Genetic Algorithms for Feature Selection and Classification of Complex Chromatographic and Spectroscopic Data

A basic methodology for analyzing large multivariate chemical data sets based on feature selection is proposed. Each chromatogram or spectrum is represented as a point in a high dimensional measurement space. A genetic algorithm for feature selection and classification is applied to the data to identify features that optimize the separation of the classes in a plot of the two or three largest principal components of the data. A good principal component plot can only be generated using features whose variance or information is primarily about differences between classes in the data. Hence, feature subsets that maximize the ratio of between-class to within-class variance are selected by the pattern recognition genetic algorithm. Furthermore, the structure of the data set can be explored, for example, new classes can be discovered by simply tuning various parameters of the fitness function of the pattern recognition genetic algorithm. The proposed method has been validated on a wide range of data. A two-step procedure for pattern recognition analysis of spectral data has been developed. First, wavelets are used to denoise and deconvolute spectral bands by decomposing each spectrum into wavelet coefficients, which represent the samples constituent frequencies. Second, the pattern recognition genetic algorithm is used to identify wavelet coefficients characteristic of the class. In several studies involving spectral library searching, this method was employed. In one study, a search pre-filter to detect the presence of carboxylic acids from vapor phase infrared spectra which has previously eluted prominent researchers has been successfully formulated and validated. In another study, this same approach has been used to develop a pattern recognition assisted infrared library searching technique to determine the model, manufacturer, and year of the vehicle from which a clear coat paint smear originated. The pattern recognition genetic algorithm has also been used to develop a potential method to identify molds in indoor environments using volatile organic compounds. A distinct profile indicative of microbial volatile organic compounds was developed from air sampling data that could be readily differentiated from the blank for both high mold count and moderate mold count exposure samples. The utility of the pattern recognition genetic algorithm for discovery of biomarker candidates from genomic and proteomic data sets has also been shown.Chemistry Departmen

Variable Selection to Improve Classification in Structure-activity Studies and Spectroscopic Analysis

A genetic algorithm for variable selection to improve classifications is explored and validated on a wide range of data. In one study, 147 tetralin and indan musks and nonmusks compiled from the literature for the purpose of investigating the relationship between molecular structure and musk odor quality were correctly classified by 45 molecular descriptors identified by the pattern recognition GA which revealed an asymmetric data structure. A 3-layer feed-forward neural network trained by back propagation was used to develop a discriminant that correctly classified all of the compounds in the training set as musk and nonmusk. The neural network was successfully validated using an external prediction set of 37 compounds. In another study, 172 tetralin-, indan- and isochroman-like compounds were combed from the published literature to investigate the relationship between chemical structure and musk odor quality. The 20 molecular structural descriptors selected by the pattern recognition GA yielded a discriminant that was successfully validated using an external validation set consisting of 19 compounds. In a third study, the development of a prototype pattern recognition library search system for the infrared spectral libraries of the paint data query database to improve the discrimination capability and permit quantification of discriminant power for automotive paint comparisons involving the original equipment manufacturer is described. The system consists of two separate but interrelated components: search prefilters to cull the library spectra to a specific assembly plant and a cross correlation library search algorithm that utilizes both forward and backward searching to identify the year, line and model of the unknown in the spectral set identified by the search prefilters. The genetic algorithm was able to identify spectral variables from the clear coat, surfacer-primer and e-coat layers of the original manufacturer�s automotive paint that were characteristic of the assembly plant of the vehicle.Chemistr