In molecular dynamics, penalized overdamped Langevin dynamics are used to model the motion of a set of particles that follow constraints up to a parameter $\varepsilon$. The most used schemes for simulating these dynamics are the Euler integrator in $\mathbb{R}^d$ and the constrained Euler integrator. Both have weak order one of accuracy, but work properly only in specific regimes depending on the size of the parameter $\varepsilon$. We propose in this paper a new consistent method with an accuracy independent of $\varepsilon$ for solving penalized dynamics on a manifold of any dimension. Moreover, this method converges to the constrained Euler scheme when $\varepsilon$ goes to zero. The numerical experiments confirm the theoretical findings, in the context of weak convergence and for the invariant measure, on a torus and on the orthogonal group in high dimension and high codimension.
相關內容
Integration：Integration, the VLSI Journal。
Explanation：集成，VLSI雜志。
Publisher：Elsevier。
SIT：
The MEK/ERK signalling pathway is involved in cell division, cell specialisation, survival and cell death. Here we study a polynomial dynamical system describing the dynamics of MEK/ERK proposed by Yeung et al. with their experimental setup, data and known biological information. The experimental dataset is a time-course of ERK measurements in different phosphorylation states following activation of either wild-type MEK or MEK mutations associated with cancer or developmental defects. We demonstrate how methods from computational algebraic geometry, differential algebra, Bayesian statistics and computational algebraic topology can inform the model reduction, identification and parameter inference of MEK variants, respectively. Throughout, we show how this algebraic viewpoint offers a rigorous and systematic analysis of such models.
We consider a generic and explicit tamed Euler--Maruyama scheme for multidimensional time-inhomogeneous stochastic differential equations with multiplicative Brownian noise. The diffusion coefficient is uniformly elliptic, H\"older continuous and weakly differentiable in the spatial variables while the drift satisfies the Ladyzhenskaya--Prodi--Serrin condition, as considered by Krylov and R\"ockner (2005). In the discrete scheme, the drift is tamed by replacing it by an approximation. A strong rate of convergence of the scheme is provided in terms of the approximation error of the drift in a suitable and possibly very weak topology. A few examples of approximating drifts are discussed in detail. The parameters of the approximating drifts can vary and be fine-tuned to achieve the standard $1/2$-strong convergence rate with a logarithmic factor.
We introduce a new class of estimators for the linear response of steady states of stochastic dynamics. We generalize the likelihood ratio approach and formulate the linear response as a product of two martingales, hence the name "martingale product estimators". We present a systematic derivation of the martingale product estimator, and show how to construct such estimator so its bias is consistent with the weak order of the numerical scheme that approximates the underlying stochastic differential equation. Motivated by the estimation of transport properties in molecular systems, we present a rigorous numerical analysis of the bias and variance for these new estimators in the case of Langevin dynamics. We prove that the variance is uniformly bounded in time and derive a specific form of the estimator for second-order splitting schemes for Langevin dynamics. For comparison, we also study the bias and variance of a Green-Kubo estimator, motivated, in part, by its variance growing linearly in time. Presented analysis shows that the new martingale product estimators, having uniformly bounded variance in time, offer a competitive alternative to the traditional Green-Kubo estimator. We compare on illustrative numerical tests the new estimators with results obtained by the Green-Kubo method.
Data from both a randomized trial and an observational study are sometimes simultaneously available for evaluating the effect of an intervention. The randomized data typically allows for reliable estimation of average treatment effects but may be limited in sample size and patient heterogeneity for estimating conditional average treatment effects for a broad range of patients. Estimates from the observational study can potentially compensate for these limitations, but there may be concerns about whether confounding and treatment effect heterogeneity have been adequately addressed. We propose an approach for combining conditional treatment effect estimators from each source such that it aggressively weights toward the randomized estimator when bias in the observational estimator is detected. This allows the combination to be consistent for a conditional causal effect, regardless of whether assumptions required for consistent estimation in the observational study are satisfied. When the bias is negligible, the estimators from each source are combined for optimal efficiency. We show the problem can be formulated as a penalized least squares problem and consider its asymptotic properties. Simulations demonstrate the robustness and efficiency of the method in finite samples, in scenarios with bias or no bias in the observational estimator. We illustrate the method by estimating the effects of hormone replacement therapy on the risk of developing coronary heart disease in data from the Women's Health Initiative.
We propose and analyse an augmented mixed finite element method for the Navier--Stokes equations written in terms of velocity, vorticity, and pressure with non-constant viscosity and no-slip boundary conditions. The weak formulation includes least-squares terms arising from the constitutive equation and from the incompressibility condition, and we use a fixed point strategies to show the existence and uniqueness of continuous and discrete solutions under the assumption of sufficiently small data. The method is constructed using any compatible finite element pair (conforming or non-conforming) for velocity and pressure as dictated by Stokes inf-sup stability, while for vorticity any generic discrete space (of arbitrary order) can be used. We establish optimal a priori error estimates. Finally, we provide a set of numerical tests in 2D and 3D illustrating the behaviour of the scheme as well as verifying the theoretical convergence rates.
Determinantal Point Process (DPPs) are statistical models for repulsive point patterns. Both sampling and inference are tractable for DPPs, a rare feature among models with negative dependence that explains their popularity in machine learning and spatial statistics. Parametric and nonparametric inference methods have been proposed in the finite case, i.e. when the point patterns live in a finite ground set. In the continuous case, only parametric methods have been investigated, while nonparametric maximum likelihood for DPPs -- an optimization problem over trace-class operators -- has remained an open question. In this paper, we show that a restricted version of this maximum likelihood (MLE) problem falls within the scope of a recent representer theorem for nonnegative functions in an RKHS. This leads to a finite-dimensional problem, with strong statistical ties to the original MLE. Moreover, we propose, analyze, and demonstrate a fixed point algorithm to solve this finite-dimensional problem. Finally, we also provide a controlled estimate of the correlation kernel of the DPP, thus providing more interpretability.
The classical Ka\v{c}anov scheme for the solution of nonlinear variational problems can be interpreted as a fixed point iteration method that updates a given approximation by solving a linear problem in each step. Based on this observation, we introduce a modified Ka\v{c}anov method, which allows for (adaptive) damping, and, thereby, to derive a new convergence analysis under more general assumptions and for a wider range of applications. For instance, in the specific context of quasilinear diffusion models, our new approach does no longer require a standard monotonicity condition on the nonlinear diffusion coefficient to hold. Moreover, we propose two different adaptive strategies for the practical selection of the damping parameters involved.
We prove hypercontractive inequalities on high dimensional expanders. As in the settings of the p-biased hypercube, the symmetric group, and the Grassmann scheme, our inequalities are effective for global functions, which are functions that are not significantly affected by a restriction of a small set of coordinates. As applications, we obtain Fourier concentration, small-set expansion, and Kruskal-Katona theorems for high dimensional expanders. Our techniques rely on a new approximate Efron-Stein decomposition for high dimensional link expanders.
A common approach to tackle a combinatorial optimization problem is to first solve a continuous relaxation and then round the obtained fractional solution. For the latter, the framework of contention resolution schemes (or CR schemes), introduced by Chekuri, Vondrak, and Zenklusen, is a general and successful tool. A CR scheme takes a fractional point $x$ in a relaxation polytope, rounds each coordinate $x_i$ independently to get a possibly non-feasible set, and then drops some elements in order to satisfy the independence constraints. Intuitively, a CR scheme is $c$-balanced if every element $i$ is selected with probability at least $c \cdot x_i$. It is known that general matroids admit a $(1-1/e)$-balanced CR scheme, and that this is (asymptotically) optimal. This is in particular true for the special case of uniform matroids of rank one. In this work, we provide a simple and explicit monotone CR scheme with a balancedness of $1 - \binom{n}{k}\:\left(1-\frac{k}{n}\right)^{n+1-k}\:\left(\frac{k}{n}\right)^k$, and show that this is optimal. As $n$ grows, this expression converges from above to $1 - e^{-k}k^k/k!$. While this asymptotic bound can be obtained by combining previously known results, these require defining an exponential-sized linear program, as well as using random sampling and the ellipsoid algorithm. Our procedure, on the other hand, has the advantage of being simple and explicit. Moreover, this scheme generalizes into an optimal CR scheme for partition matroids.
In this paper, we consider a boundary value problem (BVP) for a fourth order nonlinear functional integro-differential equation. We establish the existence and uniqueness of solution and construct a numerical method for solving it. We prove that the method is of second order accuracy and obtain an estimate for the total error. Some examples demonstrate the validity of the obtained theoretical results and the efficiency of the numerical method.
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