基于稳健判别方法的基因剪切位点识别

基因识别是生物信息学研究的一个分支.多元统计中的判别分析方法模型简单、便于解释,处理剪切位点的识别问题效果良好,但极易受到异常值的影响.对于传统判别分析方法,使用稳健统计量进行优化,得到较好的效果,并通过加权方法进一步提高了判别分析方法的稳健性,取得了更好的识别效果.加权稳健判别分析方法稳健性高、受离群值影响小,对其他分类判别问题具有很好的实际意义和参考价值.     

基于统计检验与机器学习的全基因组关联研究框架

采用统计检验和机器学习的方法来研究SNP或基因与疾病(可测性状)的关联性.先对SNP选择合适的数值编码方式,并设计了相应的统计检验流程,随后通过P值初步筛选出了与疾病或性状相关联的位点.在此基础上,对筛选出的位点,采用随机森林,XGBoost等机器学习方法,从样本外预测的角度判断SNP与疾病或性状的关联度.相关结果,显示发现运用该分析框架能较好地筛选出与疾病或性状关联的SNP(基因).并且框架由于考虑了多种分类模型,有着稳健性高,计算开销较小以及可以交叉比对等优势.框架未来在还可在金融,社交网络等方面发挥作用.     

短基因编码序列识别及基因突变检测问题研究

基于频谱分析的基因预测方法普遍有一个缺点就是对短编码序列识别效果不佳,采用多参数Z-curve方法,再运用Fisher线性判别法对短编码序列(<100bp)进行预测,并进行了仿真验证.接着对基因突变问题采用频谱和信噪比分析方法的可行性进行了研究.     

PCA-Fisher判别模型在煤层底板突水预测中的应用

针对当前煤层底板突水影响因素复杂、预测精度低及难度大等问题,通过结合主成分分析法(PCA)和Fisher判别分析法,构建了PCA-Fisher煤层底板突水判别模型,并将该判别模型应用于贵州省六盘水月亮田煤矿9号煤层对其进行底板突水危险性预测.笔者将含水层水压、隔水层厚度及煤层倾角等6个指标作为影响该煤层底板突水危险性的主要因素,把18组实测数据输入PCA-Fisher判别模型并进行煤层底板突水预测.结果显示:PCA提取的3个主成分F1、F2及F3的方差贡献率达94.179%,且判别模型的前14组训练样本正确率达85.7%;最后判别未参加训练的后4组样本,误判率为0%,其精度高达100%,结果印证了PCA-Fisher的判别模型对煤层底板突水预测的正确性.     

基于全基因组的遗传性疾病和性状的关联位点分析

研究发现,通过全基因组关联分析,找出与疾病相关的位点或基因,对于人们防治遗传病,具有重要意义.首先,考虑固定效应(SNP位点)和随机效应(人群中的群体结构和亲缘关系),建立了混合线性模型,并且利用基于FDR标准的BH法对多重检验的P值进行校正,找出最有可能的致病位点.其次,利用Fisher的P值组合方法,将基因所包含的所有SNP位点组合,找出与疾病最可能相关的基因.由于遗传疾病可能与基因所包含的位点的子集关联,我们参考已有的ARTP模型,对模型进行了改进.最后,建立多表型联合模型MultiPhen找出与10个性状有关联的位点.     

PARK18基因多态性与中国汉族人帕金森病的相关性

目的研究PARK18基因多态性与中国汉族人群帕金森病(PD)的相关性,旨在探讨PD的发病机制,为PD的风险预测提供新的遗传标记.方法选取224例PD患者(PD组)及同期体检健康者309例(对照组),采用PCR、DNA测序等方法检测比较两组PARK18基因多态性位点,分析rs3129882与PD遗传易感性的相关性.结果两组对象rs3129882基因型频率和等位基因频率分布的差异均无统计学意义(均P>0.05).rs3129882多态性与PD发生风险的关联性在3种遗传模式下均无统计学意义(均P>0.05).结论本研究暂不支持中国汉族人群中PARKl8区域rs3129882位点单核苷酸多态性与PD的发生有显著关联性.     

具有遗传性疾病和性状的遗传位点分析

随着信息技术的进步和发展,现代生物学越来越多地将这些技术用于大规模生物数据的收集、分析、挖掘等过程.大量计算机技术,特别是统计方法被用来进行复杂疾病的分析.大量研究表明,人体的许多表型性状差异以及对药物和疾病的易感性等都可能与某些位点相关联,或和包含有多个位点的基因相关联.因此,定位与性状或疾病相关联的位点在染色体或基因中的位置,能帮助研究人员了解性状和一些疾病的遗传机理,也能使人们对致病位点加以干预,防止一些遗传病的发生.利用随机森林方法、Bootstrap重抽样、logistic回归等大数据分析方法,意在解决优化生物学位点关联性分析中单一致病位点识别、多位点相互作用和多性状位点关联性分析等子问题.     

基于形式Context的格聚类与特征逼近判别

本文建立一个基于 Guo- Qiang Zhang[2 ]理论的格聚类模型与特征逼近判别模型 .如果一个统计背景 ET被解释为一个 Context CET=(Po,| =Pa) ,那么基于形式 Context的格聚类模型完全是 [FCA]的外延和内涵统一的具体表达 ,而特征逼近判别模型则是从语义谓词逻辑出发的判别方法 ,用有限特征逼近解决了无限属性的实际应用困难 .     

蛋白质结构的主成分分析及氧链糖基化位点的人工神经网络预测

糖基化是蛋白质翻译后修饰的重要形式之一,氧链糖基化是糖基化的一种主要类型,对蛋白质氧链糖基化位点进行预测具有重要的意义.以窗口长度为41的蛋白质序列为研究对象,采用稀疏编码,利用主成分分析法研究了氧链糖基化蛋白质序列的结构特点;在提取主成分的基础上,设计了一个含单隐层的BP神经网络(256—8—4),对蛋白质氧链糖基化位点进行预测,把蛋白质序列分为4类;并同直接用BP神经网络分类的结果相比较,实验结果证明提出的方法省时,准确,预测的准确率达80~90%.     

基于泛函线性模型的基因水平关联性分析

采用泛函线性模型进行基因水平关联性分析时,需要对基因片段上离散位点的遗传变异值进行数值逼近.为了改善传统样条函数在逼近时精度不高,且在推导时比较耗时的问题,文章提出了采用勒让德多项式来进行数值逼近,并利用该类多项式的正交性来提高获得泛函线性模型的效率.通过分析模拟的基因数据,文章提出的方法可以在控制好第一类统计错误的前提下,提高统计检验能力,并减少计算时间.因此,在采用泛函线性模型进行基因水平关联分析时,使用勒让德多项式估计的模型比传统的样条函数模型更有实际应用价值.     

Mathematical programming models for piecewise-linear discriminant analysis

Mathematical programming (MP) discriminant analysis models are widely used to generate linear discriminant functions that can be adopted as classification models. Nonlinear classification models may have better classification performance than linear classifiers, but although MP methods can be used to generate nonlinear discriminant functions, functions of specified form must be evaluated separately. Piecewise-linear functions can approximate nonlinear functions, and two new MP methods for generating piecewise-linear discriminant functions are developed in this paper. The first method uses maximization of classification accuracy (MCA) as the objective, while the second uses an approach based on minimization of the sum of deviations (MSD). The use of these new MP models is illustrated in an application to a test problem and the results are compared with those from standard MCA and MSD models.     

Relative and absolute error control in a finite-difference method solution of Poisson's equation

An algorithm for error control (absolute and relative) in the five-point finite-difference method applied to Poisson's equation is described. The algorithm is based on discretization of the domain of the problem by means of three rectilinear grids, each of different resolution. We discuss some hardware limitations associated with the algorithm, which are mainly due to its second-order nature. A generalization of the algorithm for finite-difference methods of arbitrary order is presented. We believe that the algorithm is a valuable addition to typical textbook discussions of the five-point finite-difference method for Poisson's equation.     

Fourth-Order Symmetric DIRK Methods for Periodic Stiff Problems

New symmetric DIRK methods specially adapted to the numerical integration of first-order stiff ODE systems with periodic solutions are obtained. Our interest is focused on the dispersion (phase errors) of the dominant components in the numerical oscillations when these methods are applied to the homogeneous linear test model. Based on this homogeneous test model we derive the dispersion conditions for symmetric DIRK methods as well as symmetric stability functions with real poles and maximal dispersion order. Two new fourth-order symmetric methods with four and five stages are obtained. One of the methods is fourth-order dispersive whereas the other method is symplectic and sixth-order dispersive. These methods have been applied to a number of test problems (linear as well as nonlinear) and some numerical results are presented to show their efficiency when they are compared with the symplectic DIRK method derived by Sanz-Serna and Abia (SIAM J. Numer. Anal. 28 (1991) 1081–1096).     

Four-stage symplectic and P-stable SDIRKN methods with dispersion of high order

New SDIRKN methods specially adapted to the numerical integration of second-order stiff ODE systems with periodic solutions are obtained. Our interest is focused on the dispersion (phase errors) of the dominant components in the numerical oscillations when these methods are applied to the homogeneous linear test model. Based on this homogeneous test model we derive the dispersion and P-stability conditions for SDIRKN methods which are assumed to be zero dissipative. Two four-stage symplectic and P-stable methods with algebraic order 4 and high order of dispersion are obtained. One of the methods is symmetric and sixth-order dispersive whereas the other method is nonsymmetric and eighth-order dispersive. These methods have been applied to a number of test problems (linear as well as nonlinear) and some numerical results are presented to show their efficiency when they are compared with other methods derived by Sharp et al. [IMA J. Numer. Anal. 10 (1990) 489–504].     

Learning multicriteria classification models from examples: Decision rules in continuous space

The classification problem statement of multicriteria decision analysis is to model the classification of the alternatives/actions according to the decision maker's preferences. These models are based on outranking relations, utility functions or (linear) discriminant functions. Model parameters can be given explicitly or learnt from a preclassified set of alternatives/actions.In this paper we propose a novel approach, the Continuous Decision (CD) method, to learn parameters of a discriminant function, and we also introduce its extension, the Continuous Decision Tree (CDT) method, which describes the classification more accurately.The proposed methods are results of integration of Machine Learning methods in Decision Analysis. From a Machine Learning point of view, the CDT method can be considered as an extension of the C4.5 decision tree building algorithm that handles only numeric criteria but applies more complex tests in the inner nodes of the tree. For the sake of easier interpretation, the decision trees are transformed to rules.     

BACKWARD ERROR ANALYSIS OF SYMPLECTIC INTEGRATORS FOR LINEAR SEPARABLE HAMILTONIAN SYSTEMS

Symplecticness, stability, and asymptotic properties of Runge-Kutta, partitioned Runge-Kutta, and Runge-Kutta-Nystrom methods applied to the simple Hamiltonian system p = -vg, q = kp are studied. Some new results in connection with P-stability are presented. The main part is focused on backward error analysis. The numerical solution produced by a symplectic method with an appropriate stepsize is the exact solution of a perturbed Hamiltonian system at discrete points. This system is studied in detail and new results are derived. Numerical examples are presented.     

Business failure prediction using the UTADIS multicriteria analysis method

Business failure prediction is one of the most essential problems in the field of financial management. The research on developing quantitative business failure prediction models has been focused on building discriminant models to distinguish among failed and non-failed firms. Several researchers in this field have proposed multivariate statistical discrimination techniques. This paper explores the applicability of multicriteria analysis to predict business failure. Four preference disaggregation methods, namely the UTADIS method and three of its variants, are compared to three well-known multivariate statistical and econometric techniques, namely discriminant analysis, logit and probit analyses. A basic (learning) sample and a holdout (testing) sample are used to perform the comparison. Through this comparison, the relative performance of all the aforementioned methods is investigated regarding their discriminating and predicting ability.     

Feature Extraction for Nonparametric Discriminant Analysis

In high-dimensional classification problems, one is often interested in finding a few important discriminant directions in order to reduce the dimensionality. Fisher's linear discriminant analysis (LDA) is a commonly used method. Although LDA is guaranteed to find the best directions when each class has a Gaussian density with a common covariance matrix, it can fail if the class densities are more general. Using a likelihood-based interpretation of Fisher's LDA criterion, we develop a general method for finding important discriminant directions without assuming the class densities belong to any particular parametric family. We also show that our method can be easily integrated with projection pursuit density estimation to produce a powerful procedure for (reduced-rank) nonparametric discriminant analysis.     

A lower bound on the performance of the quadratic discriminant function

The quadratic discriminant function is often used to separate two classes of points in a multidimensional space. When the two classes are normally distributed, this results in the optimum separation. In some cases however, the assumption of normality is a poor one and the classification error is increased. The current paper derives an upper bound for the classification error due to a quadratic decision surface. The bound is strict when the class means and covariances and the quadratic discriminant surface satisfy certain specified symmetry conditions.     

Numerical solutions of Burgers–Huxley equation by exact finite difference and NSFD schemes

In this paper, numerical solution of the Burgers–Huxley (BH) equation is presented based on the nonstandard finite difference (NSFD) scheme. At first, two exact finite difference schemes for BH equation obtained. Moreover an NSFD scheme is presented for this equation. The positivity, boundedness and local truncation error of the scheme are discussed. Finally, the numerical results of the proposed method with those of some available methods compared.