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A Subspace Version of the Powell–Yuan Trust-Region Algorithm for Equality Constrained Optimization

Journal of the Operations Research Society of China 2013年第4期1卷 425-451页

作者： Geovani Nunes Grapiglia Jinyun Yuan Ya-xiang Yuan Departamento de Matemática Universidade Federal do ParanáCentro PolitécnicoCx.postal 19.08181531-980CuritibaParanáBrazil The Capes Foundation Ministry of Education of BrazilCx.postal 25070.040-020BrasíliaDistrito FederalBrazil State Key Laboratory of Scientific/Engineering Computing Institute of Computational Mathematics and Scientific/Engineering ComputingAcademy of Mathematics and Systems ScienceChinese Academy of SciencesZhongguancundonglu 55Beijing 100190P.R.China

This paper studied subspace properties of the Celis–Dennis–Tapia(CDT)subproblem that arises in some trust-region algorithms for equality constrained opti*** analysis is an extension of that presented by Wang and Yuan(***.104:241–269,2006)for the standard trust-region *** suitable conditions,it is shown that the trial step obtained from the CDT subproblem is in the subspace spanned by all the gradient vectors of the objective function and of the constraints computed until the current *** on this observation,a subspace version of the Powell–Yuan trust-region algorithm is proposed for equality constrained optimization problems where the number of constraints is much lower than the number of variables. The convergence analysis is given and numerical results arealso reported.

关键词： Constrained optimization Trust-region methods Subspace methods

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Finite-Difference Solution of the Helmholtz Equation Based on Two Domain Decomposition Algorithms

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Journal of Applied mathematics and Physics 2013年第4期1卷 18-24页

作者： Wensheng Zhang Yunyin Dai Academy of Mathematics and Systems Science Chinese Academy of Sciences Beijing China Institute of Computational Mathematics and Scientific/Engineering Computing LSEC Beijing China

In this paper, wave simulation with the finite difference method for the Helmholtz equation based on the domain decomposition method is investigated. The method solves the problem by iteratively solving subproblems defined on smaller subdomains. Two domain decomposition algorithms both for nonoverlapping and overlapping methods are described. More numerical computations including the benchmark Marmousi model show the effectiveness of the proposed algorithms. This method can be expected to be used in the full-waveform inversion in the future.

关键词： Finite Difference Domain Decomposition Nonoverlapping Overlapping Helmholtz Equation Preconditioner

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Highlights from the 11th ISCB Student Council Symposium 2015. Dublin, Ireland. 10 July 2015

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BMC bioinformatics 2016年第3期17 Suppl 3卷 95页

作者： Katie Wilkins Mehedi Hassan Margherita Francescatto Jakob Jespersen R. Gonzalo Parra Bart Cuypers Dan DeBlasio Alexander Junge Anupama Jigisha Farzana Rahman Griet Laenen Sander Willems Lieven Thorrez Yves Moreau Nagarajan Raju Sonia Pankaj Chothani C. Ramakrishnan Masakazu Sekijima M. Michael Gromiha Paddy J Slator Nigel J Burroughs Przemysław Szałaj Zhonghui Tang Paul Michalski Oskar Luo Xingwang Li Yijun Ruan Dariusz Plewczynski Giulia Fiscon Emanuel Weitschek Massimo Ciccozzi Paola Bertolazzi Giovanni Felici Pieter Meysman Manu Vanaerschot Maya Berg Hideo Imamura Jean-Claude Dujardin Kris Laukens Westa Domanova James R. Krycer Rima Chaudhuri Pengyi Yang Fatemeh Vafaee Daniel J. Fazakerley Sean J. Humphrey David E. James Zdenka Kuncic Plant Pathology and Plant-Microbe Biology Section School of Integrative Plant Science Cornell University Ithaca USA Graduate Field of Computational Biology Cornell University Ithaca USA School of Computing & Mathematics University of South Wales Cardiff UK Department of Genome Biology for Neurodegenerative Diseases German Center for Neurodegenerative Diseases (DZNE) within the Helmholtz Association ᅟ Germany Department of Surgery Massachusetts General Hospital The Broad Institute of MIT and Harvard Boston USA Department of Systems Biology Technical University of Denmark Kemitorvet Denmark Protein Physiology Lab Facultad de Ciencias Exactas y Naturales Universidad de Buenos Aires Buenos Aires Argentina Molecular Parasitology Unit (MPU) Institute of Tropical Medicine Antwerp Belgium Advanced Database Research and Modeling (ADReM) research group University of Antwerp Antwerpen Belgium Department of Computer Science University of Arizona Tucson USA Department of Veterinary Clinical and Animal Sciences Center for non-coding RNA in Technology and Health University of Copenhagen Copenhagen Denmark University College Dublin Dublin Ireland Department of Electrical Engineering (ESAT) STADIUS Center for Dynamical Systems Signal Processing and Data Analytics KU Leuven Leuven Belgium Minds Medical IT Department Leuven Belgium Scientific Institute of Public Health (WIV-ISP) Platform of Biotechnology and Molecular Biology (PBB) Brussels Belgium Department of Development and Regeneration @ Kulak KU Leuven Kortrijk Belgium Department of Biotechnology Bhupat and Jyoti Metha School of Biosciences Indian Institute of Technology Madras Chennai India Philips Research North America Briarcliff Manor USA Global Scientific Information and Computing Center (GSIC) Tokyo Institute of Technology Tokyo Japan Systems Biology Centre University of Warwick Senate House Coventry UK Systems Biology Doctoral Training Centre University of Warwick Senate House Coventry UK Center for B

A1 Highlights from the eleventh ISCB Student Council Symposium 2015 Katie Wilkins, Mehedi Hassan, Margherita Francescatto, Jakob Jespersen, R. Gonzalo Parra, Bart Cuypers, Dan DeBlasio, Alexander Junge, Anupama Jigisha, Farzana Rahman O1 Prioritizing a drug’s targets using both gene expression and structural similarity Griet Laenen, Sander Willems, Lieven Thorrez, Yves Moreau O2 Organism specific protein-RNA recognition: A computational analysis of protein-RNA complex structures from different organisms Nagarajan Raju, Sonia Pankaj Chothani, C. Ramakrishnan, Masakazu Sekijima; M. Michael Gromiha O3 Detection of Heterogeneity in Single Particle Tracking Trajectories Paddy J Slator, Nigel J Burroughs O4 3D-NOME: 3D NucleOme Multiscale Engine for data-driven modeling of three-dimensional genome architecture Przemysław Szałaj, Zhonghui Tang, Paul Michalski, Oskar Luo, Xingwang Li, Yijun Ruan, Dariusz Plewczynski O5 A novel feature selection method to extract multiple adjacent solutions for viral genomic sequences classification Giulia Fiscon, Emanuel Weitschek, Massimo Ciccozzi, Paola Bertolazzi, Giovanni Felici O6 A Systems Biology Compendium for Leishmania donovani Bart Cuypers, Pieter Meysman, Manu Vanaerschot, Maya Berg, Hideo Imamura, Jean-Claude Dujardin, Kris Laukens O7 Unravelling signal coordination from large scale phosphorylation kinetic data Westa Domanova, James R. Krycer, Rima Chaudhuri, Pengyi Yang, Fatemeh Vafaee, Daniel J. Fazakerley, Sean J. Humphrey, David E. James, Zdenka Kuncic

关键词： Visceral Leishmaniasis Feature Selection Method Frequent Itemset Mining Leishmania Donovani Student Council

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Recent Development in Symmetries and Integrability of Difference Equations

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Frontiers of mathematics in China 2013年第5期8卷 999-1000页

作者： Xingbiao HU Qingping LIU Senyue LOU Changzheng QU Youjin ZHANG Institute of Computational Mathematics and Scientific Engineering Computing Academy of Mathematics and Systems Science Chinese Academy of Sciences Beijing 100190 China Department of Mathematics China University of Mining and Technology~Beijing i00083 China Shanghai Key Laboratory of Trustworthy Computing East China Normal University Shanghai 200062 China Faculty of Sciences Ningbo University Ningbo 315211 China Center for Nonlinear Studies Ningbo University Ningbo 315211 China Department of Mathematical Sciences Tsinghua University Beijing 100084 China

Difference equations or discrete systems are mathematical models of various fields such as physics, chemistry, biology, and economics and have been subjects of extensive study of both pure mathematicians and applied mathematicians. Through its interaction with modern integrable systems, the theory of difference equations is enriched greatly and has been undergoing a rapid development. SIDE-10, the tenth of a series of biennial conferences devoted to Symmetries and Integrability of Difference Equations and related topics, was held during 10-16 June, 2012 at Ningbo, China. It was sponsored and supported by the National Natural Science Foundation of China, Ningbo Association of Science and Technology, Ningbo University, Academy of mathematics and Systems Science of Chinese Academy of Sciences, China University of Mining and Technology （Beijing）, Tsinghua University, and Shanghai University. The conference attracted over 100 participants from more than a dozen of countries. During the conference, 44 contributed talks were arranged and the topics covered by the meeting include

关键词： Recent Development Symmetries

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Frequency-domain Elastic wave Simulation Based on the Nonoverlapping Domain Decomposition Method

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American Journal of computational mathematics 2013年第3期3卷 21-26页

作者： Wensheng Zhang Yinyun Dai Institute of Computational Mathematics and Scientific/Engineering Computing LSEC Academy of Mathematics and Systems Science Chinese Academy of Sciences Beijing P.R.China

A new wave simulation technique for the elastic wave equation in the frequency domain based on a no overlapping domain decomposition algorithm is investigated. The boundary conditions and the finite difference discrimination of the elastic wave equation are derived. The algorithm of no overlapping domain decomposition method is given. The method solves the elastic wave equation by iteratively solving sub problems defined on smaller sub domains. Numerical computations both for homogeneous and inhomogeneous media show the effectiveness of the proposed method. This method can be used in the full-waveform inversion.

关键词： Finite Difference Nonoverlapping DDM Elastic wave Equation Wave Simulation Preconditioner Absorbing Boundary Conditions

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TGV for diffusion tensors: A comparison of fidelity functions

TGV for diffusion tensors: A comparison of fidelity function...

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作者： Valkonen, Tuomo Bredies, Kristian Knoll, Florian Institute for Mathematics and Scientific Computing University of Graz Austria Department of Applied Mathematics and Theoretical Physics University of Cambridge United Kingdom Institute of Medical Engineering Graz University of Technology Austria

We study the total generalised variation regularisation of symmetric tensor fields from medical applications, namely diffusion tensor regularisation. We study the effect of the pointwise positivity constraint on the tensor field, as well as the difference between direct denoising of the tensor field first solved from the Stejskal-Tanner equation, as was done in our earlier work, and of incorporating this equation into the fidelity function. Our results indicate that the latter novel approach provides improved computational results. © de Gruyter 2013.

关键词： Tensors

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Finite-Difference Solution of the Helmholtz Equation Based on Two Domain Decomposition Algorithms

Finite-Difference Solution of the Helmholtz Equation Based o...

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2013 World Congress on engineering and Technology(CET 2013)

作者： Wensheng Zhang Yunyin Dai Institute of Computational Mathematics and Scientific/Engineering Computing LSEC Academy of Mathematics and Systems Science Chinese Academy of Sciences

关键词： Finite Difference Domain Decomposition Nonoverlapping Overlapping Helmholtz Equation Preconditioner

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Frequency-domain Elastic wave Simulation Based on the Nonoverlapping Domain Decomposition Method

Frequency-domain Elastic wave Simulation Based on the Nonove...

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The Conference on Psychology and Applications(CPA 2013);International Conference on Molecular,Atomic,Nuclear and Particle Physics(MANPP 2013);International Conference on mathematics and System Science(MSS 2013)

作者： Wensheng Zhang Yinyun Dai Institute of Computational Mathematics and Scientific/Engineering Computing LSEC Academy of Mathematics and Systems Science Chinese Academy of Sciences

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Full-waveform Velocity Inversion Based on the Acoustic Wave Equation

Full-waveform Velocity Inversion Based on the Acoustic Wave ...

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作者： Wensheng Zhang Jia Luo Institute of Computational Mathematics and Scientific/Engineering Computing LSEC Academy of Mathematics and Systems Science Chinese Academy of Sciences

Full-waveform velocity inversion based on the acoustic wave equation in the time domain is investigated in this paper. The inversion is the iterative minimization of the misfit between observed data and synthetic data obtained by a numerical solution of the wave equation. Two inversion algorithms in combination with the CG method and the BFGS method are described respectively. Numerical computations for two models including the benchmark Marmousi model with complex structure are implemented. The inversion results show that the BFGS-based algorithm behaves better in inversion than the CG-based algorithm does. Moreover, the good inversion result for Marmousi model with the BFGS-based algorithm suggests the quasi-Newton methods can provide an important tool for large-scale velocity inversion. More computations demonstrate the correctness and effectives of our inversion algorithms and code.

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Full-waveform Velocity Inversion Based on the Acoustic Wave Equation

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American Journal of computational mathematics 2013年第3期3卷 13-20页

作者： Wensheng Zhang Jia Luo Institute of Computational Mathematics and Scientific/Engineering Computing LSEC Academy of Mathematics and Systems Science Chinese Academy of Sciences Beijing P. R. China

关键词： Finite Difference Acoustic Wave Equation Full-waveform Inversion CG Method BFGS Method Marmousi Model

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