We consider continuous time Markovian processes where populations of individual agents interact stochastically according to kinetic rules. Despite the increasing prominence of such models in fields ranging from biology to smart cities, Bayesian inference for such systems remains challenging, as these are continuous time, discrete state systems with potentially infinite state-space. Here we propose a novel efficient algorithm for joint state / parameter posterior sampling in population Markov Jump processes. We introduce a class of pseudo-marginal sampling algorithms based on a random truncation method which enables a principled treatment of infinite state spaces. Extensive evaluation on a number of benchmark models shows that this approach achieves considerable savings compared to state of the art methods, retaining accuracy and fast convergence. We also present results on a synthetic biology data set showing the potential for practical usefulness of our work.
Hidden Markov Models (HMM) have been used for several years in many time series analysis or pattern recognitions tasks. HMM are often trained by means of the Baum-Welch algorithm which can be seen as a special variant of an expectation maximization (EM) algorithm. Second-order training techniques such as Variational Bayesian Inference (VI) for probabilistic models regard the parameters of the probabilistic models as random variables and define distributions over these distribution parameters, hence the name of this technique. VI can also bee regarded as a special case of an EM algorithm. In this article, we bring both together and train HMM with multivariate Gaussian output distributions with VI. The article defines the new training technique for HMM. An evaluation based on some case studies and a comparison to related approaches is part of our ongoing work.
Kernel methods are one of the mainstays of machine learning, but the problem of kernel learning remains challenging, with only a few heuristics and very little theory. This is of particular importance in methods based on estimation of kernel mean embeddings of probability measures. For characteristic kernels, which include most commonly used ones, the kernel mean embedding uniquely determines its probability measure, so it can be used to design a powerful statistical testing framework, which includes nonparametric two-sample and independence tests. In practice, however, the performance of these tests can be very sensitive to the choice of kernel and its lengthscale parameters. To address this central issue, we propose a new probabilistic model for kernel mean embeddings, the Bayesian Kernel Embedding model, combining a Gaussian process prior over the Reproducing Kernel Hilbert Space containing the mean embedding with a conjugate likelihood function, thus yielding a closed form posterior over the mean embedding. The posterior mean of our model is closely related to recently proposed shrinkage estimators for kernel mean embeddings, while the posterior uncertainty is a new, interesting feature with various possible applications. Critically for the purposes of kernel learning, our model gives a simple, closed form marginal pseudolikelihood of the observed data given the kernel hyperparameters. This marginal pseudolikelihood can either be optimized to inform the hyperparameter choice or fully Bayesian inference can be used.
Bayesian inference has great promise for the privacy-preserving analysis of sensitive data, as posterior sampling automatically preserves differential privacy, an algorithmic notion of data privacy, under certain conditions (Dimitrakakis et al., 2014; Wang et al., 2015). While this one posterior sample (OPS) approach elegantly provides privacy "for free," it is data inefficient in the sense of asymptotic relative efficiency (ARE). We show that a simple alternative based on the Laplace mechanism, the workhorse of differential privacy, is as asymptotically efficient as non-private posterior inference, under general assumptions. This technique also has practical advantages including efficient use of the privacy budget for MCMC. We demonstrate the practicality of our approach on a time-series analysis of sensitive military records from the Afghanistan and Iraq wars disclosed by the Wikileaks organization.
We reframe linear dimensionality reduction as a problem of Bayesian inference on matrix manifolds. This natural paradigm extends the Bayesian framework to dimensionality reduction tasks in higher dimensions with simpler models at greater speeds. Here an orthogonal basis is treated as a single point on a manifold and is associated with a linear subspace on which observations vary maximally. Throughout this paper, we employ the Grassmann and Stiefel manifolds for various dimensionality reduction problems, explore the connection between the two manifolds, and use Hybrid Monte Carlo for posterior sampling on the Grassmannian for the first time. We delineate in which situations either manifold should be considered. Further, matrix manifold models are used to yield scientific insight in the context of cognitive neuroscience, and we conclude that our methods are suitable for basic inference as well as accurate prediction.
We consider the problem of change-point detection in multivariate time-series. The multivariate distribution of the observations is supposed to follow a graphical model, whose graph and parameters are affected by abrupt changes throughout time. We demonstrate that it is possible to perform exact Bayesian inference whenever one considers a simple class of undirected graphs called spanning trees as possible structures. We are then able to integrate on the graph and segmentation spaces at the same time by combining classical dynamic programming with algebraic results pertaining to spanning trees. In particular, we show that quantities such as posterior distributions for change-points or posterior edge probabilities over time can efficiently be obtained. We illustrate our results on both synthetic and experimental data arising from biology and neuroscience.
Attack graphs provide compact representations of the attack paths that an attacker can follow to compromise network resources by analysing network vulnerabilities and topology. These representations are a powerful tool for security risk assessment. Bayesian inference on attack graphs enables the estimation of the risk of compromise to the system's components given their vulnerabilities and interconnections, and accounts for multi-step attacks spreading through the system. Whilst static analysis considers the risk posture at rest, dynamic analysis also accounts for evidence of compromise, e.g. from SIEM software or forensic investigation. However, in this context, exact Bayesian inference techniques do not scale well. In this paper we show how Loopy Belief Propagation - an approximate inference technique - can be applied to attack graphs, and that it scales linearly in the number of nodes for both static and dynamic analysis, making such analyses viable for larger networks. We experiment with different topologies and network clustering on synthetic Bayesian attack graphs with thousands of nodes to show that the algorithm's accuracy is acceptable and converge to a stable solution. We compare sequential and parallel versions of Loopy Belief Propagation with exact inference techniques for both static and dynamic analysis, showing the advantages of approximate inference techniques to scale to larger attack graphs.
Vector space models have become popular in distributional semantics, despite the challenges they face in capturing various semantic phenomena. We propose a novel probabilistic framework which draws on both formal semantics and recent advances in machine learning. In particular, we separate predicates from the entities they refer to, allowing us to perform Bayesian inference based on logical forms. We describe an implementation of this framework using a combination of Restricted Boltzmann Machines and feedforward neural networks. Finally, we demonstrate the feasibility of this approach by training it on a parsed corpus and evaluating it on established similarity datasets.
Bayesian inference in the presence of an intractable likelihood function is computationally challenging. When following a Markov chain Monte Carlo (MCMC) approach to approximate the posterior distribution in this context, one typically either uses MCMC schemes which target the joint posterior of the parameters and some auxiliary latent variables, or pseudo-marginal Metropolis--Hastings (MH) schemes. The latter mimic a MH algorithm targeting the marginal posterior of the parameters by approximating unbiasedly the intractable likelihood. However, in scenarios where the parameters and auxiliary variables are strongly correlated under the posterior and/or this posterior is multimodal, Gibbs sampling or Hamiltonian Monte Carlo (HMC) will perform poorly and the pseudo-marginal MH algorithm, as any other MH scheme, will be inefficient for high dimensional parameters. We propose here an original MCMC algorithm, termed pseudo-marginal HMC, which combines the advantages of both HMC and pseudo-marginal schemes. Specifically, the pseudo-marginal HMC method is controlled by a precision parameter N, controlling the approximation of the likelihood and, for any N, it samples the marginal posterior of the parameters. Additionally, as N tends to infinity, its sample trajectories and acceptance probability converge to those of an ideal, but intractable, HMC algorithm which would have access to the marginal posterior of parameters and its gradient. We demonstrate through experiments that pseudo-marginal HMC can outperform significantly both standard HMC and pseudo-marginal MH schemes.
Many algorithms for the computation of correspondences between deformable shapes rely on some variant of nearest neighbor matching in a descriptor space. Such are, for example, various point-wise correspondence recovery algorithms used as a postprocessing stage in the functional correspondence framework. In this paper, we show that such frequently used techniques in practice suffer from lack of accuracy and result in poor surjectivity. We propose an alternative recovery technique guaranteeing a bijective correspondence and producing significantly higher accuracy. We derive the proposed method from a statistical framework of Bayesian inference and demonstrate its performance on several challenging deformable 3D shape matching datasets.
Collective intelligence is believed to underly the remarkable success of human society. The formation of accurate shared beliefs is one of the key components of human collective intelligence. How are accurate shared beliefs formed in groups of fallible individuals? Answering this question requires a multiscale analysis. We must understand both the individual decision mechanisms people use, and the properties and dynamics of those mechanisms in the aggregate. As of yet, mathematical tools for such an approach have been lacking. To address this gap, we introduce a new analytical framework: We propose that groups arrive at accurate shared beliefs via distributed Bayesian inference. Distributed inference occurs through information processing at the individual level, and yields rational belief formation at the group level. We instantiate this framework in a new model of human social decision-making, which we validate using a dataset we collected of over 50,000 users of an online social trading platform where investors mimic each others' trades using real money in foreign exchange and other asset markets. We find that in this setting people use a decision mechanism in which popularity is treated as a prior distribution for which decisions are best to make. This mechanism is boundedly rational at the individual level, but we prove that in the aggregate implements a type of approximate "Thompson sampling"---a well-known and highly effective single-agent Bayesian machine learning algorithm for sequential decision-making. The perspective of distributed Bayesian inference therefore reveals how collective rationality emerges from the boundedly rational decision mechanisms people use.
We propose a general purpose variational inference algorithm that forms a natural counterpart of gradient descent for optimization. Our method iteratively transports a set of particles to match the target distribution, by applying a form of functional gradient descent that minimizes the KL divergence. Empirical studies are performed on various real world models and datasets, on which our method is competitive with existing state-of-the-art methods. The derivation of our method is based on a new theoretical result that connects the derivative of KL divergence under smooth transforms with Stein's identity and a recently proposed kernelized Stein discrepancy, which is of independent interest.
In this paper we introduce a novel framework for making exact nonparametric Bayesian inference on latent functions, that is particularly suitable for Big Data tasks. Firstly, we introduce a class of stochastic processes we refer to as string Gaussian processes (string GPs), which are not to be mistaken for Gaussian processes operating on text. We construct string GPs so that their finite-dimensional marginals exhibit suitable local conditional independence structures, which allow for scalable, distributed, and flexible nonparametric Bayesian inference, without resorting to approximations, and while ensuring some mild global regularity constraints. Furthermore, string GP priors naturally cope with heterogeneous input data, and the gradient of the learned latent function is readily available for explanatory analysis. Secondly, we provide some theoretical results relating our approach to the standard GP paradigm. In particular, we prove that some string GPs are Gaussian processes, which provides a complementary global perspective on our framework. Finally, we derive a scalable and distributed MCMC scheme for supervised learning tasks under string GP priors. The proposed MCMC scheme has computational time complexity $\mathcal{O}(N)$ and memory requirement $\mathcal{O}(dN)$, where $N$ is the data size and $d$ the dimension of the input space. We illustrate the efficacy of the proposed approach on several synthetic and real-world datasets, including a dataset with $6$ millions input points and $8$ attributes.
To construct flexible nonlinear predictive distributions, the paper introduces a family of softplus function based regression models that convolve, stack, or combine both operations by convolving countably infinite stacked gamma distributions, whose scales depend on the covariates. Generalizing logistic regression that uses a single hyperplane to partition the covariate space into two halves, softplus regressions employ multiple hyperplanes to construct a confined space, related to a single convex polytope defined by the intersection of multiple half-spaces or a union of multiple convex polytopes, to separate one class from the other. The gamma process is introduced to support the convolution of countably infinite (stacked) covariate-dependent gamma distributions. For Bayesian inference, Gibbs sampling derived via novel data augmentation and marginalization techniques is used to deconvolve and/or demix the highly complex nonlinear predictive distribution. Example results demonstrate that softplus regressions provide flexible nonlinear decision boundaries, achieving classification accuracies comparable to that of kernel support vector machine while requiring significant less computation for out-of-sample prediction.
We investigate the problem of approximate Bayesian inference for a general class of observation models by means of the expectation propagation (EP) framework for large systems under some statistical assumptions. Our approach tries to overcome the numerical bottleneck of EP caused by the inversion of large matrices. Assuming that the measurement matrices are realizations of specific types of ensembles we use the concept of freeness from random matrix theory to show that the EP cavity variances exhibit an asymptotic self-averaging property. They can be pre-computed using specific generating functions, i.e. the R- and/or S-transforms in free probability, which do not require matrix inversions. Our approach extends the framework of (generalized) approximate message passing -- assumes zero-mean iid entries of the measurement matrix -- to a general class of random matrix ensembles. The generalization is via a simple formulation of the R- and/or S-transforms of the limiting eigenvalue distribution of the Gramian of the measurement matrix. We demonstrate the performance of our approach on a signal recovery problem of nonlinear compressed sensing and compare it with that of EP.
Imbalance (on-line energy gap between contracted supply and actual demand, and associated cost) reduction is going to be a crucial service for a Power Producer and Supplier (PPS) in the deregulated energy market. PPS requires forward market interactions to procure energy as precisely as possible in order to reduce imbalance energy. This paper presents, 1) (off-line) an effective demand aggregation based strategy for creating a number of balancing groups that leads to higher predictability of group-wise aggregated demand, 2) (on-line) a robust energy storage scheduling that minimizes the imbalance for a particular balancing group considering the demand prediction uncertainty. The group formation is performed by a Probabilistic Programming approach using Bayesian Markov Chain Monte Carlo (MCMC) method after applied on the historical demand statistics. Apart from the group formation, the aggregation strategy (with the help of Bayesian Inference) also clears out the upper-limit of the required storage capacity for a formed group, fraction of which is to be utilized in on-line operation. For on-line operation, a robust energy storage scheduling method is proposed that minimizes expected imbalance energy and cost (a non-linear function of imbalance energy) while incorporating the demand uncertainty of a particular group. The proposed methods are applied on the real apartment buildings' demand data in Tokyo, Japan. Simulation results are presented to verify the effectiveness of the proposed methods.
Spike and Slab priors have been of much recent interest in signal processing as a means of inducing sparsity in Bayesian inference. Applications domains that benefit from the use of these priors include sparse recovery, regression and classification. It is well-known that solving for the sparse coefficient vector to maximize these priors results in a hard non-convex and mixed integer programming problem. Most existing solutions to this optimization problem either involve simplifying assumptions/relaxations or are computationally expensive. We propose a new greedy and adaptive matching pursuit (AMP) algorithm to directly solve this hard problem. Essentially, in each step of the algorithm, the set of active elements would be updated by either adding or removing one index, whichever results in better improvement. In addition, the intermediate steps of the algorithm are calculated via an inexpensive Cholesky decomposition which makes the algorithm much faster. Results on simulated data sets as well as real-world image recovery challenges confirm the benefits of the proposed AMP, particularly in providing a superior cost-quality trade-off over existing alternatives.
Bayesian methods for machine learning have been widely investigated, yielding principled methods for incorporating prior information into inference algorithms. In this survey, we provide an in-depth review of the role of Bayesian methods for the reinforcement learning (RL) paradigm. The major incentives for incorporating Bayesian reasoning in RL are: 1) it provides an elegant approach to action-selection (exploration/exploitation) as a function of the uncertainty in learning; and 2) it provides a machinery to incorporate prior knowledge into the algorithms. We first discuss models and methods for Bayesian inference in the simple single-step Bandit model. We then review the extensive recent literature on Bayesian methods for model-based RL, where prior information can be expressed on the parameters of the Markov model. We also present Bayesian methods for model-free RL, where priors are expressed over the value function or policy class. The objective of the paper is to provide a comprehensive survey on Bayesian RL algorithms and their theoretical and empirical properties.
To solve hard problems, AI relies on a variety of disciplines such as logic, probabilistic reasoning, machine learning and mathematical programming. Although it is widely accepted that solving real-world problems requires an integration amongst these, contemporary representation methodologies offer little support for this. In an attempt to alleviate this situation, we introduce a new declarative programming framework that provides abstractions of well-known problems such as SAT, Bayesian inference, generative models, and convex optimization. The semantics of programs is defined in terms of first-order structures with semiring labels, which allows us to freely combine and integrate problems from different AI disciplines.
Monte Carlo (MC) methods are widely used for Bayesian inference and optimization in statistics, signal processing and machine learning. A well-known class of MC methods are Markov Chain Monte Carlo (MCMC) algorithms. In order to foster better exploration of the state space, specially in high-dimensional applications, several schemes employing multiple parallel MCMC chains have been recently introduced. In this work, we describe a novel parallel interacting MCMC scheme, called {\it orthogonal MCMC} (O-MCMC), where a set of "vertical" parallel MCMC chains share information using some "horizontal" MCMC techniques working on the entire population of current states. More specifically, the vertical chains are led by random-walk proposals, whereas the horizontal MCMC techniques employ independent proposals, thus allowing an efficient combination of global exploration and local approximation. The interaction is contained in these horizontal iterations. Within the analysis of different implementations of O-MCMC, novel schemes in order to reduce the overall computational cost of parallel multiple try Metropolis (MTM) chains are also presented. Furthermore, a modified version of O-MCMC for optimization is provided by considering parallel simulated annealing (SA) algorithms. Numerical results show the advantages of the proposed sampling scheme in terms of efficiency in the estimation, as well as robustness in terms of independence with respect to initial values and the choice of the parameters.