Traditional approaches to Bayes net structure learning typically assume little regularity in graph structure other than sparseness. However, in many cases, we expect more systematicity: variables in real-world systems often group into classes that predict the kinds of probabilistic dependencies they participate in. Here we capture this form of prior knowledge in a hierarchical Bayesian framework, and exploit it to enable structure learning and type discovery from small datasets. Specifically, we present a nonparametric generative model for directed acyclic graphs as a prior for Bayes net structure learning. Our model assumes that variables come in one or more classes and that the prior probability of an edge existing between two variables is a function only of their classes. We derive an MCMC algorithm for simultaneous inference of the number of classes, the class assignments of variables, and the Bayes net structure over variables. For several realistic, sparse datasets, we show that the bias towards systematicity of connections provided by our model yields more accurate learned networks than a traditional, uniform prior approach, and that the classes found by our model are appropriate.

The National Airspace System (NAS) is a large and complex system with thousands of interrelated components: administration, control centers, airports, airlines, aircraft, passengers, etc. The complexity of the NAS creates many difficulties in management and control. One of the most pressing problems is flight delay. Delay creates high cost to airlines, complaints from passengers, and difficulties for airport operations. As demand on the system increases, the delay problem becomes more and more prominent. For this reason, it is essential for the Federal Aviation Administration to understand the causes of delay and to find ways to reduce delay. Major contributing factors to delay are congestion at the origin airport, weather, increasing demand, and air traffic management (ATM) decisions such as the Ground Delay Programs (GDP). Delay is an inherently stochastic phenomenon. Even if all known causal factors could be accounted for, macro-level national airspace system (NAS) delays could not be predicted with certainty from micro-level aircraft information. This paper presents a stochastic model that uses Bayesian Networks (BNs) to model the relationships among different components of aircraft delay and the causal factors that affect delays. A case study on delays of departure flights from Chicago O'Hare international airport (ORD) to Hartsfield-Jackson Atlanta International Airport (ATL) reveals how local and system level environmental and human-caused factors combine to affect components of delay, and how these components contribute to the final arrival delay at the destination airport.

We investigate methods for parameter learning from incomplete data that is not missing at random. Likelihood-based methods then require the optimization of a profile likelihood that takes all possible missingness mechanisms into account. Optimzing this profile likelihood poses two main difficulties: multiple (local) maxima, and its very high-dimensional parameter space. In this paper a new method is presented for optimizing the profile likelihood that addresses the second difficulty: in the proposed AI&M (adjusting imputation and mazimization) procedure the optimization is performed by operations in the space of data completions, rather than directly in the parameter space of the profile likelihood. We apply the AI&M method to learning parameters for Bayesian networks. The method is compared against conservative inference, which takes into account each possible data completion, and against EM. The results indicate that likelihood-based inference is still feasible in the case of unknown missingness mechanisms, and that conservative inference is unnecessarily weak. On the other hand, our results also provide evidence that the EM algorithm is still quite effective when the data is not missing at random.

We consider in this paper the formulation of approximate inference in Bayesian networks as a problem of exact inference on an approximate network that results from deleting edges (to reduce treewidth). We have shown in earlier work that deleting edges calls for introducing auxiliary network parameters to compensate for lost dependencies, and proposed intuitive conditions for determining these parameters. We have also shown that our method corresponds to IBP when enough edges are deleted to yield a polytree, and corresponds to some generalizations of IBP when fewer edges are deleted. In this paper, we propose a different criteria for determining auxiliary parameters based on optimizing the KL-divergence between the original and approximate networks. We discuss the relationship between the two methods for selecting parameters, shedding new light on IBP and its generalizations. We also discuss the application of our new method to approximating inference problems which are exponential in constrained treewidth, including MAP and nonmyopic value of information.

Tasks such as record linkage and multi-target tracking, which involve reconstructing the set of objects that underlie some observed data, are particularly challenging for probabilistic inference. Recent work has achieved efficient and accurate inference on such problems using Markov chain Monte Carlo (MCMC) techniques with customized proposal distributions. Currently, implementing such a system requires coding MCMC state representations and acceptance probability calculations that are specific to a particular application. An alternative approach, which we pursue in this paper, is to use a general-purpose probabilistic modeling language (such as BLOG) and a generic Metropolis-Hastings MCMC algorithm that supports user-supplied proposal distributions. Our algorithm gains flexibility by using MCMC states that are only partial descriptions of possible worlds; we provide conditions under which MCMC over partial worlds yields correct answers to queries. We also show how to use a context-specific Bayes net to identify the factors in the acceptance probability that need to be computed for a given proposed move. Experimental results on a citation matching task show that our general-purpose MCMC engine compares favorably with an application-specific system.

We introduce priors and algorithms to perform Bayesian inference in Gaussian models defined by acyclic directed mixed graphs. Such a class of graphs, composed of directed and bi-directed edges, is a representation of conditional independencies that is closed under marginalization and arises naturally from causal models which allow for unmeasured confounding. Monte Carlo methods and a variational approximation for such models are presented. Our algorithms for Bayesian inference allow the evaluation of posterior distributions for several quantities of interest, including causal effects that are not identifiable from data alone but could otherwise be inferred where informative prior knowledge about confounding is available.

In many cases it makes sense to model a relationship symmetrically, not implying any particular directionality. Consider the classical example of a recommendation system where the rating of an item by a user should symmetrically be dependent on the attributes of both the user and the item. The attributes of the (known) relationships are also relevant for predicting attributes of entities and for predicting attributes of new relations. In recommendation systems, the exploitation of relational attributes is often referred to as collaborative filtering. Again, in many applications one might prefer to model the collaborative effect in a symmetrical way. In this paper we present a relational model, which is completely symmetrical. The key innovation is that we introduce for each entity (or object) an infinite-dimensional latent variable as part of a Dirichlet process (DP) model. We discuss inference in the model, which is based on a DP Gibbs sampler, i.e., the Chinese restaurant process. We extend the Chinese restaurant process to be applicable to relational modeling. Our approach is evaluated in three applications. One is a recommendation system based on the MovieLens data set. The second application concerns the prediction of the function of yeast genes/proteins on the data set of KDD Cup 2001 using a multi-relational model. The third application involves a relational medical domain. The experimental results show that our model gives significantly improved estimates of attributes describing relationships or entities in complex relational models.

There are several existing algorithms that under appropriate assumptions can reliably identify a subset of the underlying causal relationships from observational data. This paper introduces the first computationally feasible score-based algorithm that can reliably identify causal relationships in the large sample limit for discrete models, while allowing for the possibility that there are unobserved common causes. In doing so, the algorithm does not ever need to assign scores to causal structures with unobserved common causes. The algorithm is based on the identification of so called Y substructures within Bayesian network structures that can be learned from observational data. An example of a Y substructure is A -> C, B -> C, C -> D. After providing background on causal discovery, the paper proves the conditions under which the algorithm is reliable in the large sample limit.

Bayesian Networks (BNs) are useful tools giving a natural and compact representation of joint probability distributions. In many applications one needs to learn a Bayesian Network (BN) from data. In this context, it is important to understand the number of samples needed in order to guarantee a successful learning. Previous work have studied BNs sample complexity, yet it mainly focused on the requirement that the learned distribution will be close to the original distribution which generated the data. In this work, we study a different aspect of the learning, namely the number of samples needed in order to learn the correct structure of the network. We give both asymptotic results, valid in the large sample limit, and experimental results, demonstrating the learning behavior for feasible sample sizes. We show that structure learning is a more difficult task, compared to approximating the correct distribution, in the sense that it requires a much larger number of samples, regardless of the computational power available for the learner.

The main goal of this paper is to describe a method for exact inference in general hybrid Bayesian networks (BNs) (with a mixture of discrete and continuous chance variables). Our method consists of approximating general hybrid Bayesian networks by a mixture of Gaussians (MoG) BNs. There exists a fast algorithm by Lauritzen-Jensen (LJ) for making exact inferences in MoG Bayesian networks, and there exists a commercial implementation of this algorithm. However, this algorithm can only be used for MoG BNs. Some limitations of such networks are as follows. All continuous chance variables must have conditional linear Gaussian distributions, and discrete chance nodes cannot have continuous parents. The methods described in this paper will enable us to use the LJ algorithm for a bigger class of hybrid Bayesian networks. This includes networks with continuous chance nodes with non-Gaussian distributions, networks with no restrictions on the topology of discrete and continuous variables, networks with conditionally deterministic variables that are a nonlinear function of their continuous parents, and networks with continuous chance variables whose variances are functions of their parents.