大多数面向进化的深层生成模型并未明确考虑生物学序列的潜在进化动力学，因为它是在贝叶斯系统发育推理框架内进行的。在这项研究中，我们提出了一种深层变异贝叶斯生成模型（EVOVGM）的方法，该方法共同近似局部进化参数的真实后验并生成序列比对。此外，它是由JC69，K80和GTR等连续时间马尔可夫链替代模型进行实例化和调整的。我们通过低变异的随机估计器和梯度上升算法训练模型。在这里，我们分析了VOVGM对模拟几种进化场景和不同大小的合成序列比对的一致性和有效性。最后，我们使用冠状病毒基因的序列比对来强调微调EVOVGM模型的鲁棒性。

How can we perform efficient inference and learning in directed probabilistic models, in the presence of continuous latent variables with intractable posterior distributions, and large datasets? We introduce a stochastic variational inference and learning algorithm that scales to large datasets and, under some mild differentiability conditions, even works in the intractable case. Our contributions is two-fold. First, we show that a reparameterization of the variational lower bound yields a lower bound estimator that can be straightforwardly optimized using standard stochastic gradient methods. Second, we show that for i.i.d. datasets with continuous latent variables per datapoint, posterior inference can be made especially efficient by fitting an approximate inference model (also called a recognition model) to the intractable posterior using the proposed lower bound estimator. Theoretical advantages are reflected in experimental results.

本文开发了一个贝叶斯图形模型，用于融合不同类型的计数数据。激励的应用是从不同治疗方法收集的各种高维特征的细菌群落研究。在这样的数据集中，社区之间没有明确的对应关系，每个对应都与不同的因素相对应，从而使数据融合具有挑战性。我们引入了一种灵活的多项式高斯生成模型，用于共同建模此类计数数据。该潜在变量模型通过共同的多元高斯潜在空间共同表征了观察到的数据，该空间参数化了转录组计数的多项式概率集。潜在变量的协方差矩阵诱导所有转录本之间共同依赖性的协方差矩阵，有效地融合了多个数据源。我们提出了一种可扩展的可扩展性变异期望最大化（EM）算法，用于推断模型的潜在变量和参数。推断的潜在变量为可视化数据提供了常见的维度降低，而推断的参数则提供了预测性的后验分布。除了证明变异性程序的模拟研究外，我们还将模型应用于细菌微生物组数据集。

变异推理（VI）的核心原理是将计算复杂后概率密度计算的统计推断问题转换为可拖动的优化问题。该属性使VI比几种基于采样的技术更快。但是，传统的VI算法无法扩展到大型数据集，并且无法轻易推断出越野数据点，而无需重新运行优化过程。该领域的最新发展，例如随机，黑框和摊销VI，已帮助解决了这些问题。如今，生成的建模任务广泛利用摊销VI来实现其效率和可扩展性，因为它利用参数化函数来学习近似的后验密度参数。在本文中，我们回顾了各种VI技术的数学基础，以构成理解摊销VI的基础。此外，我们还概述了最近解决摊销VI问题的趋势，例如摊销差距，泛化问题，不一致的表示学习和后验崩溃。最后，我们分析了改善VI优化的替代差异度量。

One of the core problems of modern statistics is to approximate difficult-to-compute probability densities. This problem is especially important in Bayesian statistics, which frames all inference about unknown quantities as a calculation involving the posterior density. In this paper, we review variational inference (VI), a method from machine learning that approximates probability densities through optimization. VI has been used in many applications and tends to be faster than classical methods, such as Markov chain Monte Carlo sampling. The idea behind VI is to first posit a family of densities and then to find the member of that family which is close to the target. Closeness is measured by Kullback-Leibler divergence. We review the ideas behind mean-field variational inference, discuss the special case of VI applied to exponential family models, present a full example with a Bayesian mixture of Gaussians, and derive a variant that uses stochastic optimization to scale up to massive data. We discuss modern research in VI and highlight important open problems. VI is powerful, but it is not yet well understood. Our hope in writing this paper is to catalyze statistical research on this class of algorithms.

退火重要性采样（AIS）是一种流行的算法，用于估计深层生成模型的棘手边际可能性。尽管AIS可以保证为任何一组超参数提供无偏估计，但共同的实现依赖于简单的启发式方法，例如初始和目标分布之间的几何平均桥接分布，这些分布在计算预算有限时会影响估计性性能。由于使用Markov过渡中的大都市磨碎（MH）校正步骤，因此对完全参数AI的优化仍然具有挑战性。我们提出一个具有灵活中间分布的参数AIS过程，并优化桥接分布以使用较少数量的采样步骤。一种重新聚集方法，它允许我们优化分布序列和Markov转换的参数，该参数适用于具有MH校正的大型Markov内核。我们评估了优化AIS的性能，以进行深层生成模型的边际可能性估计，并将其与其他估计器进行比较。

We marry ideas from deep neural networks and approximate Bayesian inference to derive a generalised class of deep, directed generative models, endowed with a new algorithm for scalable inference and learning. Our algorithm introduces a recognition model to represent an approximate posterior distribution and uses this for optimisation of a variational lower bound. We develop stochastic backpropagation -rules for gradient backpropagation through stochastic variables -and derive an algorithm that allows for joint optimisation of the parameters of both the generative and recognition models. We demonstrate on several real-world data sets that by using stochastic backpropagation and variational inference, we obtain models that are able to generate realistic samples of data, allow for accurate imputations of missing data, and provide a useful tool for high-dimensional data visualisation.

该报告解释，实施和扩展了“更紧密的变化界限不一定更好”所介绍的作品（T Rainforth等，2018）。我们提供了理论和经验证据，这些证据增加了重要性的重要性数量$ k $在重要性加权自动编码器（IWAE）中（Burda等，2016）降低了推理中梯度估计量的信噪比（SNR）网络，从而影响完整的学习过程。换句话说，即使增加$ k $减少了梯度的标准偏差，但它也会更快地降低真实梯度的幅度，从而增加梯度更新的相对差异。进行广泛的实验以了解$ k $的重要性。这些实验表明，更紧密的变化界限对生成网络有益，而宽松的边界对推理网络来说是可取的。通过这些见解，可以实施和研究三种方法：部分重要性加权自动编码器（PIWAE），倍增重要性加权自动编码器（MIWAE）和组合重要性加权自动编码器（CIWAE）。这三种方法中的每一种都需要IWAE作为一种特殊情况，但采用不同的重量权重，以确保较高的梯度估计器的SNR。在我们的研究和分析中，这些算法的疗效在多个数据集（如MNIST和Omniglot）上进行了测试。最后，我们证明了三种呈现的IWAE变化能够产生近似后验分布，这些分布与IWAE更接近真正的后验分布，同时匹配IWAE生成网络的性能，或者在PIWAE的情况下可能超过其表现。

近似复杂的概率密度是现代统计中的核心问题。在本文中，我们介绍了变分推理（VI）的概念，这是一种机器学习中的流行方法，该方法使用优化技术来估计复杂的概率密度。此属性允许VI汇聚速度比经典方法更快，例如Markov Chain Monte Carlo采样。概念上，VI通过选择一个概率密度函数，然后找到最接近实际概率密度的家庭 - 通常使用Kullback-Leibler（KL）发散作为优化度量。我们介绍了缩窄的证据，以促进近似的概率密度，我们审查了平均场变分推理背后的想法。最后，我们讨论VI对变分式自动编码器（VAE）和VAE-生成的对抗网络（VAE-GAN）的应用。用本文，我们的目标是解释VI的概念，并通过这种方法协助协助。

统计模型是机器学习的核心，具有广泛适用性，跨各种下游任务。模型通常由通过最大似然估计从数据估计的自由参数控制。但是，当面对现实世界数据集时，许多模型运行到一个关键问题：它们是在完全观察到的数据方面配制的，而在实践中，数据集会困扰缺失数据。来自不完整数据的统计模型估计理论在概念上类似于潜在变量模型的估计，其中存在强大的工具，例如变分推理（VI）。然而，与标准潜在变量模型相比，具有不完整数据的参数估计通常需要估计缺失变量的指数 - 许多条件分布，因此使标准的VI方法是棘手的。通过引入变分Gibbs推理（VGI），是一种新的通用方法来解决这个差距，以估计来自不完整数据的统计模型参数。我们在一组合成和实际估算任务上验证VGI，从不完整的数据中估算重要的机器学习模型，VAE和标准化流程。拟议的方法，同时通用，实现比现有的特定模型特定估计方法竞争或更好的性能。

贝叶斯神经网络具有潜在变量（BNN + LVS）通过明确建模模型不确定性（通过网络权重）和环境暂停（通过潜在输入噪声变量）来捕获预测的不确定性。在这项工作中，我们首先表明BNN + LV具有严重形式的非可识别性：可以在模型参数和潜在变量之间传输解释性，同时拟合数据。我们证明，在无限数据的极限中，网络权重和潜变量的后部模式从地面真理渐近地偏离。由于这种渐近偏差，传统的推理方法可以在实践中，产量参数概括不确定和不确定的不确定性。接下来，我们开发一种新推断过程，明确地减轻了训练期间不可识别性的影响，并产生高质量的预测以及不确定性估计。我们展示我们的推理方法在一系列合成和实际数据集中改善了基准方法。

Leveraging well-established MCMC strategies, we propose MCMC-interactive variational inference (MIVI) to not only estimate the posterior in a time constrained manner, but also facilitate the design of MCMC transitions. Constructing a variational distribution followed by a short Markov chain that has parameters to learn, MIVI takes advantage of the complementary properties of variational inference and MCMC to encourage mutual improvement. On one hand, with the variational distribution locating high posterior density regions, the Markov chain is optimized within the variational inference framework to efficiently target the posterior despite a small number of transitions. On the other hand, the optimized Markov chain with considerable flexibility guides the variational distribution towards the posterior and alleviates its underestimation of uncertainty. Furthermore, we prove the optimized Markov chain in MIVI admits extrapolation, which means its marginal distribution gets closer to the true posterior as the chain grows. Therefore, the Markov chain can be used separately as an efficient MCMC scheme. Experiments show that MIVI not only accurately and efficiently approximates the posteriors but also facilitates designs of stochastic gradient MCMC and Gibbs sampling transitions.

Variational inference uses optimization, rather than integration, to approximate the marginal likelihood, and thereby the posterior, in a Bayesian model. Thanks to advances in computational scalability made in the last decade, variational inference is now the preferred choice for many high-dimensional models and large datasets. This tutorial introduces variational inference from the parametric perspective that dominates these recent developments, in contrast to the mean-field perspective commonly found in other introductory texts.

自动编码变化贝叶斯（AEVB）是一种用于拟合潜在变量模型（无监督学习的有前途的方向）的强大而通用的算法，并且是训练变量自动编码器（VAE）的众所周知的。在本教程中，我们专注于从经典的期望最大化（EM）算法中激励AEVB，而不是确定性自动编码器。尽管自然而有些不言而喻，但在最近的深度学习文献中并未强调EM与AEVB之间的联系，我们认为强调这种联系可以改善社区对AEVB的理解。特别是，我们发现（1）优化有关推理参数的证据下限（ELBO）作为近似E-step，并且（2）优化ELBO相对于生成参数作为近似M-step；然后，与AEVB中的同时进行同时进行，然后同时拧紧并推动Elbo。我们讨论如何将近似E-Step解释为执行变异推断。详细讨论了诸如摊销和修复技巧之类的重要概念。最后，我们从划痕中得出了非深度和几个深层变量模型的AEVB训练程序，包括VAE，有条件的VAE，高斯混合物VAE和变异RNN。我们希望读者能够将AEVB认识为一种通用算法，可用于拟合广泛的潜在变量模型（不仅仅是VAE），并将AEVB应用于自己的研究领域中出现的此类模型。所有纳入型号的Pytorch代码均可公开使用。

变异推理通常从近似分布q到后p中最小化“反向” kullbeck-leibeler（kl）kl（q || p）。最近的工作研究“正向” KL KL（P || Q），它与反向KL不同并不能导致低估不确定性的变异近似值。本文介绍了运输评分攀登（TSC），该方法通过使用汉密尔顿蒙特卡洛（HMC）和新型的自适应传输图来优化KL（P || Q）。传输图通过充当潜在变量空间和扭曲空间之间变量的变化来改善HMC的轨迹。TSC使用HMC样品在优化KL时动态训练传输图（P || Q）。TSC利用协同作用，在该协同作用下，更好的运输地图会导致更好的HMC采样，从而导致更好的传输地图。我们在合成和真实数据上演示了TSC。我们发现，在训练大规模数据的变异自动编码器时，TSC可以实现竞争性能。

The choice of approximate posterior distribution is one of the core problems in variational inference. Most applications of variational inference employ simple families of posterior approximations in order to allow for efficient inference, focusing on mean-field or other simple structured approximations. This restriction has a significant impact on the quality of inferences made using variational methods. We introduce a new approach for specifying flexible, arbitrarily complex and scalable approximate posterior distributions. Our approximations are distributions constructed through a normalizing flow, whereby a simple initial density is transformed into a more complex one by applying a sequence of invertible transformations until a desired level of complexity is attained. We use this view of normalizing flows to develop categories of finite and infinitesimal flows and provide a unified view of approaches for constructing rich posterior approximations. We demonstrate that the theoretical advantages of having posteriors that better match the true posterior, combined with the scalability of amortized variational approaches, provides a clear improvement in performance and applicability of variational inference.

We develop stochastic variational inference, a scalable algorithm for approximating posterior distributions. We develop this technique for a large class of probabilistic models and we demonstrate it with two probabilistic topic models, latent Dirichlet allocation and the hierarchical Dirichlet process topic model. Using stochastic variational inference, we analyze several large collections of documents: 300K articles from Nature, 1.8M articles from The New York Times, and 3.8M articles from Wikipedia. Stochastic inference can easily handle data sets of this size and outperforms traditional variational inference, which can only handle a smaller subset. (We also show that the Bayesian nonparametric topic model outperforms its parametric counterpart.) Stochastic variational inference lets us apply complex Bayesian models to massive data sets.

即使在实践中无法计算其可能性，基于模拟的推断也能够学习模型的参数。一类方法使用用不同参数模拟的数据来推断摊销估计器，以获得似然到证据比，或等效的后函数。我们表明，可以在模型参数和模拟数据之间的相互信息最大化方面配制这种方法。我们使用此等价来重新诠释摊销推理的现有方法，并提出了两种依赖于互信息的下限的新方法。我们使用人工神经网络用于后部预测的采样轨迹，将框架应用于随机过程和混沌动态系统的推动。我们的方法提供了一个统一的框架，利用了相互信息估计的功率进行推理。

现代深度学习方法构成了令人难以置信的强大工具，以解决无数的挑战问题。然而，由于深度学习方法作为黑匣子运作，因此与其预测相关的不确定性往往是挑战量化。贝叶斯统计数据提供了一种形式主义来理解和量化与深度神经网络预测相关的不确定性。本教程概述了相关文献和完整的工具集，用于设计，实施，列车，使用和评估贝叶斯神经网络，即使用贝叶斯方法培训的随机人工神经网络。

Variational inference has become a widely used method to approximate posteriors in complex latent variables models. However, deriving a variational inference algorithm generally requires significant model-specific analysis, and these efforts can hinder and deter us from quickly developing and exploring a variety of models for a problem at hand. In this paper, we present a "black box" variational inference algorithm, one that can be quickly applied to many models with little additional derivation. Our method is based on a stochastic optimization of the variational objective where the noisy gradient is computed from Monte Carlo samples from the variational distribution. We develop a number of methods to reduce the variance of the gradient, always maintaining the criterion that we want to avoid difficult model-based derivations. We evaluate our method against the corresponding black box sampling based methods. We find that our method reaches better predictive likelihoods much faster than sampling methods. Finally, we demonstrate that Black Box Variational Inference lets us easily explore a wide space of models by quickly constructing and evaluating several models of longitudinal healthcare data.