arXiv subjects

Huan Lei

Publications and source records attributed to Huan Lei.

At least 37 records · Page 2Linked to original sources

arXiv2023

Construction of coarse-grained molecular dynamics with many-body non-Markovian memory

We introduce a machine-learning-based coarse-grained molecular dynamics (CGMD) model that faithfully retains the many-body nature of the inter-molecular dissipative interactions. Unlike common empirical CG models, the present model is constructed based on the Mori-Zwanzig formalism and naturally inherits the heterogeneous state-dependent memory term rather than matching the mean-field metrics such as the velocity auto-correlation function. Numerical results show that preserving the many-body nature of the memory term is crucial for predicting the collective transport and diffusion processes, where empirical forms generally show limitations.

physics.comp-ph↗

arXiv2023

Large-scale Training Data Search for Object Re-identification

We consider a scenario where we have access to the target domain, but cannot afford on-the-fly training data annotation, and instead would like to construct an alternative training set from a large-scale data pool such that a competitive model can be obtained. We propose a search and pruning (SnP) solution to this training data search problem, tailored to object re-identification (re-ID), an application aiming to match the same object captured by different cameras. Specifically, the search stage identifies and merges clusters of source identities which exhibit similar distributions with the target domain. The second stage, subject to a budget, then selects identities and their images from the Stage I output, to control the size of the resulting training set for efficient training. The two steps provide us with training sets 80\% smaller than the source pool while achieving a similar or even higher re-ID accuracy. These training sets are also shown to be superior to a few existing search methods such as random sampling and greedy sampling under the same budget on training data size. If we release the budget, training sets resulting from the first stage alone allow even higher re-ID accuracy. We provide interesting discussions on the specificity of our method to the re-ID problem and particularly its role in bridging the re-ID domain gap. The code is available at https://github.com/yorkeyao/SnP.

cs.CV↗

arXiv2022

Machine learning assisted coarse-grained molecular dynamics modeling of meso-scale interfacial fluids

A hallmark of meso-scale interfacial fluids is the multi-faceted, scale-dependent interfacial energy, which often manifests different characteristics across the molecular and continuum scale. The multi-scale nature imposes a challenge to construct reliable coarse-grained (CG) models, where the CG potential function needs to faithfully encode the many-body interactions arising from the unresolved atomistic interactions and account for the heterogeneous density distributions across the interface. We construct the CG models of both single- and two-component of polymeric fluid systems based on the recently developed deep coarse-grained potential (DeePCG) scheme, where each polymer molecule is modeled as a CG particle. By only using the training samples of the instantaneous force under the thermal equilibrium state, the constructed CG models can accurately reproduce both the probability density function of the void formation in bulk and the spectrum of the capillary wave across the fluid interface. More importantly, the CG models accurately predict the volume-to-area scaling transition for the apolar solvation energy, illustrating the effectiveness to probe the meso-scale collective behaviors encoded with molecular-level fidelity.

physics.comp-ph↗

arXiv2022

Data-driven construction of stochastic reduced dynamics encoded with non-Markovian features

One important problem in constructing the reduced dynamics of molecular systems is the accurate modeling of the non-Markovian behavior arising from the dynamics of unresolved variables. The main complication emerges from the lack of scale separations, where the reduced dynamics generally exhibits pronounced memory and non-white noise terms. We propose a data-driven approach to learn the reduced model of multi-dimensional resolved variables that faithfully retains the non-Markovian dynamics. Different from the common approaches based on the direct construction of the memory function, the present approach seeks a set of non-Markovian features that encode the history of the resolved variables, and establishes a joint learning of the extended Markovian dynamics in terms of both the resolved variables and these features. The training is based on matching the evolution of the correlation functions of the extended variables that can be directly obtained from the ones of the resolved variables. The constructed model essentially approximates the multi-dimensional generalized Langevin equation and ensures numerical stability without empirical treatment. We demonstrate the effectiveness of the method by constructing the reduced models of molecular systems in terms of both one-dimensional and four-dimensional resolved variables.

physics.comp-ph↗

arXiv2022

DeePN$^2$: A deep learning-based non-Newtonian hydrodynamic model

A long standing problem in the modeling of non-Newtonian hydrodynamics of polymeric flows is the availability of reliable and interpretable hydrodynamic models that faithfully encode the underlying micro-scale polymer dynamics. The main complication arises from the long polymer relaxation time, the complex molecular structure and heterogeneous interaction. DeePN$^2$, a deep learning-based non-Newtonian hydrodynamic model, has been proposed and has shown some success in systematically passing the micro-scale structural mechanics information to the macro-scale hydrodynamics for suspensions with simple polymer conformation and bond potential. The model retains a multi-scaled nature by mapping the polymer configurations into a set of symmetry-preserving macro-scale features. The extended constitutive laws for these macro-scale features can be directly learned from the kinetics of their micro-scale counterparts. In this paper, we develop DeePN$^2$ using more complex micro-structural models. We show that DeePN$^2$ can faithfully capture the broadly overlooked viscoelastic differences arising from the specific molecular structural mechanics without human intervention.

physics.comp-ph↗

arXiv2021

Effective Mori-Zwanzig equation for the reduced-order modeling of stochastic systems

Built upon the hypoelliptic analysis of the effective Mori-Zwanzig (EMZ) equation for observables of stochastic dynamical systems, we show that the obtained semigroup estimates for the EMZ equation can be used to drive prior estimates of the observable statistics for system in the equilibrium and non-equilibrium state. In addition, we introduce both first-principle and data-driven methods to approximate the EMZ memory kernel, and prove the convergence of the data-driven parametrization schemes using the regularity estimate of the memory kernel. The analysis results are validated numerically via the Monte-Carlo simulation of the Langevin dynamics for a Fermi-Pasta-Ulam chain model. With the same example, we also show the effectiveness of the proposed memory kernel approximation methods.

math-ph↗

arXiv2021

Generalized second fluctuation-dissipation theorem in the nonequilibrium steady state: Theory and applications

In this paper, we derive a generalized second fluctuation-dissipation theorem (FDT) for stochastic dynamical systems in the steady state. The established theory is built upon the Mori-type generalized Langevin equation for stochastic dynamical systems and only uses the properties of the Kolmogorov operator. The new second FDT expresses the memory kernel of the generalized Langevin equation as the correlation function of the fluctuation force plus an additional term. In particular, we show that for nonequilibrium states such as heat transport between two thermostats with different temperatures, the classical second FDT is valid even when the exact form of the steady state distribution is unknown. The obtained theoretical results enable us to construct a data-driven nanoscale fluctuating heat conduction model based on the second FDT. We numerically verify that the new model of heat transfer yields better predictions than the Green-Kubo formula for systems far from the equilibrium.

cond-mat.stat-mech↗

arXiv2021

Picasso: A CUDA-based Library for Deep Learning over 3D Meshes

We present Picasso, a CUDA-based library comprising novel modules for deep learning over complex real-world 3D meshes. Hierarchical neural architectures have proved effective in multi-scale feature extraction which signifies the need for fast mesh decimation. However, existing methods rely on CPU-based implementations to obtain multi-resolution meshes. We design GPU-accelerated mesh decimation to facilitate network resolution reduction efficiently on-the-fly. Pooling and unpooling modules are defined on the vertex clusters gathered during decimation. For feature learning over meshes, Picasso contains three types of novel convolutions namely, facet2vertex, vertex2facet, and facet2facet convolution. Hence, it treats a mesh as a geometric structure comprising vertices and facets, rather than a spatial graph with edges as previous methods do. Picasso also incorporates a fuzzy mechanism in its filters for robustness to mesh sampling (vertex density). It exploits Gaussian mixtures to define fuzzy coefficients for the facet2vertex convolution, and barycentric interpolation to define the coefficients for the remaining two convolutions. In this release, we demonstrate the effectiveness of the proposed modules with competitive segmentation results on S3DIS. The library will be made public through https://github.com/hlei-ziyan/Picasso.

cs.CV↗

arXiv2021

Potential Escalator-related Injury Identification and Prevention Based on Multi-module Integrated System for Public Health

Escalator-related injuries threaten public health with the widespread use of escalators. The existing studies tend to focus on after-the-fact statistics, reflecting on the original design and use of defects to reduce the impact of escalator-related injuries, but few attention has been paid to ongoing and impending injuries. In this study, a multi-module escalator safety monitoring system based on computer vision is designed and proposed to simultaneously monitor and deal with three major injury triggers, including losing balance, not holding on to handrails and carrying large items. The escalator identification module is utilized to determine the escalator region, namely the region of interest. The passenger monitoring module is leveraged to estimate the passengers' pose to recognize unsafe behaviors on the escalator. The dangerous object detection module detects large items that may enter the escalator and raises alarms. The processing results of the above three modules are summarized in the safety assessment module as the basis for the intelligent decision of the system. The experimental results demonstrate that the proposed system has good performance and great application potential.

cs.CV↗

arXiv2020

Machine learning based non-Newtonian fluid model with molecular fidelity

We introduce a machine-learning-based framework for constructing continuum non-Newtonian fluid dynamics model directly from a micro-scale description. Dumbbell polymer solutions are used as examples to demonstrate the essential ideas. To faithfully retain molecular fidelity, we establish a micro-macro correspondence via a set of encoders for the micro-scale polymer configurations and their macro-scale counterparts, a set of nonlinear conformation tensors. The dynamics of these conformation tensors can be derived from the micro-scale model and the relevant terms can be parametrized using machine learning. The final model named the deep non-Newtonian model (DeePN$^2$), takes the form of conventional non-Newtonian fluid dynamics models, with a new form of the objective tensor derivative. Both the formulation of the dynamic equation and the neural network representation rigorously preserve the rotational invariance, which ensures the admissibility of the constructed model. Numerical results demonstrate the accuracy of DeePN$^2$, where models based on empirical closures show limitations.

physics.comp-ph↗

arXiv2020

Data-driven molecular modeling with the generalized Langevin equation

The complexity of molecular dynamics simulations necessitates dimension reduction and coarse-graining techniques to enable tractable computation. The generalized Langevin equation (GLE) describes coarse-grained dynamics in reduced dimensions. In spite of playing a crucial role in non-equilibrium dynamics, the memory kernel of the GLE is often ignored because it is difficult to characterize and expensive to solve. To address these issues, we construct a data-driven rational approximation to the GLE. Building upon previous work leveraging the GLE to simulate simple systems, we extend these results to more complex molecules, whose many degrees of freedom and complicated dynamics require approximation methods. We demonstrate the effectiveness of our approximation by testing it against exact methods and comparing observables such as autocorrelation and transition rates.

physics.comp-ph↗

arXiv2020

Spherical Kernel for Efficient Graph Convolution on 3D Point Clouds

We propose a spherical kernel for efficient graph convolution of 3D point clouds. Our metric-based kernels systematically quantize the local 3D space to identify distinctive geometric relationships in the data. Similar to the regular grid CNN kernels, the spherical kernel maintains translation-invariance and asymmetry properties, where the former guarantees weight sharing among similar local structures in the data and the latter facilitates fine geometric learning. The proposed kernel is applied to graph neural networks without edge-dependent filter generation, making it computationally attractive for large point clouds. In our graph networks, each vertex is associated with a single point location and edges connect the neighborhood points within a defined range. The graph gets coarsened in the network with farthest point sampling. Analogous to the standard CNNs, we define pooling and unpooling operations for our network. We demonstrate the effectiveness of the proposed spherical kernel with graph neural networks for point cloud classification and semantic segmentation using ModelNet, ShapeNet, RueMonge2014, ScanNet and S3DIS datasets. The source code and the trained models can be downloaded from https://github.com/hlei-ziyan/SPH3D-GCN.

cs.CV↗

arXiv2019

Improving solution accuracy and convergence for stochastic physics parameterizations with colored noise

Stochastic parameterizations are used in numerical weather prediction and climate modeling to help capture the uncertainty in the simulations and improve their statistical properties. Convergence issues can arise when time integration methods originally developed for deterministic differential equations are applied naively to stochastic problems. (Hodyss et al 2013, 2014) demonstrated that a correction term to various deterministic numerical schemes, known in stochastic analysis as the Itô correction, can help improve solution accuracy and ensure convergence to the physically relevant solution without substantial computational overhead. The usual formulation of the Itô correction is valid only when the stochasticity is represented by {\it white} noise. In this study, a generalized formulation of the Itô correction is derived for noises of any color. The formulation is applied to a test problem described by an advection-diffusion equation forced with a spectrum of fast processes. We present numerical results for cases with both constant and spatially varying advection velocities to show that, for the same time step sizes, the introduction of the generalized Itô correction helps to substantially reduce time integration error and significantly improve the convergence rate of the numerical solutions when the forcing term in the governing equation is rough (fast varying); alternatively, for the same target accuracy, the generalized Itô correction allows for the use of significantly longer time steps and hence helps to reduce the computational cost of the numerical simulation.

math.NA↗

arXiv2019

A data-driven framework for sparsity-enhanced surrogates with arbitrary mutually dependent randomness

The challenge of quantifying uncertainty propagation in real-world systems is rooted in the high-dimensionality of the stochastic input and the frequent lack of explicit knowledge of its probability distribution. Traditional approaches show limitations for such problems. To address these difficulties, we have developed a general framework of constructing surrogate models on spaces of stochastic input with arbitrary probability measure irrespective of the mutual dependencies between individual components and the analytical form. The present Data-driven Sparsity-enhancing Rotation for Arbitrary Randomness (DSRAR) framework includes a data-driven construction of multivariate polynomial basis for arbitrary mutually dependent probability measure and a sparsity enhancement rotation procedure. This sparsity-enhancing rotation method was initially proposed in our previous work [1] for Gaussian distributions, which may not be feasible for non-Gaussian distributions due to the loss of orthogonality after the rotation. To remedy such difficulties, we developed the new approach to construct orthonormal polynomials for arbitrary mutually dependent (amdP) randomness, ensuring the constructed basis maintains the orthogonality with respect to the density of the rotated random vector, where directly applying the regular polynomial chaos including arbitrary polynomial chaos (aPC) [2] shows limitations due to the assumption of the mutual independence between the components of the random inputs. The developed DSRAR framework leads to accurate recovery of a sparse representation of the target functions. The effectiveness of our method is demonstrated in challenging problems such as PDEs and realistic molecular systems where the underlying density is implicitly represented by a large collection of sample data, as well as systems with explicitly given non-Gaussian probabilistic measures.

math.NA↗

arXiv2019

Octree guided CNN with Spherical Kernels for 3D Point Clouds

We propose an octree guided neural network architecture and spherical convolutional kernel for machine learning from arbitrary 3D point clouds. The network architecture capitalizes on the sparse nature of irregular point clouds, and hierarchically coarsens the data representation with space partitioning. At the same time, the proposed spherical kernels systematically quantize point neighborhoods to identify local geometric structures in the data, while maintaining the properties of translation-invariance and asymmetry. We specify spherical kernels with the help of network neurons that in turn are associated with spatial locations. We exploit this association to avert dynamic kernel generation during network training that enables efficient learning with high resolution point clouds. The effectiveness of the proposed technique is established on the benchmark tasks of 3D object classification and segmentation, achieving new state-of-the-art on ShapeNet and RueMonge2014 datasets.

cs.CV↗

arXiv2018

A General Framework for Enhancing Sparsity of Generalized Polynomial Chaos Expansions

Compressive sensing has become a powerful addition to uncertainty quantification when only limited data is available. In this paper we provide a general framework to enhance the sparsity of the representation of uncertainty in the form of generalized polynomial chaos expansion. We use alternating direction method to identify new sets of random variables through iterative rotations such that the new representation of the uncertainty is sparser. Consequently, we increases both the efficiency and accuracy of the compressive sensing-based uncertainty quantification method. We demonstrate that the previously developed iterative method to enhance the sparsity of Hermite polynomial expansion is a special case of this general framework. Moreover, we use Legendre and Chebyshev polynomials expansions to demonstrate the effectiveness of this method with applications in solving stochastic partial differential equations and high-dimensional (O(100)) problems.

math.NA↗

arXiv2018

Spherical Convolutional Neural Network for 3D Point Clouds

We propose a neural network for 3D point cloud processing that exploits `spherical' convolution kernels and octree partitioning of space. The proposed metric-based spherical kernels systematically quantize point neighborhoods to identify local geometric structures in data, while maintaining the properties of translation-invariance and asymmetry. The network architecture itself is guided by octree data structuring that takes full advantage of the sparse nature of irregular point clouds. We specify spherical kernels with the help of neurons in each layer that in turn are associated with spatial locations. We exploit this association to avert dynamic kernel generation during network training, that enables efficient learning with high resolution point clouds. We demonstrate the utility of the spherical convolutional neural network for 3D object classification on standard benchmark datasets.

cs.CV↗

arXiv2017

Atomic radius and charge parameter uncertainty in biomolecular solvation energy calculations

Atomic radii and charges are two major parameters used in implicit solvent electrostatics and energy calculations. The optimization problem for charges and radii is under-determined, leading to uncertainty in the values of these parameters and in the results of solvation energy calculations using these parameters. This paper presents a new method for quantifying this uncertainty in implicit solvation calculations of small molecules using surrogate models based on generalized polynomial chaos (gPC) expansions. There are relatively few atom types used to specify radii parameters in implicit solvation calculations; therefore, surrogate models for these low-dimensional spaces could be constructed using least-squares fitting. However, there are many more types of atomic charges; therefore, construction of surrogate models for the charge parameter space requires compressed sensing combined with an iterative rotation method to enhance problem sparsity. We demonstrate the application of the method by presenting results for the uncertainties in small molecule solvation energies based on these approaches. The method presented in this paper is a promising approach for efficiently quantifying uncertainty in a wide range of force field parameterization problems, including those beyond continuum solvation calculations.The intent of this study is to provide a way for developers of implicit solvent model parameter sets to understand the sensitivity of their target properties (solvation energy) on underlying choices for solute radius and charge parameters.

q-bio.BM↗