Detailed dynamical systems models used in life sciences may include dozens or even hundreds of state variables. Models of large dimension are not only harder from the numerical perspective (e.g., for parameter estimation or simulation), but it is also becoming challenging to derive mechanistic insights from such models. Exact model reduction is a way to address this issue by finding a self-consistent lower-dimensional projection of the corresponding dynamical system. A recent algorithm CLUE allows one to construct an exact linear reduction of the smallest possible dimension such that the fixed variables of interest are preserved. However, CLUE is restricted to systems with polynomial dynamics. Since rational dynamics occurs frequently in the life sciences (e.g., Michaelis-Menten or Hill kinetics), it is desirable to extend CLUE to the models with rational dynamics. In this paper, we present an extension of CLUE to the case of rational dynamics and demonstrate its applicability on examples from literature. Our implementation is available in version 1.5 of CLUE at //github.com/pogudingleb/CLUE.
This work proposes a new framework of model reduction for parametric complex systems. The framework employs a popular model reduction technique dynamic mode decomposition (DMD), which is capable of combining data-driven learning and physics ingredients based on the Koopman operator theory. In the offline step of the proposed framework, DMD constructs a low-rank linear surrogate model for the high dimensional quantities of interest (QoIs) derived from the (nonlinear) complex high fidelity models (HFMs) of unknown forms. Then in the online step, the resulting local reduced order bases (ROBs) and parametric reduced order models (PROMs) at the training parameter sample points are interpolated to construct a new PROM with the corresponding ROB for a new set of target/test parameter values. The interpolations need to be done on the appropriate manifolds within consistent sets of generalized coordinates. The proposed framework is illustrated by numerical examples for both linear and nonlinear problems. In particular, its advantages in computational costs and accuracy are demonstrated by the comparisons with projection-based proper orthogonal decomposition (POD)-PROM and Kriging.
We formulate the quadratic eigenvalue problem underlying the mathematical model of a linear vibrational system as an eigenvalue problem of a diagonal-plus-low-rank matrix $A$. The eigenvector matrix of $A$ has a Cauchy-like structure. Optimal viscosities are those for which $trace(X)$ is minimal, where $X$ is the solution of the Lyapunov equation $AX+XA^{*}=GG^{*}$. Here $G$ is a low-rank matrix which depends on the eigenfrequencies that need to be damped. After initial eigenvalue decomposition of linearized problem which requires $O(n^3)$ operations, our algorithm computes optimal viscosities for each choice of external dampers in $O(n^2)$ operations, provided that the number of dampers is small. Hence, the subsequent optimization is order of magnitude faster than in the standard approach which solves Lyapunov equation in each step, thus requiring $O(n^3)$ operations. Our algorithm is based on $O(n^2)$ eigensolver for complex symmetric diagonal-plus-rank-one matrices and fast $O(n^2)$ multiplication of linked Cauchy-like matrices.
Linear mixed models (LMMs) are instrumental for regression analysis with structured dependence, such as grouped, clustered, or multilevel data. However, selection among the covariates--while accounting for this structured dependence--remains a challenge. We introduce a Bayesian decision analysis for subset selection with LMMs. Using a Mahalanobis loss function that incorporates the structured dependence, we derive optimal linear coefficients for (i) any given subset of variables and (ii) all subsets of variables that satisfy a cardinality constraint. Crucially, these estimates inherit shrinkage or regularization and uncertainty quantification from the underlying Bayesian model, and apply for any well-specified Bayesian LMM. More broadly, our decision analysis strategy deemphasizes the role of a single "best" subset, which is often unstable and limited in its information content, and instead favors a collection of near-optimal subsets. This collection is summarized by key member subsets and variable-specific importance metrics. Customized subset search and out-of-sample approximation algorithms are provided for more scalable computing. These tools are applied to simulated data and a longitudinal physical activity dataset, and demonstrate excellent prediction, estimation, and selection ability.
We propose a novel framework for learning a low-dimensional representation of data based on nonlinear dynamical systems, which we call dynamical dimension reduction (DDR). In the DDR model, each point is evolved via a nonlinear flow towards a lower-dimensional subspace; the projection onto the subspace gives the low-dimensional embedding. Training the model involves identifying the nonlinear flow and the subspace. Following the equation discovery method, we represent the vector field that defines the flow using a linear combination of dictionary elements, where each element is a pre-specified linear/nonlinear candidate function. A regularization term for the average total kinetic energy is also introduced and motivated by optimal transport theory. We prove that the resulting optimization problem is well-posed and establish several properties of the DDR method. We also show how the DDR method can be trained using a gradient-based optimization method, where the gradients are computed using the adjoint method from optimal control theory. The DDR method is implemented and compared on synthetic and example datasets to other dimension reductions methods, including PCA, t-SNE, and Umap.
We describe a numerical algorithm for approximating the equilibrium-reduced density matrix and the effective (mean force) Hamiltonian for a set of system spins coupled strongly to a set of bath spins when the total system (system+bath) is held in canonical thermal equilibrium by weak coupling with a "super-bath". Our approach is a generalization of now standard typicality algorithms for computing the quantum expectation value of observables of bare quantum systems via trace estimators and Krylov subspace methods. In particular, our algorithm makes use of the fact that the reduced system density, when the bath is measured in a given random state, tends to concentrate about the corresponding thermodynamic averaged reduced system density. Theoretical error analysis and numerical experiments are given to validate the accuracy of our algorithm. Further numerical experiments demonstrate the potential of our approach for applications including the study of quantum phase transitions and entanglement entropy for long-range interaction systems.
The metriplectic formalism is useful for describing complete dynamical systems which conserve energy and produce entropy. This creates challenges for model reduction, as the elimination of high-frequency information will generally not preserve the metriplectic structure which governs long-term stability of the system. Based on proper orthogonal decomposition, a provably convergent metriplectic reduced-order model is formulated which is guaranteed to maintain the algebraic structure necessary for energy conservation and entropy formation. Numerical results on benchmark problems show that the proposed method is remarkably stable, leading to improved accuracy over long time scales at a moderate increase in cost over naive methods.
Let $X^{(n)}$ be an observation sampled from a distribution $P_{\theta}^{(n)}$ with an unknown parameter $\theta,$ $\theta$ being a vector in a Banach space $E$ (most often, a high-dimensional space of dimension $d$). We study the problem of estimation of $f(\theta)$ for a functional $f:E\mapsto {\mathbb R}$ of some smoothness $s>0$ based on an observation $X^{(n)}\sim P_{\theta}^{(n)}.$ Assuming that there exists an estimator $\hat \theta_n=\hat \theta_n(X^{(n)})$ of parameter $\theta$ such that $\sqrt{n}(\hat \theta_n-\theta)$ is sufficiently close in distribution to a mean zero Gaussian random vector in $E,$ we construct a functional $g:E\mapsto {\mathbb R}$ such that $g(\hat \theta_n)$ is an asymptotically normal estimator of $f(\theta)$ with $\sqrt{n}$ rate provided that $s>\frac{1}{1-\alpha}$ and $d\leq n^{\alpha}$ for some $\alpha\in (0,1).$ We also derive general upper bounds on Orlicz norm error rates for estimator $g(\hat \theta)$ depending on smoothness $s,$ dimension $d,$ sample size $n$ and the accuracy of normal approximation of $\sqrt{n}(\hat \theta_n-\theta).$ In particular, this approach yields asymptotically efficient estimators in some high-dimensional exponential models.
The stochastic gradient Langevin Dynamics is one of the most fundamental algorithms to solve sampling problems and non-convex optimization appearing in several machine learning applications. Especially, its variance reduced versions have nowadays gained particular attention. In this paper, we study two variants of this kind, namely, the Stochastic Variance Reduced Gradient Langevin Dynamics and the Stochastic Recursive Gradient Langevin Dynamics. We prove their convergence to the objective distribution in terms of KL-divergence under the sole assumptions of smoothness and Log-Sobolev inequality which are weaker conditions than those used in prior works for these algorithms. With the batch size and the inner loop length set to $\sqrt{n}$, the gradient complexity to achieve an $\epsilon$-precision is $\tilde{O}((n+dn^{1/2}\epsilon^{-1})\gamma^2 L^2\alpha^{-2})$, which is an improvement from any previous analyses. We also show some essential applications of our result to non-convex optimization.
We introduce a novel methodology for particle filtering in dynamical systems where the evolution of the signal of interest is described by a SDE and observations are collected instantaneously at prescribed time instants. The new approach includes the discretisation of the SDE and the design of efficient particle filters for the resulting discrete-time state-space model. The discretisation scheme converges with weak order 1 and it is devised to create a sequential dependence structure along the coordinates of the discrete-time state vector. We introduce a class of space-sequential particle filters that exploits this structure to improve performance when the system dimension is large. This is numerically illustrated by a set of computer simulations for a stochastic Lorenz 96 system with additive noise. The new space-sequential particle filters attain approximately constant estimation errors as the dimension of the Lorenz 96 system is increased, with a computational cost that increases polynomially, rather than exponentially, with the system dimension. Besides the new numerical scheme and particle filters, we provide in this paper a general framework for discrete-time filtering in continuous-time dynamical systems described by a SDE and instantaneous observations. Provided that the SDE is discretised using a weakly-convergent scheme, we prove that the marginal posterior laws of the resulting discrete-time state-space model converge to the posterior marginal posterior laws of the original continuous-time state-space model under a suitably defined metric. This result is general and not restricted to the numerical scheme or particle filters specifically studied in this manuscript.
Bayesian model selection provides a powerful framework for objectively comparing models directly from observed data, without reference to ground truth data. However, Bayesian model selection requires the computation of the marginal likelihood (model evidence), which is computationally challenging, prohibiting its use in many high-dimensional Bayesian inverse problems. With Bayesian imaging applications in mind, in this work we present the proximal nested sampling methodology to objectively compare alternative Bayesian imaging models for applications that use images to inform decisions under uncertainty. The methodology is based on nested sampling, a Monte Carlo approach specialised for model comparison, and exploits proximal Markov chain Monte Carlo techniques to scale efficiently to large problems and to tackle models that are log-concave and not necessarily smooth (e.g., involving l_1 or total-variation priors). The proposed approach can be applied computationally to problems of dimension O(10^6) and beyond, making it suitable for high-dimensional inverse imaging problems. It is validated on large Gaussian models, for which the likelihood is available analytically, and subsequently illustrated on a range of imaging problems where it is used to analyse different choices of dictionary and measurement model.