Esub8: A novel tool to predict protein subcellular localizations in eukaryotic organisms
BackgroundSubcellular localization of a new protein sequence is very important and fruitful for understanding its function. As the number of new genomes has dramatically increased over recent years, a reliable and efficient system to predict protein subcellular location is urgently needed.ResultsEsub8 was developed to predict protein subcellular localizations for eukaryotic proteins based on amino acid composition. In this research, the proteins are classified into the following eight groups: chloroplast, cytoplasm, extracellular, Golgi apparatus, lysosome, mitochondria, nucleus and peroxisome. We know subcellular localization is a typical classification problem; consequently, a one-against-one (1-v-1) multi-class support vector machine was introduced to construct the classifier. Unlike previous methods, ours considers the order information of protein sequences by a different method. Our method is tested in three subcellular localization predictions for prokaryotic proteins and four subcellular localization predictions for eukaryotic proteins on Reinhardt's dataset. The results are then compared to several other methods. The total prediction accuracies of two tests are both 100% by a self-consistency test, and are 92.9% and 84.14% by the jackknife test, respectively. Esub8 also provides excellent results: the total prediction accuracies are 100% by a self-consistency test and 87% by the jackknife test.ConclusionsOur method represents a different approach for predicting protein subcellular localization and achieved a satisfactory result; furthermore, we believe Esub8 will be a useful tool for predicting protein subcellular localizations in eukaryotic organisms.

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 combinational feature selection and ensemble neural network method for classification of gene expression data
abstract: 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: 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: 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: Mining interesting knowledge using DM-II
abstract: Data mining aims to develop a new generation of tools to intelligently assist humans in analyzing mountains of data. Over the past few years, great progress has been made in both research and applications of data mining. Data mining systems have helped many businesses by exposing previously unknown patterns in their databases, which were used to improve profits, enhance customer services, and ultimately achieve a competitive advantage. In this paper, we present our unique data mining system DM-II (Data Mining Integration and Interestingness). DM-II is a PC-based system working in Windows 95/98/NT environment. Apart from the normal components of a data mining system, DM-II has a number of unique and advanced sub-systems. These sub-systems have been applied in many real-life applications, including education applications, insurance application, accident application, disease application, drug screening application, image classification, etc. Here, we focus on discussing the following sub-systems: CBA: CBA originally stands for Classification-Based on Associations [lo]. It has now been extended with a number of other advanced features. In all, CBA has the following capabilities: Building classifiers using association rules: Traditionally, association rule mining and classifier building are regarded as two different data mining tasks. CBA unifies the two tasks. It is able to ,generate association rules and builds a classifier using a special subset of the association rules. What is significant is that CBA, in general, produces more accurate classifiers compared to the state-ofthe-art classification system C4.5 [ 161. It also helps to solve some outstanding problems with the existing classification systems. Pruning and summarizing the discovered associations: One major problem with association

title: The design of nonuniform-band maximally decimated filter banks
abstract: A design method for nonuniform-band maximally decimated filter banks is presented. It is based on the quadrature mirror filter (QMF) design method and allows the direct frequency domain design of two-band filter banks having arbitrary rational decimation ratios. The numerical design of nonuniform-band filter banks is achieved using a simple structure in which elementary modulators are used in the highpass channel to obtain almost-perfect reconstruction.<<ETX>>

title: Business applications of data mining
abstract: They help identify and predict individual, as well as aggregate, behavior, as illustrated by four application domains: direct mail, retail, automobile insurance, and health care.

title: Nesting One-Against-One Algorithm Based on SVMs for Pattern Classification
abstract: Support vector machines (SVMs), which were originally designed for binary classifications, are an excellent tool for machine learning. For the multiclass classifications, they are usually converted into binary ones before they can be used to classify the examples. In the one-against-one algorithm with SVMs, there exists an unclassifiable region where the data samples cannot be classified by its decision function. This paper extends the one-against-one algorithm to handle this problem. We also give the convergence and computational complexity analysis of the proposed method. Finally, one-against-one, fuzzy decision function (FDF), and decision-directed acyclic graph (DDAG) algorithms and our proposed method are compared using five University of California at Irvine (UCI) data sets. The results report that the proposed method can handle the unclassifiable region better than others.

title: A Chinese question classification using one-vs-one method as a learning tool
abstract: Question classification plays an important role in the question answering system and the errors of question classification will probably result in the failure of question answering. Thus, how to enhance the accuracy is an open question. In order to enhance the accuracies of the Chinese question classification, this paper extends one-against-one method based on SVMs to resolve the problems. The results show the good performance of the algorithm for Chinese question classification problems.