Systematic benchmarking of microarray data feature extraction and classification
A combination of microarrays with classification methods is a promising approach to supporting clinical management decisions in oncology. The aim of this paper is to systematically benchmark the role of classification models. Each classification model is a combination of one feature extraction method and one classification method. We consider four feature extraction methods and five classification methods, from which 20 classification models can be derived. The feature extraction methods are t-statistics, non-parametric Wilcoxon statistics, ad hoc signal-to-noise statistics, and principal component analysis (PCA), and the classification methods are Fisher linear discriminant analysis (FLDA), the support vector machine (SVM), the k nearest-neighbour classifier (kNN), diagonal linear discriminant analysis (DLDA), and diagonal quadratic discriminant analysis (DQDA). Twenty randomizations of each of three binary cancer classification problems derived from publicly available datasets are examined. PCA plus FLDA is found to be the optimal classification model.

title: Characterizing the dynamic connectivity between genes by variable parameter regression and Kalman filtering based on temporal gene expression data
abstract: One popular method for analyzing functional connectivity between genes is to cluster genes with similar expression profiles. The most popular metrics measuring the similarity (or dissimilarity) among genes include Pearson's correlation, linear regression coefficient and Euclidean distance. As these metrics only give some constant values, they can only depict a stationary connectivity between genes. However, the functional connectivity between genes usually changes with time. Here, we introduce a novel insight for characterizing the relationship between genes and find out a proper mathematical model, variable parameter regression and Kalman filtering to model it.



We applied our algorithm to some simulated data and two pairs of real gene expression data. The changes of connectivity in simulated data are closely identical with the truth and the results of two pairs of gene expression data show that our method has successfully demonstrated the dynamic connectivity between genes.

title: A Neural Network Approach To Shape From Shading
abstract: In this paper, we propose a method of recovering shape from shading that solves directly for the surface height using neural networks. The main motivation of this paper is to provide an answer to the open problem proposed by Zhou and Chellappa [11]. We first formulate the shape from shading problem by combining a triangular element surface model with a linearized reflectance map. Then, we use a linear feed-forward network architecture with six layers to compute the surface height with a singular value decomposition. The weights in the model initialized using eigenvectors and eigen-values of the stiffness matrix of objective functional. Experimental results show that our solution is very effective.

title: Twi-Map Support Vector Machine for Multi-classification Problems
abstract: In this paper, a novel method called Twi-Map Support Vector Machines (TMSVM) for multi-classification problems is presented. Our ideas are as follows: Firstly, the training data set is mapped into a high-dimensional feature space. Secondly, we calculate the distances between the training data points and hyperplanes. Thirdly, we view the new vector consisting of the distances as new training data point. Finally, we map the new training data points into another high-dimensional feature space with the same kernel function and construct the optimal hyperplanes. In order to examine the training accuracy and the generalization performance of the proposed algorithm, One-against-One algorithm, Fuzzy Least Square Support Vector Machine (FLS-SVM) and the proposed algorithm are applied to five UCI data sets. Comparison results obtained by using three algorithms are given. The results show that the training accuracy and the testing one of the proposed algorithm are higher than those of One-against-One and FLS-SVM.

title: Support Vector Machines for Text Categorization in Chinese Question Classification
abstract: Question classification plays a crucial important role in the question answering system because categorizing a given question is beneficial to identify an answer in the documents. The goal of question classification is to accurately assign labels to question based on expected answer type. Recently, many machine learning algorithms are used for question classification. However many research results show that SVM perform best in this task, because it is well known to work well for nonlinear, sparse, high dimensional problems. In this experiment, we perform the One-against-One SVM algorithm and a feature extraction method of Chinese questions to get high classification accuracy

title: A singular integral of the composite operator
abstract: We establish the Poincare-type inequalities for the composition of the homotopy operator and the projection operator. We also obtain some estimates for the integral of the composite operator with a singular density.

title: Web Data Mining: Exploring Hyperlinks, Contents, and Usage Data
abstract: Web mining aims to discover useful information and knowledge from Web hyperlinks, page contents, and usage data. Although Web mining uses many conventional data mining techniques, it is not purely an application of traditional data mining due to the semi-structured and unstructured nature of the Web data. The field has also developed many of its own algorithms and techniques. Liu has written a comprehensive text on Web mining, which consists of two parts. The first part covers the data mining and machine learning foundations, where all the essential concepts and algorithms of data mining and machine learning are presented. The second part covers the key topics of Web mining, where Web crawling, search, social network analysis, structured data extraction, information integration, opinion mining and sentiment analysis, Web usage mining, query log mining, computational advertising, and recommender systems are all treated both in breadth and in depth. His book thus brings all the related concepts and algorithms together to form an authoritative and coherent text.The book offers a rich blend of theory and practice. It is suitable for students, researchers and practitioners interested in Web mining and data mining both as a learning text and as a reference book. Professors can readily use it for classes on data mining, Web mining, and text mining. Additional teaching materials such as lecture slides, datasets, and implemented algorithms are available online.

title: Text Classification by Labeling Words
abstract: Traditionally, text classifiers are built from labeled training examples. Labeling is usually done manually by human experts (or the users), which is a labor intensive and time consuming process. In the past few years, researchers investigated various forms of semi-supervised learning to reduce the burden of manual labeling. In this paper, we propose a different approach. Instead of labeling a set of documents, the proposed method labels a set of representative words for each class. It then uses these words to extract a set of documents for each class from a set of unlabeled documents to form the initial training set. The EM algorithm is then applied to build the classifier. The key issue of the approach is how to obtain a set of representative words for each class. One way is to ask the user to provide them, which is difficult because the user usually can only give a few words (which are insufficient for accurate learning). We propose a method to solve the problem. It combines clustering and feature selection. The technique can effectively rank the words in the unlabeled set according to their importance. The user then selects/labels some words from the ranked list for each class. This process requires less effort than providing words with no help or manual labelillg of documents. Our results show that the new method is highly effective and promising.