State-space models (SSMs) provide a flexible framework for modelling time-series data. Consequently, SSMs are ubiquitously applied in areas such as engineering, econometrics and epidemiology. In this paper we provide a fast approach for approximate Bayesian inference in SSMs using the tools of deep learning and variational inference.
We present further development and the first public release of our multimodal nested sampling algorithm, called MultiNest. This Bayesian inference tool calculates the evidence, with an associated error estimate, and produces posterior samples from distributions that may contain multiple modes and pronounced (curving) degeneracies in high dimensions. The developments presented here lead to further substantial improvements in sampling efficiency and robustness, as compared to the original algorithm presented in Feroz & Hobson (2008), which itself significantly outperformed existing MCMC techniques in a wide range of astrophysical inference problems. The accuracy and economy of the MultiNest algorithm is demonstrated by application to two toy problems and to a cosmological inference problem focussing on the extension of the vanilla $\Lambda$CDM model to include spatial curvature and a varying equation of state for dark energy. The MultiNest software, which is fully parallelized using MPI and includes an interface to CosmoMC, is available at http://www.mrao.cam.ac.uk/software/multinest/. It will also be released as part of the SuperBayeS package, for the analysis of supersymmetric theories of particle physics, at http://www.superbayes.org
In this paper we present an algorithm for rapid Bayesian analysis that combines the benefits of nested sampling and artificial neural networks. The blind accelerated multimodal Bayesian inference (BAMBI) algorithm implements the MultiNest package for nested sampling as well as the training of an artificial neural network (NN) to learn the likelihood function. In the case of computationally expensive likelihoods, this allows the substitution of a much more rapid approximation in order to increase significantly the speed of the analysis. We begin by demonstrating, with a few toy examples, the ability of a NN to learn complicated likelihood surfaces. BAMBI's ability to decrease running time for Bayesian inference is then demonstrated in the context of estimating cosmological parameters from Wilkinson Microwave Anisotropy Probe and other observations. We show that valuable speed increases are achieved in addition to obtaining NNs trained on the likelihood functions for the different model and data combinations. These NNs can then be used for an even faster follow-up analysis using the same likelihood and different priors. This is a fully general algorithm that can be applied, without any pre-processing, to other problems with computationally expensive likelihood functions.
The benefits of automating design cycles for Bayesian inference-based algorithms are becoming increasingly recognized by the machine learning community. As a result, interest in probabilistic programming frameworks has much increased over the past few years. This paper explores a specific probabilistic programming paradigm, namely message passing in Forney-style factor graphs (FFGs), in the context of automated design of efficient Bayesian signal processing algorithms. To this end, we developed "ForneyLab" (https://github.com/biaslab/ForneyLab.jl) as a Julia toolbox for message passing-based inference in FFGs. We show by example how ForneyLab enables automatic derivation of Bayesian signal processing algorithms, including algorithms for parameter estimation and model comparison. Crucially, due to the modular makeup of the FFG framework, both the model specification and inference methods are readily extensible in ForneyLab. In order to test this framework, we compared variational message passing as implemented by ForneyLab with automatic differentiation variational inference (ADVI) and Monte Carlo methods as implemented by state-of-the-art tools "Edward" and "Stan". In terms of performance, extensibility and stability issues, ForneyLab appears to enjoy an edge relative to its competitors for automated inference in state-space models.
Uncertainty estimation in deep neural networks is essential for designing reliable and robust AI systems. Applications such as video surveillance for identifying suspicious activities are designed with deep neural networks (DNNs), but DNNs do not provide uncertainty estimates. Capturing reliable uncertainty estimates in safety and security critical applications will help to establish trust in the AI system. Our contribution is to apply Bayesian deep learning framework to visual activity recognition application and quantify model uncertainty along with principled confidence. We utilize the stochastic variational inference technique while training the Bayesian DNNs to infer the approximate posterior distribution around model parameters and perform Monte Carlo sampling on the posterior of model parameters to obtain the predictive distribution. We show that the Bayesian inference applied to DNNs provide reliable confidence measures for visual activity recognition task as compared to conventional DNNs. We also show that our method improves the visual activity recognition precision-recall AUC by 6.2% compared to non-Bayesian baseline. We evaluate our models on Moments-In-Time (MiT) activity recognition dataset by selecting a subset of in- and out-of-distribution video samples.
The problem of state estimation for unobservable distribution systems is considered. A deep learning approach to Bayesian state estimation is proposed for real-time applications. The proposed technique consists of distribution learning of stochastic power injection, a Monte Carlo technique for the training of a deep neural network for state estimation, and a Bayesian bad-data detection and filtering algorithm. Structural characteristics of the deep neural networks are investigated. Simulations illustrate the accuracy of Bayesian state estimation for unobservable systems and demonstrate the benefit of employing a deep neural network. Numerical results show the robustness of Bayesian state estimation against modeling and estimation errors and the presence of bad and missing data. Comparing with pseudo-measurement techniques, direct Bayesian state estimation via deep learning neural network outperforms existing benchmarks.
Quantum Graphical Models (QGMs) generalize classical graphical models by adopting the formalism for reasoning about uncertainty from quantum mechanics. Unlike classical graphical models, QGMs represent uncertainty with density matrices in complex Hilbert spaces. Hilbert space embeddings (HSEs) also generalize Bayesian inference in Hilbert spaces. We investigate the link between QGMs and HSEs and show that the sum rule and Bayes rule for QGMs are equivalent to the kernel sum rule in HSEs and a special case of Nadaraya-Watson kernel regression, respectively. We show that these operations can be kernelized, and use these insights to propose a Hilbert Space Embedding of Hidden Quantum Markov Models (HSE-HQMM) to model dynamics. We present experimental results showing that HSE-HQMMs are competitive with state-of-the-art models like LSTMs and PSRNNs on several datasets, while also providing a nonparametric method for maintaining a probability distribution over continuous-valued features.
When the cost of misclassifying a sample is high, it is useful to have an accurate estimate of uncertainty in the prediction for that sample. There are also multiple types of uncertainty which are best estimated in different ways, for example, uncertainty that is intrinsic to the training set may be well-handled by a Bayesian approach, while uncertainty introduced by shifts between training and query distributions may be better-addressed by density/support estimation. In this paper, we examine three types of uncertainty: model capacity uncertainty, intrinsic data uncertainty, and open set uncertainty, and review techniques that have been derived to address each one. We then introduce a unified hierarchical model, which combines methods from Bayesian inference, invertible latent density inference, and discriminative classification in a single end-to-end deep neural network topology to yield efficient per-sample uncertainty estimation in a detection context. This approach addresses all three uncertainty types and can readily accommodate prior/base rates for binary detection. We then discuss how to extend this model to a more generic multiclass recognition context.
A theoretical performance analysis of the graph neural network (GNN) is presented. For classification tasks, the neural network approach has the advantage in terms of flexibility that it can be employed in a data-driven manner, whereas Bayesian inference requires the assumption of a specific model. A fundamental question is then whether GNN has a high accuracy in addition to this flexibility. Moreover, whether the achieved performance is predominately a result of the backpropagation or the architecture itself is a matter of considerable interest. To gain a better insight into these questions, a mean-field theory of a minimal GNN architecture is developed for the graph partitioning problem. This demonstrates a good agreement with numerical experiments.
We propose a general statistical framework for clustering multiple time series that exhibit nonlinear dynamics into an a-priori-unknown number of sub-groups. Our motivation comes from neuroscience, where an important problem is to identify, within a large assembly of neurons, subsets that respond similarly to a stimulus or contingency. Upon modeling the multiple time series as the output of a Dirichlet process mixture of nonlinear state-space models, we derive a Metropolis-within-Gibbs algorithm for full Bayesian inference that alternates between sampling cluster assignments and sampling parameter values that form the basis of the clustering. The Metropolis step employs recent innovations in particle-based methods. We apply the framework to clustering time series acquired from the prefrontal cortex of mice in an experiment designed to characterize the neural underpinnings of fear.
Parametric statistical models that are implicitly defined in terms of a stochastic data generating process are used in a wide range of scientific disciplines because they enable accurate modeling. However, learning the parameters from observed data is generally very difficult because their likelihood function is typically intractable. Likelihood-free Bayesian inference methods have been proposed which include the frameworks of approximate Bayesian computation (ABC), synthetic likelihood, and its recent generalization that performs likelihood-free inference by ratio estimation (LFIRE). A major difficulty in all these methods is choosing summary statistics that reduce the dimensionality of the data to facilitate inference. While several methods for choosing summary statistics have been proposed for ABC, the literature for synthetic likelihood and LFIRE is very thin to date. We here address this gap in the literature, focusing on the important special case of time-series models. We show that convolutional neural networks trained to predict the input parameters from the data provide suitable summary statistics for LFIRE. On a wide range of time-series models, a single neural network architecture produced equally or more accurate posteriors than alternative methods.
State space models (SSMs) are a flexible approach to modeling complex time series. However, inference in SSMs is often computationally prohibitive for long time series. Stochastic gradient MCMC (SGMCMC) is a popular method for scalable Bayesian inference for large independent data. Unfortunately when applied to dependent data, such as in SSMs, SGMCMC's stochastic gradient estimates are biased as they break crucial temporal dependencies. To alleviate this, we propose stochastic gradient estimators that control this bias by performing additional computation in a `buffer' to reduce breaking dependencies. Furthermore, we derive error bounds for this bias and show a geometric decay under mild conditions. Using these estimators, we develop novel SGMCMC samplers for discrete, continuous and mixed-type SSMs with analytic message passing. Our experiments on real and synthetic data demonstrate the effectiveness of our SGMCMC algorithms compared to batch MCMC, allowing us to scale inference to long time series with millions of time points.
Stochastic variational inference is an established way to carry out approximate Bayesian inference for deep models. While there have been effective proposals for good initializations for loss minimization in deep learning, far less attention has been devoted to the issue of initialization of stochastic variational inference. We address this by proposing a novel layer-wise initialization strategy based on Bayesian linear models. The proposed method is extensively validated on regression and classification tasks, including Bayesian DeepNets and ConvNets, showing faster and better convergence compared to alternatives inspired by the literature on initializations for loss minimization.
Eye Movement analysis with Hidden Markov Models (EMHMM) is a method for modeling eye fixation sequences using hidden Markov models (HMMs). In this report, we run a simulation study to investigate the estimation error for learning HMMs with variational Bayesian inference, with respect to the number of sequences and the sequence lengths. We also relate the estimation error measured by KL divergence and L1-norm to a corresponding distortion in the ground-truth HMM parameters.
The vast majority of network datasets contains errors and omissions, although this is rarely incorporated in traditional network analysis. Recently, an increasing effort has been made to fill this methodological gap by developing network reconstruction approaches based on Bayesian inference. These approaches, however, rely on assumptions of uniform error rates and on direct estimations of the existence of each edge via repeated measurements, something that is currently unavailable for the majority of network data. Here we develop a Bayesian reconstruction approach that lifts these limitations by not only allowing for heterogeneous errors, but also for single edge measurements without direct error estimates. Our approach works by coupling the inference approach with structured generative network models, which enable the correlations between edges to be used as reliable uncertainty estimates. Although our approach is general, we focus on the stochastic block model as the basic generative process, from which efficient nonparametric inference can be performed, and yields a principled method to infer hierarchical community structure from noisy data. We demonstrate the efficacy of our approach with a variety of empirical and artificial networks.
A significant part of MCMC methods can be considered as the Metropolis-Hastings (MH) algorithm with different proposal distributions. From this point of view, the problem of constructing a sampler can be reduced to the question - how to choose a proposal for the MH algorithm? To address this question, we propose to learn an independent sampler that maximizes the acceptance rate of the MH algorithm, which, as we demonstrate, is highly related to the conventional variational inference. For Bayesian inference, the proposed method compares favorably against alternatives to sample from the posterior distribution. Under the same approach, we step beyond the scope of classical MCMC methods and deduce the Generative Adversarial Networks (GANs) framework from scratch, treating the generator as the proposal and the discriminator as the acceptance test. On real-world datasets, we improve Frechet Inception Distance and Inception Score, using different GANs as a proposal distribution for the MH algorithm. In particular, we demonstrate improvements of recently proposed BigGAN model on ImageNet.
Bayesian inference is known to provide a general framework for incorporating prior knowledge or specific properties into machine learning models via carefully choosing a prior distribution. In this work, we propose a new type of prior distributions for convolutional neural networks, deep weight prior (DWP), that exploit generative models to encourage a specific structure of trained convolutional filters e.g., spatial correlations of weights. We define DWP in the form of an implicit distribution and propose a method for variational inference with such type of implicit priors. In experiments, we show that DWP improves the performance of Bayesian neural networks when training data are limited, and initialization of weights with samples from DWP accelerates training of conventional convolutional neural networks.
Most of agents that learn policy for tasks with reinforcement learning (RL) lack the ability to communicate with people, which makes human-agent collaboration challenging. We believe that, in order for RL agents to comprehend utterances from human colleagues, RL agents must infer the mental states that people attribute to them because people sometimes infer an interlocutor's mental states and communicate on the basis of this mental inference. This paper proposes PublicSelf model, which is a model of a person who infers how the person's own behavior appears to their colleagues. We implemented the PublicSelf model for an RL agent in a simulated environment and examined the inference of the model by comparing it with people's judgment. The results showed that the agent's intention that people attributed to the agent's movement was correctly inferred by the model in scenes where people could find certain intentionality from the agent's behavior.
Many probabilistic models of interest in scientific computing and machine learning have expensive, black-box likelihoods that prevent the application of standard techniques for Bayesian inference, such as MCMC, which would require access to the gradient or a large number of likelihood evaluations. We introduce here a novel sample-efficient inference framework, Variational Bayesian Monte Carlo (VBMC). VBMC combines variational inference with Gaussian-process based, active-sampling Bayesian quadrature, using the latter to efficiently approximate the intractable integral in the variational objective. Our method produces both a nonparametric approximation of the posterior distribution and an approximate lower bound of the model evidence, useful for model selection. We demonstrate VBMC both on several synthetic likelihoods and on a neuronal model with data from real neurons. Across all tested problems and dimensions (up to $D = 10$), VBMC performs consistently well in reconstructing the posterior and the model evidence with a limited budget of likelihood evaluations, unlike other methods that work only in very low dimensions. Our framework shows great promise as a novel tool for posterior and model inference with expensive, black-box likelihoods.
Understanding the uncertainty of a neural network's (NN) predictions is essential for many purposes. The Bayesian framework provides a principled approach to this, however applying it to NNs is challenging due to large numbers of parameters and data. Ensembling NNs provides an easily implementable, scalable method for uncertainty quantification, however, it has been criticised for not being Bayesian. This work proposes one modification to the usual process that we argue does result in approximate Bayesian inference; regularising parameters about values drawn from a distribution which can be set equal to the prior. A theoretical analysis of the procedure in a simplified setting suggests the recovered posterior is centred correctly but tends to have an underestimated marginal variance, and overestimated correlation. However, two conditions can lead to exact recovery. We argue that these conditions are partially present in NNs. Empirical evaluations demonstrate it has an advantage over standard ensembling, and is competitive with variational methods.