A combinational feature selection and ensemble neural network method for classification of gene expression data
BackgroundMicroarray experiments are becoming a powerful tool for clinical diagnosis, as they have the potential to discover gene expression patterns that are characteristic for a particular disease. To date, this problem has received most attention in the context of cancer research, especially in tumor classification. Various feature selection methods and classifier design strategies also have been generally used and compared. However, most published articles on tumor classification have applied a certain technique to a certain dataset, and recently several researchers compared these techniques based on several public datasets. But, it has been verified that differently selected features reflect different aspects of the dataset and some selected features can obtain better solutions on some certain problems. At the same time, faced with a large amount of microarray data with little knowledge, it is difficult to find the intrinsic characteristics using traditional methods. In this paper, we attempt to introduce a combinational feature selection method in conjunction with ensemble neural networks to generally improve the accuracy and robustness of sample classification.ResultsWe validate our new method on several recent publicly available datasets both with predictive accuracy of testing samples and through cross validation. Compared with the best performance of other current methods, remarkably improved results can be obtained using our new strategy on a wide range of different datasets.ConclusionsThus, we conclude that our methods can obtain more information in microarray data to get more accurate classification and also can help to extract the latent marker genes of the diseases for better diagnosis and treatment.

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: 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: Systematic benchmarking of microarray data feature extraction and classification
abstract: 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: Multi-Agent Based Network Management Task Decomposition and Scheduling
abstract: The rapid development of Internet makes network management on large-scale network a critical issue. But with the management task of large-scale network becoming more complicated, neither centralized network management nor agent based network management can satisfy the increasing demands. This paper presents a network management framework to support dynamic scheduling decisions. In this framework, some algorithms are proposed to decompose the whole network management task into several groups of sub-tasks. During the course of decomposition, different priorities are assigned to sub-tasks. Then based on the priorities of these sub-tasks, the strategies of agent scheduling are established. Priority-ranked sub-tasks are grouped according to their inter-dependences. Sub-tasks with the same priority are put into the same group and they can be performed in parallel manner, while different groups of sub-tasks with different priorities must be implemented according to the order of their priorities. An experiment has been done with the algorithms, the results of which demonstrate the advantage of the algorithms.

title: Learning to Classify Texts Using Positive and Unlabeled Data
abstract: In traditional text classification, a classifier is built using labeled training documents of every class. This paper studies a different problem. Given a set P of documents of a particular class (called positive class) and a set U of unlabeled documents that contains documents from class P and also other types of documents (called negative class documents), we want to build a classifier to classify the documents in U into documents from P and documents not from P. The key feature of this problem is that there is no labeled negative document, which makes traditional text classification techniques inapplicable. In this paper, we propose an effective technique to solve the problem. It combines the Rocchio method and the SVM technique for classifier building. Experimental results show that the new method outperforms existing methods significantly.

title: Improving an Association Rule Based Classifier
abstract: Existing classification algorithms in machine learning mainly use heuristic search to find a subset of regularities in data for classification. In the past few years, extensive research was done in the database community on learning rules using exhaustive search under the name of association rule mining. Although the whole set of rules may not be used directly for accurate classification, effective classifiers have been built using the rules. This paper aims to improve such an exhaustive search based classification system CBA (Classification Based on Associations). The main strength of this system is that it is able to use the most accurate rules for classification. However, it also has weaknesses. This paper proposes two new techniques to deal with these weaknesses. This results in remarkably accurate classifiers. Experiments on a set of 34 benchmark datasets show that on average the new techniques reduce the error of CBA by 17% and is superior to CBA on 26 of the 34 datasets. They reduce the error of C4.5 by 19%, and improve performance on 29 datasets. Similar good results are also achieved against RIPPER, LB and a Naive-Bayes classifier.

title: Boundary Constrained Manifold Unfolding

title: Guest Editors' Introduction: Special Section on Intelligent Data Preparation