Identification of disease-causing genes using microarray data mining and gene ontology

Background: One of the best and most accurate methods for identifying disease-causing genes is monitoring gene expression values in different samples using microarray technology. One of the shortcomings of microarray data is that they provide a small quantity of samples with respect to the number of genes. This problem reduces the classification accuracy of the methods, so gene selection is essential to improve the predictive accuracy and to identify potential marker genes for a disease. Among numerous existing methods for gene selection, support vector machine-based recursive feature elimination (SVMRFE) has become one of the leading methods, but its performance can be reduced because of the small sample size, noisy data and the fact that the method does not remove redundant genes. Methods: We propose a novel framework for gene selection which uses the advantageous features of conventional methods and addresses their weaknesses. In fact, we have combined the Fisher method and SVMRFE to utilize the advantages of a filtering method as well as an embedded method. Furthermore, we have added a redundancy reduction stage to address the weakness of the Fisher method and SVMRFE. In addition to gene expression values, the proposed method uses Gene Ontology which is a reliable source of information on genes. The use of Gene Ontology can compensate, in part, for the limitations of microarrays, such as having a small number of samples and erroneous measurement results. Results: The proposed method has been applied to colon, Diffuse Large B-Cell Lymphoma (DLBCL) and prostate cancer datasets. The empirical results show that our method has improved classification performance in terms of accuracy, sensitivity and specificity. In addition, the study of the molecular function of selected genes strengthened the hypothesis that these genes are involved in the process of cancer growth. Conclusions: The proposed method addresses the weakness of conventional methods by adding a redundancy reduction stage and utilizing Gene Ontology information. It predicts marker genes for colon, DLBCL and prostate cancer with a high accuracy. The predictions made in this study can serve as a list of candidates for subsequent wet-lab verification and might help in the search for a cure for cancers

Fractal dimension for clustering and unsupervised and supervised feature selection.

Data mining refers to the automation of data analysis to extract patterns from large amounts of data. A major breakthrough in modelling natural patterns is the recognition that nature is fractal, not Euclidean. Fractals are capable of modelling self-similarity, infinite details, infinite length and the absence of smoothness. This research was aimed at simplifying the discovery and detection of groups in data using fractal dimension. These data mining tasks were addressed efficiently. The first task defines groups of instances (clustering), the second selects useful features from non-defined (unsupervised) groups of instances and the third selects useful features from pre-defined (supervised) groups of instances. Improvements are shown on two data mining classification models: hierarchical clustering and Artificial Neural Networks (ANN). For clustering tasks, a new two-phase clustering algorithm based on the Fractal Dimension (FD), compactness and closeness of clusters is presented. The proposed method, uses self-similarity properties of the data, first divides the data into sufficiently large sub-clusters with high compactness. In the second stage, the algorithm merges the sub-clusters that are close to each other and have similar complexity. The final clusters are obtained through a very natural and fully deterministic way. The selection of different feature subspaces leads to different cluster interpretations. An unsupervised embedded feature selection algorithm, able to detect relevant and redundant features, is presented. This algorithm is based on the concept of fractal dimension. The level of relevance in the features is quantified using a new proposed entropy measure, which is less complex than the current state-of-the-art technology. The proposed algorithm is able to maintain and in some cases improve the quality of the clusters in reduced feature spaces. For supervised feature selection, for classification purposes, a new algorithm is proposed that maximises the relevance and minimises the redundancy of the features simultaneously. This algorithm makes use of the FD and the Mutual Information (MI) techniques, and combines them to create a new measure of feature usefulness and to produce a simpler and non-heuristic algorithm. The similar nature of the two techniques, FD and MI, makes the proposed algorithm more suitable for a straightforward global analysis of the data

An Empirical Comparative Study on the Two Methods of Eliciting Singers’ Emotions in Singing: Self-Imagination and VR Training

Emotional singing can affect vocal performance and the audience’s engagement. Chinese universities use traditional training techniques for teaching theoretical and applied knowledge. Self-imagination is the predominant training method for emotional singing. Recently, virtual reality (VR) technologies have been applied in several fields for training purposes. In this empirical comparative study, a VR training task was implemented to elicit emotions from singers and further assist them with improving their emotional singing performance. The VR training method was compared against the traditional self-imagination method. By conducting a two-stage experiment, the two methods were compared in terms of emotions’ elicitation and emotional singing performance. In the first stage, electroencephalographic (EEG) data were collected from the subjects. In the second stage, self-rating reports and third-party teachers’ evaluations were collected. The EEG data were analyzed by adopting the max-relevance and min-redundancy algorithm for feature selection and the support vector machine (SVM) for emotion recognition. Based on the results of EEG emotion classification and subjective scale, VR can better elicit the positive, neutral, and negative emotional states from the singers than not using this technology (i.e., self-imagination). Furthermore, due to the improvement of emotional activation, VR brings the improvement of singing performance. The VR hence appears to be an effective approach that may improve and complement the available vocal music teaching methods

High-Dimensional Feature Selection by Feature-Wise Kernelized Lasso

The goal of supervised feature selection is to find a subset of input features that are responsible for predicting output values. The least absolute shrinkage and selection operator (Lasso) allows computationally efficient feature selection based on linear dependency between input features and output values. In this paper, we consider a feature-wise kernelized Lasso for capturing non-linear input-output dependency. We first show that, with particular choices of kernel functions, non-redundant features with strong statistical dependence on output values can be found in terms of kernel-based independence measures. We then show that the globally optimal solution can be efficiently computed; this makes the approach scalable to high-dimensional problems. The effectiveness of the proposed method is demonstrated through feature selection experiments with thousands of features.Comment: 18 page

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