Learning Bayesian networks is often cast as an optimization problem, where the computational task is to find a structure that maximizes a statistically motivated score. By and large, existing learning tools address this optimization problem using standard heuristic search techniques. Since the search space is extremely large, such search procedures can spend most of the time examining candidates that are extremely unreasonable. This problem becomes critical when we deal with data sets that are large either in the number of instances, or the number of attributes. In this paper, we introduce an algorithm that achieves faster learning by restricting the search space. This iterative algorithm restricts the parents of each variable to belong to a small subset of candidates. We then search for a network that satisfies these constraints. The learned network is then used for selecting better candidates for the next iteration. We evaluate this algorithm both on synthetic and real-life data. Our results show that it is significantly faster than alternative search procedures without loss of quality in the learned structures.

In recent years there ha-- been significant progress in algorithms and methods for inducing Bayesian networks from data. However, in complex data analysis problems, we need to go beyond being satisfied with inducing networks with high scores. We need to provide confidence measures on features of these networks: Is the existence of an edge between two nodes warranted? Is the Markov blanket of a given node robust? Can we say something about the ordering of the variables? We should be able to address these questions, even when the amount of data is not enough to induce a high scoring network. In this paper we propose Efron's Bootstrap a-- a computationally efficient approach for answering these questions. In addition, we propose to use these confidence measures to induce better structures from the data, and to detect the presence of latent variables.

We present a hybrid constraint-based/Bayesian algorithm for learning causal networks in the presence of sparse data. The algorithm searches the space of equivalence classes of models (essential graphs) using a heuristic based on conventional constraint-based techniques. Each essential graph is then converted into a directed acyclic graph and scored using a Bayesian scoring metric. Two variants of the algorithm are developed and tested using data from randomly generated networks of sizes from 15 to 45 nodes with data sizes ranging from 250 to 2000 records. Both variations are compared to, and found to consistently outperform two variations of greedy search with restarts.

Recent work on loglinear models in probabilistic constraint logic programming is applied to first-order probabilistic reasoning. Probabilities are defined directly on the proofs of atomic formulae, and by marginalisation on the atomic formulae themselves. We use Stochastic Logic Programs (SLPs) composed of labelled and unlabelled definite clauses to define the proof probabilities. We have a conservative extension of first-order reasoning, so that, for example, there is a one-one mapping between logical and random variables. We show how, in this framework, Inductive Logic Programming (ILP) can be used to induce the features of a loglinear model from data. We also compare the presented framework with other approaches to first-order probabilistic reasoning.

This paper describes a Bayesian method for combining an arbitrary mixture of observational and experimental data in order to learn causal Bayesian networks. Observational data are passively observed. Experimental data, such as that produced by randomized controlled trials, result from the experimenter manipulating one or more variables (typically randomly) and observing the states of other variables. The paper presents a Bayesian method for learning the causal structure and parameters of the underlying causal process that is generating the data, given that (1) the data contains a mixture of observational and experimental case records, and (2) the causal process is modeled as a causal Bayesian network. This learning method was applied using as input various mixtures of experimental and observational data that were generated from the ALARM causal Bayesian network. In these experiments, the absolute and relative quantities of experimental and observational data were varied systematically. For each of these training datasets, the learning method was applied to predict the causal structure and to estimate the causal parameters that exist among randomly selected pairs of nodes in ALARM that are not confounded. The paper reports how these structure predictions and parameter estimates compare with the true causal structures and parameters as given by the ALARM network.

In this paper, we empirically evaluate algorithms for learning four types of Bayesian network (BN) classifiers - Naive-Bayes, tree augmented Naive-Bayes, BN augmented Naive-Bayes and general BNs, where the latter two are learned using two variants of a conditional-independence (CI) based BN-learning algorithm. Experimental results show the obtained classifiers, learned using the CI based algorithms, are competitive with (or superior to) the best known classifiers, based on both Bayesian networks and other formalisms; and that the computational time for learning and using these classifiers is relatively small. Moreover, these results also suggest a way to learn yet more effective classifiers; we demonstrate empirically that this new algorithm does work as expected. Collectively, these results argue that BN classifiers deserve more attention in machine learning and data mining communities.

Dynamic Bayesian networks provide a compact and natural representation for complex dynamic systems. However, in many cases, there is no expert available from whom a model can be elicited. Learning provides an alternative approach for constructing models of dynamic systems. In this paper, we address some of the crucial computational aspects of learning the structure of dynamic systems, particularly those where some relevant variables are partially observed or even entirely unknown. Our approach is based on the Structural Expectation Maximization (SEM) algorithm. The main computational cost of the SEM algorithm is the gathering of expected sufficient statistics. We propose a novel approximation scheme that allows these sufficient statistics to be computed efficiently. We also investigate the fundamental problem of discovering the existence of hidden variables without exhaustive and expensive search. Our approach is based on the observation that, in dynamic systems, ignoring a hidden variable typically results in a violation of the Markov property. Thus, our algorithm searches for such violations in the data, and introduces hidden variables to explain them. We provide empirical results showing that the algorithm is able to learn the dynamics of complex systems in a computationally tractable way.

This paper examines the use of Bayesian Networks to tackle one of the tougher problems in requirements engineering, translating user requirements into system requirements. The approach taken is to model domain knowledge as Bayesian Network fragments that are glued together to form a complete view of the domain specific system requirements. User requirements are introduced as evidence and the propagation of belief is used to determine what are the appropriate system requirements as indicated by user requirements. This concept has been demonstrated in the development of a system specification and the results are presented here.

Diagnosis and prediction in some domains, like medical and industrial diagnosis, require a representation that combines uncertainty management and temporal reasoning. Based on the fact that in many cases there are few state changes in the temporal range of interest, we propose a novel representation called Temporal Nodes Bayesian Networks (TNBN). In a TNBN each node represents an event or state change of a variable, and an arc corresponds to a causal-temporal relationship. The temporal intervals can differ in number and size for each temporal node, so this allows multiple granularity. Our approach is contrasted with a dynamic Bayesian network for a simple medical example. An empirical evaluation is presented for a more complex problem, a subsystem of a fossil power plant, in which this approach is used for fault diagnosis and prediction with good results.

Next-generation sequencing technologies provide a revolutionary tool for generating gene expression data. Starting with a fixed RNA sample, they construct a library of millions of differentially abundant short sequence tags or "reads", which constitute a fundamentally discrete measure of the level of gene expression. A common limitation in experiments using these technologies is the low number or even absence of biological replicates, which complicates the statistical analysis of digital gene expression data. Analysis of this type of data has often been based on modified tests originally devised for analysing microarrays; both these and even de novo methods for the analysis of RNA-seq data are plagued by the common problem of low replication. We propose a novel, non-parametric Bayesian approach for the analysis of digital gene expression data. We begin with a hierarchical model for modelling over-dispersed count data and a blocked Gibbs sampling algorithm for inferring the posterior distribution of model parameters conditional on these counts. The algorithm compensates for the problem of low numbers of biological replicates by clustering together genes with tag counts that are likely sampled from a common distribution and using this augmented sample for estimating the parameters of this distribution. The number of clusters is not decided a priori, but it is inferred along with the remaining model parameters. We demonstrate the ability of this approach to model biological data with high fidelity by applying the algorithm on a public dataset obtained from cancerous and non-cancerous neural tissues.