Date on Master's Thesis/Doctoral Dissertation

5-2010

Document Type

Doctoral Dissertation

Degree Name

Ph. D.

Department

Computer Engineering and Computer Science

Committee Chair

Rouchka, Eric Christian

Author's Keywords

Hyper basis function network; Regularization; Transcription start sites

Subject

Neural networks (Computer science); Bioinformatics

Abstract

A hyper basis function network (HyperBF) is a generalized radial basis function network (RBF) where the activation function is a radial function of a weighted distance. The local weighting of the distance accounts for the variation in local scaling and discriminative power along each feature. Such generalization makes HyperBF networks capable of interpolating decision functions with high accuracy. However, such complexity makes HyperBF networks susceptible to overfitting. Moreover, training a HyperBF network demands weights, centers and local scaling factors to be optimized simultaneously. In the case of a relatively large dataset with a large network structure, such optimization becomes computationally challenging. In this work, a new regularization method that performs soft local dimension reduction and weight decay is presented. The regularized HyperBF (Reduced HyperBF) network is shown to provide classification accuracy comparable to a Support Vector Machines (SVM) while requiring a significantly smaller network structure. Furthermore, the soft local dimension reduction is shown to be informative for ranking features based on their localized discriminative power. In addition, a practical training approach for constructing HyperBF networks is presented. This approach uses hierarchal clustering to initialize neurons followed by a gradient optimization using a scaled Rprop algorithm with a localized partial backtracking step (iSRprop). Experimental results on a number of datasets show a faster and smoother convergence than the regular Rprop algorithm. The proposed Reduced HyperBF network is applied to two problems in bioinformatics. The first is the detection of transcription start sites (TSS) in human DNA. A novel method for improving the accuracy of TSS recognition for recently published methods is proposed. This method incorporates a new metric feature based on oligonucleotide positional frequencies. The second application is the accurate classification of microarray samples. A new feature selection algorithm based on a Reduced HyperBF network is proposed. The method is applied to two microarray datasets and is shown to select a minimal subset of features with high discriminative information. The algorithm is compared to two widely used methods and is shown to provide competitive results. In both applications, the final Reduced HyperBF network is used for higher level analysis. Significant neurons can indicate subpopulations, while local active features provide insight into the characteristics of the subpopulation in specific and the whole class in general.

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