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Laplacian normalization and random walk on heterogeneous networks for disease-gene prioritization

Computational biology and chemistry 2015年 57卷 21-8页

作者： Zhi-Qin Zhao Guo-Sheng Han Zu-Guo Yu Jinyan Li Hunan Key Laboratory for Computation and Simulation in Science and Engineering and Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education Xiangtan University Xiangtan Hunan 411105 China. Hunan Key Laboratory for Computation and Simulation in Science and Engineering and Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education Xiangtan University Xiangtan Hunan 411105 China School of Mathematical Sciences Queensland University of Technology GPO Box 2434 Brisbane Q4001 Australia. Electronic address: yuzg1970@***. Advanced Analytics Institute & Centre for Health Technologies University of Technology Sydney Broadway NSW 2007 Australia. Electronic address: jinyan.li@uts.edu.au.

Random walk on heterogeneous networks is a recently emerging approach to effective disease gene prioritization. Laplacian normalization is a technique capable of normalizing the weight of edges in a network. We use this technique to normalize the gene matrix and the phenotype matrix before the construction of the heterogeneous network, and also use this idea to define the transition matrices of the heterogeneous network. Our method has remarkably better performance than the existing methods for recovering known gene-phenotype relationships. The Shannon information entropy of the distribution of the transition probabilities in our networks is found to be smaller than the networks constructed by the existing methods, implying that a higher number of top-ranked genes can be verified as disease genes. In fact, the most probable gene-phenotype relationships ranked within top 3 or top 5 in our gene lists can be confirmed by the OMIM database for many cases. Our algorithms have shown remarkably superior performance over the state-of-the-art algorithms for recovering gene-phenotype relationships. All Matlab codes can be available upon email request.

关键词： Disease genes and phenotypes Heterogeneous network Laplacian normalization Leave-one-out cross-validation Random walk with restart Shannon information entropy

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Non-fragile Observer Design for Fractional-order One-sided Lipschitz Nonlinear Systems

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International Journal of Automation and computing 2013年第4期10卷 296-302页

作者： Yong-Hong Lan Wen-Jie Li Yan Zhou Yi-Ping Luo School of Information Engineering Xiangtan University Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education Xiangtan University Institute of Intelligent Control Hunan Institute of Engineering

This paper is concerned with the problem of the full-order observer design for a class of fractional-order Lipschitz nonlinear systems. By introducing a continuous frequency distributed equivalent model and using an indirect Lyapunov approach, the sufficient condition for asymptotic stability of the full-order observer error dynamic system is presented. The stability condition is obtained in terms of LMI, which is less conservative than the existing one. A numerical example demonstrates the validity of this approach.

关键词： Fractional-order nonlinear system observer design indirect Lyapunov approach linear matrix inequality （LMI）.

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A structural description: ordered AND/OR graph

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Journal of Information and Computational Science 2013年第11期10卷 3323-3330页

作者： Chen, Jie Zhang, Yanping Zhao, Shu School of Computer Science and Technology Anhui University Hefei 230039 China Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education Anhui University Hefei 230039 China

In the real word, the complex problems usually have netted structure, namely netted problems. The general methods to solve this kind of problems are based on the sequence structural description or tree structural description of problem. But the netted structure of complex problem cannot be simple pictured by sequence or tree. To precisely describe the structure of netted problem and simplify the solution procedure, ordered AND/OR graph is proposed in this paper to depict the problem structure. The graph has the hierarchy of tree structure, as well as nodes in this graph have AND relation and OR relation. More importantly, among the siblings from the same father node there exits order relationships. In this paper, an applicable example is given, and experiments show that the description of structure of netted problem is effective. © 2013 Binary Information Press.

关键词： Forestry

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Controlling chaos in mixed TCP and UDP model

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Journal of Computational Information Systems 2013年第23期9卷 9341-9346页

作者： Ding, Dawei Qiu, Sen Guo, Fan Zhang, Kun Xu, Xianfan Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education Anhui University Hefei 230039 China School of Electronics and Information Engineering Anhui University Hefei 230601 China

In this paper, a discrete time model of the mixed TCP and UDP connection with the RED is introduced. We use this one order discrete-time model to explain the instability, bifurcation and chaotic behaviors of the system. Then a time delayed feedback control approaches is applied to control the system in order to stabilize the chaotic behavior of average queue size. From numerical simulation it is concluded that the chaotic orbit can be stabilize to a fixed point when feedback parameter is properly chosen. Copyright © 2013 Binary Information Press.

关键词： Transmission control protocol

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A high order composite scheme for the second order elliptic problem with nonlocal boundary and its fast algorithm

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Applied Mathematics and Computation 2014年 227卷 212-221页

作者： Cunyun Nie Shi Shu Haiyuan Yu Qianjiang An Department of Mathematics and Physics The Hunan Institution of Engineering Xiangtan City Hunan 411104 China Hunan Key Laboratory for Computation & Simulation in Science and Engineering Key Laboratory of Intelligent Computing & Information Processing of Ministry of Education Xiangtan University Hunan 411105 China Department of Mathematics The Institute of Tongren Guizhou 554300 China

The elliptic problem with nonlocal boundary condition is widely applied in the field of science and engineering. Firstly, we construct a linear finite element scheme for the nonlocal boundary problem, and derive the optimal L 2 error estimate. Then, based on the quadratic finite element and the extrapolation linear finite element methods, we present a composite scheme, and prove that it is convergent order three. Furthermore, we design an upper triangular preconditioning algorithm for the linear finite element discrete system. Finally, numerical results not only validate that the new algorithm is efficient, but also show that the new scheme is convergent order three, furthermore order four on uniform grids.

关键词： The elliptic problem with nonlocal boundary condition The finite element method An upper triangular preconditioner Algebraic multigrid method

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Topological properties and fractal analysis of a recurrence network constructed from fractional Brownian motions

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Physical Review E 2014年第3期89卷 032814-032814页

作者： Jin-Long Liu Zu-Guo Yu Vo Anh Hunan Key Laboratory for Computation and Simulation in Science and Engineering and Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education Xiangtan University Xiangtan Hunan 411105 China School of Mathematical Sciences Queensland University of Technology GPO Box 2434 Brisbane Q4001 Australia

Many studies have shown that we can gain additional information on time series by investigating their accompanying complex networks. In this work, we investigate the fundamental topological and fractal properties of recurrence networks constructed from fractional Brownian motions (FBMs). First, our results indicate that the constructed recurrence networks have exponential degree distributions; the average degree exponent 〈λ〉 increases first and then decreases with the increase of Hurst index H of the associated FBMs; the relationship between H and 〈λ〉 can be represented by a cubic polynomial function. We next focus on the motif rank distribution of recurrence networks, so that we can better understand networks at the local structure level. We find the interesting superfamily phenomenon, i.e., the recurrence networks with the same motif rank pattern being grouped into two superfamilies. Last, we numerically analyze the fractal and multifractal properties of recurrence networks. We find that the average fractal dimension 〈dB〉 of recurrence networks decreases with the Hurst index H of the associated FBMs, and their dependence approximately satisfies the linear formula 〈dB〉≈2−H, which means that the fractal dimension of the associated recurrence network is close to that of the graph of the FBM. Moreover, our numerical results of multifractal analysis show that the multifractality exists in these recurrence networks, and the multifractality of these networks becomes stronger at first and then weaker when the Hurst index of the associated time series becomes larger from 0.4 to 0.95. In particular, the recurrence network with the Hurst index H=0.5 possesses the strongest multifractality. In addition, the dependence relationships of the average information dimension 〈D(1)〉 and the average correlation dimension 〈D(2)〉 on the Hurst index H can also be fitted well with linear functions. Our results strongly suggest that the recurrence network inherits the basic characteristic

关键词： TOPOLOGICAL property FRACTAL analysis BROWNIAN motion CORRELATION (Statistics) RECURSIVE sequences (Mathematics) COMPUTER networks

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Control of Hopf bifurcation in Internet congestion control model via time-delayed feedback control

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Information Technology Journal 2013年第18期12卷 4493-4497页

作者： Xu, Xian-Fan Fan, Guo Ding, Da-Wei Yi, Liu Han, Liu-Jun School of Electronics and Information Engineering Anhui University 230601 Hefei China Key Laboratory of Intelligent Computing and Signal Processing Ministry of Education Anhui University 230039 Hefei China

In this study, we are concerned with controlling Hopf bifurcation in a dual model of Internet congestion control algorithms. The stability of this system depends on a communication delay parameter, and Hopf bifurcation occurs when the communication delay passes through a critical value. Comparing with previous work, a time-delayed feedback method is proposed to postpone the onset of undesired Hopf bifurcation and improve stability of the dual model. Theoretical analysis and numerical simulation are provided to verify the effectiveness of our method. © 2013 Asian Network for Scientific Information.

关键词： Hopf bifurcation

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Crank-Nicolson difference scheme for the coupled nonlinear Schrödinger equations with the Riesz space fractional derivative

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Journal of Computational Physics 2013年 242卷 670-681页

作者： Wang, Dongling Xiao, Aiguo Yang, Wei Hunan Key Laboratory for Computation and Simulation in Science and Engineering Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education Xiangtan University Xiangtan Hunan 411105 China

In this paper, the Crank-Nicolson (CN) difference scheme for the coupled nonlinear Schrödinger equations with the Riesz space fractional derivative is studied. The existence of this difference solution is proved by the Brouwer fixed point theorem. The stability and convergence of the CN scheme are discussed in the L2 norm. When the fractional order is two, all those results are in accord with the difference scheme developed for the classical non-fractional coupled nonlinear Schrödinger equations. Some numerical examples are also presented. © 2013 Elsevier Inc.

关键词： Nonlinear equations

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Multifractal analysis of weighted networks by a modified sandbox algorithm

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Scientific reports 2015年第1期5卷 17628页

作者： Yu-Qin Song Jin-Long Liu Zu-Guo Yu Bao-Gen Li Hunan Key Laboratory for Computation and Simulation in Science and Engineering and Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education Xiangtan University Xiangtan Hunan 411105 China. College of Science Hunan University of technology Zhuzhou Hunan 412007 China. School of Mathematical Sciences Queensland University of Technology Brisbane Q4001 Australia.

Complex networks have attracted growing attention in many fields. As a generalization of fractal analysis, multifractal analysis (MFA) is a useful way to systematically describe the spatial heterogeneity of both theoretical and experimental fractal patterns. Some algorithms for MFA of unweighted complex networks have been proposed in the past a few years, including the sandbox (SB) algorithm recently employed by our group. In this paper, a modified SB algorithm (we call it SBw algorithm) is proposed for MFA of weighted networks. First, we use the SBw algorithm to study the multifractal property of two families of weighted fractal networks (WFNs): "Sierpinski" WFNs and "Cantor dust" WFNs. We also discuss how the fractal dimension and generalized fractal dimensions change with the edge-weights of the WFN. From the comparison between the theoretical and numerical fractal dimensions of these networks, we can find that the proposed SBw algorithm is efficient and feasible for MFA of weighted networks. Then, we apply the SBw algorithm to study multifractal properties of some real weighted networks - collaboration networks. It is found that the multifractality exists in these weighted networks, and is affected by their edge-weights.

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Bacterial foraging algorithm based on quantum-behaved particle swarm optimization and opposition-based learning

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Journal of Computational Information Systems 2013年第3期9卷 1157-1165页

作者： Mai, Xiongfa Li, Ling Science Computing and Intelligent Information Processing of GuangXi Higher Education Key Laboratory Guangxi Teachers Education University Nanning 530023 China Ministry of Education Nanning 530001 China

Bacterial Foraging Optimization(BFA) algorithm has recently emerged as a very powerful technique for real parameter optimization, but the E. coli algorithm depends on random search directions which may lead to delay in reaching the global solution, while the reproduction step of BFA may reduce its diversity for in this step one better bacterium split into two same bacterium. In order to overcome the delay in optimization and to further enhance the performance of BFA, a bacterial foraging algorithm based on QPSO and OBL(OQ-BFA) is presented. The new algorithm is proposed to combine all algorithms' advantages in order to get better optimization values. Simulation results on eight benchmark functions show that the proposed algorithm is superior to the BFA, QPSO and BF-PSO. Copyright © 2013 Binary Information Press.

关键词： Escherichia coli

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