Variational autoencoders model high-dimensional data by positing low-dimensional latent variables that are mapped through a flexible distribution parametrized by a neural network. Unfortunately, variational autoencoders often suffer from posterior collapse: the posterior of the latent variables is equal to its prior, rendering the variational autoencoder useless as a means to produce meaningful representations. Existing approaches to posterior collapse often attribute it to the use of neural networks or optimization issues due to variational approximation. In this paper, we consider posterior collapse as a problem of latent variable non-identifiability. We prove that the posterior collapses if and only if the latent variables are non-identifiable in the generative model. This fact implies that posterior collapse is not a phenomenon specific to the use of flexible distributions or approximate inference. Rather, it can occur in classical probabilistic models even with exact inference, which we also demonstrate. Based on these results, we propose a class of latent-identifiable variational autoencoders, deep generative models which enforce identifiability without sacrificing flexibility. This model class resolves the problem of latent variable non-identifiability by leveraging bijective Brenier maps and parameterizing them with input convex neural networks, without special variational inference objectives or optimization tricks. Across synthetic and real datasets, latent-identifiable variational autoencoders outperform existing methods in mitigating posterior collapse and providing meaningful representations of the data.

This paper revisits a fundamental problem in statistical inference from a non-asymptotic theoretical viewpoint $\unicode{x2013}$ the construction of confidence sets. We establish a finite-sample bound for the estimator, characterizing its asymptotic behavior in a non-asymptotic fashion. An important feature of our bound is that its dimension dependency is captured by the effective dimension $\unicode{x2013}$ the trace of the limiting sandwich covariance $\unicode{x2013}$ which can be much smaller than the parameter dimension in some regimes. We then illustrate how the bound can be used to obtain a confidence set whose shape is adapted to the optimization landscape induced by the loss function. Unlike previous works that rely heavily on the strong convexity of the loss function, we only assume the Hessian is lower bounded at optimum and allow it to gradually becomes degenerate. This property is formalized by the notion of generalized self-concordance which originated from convex optimization. Moreover, we demonstrate how the effective dimension can be estimated from data and characterize its estimation accuracy. We apply our results to maximum likelihood estimation with generalized linear models, score matching with exponential families, and hypothesis testing with Rao's score test.

Multi-fidelity Kriging model is a promising technique in surrogate-based design as it can balance the model accuracy and cost of sample preparation by fusing low- and high-fidelity data. However, the cost for building a multi-fidelity Kriging model increases significantly with the increase of the problem dimension. To attack this issue, an efficient Hierarchical Kriging modeling method is proposed. In building the low-fidelity model, the maximal information coefficient is utilized to calculate the relative value of the hyperparameter. With this, the maximum likelihood estimation problem for determining the hyperparameters is transformed as a one-dimension optimization problem, which can be solved in an efficient manner and thus improve the modeling efficiency significantly. A local search is involved further to exploit the search space of hyperparameters to improve the model accuracy. The high-fidelity model is built in a similar manner with the hyperparameter of the low-fidelity model served as the relative value of the hyperparameter for high-fidelity model. The performance of the proposed method is compared with the conventional tuning strategy, by testing them over ten analytic problems and an engineering problem of modeling the isentropic efficiency of a compressor rotor. The empirical results demonstrate that the modeling time of the proposed method is reduced significantly without sacrificing the model accuracy. For the modeling of the isentropic efficiency of the compressor rotor, the cost saving associated with the proposed method is about 90% compared with the conventional strategy. Meanwhile, the proposed method achieves higher accuracy.

Uncertainty quantification is crucial to inverse problems, as it could provide decision-makers with valuable information about the inversion results. For example, seismic inversion is a notoriously ill-posed inverse problem due to the band-limited and noisy nature of seismic data. It is therefore of paramount importance to quantify the uncertainties associated to the inversion process to ease the subsequent interpretation and decision making processes. Within this framework of reference, sampling from a target posterior provides a fundamental approach to quantifying the uncertainty in seismic inversion. However, selecting appropriate prior information in a probabilistic inversion is crucial, yet non-trivial, as it influences the ability of a sampling-based inference in providing geological realism in the posterior samples. To overcome such limitations, we present a regularized variational inference framework that performs posterior inference by implicitly regularizing the Kullback-Leibler divergence loss with a CNN-based denoiser by means of the Plug-and-Play methods. We call this new algorithm Plug-and-Play Stein Variational Gradient Descent (PnP-SVGD) and demonstrate its ability in producing high-resolution, trustworthy samples representative of the subsurface structures, which we argue could be used for post-inference tasks such as reservoir modelling and history matching. To validate the proposed method, numerical tests are performed on both synthetic and field post-stack seismic data.

Objective: Convolutional neural networks (CNNs) have demonstrated promise in automated cardiac magnetic resonance image segmentation. However, when using CNNs in a large real-world dataset, it is important to quantify segmentation uncertainty and identify segmentations which could be problematic. In this work, we performed a systematic study of Bayesian and non-Bayesian methods for estimating uncertainty in segmentation neural networks. Methods: We evaluated Bayes by Backprop, Monte Carlo Dropout, Deep Ensembles, and Stochastic Segmentation Networks in terms of segmentation accuracy, probability calibration, uncertainty on out-of-distribution images, and segmentation quality control. Results: We observed that Deep Ensembles outperformed the other methods except for images with heavy noise and blurring distortions. We showed that Bayes by Backprop is more robust to noise distortions while Stochastic Segmentation Networks are more resistant to blurring distortions. For segmentation quality control, we showed that segmentation uncertainty is correlated with segmentation accuracy for all the methods. With the incorporation of uncertainty estimates, we were able to reduce the percentage of poor segmentation to 5% by flagging 31--48% of the most uncertain segmentations for manual review, substantially lower than random review without using neural network uncertainty (reviewing 75--78% of all images). Conclusion: This work provides a comprehensive evaluation of uncertainty estimation methods and showed that Deep Ensembles outperformed other methods in most cases. Significance: Neural network uncertainty measures can help identify potentially inaccurate segmentations and alert users for manual review.

The traditional statistical inference is static, in the sense that the estimate of the quantity of interest does not affect the future evolution of the quantity. In some sequential estimation problems however, the future values of the quantity to be estimated depend on the estimate of its current value. This type of estimation problems has been formulated as the dynamic inference problem. In this work, we formulate the Bayesian learning problem for dynamic inference, where the unknown quantity-generation model is assumed to be randomly drawn according to a random model parameter. We derive the optimal Bayesian learning rules, both offline and online, to minimize the inference loss. Moreover, learning for dynamic inference can serve as a meta problem, such that all familiar machine learning problems, including supervised learning, imitation learning and reinforcement learning, can be cast as its special cases or variants. Gaining a good understanding of this unifying meta problem thus sheds light on a broad spectrum of machine learning problems as well.

In this paper we derive a PAC-Bayesian-Like error bound for a class of stochastic dynamical systems with inputs, namely, for linear time-invariant stochastic state-space models (stochastic LTI systems for short). This class of systems is widely used in control engineering and econometrics, in particular, they represent a special case of recurrent neural networks. In this paper we 1) formalize the learning problem for stochastic LTI systems with inputs, 2) derive a PAC-Bayesian-Like error bound for such systems, 3) discuss various consequences of this error bound.

You tagged this question with the tag "Maximum Likelihood". In maximum likelihood estimation you explicitly maximize an objective function (namely the likelihood). It just so happens that for an observation that we assume to be drawn from a Gaussian random variable, the likelihood function usually takes a nice form after you take a logarithm. Then there is usually a leading negation, encouraging the entrepreneurial optimizer to switch away from maximizing the objective to minimizing the negative of objective, or roughly the "cost". For discrete maximum likelihood estimation the "cost" also has another meaningful name since it takes the same form as the euclidean distance in the observation space.

Model estimates obtained from traditional subspace identification methods may be subject to significant variance. This elevated variance is aggravated in the cases of large models or of a limited sample size. Common solutions to reduce the effect of variance are regularized estimators, shrinkage estimators and Bayesian estimation. In the current work we investigate the latter two solutions, which have not yet been applied to subspace identification. Our experimental results show that our proposed estimators may reduce the estimation risk up to $40\%$ of that of traditional subspace methods.

Rapid advancements in collection, processing, and dissemination of multi-platform molecular and genomics (multi-omics, in short) data has resulted in enormous opportunities to aggregate such data in order to understand, prevent, and treat diseases. This has catalyzed development of integrative methods that can collectively mine multiple types and scales of multi-omics data, in order to provide a more holistic view of human disease evolution and progression (Subramanian et al. 2020). Specifically, in the context of cancer, a disease driven predominantly by agglomerations of several molecular changes (Sun et al. 2021), the importance of synthesizing information from multi-platform omics and clinical sources to understand the cellular basis of the disease is even further underscored. Cellular oncological mechanisms, triggered at different molecular levels of the DNA RNA Protein path, can confer profound phenotypic advantages/disadvantages. While significant improvements have been made in multi-omics data integration methods to unveil such mechanisms, focused on both prognosis (Duan et al. 2021) and treatment (Finotello et al. 2020), the precise functions governing them need detailed and data-driven de-novo evaluations. Our work, in the same vein, aims at two different but inter-related scientific axes: (i) selection of biomarkers associated with cancer prognosis and clinical outcomes, and (ii) learning the mechanism of these biomarkers' effects upon such outcomes via integrating upstream molecular information - we provide some additional scientific context below. Classes of Integrative Omics Models First, we briefly discuss existing integrative omics approaches in order to contextualize the need for our framework. Broadly, most of the existing integrative statistical methods can be classified into two categories - horizontal (meta-analysis type) and vertical (multi-omics) integration procedures (Tseng et al. 2015).