Model-based approaches bear great promise for decision making of agents interacting with the physical world. In the context of spatial environments, different types of problems such as localisation, mapping, navigation or autonomous exploration are typically adressed with specialised methods, often relying on detailed knowledge of the system at hand. We express these tasks as probabilistic inference and planning under the umbrella of deep sequential generative models. Using the frameworks of variational inference and neural networks, our method inherits favourable properties such as flexibility, scalability and the ability to learn from data. The method performs comparably to specialised state-of-the-art methodology in two distinct simulated environments.
In this article, we propose a new class of priors for Bayesian inference with multiple Gaussian graphical models. We introduce fully Bayesian treatments of two popular procedures, the group graphical lasso and the fused graphical lasso, and extend them to a continuous spike-and-slab framework to allow self-adaptive shrinkage and model selection simultaneously. We develop an EM algorithm that performs fast and dynamic explorations of posterior modes. Our approach selects sparse models efficiently with substantially smaller bias than would be induced by alternative regularization procedures. The performance of the proposed methods are demonstrated through simulation and two real data examples.
The aim of this work is to enable inference of deep networks that retain high accuracy for the least possible model complexity, with the latter deduced from the data during inference. To this end, we revisit deep networks that comprise competing linear units, as opposed to nonlinear units that do not entail any form of (local) competition. In this context, our main technical innovation consists in an inferential setup that leverages solid arguments from Bayesian nonparametrics. We infer both the needed set of connections or locally competing sets of units, as well as the required floating-point precision for storing the network parameters. Specifically, we introduce auxiliary discrete latent variables representing which initial network components are actually needed for modeling the data at hand, and perform Bayesian inference over them by imposing appropriate stick-breaking priors. As we experimentally show using benchmark datasets, our approach yields networks with less computational footprint than the state-of-the-art, and with no compromises in predictive accuracy.
In Bayesian inference, the posterior distributions are difficult to obtain analytically for complex models such as neural networks. Variational inference usually uses a parametric distribution for approximation, from which we can easily draw samples. Recently discrete approximation by particles has attracted attention because of its high expression ability. An example is Stein variational gradient descent (SVGD), which iteratively optimizes particles. Although SVGD has been shown to be computationally efficient empirically, its theoretical properties have not been clarified yet and no finite sample bound of the convergence rate is known. Another example is the Stein points (SP) method, which minimizes kernelized Stein discrepancy directly. Although a finite sample bound is assured theoretically, SP is computationally inefficient empirically, especially in high-dimensional problems. In this paper, we propose a novel method named maximum mean discrepancy minimization by the Frank-Wolfe algorithm (MMD-FW), which minimizes MMD in a greedy way by the FW algorithm. Our method is computationally efficient empirically and we show that its finite sample convergence bound is in a linear order in finite dimensions.
Infectious diseases are studied to understand their spreading mechanisms, to evaluate control strategies and to predict the risk and course of future outbreaks. Because people only interact with a small number of individuals, and because the structure of these interactions matters for spreading processes, the pairwise relationships between individuals in a population can be usefully represented by a network. Although the underlying processes of transmission are different, the network approach can be used to study the spread of pathogens in a contact network or the spread of rumors in an online social network. We study simulated simple and complex epidemics on synthetic networks and on two empirical networks, a social / contact network in an Indian village and an online social network in the U.S. Our goal is to learn simultaneously about the spreading process parameters and the source node (first infected node) of the epidemic, given a fixed and known network structure, and observations about state of nodes at several points in time. Our inference scheme is based on approximate Bayesian computation (ABC), an inference technique for complex models with likelihood functions that are either expensive to evaluate or analytically intractable. ABC enables us to adopt a Bayesian approach to the problem despite the posterior distribution being very complex. Our method is agnostic about the topology of the network and the nature of the spreading process. It generally performs well and, somewhat counter-intuitively, the inference problem appears to be easier on more heterogeneous network topologies, which enhances its future applicability to real-world settings where few networks have homogeneous topologies.
In programming by example, users "write" programs by generating a small number of input-output examples and asking the computer to synthesize consistent programs. We consider a challenging problem in this domain: learning regular expressions (regexes) from positive and negative example strings. This problem is challenging, as (1) user-generated examples may not be informative enough to sufficiently constrain the hypothesis space, and (2) even if user-generated examples are in principle informative, there is still a massive search space to examine. We frame regex induction as the problem of inferring a probabilistic regular grammar and propose an efficient inference approach that uses a novel stochastic process recognition model. This model incrementally "grows" a grammar using positive examples as a scaffold. We show that this approach is competitive with human ability to learn regexes from examples.
Super-resolution fluorescence microscopy, with a resolution beyond the diffraction limit of light, has become an indispensable tool to directly visualize biological structures in living cells at a nanometer-scale resolution. Despite advances in high-density super-resolution fluorescent techniques, existing methods still have bottlenecks, including extremely long execution time, artificial thinning and thickening of structures, and lack of ability to capture latent structures. Here we propose a novel deep learning guided Bayesian inference approach, DLBI, for the time-series analysis of high-density fluorescent images. Our method combines the strength of deep learning and statistical inference, where deep learning captures the underlying distribution of the fluorophores that are consistent with the observed time-series fluorescent images by exploring local features and correlation along time-axis, and statistical inference further refines the ultrastructure extracted by deep learning and endues physical meaning to the final image. Comprehensive experimental results on both real and simulated datasets demonstrate that our method provides more accurate and realistic local patch and large-field reconstruction than the state-of-the-art method, the 3B analysis, while our method is more than two orders of magnitude faster. The main program is available at https://github.com/lykaust15/DLBI
We present a scalable approach to performing approximate fully Bayesian inference in generic state space models. The proposed method is an alternative to particle MCMC that provides fully Bayesian inference of both the dynamic latent states and the static parameters of the model. We build up on recent advances in computational statistics that combine variational methods with sequential Monte Carlo sampling and we demonstrate the advantages of performing full Bayesian inference over the static parameters rather than just performing variational EM approximations. We illustrate how our approach enables scalable inference in multivariate stochastic volatility models and self-exciting point process models that allow for flexible dynamics in the latent intensity function.
Approximate Bayesian Computation (ABC) provides methods for Bayesian inference in simulation-based stochastic models which do not permit tractable likelihoods. We present a new ABC method which uses probabilistic neural emulator networks to learn synthetic likelihoods on simulated data -- both local emulators which approximate the likelihood for specific observed data, as well as global ones which are applicable to a range of data. Simulations are chosen adaptively using an acquisition function which takes into account uncertainty about either the posterior distribution of interest, or the parameters of the emulator. Our approach does not rely on user-defined rejection thresholds or distance functions. We illustrate inference with emulator networks on synthetic examples and on a biophysical neuron model, and show that emulators allow accurate and efficient inference even on high-dimensional problems which are challenging for conventional ABC approaches.
We design a new myopic strategy for a wide class of sequential design of experiment (DOE) problems, where the goal is to collect data in order to to fulfil a certain problem specific goal. Our approach, Myopic Posterior Sampling (MPS), is inspired by the classical posterior (Thompson) sampling algorithm for multi-armed bandits and leverages the flexibility of probabilistic programming and approximate Bayesian inference to address a broad set of problems. Empirically, this general-purpose strategy is competitive with more specialised methods in a wide array of DOE tasks, and more importantly, enables addressing complex DOE goals where no existing method seems applicable. On the theoretical side, we leverage ideas from adaptive submodularity and reinforcement learning to derive conditions under which MPS achieves sublinear regret against natural benchmark policies.
Accurate statistical models of neural spike responses can characterize the information carried by neural populations. But the limited samples of spike counts during recording usually result in model overfitting. Besides, current models assume spike counts to be Poisson-distributed, which ignores the fact that many neurons demonstrate over-dispersed spiking behaviour. Although the Negative Binomial Generalized Linear Model (NB-GLM) provides a powerful tool for modeling over-dispersed spike counts, the maximum likelihood-based standard NB-GLM leads to highly variable and inaccurate parameter estimates. Thus, we propose a hierarchical parametric empirical Bayes method to estimate the neural spike responses among neuronal population. Our method integrates both Generalized Linear Models (GLMs) and empirical Bayes theory, which aims to (1) improve the accuracy and reliability of parameter estimation, compared to the maximum likelihood-based method for NB-GLM and Poisson-GLM; (2) effectively capture the over-dispersion nature of spike counts from both simulated data and experimental data; and (3) provide insight into both neural interactions and spiking behaviours of the neuronal populations. We apply our approach to study both simulated data and experimental neural data. The estimation of simulation data indicates that the new framework can accurately predict mean spike counts simulated from different models and recover the connectivity weights among neural populations. The estimation based on retinal neurons demonstrate the proposed method outperforms both NB-GLM and Poisson-GLM in terms of the predictive log-likelihood of held-out data. Codes are available in https://doi.org/10.5281/zenodo.4704423
Semi-implicit variational inference (SIVI) is introduced to expand the commonly used analytic variational distribution family, by mixing the variational parameter with a flexible distribution. This mixing distribution can assume any density function, explicit or not, as long as independent random samples can be generated via reparameterization. Not only does SIVI expand the variational family to incorporate highly flexible variational distributions, including implicit ones that have no analytic density functions, but also sandwiches the evidence lower bound (ELBO) between a lower bound and an upper bound, and further derives an asymptotically exact surrogate ELBO that is amenable to optimization via stochastic gradient ascent. With a substantially expanded variational family and a novel optimization algorithm, SIVI is shown to closely match the accuracy of MCMC in inferring the posterior in a variety of Bayesian inference tasks.
We reconsider a nonparametric density model based on Gaussian processes. By augmenting the model with latent P\'olya--Gamma random variables and a latent marked Poisson process we obtain a new likelihood which is conjugate to the model's Gaussian process prior. The augmented posterior allows for efficient inference by Gibbs sampling and an approximate variational mean field approach. For the latter we utilise sparse GP approximations to tackle the infinite dimensionality of the problem. The performance of both algorithms and comparisons with other density estimators are demonstrated on artificial and real datasets with up to several thousand data points.
In this work, a novel sequential Monte Carlo filter is introduced which aims at efficient sampling of high-dimensional state spaces with a limited number of particles. Particles are pushed forward from the prior to the posterior density using a sequence of mappings that minimizes the Kullback-Leibler divergence between the posterior and the sequence of intermediate densities. The sequence of mappings represents a gradient flow. A key ingredient of the mappings is that they are embedded in a reproducing kernel Hilbert space, which allows for a practical and efficient algorithm. The embedding provides a direct means to calculate the gradient of the Kullback-Leibler divergence leading to quick convergence using well-known gradient-based stochastic optimization algorithms. Evaluation of the method is conducted in the chaotic Lorenz-63 system, the Lorenz-96 system, which is a coarse prototype of atmospheric dynamics, and an epidemic model that describes cholera dynamics. No resampling is required in the mapping particle filter even for long recursive sequences. The number of effective particles remains close to the total number of particles in all the experiments.
We present a novel model architecture which leverages deep learning tools to perform exact Bayesian inference on sets of high dimensional, complex observations. Our model is provably exchangeable, meaning that the joint distribution over observations is invariant under permutation: this property lies at the heart of Bayesian inference. The model does not require variational approximations to train, and new samples can be generated conditional on previous samples, with cost linear in the size of the conditioning set. The advantages of our architecture are demonstrated on learning tasks that require generalisation from short observed sequences while modelling sequence variability, such as conditional image generation, few-shot learning, and anomaly detection.
Incentive mechanisms for crowdsourcing are designed to incentivize financially self-interested workers to generate and report high-quality labels. Existing mechanisms are often developed as one-shot static solutions, assuming a certain level of knowledge about worker models (expertise levels, costs of exerting efforts, etc.). In this paper, we propose a novel inference aided reinforcement mechanism that learns to incentivize high-quality data sequentially and requires no such prior assumptions. Specifically, we first design a Gibbs sampling augmented Bayesian inference algorithm to estimate workers' labeling strategies from the collected labels at each step. Then we propose a reinforcement incentive learning (RIL) method, building on top of the above estimates, to uncover how workers respond to different payments. RIL dynamically determines the payment without accessing any ground-truth labels. We theoretically prove that RIL is able to incentivize rational workers to provide high-quality labels. Empirical results show that our mechanism performs consistently well under both rational and non-fully rational (adaptive learning) worker models. Besides, the payments offered by RIL are more robust and have lower variances compared to the existing one-shot mechanisms.
This paper introduces Wasserstein variational inference, a new form of approximate Bayesian inference based on optimal transport theory. Wasserstein variational inference uses a new family of divergences that includes both f-divergences and the Wasserstein distance as special cases. The gradients of the Wasserstein variational loss are obtained by backpropagating through the Sinkhorn iterations. This technique results in a very stable likelihood-free training method that can be used with implicit distributions and probabilistic programs. Using the Wasserstein variational inference framework, we introduce several new forms of autoencoders and test their robustness and performance against existing variational autoencoding techniques.
We formalize the problem of learning interdomain correspondences in the absence of paired data as Bayesian inference in a latent variable model (LVM), where one seeks the underlying hidden representations of entities from one domain as entities from the other domain. First, we introduce implicit latent variable models, where the prior over hidden representations can be specified flexibly as an implicit distribution. Next, we develop a new variational inference (VI) algorithm for this model based on minimization of the symmetric Kullback-Leibler (KL) divergence between a variational joint and the exact joint distribution. Lastly, we demonstrate that the state-of-the-art cycle-consistent adversarial learning (CYCLEGAN) models can be derived as a special case within our proposed VI framework, thus establishing its connection to approximate Bayesian inference methods.
We present the very first robust Bayesian Online Changepoint Detection algorithm through General Bayesian Inference (GBI) with $\beta$-divergences. The resulting inference procedure is doubly robust for both the parameter and the changepoint (CP) posterior, with linear time and constant space complexity. We provide a construction for exponential models and demonstrate it on the Bayesian Linear Regression model. In so doing, we make two additional contributions: Firstly, we make GBI scalable using Structural Variational approximations that are exact as $\beta \to 0$. Secondly, we give a principled way of choosing the divergence parameter $\beta$ by minimizing expected predictive loss on-line. Reducing False Discovery Rates of CPs from more than 90% to 0% on real world data, this offers the state of the art.
The multiresolution Gaussian process (GP) has gained increasing attention as a viable approach towards improving the quality of approximations in GPs that scale well to large-scale data. Most of the current constructions assume full independence across resolutions. This assumption simplifies the inference, but it underestimates the uncertainties in transitioning from one resolution to another. This in turn results in models which are prone to overfitting in the sense of excessive sensitivity to the chosen resolution, and predictions which are non-smooth at the boundaries. Our contribution is a new construction which instead assumes conditional independence among GPs across resolutions. We show that relaxing the full independence assumption enables robustness against overfitting, and that it delivers predictions that are smooth at the boundaries. Our new model is compared against current state of the art on 2 synthetic and 9 real-world datasets. In most cases, our new conditionally independent construction performed favorably when compared against models based on the full independence assumption. In particular, it exhibits little to no signs of overfitting.