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The perfectly matched layer (PML) formulation is a prominent way of handling radiation problems in unbounded domain and has gained interest due to its simple implementation in finite element codes. However, its simplicity can be advanced further using the isogeometric framework. This work presents a spline based PML formulation which avoids additional coordinate transformation as the formulation is based on the same space in which the numerical solution is sought. The procedure can be automated for any convex artificial boundary. This removes restrictions on the domain construction using PML and can therefore reduce computational cost and improve mesh quality. The usage of spline basis functions with higher continuity also improves the accuracy of the numerical solution.

This paper presents a control framework on Lie groups by designing the control objective in its Lie algebra. Control on Lie groups is challenging due to its nonlinear nature and difficulties in system parameterization. Existing methods to design the control objective on a Lie group and then derive the gradient for controller design are non-trivial and can result in slow convergence in tracking control. We show that with a proper left-invariant metric, setting the gradient of the cost function as the tracking error in the Lie algebra leads to a quadratic Lyapunov function that enables globally exponential convergence. In the PD control case, we show that our controller can maintain an exponential convergence rate even when the initial error is approaching $\pi$ in SO(3). We also show the merit of this proposed framework in trajectory optimization. The proposed cost function enables the iterative Linear Quadratic Regulator (iLQR) to converge much faster than the Differential Dynamic Programming (DDP) with a well-adopted cost function when the initial trajectory is poorly initialized on SO(3).

Community detection refers to the problem of clustering the nodes of a network into groups. Existing inferential methods for community structure mainly focus on unweighted (binary) networks. Many real-world networks are nonetheless weighted and a common practice is to dichotomize a weighted network to an unweighted one which is known to result in information loss. Literature on hypothesis testing in the latter situation is still missing. In this paper, we study the problem of testing the existence of community structure in weighted networks. Our contributions are threefold: (a). We use the (possibly infinite-dimensional) exponential family to model the weights and derive the sharp information-theoretic limit for the existence of consistent test. Within the limit, any test is inconsistent; and beyond the limit, we propose a useful consistent test. (b). Based on the information-theoretic limits, we provide the first formal way to quantify the loss of information incurred by dichotomizing weighted graphs into unweighted graphs in the context of hypothesis testing. (c). We propose several new and practically useful test statistics. Simulation study show that the proposed tests have good performance. Finally, we apply the proposed tests to an animal social network.

Approximate-message passing (AMP) algorithms have become an important element of high-dimensional statistical inference, mostly due to their adaptability and concentration properties, the state evolution (SE) equations. This is demonstrated by the growing number of new iterations proposed for increasingly complex problems, ranging from multi-layer inference to low-rank matrix estimation with elaborate priors. In this paper, we address the following questions: is there a structure underlying all AMP iterations that unifies them in a common framework? Can we use such a structure to give a modular proof of state evolution equations, adaptable to new AMP iterations without reproducing each time the full argument ? We propose an answer to both questions, showing that AMP instances can be generically indexed by an oriented graph. This enables to give a unified interpretation of these iterations, independent from the problem they solve, and a way of composing them arbitrarily. We then show that all AMP iterations indexed by such a graph admit rigorous SE equations, extending the reach of previous proofs, and proving a number of recent heuristic derivations of those equations. Our proof naturally includes non-separable functions and we show how existing refinements, such as spatial coupling or matrix-valued variables, can be combined with our framework.

Numerical solution of heterogeneous Helmholtz problems presents various computational challenges, with descriptive theory remaining out of reach for many popular approaches. Robustness and scalability are key for practical and reliable solvers in large-scale applications, especially for large wave number problems. In this work we explore the use of a GenEO-type coarse space to build a two-level additive Schwarz method applicable to highly indefinite Helmholtz problems. Through a range of numerical tests on a 2D model problem, discretised by finite elements on pollution-free meshes, we observe robust convergence, iteration counts that do not increase with the wave number, and good scalability of our approach. We further provide results showing a favourable comparison with the DtN coarse space. Our numerical study shows promise that our solver methodology can be effective for challenging heterogeneous applications.

This paper introduces a new simulation-based inference procedure to model and sample from multi-dimensional probability distributions given access to i.i.d. samples, circumventing the usual approaches of explicitly modeling the density function or designing Markov chain Monte Carlo. Motivated by the seminal work on distance and isomorphism between metric measure spaces, we propose a new notion called the Reversible Gromov-Monge (RGM) distance and study how RGM can be used to design new transform samplers to perform simulation-based inference. Our RGM sampler can also estimate optimal alignments between two heterogeneous metric measure spaces $(\mathcal{X}, \mu, c_{\mathcal{X}})$ and $(\mathcal{Y}, \nu, c_{\mathcal{Y}})$ from empirical data sets, with estimated maps that approximately push forward one measure $\mu$ to the other $\nu$, and vice versa. Analytic properties of the RGM distance are derived; statistical rate of convergence, representation, and optimization questions regarding the induced sampler are studied. Synthetic and real-world examples showcasing the effectiveness of the RGM sampler are also demonstrated.

Molecular mechanics (MM) potentials have long been a workhorse of computational chemistry. Leveraging accuracy and speed, these functional forms find use in a wide variety of applications in biomolecular modeling and drug discovery, from rapid virtual screening to detailed free energy calculations. Traditionally, MM potentials have relied on human-curated, inflexible, and poorly extensible discrete chemical perception rules or applying parameters to small molecules or biopolymers, making it difficult to optimize both types and parameters to fit quantum chemical or physical property data. Here, we propose an alternative approach that uses graph neural networks to perceive chemical environments, producing continuous atom embeddings from which valence and nonbonded parameters can be predicted using invariance-preserving layers. Since all stages are built from smooth neural functions, the entire process is modular and end-to-end differentiable with respect to model parameters, allowing new force fields to be easily constructed, extended, and applied to arbitrary molecules. We show that this approach is not only sufficiently expressive to reproduce legacy atom types, but that it can learn to accurately reproduce and extend existing molecular mechanics force fields. Trained with arbitrary loss functions, it can construct entirely new force fields self-consistently applicable to both biopolymers and small molecules directly from quantum chemical calculations, with superior fidelity than traditional atom or parameter typing schemes. When trained on the same quantum chemical small molecule dataset used to parameterize the openff-1.2.0 small molecule force field augmented with a peptide dataset, the resulting espaloma model shows superior accuracy vis-\`a-vis experiments in computing relative alchemical free energy calculations for a popular benchmark set.

Collision avoidance is a widely investigated topic in robotic applications. When applying collision avoidance techniques to a mobile robot, how to deal with the spatial structure of the robot still remains a challenge. In this paper, we design a configuration-aware safe control law by solving a Quadratic Programming (QP) with designed Control Barrier Functions (CBFs) constraints, which can safely navigate a mobile robotic arm to a desired region while avoiding collision with environmental obstacles. The advantage of our approach is that it correctly and in an elegant way incorporates the spatial structure of the mobile robotic arm. This is achieved by merging geometric restrictions among mobile robotic arm links into CBFs constraints. Simulations on a rigid rod and the modeled mobile robotic arm are performed to verify the feasibility and time-efficiency of proposed method. Numerical results about the time consuming for different degrees of freedom illustrate that our method scales well with dimension.

We provide a decision theoretic analysis of bandit experiments. The setting corresponds to a dynamic programming problem, but solving this directly is typically infeasible. Working within the framework of diffusion asymptotics, we define suitable notions of asymptotic Bayes and minimax risk for bandit experiments. For normally distributed rewards, the minimal Bayes risk can be characterized as the solution to a nonlinear second-order partial differential equation (PDE). Using a limit of experiments approach, we show that this PDE characterization also holds asymptotically under both parametric and non-parametric distribution of the rewards. The approach further describes the state variables it is asymptotically sufficient to restrict attention to, and therefore suggests a practical strategy for dimension reduction. The upshot is that we can approximate the dynamic programming problem defining the bandit experiment with a PDE which can be efficiently solved using sparse matrix routines. We derive the optimal Bayes and minimax policies from the numerical solutions to these equations. The proposed policies substantially dominate existing methods such as Thompson sampling. The framework also allows for substantial generalizations to the bandit problem such as time discounting and pure exploration motives.

Many mathematical objects can be represented as functors from finitely-presented categories $\mathsf{C}$ to $\mathsf{Set}$. For instance, graphs are functors to $\mathsf{Set}$ from the category with two parallel arrows. Such functors are known informally as $\mathsf{C}$-sets. In this paper, we describe and implement an extension of $\mathsf{C}$-sets having data attributes with fixed types, such as graphs with labeled vertices or real-valued edge weights. We call such structures "acsets," short for "attributed $\mathsf{C}$-sets." Derived from previous work on algebraic databases, acsets are a joint generalization of graphs and data frames. They also encompass more elaborate graph-like objects such as wiring diagrams and Petri nets with rate constants. We develop the mathematical theory of acsets and then describe a generic implementation in the Julia programming language, which uses advanced language features to achieve performance comparable with specialized data structures.