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作者： Sandberg, Richard L. Raines, Kevin S. Salha, Sara Jiang, Huaidong Rodríguez, Jose A. Fahimian, Benjamin P. Kapteyn, Henry C. Murnane, Margaret M. Du, Jincheng Miao, Jianwei Department of Physics JILA University of Colorado at Boulder Boulder CO 80309-0440 United States Physical Chemistry and Applied Spectroscopy Los Alamos National Laboratory Los Alamos NM 8 7545 United States Department of Physics and Astronomy California NanoSystems Institute University of of California Los Angeles CA 90095 United States Molecular Biology Institute University of California Los Angeles CA 90095 United States Department of Materials Science and Engineering Center for Advanced Scientific Computing and Modeling University of North Texas Denton TX 76203 United States

We demonstrate that high numerical aperture coherent diffractive imaging enables three-dimensional imaging from a single exposure angle under certain conditions. We demonstrate this technique, called ankylography, wit... 详细信息

ISBN: (纸本)9781557528902

关键词： X ray lasers

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A Markovian Model for Default Risk in a Network of Sectors

A Markovian Model for Default Risk in a Network of Sectors

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The Second International Conference on Business Intelligence and Financial Engineering(BIFE 2009)(第二届商务智能与金融工程国际会议)

作者： Hao Jiang Wai-Ki Ching Liang Sun Ho-Yin Leung Advanced Modeling and Applied Computing Laboratory Department of Mathematics The University of Hong Advanced Modeling and Applied Computing Laboratory Department of Mathematics The University of Hong

In this paper, we study the problem of modeling the dependence of defaults in different sectors. We consider multiple default data sequences as a network and model them by using a Markov chain model. The new network model allows us to compute two important risk measures, namely, Value-at-Risk (VaR) and Expected Shortfall (ES). Numerical experiments are given to illustrate the practical implementation of the model. We also perform empirical studies of the model using real default data sequences and analyze the empirical behaviors of the risk measures arising from the model.

关键词： Bonding Mathematical model Laboratories mathematics Computer networks Reactive power Yttrium Business Intelligent networks Sun

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Three-dimensional coherent x-ray diffractive imaging from a single view

Three-dimensional coherent x-ray diffractive imaging from a ...

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Conference on Lasers and Electro-Optics (CLEO)

作者： Richard L. Sandberg Kevin S. Raines Sara Salha Huaidong Jiang Jose A. Rodríguez Benjamin P. Fahimian Henry C. Kapteyn Margaret M. Murnane Jincheng Du Jianwei Miao Department of Physics and JILA University of Colorado at Boulder Boulder CO USA Now at Physical Chemistry and Applied Spectroscopy Los Alamos National Laboratory Los Alamos NM USA Department of Physics and Astronomy and California NanoSystems Institute University of California Los Angeles CA USA Department of Physics and Astronomy and California NanoSystems Institute University of of California Los Angeles California USA Molecular Biology Institute University of California Los Angeles California USA Department of Materials Science & Engineering Center for Advanced Scientific Computing and Modeling University of North Texas Denton Texas USA

ISBN: (纸本)9781557528896

关键词： X-ray imaging X-ray diffraction Optical imaging X-ray lasers Free electron lasers Image reconstruction Testing Apertures Ultrafast optics Image resolution

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Finite-Horizon Control of Genetic Regulatory Networks with Multiple Hard-Constraints

Finite-Horizon Control of Genetic Regulatory Networks with M...

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第三届最优化与系统生物学国际研讨会

作者： Wai-Ki Ching Yang Cong Advanced Modeling and Applied Computing Laboratory Department of MathematicsThe University of Hong Kong

Probabilistic Boolean Networks(PBNs) provide a convenient tool for studying the interactions among different genes while allowing *** paper deals with the issue of finite-horizon control with multiple hard-constraints in a *** precisely,under the constraint of the number of times that each control method can be applied,we develop a control strategy by which the state of a given genetic network falls into a desired state set with a prescribed minimum *** propose an efficient algorithm to find the feasible *** upper bound for the computational cost is also *** numerical experiment is then conducted to demonstrate the efficiency of our proposed method.

关键词： Probability Boolean Networks Finite-Horizon Multiple Hard-Constraints Intervention Markov Chain Optimal Control

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A Study of Network-based Kernel Methods on Protein-Protein Interaction for Protein Functions Prediction

A Study of Network-based Kernel Methods on Protein-Protein I...

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第三届最优化与系统生物学国际研讨会

作者： Wai-Ki Ching Limin Li Yat-Ming Chan Hiroshi Mamitsuka Advanced Modeling and Applied Computing Laboratory Department of MathematicsThe University of Hong Kong

Predicting protein functions is an important issue in the post-genomic *** this paper, we studied several network-based kernels including Local Linear Embedding(LLE) kernel method, Diffusion kernel and Laplacian Kernel to uncover the relationship between proteins functions and Protein-Protein Interactions(PPI).We first construct kernels based on PPI networks,we then apply Support Vector Machine(SVM) techniques to classify proteins into different functional groups.5-fold cross validation is then applied to the selected 359 GO terms to compare the performance of different kernels and guilt-by-association methods including neighbor counting methods and Chisquare *** we made predictions of functions of some unknown genes and verified the preciseness of our prediction in part by the information of other data source.

关键词： Protein Function Prediction Kernel Method Local Linear Embedding(LLE) Kernel Laplacian Kernel Diffusion Kernel Support Vector Machine

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Efficient computation of impact degrees for multiple reactions in metabolic networks with cycles

Efficient computation of impact degrees for multiple reactio...

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3rd ACM International Workshop on Data and Text Mining in Bioinformatics, DTMBIO'09, Co-located with the 18th ACM International Conference on Information and Knowledge Management, CIKM 2009

作者： Cong, Yang Tamura, Takeyuki Akutsu, Tatsuya Ching, Wai-Ki Advanced Modeling and Applied Computing Laboratory Department of Mathematics University of Hong Kong Pokfulam Road Hong Kong Hong Kong Bioinformatics Center Institute for Chemical Research Kyoto University Gokasho Uji Kyoto 611-0011 Japan

ISBN: (纸本)9781605588032

Analysis of the robustness of a metabolic network against of single or multiple reaction(s) is useful for mining important enzymes/genes. For that purpose, the impact degree was proposed by Jiang et al. In this short paper, we extend the impact degree for metabolic networks containing cycles and develop a simple algorithm for its computation. Furthermore, we propose an improved algorithm for computing impact degrees for deletions of multiple reactions. The results of preliminary computational experiments suggest that the improved algorithm is several tens of times faster than a simple algorithm. Copyright 2009 ACM.

关键词： Metabolism

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Scaling to 150K cores: Recent algorithm and performance engineering developments enabling XGC1 to run at scale

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Journal of Physics: Conference Series 2009年第1期180卷

作者： Mark F Adams Seung-Hoe Ku Patrick Worley Ed D'Azevedo Julian C Cummings C-S Chang Department of Applied Physics and Applied Mathematics Columbia University Courant Institute of Mathematical Sciences New York University Computer Science and Mathematics Division Oak Ridge National Laboratory Center for Advanced Computing Research California Institute of Technology

Particle-in-cell (PIC) methods have proven to be effective in discretizing the Vlasov-Maxwell system of equations describing the core of toroidal burning plasmas for many decades. Recent physical understanding of the importance of edge physics for stability and transport in tokamaks has lead to development of the first fully toroidal edge PIC code – XGC1. The edge region poses special problems in meshing for PIC methods due to the lack of closed flux surfaces, which makes field-line following meshes and coordinate systems problematic. We present a solution to this problem with a semi-field line following mesh method in a cylindrical coordinate system. Additionally, modern supercomputers require highly concurrent algorithms and implementations, with all levels of the memory hierarchy being efficiently utilized to realize optimal code performance. This paper presents a mesh and particle partitioning method, suitable to our meshing strategy, for use on highly concurrent cache-based computing platforms.

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A Heuristic Method for Generating Probabilistic Boolean Networks from a Prescribed Transition Probability Matrix

A Heuristic Method for Generating Probabilistic Boolean Netw...

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第二届最优化与系统生物学国际研讨会

作者： Wai-Ki Ching Xi Chen Nam-Kiu Tsing Ho-Yin Leung Advanced Modeling and Applied Computing Laboratory Department of Mathematics The University of Hong Kong

Probabilistic Boolean Networks (PBNs) have received much attention for modeling genetic regulatory networks. In this paper, we propose efficient algorithms for constructing a probabilistic Boolean network when its transition probability matrix is given. This is an important inverse problem in network inference from steady-state data, as most microarray data sets are assumed to be obtained from sampling the steady-state.

关键词： Boolean Networks Probabilistic Boolean Networks Inverse Problem Transition Probability Matrix.

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Some Infection Models for the Development of AIDS

Some Infection Models for the Development of AIDS

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第二届最优化与系统生物学国际研讨会

作者： Wai-Ki Ching Yang Cong Tuen-Wai Ng Zheng-Jian Bai Advanced Modeling and Applied Computing Laboratory Department of Mathematics The University of Hong Kong Department of Information and Computational Mathematics Xiamen University

The co-infection of HIV viruses can affect the viral evolution in vivo. Wodarz and Levy 2007 [1] study the effect of HIV co-infection by investigating the values of the virus cytopathicity when the basic reproductive ratio of the virus and the total number of the target cells reach their extreme point respectively. Here based on their ideas, we further extended the discussion to a more general model.

关键词： HIV Dynamics Mathematical Models

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A simplified multivariate Markov chain model for the construction and control of genetic regulatory networks

A simplified multivariate Markov chain model for the constru...

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2nd International Conference on Bioinformatics and Biomedical Engineering, iCBBE 2008

作者： Zhang, Shu-Qin Ching, Wai-Ki Jiao, Yue Wu, Ling-Yun Chan, Raymond H. School of Mathematical Sciences Fudan University Shanghai200433 China Advanced Modeling and Applied Computing Laboratory Department of Mathematics University of Hong Kong Pokfulam Road Hong Kong Hong Kong Institute of Applied Mathematics Academy of Mathematics and System Sciences Chinese Academy of Sciences Department of Mathematics Chinese University of Hong Kong Shatin N.T. Hong Kong

ISBN: (纸本)9781424417483

The construction and control of genetic regulatory networks using gene expression data is an important research topic in bioinformatics. Probabilistic Boolean Networks (PBNs) have been served as an effective tool for this purpose. However, PBNs are difficult to be used in practice when the number of genes is large because of the huge computational cost. In this paper, we propose a simplified multivariate Markov model for approximating a PBN. The new model can preserve the strength of PBNs and at the same time reduce the complexity of the network and therefore the computational cost. We then present an optimal control model with hard constraints for the purpose of control/intervention of a genetic regulatory network. Numerical experimental examples based on the yeast data are then given to demonstrate the effectiveness of our proposed model and control policy. © 2008 IEEE.

关键词： Gene expression

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