We describe scoring metrics for learning Bayesian networks from a combination of user knowledge and statistical data. We identify two important properties of metrics, which we call event equivalence and parameter modularity. These properties have been mostly ignored, but when combined, greatly simplify the encoding of a user’s prior knowledge. In particular, a user can express his knowledge—for the most part—as a single prior Bayesian network for the domain. 1

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DNA hybridization arrays simultaneously measure the expression level for thousands of genes. These measurements provide a “snapshot ” of transcription levels within the cell. A major challenge in computational biology is to uncover, from such measurements, gene/protein interactions and key biological features of cellular systems. In this paper, we propose a new framework for discovering interactions between genes based on multiple expression measurements. This framework builds on the use of Bayesian networks for representing statistical dependencies. A Bayesian network is a graph-based model of joint multivariate probability distributions that captures properties of conditional independence between variables. Such models are attractive for their ability to describe complex stochastic processes and because they provide a clear methodology for learning from (noisy) observations. We start by showing how Bayesian networks can describe interactions between genes. We then describe a method for recovering gene interactions from microarray data using tools for learning Bayesian networks. Finally, we demonstrate this method on the S. cerevisiae cell-cycle measurements of Spellman et al. (1998). Key words: gene expression, microarrays, Bayesian methods. 1.

We examine a graphical representation of uncertain knowledge called a Bayesian network. The representation is easy to construct and interpret, yet has formal probabilistic semantics making it suitable for statistical manipulation. We show how we can use the representation to learn new knowledge by combining domain knowledge with statistical data. 1 Introduction Many techniques for learning rely heavily on data. In contrast, the knowledge encoded in expert systems usually comes solely from an expert. In this paper, we examine a knowledge representation, called a Bayesian network, that lets us have the best of both worlds. Namely, the representation allows us to learn new knowledge by combining expert domain knowledge and statistical data. A Bayesian network is a graphical representation of uncertain knowledge that most people find easy to construct and interpret. In addition, the representation has formal probabilistic semantics, making it suitable for statistical manipulation (Howard,...

■ Data mining and knowledge discovery in databases have been attracting a significant amount of research, industry, and media attention of late. What is all the excitement about? This article provides an overview of this emerging field, clarifying how data mining and knowledge discovery in databases are related both to each other and to related fields, such as machine learning, statistics, and databases. The article mentions particular real-world applications, specific data-mining techniques, challenges involved in real-world applications of knowledge discovery, and current and future research directions in the field. Across a wide variety of fields, data are

We discuss Bayesian methods for learning Bayesian networks when data sets are incomplete. In particular, we examine asymptotic approximations for the marginal likelihood of incomplete data given a Bayesian network. We consider the Laplace approximation and the less accurate but more efficient BIC/MDL approximation. We also consider approximations proposed by Draper (1993) and Cheeseman and Stutz (1995). These approximations are as efficient as BIC/MDL, but their accuracy has not been studied in any depth. We compare the accuracy of these approximations under the assumption that the Laplace approximation is the most accurate. In experiments using synthetic data generated from discrete naive-Bayes models having a hidden root node, we find that (1) the BIC/MDL measure is the least accurate, having a bias in favor of simple models, and (2) the Draper and CS measures are the most accurate. 1

Genome-wide expression profiles of genetic mutants provide a wide variety of measurements of cellular responses to perturbations. Typical analysis of such data identifies genes affected by perturbation and uses clustering to group genes of similar function. In this paper we discover a finer structure of interactions between genes, such as causality, mediation, activation, and inhibition by using a Bayesian network framework. We extend this framework to correctly handle perturbations, and to identify significant subnetworks of interacting genes. We apply this method to expression data of S. cerevisiae mutants and uncover a variety of structured metabolic, signaling and regulatory pathways. Contact: danab@cs.huji.ac.il

In this paper we prove the so-called "Meek Conjecture". In particular, we show that if a is an independence map of another DAG then there exists a finite sequence of edge additions and covered edge reversals in such that (1) after each edge modification and (2) after all modifications H.

Approaches to learning Bayesian networks from data typically combine a scoring metric with a heuristic search procedure. Given aBayesian network structure, many of the scoring metrics derived in the literature return a score for the entire equivalence class to which the structure belongs. When using such a metric, it is appropriate for the heuristic search algorithm to searchover equivalence classes of Bayesian networks as opposed to individual structures. We present the general formulation of a search space for which the states of the search correspond to equivalence classes of structures. Using this space, anyoneofanumber of heuristic searchalgorithms can easily be applied. We compare greedy search performance in the proposed search space to greedy search performance in a search space for which the states correspond to individual Bayesian network structures. 1

Machine Learning research has been making great progress in many directions. This article summarizes four of these directions and discusses some current open problems. The four directions are (a) improving classification accuracy by learning ensembles of classifiers, (b) methods for scaling up supervised learning algorithms, (c) reinforcement learning, and (d) learning complex stochastic models.