Wavelet feature extraction and genetic algorithm for biomarker detection in colorectal cancer data

Biomarkers which predict patient’s survival can play an important role in medical diagnosis and treatment. How to select the significant biomarkers from hundreds of protein markers is a key step in survival analysis. In this paper a novel method is proposed to detect the prognostic biomarkers ofsurvival in colorectal cancer patients using wavelet analysis, genetic algorithm, and Bayes classifier. One dimensional discrete wavelet transform (DWT) is normally used to reduce the dimensionality of biomedical data. In this study one dimensional continuous wavelet transform (CWT) was proposed to extract the features of colorectal cancer data. One dimensional CWT has no ability to reduce dimensionality of data, but captures the missing features of DWT, and is complementary part of DWT. Genetic algorithm was performed on extracted wavelet coefficients to select the optimized features, using Bayes classifier to build its fitness function. The corresponding protein markers were located based on the position of optimized features. Kaplan-Meier curve and Cox regression model 2 were used to evaluate the performance of selected biomarkers. Experiments were conducted on colorectal cancer dataset and several significant biomarkers were detected. A new protein biomarker CD46 was found to significantly associate with survival time

Effective Discriminative Feature Selection with Non-trivial Solutions

Feature selection and feature transformation, the two main ways to reduce dimensionality, are often presented separately. In this paper, a feature selection method is proposed by combining the popular transformation based dimensionality reduction method Linear Discriminant Analysis (LDA) and sparsity regularization. We impose row sparsity on the transformation matrix of LDA through ${\ell}_{2,1}$-norm regularization to achieve feature selection, and the resultant formulation optimizes for selecting the most discriminative features and removing the redundant ones simultaneously. The formulation is extended to the ${\ell}_{2,p}$-norm regularized case: which is more likely to offer better sparsity when $0<p<1$. Thus the formulation is a better approximation to the feature selection problem. An efficient algorithm is developed to solve the ${\ell}_{2,p}$-norm based optimization problem and it is proved that the algorithm converges when $0<p\le 2$. Systematical experiments are conducted to understand the work of the proposed method. Promising experimental results on various types of real-world data sets demonstrate the effectiveness of our algorithm

Dimensionality reduction of clustered data sets

We present a novel probabilistic latent variable model to perform linear dimensionality reduction on data sets which contain clusters. We prove that the maximum likelihood solution of the model is an unsupervised generalisation of linear discriminant analysis. This provides a completely new approach to one of the most established and widely used classification algorithms. The performance of the model is then demonstrated on a number of real and artificial data sets

Feature Augmentation via Nonparametrics and Selection (FANS) in High Dimensional Classification

We propose a high dimensional classification method that involves nonparametric feature augmentation. Knowing that marginal density ratios are the most powerful univariate classifiers, we use the ratio estimates to transform the original feature measurements. Subsequently, penalized logistic regression is invoked, taking as input the newly transformed or augmented features. This procedure trains models equipped with local complexity and global simplicity, thereby avoiding the curse of dimensionality while creating a flexible nonlinear decision boundary. The resulting method is called Feature Augmentation via Nonparametrics and Selection (FANS). We motivate FANS by generalizing the Naive Bayes model, writing the log ratio of joint densities as a linear combination of those of marginal densities. It is related to generalized additive models, but has better interpretability and computability. Risk bounds are developed for FANS. In numerical analysis, FANS is compared with competing methods, so as to provide a guideline on its best application domain. Real data analysis demonstrates that FANS performs very competitively on benchmark email spam and gene expression data sets. Moreover, FANS is implemented by an extremely fast algorithm through parallel computing.Comment: 30 pages, 2 figure

Latent Fisher Discriminant Analysis

Linear Discriminant Analysis (LDA) is a well-known method for dimensionality reduction and classification. Previous studies have also extended the binary-class case into multi-classes. However, many applications, such as object detection and keyframe extraction cannot provide consistent instance-label pairs, while LDA requires labels on instance level for training. Thus it cannot be directly applied for semi-supervised classification problem. In this paper, we overcome this limitation and propose a latent variable Fisher discriminant analysis model. We relax the instance-level labeling into bag-level, is a kind of semi-supervised (video-level labels of event type are required for semantic frame extraction) and incorporates a data-driven prior over the latent variables. Hence, our method combines the latent variable inference and dimension reduction in an unified bayesian framework. We test our method on MUSK and Corel data sets and yield competitive results compared to the baseline approach. We also demonstrate its capacity on the challenging TRECVID MED11 dataset for semantic keyframe extraction and conduct a human-factors ranking-based experimental evaluation, which clearly demonstrates our proposed method consistently extracts more semantically meaningful keyframes than challenging baselines.Comment: 12 page