Estimating hidden processes from non-linear noisy observations is particularly difficult when the parameters of these processes are not known. This paper adopts a machine learning approach to devise variational Bayesian inference for such scenarios. In particular, a random process generated by the autoregressive moving average (ARMA) linear model is inferred from non-linearity noise observations. The posterior distribution of hidden states are approximated by a set of weighted particles generated by the sequential Monte carlo (SMC) algorithm involving sampling with importance sampling resampling (SISR). Numerical efficiency and estimation accuracy of the proposed inference method are evaluated by computer simulations. Furthermore, the proposed inference method is demonstrated on a practical problem of estimating the missing values in the gene expression time series assuming vector autoregressive (VAR) data model.
We address the problem of continual learning in multi-task Gaussian process (GP) models for handling sequential input-output observations. Our approach extends the existing prior-posterior recursion of online Bayesian inference, i.e.\ past posterior discoveries become future prior beliefs, to the infinite functional space setting of GP. For a reason of scalability, we introduce variational inference together with an sparse approximation based on inducing inputs. As a consequence, we obtain tractable continual lower-bounds where two novel Kullback-Leibler (KL) divergences intervene in a natural way. The key technical property of our method is the recursive reconstruction of conditional GP priors conditioned on the variational parameters learned so far. To achieve this goal, we introduce a novel factorization of past variational distributions, where the predictive GP equation propagates the posterior uncertainty forward. We then demonstrate that it is possible to derive GP models over many types of sequential observations, either discrete or continuous and amenable to stochastic optimization. The continual inference approach is also applicable to scenarios where potential multi-channel or heterogeneous observations might appear. Extensive experiments demonstrate that the method is fully scalable, shows a reliable performance and is robust to uncertainty error propagation over a plenty of synthetic and real-world datasets.
We perform theoretical and algorithmic studies for the problem of clustering and semi-supervised classification on graphs with both pairwise relational information and single-point feature information, upon a joint stochastic block model for generating synthetic graphs with both edges and node features. Asymptotically exact analysis based on the Bayesian inference of the underlying model are conducted, using the cavity method in statistical physics. Theoretically, we identify a phase transition of the generative model, which puts fundamental limits on the ability of all possible algorithms in the clustering task of the underlying model. Algorithmically, we propose a belief propagation algorithm that is asymptotically optimal on the generative model, and can be further extended to a belief propagation graph convolution neural network (BPGCN) for semi-supervised classification on graphs. For the first time, well-controlled benchmark datasets with asymptotially exact properties and optimal solutions could be produced for the evaluation of graph convolution neural networks, and for the theoretical understanding of their strengths and weaknesses. In particular, on these synthetic benchmark networks we observe that existing graph convolution neural networks are subject to an sparsity issue and an ovefitting issue in practice, both of which are successfully overcome by our BPGCN. Moreover, when combined with classic neural network methods, BPGCN yields extraordinary classification performances on some real-world datasets that have never been achieved before.
Bayesian inference in state-space models is challenging due to high-dimensional state trajectories. A viable approach is particle Markov chain Monte Carlo, combining MCMC and sequential Monte Carlo to form "exact approximations" to otherwise intractable MCMC methods. The performance of the approximation is limited to that of the exact method. We focus on particle Gibbs and particle Gibbs with ancestor sampling, improving their performance beyond that of the underlying Gibbs sampler (which they approximate) by marginalizing out one or more parameters. This is possible when the parameter prior is conjugate to the complete data likelihood. Marginalization yields a non-Markovian model for inference, but we show that, in contrast to the general case, this method still scales linearly in time. While marginalization can be cumbersome to implement, recent advances in probabilistic programming have enabled its automation. We demonstrate how the marginalized methods are viable as efficient inference backends in probabilistic programming, and demonstrate with examples in ecology and epidemiology.
Causal inference can be formalized as Bayesian inference that combines a prior distribution over causal models and likelihoods that account for both observations and interventions. We show that it is possible to implement this approach using a sufficiently expressive probabilistic programming language. Priors are represented using probabilistic programs that generate source code in a domain specific language. Interventions are represented using probabilistic programs that edit this source code to modify the original generative process. This approach makes it straightforward to incorporate data from atomic interventions, as well as shift interventions, variance-scaling interventions, and other interventions that modify causal structure. This approach also enables the use of general-purpose inference machinery for probabilistic programs to infer probable causal structures and parameters from data. This abstract describes a prototype of this approach in the Gen probabilistic programming language.
Real-world autonomous systems often employ probabilistic predictive models of human behavior during planning to reason about their future motion. Since accurately modeling human behavior a priori is challenging, such models are often parameterized, enabling the robot to adapt predictions based on observations by maintaining a distribution over the model parameters. Although this enables data and priors to improve the human model, observation models are difficult to specify and priors may be incorrect, leading to erroneous state predictions that can degrade the safety of the robot motion plan. In this work, we seek to design a predictor which is more robust to misspecified models and priors, but can still leverage human behavioral data online to reduce conservatism in a safe way. To do this, we cast human motion prediction as a Hamilton-Jacobi reachability problem in the joint state space of the human and the belief over the model parameters. We construct a new continuous-time dynamical system, where the inputs are the observations of human behavior, and the dynamics include how the belief over the model parameters change. The results of this reachability computation enable us to both analyze the effect of incorrect priors on future predictions in continuous state and time, as well as to make predictions of the human state in the future. We compare our approach to the worst-case forward reachable set and a stochastic predictor which uses Bayesian inference and produces full future state distributions. Our comparisons in simulation and in hardware demonstrate how our framework can enable robust planning while not being overly conservative, even when the human model is inaccurate.
In this paper, we consider the sigmoid Gaussian Hawkes process model: the baseline intensity and triggering kernel of Hawkes process are both modeled as the sigmoid transformation of random trajectories drawn from Gaussian processes (GP). By introducing auxiliary latent random variables (branching structure, P\'{o}lya-Gamma random variables and latent marked Poisson processes), the likelihood is converted to two decoupled components with a Gaussian form which allows for an efficient conjugate analytical inference. Using the augmented likelihood, we derive an expectation-maximization (EM) algorithm to obtain the maximum a posteriori (MAP) estimate. Furthermore, we extend the EM algorithm to an efficient approximate Bayesian inference algorithm: mean-field variational inference. We demonstrate the performance of two algorithms on simulated fictitious data. Experiments on real data show that our proposed inference algorithms can recover well the underlying prompting characteristics efficiently.
Graph convolutional neural networks (GCNN) have been successfully applied to many different graph based learning tasks including node and graph classification, matrix completion, and learning of node embeddings. Despite their impressive performance, the techniques have a limited capability to incorporate the uncertainty in the underlined graph structure. In order to address this issue, a Bayesian GCNN (BGCN) framework was recently proposed. In this framework, the observed graph is considered to be a random realization from a parametric random graph model and the joint Bayesian inference of the graph and GCNN weights is performed. In this paper, we propose a non-parametric generative model for graphs and incorporate it within the BGCN framework. In addition to the observed graph, our approach effectively uses the node features and training labels in the posterior inference of graphs and attains superior or comparable performance in benchmark node classification tasks.
Stein variational gradient descent (SVGD) is a particle-based inference algorithm that leverages gradient information for efficient approximate inference. In this work, we enhance SVGD by leveraging preconditioning matrices, such as the Hessian and Fisher information matrix, to incorporate geometric information into SVGD updates. We achieve this by presenting a generalization of SVGD that replaces the scalar-valued kernels in vanilla SVGD with more general matrix-valued kernels. This yields a significant extension of SVGD, and more importantly, allows us to flexibly incorporate various preconditioning matrices to accelerate the exploration in the probability landscape. Empirical results show that our method outperforms vanilla SVGD and a variety of baseline approaches over a range of real-world Bayesian inference tasks.
This paper tackles the challenge presented by small-data to the task of Bayesian inference. A novel methodology, based on manifold learning and manifold sampling, is proposed for solving this computational statistics problem under the following assumptions: 1) neither the prior model nor the likelihood function are Gaussian and neither can be approximated by a Gaussian measure; 2) the number of functional input (system parameters) and functional output (quantity of interest) can be large; 3) the number of available realizations of the prior model is small, leading to the small-data challenge typically associated with expensive numerical simulations; the number of experimental realizations is also small; 4) the number of the posterior realizations required for decision is much larger than the available initial dataset. The method and its mathematical aspects are detailed. Three applications are presented for validation: The first two involve mathematical constructions aimed to develop intuition around the method and to explore its performance. The third example aims to demonstrate the operational value of the method using a more complex application related to the statistical inverse identification of the non-Gaussian matrix-valued random elasticity field of a damaged biological tissue (osteoporosis in a cortical bone) using ultrasonic waves.
Deep learning has been successfully applied to the segmentation of 3D Computed Tomography (CT) scans. Establishing the credibility of these segmentations requires uncertainty quantification (UQ) to identify untrustworthy predictions. Recent UQ architectures include Monte Carlo dropout networks (MCDNs), which approximate deep Gaussian processes, and Bayesian neural networks (BNNs), which learn the distribution of the weight space. BNNs are advantageous over MCDNs for UQ but are thought to be computationally infeasible in high dimension, and neither architecture has produced interpretable geometric uncertainty maps. We propose a novel 3D Bayesian convolutional neural network (BCNN), the first deep learning method which generates statistically credible geometric uncertainty maps and scales for application to 3D data. We present experimental results on CT scans of graphite electrodes and laser-welded metals and show that our BCNN outperforms an MCDN in recent uncertainty metrics. The geometric uncertainty maps generated by our BCNN capture distributions of sigmoid values that are interpretable as confidence intervals, critical for applications that rely on deep learning for high-consequence decisions. Code available at https://github.com/sandialabs/bcnn.
In classic papers, Zellner demonstrated that Bayesian inference could be derived as the solution to an information theoretic functional. Below we derive a generalized form of this functional as a variational lower bound of a predictive information bottleneck objective. This generalized functional encompasses most modern inference procedures and suggests novel ones.
We study generalized Bayesian inference under misspecification, i.e. when the model is 'wrong but useful'. Generalized Bayes equips the likelihood with a learning rate $\eta$. We show that for generalized linear models (GLMs), $\eta$-generalized Bayes concentrates around the best approximation of the truth within the model for specific $\eta \neq 1$, even under severely misspecified noise, as long as the tails of the true distribution are exponential. We derive MCMC samplers for generalized Bayesian lasso and logistic regression and give examples of both simulated and real-world data in which generalized Bayes substantially outperforms standard Bayes.
Recent work has argued that neural networks can be understood theoretically by taking the number of channels to infinity, at which point the outputs become Gaussian process (GP) distributed. However, we note that infinite Bayesian neural networks lack a key facet of the behaviour of real neural networks: the fixed kernel, determined only by network hyperparameters, implies that they cannot do any form of representation learning. The lack of representation or equivalently kernel learning leads to less flexibility and hence worse performance, giving a potential explanation for the inferior performance of infinite networks observed in the literature (e.g. Novak et al. 2019). We give analytic results characterising the prior over representations and representation learning in finite deep linear networks. We show empirically that the representations in SOTA architectures such as ResNets trained with SGD are much closer to those suggested by our deep linear results than by the corresponding infinite network. This motivates the introduction of a new class of network: infinite networks with bottlenecks, which inherit the theoretical tractability of infinite networks while at the same time allowing representation learning.
Markov chain Monte Carlo (MCMC) methods have not been broadly adopted in Bayesian neural networks (BNNs). This paper initially reviews the main challenges in sampling from the parameter posterior of a neural network via MCMC. Such challenges culminate to lack of convergence to the parameter posterior. Nevertheless, this paper shows that a non-converged Markov chain, generated via MCMC sampling from the parameter space of a neural network, can yield via Bayesian marginalization a valuable posterior predictive distribution of the output of the neural network. Classification examples based on multilayer perceptrons showcase highly accurate posterior predictive distributions. The postulate of limited scope for MCMC developments in BNNs is partially valid; an asymptotically exact parameter posterior seems less plausible, yet an accurate posterior predictive distribution is a tenable research avenue.
We introduce a recent symplectic integration scheme derived for solving physically motivated systems with non-separable Hamiltonians. We show its relevance to Riemannian manifold Hamiltonian Monte Carlo (RMHMC) and provide an alternative to the currently used generalised leapfrog symplectic integrator, which relies on solving multiple fixed point iterations to convergence. Via this approach, we are able to reduce the number of higher-order derivative calculations per leapfrog step. We explore the implications of this integrator and demonstrate its efficacy in reducing the computational burden of RMHMC. Our code is provided in a new open-source Python package, hamiltorch.
We address tracking and prediction of multiple moving objects in visual data streams as inference and sampling in a disentangled latent state-space model. By encoding objects separately and including explicit position information in the latent state space, we perform tracking via amortized variational Bayesian inference of the respective latent positions. Inference is implemented in a modular neural framework tailored towards our disentangled latent space. Generative and inference model are jointly learned from observations only. Comparing to related prior work, we empirically show that our Markovian state-space assumption enables faithful and much improved long-term prediction well beyond the training horizon. Further, our inference model correctly decomposes frames into objects, even in the presence of occlusions. Tracking performance is increased significantly over prior art.
Recently, different machine learning methods have been introduced to tackle the challenging few-shot learning scenario that is, learning from a small labeled dataset related to a specific task. Common approaches have taken the form of meta-learning: learning to learn on the new problem given the old. Following the recognition that meta-learning is implementing learning in a multi-level model, we present a Bayesian treatment for the meta-learning inner loop through the use of deep kernels. As a result we can learn a kernel that transfers to new tasks; we call this Deep Kernel Transfer (DKT). This approach has many advantages: is straightforward to implement as a single optimizer, provides uncertainty quantification, and does not require estimation of task-specific parameters. We empirically demonstrate that DKT outperforms several state-of-the-art algorithms in few-shot classification, and is the state of the art for cross-domain adaptation and regression. We conclude that complex meta-learning routines can be replaced by a simpler Bayesian model without loss of accuracy.
For mobile robots to operate autonomously in general environments, perception is required in the form of a dense metric map. For this purpose, we present the stochastic triangular mesh (STM) mapping technique: a 2.5-D representation of the surface of the environment using a continuous mesh of triangular surface elements, where each surface element models the mean plane and roughness of the underlying surface. In contrast to existing mapping techniques, a STM map models the structure of the environment by ensuring a continuous model, while also being able to be incrementally updated with linear computational cost in the number of measurements. We reduce the effect of uncertainty in the robot pose (position and orientation) by using landmark-relative submaps. The uncertainty in the measurements and robot pose are accounted for by the use of Bayesian inference techniques during the map update. We demonstrate that a STM map can be used with sensors that generate point measurements, such as light detection and ranging (LiDAR) sensors and stereo cameras. We show that a STM map is a more accurate model than the only comparable online surface mapping technique$\unicode{x2014}$a standard elevation map$\unicode{x2014}$and we also provide qualitative results on practical datasets.
Likelihood-free inference involves inferring parameter values given observed data and a simulator model. The simulator is computer code which takes parameters, performs stochastic calculations, and outputs simulated data. In this work, we view the simulator as a function whose inputs are (1) the parameters and (2) a vector of pseudo-random draws. We attempt to infer all these inputs conditional on the observations. This is challenging as the resulting posterior can be high dimensional and involve strong dependence. We approximate the posterior using normalizing flows, a flexible parametric family of densities. Training data is generated by likelihood-free importance sampling with a large bandwidth value epsilon, which makes the target similar to the prior. The training data is "distilled" by using it to train an updated normalizing flow. The process is iterated, using the updated flow as the importance sampling proposal, and slowly reducing epsilon so the target becomes closer to the posterior. Unlike most other likelihood-free methods, we avoid the need to reduce data to low dimensional summary statistics, and hence can achieve more accurate results. We illustrate our method in two challenging examples, on queuing and epidemiology.