Bayesian Structural Inference for Hidden Processes

We introduce a Bayesian approach to discovering patterns in structurally complex processes. The proposed method of Bayesian Structural Inference (BSI) relies on a set of candidate unifilar HMM (uHMM) topologies for inference of process structure from a data series. We employ a recently developed exact enumeration of topological epsilon-machines. (A sequel then removes the topological restriction.) This subset of the uHMM topologies has the added benefit that inferred models are guaranteed to be epsilon-machines, irrespective of estimated transition probabilities. Properties of epsilon-machines and uHMMs allow for the derivation of analytic expressions for estimating transition probabilities, inferring start states, and comparing the posterior probability of candidate model topologies, despite process internal structure being only indirectly present in data. We demonstrate BSI's effectiveness in estimating a process's randomness, as reflected by the Shannon entropy rate, and its structure, as quantified by the statistical complexity. We also compare using the posterior distribution over candidate models and the single, maximum a posteriori model for point estimation and show that the former more accurately reflects uncertainty in estimated values. We apply BSI to in-class examples of finite- and infinite-order Markov processes, as well to an out-of-class, infinite-state hidden process.Comment: 20 pages, 11 figures, 1 table; supplementary materials, 15 pages, 11 figures, 6 tables; http://csc.ucdavis.edu/~cmg/compmech/pubs/bsihp.ht

Dirichlet Bayesian Network Scores and the Maximum Relative Entropy Principle

A classic approach for learning Bayesian networks from data is to identify a maximum a posteriori (MAP) network structure. In the case of discrete Bayesian networks, MAP networks are selected by maximising one of several possible Bayesian Dirichlet (BD) scores; the most famous is the Bayesian Dirichlet equivalent uniform (BDeu) score from Heckerman et al (1995). The key properties of BDeu arise from its uniform prior over the parameters of each local distribution in the network, which makes structure learning computationally efficient; it does not require the elicitation of prior knowledge from experts; and it satisfies score equivalence. In this paper we will review the derivation and the properties of BD scores, and of BDeu in particular, and we will link them to the corresponding entropy estimates to study them from an information theoretic perspective. To this end, we will work in the context of the foundational work of Giffin and Caticha (2007), who showed that Bayesian inference can be framed as a particular case of the maximum relative entropy principle. We will use this connection to show that BDeu should not be used for structure learning from sparse data, since it violates the maximum relative entropy principle; and that it is also problematic from a more classic Bayesian model selection perspective, because it produces Bayes factors that are sensitive to the value of its only hyperparameter. Using a large simulation study, we found in our previous work (Scutari, 2016) that the Bayesian Dirichlet sparse (BDs) score seems to provide better accuracy in structure learning; in this paper we further show that BDs does not suffer from the issues above, and we recommend to use it for sparse data instead of BDeu. Finally, will show that these issues are in fact different aspects of the same problem and a consequence of the distributional assumptions of the prior.Comment: 20 pages, 4 figures; extended version submitted to Behaviormetrik

Hyperparameter Estimation in Bayesian MAP Estimation: Parameterizations and Consistency

The Bayesian formulation of inverse problems is attractive for three primary reasons: it provides a clear modelling framework; means for uncertainty quantification; and it allows for principled learning of hyperparameters. The posterior distribution may be explored by sampling methods, but for many problems it is computationally infeasible to do so. In this situation maximum a posteriori (MAP) estimators are often sought. Whilst these are relatively cheap to compute, and have an attractive variational formulation, a key drawback is their lack of invariance under change of parameterization. This is a particularly significant issue when hierarchical priors are employed to learn hyperparameters. In this paper we study the effect of the choice of parameterization on MAP estimators when a conditionally Gaussian hierarchical prior distribution is employed. Specifically we consider the centred parameterization, the natural parameterization in which the unknown state is solved for directly, and the noncentred parameterization, which works with a whitened Gaussian as the unknown state variable, and arises when considering dimension-robust MCMC algorithms; MAP estimation is well-defined in the nonparametric setting only for the noncentred parameterization. However, we show that MAP estimates based on the noncentred parameterization are not consistent as estimators of hyperparameters; conversely, we show that limits of finite-dimensional centred MAP estimators are consistent as the dimension tends to infinity. We also consider empirical Bayesian hyperparameter estimation, show consistency of these estimates, and demonstrate that they are more robust with respect to noise than centred MAP estimates. An underpinning concept throughout is that hyperparameters may only be recovered up to measure equivalence, a well-known phenomenon in the context of the Ornstein-Uhlenbeck process.Comment: 36 pages, 8 figure

An Empirical-Bayes Score for Discrete Bayesian Networks

Bayesian network structure learning is often performed in a Bayesian setting, by evaluating candidate structures using their posterior probabilities for a given data set. Score-based algorithms then use those posterior probabilities as an objective function and return the maximum a posteriori network as the learned model. For discrete Bayesian networks, the canonical choice for a posterior score is the Bayesian Dirichlet equivalent uniform (BDeu) marginal likelihood with a uniform (U) graph prior (Heckerman et al., 1995). Its favourable theoretical properties descend from assuming a uniform prior both on the space of the network structures and on the space of the parameters of the network. In this paper, we revisit the limitations of these assumptions; and we introduce an alternative set of assumptions and the resulting score: the Bayesian Dirichlet sparse (BDs) empirical Bayes marginal likelihood with a marginal uniform (MU) graph prior. We evaluate its performance in an extensive simulation study, showing that MU+BDs is more accurate than U+BDeu both in learning the structure of the network and in predicting new observations, while not being computationally more complex to estimate.Comment: 12 pages, PGM 201

Log-Concave Duality in Estimation and Control

In this paper we generalize the estimation-control duality that exists in the linear-quadratic-Gaussian setting. We extend this duality to maximum a posteriori estimation of the system's state, where the measurement and dynamical system noise are independent log-concave random variables. More generally, we show that a problem which induces a convex penalty on noise terms will have a dual control problem. We provide conditions for strong duality to hold, and then prove relaxed conditions for the piecewise linear-quadratic case. The results have applications in estimation problems with nonsmooth densities, such as log-concave maximum likelihood densities. We conclude with an example reconstructing optimal estimates from solutions to the dual control problem, which has implications for sharing solution methods between the two types of problems