70,777 research outputs found
Non-Redundant Spectral Dimensionality Reduction
Spectral dimensionality reduction algorithms are widely used in numerous
domains, including for recognition, segmentation, tracking and visualization.
However, despite their popularity, these algorithms suffer from a major
limitation known as the "repeated Eigen-directions" phenomenon. That is, many
of the embedding coordinates they produce typically capture the same direction
along the data manifold. This leads to redundant and inefficient
representations that do not reveal the true intrinsic dimensionality of the
data. In this paper, we propose a general method for avoiding redundancy in
spectral algorithms. Our approach relies on replacing the orthogonality
constraints underlying those methods by unpredictability constraints.
Specifically, we require that each embedding coordinate be unpredictable (in
the statistical sense) from all previous ones. We prove that these constraints
necessarily prevent redundancy, and provide a simple technique to incorporate
them into existing methods. As we illustrate on challenging high-dimensional
scenarios, our approach produces significantly more informative and compact
representations, which improve visualization and classification tasks
Dimension Reduction by Mutual Information Discriminant Analysis
In the past few decades, researchers have proposed many discriminant analysis
(DA) algorithms for the study of high-dimensional data in a variety of
problems. Most DA algorithms for feature extraction are based on
transformations that simultaneously maximize the between-class scatter and
minimize the withinclass scatter matrices. This paper presents a novel DA
algorithm for feature extraction using mutual information (MI). However, it is
not always easy to obtain an accurate estimation for high-dimensional MI. In
this paper, we propose an efficient method for feature extraction that is based
on one-dimensional MI estimations. We will refer to this algorithm as mutual
information discriminant analysis (MIDA). The performance of this proposed
method was evaluated using UCI databases. The results indicate that MIDA
provides robust performance over different data sets with different
characteristics and that MIDA always performs better than, or at least
comparable to, the best performing algorithms.Comment: 13pages, 3 tables, International Journal of Artificial Intelligence &
Application
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
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