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

Nonlinear Supervised Dimensionality Reduction via Smooth Regular Embeddings

The recovery of the intrinsic geometric structures of data collections is an important problem in data analysis. Supervised extensions of several manifold learning approaches have been proposed in the recent years. Meanwhile, existing methods primarily focus on the embedding of the training data, and the generalization of the embedding to initially unseen test data is rather ignored. In this work, we build on recent theoretical results on the generalization performance of supervised manifold learning algorithms. Motivated by these performance bounds, we propose a supervised manifold learning method that computes a nonlinear embedding while constructing a smooth and regular interpolation function that extends the embedding to the whole data space in order to achieve satisfactory generalization. The embedding and the interpolator are jointly learnt such that the Lipschitz regularity of the interpolator is imposed while ensuring the separation between different classes. Experimental results on several image data sets show that the proposed method outperforms traditional classifiers and the supervised dimensionality reduction algorithms in comparison in terms of classification accuracy in most settings

Confident Kernel Sparse Coding and Dictionary Learning

In recent years, kernel-based sparse coding (K-SRC) has received particular attention due to its efficient representation of nonlinear data structures in the feature space. Nevertheless, the existing K-SRC methods suffer from the lack of consistency between their training and test optimization frameworks. In this work, we propose a novel confident K-SRC and dictionary learning algorithm (CKSC) which focuses on the discriminative reconstruction of the data based on its representation in the kernel space. CKSC focuses on reconstructing each data sample via weighted contributions which are confident in its corresponding class of data. We employ novel discriminative terms to apply this scheme to both training and test frameworks in our algorithm. This specific design increases the consistency of these optimization frameworks and improves the discriminative performance in the recall phase. In addition, CKSC directly employs the supervised information in its dictionary learning framework to enhance the discriminative structure of the dictionary. For empirical evaluations, we implement our CKSC algorithm on multivariate time-series benchmarks such as DynTex++ and UTKinect. Our claims regarding the superior performance of the proposed algorithm are justified throughout comparing its classification results to the state-of-the-art K-SRC algorithms.Comment: 10 pages, ICDM 2018 conferenc

Sparse multinomial kernel discriminant analysis (sMKDA)

Dimensionality reduction via canonical variate analysis (CVA) is important for pattern recognition and has been extended variously to permit more flexibility, e.g. by "kernelizing" the formulation. This can lead to over-fitting, usually ameliorated by regularization. Here, a method for sparse, multinomial kernel discriminant analysis (sMKDA) is proposed, using a sparse basis to control complexity. It is based on the connection between CVA and least-squares, and uses forward selection via orthogonal least-squares to approximate a basis, generalizing a similar approach for binomial problems. Classification can be performed directly via minimum Mahalanobis distance in the canonical variates. sMKDA achieves state-of-the-art performance in terms of accuracy and sparseness on 11 benchmark datasets

Localized Linear Discriminant Analysis

Despite its age, the Linear Discriminant Analysis performs well even in situations where the underlying premises like normally distributed data with constant covariance matrices over all classes are not met. It is, however, a global technique that does not regard the nature of an individual observation to be classified. By weighting each training observation according to its distance to the observation of interest, a global classifier can be transformed into an observation specific approach. So far, this has been done for logistic discrimination. By using LDA instead, the computation of the local classifier is much simpler. Moreover, it is ready for applications in multi-class situations. --classification,local models,LDA

2D Face Recognition System Based on Selected Gabor Filters and Linear Discriminant Analysis LDA

We present a new approach for face recognition system. The method is based on 2D face image features using subset of non-correlated and Orthogonal Gabor Filters instead of using the whole Gabor Filter Bank, then compressing the output feature vector using Linear Discriminant Analysis (LDA). The face image has been enhanced using multi stage image processing technique to normalize it and compensate for illumination variation. Experimental results show that the proposed system is effective for both dimension reduction and good recognition performance when compared to the complete Gabor filter bank. The system has been tested using CASIA, ORL and Cropped YaleB 2D face images Databases and achieved average recognition rate of 98.9 %