Elizabeth P. Chou

Elizabeth Chou, Catie McVey, Yin-Chen Hsieh et al.

With histograms as its foundation, we develop Categorical Exploratory Data Analysis (CEDA) under the extreme-$K$ sample problem, and illustrate its universal applicability through four 1D categorical datasets. Given a sizable $K$, CEDA's ultimate goal amounts to discover by data's information content via carrying out two data-driven computational tasks: 1) establish a tree geometry upon $K$ populations as a platform for discovering a wide spectrum of patterns among populations; 2) evaluate each geometric pattern's reliability. In CEDA developments, each population gives rise to a row vector of categories proportions. Upon the data matrix's row-axis, we discuss the pros and cons of Euclidean distance against its weighted version for building a binary clustering tree geometry. The criterion of choice rests on degrees of uniformness in column-blocks framed by this binary clustering tree. Each tree-leaf (population) is then encoded with a binary code sequence, so is tree-based pattern. For evaluating reliability, we adopt row-wise multinomial randomness to generate an ensemble of matrix mimicries, so an ensemble of mimicked binary trees. Reliability of any observed pattern is its recurrence rate within the tree ensemble. A high reliability value means a deterministic pattern. Our four applications of CEDA illuminate four significant aspects of extreme-$K$ sample problems.

Elizabeth P. Chou, Tzu-Wei Ko

The current study proposes a dimension reduction method, stepwise support vector machine (SVM), to reduce the dimensions of large p small n datasets. The proposed method is compared with other dimension reduction methods, namely, the Pearson product difference correlation coefficient (PCCs), recursive feature elimination based on random forest (RF-RFE), and principal component analysis (PCA), by using five gene expression datasets. Additionally, the prediction performance of the variables selected by our method is evaluated. The study found that stepwise SVM can effectively select the important variables and achieve good prediction performance. Moreover, the predictions of stepwise SVM for reduced datasets was better than those for the unreduced datasets. The performance of stepwise SVM was more stable than that of PCA and RF-RFE, but the performance difference with respect to PCCs was minimal. It is necessary to reduce the dimensions of large p small n datasets. We believe that stepwise SVM can effectively eliminate noise in data and improve the prediction accuracy in any large p small n dataset.