Dimensionality reduction using genetic algorithms

Pattern recognition generally requires that objects be described in terms of a set of measurable features. The selection and quality of the features representing each pattern have a considerable bearing on the success of subsequent pattern classification. Feature extraction is the process of deriving new features from the original features in order to reduce the cost of feature measurement, increase classifier efficiency, and allow higher classification accuracy. Many current feature extraction techniques involve linear transformations of the original pattern vectors to new vectors of lower dimensionality. While this is useful for data visualization and increasing classification efficiency, it does not necessarily reduce the number of features that must be measured since each new feature may be a linear combination of all of the features in the original pattern vector. Here, we present a new approach to feature extraction in which feature selection, feature extraction, and classifier training are performed simultaneously using a genetic algorithm. The genetic algorithm optimizes a vector of feature weights, which are used to scale the individual features in the original pattern vectors in either a linear or a nonlinear fashion. A masking vector is also employed to perform simultaneous selection of a subset of the features. We employ this technique in combination with the nearest neighbor classification rule, and compare the results with classical feature selection and extraction techniques, including sequential floating forward feature selection, and linear discriminant analysis. We also present results for the identification of favorable water-binding sites on protein surfaces, an important problem in biochemistry and drug design.