Comparing Prediction Accuracy for Supervised Techniques in Gene Expression Data

Classification is one of the most important tasks for different application such as text categorization, tone recognition, image classification, micro-array gene expression, proteins structure predictions, data classification etc. Microarray based gene expression profiling has been emerged as an efficient technique for cancer classification, as well as for diagnosis, prognosis, and treatment purposes. The classification of different tumor types is of great significance in cancer diagnosis and drug innovation. One challenging area in the studies of gene expression data is the classification of different types of tumors into correct classes. Diagonal discriminant analysis, regularized discriminant analysis, support vector machines and k-nearest neighbor have been suggested as among the best methods for small sample size situations. The methods are applied to datasets from four recently published cancer gene expression studies. Four publicly available microarray data sets are Leukemia, Lymphoma, SRBCT & Prostate. The performance of the classification technique has been evaluated according to the percentage of misclassification through hold-out cross validation

Comparing Prediction Accuracy for Machine Learning and Other Classical Approaches in Gene Expression Data

Microarray based gene expression profiling has been emerged as an efficient technique for cancer classification, as well as for diagnosis, prognosis, and treatment purposes. The classification of different tumor types is of great significance in cancer diagnosis and drug innovation. Using a large number of genes to classify samples based on a small number of microarrays remains a difficult problem. Feature selection techniques can be used to extract the marker genes which influence the classification accuracy effectively by eliminating the unwanted noisy and redundant genes. Quite a number of methods have been proposed in recent years with promising results. But there are still a lot of issues which need to be addressed and understood. Diagonal discriminant analysis, regularized discriminant analysis, support vector machines and k-nearest neighbor have been suggested as among the best methods for small sample size situations. In this paper, we have compared the performance of different discrimination methods for the classification of tumors based on gene expression data. The methods are applied to datasets from four recently published cancer gene expression studies. The performance of the classification technique has been evaluated for varying number of selected features in terms of misclassification rate  using hold-out cross validation. Our study shows that KNN, RDA and SVM with linear kernel methods have lower misclassification rate than the other algorithms. Keywords: microarray, gene expression, KNN, DLDA, RDA, SV

Discriminant feature pursuit: from statistical learning to informative learning.

Lin Dahua.Thesis (M.Phil.)--Chinese University of Hong Kong, 2006.Includes bibliographical references (leaves 233-250).Abstracts in English and Chinese.Abstract --- p.iAcknowledgement --- p.iiiChapter 1 --- Introduction --- p.1Chapter 1.1 --- The Problem We are Facing --- p.1Chapter 1.2 --- Generative vs. Discriminative Models --- p.2Chapter 1.3 --- Statistical Feature Extraction: Success and Challenge --- p.3Chapter 1.4 --- Overview of Our Works --- p.5Chapter 1.4.1 --- New Linear Discriminant Methods: Generalized LDA Formulation and Performance-Driven Sub space Learning --- p.5Chapter 1.4.2 --- Coupled Learning Models: Coupled Space Learning and Inter Modality Recognition --- p.6Chapter 1.4.3 --- Informative Learning Approaches: Conditional Infomax Learning and Information Chan- nel Model --- p.6Chapter 1.5 --- Organization of the Thesis --- p.8Chapter I --- History and Background --- p.10Chapter 2 --- Statistical Pattern Recognition --- p.11Chapter 2.1 --- Patterns and Classifiers --- p.11Chapter 2.2 --- Bayes Theory --- p.12Chapter 2.3 --- Statistical Modeling --- p.14Chapter 2.3.1 --- Maximum Likelihood Estimation --- p.14Chapter 2.3.2 --- Gaussian Model --- p.15Chapter 2.3.3 --- Expectation-Maximization --- p.17Chapter 2.3.4 --- Finite Mixture Model --- p.18Chapter 2.3.5 --- A Nonparametric Technique: Parzen Windows --- p.21Chapter 3 --- Statistical Learning Theory --- p.24Chapter 3.1 --- Formulation of Learning Model --- p.24Chapter 3.1.1 --- Learning: Functional Estimation Model --- p.24Chapter 3.1.2 --- Representative Learning Problems --- p.25Chapter 3.1.3 --- Empirical Risk Minimization --- p.26Chapter 3.2 --- Consistency and Convergence of Learning --- p.27Chapter 3.2.1 --- Concept of Consistency --- p.27Chapter 3.2.2 --- The Key Theorem of Learning Theory --- p.28Chapter 3.2.3 --- VC Entropy --- p.29Chapter 3.2.4 --- Bounds on Convergence --- p.30Chapter 3.2.5 --- VC Dimension --- p.35Chapter 4 --- History of Statistical Feature Extraction --- p.38Chapter 4.1 --- Linear Feature Extraction --- p.38Chapter 4.1.1 --- Principal Component Analysis (PCA) --- p.38Chapter 4.1.2 --- Linear Discriminant Analysis (LDA) --- p.41Chapter 4.1.3 --- Other Linear Feature Extraction Methods --- p.46Chapter 4.1.4 --- Comparison of Different Methods --- p.48Chapter 4.2 --- Enhanced Models --- p.49Chapter 4.2.1 --- Stochastic Discrimination and Random Subspace --- p.49Chapter 4.2.2 --- Hierarchical Feature Extraction --- p.51Chapter 4.2.3 --- Multilinear Analysis and Tensor-based Representation --- p.52Chapter 4.3 --- Nonlinear Feature Extraction --- p.54Chapter 4.3.1 --- Kernelization --- p.54Chapter 4.3.2 --- Dimension reduction by Manifold Embedding --- p.56Chapter 5 --- Related Works in Feature Extraction --- p.59Chapter 5.1 --- Dimension Reduction --- p.59Chapter 5.1.1 --- Feature Selection --- p.60Chapter 5.1.2 --- Feature Extraction --- p.60Chapter 5.2 --- Kernel Learning --- p.61Chapter 5.2.1 --- Basic Concepts of Kernel --- p.61Chapter 5.2.2 --- The Reproducing Kernel Map --- p.62Chapter 5.2.3 --- The Mercer Kernel Map --- p.64Chapter 5.2.4 --- The Empirical Kernel Map --- p.65Chapter 5.2.5 --- Kernel Trick and Kernelized Feature Extraction --- p.66Chapter 5.3 --- Subspace Analysis --- p.68Chapter 5.3.1 --- Basis and Subspace --- p.68Chapter 5.3.2 --- Orthogonal Projection --- p.69Chapter 5.3.3 --- Orthonormal Basis --- p.70Chapter 5.3.4 --- Subspace Decomposition --- p.70Chapter 5.4 --- Principal Component Analysis --- p.73Chapter 5.4.1 --- PCA Formulation --- p.73Chapter 5.4.2 --- Solution to PCA --- p.75Chapter 5.4.3 --- Energy Structure of PCA --- p.76Chapter 5.4.4 --- Probabilistic Principal Component Analysis --- p.78Chapter 5.4.5 --- Kernel Principal Component Analysis --- p.81Chapter 5.5 --- Independent Component Analysis --- p.83Chapter 5.5.1 --- ICA Formulation --- p.83Chapter 5.5.2 --- Measurement of Statistical Independence --- p.84Chapter 5.6 --- Linear Discriminant Analysis --- p.85Chapter 5.6.1 --- Fisher's Linear Discriminant Analysis --- p.85Chapter 5.6.2 --- Improved Algorithms for Small Sample Size Problem . --- p.89Chapter 5.6.3 --- Kernel Discriminant Analysis --- p.92Chapter II --- Improvement in Linear Discriminant Analysis --- p.100Chapter 6 --- Generalized LDA --- p.101Chapter 6.1 --- Regularized LDA --- p.101Chapter 6.1.1 --- Generalized LDA Implementation Procedure --- p.101Chapter 6.1.2 --- Optimal Nonsingular Approximation --- p.103Chapter 6.1.3 --- Regularized LDA algorithm --- p.104Chapter 6.2 --- A Statistical View: When is LDA optimal? --- p.105Chapter 6.2.1 --- Two-class Gaussian Case --- p.106Chapter 6.2.2 --- Multi-class Cases --- p.107Chapter 6.3 --- Generalized LDA Formulation --- p.108Chapter 6.3.1 --- Mathematical Preparation --- p.108Chapter 6.3.2 --- Generalized Formulation --- p.110Chapter 7 --- Dynamic Feedback Generalized LDA --- p.112Chapter 7.1 --- Basic Principle --- p.112Chapter 7.2 --- Dynamic Feedback Framework --- p.113Chapter 7.2.1 --- Initialization: K-Nearest Construction --- p.113Chapter 7.2.2 --- Dynamic Procedure --- p.115Chapter 7.3 --- Experiments --- p.115Chapter 7.3.1 --- Performance in Training Stage --- p.116Chapter 7.3.2 --- Performance on Testing set --- p.118Chapter 8 --- Performance-Driven Subspace Learning --- p.119Chapter 8.1 --- Motivation and Principle --- p.119Chapter 8.2 --- Performance-Based Criteria --- p.121Chapter 8.2.1 --- The Verification Problem and Generalized Average Margin --- p.122Chapter 8.2.2 --- Performance Driven Criteria based on Generalized Average Margin --- p.123Chapter 8.3 --- Optimal Subspace Pursuit --- p.125Chapter 8.3.1 --- Optimal threshold --- p.125Chapter 8.3.2 --- Optimal projection matrix --- p.125Chapter 8.3.3 --- Overall procedure --- p.129Chapter 8.3.4 --- Discussion of the Algorithm --- p.129Chapter 8.4 --- Optimal Classifier Fusion --- p.130Chapter 8.5 --- Experiments --- p.131Chapter 8.5.1 --- Performance Measurement --- p.131Chapter 8.5.2 --- Experiment Setting --- p.131Chapter 8.5.3 --- Experiment Results --- p.133Chapter 8.5.4 --- Discussion --- p.139Chapter III --- Coupled Learning of Feature Transforms --- p.140Chapter 9 --- Coupled Space Learning --- p.141Chapter 9.1 --- Introduction --- p.142Chapter 9.1.1 --- What is Image Style Transform --- p.142Chapter 9.1.2 --- Overview of our Framework --- p.143Chapter 9.2 --- Coupled Space Learning --- p.143Chapter 9.2.1 --- Framework of Coupled Modelling --- p.143Chapter 9.2.2 --- Correlative Component Analysis --- p.145Chapter 9.2.3 --- Coupled Bidirectional Transform --- p.148Chapter 9.2.4 --- Procedure of Coupled Space Learning --- p.151Chapter 9.3 --- Generalization to Mixture Model --- p.152Chapter 9.3.1 --- Coupled Gaussian Mixture Model --- p.152Chapter 9.3.2 --- Optimization by EM Algorithm --- p.152Chapter 9.4 --- Integrated Framework for Image Style Transform --- p.154Chapter 9.5 --- Experiments --- p.156Chapter 9.5.1 --- Face Super-resolution --- p.156Chapter 9.5.2 --- Portrait Style Transforms --- p.157Chapter 10 --- Inter-Modality Recognition --- p.162Chapter 10.1 --- Introduction to the Inter-Modality Recognition Problem . . . --- p.163Chapter 10.1.1 --- What is Inter-Modality Recognition --- p.163Chapter 10.1.2 --- Overview of Our Feature Extraction Framework . . . . --- p.163Chapter 10.2 --- Common Discriminant Feature Extraction --- p.165Chapter 10.2.1 --- Formulation of the Learning Problem --- p.165Chapter 10.2.2 --- Matrix-Form of the Objective --- p.168Chapter 10.2.3 --- Solving the Linear Transforms --- p.169Chapter 10.3 --- Kernelized Common Discriminant Feature Extraction --- p.170Chapter 10.4 --- Multi-Mode Framework --- p.172Chapter 10.4.1 --- Multi-Mode Formulation --- p.172Chapter 10.4.2 --- Optimization Scheme --- p.174Chapter 10.5 --- Experiments --- p.176Chapter 10.5.1 --- Experiment Settings --- p.176Chapter 10.5.2 --- Experiment Results --- p.177Chapter IV --- A New Perspective: Informative Learning --- p.180Chapter 11 --- Toward Information Theory --- p.181Chapter 11.1 --- Entropy and Mutual Information --- p.181Chapter 11.1.1 --- Entropy --- p.182Chapter 11.1.2 --- Relative Entropy (Kullback Leibler Divergence) --- p.184Chapter 11.2 --- Mutual Information --- p.184Chapter 11.2.1 --- Definition of Mutual Information --- p.184Chapter 11.2.2 --- Chain rules --- p.186Chapter 11.2.3 --- Information in Data Processing --- p.188Chapter 11.3 --- Differential Entropy --- p.189Chapter 11.3.1 --- Differential Entropy of Continuous Random Variable . --- p.189Chapter 11.3.2 --- Mutual Information of Continuous Random Variable . --- p.190Chapter 12 --- Conditional Infomax Learning --- p.191Chapter 12.1 --- An Overview --- p.192Chapter 12.2 --- Conditional Informative Feature Extraction --- p.193Chapter 12.2.1 --- Problem Formulation and Features --- p.193Chapter 12.2.2 --- The Information Maximization Principle --- p.194Chapter 12.2.3 --- The Information Decomposition and the Conditional Objective --- p.195Chapter 12.3 --- The Efficient Optimization --- p.197Chapter 12.3.1 --- Discrete Approximation Based on AEP --- p.197Chapter 12.3.2 --- Analysis of Terms and Their Derivatives --- p.198Chapter 12.3.3 --- Local Active Region Method --- p.200Chapter 12.4 --- Bayesian Feature Fusion with Sparse Prior --- p.201Chapter 12.5 --- The Integrated Framework for Feature Learning --- p.202Chapter 12.6 --- Experiments --- p.203Chapter 12.6.1 --- A Toy Problem --- p.203Chapter 12.6.2 --- Face Recognition --- p.204Chapter 13 --- Channel-based Maximum Effective Information --- p.209Chapter 13.1 --- Motivation and Overview --- p.209Chapter 13.2 --- Maximizing Effective Information --- p.211Chapter 13.2.1 --- Relation between Mutual Information and Classification --- p.211Chapter 13.2.2 --- Linear Projection and Metric --- p.212Chapter 13.2.3 --- Channel Model and Effective Information --- p.213Chapter 13.2.4 --- Parzen Window Approximation --- p.216Chapter 13.3 --- Parameter Optimization on Grassmann Manifold --- p.217Chapter 13.3.1 --- Grassmann Manifold --- p.217Chapter 13.3.2 --- Conjugate Gradient Optimization on Grassmann Manifold --- p.219Chapter 13.3.3 --- Computation of Gradient --- p.221Chapter 13.4 --- Experiments --- p.222Chapter 13.4.1 --- A Toy Problem --- p.222Chapter 13.4.2 --- Face Recognition --- p.223Chapter 14 --- Conclusion --- p.23

1 Regularized Discriminant Analysis for Face Recognition

This paper studies Regularized Discriminant Analysis (RDA) in the context of face recognition. We check RDA sensitivity to different photometric preprocessing methods and compare its performance to other classifiers. Our study shows that RDA is better able to extract the relevant discriminatory information from training data than the other classifiers tested, thus obtaining a lower error rate. Moreover, RDA is robust under various lighting conditions while the other classifiers perform badly when no photometric method is applied