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We construct a family of genealogy-valued Markov processes that are induced by a continuous-time Markov population process. We derive exact expressions for the likelihood of a given genealogy conditional on the history of the underlying population process. These lead to a nonlinear filtering equation which can be used to design efficient Monte Carlo inference algorithms. We demonstrate these calculations with several examples. Existing full-information approaches for phylodynamic inference are special cases of the theory.

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 Processing 是一門開源編程語言和與之配套的集成開發環境(IDE)的名稱。Processing 在電子藝術和視覺設計社區被用來教授編程基礎,并運用于大量的新媒體和互動藝術作品中。

In this study, we generalize a problem of sampling a scalar Gauss Markov Process, namely, the Ornstein-Uhlenbeck (OU) process, where the samples are sent to a remote estimator and the estimator makes a causal estimate of the observed realtime signal. In recent years, the problem is solved for stable OU processes. We present solutions for the optimal sampling policy that exhibits a smaller estimation error for both stable and unstable cases of the OU process along with a special case when the OU process turns to a Wiener process. The obtained optimal sampling policy is a threshold policy. However, the thresholds are different for all three cases. Later, we consider additional noise with the sample when the sampling decision is made beforehand. The estimator utilizes noisy samples to make an estimate of the current signal value. The mean-square error (mse) is changed from previous due to noise and the additional term in the mse is solved which provides performance upper bound and room for a pursuing further investigation on this problem to find an optimal sampling strategy that minimizes the estimation error when the observed samples are noisy. Numerical results show performance degradation caused by the additive noise.

In a first part, we present a mathematical analysis of a general methodology of a probabilistic learning inference that allows for estimating a posterior probability model for a stochastic boundary value problem from a prior probability model. The given targets are statistical moments for which the underlying realizations are not available. Under these conditions, the Kullback-Leibler divergence minimum principle is used for estimating the posterior probability measure. A statistical surrogate model of the implicit mapping, which represents the constraints, is introduced. The MCMC generator and the necessary numerical elements are given to facilitate the implementation of the methodology in a parallel computing framework. In a second part, an application is presented to illustrate the proposed theory and is also, as such, a contribution to the three-dimensional stochastic homogenization of heterogeneous linear elastic media in the case of a non-separation of the microscale and macroscale. For the construction of the posterior probability measure by using the probabilistic learning inference, in addition to the constraints defined by given statistical moments of the random effective elasticity tensor, the second-order moment of the random normalized residue of the stochastic partial differential equation has been added as a constraint. This constraint guarantees that the algorithm seeks to bring the statistical moments closer to their targets while preserving a small residue.

The existence of the {\em typical set} is key for data compression strategies and for the emergence of robust statistical observables in macroscopic physical systems. Standard approaches derive its existence from a restricted set of dynamical constraints. However, given the enormous consequences for the understanding of the system's dynamics, and its role underlying the presence of stable, almost deterministic statistical patterns, a question arises whether typical sets exist in much more general scenarios. We demonstrate here that the typical set can be defined and characterized from general forms of entropy for a much wider class of stochastic processes than it was previously thought. This includes processes showing arbitrary path dependence, long range correlations or dynamic sampling spaces; suggesting that typicality is a generic property of stochastic processes, regardless of their complexity. Our results impact directly in the understanding of the stability of complex systems, open the door to new data compression strategies and points to the existence of statistical mechanics-like approaches to systems arbitrarily away from equilibrium with dynamic phase spaces. We argue that the potential emergence of robust properties in complex stochastic systems provided by the existence of typical sets has special relevance to biological systems.

We study entropy-regularized constrained Markov decision processes (CMDPs) under the soft-max parameterization, in which an agent aims to maximize the entropy-regularized value function while satisfying constraints on the expected total utility. By leveraging the entropy regularization, our theoretical analysis shows that its Lagrangian dual function is smooth and the Lagrangian duality gap can be decomposed into the primal optimality gap and the constraint violation. Furthermore, we propose an accelerated dual-descent method for entropy-regularized CMDPs. We prove that our method achieves the global convergence rate $\widetilde{\mathcal{O}}(1/T)$ for both the optimality gap and the constraint violation for entropy-regularized CMDPs. A discussion about a linear convergence rate for CMDPs with a single constraint is also provided.

We present a novel hybrid strategy based on machine learning to improve curvature estimation in the level-set method. The proposed inference system couples enhanced neural networks with standard numerical schemes to compute curvature more accurately. The core of our hybrid framework is a switching mechanism that relies on well established numerical techniques to gauge curvature. If the curvature magnitude is larger than a resolution-dependent threshold, it uses a neural network to yield a better approximation. Our networks are multilayer perceptrons fitted to synthetic data sets composed of sinusoidal- and circular-interface samples at various configurations. To reduce data set size and training complexity, we leverage the problem's characteristic symmetry and build our models on just half of the curvature spectrum. These savings lead to a powerful inference system able to outperform any of its numerical or neural component alone. Experiments with stationary, smooth interfaces show that our hybrid solver is notably superior to conventional numerical methods in coarse grids and along steep interface regions. Compared to prior research, we have observed outstanding gains in precision after training the regression model with data pairs from more than a single interface type and transforming data with specialized input preprocessing. In particular, our findings confirm that machine learning is a promising venue for reducing or removing mass loss in the level-set method.

Our goal is to recover time-delayed latent causal variables and identify their relations from measured temporal data. Estimating causally-related latent variables from observations is particularly challenging as the latent variables are not uniquely recoverable in the most general case. In this work, we consider both a nonparametric, nonstationary setting and a parametric setting for the latent processes and propose two provable conditions under which temporally causal latent processes can be identified from their nonlinear mixtures. We propose LEAP, a theoretically-grounded framework that extends Variational AutoEncoders (VAEs) by enforcing our conditions through proper constraints in causal process prior. Experimental results on various datasets demonstrate that temporally causal latent processes are reliably identified from observed variables under different dependency structures and that our approach considerably outperforms baselines that do not properly leverage history or nonstationarity information. This demonstrates that using temporal information to learn latent processes from their invertible nonlinear mixtures in an unsupervised manner, for which we believe our work is one of the first, seems promising even without sparsity or minimality assumptions.

Incorporating high-level knowledge is an effective way to expedite reinforcement learning (RL), especially for complex tasks with sparse rewards. We investigate an RL problem where the high-level knowledge is in the form of reward machines, i.e., a type of Mealy machine that encodes the reward functions. We focus on a setting in which this knowledge is a priori not available to the learning agent. We develop an iterative algorithm that performs joint inference of reward machines and policies for RL (more specifically, q-learning). In each iteration, the algorithm maintains a hypothesis reward machine and a sample of RL episodes. It derives q-functions from the current hypothesis reward machine, and performs RL to update the q-functions. While performing RL, the algorithm updates the sample by adding RL episodes along which the obtained rewards are inconsistent with the rewards based on the current hypothesis reward machine. In the next iteration, the algorithm infers a new hypothesis reward machine from the updated sample. Based on an equivalence relationship we defined between states of reward machines, we transfer the q-functions between the hypothesis reward machines in consecutive iterations. We prove that the proposed algorithm converges almost surely to an optimal policy in the limit if a minimal reward machine can be inferred and the maximal length of each RL episode is sufficiently long. The experiments show that learning high-level knowledge in the form of reward machines can lead to fast convergence to optimal policies in RL, while standard RL methods such as q-learning and hierarchical RL methods fail to converge to optimal policies after a substantial number of training steps in many tasks.

This paper proposes a model-free Reinforcement Learning (RL) algorithm to synthesise policies for an unknown Markov Decision Process (MDP), such that a linear time property is satisfied. We convert the given property into a Limit Deterministic Buchi Automaton (LDBA), then construct a synchronized MDP between the automaton and the original MDP. According to the resulting LDBA, a reward function is then defined over the state-action pairs of the product MDP. With this reward function, our algorithm synthesises a policy whose traces satisfies the linear time property: as such, the policy synthesis procedure is "constrained" by the given specification. Additionally, we show that the RL procedure sets up an online value iteration method to calculate the maximum probability of satisfying the given property, at any given state of the MDP - a convergence proof for the procedure is provided. Finally, the performance of the algorithm is evaluated via a set of numerical examples. We observe an improvement of one order of magnitude in the number of iterations required for the synthesis compared to existing approaches.

We show that the output of a (residual) convolutional neural network (CNN) with an appropriate prior over the weights and biases is a Gaussian process (GP) in the limit of infinitely many convolutional filters, extending similar results for dense networks. For a CNN, the equivalent kernel can be computed exactly and, unlike "deep kernels", has very few parameters: only the hyperparameters of the original CNN. Further, we show that this kernel has two properties that allow it to be computed efficiently; the cost of evaluating the kernel for a pair of images is similar to a single forward pass through the original CNN with only one filter per layer. The kernel equivalent to a 32-layer ResNet obtains 0.84% classification error on MNIST, a new record for GPs with a comparable number of parameters.

Stochastic gradient Markov chain Monte Carlo (SGMCMC) has become a popular method for scalable Bayesian inference. These methods are based on sampling a discrete-time approximation to a continuous time process, such as the Langevin diffusion. When applied to distributions defined on a constrained space, such as the simplex, the time-discretisation error can dominate when we are near the boundary of the space. We demonstrate that while current SGMCMC methods for the simplex perform well in certain cases, they struggle with sparse simplex spaces; when many of the components are close to zero. However, most popular large-scale applications of Bayesian inference on simplex spaces, such as network or topic models, are sparse. We argue that this poor performance is due to the biases of SGMCMC caused by the discretization error. To get around this, we propose the stochastic CIR process, which removes all discretization error and we prove that samples from the stochastic CIR process are asymptotically unbiased. Use of the stochastic CIR process within a SGMCMC algorithm is shown to give substantially better performance for a topic model and a Dirichlet process mixture model than existing SGMCMC approaches.

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