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Motivation: The branching processes model yields unevenly stochastically distributed data that consists of sparse and dense regions. The work tries to solve the problem of a precise evaluation of a parameter for this type of model. The application of the branching processes model to cancer cell evolution has many difficulties like high dimensionality and the rare appearance of a result of interest. Moreover, we would like to solve the ambitious task of obtaining the coefficients of the model reflecting the relationship of driver genes mutations and cancer hallmarks on the basis of personal data of variant allele frequencies. Results: The Approximate Bayesian computation method based on the Isolation kernel is designed. The method includes a transformation row data to a Hilbert space (mapping) and measures the similarity between simulation points and maxima weighted Isolation kernel mapping related to the observation point. Also, we designed a heuristic algorithm to find parameter estimation without gradient calculation and dimension-independent. The advantage of the proposed machine learning method is shown for multidimensional test data as well as for an example of cancer cell evolution.

Robust estimation of a mean vector, a topic regarded as obsolete in the traditional robust statistics community, has recently surged in machine learning literature in the last decade. The latest focus is on the sub-Gaussian performance and computability of the estimators in a non-asymptotic setting. Numerous traditional robust estimators are computationally intractable, which partly contributes to the renewal of the interest in the robust mean estimation. Robust centrality estimators, however, include the trimmed mean and the sample median. The latter has the best robustness but suffers a low-efficiency drawback. Trimmed mean and median of means, %as robust alternatives to the sample mean, and achieving sub-Gaussian performance have been proposed and studied in the literature. This article investigates the robustness of leading sub-Gaussian estimators of mean and reveals that none of them can resist greater than $25\%$ contamination in data and consequently introduces an outlyingness induced winsorized mean which has the best possible robustness (can resist up to $50\%$ contamination without breakdown) meanwhile achieving high efficiency. Furthermore, it has a sub-Gaussian performance for uncontaminated samples and a bounded estimation error for contaminated samples at a given confidence level in a finite sample setting. It can be computed in linear time.

Multifidelity approximation is an important technique in scientific computation and simulation. In this paper, we introduce a bandit-learning approach for leveraging data of varying fidelities to achieve precise estimates of the parameters of interest. Under a linear model assumption, we formulate a multifidelity approximation as a modified stochastic bandit, and analyze the loss for a class of policies that uniformly explore each model before exploiting. Utilizing the estimated conditional mean-squared error, we propose a consistent algorithm, adaptive Explore-Then-Commit (AETC), and establish a corresponding trajectory-wise optimality result. These results are then extended to the case of vector-valued responses, where we demonstrate that the algorithm is efficient without the need to worry about estimating high-dimensional parameters. The main advantage of our approach is that we require neither hierarchical model structure nor \textit{a priori} knowledge of statistical information (e.g., correlations) about or between models. Instead, the AETC algorithm requires only knowledge of which model is a trusted high-fidelity model, along with (relative) computational cost estimates of querying each model. Numerical experiments are provided at the end to support our theoretical findings.

Bayesian bandit algorithms with approximate inference have been widely used in practice with superior performance. Yet, few studies regarding the fundamental understanding of their performances are available. In this paper, we propose a Bayesian bandit algorithm, which we call Generalized Bayesian Upper Confidence Bound (GBUCB), for bandit problems in the presence of approximate inference. Our theoretical analysis demonstrates that in Bernoulli multi-armed bandit, GBUCB can achieve $O(\sqrt{T}(\log T)^c)$ frequentist regret if the inference error measured by symmetrized Kullback-Leibler divergence is controllable. This analysis relies on a novel sensitivity analysis for quantile shifts with respect to inference errors. To our best knowledge, our work provides the first theoretical regret bound that is better than $o(T)$ in the setting of approximate inference. Our experimental evaluations on multiple approximate inference settings corroborate our theory, showing that our GBUCB is consistently superior to BUCB and Thompson sampling.

Uncertainty estimation in deep models is essential in many real-world applications and has benefited from developments over the last several years. Recent evidence suggests that existing solutions dependent on simple Gaussian formulations may not be sufficient. However, moving to other distributions necessitates Monte Carlo (MC) sampling to estimate quantities such as the KL divergence: it could be expensive and scales poorly as the dimensions of both the input data and the model grow. This is directly related to the structure of the computation graph, which can grow linearly as a function of the number of MC samples needed. Here, we construct a framework to describe these computation graphs, and identify probability families where the graph size can be independent or only weakly dependent on the number of MC samples. These families correspond directly to large classes of distributions. Empirically, we can run a much larger number of iterations for MC approximations for larger architectures used in computer vision with gains in performance measured in confident accuracy, stability of training, memory and training time.

Purpose: To develop a deep learning-based Bayesian inference for MRI reconstruction. Methods: We modeled the MRI reconstruction problem with Bayes's theorem, following the recently proposed PixelCNN++ method. The image reconstruction from incomplete k-space measurement was obtained by maximizing the posterior possibility. A generative network was utilized as the image prior, which was computationally tractable, and the k-space data fidelity was enforced by using an equality constraint. The stochastic backpropagation was utilized to calculate the descent gradient in the process of maximum a posterior, and a projected subgradient method was used to impose the equality constraint. In contrast to the other deep learning reconstruction methods, the proposed one used the likelihood of prior as the training loss and the objective function in reconstruction to improve the image quality. Results: The proposed method showed an improved performance in preserving image details and reducing aliasing artifacts, compared with GRAPPA, $\ell_1$-ESPRiT, and MODL, a state-of-the-art deep learning reconstruction method. The proposed method generally achieved more than 5 dB peak signal-to-noise ratio improvement for compressed sensing and parallel imaging reconstructions compared with the other methods. Conclusion: The Bayesian inference significantly improved the reconstruction performance, compared with the conventional $\ell_1$-sparsity prior in compressed sensing reconstruction tasks. More importantly, the proposed reconstruction framework can be generalized for most MRI reconstruction scenarios.

The Bayesian paradigm has the potential to solve core issues of deep neural networks such as poor calibration and data inefficiency. Alas, scaling Bayesian inference to large weight spaces often requires restrictive approximations. In this work, we show that it suffices to perform inference over a small subset of model weights in order to obtain accurate predictive posteriors. The other weights are kept as point estimates. This subnetwork inference framework enables us to use expressive, otherwise intractable, posterior approximations over such subsets. In particular, we implement subnetwork linearized Laplace: We first obtain a MAP estimate of all weights and then infer a full-covariance Gaussian posterior over a subnetwork. We propose a subnetwork selection strategy that aims to maximally preserve the model's predictive uncertainty. Empirically, our approach is effective compared to ensembles and less expressive posterior approximations over full networks.

Markov Logic Networks (MLNs), which elegantly combine logic rules and probabilistic graphical models, can be used to address many knowledge graph problems. However, inference in MLN is computationally intensive, making the industrial-scale application of MLN very difficult. In recent years, graph neural networks (GNNs) have emerged as efficient and effective tools for large-scale graph problems. Nevertheless, GNNs do not explicitly incorporate prior logic rules into the models, and may require many labeled examples for a target task. In this paper, we explore the combination of MLNs and GNNs, and use graph neural networks for variational inference in MLN. We propose a GNN variant, named ExpressGNN, which strikes a nice balance between the representation power and the simplicity of the model. Our extensive experiments on several benchmark datasets demonstrate that ExpressGNN leads to effective and efficient probabilistic logic reasoning.

Knowledge graph reasoning, which aims at predicting the missing facts through reasoning with the observed facts, is critical to many applications. Such a problem has been widely explored by traditional logic rule-based approaches and recent knowledge graph embedding methods. A principled logic rule-based approach is the Markov Logic Network (MLN), which is able to leverage domain knowledge with first-order logic and meanwhile handle their uncertainty. However, the inference of MLNs is usually very difficult due to the complicated graph structures. Different from MLNs, knowledge graph embedding methods (e.g. TransE, DistMult) learn effective entity and relation embeddings for reasoning, which are much more effective and efficient. However, they are unable to leverage domain knowledge. In this paper, we propose the probabilistic Logic Neural Network (pLogicNet), which combines the advantages of both methods. A pLogicNet defines the joint distribution of all possible triplets by using a Markov logic network with first-order logic, which can be efficiently optimized with the variational EM algorithm. In the E-step, a knowledge graph embedding model is used for inferring the missing triplets, while in the M-step, the weights of logic rules are updated based on both the observed and predicted triplets. Experiments on multiple knowledge graphs prove the effectiveness of pLogicNet over many competitive baselines.

A fundamental computation for statistical inference and accurate decision-making is to compute the marginal probabilities or most probable states of task-relevant variables. Probabilistic graphical models can efficiently represent the structure of such complex data, but performing these inferences is generally difficult. Message-passing algorithms, such as belief propagation, are a natural way to disseminate evidence amongst correlated variables while exploiting the graph structure, but these algorithms can struggle when the conditional dependency graphs contain loops. Here we use Graph Neural Networks (GNNs) to learn a message-passing algorithm that solves these inference tasks. We first show that the architecture of GNNs is well-matched to inference tasks. We then demonstrate the efficacy of this inference approach by training GNNs on a collection of graphical models and showing that they substantially outperform belief propagation on loopy graphs. Our message-passing algorithms generalize out of the training set to larger graphs and graphs with different structure.