The classical approach to inverse problems is based on the optimization of a misfit function. Despite its computational appeal, such an approach suffers from many shortcomings, e.g., non-uniqueness of solutions, modeling prior knowledge, etc. The Bayesian formalism to inverse problems avoids most of the difficulties encountered by the optimization approach, albeit at an increased computational cost. In this work, we use information theoretic arguments to cast the Bayesian inference problem in terms of an optimization problem. The resulting scheme combines the theoretical soundness of fully Bayesian inference with the computational efficiency of a simple optimization.
Bayesian entity resolution merges together multiple, noisy databases and returns the minimal collection of unique individuals represented, together with their true, latent record values. Bayesian methods allow flexible generative models that share power across databases as well as principled quantification of uncertainty for queries of the final, resolved database. However, existing Bayesian methods for entity resolution use Markov monte Carlo method (MCMC) approximations and are too slow to run on modern databases containing millions or billions of records. Instead, we propose applying variational approximations to allow scalable Bayesian inference in these models. We derive a coordinate-ascent approximation for mean-field variational Bayes, qualitatively compare our algorithm to existing methods, note unique challenges for inference that arise from the expected distribution of cluster sizes in entity resolution, and discuss directions for future work in this domain.
The ever-increasing size of modern data sets combined with the difficulty of obtaining label information has made semi-supervised learning one of the problems of significant practical importance in modern data analysis. We revisit the approach to semi-supervised learning with generative models and develop new models that allow for effective generalisation from small labelled data sets to large unlabelled ones. Generative approaches have thus far been either inflexible, inefficient or non-scalable. We show that deep generative models and approximate Bayesian inference exploiting recent advances in variational methods can be used to provide significant improvements, making generative approaches highly competitive for semi-supervised learning.
One of the most fundamental problems in causal inference is the estimation of a causal effect when variables are confounded. This is difficult in an observational study, because one has no direct evidence that all confounders have been adjusted for. We introduce a novel approach for estimating causal effects that exploits observational conditional independencies to suggest "weak" paths in a unknown causal graph. The widely used faithfulness condition of Spirtes et al. is relaxed to allow for varying degrees of "path cancellations" that imply conditional independencies but do not rule out the existence of confounding causal paths. The outcome is a posterior distribution over bounds on the average causal effect via a linear programming approach and Bayesian inference. We claim this approach should be used in regular practice along with other default tools in observational studies.
Identifying small subsets of features that are relevant for prediction and/or classification tasks is a central problem in machine learning and statistics. The feature selection task is especially important, and computationally difficult, for modern datasets where the number of features can be comparable to, or even exceed, the number of samples. Here, we show that feature selection with Bayesian inference takes a universal form and reduces to calculating the magnetizations of an Ising model, under some mild conditions. Our results exploit the observation that the evidence takes a universal form for strongly-regularizing priors --- priors that have a large effect on the posterior probability even in the infinite data limit. We derive explicit expressions for feature selection for generalized linear models, a large class of statistical techniques that include linear and logistic regression. We illustrate the power of our approach by analyzing feature selection in a logistic regression-based classifier trained to distinguish between the letters B and D in the notMNIST dataset.
We propose a nonparametric Bayesian probabilistic latent variable model for multi-view anomaly detection, which is the task of finding instances that have inconsistent views. With the proposed model, all views of a non-anomalous instance are assumed to be generated from a single latent vector. On the other hand, an anomalous instance is assumed to have multiple latent vectors, and its different views are generated from different latent vectors. By inferring the number of latent vectors used for each instance with Dirichlet process priors, we obtain multi-view anomaly scores. The proposed model can be seen as a robust extension of probabilistic canonical correlation analysis for noisy multi-view data. We present Bayesian inference procedures for the proposed model based on a stochastic EM algorithm. The effectiveness of the proposed model is demonstrated in terms of performance when detecting multi-view anomalies and imputing missing values in multi-view data with anomalies.
A wide range of evidence points toward the existence of a common algorithm underlying the processing of information throughout the cerebral cortex. Several hypothesized features of this cortical algorithm are reviewed, including sparse distributed representation, Bayesian inference, hierarchical organization composed of alternating template matching and pooling layers, temporal slowness and predictive coding. Hierarchical Temporal Memory (HTM) is a family of learning algorithms and corresponding theories of cortical function that embodies these principles. HTM has previously been applied mainly to perceptual tasks typical of posterior cortex. In order to evaluate HTM as a candidate model of cortical function, it is necessary also to investigate its compatibility with the requirements of frontal cortical function. To this end, a variety of models of frontal cortical function are reviewed and integrated, to arrive at the hypothesis that frontal functions including attention, working memory and action selection depend largely upon the same basic algorithms as do posterior functions, with the notable additions of a mechanism for the active maintenance of representations and of multiple cortico-striato-thalamo-cortical loops that allow communication between regions of frontal cortex to be gated in an adaptive manner. Computational models of this system are reviewed. Finally, there is a discussion of how HTM can contribute to the understanding of frontal cortical function, and of what the requirements of frontal cortical function mean for the future development of HTM.
Rodent hippocampal population codes represent important spatial information about the environment during navigation. Several computational methods have been developed to uncover the neural representation of spatial topology embedded in rodent hippocampal ensemble spike activity. Here we extend our previous work and propose a nonparametric Bayesian approach to infer rat hippocampal population codes during spatial navigation. To tackle the model selection problem, we leverage a nonparametric Bayesian model. Specifically, to analyze rat hippocampal ensemble spiking activity, we apply a hierarchical Dirichlet process-hidden Markov model (HDP-HMM) using two Bayesian inference methods, one based on Markov chain Monte Carlo (MCMC) and the other based on variational Bayes (VB). We demonstrate the effectiveness of our Bayesian approaches on recordings from a freely-behaving rat navigating in an open field environment. We find that MCMC-based inference with Hamiltonian Monte Carlo (HMC) hyperparameter sampling is flexible and efficient, and outperforms VB and MCMC approaches with hyperparameters set by empirical Bayes.
This dissertation shows that careful injection of noise into sample data can substantially speed up Expectation-Maximization algorithms. Expectation-Maximization algorithms are a class of iterative algorithms for extracting maximum likelihood estimates from corrupted or incomplete data. The convergence speed-up is an example of a noise benefit or "stochastic resonance" in statistical signal processing. The dissertation presents derivations of sufficient conditions for such noise-benefits and demonstrates the speed-up in some ubiquitous signal-processing algorithms. These algorithms include parameter estimation for mixture models, the $k$-means clustering algorithm, the Baum-Welch algorithm for training hidden Markov models, and backpropagation for training feedforward artificial neural networks. This dissertation also analyses the effects of data and model corruption on the more general Bayesian inference estimation framework. The main finding is a theorem guaranteeing that uniform approximators for Bayesian model functions produce uniform approximators for the posterior pdf via Bayes theorem. This result also applies to hierarchical and multidimensional Bayesian models.
We present the Bayesian Echo Chamber, a new Bayesian generative model for social interaction data. By modeling the evolution of people's language usage over time, this model discovers latent influence relationships between them. Unlike previous work on inferring influence, which has primarily focused on simple temporal dynamics evidenced via turn-taking behavior, our model captures more nuanced influence relationships, evidenced via linguistic accommodation patterns in interaction content. The model, which is based on a discrete analog of the multivariate Hawkes process, permits a fully Bayesian inference algorithm. We validate our model's ability to discover latent influence patterns using transcripts of arguments heard by the US Supreme Court and the movie "12 Angry Men." We showcase our model's capabilities by using it to infer latent influence patterns from Federal Open Market Committee meeting transcripts, demonstrating state-of-the-art performance at uncovering social dynamics in group discussions.
A key quantity of interest in Bayesian inference are expectations of functions with respect to a posterior distribution. Markov Chain Monte Carlo is a fundamental tool to consistently compute these expectations via averaging samples drawn from an approximate posterior. However, its feasibility is being challenged in the era of so called Big Data as all data needs to be processed in every iteration. Realising that such simulation is an unnecessarily hard problem if the goal is estimation, we construct a computationally scalable methodology that allows unbiased estimation of the required expectations -- without explicit simulation from the full posterior. The scheme's variance is finite by construction and straightforward to control, leading to algorithms that are provably unbiased and naturally arrive at a desired error tolerance. This is achieved at an average computational complexity that is sub-linear in the size of the dataset and its free parameters are easy to tune. We demonstrate the utility and generality of the methodology on a range of common statistical models applied to large-scale benchmark and real-world datasets.
We consider the problem of approximate Bayesian inference in log-supermodular models. These models encompass regular pairwise MRFs with binary variables, but allow to capture high-order interactions, which are intractable for existing approximate inference techniques such as belief propagation, mean field, and variants. We show that a recently proposed variational approach to inference in log-supermodular models -L-FIELD- reduces to the widely-studied minimum norm problem for submodular minimization. This insight allows to leverage powerful existing tools, and hence to solve the variational problem orders of magnitude more efficiently than previously possible. We then provide another natural interpretation of L-FIELD, demonstrating that it exactly minimizes a specific type of R\'enyi divergence measure. This insight sheds light on the nature of the variational approximations produced by L-FIELD. Furthermore, we show how to perform parallel inference as message passing in a suitable factor graph at a linear convergence rate, without having to sum up over all the configurations of the factor. Finally, we apply our approach to a challenging image segmentation task. Our experiments confirm scalability of our approach, high quality of the marginals, and the benefit of incorporating higher-order potentials.
We consider a dictionary learning problem whose objective is to design a dictionary such that the signals admits a sparse or an approximate sparse representation over the learned dictionary. Such a problem finds a variety of applications such as image denoising, feature extraction, etc. In this paper, we propose a new hierarchical Bayesian model for dictionary learning, in which a Gaussian-inverse Gamma hierarchical prior is used to promote the sparsity of the representation. Suitable priors are also placed on the dictionary and the noise variance such that they can be reasonably inferred from the data. Based on the hierarchical model, a variational Bayesian method and a Gibbs sampling method are developed for Bayesian inference. The proposed methods have the advantage that they do not require the knowledge of the noise variance \emph{a priori}. Numerical results show that the proposed methods are able to learn the dictionary with an accuracy better than existing methods, particularly for the case where there is a limited number of training signals.
Approximate Bayesian computation (ABC) is a powerful and elegant framework for performing inference in simulation-based models. However, due to the difficulty in scaling likelihood estimates, ABC remains useful for relatively low-dimensional problems. We introduce Hamiltonian ABC (HABC), a set of likelihood-free algorithms that apply recent advances in scaling Bayesian learning using Hamiltonian Monte Carlo (HMC) and stochastic gradients. We find that a small number forward simulations can effectively approximate the ABC gradient, allowing Hamiltonian dynamics to efficiently traverse parameter spaces. We also describe a new simple yet general approach of incorporating random seeds into the state of the Markov chain, further reducing the random walk behavior of HABC. We demonstrate HABC on several typical ABC problems, and show that HABC samples comparably to regular Bayesian inference using true gradients on a high-dimensional problem from machine learning.
Computer vision is hard because of a large variability in lighting, shape, and texture; in addition the image signal is non-additive due to occlusion. Generative models promised to account for this variability by accurately modelling the image formation process as a function of latent variables with prior beliefs. Bayesian posterior inference could then, in principle, explain the observation. While intuitively appealing, generative models for computer vision have largely failed to deliver on that promise due to the difficulty of posterior inference. As a result the community has favoured efficient discriminative approaches. We still believe in the usefulness of generative models in computer vision, but argue that we need to leverage existing discriminative or even heuristic computer vision methods. We implement this idea in a principled way with an "informed sampler" and in careful experiments demonstrate it on challenging generative models which contain renderer programs as their components. We concentrate on the problem of inverting an existing graphics rendering engine, an approach that can be understood as "Inverse Graphics". The informed sampler, using simple discriminative proposals based on existing computer vision technology, achieves significant improvements of inference.
Approximate Bayesian Computation (ABC) are likelihood-free Monte Carlo methods. ABC methods use a comparison between simulated data, using different parameters drew from a prior distribution, and observed data. This comparison process is based on computing a distance between the summary statistics from the simulated data and the observed data. For complex models, it is usually difficult to define a methodology for choosing or constructing the summary statistics. Recently, a nonparametric ABC has been proposed, that uses a dissimilarity measure between discrete distributions based on empirical kernel embeddings as an alternative for summary statistics. The nonparametric ABC outperforms other methods including ABC, kernel ABC or synthetic likelihood ABC. However, it assumes that the probability distributions are discrete, and it is not robust when dealing with few observations. In this paper, we propose to apply kernel embeddings using an smoother density estimator or Parzen estimator for comparing the empirical data distributions, and computing the ABC posterior. Synthetic data and real data were used to test the Bayesian inference of our method. We compare our method with respect to state-of-the-art methods, and demonstrate that our method is a robust estimator of the posterior distribution in terms of the number of observations.
General results from statistical learning theory suggest to understand not only brain computations, but also brain plasticity as probabilistic inference. But a model for that has been missing. We propose that inherently stochastic features of synaptic plasticity and spine motility enable cortical networks of neurons to carry out probabilistic inference by sampling from a posterior distribution of network configurations. This model provides a viable alternative to existing models that propose convergence of parameters to maximum likelihood values. It explains how priors on weight distributions and connection probabilities can be merged optimally with learned experience, how cortical networks can generalize learned information so well to novel experiences, and how they can compensate continuously for unforeseen disturbances of the network. The resulting new theory of network plasticity explains from a functional perspective a number of experimental data on stochastic aspects of synaptic plasticity that previously appeared to be quite puzzling.
Markov chain Monte Carlo methods are often deemed too computationally intensive to be of any practical use for big data applications, and in particular for inference on datasets containing a large number $n$ of individual data points, also known as tall datasets. In scenarios where data are assumed independent, various approaches to scale up the Metropolis-Hastings algorithm in a Bayesian inference context have been recently proposed in machine learning and computational statistics. These approaches can be grouped into two categories: divide-and-conquer approaches and, subsampling-based algorithms. The aims of this article are as follows. First, we present a comprehensive review of the existing literature, commenting on the underlying assumptions and theoretical guarantees of each method. Second, by leveraging our understanding of these limitations, we propose an original subsampling-based approach which samples from a distribution provably close to the posterior distribution of interest, yet can require less than $O(n)$ data point likelihood evaluations at each iteration for certain statistical models in favourable scenarios. Finally, we have only been able so far to propose subsampling-based methods which display good performance in scenarios where the Bernstein-von Mises approximation of the target posterior distribution is excellent. It remains an open challenge to develop such methods in scenarios where the Bernstein-von Mises approximation is poor.
In this paper we propose the first non-parametric Bayesian model using Gaussian Processes to make inference on Poisson Point Processes without resorting to gridding the domain or to introducing latent thinning points. Unlike competing models that scale cubically and have a squared memory requirement in the number of data points, our model has a linear complexity and memory requirement. We propose an MCMC sampler and show that our model is faster, more accurate and generates less correlated samples than competing models on both synthetic and real-life data. Finally, we show that our model easily handles data sizes not considered thus far by alternate approaches.
We define the task of salient structure (SS) detection to unify the saliency-related tasks like fixation prediction, salient object detection, and other detection of structures of interest. In this study, we propose a unified framework for SS detection by modeling the two-pathway-based guided search strategy of biological vision. Firstly, context-based spatial prior (CBSP) is extracted based on the layout of edges in the given scene along a fast visual pathway, called non-selective pathway. This is a rough and non-selective estimation of the locations where the potential SSs present. Secondly, another flow of local feature extraction is executed in parallel along the selective pathway. Finally, Bayesian inference is used to integrate local cues guided by CBSP, and to predict the exact locations of SSs in the input scene. The proposed model is invariant to size and features of objects. Experimental results on four datasets (two fixation prediction datasets and two salient object datasets) demonstrate that our system achieves competitive performance for SS detection (i.e., both the tasks of fixation prediction and salient object detection) comparing to the state-of-the-art methods.