Benhui Chen

Local linear multi-SVM method for gene function classification

This paper proposes a local linear multi-SVM method based on composite kernel for solving classification tasks in gene function prediction. The proposed method realizes a nonlinear separating boundary by estimating a series of piecewise linear boundaries. Firstly, according to the distribution information of training data, a guided partitioning approach composed of separating boundary detection and clustering technique is used to obtain local subsets, and each subset is utilized to capture prior knowledge of corresponding local linear boundary. Secondly, a composite kernel is introduced to realize the local linear multi-SVM model. Instead of building multiple local SVM models separately, the prior knowledge of local subsets is used to construct a composite kernel, then the local linear multi-SVM model is realized by using the composite kernel exactly in the same way as a single SVM model. Experimental results on benchmark datasets demonstrate that the proposed method improves the classification performance efficiently.

A novel EDAs based method for HP model protein folding

The protein structure prediction (PSP) problem is one of the most important problems in computational biology. This paper proposes a novel Estimation of Distribution Algorithms (EDAs) based method to solve the PSP problem on HP model. Firstly, a composite fitness function containing the information of folding structure core formation is introduced to replace the traditional fitness function of HP model. It can help to select more optimum individuals for probabilistic model of EDAs algorithm. And a set of guided operators are used to increase the diversity of population and the likelihood of escaping from local optima. Secondly, an improved backtracking repairing algorithm is proposed to repair invalid individuals sampled by the probabilistic model of EDAs for the long sequence protein instances. A detection procedure of feasibility is added to avoid entering invalid closed areas when selecting directions for the residues. Thus, it can significant reduce the number of backtracking operation and the computational cost for long sequence protein. Experimental results demonstrate that the proposed method outperform the basic EDAs method. At the same time, it is very competitive with the other existing algorithms for the PSP problem on lattice HP models.

An improved multi-label classification method and its application to functional genomics

In this paper, a multi-label classification method based on label ranking and delicate boundary Support Vector Machine (SVM) is proposed for solving the functional genomics applications. Firstly, an improved probabilistic SVM with delicate decision boundary is used as scoring approach to obtain a proper label rank. Secondly, an instance-dependent thresholding strategy is proposed to decide classification results. A d-folds validation approach is utilised to determine a set of target thresholds for all training samples as teachers, then an appropriate instance-dependent threshold for each testing instance is obtained by applying k-Nearest Neighbours (KNN) strategy on this teacher threshold set.

Improving multi-label classification performance by label constraints

Multi-label classification is an extension of traditional classification problem in which each instance is associated with a set of labels. For some multi-label classification tasks, labels are usually overlapped and correlated, and some implicit constraint rules are existed among the labels. This paper presents an improved multi-label classification method based on label ranking strategy and label constraints. Firstly, one-against-all decomposition technique is used to divide a multilabel classification task into multiple independent binary classification sub-problems. One binary SVM classifier is trained for each label. Secondly, based on training data, label constraint rules are mined by association rule learning method. Thirdly, a correction model based on label constraints is used to correct the probabilistic outputs of SVM classifiers for label ranking. Experiment results on three well-known multi-label benchmark datasets show that the proposed method outperforms some conventional multi-label classification methods.

An adaptive niching EDA based on clustering analysis

Estimation of Distribution Algorithms (EDAs) still suffer from the drawback of premature convergence for solving the optimization problems with irregular and complex multimodal landscapes. In this paper, we propose an adaptive niching EDA based on Affinity Propagation (AP) clustering analysis. The AP clustering is used to adaptively partition the niches and mine searching information from the evolution process. The obtained information is successfully utilized to improve the EDA performance by a balance niching searching strategy. Two different categories of optimization problems are used to evaluate the proposed adaptive niching EDA. The first is the continuous EDA based on single Gaussian probabilistic model to solve two benchmark functional multimodal optimization problems. The second is a real complicated discrete EDA optimization problem, the protein 3-D HP model based on k-order Markov probabilistic model. The experiment studies demonstrate that the proposed adaptive niching EDA is an efficient method.

Network Administrator Assistance System Based on Fuzzy C-means Analysis

In this research we design a network administrator assistance system based on traffic measurement and fuzzy c-means (FCM) clustering analysis method. Network traffic measurement is an essential tool for monitoring and controlling communication network. It can provide valuable information about network trafficload patterns and performances. The proposed system utilizes the FCM method to analyze users’ network behaviors and traffic-load patterns based on traffic measurement data of IP network. Analysis results can be used as assistance for administrator to determine efficient controlling and configuring parameters of network management systems. The system is applied in Dali University campus network, and it is effective in practice.

Combining binary-SVM and pairwise label constraints for multi-label classification

Multi-label classification is an extension of traditional classification problem in which each instance is associated with a set of labels. Recent research has shown that the ranking approach is an effective way to solve this problem. In the multi-labeled sets, classes are often related to each other. Some implicit constraint rules are existed among the labels. So we present a novel multi-label ranking algorithm inspired by the pairwise constraint rules mined from the training set to enhance the existing method. In this method, one-against-all decomposition technique is used firstly to divide a multi-label problem into binary class sub-problems. A rank list is generated by combining the probabilistic outputs of each binary Support Vector Machine (SVM) classifier. Label constraint rules are learned by minimizing the ranking loss. Experimental performance evaluation on well-known multi-label benchmark datasets show that our method improves the classification accuracy efficiently, compared with some existed methods.

An improved multi-label classification based on label ranking and delicate boundary SVM

In this paper, an improved multi-label classification is proposed based on label ranking and delicate decision boundary SVM. Firstly, an improved probabilistic SVM with delicate decision boundary is used as the scoring method to obtain a proper label rank. It can improve the probabilistic label rank by introducing the information of overlapped training samples into learning procedure. Secondly, a threshold selection related with input instance and label rank is proposed to decide the classification results. It can estimate an appropriate threshold for each testing instance according to the characteristics of instance and label rank. Experimental results on four multi-label benchmark datasets show that the proposed method improves the performance of classification efficiently, compared with binary SVM method and some existing well-known methods.

A novel clustering based niching EDA for protein folding

Protein structure prediction (PSP) is one of the most important problems in computational biology. And it also is a very difficult optimization task, especially for long sequence instances. This paper proposes a novel clustering based niching EDA for HP model folding problem. The EDA individuals are clustered by the affinity propagation clustering method before submitting them to niching clearing. A cluster can be seen as a niche in clearing procedure. The niche clearing radius can be adaptively determined by clustering. And an approach based on Boltzmann scheme is proposed to determine the niche capacity according to the adaptive clearing radius and niche fitness. Experimental results demonstrate that the proposed method outperforms the basic EDAs method. At the same time, it is very competitive with other existing algorithms for the PSP problem on lattice HP models.

Composite kernel based SVM for hierarchical multi-label gene function classification

This paper proposes a hierarchical multi-label classification method based on SVM with composite kernel for solving gene function prediction. The hierarchical multi-label classification problem is resolved into a set of binary classification tasks. A composite kernel based SVM (ck-SVM) is introduced to deal with the binary classification tasks. In estimation procedure of ck-SVM, a supervised clustering with over-sampling strategy is introduced for solving imbalance dataset learning problem and improve classification performance. Experimental results on benchmark datasets demonstrate that the proposed method improves the classification performance efficiently.