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Estimation in the group action channel

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arXiv 2018年

作者： Abbe, Emmanuel Pereira, João M. Singer, Amit Program in Applied and Computational Mathematics Princeton University PrincetonNJ United States Electrical Engineering Department Princeton University PrincetonNJ United States Department of Mathematics Princeton University PrincetonNJ United States

MSC Codes 94A15, 62B10We analyze the problem of estimating a signal from multiple measurements on a group action channel that linearly transforms a signal by a random group action followed by a fixed projection and additive Gaussian noise. This channel is motivated by applications such as multi-reference alignment and cryoelectron microscopy. We focus on the large noise regime prevalent in these applications. We give a lower bound on the mean square error (MSE) of any asymptotically unbiased estimator of the signal's orbit in terms of the signal's moment tensors, which implies that the MSE is bounded away from 0 when N=σ2dis bounded from above, where N is the number of observations, σ is the noise standard deviation, and d is the so-called moment order cutoff. In contrast, the maximum likelihood estimator is shown to be consistent if N=σ2ddiverges. Copyright © 2018, The Authors. All rights reserved.

关键词： Mean square error

Multireference alignment is easier with an aperiodic translation distribution

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arXiv 2017年

作者： Abbe, Emmanuel Bendory, Tamir Leeb, William Pereira, João M. Sharon, Nir Singer, Amit Program in Applied and Computational Mathematics Princeton University PrincetonNJ United States Electrical Engineering Department Princeton University PrincetonNJ United States Department of Mathematics Princeton University PrincetonNJ United States

In the multireference alignment model, a signal is observed by the action of a random circular translation and the addition of Gaussian noise. The goal is to recover the signal's orbit by accessing multiple independent observations. Of particular interest is the sample complexity, i.e., the number of observations/samples needed in terms of the signal-to-noise ratio (the signal energy divided by the noise variance) in order to drive the mean-square error (MSE) to zero. Previous work showed that if the translations are drawn from the uniform distribution, then, in the low SNR regime, the sample complexity of the problem scales as ω(1/SNR3). In this work, using a generalization of the Chapman-Robbins bound for orbits and expansions of the X2divergence at low SNR, we show that in the same regime the sample complexity for any aperiodic translation distribution scales as ω(1/SNR2). This rate is achieved by a simple spectral algorithm. We propose two additional algorithms based on non-convex optimization and expectation-maximization. We also draw a connection between the multireference alignment problem and the spiked covariance model. Copyright © 2017, The Authors. All rights reserved.

关键词： Maximum principle

First-principles characterization of Ni diffusion kinetics in β-NiAl

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Physical Review B 2008年第18期78卷 184105-184105页

作者： Kristen A. Marino Emily A. Carter Department of Chemical Engineering Princeton University Princeton New Jersey 08544-5263 USA Department of Mechanical and Aerospace Engineering and Program in Applied and Computational Mathematics Princeton University Princeton New Jersey 08544-5263 USA

First-principles density functional theory calculations are performed to examine five postulated diffusion mechanisms for Ni in NiAl: next-nearest-neighbor (NNN) jumps, the triple defect mechanism, and three variants of the six-jump cycle. In contrast to most previous theoretical work, which employed empirical interatomic potentials, we provide a more accurate nonempirical description of the mechanisms. For each pathway, we calculate the activation energy and the pre-exponential factor for the diffusion constant. Although our quantum mechanics calculations are performed at 0 K, we show that it is critical to include the effect of temperature on the pre-exponential factor. We predict that the triple defect mechanism and [110] six-jump cycle both are likely contributors to Ni diffusion in NiAl since their activation energies and pre-exponential factors are in very good agreement with experimental data. Although the activation energy and pre-exponential factor of NNN jumps agree well with experiment, experimental evidence suggests that this is not a dominant contributor to Ni diffusion. Lastly, the activation energies of the [100] bent and straight six-jump cycles are 1 eV higher than the experimental value, allowing us to exclude both [100] cycle mechanisms.

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Comment on “Jamming at zero temperature and zero applied stress: The epitome of disorder”

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Physical Review E 2004年第4期70卷 043301-043301页

作者： Aleksandar Donev Salvatore Torquato Frank H. Stillinger Robert Connelly Program in Applied and Computational Mathematics Princeton University Princeton New Jersey 08544 USA Materials Institute Princeton University Princeton New Jersey 08544 USA Department of Chemistry Princeton University Princeton New Jersey 08544 USA Department of Mathematics Cornell University Ithaca New York 14853 USA

O’Hern, Silbert, Liu, and Nagel [Phys. Rev. E. 68, 011306 (2003)] claim that a special point J of a “jamming phase diagram” (in density, temperature, stress space) is related to random close packing of hard spheres and that it represents, for their suggested definitions of jammed and random, the recently introduced maximally random jammed state. We point out several difficulties with their definitions and question some of their claims. Furthermore, we discuss the connections between their algorithm and other hard-sphere packing algorithms in the literature.

关键词： .RCp Phys Rev Hard Spheres hard-sphere well-de jamming point out maximally claim special point nitions jammed MRJ OSLN

Ab Initio Generalized Langevin Equation

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arXiv 2022年

作者： Xie, Pinchen Car, Roberto Weinan, E. Program in Applied and Computational Mathematics Princeton University PrincetonNJ08544 United States Department of Chemistry Department of Physics Program in Applied and Computational Mathematics Princeton Institute for the Science and Technology of Materials Princeton University PrincetonNJ08544 United States AI for Science Institute Beijing China Center for Machine Learning Research School of Mathematical Sciences Peking University Beijing China

We introduce a machine learning-based approach called ab initio generalized Langevin equation (AIGLE) to model the dynamics of slow collective variables in materials and molecules. In this scheme, the parameters are learned from atomistic simulations based on ab initio quantum mechanical models. Force field, memory kernel, and noise generator are constructed in the context of the Mori-Zwanzig formalism, under the constraint of the fluctuation-dissipation theorem. Combined with deep potential molecular dynamics and electronic density functional theory, this approach opens the way to multi-scale modeling in a variety of situations. Here, we demonstrate this capability with a study of two mesoscale processes in crystalline lead titanate, namely the field-driven dynamics of a planar ferroelectric domain wall, and the dynamics of an extensive lattice of coarse-grained electric dipoles. In the first case, AIGLE extends the reach of ab initio simulations to a regime of noise-driven motions not accessible to molecular dynamics. In the second case, AIGLE deals with an extensive set of collective variables by adopting a local approximation for the memory kernel and retaining only short-range noise correlations. The scheme is computationally more efficient than molecular dynamics by several orders of magnitude, and mimics the microscopic dynamics at low frequencies where it reproduces accurately the dominant far-infrared absorption frequency. © 2022, CC BY.

关键词： Molecular dynamics

DeePMD-kit: A deep learning package for many-body potential energy representation and molecular dynamics

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arXiv 2017年

作者： Wang, Han Zhang, Linfeng Han, Jiequn Weinan, E. Institute of Applied Physics and Computational Mathematics Fenghao East Road 2 Beijing100094 China CAEP Software Center for High Performance Numerical Simulation Huayuan Road 6 Beijing100088 China Program in Applied and Computational Mathematics Princeton University PrincetonNJ08544 United States Department of Mathematics and Program in Applied and Computational Mathematics Princeton University PrincetonNJ08544 United States Center for Data Science Beijing International Center for Mathematical Research Peking University Beijing Institute of Big Data Research Beijing100871 China

Recent developments in many-body potential energy representation via deep learning have brought new hopes to addressing the accuracy-versus-efficiency dilemma in molecular simulations. Here we describe DeePMD-kit, a package written in Python/C++ that has been designed to minimize the effort required to build deep learning based representation of potential energy and force field and to perform molecular dynamics. Potential applications of DeePMD-kit span from finite molecules to extended systems and from metallic systems to chemically bonded systems. DeePMD-kit is interfaced with TensorFlow, one of the most popular deep learning frameworks, making the training process highly automatic and efficient. On the other end, DeePMD-kit is interfaced with high-performance classical molecular dynamics and quantum (path-integral) molecular dynamics packages, i.e., LAMMPS and the i-PI, respectively. Thus, upon training, the potential energy and force field models can be used to perform efficient molecular simulations for different purposes. As an example of the many potential applications of the package, we use DeePMD-kit to learn the interatomic potential energy and forces of a water model using data obtained from density functional theory. We demonstrate that the resulted molecular dynamics model reproduces accurately the structural information contained in the original model. Copyright © 2017, The Authors. All rights reserved.

关键词： Potential energy

Benchmark problems for phase retrieval

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arXiv 2017年

作者： Elser, Veit Lan, Ti-Yen Bendory, Tamir Department of Physics Cornell University IthacaNY14853-2501 United States Program in Applied and Computational Mathematics Princeton University Princeton08544-1000 United States

In recent years, the mathematical and algorithmic aspects of the phase retrieval problem have received considerable attention. Many papers in this area mention crystallography as a principal application. In crystallography, the signal to be recovered is periodic and comprised of atomic distributions arranged homogeneously in the unit cell of the crystal. The crystallographic problem is both the leading application and one of the hardest forms of phase retrieval. We have constructed a graded set of benchmark problems for evaluating algorithms that perform this type of phase retrieval. The data, publicly available online1, is provided in an easily interpretable format. We also propose a simple and unambiguous success/failure criterion based on the actual needs in crystallography. Baseline runtimes were obtained with an iterative algorithm that is similar but more transparent than those used in crystallography. Empirically,the runtimes grow exponentially with respect to a new hardness parameter: the sparsity of the signal autocorrelation. We also review the algorithms used by the leading software packages. This set of benchmark problems, we hope, will encourage the development of new algorithms for the phase retrieval problem in general, and crystallography in particular. Copyright © 2017, The Authors. All rights reserved.

关键词： Benchmarking

Bayesian Spectral Graph Denoising with Smoothness Prior

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Bayesian Spectral Graph Denoising with Smoothness Prior

Annual Conference on Information Sciences and Systems (CISS)

作者： Sam Leone Xingzhi Sun Michael Perlmutter Smita Krishnaswamy Program for Applied Mathematics Yale University Department of Computer Science Yale University Department of Mathematics Boise State University Department of Genetics Yale School of Medicine Wu Tsai Institute Yale University FAIR Meta AI Computational Biology and Bioinformatics Program Yale University

Here we consider the problem of denoising features associated to complex data, modeled as signals on a graph, via a smoothness prior. This is motivated in part by settings such as single-cell RNA where the data is very high-dimensional, but its structure can be captured via an affinity graph. This allows us to utilize ideas from graph signal processing. In particular, we present algorithms for the cases where the signal is perturbed by Gaussian noise, dropout, and uniformly distributed noise. The signals are assumed to follow a prior distribution defined in the frequency domain which favors signals which are smooth across the edges of the graph. By pairing this prior distribution with our three models of noise generation, we propose Maximum A Posteriori (M.A.P.) estimates of the true signal in the presence of noisy data and provide algorithms for computing the M.A.P. Finally, we demonstrate the algorithms’ ability to effectively restore signals from white noise on image data and from severe dropout in single-cell RNA sequence data.

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A fourth-order accurate finite volume method for ideal mhd via upwind constrained transport

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arXiv 2017年

作者： Felker, Kyle Gerard Stone, James Program in Applied and Computational Mathematics Princeton University PrincetonNJ08544 United States Department of Astrophysical Sciences Princeton University PrincetonNJ08544 United States

We present a fourth-order accurate finite volume method for the solution of ideal magnetohydrodynamics (MHD). The numerical method combines high-order quadrature rules in the solution of semi-discrete formulations of hyperbolic conservation laws with the upwind constrained transport (UCT) framework to ensure that the divergence-free constraint of the magnetic field is satisfied. A novel implementation of UCT that uses the piecewise parabolic method (PPM) for the reconstruction of magnetic fields at cell corners in 2D is introduced. The resulting scheme can be expressed as the extension of the second-order accurate constrained transport (CT) Godunov-type scheme that is currently used in the Athena astrophysics code. After validating the base algorithm on a series of hydrodynamics test problems, we present the results of multidimensional MHD test problems which demonstrate formal fourth-order convergence for smooth problems, robustness for discontinuous problems, and improved accuracy relative to the second-order scheme. Copyright © 2017, The Authors. All rights reserved.

关键词： Numerical methods