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Recently, there has been much interest in reverse engineering genetic networks from time series data. In this paper, we show that most of the proposed discrete time models — including the boolean network model [Kau93, SS96], the linear model of D’haeseleer et al. [DWFS99], and the nonlinear model of Weaver et al. [WWS99] — are all special cases of a general class of models called Dynamic Bayesian Networks (DBNs). The advantages of DBNs include the ability to model stochasticity, to incorporate prior knowledge, and to handle hidden variables and missing data in a principled way. This paper provides a review of techniques for learning DBNs. Keywords: Genetic networks, boolean networks, Bayesian networks, neural networks, reverse engineering, machine learning. 1

We propose a new definition of actual causes, using structural equations to model counterfactuals. We show that the definition yields a plausible and elegant account of causation that handles well examples which have caused problems for other definitions

Mining for association rules in market basket data has proved a fruitful area of research. Measures such as conditional probability (confidence) and correlation have been used to infer rules of the form "the existence of item A implies the existence of item B." However, such rules indicate only a statistical relationship between A and B. They do not specify the nature of the relationship: whether the presence of A causes the presence of B, or the converse, or some other attribute or phenomenon causes both to appear together. In applications, knowing such causal relationships is extremely useful for enhancing understanding and effecting change. While distinguishing causality from correlation is a truly difficult problem, recent work in statistics and Bayesian learning provide some avenues of attack. In these fields, the goal has generally been to learn complete causal models, which are essentially impossible to learn in large-scale data mining applications with a large number of variab...

Causal models defined in terms of a collection of equations, as defined by Pearl, are axiomatized here. Axiomatizations are provided for three successively more general classes of causal models: (1) the class of recursive theories (those without feedback), (2) the class of theories where the solutions to the equations are unique, (3) arbitrary theories (where the equations may not have solutions and, if they do, they are not necessarily unique). It is shown that to reason about causality in the most general third class, we must extend the language used by Galles and Pearl (1997, 1998). In addition, the complexity of the decision procedures is characterized for all the languages and classes of models considered. 1. Introduction The important role of causal reasoning---in prediction, explanation, and counterfactual reasoning---has been argued eloquently in a number of recent papers and books (Chajewska & Halpern, 1997; Heckerman & Shachter, 1995; Henrion & Druzdzel, 1990; Druzdz...

Introduction The introduction of Bayesian networks (Pearl 1986b) and associated local computation algorithms (Lauritzen and Spiegelhalter 1988, Shenoy and Shafer 1990, Jensen, Lauritzen and Olesen 1990) has initiated a renewed interest for understanding causal concepts in connection with modelling complex stochastic systems. It has become clear that graphical models, in particular those based upon directed acyclic graphs, have natural causal interpretations and thus form a base for a language in which causal concepts can be discussed and analysed in precise terms. As a consequence there has been an explosion of writings, not primarily within mainstream statistical literature, concerned with the exploitation of this language to clarify and extend causal concepts. Among these we mention in particular books by Spirtes, Glymour and Scheines (1993), Shafer (1996), and Pearl (2000) as well as the collection of papers in Glymour and Cooper (1999). Very briefly, but fundamentally,

One of the benefits of belief networks and influence diagrams is that so much knowledge is captured in the graphical structure. In particular, statements of conditional irrelevance (or independence) can be verified in time linear in the size of the graph. To resolve a particular inference query or decision problem, only some of the possible states and probability distributions must be specified, the“requisite information.” This paper presents a new, simple, and efficient “Bayes-ball ” algorithm which is wellsuited to both new students of belief networks and state of the art implementations. The Bayes-ball algorithm determines irrelevant sets and requisite information more efficiently than existing methods, and is linear in the size of the graph for belief networks and influence diagrams.

A probabilistic network is a graphical model that encodes probabilistic relationships between variables of interest. Such a model records qualitative influences between variables in addition to the numerical parameters of the probability distribution. As such it provides an ideal form for combining prior knowledge, which might be limited solely to experience of the influences between some of the variables of interest, and data. In this paper, we first show how data can be used to revise initial estimates of the parameters of a model. We then progress to showing how the structure of the model can be revised as data is obtained. Techniques for learning with incomplete data are also covered.

As probabilistic systems gain popularity and are coming into wider use, the need for a mechanism that explains the system's findings and recommendations becomes more critical. The system will also need a mechanism for ordering competing explanations. We examine two representative approaches to explanation in the literature--- one due to G ardenfors and one due to Pearl---and show that both suffer from significant problems. We propose an approach to defining a notion of "better explanation" that combines some of the features of both together with more recent work by Pearl and others on causality. 1 INTRODUCTION Probabilistic inference is often hard for humans to understand. Even a simple inference in a small domain may seem counterintuitive and surprising; the situation only gets worse for large and complex domains. Thus, a system doing probabilistic inference must be able to explain its findings and recommendations to evoke confidence on the part of the user. Indeed, in experiments wi...

We develop and extend existing decision-theoretic methods for troubleshooting a nonfunctioning device. Traditionally, diagnosis with Bayesian networks has focused on belief updating -- determining the probabilities of various faults given current observations. In this paper, we extend this paradigm to include taking actions. In particular, we consider three classes of actions: (1) we can make observations regarding the behavior of a device and infer likely faults as in traditional diagnosis, (2) we can repair a component and then observe the behavior of the device to infer likely faults, and (3) we can change the configuration of the device, observe its new behavior, and infer the likelihood of faults. Analysis of latter two classes of troubleshooting actions requires incorporating notions of persistence into the belief-network formalism used for probabilistic inference.