The authors provide a didactic treatment of nonlinear (categorical) principal components analysis (PCA). This method is the nonlinear equivalent of standard PCA and reduces the observed variables to a number of uncorrelated principal components. The most important advantages of nonlinear over linear PCA are that it incorporates nominal and ordinal variables and that it can handle and discover n...

Traditional principal components analysis (PCA) techniques for face recognition are based on batch-mode training using a pre-available image set. Real world applications require that the training set be dynamic of evolving nature where within the framework of continuous learning, new training images are continuously added to the original set; this would trigger a costly continuous re-computatio...

Sparse principal component analysis combines the idea of sparsity with principal component analysis (PCA). There are two kinds of sparse PCA; sparse loading PCA (slPCA) which keeps all the variables but zeroes out some of their loadings; and sparse variable PCA (svPCA) which removes whole variables by simultaneously zeroing out all the loadings on some variables. In this paper we propose a mode...

Prostate cancer (PCa) is a global disease causing large numbers of deaths every year. Recent studies have indicated the RTK/ERK pathway might be a key pathway in the development of PCa. However, the exact association and evolution-based mechanism remain unclear. This study was conducted by combining genotypic and phenotypic data from the Chinese Consortium for Prostate Cancer Genetics (ChinaPCa...

Most correlation clustering algorithms rely on principal component analysis (PCA) as a correlation analysis tool. The correlation of each cluster is learned by applying PCA to a set of sample points. Since PCA is rather sensitive to outliers, if a small fraction of these points does not correspond to the correct correlation of the cluster, the algorithms are usually misled or even fail to detec...

A popular approach for dimensionality reduction and data analysis is principal component analysis (PCA). A limiting factor with PCA is that it does not inform us on which of the original features are important. There is a recent interest in sparse PCA (SPCA). By applying an L1 regularizer to PCA, a sparse transformation is achieved. However, true feature selection may not be achieved as non-spa...

Epigenetic changes have been suggested to drive prostate cancer (PCa) development and progression. Therefore, in this study, we aimed to identify novel epigenetics-related genes in PCa tissues, and to examine their expression in metastatic PCa cell lines. We analyzed the expression of epigenetics-related genes via a clustering analysis based on ge...

BACKGROUND Lysosome-associated protein transmembrane 4b-35 (LAPTM4B-35) is a member of the mammalian 4-tetratransmembrane spanning protein superfamily, which is overexpressed in several solid malignancies. However, the expression of LAPTM4B-35 and its role in the progression of prostate cancer (PCa) is unknown. The aim of the present study was to investigate the LAPTM4B-35 expression in PCa and...

Objective Yes associated protein 1 (YAP1) is a member of the Hippo pathway, acting as a transcriptional coactivator. To elucidate the role of YAP1 and phosphorylated (p)YAP1 in prostate cancer (PCa) tumorigenesis, we investigated their expression in clinical samples of PCa and cell lines. Methods Fifty-four tumor, adjacent nontumor, and prostate intraepithelial neoplasia (PIN) tissues from pa...

METHOD Genome-wide expression profiling is a widely used approach for characterizing heterogeneous populations of cells, tissues, biopsies, or other biological specimen. The exploratory analysis of such data typically relies on generic unsupervised methods, e.g. principal component analysis (PCA) or hierarchical clustering. However, generic methods fail to exploit prior knowledge about the mole...