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

Structured Sparsity: Discrete and Convex approaches

Compressive sensing (CS) exploits sparsity to recover sparse or compressible signals from dimensionality reducing, non-adaptive sensing mechanisms. Sparsity is also used to enhance interpretability in machine learning and statistics applications: While the ambient dimension is vast in modern data analysis problems, the relevant information therein typically resides in a much lower dimensional space. However, many solutions proposed nowadays do not leverage the true underlying structure. Recent results in CS extend the simple sparsity idea to more sophisticated {\em structured} sparsity models, which describe the interdependency between the nonzero components of a signal, allowing to increase the interpretability of the results and lead to better recovery performance. In order to better understand the impact of structured sparsity, in this chapter we analyze the connections between the discrete models and their convex relaxations, highlighting their relative advantages. We start with the general group sparse model and then elaborate on two important special cases: the dispersive and the hierarchical models. For each, we present the models in their discrete nature, discuss how to solve the ensuing discrete problems and then describe convex relaxations. We also consider more general structures as defined by set functions and present their convex proxies. Further, we discuss efficient optimization solutions for structured sparsity problems and illustrate structured sparsity in action via three applications.Comment: 30 pages, 18 figure

Bibliometric Mapping of the Computational Intelligence Field

In this paper, a bibliometric study of the computational intelligence field is presented. Bibliometric maps showing the associations between the main concepts in the field are provided for the periods 1996–2000 and 2001–2005. Both the current structure of the field and the evolution of the field over the last decade are analyzed. In addition, a number of emerging areas in the field are identified. It turns out that computational intelligence can best be seen as a field that is structured around four important types of problems, namely control problems, classification problems, regression problems, and optimization problems. Within the computational intelligence field, the neural networks and fuzzy systems subfields are fairly intertwined, whereas the evolutionary computation subfield has a relatively independent position.neural networks;bibliometric mapping;fuzzy systems;bibliometrics;computational intelligence;evolutionary computation

Wavelet-Based Kernel Construction for Heart Disease Classification

© 2019 ADVANCES IN ELECTRICAL AND ELECTRONIC ENGINEERINGHeart disease classification plays an important role in clinical diagnoses. The performance improvement of an Electrocardiogram classifier is therefore of great relevance, but it is a challenging task too. This paper proposes a novel classification algorithm using the kernel method. A kernel is constructed based on wavelet coefficients of heartbeat signals for a classifier with high performance. In particular, a wavelet packet decomposition algorithm is applied to heartbeat signals to obtain the Approximation and Detail coefficients, which are used to calculate the parameters of the kernel. A principal component analysis algorithm with the wavelet-based kernel is employed to choose the main features of the heartbeat signals for the input of the classifier. In addition, a neural network with three hidden layers in the classifier is utilized for classifying five types of heart disease. The electrocardiogram signals in nine patients obtained from the MIT-BIH database are used to test the proposed classifier. In order to evaluate the performance of the classifier, a multi-class confusion matrix is applied to produce the performance indexes, including the Accuracy, Recall, Precision, and F1 score. The experimental results show that the proposed method gives good results for the classification of the five mentioned types of heart disease.Peer reviewedFinal Published versio