arXiv subjects

Xiu Yang

Publications and source records attributed to Xiu Yang.

At least 37 records · Page 2Linked to original sources

arXiv2021

A general framework of rotational sparse approximation in uncertainty quantification

This paper proposes a general framework to estimate coefficients of generalized polynomial chaos (gPC) used in uncertainty quantification via rotational sparse approximation. In particular, we aim to identify a rotation matrix such that the gPC expansion of a set of random variables after the rotation has a sparser representation. However, this rotational approach alters the underlying linear system to be solved, which makes finding the sparse coefficients more difficult than the case without rotation. To solve this problem, we examine several popular nonconvex regularizations in compressive sensing (CS) that perform better than the classic l1 approach empirically. All these regularizations can be minimized by the alternating direction method of multipliers (ADMM). Numerical examples show superior performance of the proposed combination of rotation and nonconvex sparse promoting regularizations over the ones without rotation and with rotation but using the convex l1 approach.

stat.CO↗

arXiv2021

An asymptotically compatible probabilistic collocation method for randomly heterogeneous nonlocal problems

In this paper we present an asymptotically compatible meshfree method for solving nonlocal equations with random coefficients, describing diffusion in heterogeneous media. In particular, the random diffusivity coefficient is described by a finite-dimensional random variable or a truncated combination of random variables with the Karhunen-Loève decomposition, then a probabilistic collocation method (PCM) with sparse grids is employed to sample the stochastic process. On each sample, the deterministic nonlocal diffusion problem is discretized with an optimization-based meshfree quadrature rule. We present rigorous analysis for the proposed scheme and demonstrate convergence for a number of benchmark problems, showing that it sustains the asymptotic compatibility spatially and achieves an algebraic or sub-exponential convergence rate in the random coefficients space as the number of collocation points grows. Finally, to validate the applicability of this approach we consider a randomly heterogeneous nonlocal problem with a given spatial correlation structure, demonstrating that the proposed PCM approach achieves substantial speed-up compared to conventional Monte Carlo simulations.

math.NA↗

arXiv2021

Augmented Gaussian Random Field: Theory and Computation

We propose the novel augmented Gaussian random field (AGRF), which is a universal framework incorporating the data of observable and derivatives of any order. Rigorous theory is established. We prove that under certain conditions, the observable and its derivatives of any order are governed by a single Gaussian random field, which is the aforementioned AGRF. As a corollary, the statement ``the derivative of a Gaussian process remains a Gaussian process'' is validated, since the derivative is represented by a part of the AGRF. Moreover, a computational method corresponding to the universal AGRF framework is constructed. Both noiseless and noisy scenarios are considered. Formulas of the posterior distributions are deduced in a nice closed form. A significant advantage of our computational method is that the universal AGRF framework provides a natural way to incorporate arbitrary order derivatives and deal with missing data. We use four numerical examples to demonstrate the effectiveness of the computational method. The numerical examples are composite function, damped harmonic oscillator, Korteweg-De Vries equation, and Burgers' equation.

math.ST↗

arXiv2021

Graphical Gaussian Process Regression Model for Aqueous Solvation Free Energy Prediction of Organic Molecules in Redox Flow Battery

The solvation free energy of organic molecules is a critical parameter in determining emergent properties such as solubility, liquid-phase equilibrium constants, and pKa and redox potentials in an organic redox flow battery. In this work, we present a machine learning (ML) model that can learn and predict the aqueous solvation free energy of an organic molecule using Gaussian process regression method based on a new molecular graph kernel. To investigate the performance of the ML model on electrostatic interaction, the nonpolar interaction contribution of solvent and the conformational entropy of solute in solvation free energy, three data sets with implicit or explicit water solvent models, and contribution of conformational entropy of solute are tested. We demonstrate that our ML model can predict the solvation free energy of molecules at chemical accuracy with a mean absolute error of less than 1 kcal/mol for subsets of the QM9 dataset and the Freesolv database. To solve the general data scarcity problem for a graph-based ML model, we propose a dimension reduction algorithm based on the distance between molecular graphs, which can be used to examine the diversity of the molecular data set. It provides a promising way to build a minimum training set to improve prediction for certain test sets where the space of molecular structures is predetermined.

cs.CE↗

arXiv2021

A Physics-Informed Neural Network Framework For Partial Differential Equations on 3D Surfaces: Time-Dependent Problems

In this paper, we show a physics-informed neural network solver for the time-dependent surface PDEs. Unlike the traditional numerical solver, no extension of PDE and mesh on the surface is needed. We show a simplified prior estimate of the surface differential operators so that PINN's loss value will be an indicator of the residue of the surface PDEs. Numerical experiments verify efficacy of our algorithm.

cs.LG↗

arXiv2020

Multifidelity Data Fusion via Gradient-Enhanced Gaussian Process Regression

We propose a data fusion method based on multi-fidelity Gaussian process regression (GPR) framework. This method combines available data of the quantity of interest (QoI) and its gradients with different fidelity levels, namely, it is a Gradient-enhanced Cokriging method (GE-Cokriging). It provides the approximations of both the QoI and its gradients simultaneously with uncertainty estimates. We compare this method with the conventional multi-fidelity Cokriging method that does not use gradients information, and the result suggests that GE-Cokriging has a better performance in predicting both QoI and its gradients. Moreover, GE-Cokriging even shows better generalization result in some cases where Cokriging performs poorly due to the singularity of the covariance matrix. We demonstrate the application of GE-Cokriging in several practical cases including reconstructing the trajectories and velocity of an underdamped oscillator with respect to time simultaneously, and investigating the sensitivity of power factor of a load bus with respect to varying power inputs of a generator bus in a large scale power system. We also show that though GE-Cokriging method requires a little bit higher computational cost than Cokriging method, the result of accuracy comparison shows that this cost is usually worth it.

cs.CE↗

arXiv2020

Nonnegativity-Enforced Gaussian Process Regression

Gaussian Process (GP) regression is a flexible non-parametric approach to approximate complex models. In many cases, these models correspond to processes with bounded physical properties. Standard GP regression typically results in a proxy model which is unbounded for all temporal or spacial points, and thus leaves the possibility of taking on infeasible values. We propose an approach to enforce the physical constraints in a probabilistic way under the GP regression framework. In addition, this new approach reduces the variance in the resulting GP model.

cs.LG↗

arXiv2019

A New Approach For Learning Coarse-Grained Potentials with Application to Immiscible Fluids

Even though atomistic and coarse-grained (CG) models have been used to simulate liquid nanodroplets in vapor, very few rigorous studies of the liquid-liquid interface structure are available, and most of them are limited to planar interfaces. In this work, we evaluate several existing force fields (FF)s, including two atomistic and three CG FFs, with respect to modeling the interface structure and thermodynamic properties of the water-hexane interface. Both atomistic FFs are able to quantitatively reproduce the interfacial tension and the coexisting densities of the experimentally-observed planar interface. We use the atomistic FFs to model water droplets in hexane and use these simulations to test the CG FFs. We find that the tested CG FFs cannot reproduce the interfacial tensions of planar and/or curved interfaces. Finally, we propose a new approach for learning CG potentials within the CG SDK (Shinoda-DeVane-Klein) FF framework from atomistic simulation data. We demonstrate that the new potential significantly improves the prediction of both the interfacial tension and structure of water-hexane planar and curved interfaces.

physics.chem-ph↗

arXiv2019

Engineering Structural Robustness in Power Grid Networks Susceptible to Coherent Swing Instability

Networked power grid systems are susceptible to a phenomenon known as Coherent Swing Instability (CSI), in which a subset of machines in the grid lose synchrony with the rest of the network. We develop network level evaluation metrics to (i) identify community substructures in the power grid network, (ii) determine weak points in the network that are particularly sensitive to CSI, and (iii) produce an engineering approach for the addition of transmission lines to reduce the incidences of CSI in existing networks, or design new power grid networks that are robust to CSI by their network design. For simulations on a reduced model for the American Northeast power grid, where a block of buses representing the New England region exhibit a strong propensity for CSI, we show that modifying the network's connectivity structure can markedly improve the grid's resilience to CSI. Our analysis provides a versatile diagnostic tool for evaluating the efficacy of adding lines to a power grid which is known to be prone to CSI. This is a particularly relevant problem in large-scale power systems, where improving stability and robustness to interruptions by increasing overall network connectivity is not feasible due to financial and infrastructural constraints.

physics.soc-ph↗

arXiv2018

When Bifidelity Meets CoKriging: An Efficient Physics-Informed Multifidelity Method

In this work, we propose a framework that combines the approximation-theory-based multifidelity method and Gaussian-process-regression-based multifidelity method to achieve data-model convergence when stochastic simulation models and sparse accurate observation data are available. Specifically, the two types of multifidelity methods we use are the bifidelity and CoKriging methods. The new approach uses the bifidelity method to efficiently estimate the empirical mean and covariance of the stochastic simulation outputs, then it uses these statistics to construct a Gaussian process (GP) representing low-fidelity in CoKriging. We also combine the bifidelity method with Kriging, where the approximated empirical statistics are used to construct the GP as well. We prove that the resulting posterior mean by the new physics-informed approach preserves linear physical constraints up to an error bound. By using this method, we can obtain an accurate construction of a state of interest based on a partially correct physical model and a few accurate observations. We present numerical examples to demonstrate performance of the method.

stat.ML↗

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

Physics-Informed CoKriging: A Gaussian-Process-Regression-Based Multifidelity Method for Data-Model Convergence

In this work, we propose a new Gaussian process regression (GPR)-based multifidelity method: physics-informed CoKriging (CoPhIK). In CoKriging-based multifidelity methods, the quantities of interest are modeled as linear combinations of multiple parameterized stationary Gaussian processes (GPs), and the hyperparameters of these GPs are estimated from data via optimization. In CoPhIK, we construct a GP representing low-fidelity data using physics-informed Kriging (PhIK), and model the discrepancy between low- and high-fidelity data using a parameterized GP with hyperparameters identified via optimization. Our approach reduces the cost of optimization for inferring hyperparameters by incorporating partial physical knowledge. We prove that the physical constraints in the form of deterministic linear operators are satisfied up to an error bound. Furthermore, we combine CoPhIK with a greedy active learning algorithm for guiding the selection of additional observation locations. The efficiency and accuracy of CoPhIK are demonstrated for reconstructing the partially observed modified Branin function, reconstructing the sparsely observed state of a steady state heat transport problem, and learning a conservative tracer distribution from sparse tracer concentration measurements.

stat.ML↗

arXiv2018

Sliced-Inverse-Regression-Aided Rotated Compressive Sensing Method for Uncertainty Quantification

Compressive-sensing-based uncertainty quantification methods have become a pow- erful tool for problems with limited data. In this work, we use the sliced inverse regression (SIR) method to provide an initial guess for the alternating direction method, which is used to en- hance sparsity of the Hermite polynomial expansion of stochastic quantity of interest. The sparsity improvement increases both the efficiency and accuracy of the compressive-sensing- based uncertainty quantification method. We demonstrate that the initial guess from SIR is more suitable for cases when the available data are limited (Algorithm 4). We also propose another algorithm (Algorithm 5) that performs dimension reduction first with SIR. Then it constructs a Hermite polynomial expansion of the reduced model. This method affords the ability to approximate the statistics accurately with even less available data. Both methods are non-intrusive and require no a priori information of the sparsity of the system. The effec- tiveness of these two methods (Algorithms 4 and 5) are demonstrated using problems with up to 500 random dimensions.

math.NA↗

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↗

arXiv2017

PDF estimation for power grid systems via sparse regression

We present a numerical approach for estimating the probability density function (PDF) of quantities of interest (QoIs) of power grid systems subject to uncertain power generation and load fluctuations. In our approach, generation and load fluctuations are modeled by means of autocorrelated-in-time random processes, which are approximated in terms of a finite set of random parameters by means of Karhunen-Loève approximations. The map from random parameters to QoIs is approximated by means of Hermite polynomial expansions. We propose a new approach based on compressive sensing to estimate the coefficients in the Hermite expansions from a small number of realizations (sampling points). Linear transforms identified by iterative rotations are introduced to improve the sparsity of the Hermite representations, exploiting the intrinsic low-dimensional structure of the map. As such, the proposed approach significantly reduces the required number of sampling points to achieve a given accuracy compared to the standard least squares method. The proposed approach is employed to estimate the PDF of relative angular velocities and bus voltages of systems of classical machines driven by autocorrelated random generation. More accurate PDF estimates, as measured by the Kullback-Leibler divergence, are achieved using fewer realizations than required by basic Monte Carlo sampling.

stat.AP↗

arXiv2016

Systematic parameter inference in stochastic mesoscopic modeling

We propose a method to efficiently determine the optimal coarse-grained force field in mesoscopic stochastic simulations of Newtonian fluid and polymer melt systems modeled by dissipative particle dynamics (DPD) and energy conserving dissipative particle dynamics (eDPD). The response surfaces of various target properties (viscosity, diffusivity, pressure, etc.) with respect to model parameters are constructed based on the generalized polynomial chaos (gPC) expansion using simulation results on sampling points (e.g., individual parameter sets). To alleviate the computational cost to evaluate the target properties, we employ the compressive sensing method to compute the coefficients of the dominant gPC terms given the prior knowledge that the coefficients are sparse. The proposed method shows comparable accuracy with the standard probabilistic collocation method (PCM) while it imposes a much weaker restriction on the number of the simulation samples especially for systems with high dimensional parametric space. Fully access to the response surfaces within the confidence range enables us to infer the optimal force parameters given the desirable values of target properties at the macroscopic scale. Moreover, it enables us to investigate the intrinsic relationship between the model parameters, identify possible degeneracies in the parameter space, and optimize the model by eliminating model redundancies. The proposed method provides an efficient alternative approach for constructing mesoscopic models by inferring model parameters to recover target properties of the physics systems (e.g., from experimental measurements), where those force field parameters and formulation cannot be derived from the microscopic level in a straight forward way.

physics.comp-ph↗

arXiv2015

Enhancing Sparsity of Hermite Polynomial Expansions by Iterative Rotations

Compressive sensing has become a powerful addition to uncertainty quantification in recent years. This paper identifies new bases for random variables through linear mappings such that the representation of the quantity of interest is more sparse with new basis functions associated with the new random variables. This sparsity increases both the efficiency and accuracy of the compressive sensing-based uncertainty quantification method. Specifically, we consider rotation-based linear mappings which are determined iteratively for Hermite polynomial expansions. We demonstrate the effectiveness of the new method with applications in solving stochastic partial differential equations and high-dimensional ($\mathcal{O}(100)$) problems.

math.ST↗

arXiv2015

Quantifying the influence of conformational uncertainty in biomolecular solvation

Biomolecules exhibit conformational fluctuations near equilibrium states, inducing uncertainty in various biological properties in a dynamic way. We have developed a general method to quantify the uncertainty of target properties induced by conformational fluctuations. Using a generalized polynomial chaos (gPC) expansion, we construct a surrogate model of the target property with respect to varying conformational states. We also propose a method to increase the sparsity of the gPC expansion by defining a set of conformational "active space" random variables. With the increased sparsity, we employ the compressive sensing method to accurately construct the surrogate model. We demonstrate the performance of the surrogate model by evaluating fluctuation-induced uncertainty in solvent-accessible surface area for the bovine trypsin inhibitor protein system and show that the new approach offers more accurate statistical information than standard Monte Carlo approaches. Further more, the constructed surrogate model also enables us to directly evaluate the target property under various conformational states, yielding a more accurate response surface than standard sparse grid collocation methods. In particular, the new method provides higher accuracy in high-dimensional systems, such as biomolecules, where sparse grid performance is limited by the accuracy of the computed quantity of interest. Our new framework is generalizable and can be used to investigate the uncertainty of a wide variety of target properties in biomolecular systems.

q-bio.BM↗