的基础上,构建了考虑位点保守性和伪计数的位置关联性打分方程.预测结果表明,在最佳阈值之下,该算法对转录因子结合位点的假阳率低于0.01%.     

蛋白质中RNA-结合残基预测的随机森林模型

构建了用于预测蛋白质序列中RNA-结合残基的分类模型.在模型的特征提取方面,除了与功能相关的结构特征和序列正交编码信息以外,还提出了一个新颖的特征PSSM-PP.该特征不仅包含蛋白质序列的进化保守特征,还包含与蛋白质和RNA结合有关的氨基酸理化特征.在设计模型时,考虑到样本数据量大的问题,选用了快速的随机森林算法.该预测模型总体预测准确率达到87.02％,特异性达到95.62％,敏感性达51.16％,Matthew相关系数为0.533 6.此外,还构建了RNA结合残基的预测平台.     

PowerPoint文档自动阅卷的设计与实现

本文利用VBA技术对PowerPoint文档对象属性进行分析,并且对PowerPoint操作进行分类编码,运用阅卷信息语言生成系统生成标准阅卷信息,然后运用VB工具,查询、匹配数据库和考生操作的VBA属性值,从而实现PowerPoint文档的评分与自动阅卷。     

基于时间序列的模糊聚类与规则提取信用评价模型

提出基于多维时间序列模糊聚类与模糊规则提取技术相结合的模糊分类系统,将其应用于信用评价研究.该方法利用投影寻踪技术对多维时间序列数据进行降维处理并进行模糊分类;根据分类结果和最佳投影值提取模糊规则,采用梯形分布法生成三个模糊隶属函数;最后根据计算模糊贴近度确定样本的信用级别.实例证明该方法具有良好的评价效果和实用价值.     

基于语义相似度与XGBoost算法的英语作文智能评价框架研究

作文智能评分和评语智能生成能极大减轻评阅专家的工作量、节约人力成本。目前,评分和评语结果的准确性与公平性尚不高。近年来,机器学习和自然语言处理等技术的快速发展,在一定程度上提升了文本分类、机器翻译等任务的性能,但仍有许多新的研究成果尚未应用于作文智能评价。本研究综合了词向量(word2vec)、段落向量(paragraph2vec)、词性向量(pos2vec)和LDA (latent dirichlet allocation)等特征,共同组合为作文的语义表示向量;采用基于kNN (k nearest neighbors)算法的语义相似度模型,得到作文的评语标签;采用基于XGBoost(extreme gradient boosting)的回归模型计算英语作文的评分值;并以900篇大学生英语作文为样本,构造算例进行验证。最后表明,提出的智能评价框架在英语作文自动评分和评语生成的准确性上,都要高于传统方法。