Principal Component Linear

Two fundamentally different statistical approaches to biomarker selection are possible. With the first, experimental data can be used to construct multivariate statistical models of increasing complexity and predictive power - well-known examples are Partial Least Square Discriminant Analysis (PLS-DA) (Barker Rayens, 2003 Kemsley, 1996 Szymanska et al., 2011) or Principal Component Linear Discriminant Analysis (PC-LDA) (Smit et al., 2007 Werf et al., 2006). Inspection of the model coefficients then should point to those variables that are important for class discrimination. As an alternative, univariate statistical tests can be... 

We have to apply projection techniques which allow us to plot the hyperspaces onto two- or three-dimensional space. Principal Component Analysis (PCA) is a method that is fit for performing this task it is described in Section 9.4.4. PCA operates with latent variables, which are linear combinations of the original variables. 

To gain insight into chemometric methods such as correlation analysis, Multiple Linear Regression Analysis, Principal Component Analysis, Principal Component Regression, and Partial Least Squares regression/Projection to Latent Structures... 

Kohonen network Conceptual clustering Principal Component Analysis (PCA) Decision trees Partial Least Squares (PLS) Multiple Linear Regression (MLR) Counter-propagation networks Back-propagation networks Genetic algorithms (GA)... 

The previously mentioned data set with a total of 115 compounds has already been studied by other statistical methods such as Principal Component Analysis (PCA), Linear Discriminant Analysis, and the Partial Least Squares (PLS) method [39]. Thus, the choice and selection of descriptors has already been accomplished. 

Consider the data shown in Figure 9.32. It is easy to see that there is a high degree ( correlation between the x and the y values. If we were to define a new variable, z = x +, then we could express most of the variation in the data as the values of this new variabl 2. The new variable is called a principal component. In general, a principal component is linear combination of the variables ... 

An alternative to principal components analysis is factor analysis. This is a technique which can identify multicollinearities in the set - these are descriptors which are correlated with a linear combination of two or more other descriptors. Factor analysis is related to (and... 

Multiple linear regression is strictly a parametric supervised learning technique. A parametric technique is one which assumes that the variables conform to some distribution (often the Gaussian distribution) the properties of the distribution are assumed in the underlying statistical method. A non-parametric technique does not rely upon the assumption of any particular distribution. A supervised learning method is one which uses information about the dependent variable to derive the model. An unsupervised learning method does not. Thus cluster analysis, principal components analysis and factor analysis are all examples of unsupervised learning techniques. 

How does principal component analysis work Consider, for example, the two-dimensional distribution of points shown in Figure 7a. This distribution clearly has a strong linear component and is closer to a one-dimensional distribution than to a full two-dimensional distribution. However, from the one-dimensional projections of this distribution on the two orthogonal axes X and Y you would not know that. In fact, you would probably conclude, based only on these projections, that the data points are homogeneously distributed in two dimensions. A simple axes rotation is all it takes to reveal that the data points... 

We now consider a type of analysis in which the data (which may consist of solvent properties or of solvent effects on rates, equilibria, and spectra) again are expressed as a linear combination of products as in Eq. (8-81), but now the statistical treatment yields estimates of both a, and jc,. This method is called principal component analysis or factor analysis. A key difference between multiple linear regression analysis and principal component analysis (in the chemical setting) is that regression analysis adopts chemical models a priori, whereas in factor analysis the chemical significance of the factors emerges (if desired) as a result of the analysis. We will not explore the statistical procedure, but will cite some results. We have already encountered examples in Section 8.2 on the classification of solvents and in the present section in the form of the Swain et al. treatment leading to Eq. (8-74). 

Initially, the whole data set was analyzed by the linear PCA. By examining the behaviors of the process data in the projection spaces defined by small number of principal components, it... 

Principal Component Analysis (PCA). Principal component analysis is an extremely important method within the area of chemometrics. By this type of mathematical treatment one finds the main variation in a multidimensional data set by creating new linear combinations of the raw data (e.g. spectral variables) [4]. The method is superior when dealing with highly collinear variables as is the case in most spectroscopic techniques two neighbor wavelengths show almost the same variation. 

In a general way, we can state that the projection of a pattern of points on an axis produces a point which is imaged in the dual space. The matrix-to-vector product can thus be seen as a device for passing from one space to another. This property of swapping between spaces provides a geometrical interpretation of many procedures in data analysis such as multiple linear regression and principal components analysis, among many others [12] (see Chapters 10 and 17). 

A first introduction to principal components analysis (PCA) has been given in Chapter 17. Here, we present the method from a more general point of view, which encompasses several variants of PCA. Basically, all these variants have in common that they produce linear combinations of the original columns in a measurement table. These linear combinations represent a kind of abstract measurements or factors that are better descriptors for structure or pattern in the data than the original measurements [1]. The former are also referred to as latent variables [2], while the latter are called manifest variables. Often one finds that a few of these abstract measurements account for a large proportion of the variation in the data. In that case one can study structure and pattern in a reduced space which is possibly two- or three-dimensional. 

Each column of S represents a row-principal component of X and can be interpreted as a linear combination of the columns of X using the elements of V as weighting coefficients ... 

In the method of linear discriminant analysis, one therefore seeks a linear function of the variables, D, which maximizes the ratio between both variances. Geometrically, this means that we look for a line through the cloud of points, such that the projections of the points of the two groups are separated as much as possible. The approach is comparable to principal components, where one seeks a line that explains best the variation in the data (see Chapter 17). The principal component line and the discriminant function often more or less coincide (as is the case in Fig. 33.8a) but this is not necessarily so, as shown in Fig. 33.8b. 

Fig. 33.8. Situation where principal component (PC) and linear discriminant function (DF) are essentially the same (a) and very different (b).

In order to apply RBL or GRAFA successfully some attention has to be paid to the quality of the data. Like any other multivariate technique, the results obtained by RBL and GRAFA are affected by non-linearity of the data and heteroscedast-icity of the noise. By both phenomena the rank of the data matrix is higher than the number of species present in the sample. This has been demonstrated on the PCA results obtained for an anthracene standard solution eluted and detected by three different brands of diode array detectors [37]. In all three cases significant second eigenvalues were obtained and structure is seen in the second principal component. 

Note that the lipophilicity parameter log P is defined as a decimal logarithm. The parabolic equation is only non-linear in the variable log P, but is linear in the coefficients. Hence, it can be solved by multiple linear regression (see Section 10.8). The bilinear equation, however, is non-linear in both the variable P and the coefficients, and can only be solved by means of non-linear regression techniques (see Chapter 11). It is approximately linear with a positive slope (/ ,) for small values of log P, while it is also approximately linear with a negative slope b + b for large values of log P. The term bilinear is used in this context to indicate that the QSAR model can be resolved into two linear relations for small and for large values of P, respectively. This definition differs from the one which has been introduced in the context of principal components analysis in Chapter 17. 

While principal components models are used mostly in an unsupervised or exploratory mode, models based on canonical variates are often applied in a supervisory way for the prediction of biological activities from chemical, physicochemical or other biological parameters. In this section we discuss briefly the methods of linear discriminant analysis (LDA) and canonical correlation analysis (CCA). Although there has been an early awareness of these methods in QSAR [7,50], they have not been widely accepted. More recently they have been superseded by the successful introduction of partial least squares analysis (PLS) in QSAR. Nevertheless, the early pattern recognition techniques have prepared the minds for the introduction of modem chemometric approaches. 

Techniques for multivariate input analysis reduce the data dimensionality by projecting the variables on a linear or nonlinear hypersurface and then describe the input data with a smaller number of attributes of the hypersurface. Among the most popular methods based on linear projection is principal component analysis (PCA). Those based on nonlinear projection are nonlinear PCA (NLPCA) and clustering methods. 

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