Principal component analysis -based approach

Steindl, T. M., Crump, C. E., Hayden, E. G., Langer, T. Pharmacophore modeling, docking, and principal component analysis based clustering combined computer-assisted approaches to identify new inhibitors of the human rhinovirus coat protein. 7. Med. Chem. 2005, 4S(20), 6250-6260. 

A method of resolution that makes a very few a priori assumptions is based on principal components analysis. The various forms of this approach are based on the self-modeling curve resolution developed in 1971 (55). The method requites a data matrix comprised of spectroscopic scans obtained from a two-component system in which the concentrations of the components are varying over the sample set. Such a data matrix could be obtained, for example, from a chromatographic analysis where spectroscopic scans are obtained at several points in time as an overlapped peak elutes from the column. 

We are about to enter what is, to many, a mysterious world—the world of factor spaces and the factor based techniques, Principal Component Analysis (PCA, sometimes known as Factor Analysis) and Partial Least-Squares (PLS) in latent variables. Our goal here is to thoroughly explore these topics using a data-centric approach to dispell the mysteries. When you complete this chapter, neither factor spaces nor the rhyme at the top of this page will be mysterious any longer. As we will see, it s all in your point of view. 

Wu et al. [46] used the approach of an artificial neural network and applied it to drug release from osmotic pump tablets based on several coating parameters. Gabrielsson et al. [47] applied several different multivariate methods for both screening and optimization applied to the general topic of tablet formulation they included principal component analysis and... 

Computational methods have been applied to determine the connections in systems that are not well-defined by canonical pathways. This is either done by semi-automated and/or curated literature causal modeling [1] or by statistical methods based on large-scale data from expression or proteomic studies (a mostly theoretical approach is given by reference [2] and a more applied approach is in reference [3]). Many methods, including clustering, Bayesian analysis and principal component analysis have been used to find relationships and "fingerprints" in gene expression data [4]. 

A principal components multivariate statistical approach (SIMCA) was evaluated and applied to interpretation of isomer specific analysis of polychlorinated biphenyls (PCBs) using both a microcomputer and a main frame computer. Capillary column gas chromatography was employed for separation and detection of 69 individual PCB isomers. Computer programs were written in AMSII MUMPS to provide a laboratory data base for data manipulation. This data base greatly assisted the analysts in calculating isomer concentrations and data management. Applications of SIMCA for quality control, classification, and estimation of the composition of multi-Aroclor mixtures are described for characterization and study of complex environmental residues. 

There are many advantages in using this approach to feature selection. First, chance classification is not a serious problem because the bulk of the variance or information content of the feature subset selected is about the classification problem of interest. Second, features that contain discriminatory information about a particular classification problem are usually correlated, which is why feature selection methods using principal component analysis or other variance-based methods are generally preferred. Third, the principal component plot... 

A generalised structure of an electronic nose is shown in Fig. 15.9. The sensor array may be QMB, conducting polymer, MOS or MS-based sensors. The data generated by each sensor are processed by a pattern-recognition algorithm and the results are then analysed. The ability to characterise complex mixtures without the need to identify and quantify individual components is one of the main advantages of such an approach. The pattern-recognition methods maybe divided into non-supervised (e.g. principal component analysis, PCA) and supervised (artificial neural network, ANN) methods also a combination of both can be used. 

The molecular specificity of Fourier transform infrared (FTIR) lends itself quite well to applications in pharmaceutical development labs, as pointed out in a review article with some historical perspective.10 One of the more common applications of mid-IR in development is a real-time assessment of reaction completion when used in conjunction with standard multivariate statistical tools, such as partial least squares (PLS) and principal component analysis (PCA).18,19 Another clever use of FTIR is illustrated in Figure 9.1, where the real-time response of a probe-based spectroscopic analyzer afforded critical control in the charge of an activating agent (trifluoroacetic anhydride) to activate lactol. Due to stability and reactivity concerns, the in situ spectroscopic approach was... 

A second approach to determining optimum TLC systems is based on principal components analysis. This is another statistical approach aimed at the identification of pharmaceuticals [76]. By using this approach on 360 drugs, 4 mobile phases from a set of 40 were chosen as giving the most diverse chromatographic information. Table 3.7 lists the four chosen mobile phases. 

A second and orthogonally equivariant approach to robust PCA uses projection pursuit (PP) techniques. These methods maximize a robust measure of spread to obtain consecutive directions on which the data points are projected. In Hubert et al. [46], a projection pursuit (PP) algorithm is presented, based on the ideas of Li and Chen [47] and Croux and Ruiz-Gazen [48], The algorithm is called RAPCA, which stands for reflection algorithm for principal components analysis. 

The McReynolds data were standardized and subjected to principal component analysis by several groups of workers who were able to reduce the data to three statistical components. Burns and Hawkes42 further refined the calculations to produce four quasi-theoretical indices that measure dispersion, polarity, acidity, and basicity. Hawkes has described this process in a more recent paper43 in which his group confirmed and refined these calculations with spectroscopic measurements. In addition to justifying their approach, they provide four indices for each of the 26 common liquid phases that were identified earlier as being the most important.36 The dispersion index is calculated from refractive indices, but the other three indices are based at least partially on chromatographic data. 

In organic chemistry, decomposition of molecules into substituents and molecular frameworks is a natural way to characterize molecular structures. In QSAR, both the Hansch-Fujita " and the Free-Wilson classical approaches are based on this decomposition, but only the second one explicitly accounts for the presence or the absence of substituent(s) attached to molecular framework at a certain position. While the multiple linear regression technique was associated with the Free-Wilson method, recent modifications of this approach involve more sophisticated statistical and machine-learning approaches, such as the principal component analysis and neural networks. ... 

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