Chemometrics clustering

Fig. 2 Generation of spectroscopic FTIR images, a Native sample, here a thin section of biological tissue, b FTIR spectra are collected at every pixel of the native sample. Bad spectra, e.g. from areas outside the sample, have already been removed, c Good spectra have been subject to a chemometric cluster analysis. Pixels are color-coded according to the cluster membership (spectral staining). Slightest chemical differences across the sample are now clearly revealed...

Calibration-check sample Chemometrics Cluster analysis Control chart Correlation coefficient Dependent variable Duplicates EDA... 

Evidence of the appHcation of computers and expert systems to instmmental data interpretation is found in the new discipline of chemometrics (qv) where the relationship between data and information sought is explored as a problem of mathematics and statistics (7—10). One of the most useful insights provided by chemometrics is the realization that a cluster of measurements of quantities only remotely related to the actual information sought can be used in combination to determine the information desired by inference. Thus, for example, a combination of viscosity, boiling point, and specific gravity data can be used to a characterize the chemical composition of a mixture of solvents (11). The complexity of such a procedure is accommodated by performing a multivariate data analysis. 

T. Fearn, Flat or natural A note on the choice of calibration samples, pp. 61-66 in Ref. [1]. T. Naes and T. Isaksson, Splitting of calibration data by cluster-analysis. J. Chemometr, 5 (1991)49-65. 

Multivariate chemometric techniques have subsequently broadened the arsenal of tools that can be applied in QSAR. These include, among others. Multivariate ANOVA [9], Simplex optimization (Section 26.2.2), cluster analysis (Chapter 30) and various factor analytic methods such as principal components analysis (Chapter 31), discriminant analysis (Section 33.2.2) and canonical correlation analysis (Section 35.3). An advantage of multivariate methods is that they can be applied in... 

To highlight and explain the quantitative chemical differences between the pitches found in the two archaeological sites, a chemometric evaluation of the GC/MS data (normalized peak areas) by means of principal component analysis (PCA) was performed. The PCA scatter plot of the first two principal components (Figure 8.6) highlights that the samples from Pisa and Fayum are almost completely separated into two clusters and that samples from Fayum form a relatively compact cluster, while the Pisa samples are... 

Also, we do not cover several typical chemometrics types of analyses, such as cluster analysis, experimental design, pattern recognition, classification, neural networks, wavelet transforms, qualimetrics etc. This explains our decision not to include the word chemometrics in the title. 

The final methodological chapter (Chapter 6) is devoted to cluster analysis. Besides a general treatment of different clustering approaches, also more specific problems in chemometrics are included, like clustering binary vectors indicating presence or absence of certain substructures. 

Kowalski and Bender presented chemometrics (at this time called pattern recognition and roughly considered as a branch of artificial intelligence) in a broader scope as a general approach to interpret chemical data, especially by mapping multivariate data with the purposes of cluster analysis and classification (Kowalski and Bender 1972). 

A comprehensive two-volume Handbook of Chemometrics and Qualimetrics has been published by D. L. Massart et al. (1997) and B. G. M. Vandeginste et al. (1998) predecessors of this work and historically interesting are Chemometrics A Textbook (Massart et al. 1988), Evaluation and Optimization of Laboratory Methods and Analytical Procedures (Massart et al. 1978), and The Interpretation of Analytical Chemical Data by the Use of Cluster Analysis (Massart and Kaufmann 1983). A classical reference is still Multivariate Calibration (Martens and Naes 1989). A dictionary with extensive explanations containing about 1700 entries is The Data Analysis Handbook (Frank and Todeschini 1994). 

Since the value of H depends on the choice of , modifications of this procedure have been proposed (Fernandez Piema and Massart 2000). Another modification of the Hopkins statistic—published in the chemometrics literature—concern the distributions of the values of the used variables (Hodes 1992 Jurs and Lawson 1991 Lawson and Jurs 1990). The Hopkins statistic has been suggested for an evaluation of variable selection methods with the aim to find a variable set (for instance, molecular descriptors) that gives distinct clustering of the objects (for instance, chemical structures)—hoping that the clusters reflect, for instance, different biological activities (Lawson and Jurs 1990). 

In most applications chemometric methods are applied to analytical data in an off-line mode that is, data has already been obtained by conventional techniques and is then applied to a particular chemometric method. Examples of this use are in cluster analysis and in pattern recognition. They are applied to spectroscopic, chromatographic, and other analytical data. 

A number of chemometric tools have been employed for these classifications, including partial least squares - hierarchical cluster analysis (PLS-HCA) for Viagra tablets [98] and antimalarial artesunate tablets [99]. de Peinder et al. used partial least squares discriminant analysis (PLS-DA) models to distinguish genuine from counterfeit Lipitor tablets even when the real API was present [100]. The counterfeit samples also were found to have poorer API distribution than the genuine ones based on spectra collected in a cross pattern on the tablet. 

CONTENTS 1. Chemometrics and the Analytical Process. 2. Precision and Accuracy. 3. Evaluation of Precision and Accuracy. Comparison of Two Procedures. 4. Evaluation of Sources of Variation in Data. Analysis of Variance. 5. Calibration. 6. Reliability and Drift. 7. Sensitivity and Limit of Detection. 8. Selectivity and Specificity. 9. Information. 10. Costs. 11. The Time Constant. 12. Signals and Data. 13. Regression Methods. 14. Correlation Methods. 15. Signal Processing. 16. Response Surfaces and Models. 17. Exploration of Response Surfaces. 18. Optimization of Analytical Chemical Methods. 19. Optimization of Chromatographic Methods. 20. The Multivariate Approach. 21. Principal Components and Factor Analysis. 22. Clustering Techniques. 23. Supervised Pattern Recognition. 24. Decisions in the Analytical Laboratory. 

Principal component analysis is a popular statistical method that tries to explain the covariance structure of data by means of a small number of components. These components are linear combinations of the original variables, and often allow for an interpretation and a better understanding of the different sources of variation. Because PCA is concerned with data reduction, it is widely used for the analysis of high-dimensional data, which are frequently encountered in chemometrics. PCA is then often the first step of the data analysis, followed by classification, cluster analysis, or other multivariate techniques [44], It is thus important to find those principal components that contain most of the information. 

FIGURE 9.4 Are there two or four clusters in the data (Adapted from Brereton, R.G., Ed., Multivariate Pattern Recognition in Chemometrics, Elsevier Science Publishers, Amsterdam, 1992. With permission.)... 

One of the emerging biological and biomedical application areas for vibrational spectroscopy and chemometrics is the characterization and discrimination of different types of microorganisms [74]. A recent review of various FTIR (Fourier transform infrared spectrometry) techniques describes such chemometrics methods as hierarchical cluster analysis (HCA), principal component analysis (PCA), and artificial neural networks (ANN) for use in taxonomical classification, discrimination according to susceptibility to antibiotic agents, etc. [74],... 

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