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55
Modelling gene expression data using dynamic bayesian networks
, 1999
"... 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 ..."
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Cited by 170 (1 self)
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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
Causes and explanations: A structuralmodel approach
 In Proceedings IJCAI01
, 2001
"... 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 ..."
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Cited by 134 (10 self)
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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
Scalable Techniques for Mining Causal Structures
 Data Mining and Knowledge Discovery
, 1998
"... 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 ..."
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Cited by 93 (1 self)
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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 largescale data mining applications with a large number of variab...
Axiomatizing causal reasoning
 Uncertainty in Artificial Intelligence
, 1998
"... 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 solutio ..."
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Cited by 70 (5 self)
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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.
Causal Inference from Graphical Models
, 2001
"... 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 ..."
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Cited by 62 (4 self)
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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,
Bayesball: The rational pastime (for determining irrelevance and requisite information in belief networks and influence diagrams
 In Uncertainty in Artificial Intelligence
, 1998
"... 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 d ..."
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Cited by 45 (3 self)
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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 “Bayesball ” algorithm which is wellsuited to both new students of belief networks and state of the art implementations. The Bayesball 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.
Learning Probabilistic Networks
 THE KNOWLEDGE ENGINEERING REVIEW
, 1998
"... 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 combini ..."
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Cited by 41 (2 self)
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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.
DecisionTheoretic Troubleshooting: A Framework for Repair and Experiment
 IN PROCEEDINGS OF THE TWELFTH CONFERENCE ON UNCERTAINTY IN ARTIFICIAL INTELLIGENCE
, 1996
"... We develop and extend existing decisiontheoretic 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 paradi ..."
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Cited by 25 (0 self)
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We develop and extend existing decisiontheoretic 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 beliefnetwork formalism used for probabilistic inference.
Defining Explanation in Probabilistic Systems
 In Proc. UAI97
, 1997
"... 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 ..."
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Cited by 23 (3 self)
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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 Pearland 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...