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We develop deep Poisson-gamma dynamical systems (DPGDS) to model sequentially observed multivariate count data, improving previously proposed models by not only mining deep hierarchical latent structure from the data, but also capturing both first-order and long-range temporal dependencies. Using sophisticated but simple-to-implement data augmentation techniques, we derived closed-form Gibbs sampling update equations by first backward and upward propagating auxiliary latent counts, and then forward and downward sampling latent variables. Moreover, we develop stochastic gradient MCMC inference that is scalable to very long multivariate count time series. Experiments on both synthetic and a variety of real-world data demonstrate that the proposed model not only has excellent predictive performance, but also provides highly interpretable multilayer latent structure to represent hierarchical and temporal information propagation.
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We present a novel offline-online method to mitigate the computational burden of the characterization of conditional beliefs in statistical learning. In the offline phase, the proposed method learns the joint law of the belief random variables and the observational random variables in the tensor-train (TT) format. In the online phase, it utilizes the resulting order-preserving conditional transport map to issue real-time characterization of the conditional beliefs given new observed information. Compared with the state-of-the-art normalizing flows techniques, the proposed method relies on function approximation and is equipped with thorough performance analysis. This also allows us to further extend the capability of transport maps in challenging problems with high-dimensional observations and high-dimensional belief variables. On the one hand, we present novel heuristics to reorder and/or reparametrize the variables to enhance the approximation power of TT. On the other, we integrate the TT-based transport maps and the parameter reordering/reparametrization into layered compositions to further improve the performance of the resulting transport maps. We demonstrate the efficiency of the proposed method on various statistical learning tasks in ordinary differential equations (ODEs) and partial differential equations (PDEs).
We propose a new method for modeling the distribution function of high dimensional extreme value distributions. The Pickands dependence function models the relationship between the covariates in the tails, and we learn this function using a neural network that is designed to satisfy its required properties. Moreover, we present new methods for recovering the spectral representation of extreme distributions and propose a generative model for sampling from extreme copulas. Numerical examples are provided demonstrating the efficacy and promise of our proposed methods.
During the past five years the Bayesian deep learning community has developed increasingly accurate and efficient approximate inference procedures that allow for Bayesian inference in deep neural networks. However, despite this algorithmic progress and the promise of improved uncertainty quantification and sample efficiency there are---as of early 2020---no publicized deployments of Bayesian neural networks in industrial practice. In this work we cast doubt on the current understanding of Bayes posteriors in popular deep neural networks: we demonstrate through careful MCMC sampling that the posterior predictive induced by the Bayes posterior yields systematically worse predictions compared to simpler methods including point estimates obtained from SGD. Furthermore, we demonstrate that predictive performance is improved significantly through the use of a cold posterior that overcounts evidence. Such cold posteriors sharply deviate from the Bayesian paradigm but are commonly used as heuristic in Bayesian deep learning papers. We put forward several hypotheses that could explain cold posteriors and evaluate the hypotheses through experiments. Our work questions the goal of accurate posterior approximations in Bayesian deep learning: If the true Bayes posterior is poor, what is the use of more accurate approximations? Instead, we argue that it is timely to focus on understanding the origin of the improved performance of cold posteriors.
Neural networks have excelled at regression and classification problems when the input space consists of scalar variables. As a result of this proficiency, several popular packages have been developed that allow users to easily fit these kinds of models. However, the methodology has excluded the use of functional covariates and to date, there exists no software that allows users to build deep learning models with this generalized input space. To the best of our knowledge, the functional neural network (FuncNN) library is the first such package in any programming language; the library has been developed for R and is built on top of the keras architecture. Throughout this paper, several functions are introduced that provide users an avenue to easily build models, generate predictions, and run cross-validations. A summary of the underlying methodology is also presented. The ultimate contribution is a package that provides a set of general modelling and diagnostic tools for data problems in which there exist both functional and scalar covariates.
We introduce a flexible, scalable Bayesian inference framework for nonlinear dynamical systems characterised by distinct and hierarchical variability at the individual, group, and population levels. Our model class is a generalisation of nonlinear mixed-effects (NLME) dynamical systems, the statistical workhorse for many experimental sciences. We cast parameter inference as stochastic optimisation of an end-to-end differentiable, block-conditional variational autoencoder. We specify the dynamics of the data-generating process as an ordinary differential equation (ODE) such that both the ODE and its solver are fully differentiable. This model class is highly flexible: the ODE right-hand sides can be a mixture of user-prescribed or white-box sub-components and neural network or black-box sub-components. Using stochastic optimisation, our amortised inference algorithm could seamlessly scale up to massive data collection pipelines (common in labs with robotic automation). Finally, our framework supports interpretability with respect to the underlying dynamics, as well as predictive generalization to unseen combinations of group components (also called zero-shot learning). We empirically validate our method by predicting the dynamic behaviour of bacteria that were genetically engineered to function as biosensors. Our implementation of the framework, the dataset, and all code to reproduce the experimental results is available at https://www.github.com/Microsoft/vi-hds .
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