Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

Fast parallel algorithms for short-range molecular dynamics

We consider the class of iterative shrinkage-thresholding algorithms (ISTA) for solving linear inverse problems arising in signal/image processing. This class of methods, which can be viewed as an extension of the classical gradient algorithm, is attractive due to its simplicity and thus is adequate for solving large-scale problems even with dense matrix data. However, such methods are also known to converge quite slowly. In this paper we present a new fast iterative shrinkage-thresholding algorithm (FISTA) which preserves the computational simplicity of ISTA but with a global rate of convergence which is proven to be significantly better, both theoretically and practically. Initial promising numerical results for wavelet-based image deblurring demonstrate the capabilities of FISTA which is shown to be faster than ISTA by several orders of magnitude.

http://people.rennes.inria.fr/Cedric.Herzet/Cedric.Herzet/Sparse_Seminar/Entrees/2012/11/12_A_Fast_Iterative_Shrinkage-Thresholding_Algorithmfor_Linear_Inverse_Problems_(A._Beck,_M._Teboulle)_files/Breck_2009.pdf

A Fast Iterative Shrinkage-Thresholding Algorithm for Linear Inverse Problems

We consider linear inverse problems where the solution is assumed to have a sparse expansion on an arbitrary preassigned orthonormal basis. We prove that replacing the usual quadratic regularizing penalties by weighted p-penalties on the coefficients of such expansions, with 1 ≤ p ≤ 2, still regularizes the problem. Use of such p-penalized problems with p < 2 is often advocated when one expects the underlying ideal noiseless solution to have a sparse expansion with respect to the basis under consideration. To compute the corresponding regularized solutions, we analyze an iterative algorithm that amounts to a Landweber iteration with thresholding (or nonlinear shrinkage) applied at each iteration step. We prove that this algorithm converges in norm. © 2004 Wiley Periodicals, Inc.

/pdf/an-iterative-thresholding-algorithm-for-linear-inverse-565i4q2jj2.pdf

An Iterative Thresholding Algorithm for Linear Inverse Problems with a Sparsity Constraint

Thank you very much for downloading table of integrals series and products. Maybe you have knowledge that, people have look hundreds times for their chosen books like this table of integrals series and products, but end up in harmful downloads. Rather than reading a good book with a cup of coffee in the afternoon, instead they cope with some harmful virus inside their laptop. table of integrals series and products is available in our book collection an online access to it is set as public so you can get it instantly. Our book servers saves in multiple locations, allowing you to get the most less latency time to download any of our books like this one. Merely said, the table of integrals series and products is universally compatible with any devices to read.

Table Of Integrals Series And Products

A fruitful direction for future data mining research will be the development of techniques that incorporate privacy concerns. Specifically, we address the following question. Since the primary task in data mining is the development of models about aggregated data, can we develop accurate models without access to precise information in individual data records? We consider the concrete case of building a decision-tree classifier from training data in which the values of individual records have been perturbed. The resulting data records look very different from the original records and the distribution of data values is also very different from the original distribution. While it is not possible to accurately estimate original values in individual data records, we propose a novel reconstruction procedure to accurately estimate the distribution of original data values. By using these reconstructed distributions, we are able to build classifiers whose accuracy is comparable to the accuracy of classifiers built with the original data.

Privacy-preserving data mining

Preface. 1. Introduction: Examples of Inverse Problems. 2. Ill-Posed Linear Operator Equations. 3. Regularization Operators. 4. Continuous Regularization Methods. 5. Tikhonov Regularization. 6. Iterative Regularization Methods. 7. The Conjugate Gradient Method. 8. Regularization with Differential Operators. 9. Numerical Realization. 10. Tikhonov Regularization of Nonlinear Problems. 11. Iterative Methods for Nonlinear Problems. A. Appendix: A.1. Weighted Polynomial Minimization Problems. A.2. Orthogonal Polynomials. A.3. Christoffel Functions. Bibliography. Index.

Regularization of Inverse Problems

In this paper we prove that the Landweber iteration is a stable method for solving nonlinear ill-posed problems. For perturbed data with noise level \(\delta \) we propose a stopping rule that yields the convergence rate\(O (\delta ^{1/2}\) ) under appropriate conditions. We illustrate these conditions for a few examples.

A convergence analysis of the Landweber iteration for nonlinear ill-posed problems

Regularization methods for large-scale problems

1. Preface and Notation 2. Conjugate gradient type methods 3. Regularizing properties of MR and CGNE 4. Regularizing properties of CG and CGME 5. On the number of iterations 6. A minimal residual method for indefinite problems References Index

Conjugate Gradient Type Methods for Ill-Posed Problems

The first part of this paper studies a Levenberg - Marquardt scheme for nonlinear inverse problems where the corresponding Lagrange (or regularization) parameter is chosen from an inexact Newton strategy While the convergence analysis of standard implementations based on trust region strategies always requires the invertibility of the Frechet derivative of the nonlinear operator at the exact solution, the new Levenberg - Marquardt scheme is suitable for ill-posed problems as long as the Taylor remainder is of second order in the interpolating metric between the range and domain topologies Estimates of this type are established in the second part of the paper for ill-posed parameter identification problems arising in inverse groundwater hydrology Both transient and steady-state data are investigated Finally, the numerical performance of the new Levenberg - Marquardt scheme is studied and compared to a usual implementation on a realistic but synthetic two-dimensional model problem from the engineering literature

/pdf/a-regularizing-levenberg-marquardt-scheme-with-applications-42wqcngv07.pdf

Martin Hanke

Papers

Regularization of Inverse Problems

A convergence analysis of the Landweber iteration for nonlinear ill-posed problems

Regularization methods for large-scale problems

Conjugate Gradient Type Methods for Ill-Posed Problems

A regularizing Levenberg - Marquardt scheme, with applications to inverse groundwater filtration problems