11,433 research outputs found

    A Variational Approach to Parameter Estimation in Ordinary Differential Equations

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    Ordinary differential equations are widely-used in the field of systems biology and chemical engineering to model chemical reaction networks. Numerous techniques have been developed to estimate parameters like rate constants, initial conditions or steady state concentrations from time-resolved data. In contrast to this countable set of parameters, the estimation of entire courses of network components corresponds to an innumerable set of parameters. The approach presented in this work is able to deal with course estimation for extrinsic system inputs or intrinsic reactants, both not being constrained by the reaction network itself. Our method is based on variational calculus which is carried out analytically to derive an augmented system of differential equations including the unconstrained components as ordinary state variables. Finally, conventional parameter estimation is applied to the augmented system resulting in a combined estimation of courses and parameters. The combined estimation approach takes the uncertainty in input courses correctly into account. This leads to precise parameter estimates and correct confidence intervals. In particular this implies that small motifs of large reaction networks can be analysed independently of the rest. By the use of variational methods, elements from control theory and statistics are combined allowing for future transfer of methods between the two fields

    Variational mean-field algorithm for efficient inference in large systems of stochastic differential equations

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    This work introduces a Gaussian variational mean-field approximation for inference in dynamical systems which can be modeled by ordinary stochastic differential equations. This new approach allows one to express the variational free energy as a functional of the marginal moments of the approximating Gaussian process. A restriction of the moment equations to piecewise polynomial functions, over time, dramatically reduces the complexity of approximate inference for stochastic differential equation models and makes it comparable to that of discrete time hidden Markov models. The algorithm is demonstrated on state and parameter estimation for nonlinear problems with up to 1000 dimensional state vectors and compares the results empirically with various well-known inference methodologies

    Parametric Estimation of Ordinary Differential Equations with Orthogonality Conditions

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    Differential equations are commonly used to model dynamical deterministic systems in applications. When statistical parameter estimation is required to calibrate theoretical models to data, classical statistical estimators are often confronted to complex and potentially ill-posed optimization problem. As a consequence, alternative estimators to classical parametric estimators are needed for obtaining reliable estimates. We propose a gradient matching approach for the estimation of parametric Ordinary Differential Equations observed with noise. Starting from a nonparametric proxy of a true solution of the ODE, we build a parametric estimator based on a variational characterization of the solution. As a Generalized Moment Estimator, our estimator must satisfy a set of orthogonal conditions that are solved in the least squares sense. Despite the use of a nonparametric estimator, we prove the root-nn consistency and asymptotic normality of the Orthogonal Conditions estimator. We can derive confidence sets thanks to a closed-form expression for the asymptotic variance. Finally, the OC estimator is compared to classical estimators in several (simulated and real) experiments and ODE models in order to show its versatility and relevance with respect to classical Gradient Matching and Nonlinear Least Squares estimators. In particular, we show on a real dataset of influenza infection that the approach gives reliable estimates. Moreover, we show that our approach can deal directly with more elaborated models such as Delay Differential Equation (DDE).Comment: 35 pages, 5 figure

    AReS and MaRS - Adversarial and MMD-Minimizing Regression for SDEs

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    Stochastic differential equations are an important modeling class in many disciplines. Consequently, there exist many methods relying on various discretization and numerical integration schemes. In this paper, we propose a novel, probabilistic model for estimating the drift and diffusion given noisy observations of the underlying stochastic system. Using state-of-the-art adversarial and moment matching inference techniques, we avoid the discretization schemes of classical approaches. This leads to significant improvements in parameter accuracy and robustness given random initial guesses. On four established benchmark systems, we compare the performance of our algorithms to state-of-the-art solutions based on extended Kalman filtering and Gaussian processes.Comment: Published at the Thirty-sixth International Conference on Machine Learning (ICML 2019

    A variational approach to path estimation and parameter inference of hidden diffusion processes

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    We consider a hidden Markov model, where the signal process, given by a diffusion, is only indirectly observed through some noisy measurements. The article develops a variational method for approximating the hidden states of the signal process given the full set of observations. This, in particular, leads to systematic approximations of the smoothing densities of the signal process. The paper then demonstrates how an efficient inference scheme, based on this variational approach to the approximation of the hidden states, can be designed to estimate the unknown parameters of stochastic differential equations. Two examples at the end illustrate the efficacy and the accuracy of the presented method.Comment: 37 pages, 2 figures, revise

    Methods for the identification of material parameters in distributed models for flexible structures

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    Theoretical and numerical results are presented for inverse problems involving estimation of spatially varying parameters such as stiffness and damping in distributed models for elastic structures such as Euler-Bernoulli beams. An outline of algorithms used and a summary of computational experiences are presented
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