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arXiv 2023年

作者： Zeng, Jinzhe Zhang, Duo Lu, Denghui Mo, Pinghui Li, Zeyu Chen, Yixiao Rynik, Marián Huang, Li'ang Li, Ziyao Shi, Shaochen Wang, Yingze Ye, Haotian Tuo, Ping Yang, Jiabin Ding, Ye Li, Yifan Tisi, Davide Zeng, Qiyu Bao, Han Xia, Yu Huang, Jiameng Muraoka, Koki Wang, Yibo Chang, Junhan Yuan, Fengbo Bore, Sigbjørn Løland Cai, Chun Lin, Yinnian Wang, Bo Xu, Jiayan Zhu, Jia-Xin Luo, Chenxing Zhang, Yuzhi Goodall, Rhys E.A. Liang, Wenshuo Singh, Anurag Kumar Yao, Sikai Zhang, Jingchao Wentzcovitch, Renata Han, Jiequn Liu, Jie Jia, Weile York, Darrin M. Weinan, E. Car, Roberto Zhang, Linfeng Wang, Han Laboratory for Biomolecular Simulation Research Institute for Quantitative Biomedicine Department of Chemistry and Chemical Biology Rutgers University PiscatawayNJ08854 United States AI for Science Institute Beijing100080 China DP Technology Beijing100080 China Academy for Advanced Interdisciplinary Studies Peking University Beijing100871 China HEDPS CAPT College of Engineering Peking University Beijing100871 China College of Electrical and Information Engineering Hunan University Changsha China Yuanpei College Peking University Beijing100871 China Program in Applied and Computational Mathematics Princeton University PrincetonNJ08540 United States Department of Experimental Physics Comenius University Mlynská Dolina F2 Bratislava842 48 Slovakia Center for Quantum Information Institute for Interdisciplinary Information Sciences Tsinghua University Beijing100084 China Center for Data Science Peking University Beijing100871 China ByteDance Research Zhonghang Plaza No. 43 North 3rd Ring West Road Haidian District Beijing China College of Chemistry and Molecular Engineering Peking University Beijing100871 China Baidu Inc. Beijing China Key Laboratory of Structural Biology of Zhejiang Province School of Life Sciences Westlake University Zhejiang Hangzhou China Westlake AI Therapeutics Lab Westlake Laboratory of Life Sciences and Biomedicine Zhejiang Hangzhou China Department of Chemistry Princeton University PrincetonNJ08544 United States SISSA Scuola Internazionale Superiore di Studi Avanzati Trieste34136 Italy Laboratory of Computational Science and Modeling Institute of Materials École Polytechnique Fédérale de Lausanne Lausanne1015 Switzerland Department of Physics National University of Defense Technology Hunan Changsha410073 China State Key Lab of Processors Institute of Computing Technology Chinese Academy of Sciences Beijing China University of Chinese Academy of Sciences Beijing China School of Electronics Engineerin

DeePMD-kit is a powerful open-source software package that facilitates molecular dynamics simulations using machine learning potentials (MLP) known as Deep Potential (DP) models. This package, which was released in 2017, has been widely used in the fields of physics, chemistry, biology, and material science for studying atomistic systems. The current version of DeePMD-kit offers numerous advanced features such as DeepPot-SE, attention-based and hybrid descriptors, the ability to fit tensile properties, type embedding, model deviation, Deep Potential - Range Correction (DPRc), Deep Potential Long Range (DPLR), GPU support for customized operators, model compression, non-von Neumann molecular dynamics (NVNMD), and improved usability, including documentation, compiled binary packages, graphical user interfaces (GUI), and application programming interfaces (API). This article presents an overview of the current major version of the DeePMD-kit package, highlighting its features and technical details. Additionally, the article benchmarks the accuracy and efficiency of different models and discusses ongoing developments. © 2023, CC BY-NC-ND.

关键词： Molecular dynamics

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The barron space and the flow-induced function spaces for neural network models

arXiv

引用

arXiv 2019年

作者： Weinan, E. Ma, Chao Wu, Lei Department of Mathematics Princeton University United States Program in Applied and Computational Mathematics Princeton University United States Beijing Institute of Big Data Research China

One of the key issues in the analysis of machine learning models is to identify the appropriate function space and norm for the model. This is the set of functions endowed with a quantity which can control the approximation and estimation errors by a particular machine learning model. In this paper, we address this issue for two representative neural network models: The two-layer networks and the residual neural networks. We define the Barron space and show that it is the right space for two-layer neural network models in the sense that optimal direct and inverse approximation theorems hold for functions in the Barron space. For residual neural network models, we construct the so-called flow-induced function space, and prove direct and inverse approximation theorems for this space. In addition, we show that the Rademacher complexity for bounded sets under these norms has the optimal upper bounds. Copyright © 2019, The Authors. All rights reserved.

关键词： Functional analysis

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Deep neural network for Wannier function centers

arXiv

引用

arXiv 2019年

作者： Zhang, Linfeng Chen, Mohan Wu, Xifan Wang, Han Weinan, E. Car, Roberto Program in Applied and Computational Mathematics Princeton University PrincetonNJ08544 United States CAPT HEDPS College of Engineering Peking University Beijing100871 China Department of Physics Temple University PhiladelphiaPA19122 United States Laboratory of Computational Physics Institute of Applied Physics and Computational Mathematics Huayuan Road 6 Beijing100088 China Department of Mathematics and Program in Applied and Computational Mathematics Princeton University PrincetonNJ08544 United States Beijing Institute of Big Data Research Beijing100871 China 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

We introduce a deep neural network (DNN) model that assigns the position of the centers of the electronic charge in the snapshots of a molecular dynamics trajectory. The electronic centers are uniquely specified by the unitary transformation that maps the occupied eigenstates onto maximally localized Wannier functions. In combination with deep potential molecular dynamics, a DNN approach to model the atomic potential energy surface at the ab initio density functional level of theory, the scheme makes possible to predict the dielectric properties of insulators for samples and trajectories inaccessible to direct ab initio simulation, without loss of accuracy. As an example, we report calculations of the infrared absorption spectra of light and heavy water at a dispersion inclusive hybrid functional level of theory, finding good agreement with experiment. Extensions to other spectroscopies, like Raman and sum frequency generation, are discussed. Copyright © 2019, The Authors. All rights reserved.

关键词： Quantum chemistry

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CONVERGENCE OF A TIME-STEPPING SCHEME TO THE FREE BOUNDARY IN THE SUPERCOOLED STEFAN PROBLEM

arXiv

引用

arXiv 2020年

作者： Kaushansky, Vadim Reisinger, Christoph Shkolnikov, Mykhaylo Song, Zhuo Qun Department of Mathematics University of California Los AngelesCA90095 United States Mathematical Institute University of Oxford Andrew Wiles Building Radcliffe Observatory Quarter OxfordOX2 6GG United Kingdom ORFE Department Bendheim Center for Finance and Program in Applied & Computational Mathematics Princeton University Princeton NJ08544 United States Department of Mathematics Princeton University Princeton NJ08544 United States

The supercooled Stefan problem and its variants describe the freezing of a supercooled liquid in physics, as well as the large system limits of systemic risk models in finance and of integrate-and-fire models in neuroscience. Adopting the physics terminology, the supercooled Stefan problem is known to feature a finite-time blow-up of the freezing rate for a wide range of initial temperature distributions in the liquid. Such a blow-up can result in a discontinuity of the liquid-solid boundary. In this paper, we prove that the natural Euler time-stepping scheme applied to a probabilistic formulation of the supercooled Stefan problem converges to the liquid-solid boundary of its physical solution globally in time, in the Skorokhod M1 topology. In the course of the proof, we give an explicit bound on the rate of local convergence for the time-stepping scheme. We also run numerical tests to compare our theoretical results to the practically observed convergence *** Codes 80A22, 35B44, 65N20, 60H30 Copyright © 2020, The Authors. All rights reserved.

关键词： Supercooling

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Spectral neighbor joining for reconstruction of latent tree models

arXiv

引用

arXiv 2020年

作者： Jaffe, Ariel Amsel, Noah Nadler, Boaz Chang, Joseph T. Kluger, Yuval Program in Applied Mathematics Yale University New HavenCT06511 United States Department of Computer Science Weizmann Institute of Science Rehovot76100 Israel Department of Statistics Yale University New HavenCT06520 United States Interdepartmental Program in Computational Biology and Bioinformatics New HavenCT06511 Singapore Department of Pathology New HavenCT06511 United States

A key assumption in multiple scientific applications is that the distribution of observed data can be modeled by a latent tree graphical model. An important example is phylogenetics, where the tree models the evolutionary lineages of various organisms. Given a set of independent realizations of the random variables at the leaves of the tree, a common task is to infer the underlying tree topology. In this work we develop Spectral Neighbor Joining (SNJ), a novel method to recover latent tree graphical models. In contrast to distance based methods, SNJ is based on a spectral measure of similarity between all pairs of observed variables. We prove that SNJ is consistent, and derive a sufficient condition for correct tree recovery from an estimated similarity matrix. Combining this condition with a concentration of measure result on the similarity matrix, we bound the number of samples required to recover the tree with high probability. We illustrate via extensive simulations that SNJ requires fewer samples to accurately recover trees in regimes where the tree contains a large number of leaves or long edges. We provide theoretical support for this observation by analyzing the model of a perfect binary tree. Copyright © 2020, The Authors. All rights reserved.

关键词： Recovery

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Convergence acceleration of ensemble Kalman inversion in nonlinear settings

arXiv

引用

arXiv 2019年

作者： Chada, Neil K. Tong, Xin T. Applied Mathematics and Computational Science Program King Abdullah University of Science and Technology Thuwal23955 Saudi Arabia Department of Mathematics National University of Singapore 119077 Singapore

Many data-science problems can be formulated as an inverse problem, where the parameters are estimated by minimizing a proper loss function. When complicated black-box models are involved, derivative-free optimization tools are often needed. The ensemble Kalman filter (EnKF) is a particle-based derivative-free Bayesian algorithm originally designed for data assimilation. Recently, it has been applied to inverse problems for computational efficiency. The resulting algorithm, known as ensemble Kalman inversion (EKI), involves running an ensemble of particles with EnKF update rules so they can converge to a minimizer. In this article, we investigate EKI convergence in general nonlinear settings. To improve convergence speed and stability, we consider applying EKI with non-constant step-sizes and covariance inflation. We prove that EKI can hit critical points with finite steps in non-convex settings. We further prove that EKI converges to the global minimizer polynomially fast if the loss function is strongly convex. We verify the analysis presented with numerical experiments on two inverse problems. Copyright © 2019, The Authors. All rights reserved.

关键词： Inverse problems

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A Mathematical Model for Linguistic Universals

arXiv

引用

arXiv 2019年

作者： Weinan, E. Zhou, Yajun Department of Mathematics & Program in Applied and Computational Mathematics Princeton University PrincetonNJ08544 United States Beijing Institute of Big Data Research Beijing100871 China

Inspired by chemical kinetics and neurobiology, we propose a mathematical theory for pattern recurrence in text documents, applicable to a wide variety of languages. We present a Markov model at the discourse level for Steven Pinker’s "mentalese", or chains of mental states that transcend the spoken/written forms. Such (potentially) universal temporal structures of textual patterns lead us to a language-independent semantic representation, or a translationally-invariant word embedding, thereby forming the common ground for both comprehensibility within a given language and translatability between different languages. Applying our model to documents of moderate lengths, without relying on external knowledge bases, we reconcile Noam Chomsky’s "poverty of stimulus" paradox with statistical learning of natural languages. Copyright © 2019, The Authors. All rights reserved.

关键词： Markov processes

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Reed-Muller Codes Polarize

Reed-Muller Codes Polarize

引用

Annual IEEE Symposium on Foundations of Computer Science

作者： Emmanuel Abbe Min Ye Mathematics Institute and the School of Computer and Communication Sciences at EPFL Switzerland Program in Applied and Computational Mathematics in Princeton University USA Department of Electrical Engineering Princeton University USA

Reed-Muller (RM) codes were introduced in 1954 and have long been conjectured to achieve Shannon's capacity on symmetric channels. The activity on this conjecture has recently been revived with the emergence of polar codes. RM codes and polar codes are generated by the same matrix G_m= [1/1 0/1] ^⊗m but using different subset of rows. RM codes select simply rows having largest weights. Polar codes select instead rows having the largest conditional mutual information proceeding top to down in G_m; while this is a more elaborate and channel-dependent rule, the top-to-down ordering allows Arikan to show that the conditional mutual information polarizes, and this gives directly a capacity-achieving code on any symmetric channel. RM codes are yet to be proved to have such a property, despite the recent success for the erasure channel. In this paper, we connect RM codes to polarization theory. We show that proceeding in the RM code ordering, i.e., not top-to-down but from the lightest to the heaviest rows in G_m, the conditional mutual information again polarizes. We further demonstrate that it does so faster than for polar codes. This implies that G_m contains another code, different than the polar code and called here the twin-RM code, that is provably capacity-achieving on any symmetric channel. This gives in particular a necessary condition for RM codes to achieve capacity on symmetric channels. It further gives a sufficient condition if the rows with largest conditional mutual information correspond to the heaviest rows, i.e., if the twin-RM code is the RM code. We demonstrate here that the two codes are at least similar and give further evidence that they are indeed the same.

关键词： Polar codes Mutual information Channel capacity Decoding Entropy Boolean functions

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Hyper-molecules: On the representation and recovery of dynamical structures, with application to flexible macro-molecular structures in cryo-EM

arXiv

引用

arXiv 2019年

作者： Lederman, Roy R. Andén, Joakim Singer, Amit Department of Statistics and Data Science Yale University New HavenCT United States Center for Computational Mathematics Flatiron Institute New YorkNY United States Department of Mathematics and Program in Applied and Computational Mathematics Princeton University PrincetonNJ United States

Cryo-electron microscopy (cryo-EM), the subject of the 2017 Nobel Prize in Chemistry, is a technology for determining the 3-D structure of macromolecules from many noisy 2-D projections of instances of these macromolecules, whose orientations and positions are unknown. The molecular structures are not rigid objects, but flexible objects involved in dynamical processes. The different conformations are exhibited by different instances of the macromolecule observed in a cryo-EM experiment, each of which is recorded as a particle image. The range of conformations and the conformation of each particle are not known a priori;one of the great promises of cryo-EM is to map this conformation space. Remarkable progress has been made in determining rigid structures from homogeneous samples of molecules in spite of the unknown orientation of each particle image and significant progress has been made in recovering a few distinct states from mixtures of rather distinct conformations, but more complex heterogeneous samples remain a major challenge. We introduce the "hyper-molecule" framework for modeling structures across different states of heterogeneous molecules, including continuums of states. The key idea behind this framework is representing heterogeneous macromolecules as high-dimensional objects, with the additional dimensions representing the conformation space. This idea is then refined to model properties such as localized heterogeneity. In addition, we introduce an algorithmic framework for recovering such maps of heterogeneous objects from experimental data using a Bayesian formulation of the problem and Markov chain Monte Carlo (MCMC) algorithms to address the computational challenges in recovering these high dimensional hyper-molecules. We demonstrate these ideas in a prototype applied to synthetic data. Copyright © 2019, The Authors. All rights reserved.

关键词： Medical imaging

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Effective Elastic Wave Characteristics of Composite Media

arXiv

引用

arXiv 2020年

作者： Kim, Jaeuk Torquato, S. Department of Physics Princeton University PrincetonNJ08544 United States Department of Chemistry Princeton University PrincetonNJ08544 United States Princeton Institute for the Science and Technology of Materials Princeton University PrincetonNJ08544 United States Program in Applied and Computational Mathematics Princeton University PrincetonNJ08544 United States

We derive exact expressions for effective elastodynamic properties of two-phase composites in the long-wavelength (quasistatic) regime via homogenized constitutive relations that are local in space. This is accomplished by extending the "strong-contrast" expansion formalism that was previously applied to the static problem. These strong-contrast expansions explicitly incorporate complete microstructural information of the composite via an infinite set of n-point correlation functions. Utilizing the rapid-convergence properties of these series expansions (even for extreme contrast ratios), we extract accurate approximations that depend on the microstructure via the spectral density, which is easy to compute or measure for any composite. We also investigate the predictive power of modifications of such approximation formulas postulated elsewhere [J. Kim and S. Torquato, Proc. Nat. Acad. Sci. 117, 8764 (2020)] to extend their applicability beyond the quasistatic regime. The accuracy of these nonlocal microstructure-dependent approximations is validated by comparison to full-waveform simulation results for certain models of dispersions. We apply our formulas to a variety of models of nonhyperuniform and hyperuniform disordered composites. We demonstrate that hyperuniform systems are less lossy than their nonhyperuniform counterparts in the quasistatic regime, and stealthy hyperuniform media can be perfectly transparent for a wide range of wavenumbers. Finally, we discuss how to utilize our approximations for engineering composites with prescribed elastic wave characteristics. Copyright © 2020, The Authors. All rights reserved.

关键词： Microstructure

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