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Dynamic Bayesian Networks: Representation, Inference and Learning
, 2002
"... Modelling sequential data is important in many areas of science and engineering. Hidden Markov models (HMMs) and Kalman filter models (KFMs) are popular for this because they are simple and flexible. For example, HMMs have been used for speech recognition and biosequence analysis, and KFMs have bee ..."
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Cited by 770 (3 self)
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Modelling sequential data is important in many areas of science and engineering. Hidden Markov models (HMMs) and Kalman filter models (KFMs) are popular for this because they are simple and flexible. For example, HMMs have been used for speech recognition and biosequence analysis, and KFMs have been used for problems ranging from tracking planes and missiles to predicting the economy. However, HMMs
and KFMs are limited in their “expressive power”. Dynamic Bayesian Networks (DBNs) generalize HMMs by allowing the state space to be represented in factored form, instead of as a single discrete random variable. DBNs generalize KFMs by allowing arbitrary probability distributions, not just (unimodal) linearGaussian. In this thesis, I will discuss how to represent many different kinds of models as DBNs, how to perform exact and approximate inference in DBNs, and how to learn DBN models from sequential data.
In particular, the main novel technical contributions of this thesis are as follows: a way of representing
Hierarchical HMMs as DBNs, which enables inference to be done in O(T) time instead of O(T 3), where T is the length of the sequence; an exact smoothing algorithm that takes O(log T) space instead of O(T); a simple way of using the junction tree algorithm for online inference in DBNs; new complexity bounds on exact online inference in DBNs; a new deterministic approximate inference algorithm called factored frontier; an analysis of the relationship between the BK algorithm and loopy belief propagation; a way of
applying RaoBlackwellised particle filtering to DBNs in general, and the SLAM (simultaneous localization
and mapping) problem in particular; a way of extending the structural EM algorithm to DBNs; and a variety of different applications of DBNs. However, perhaps the main value of the thesis is its catholic presentation of the field of sequential data modelling.
Mediation in experimental and nonexperimental studies: new procedures and recommendations
 PSYCHOLOGICAL METHODS
, 2002
"... Mediation is said to occur when a causal effect of some variable X on an outcome Y is explained by some intervening variable M. The authors recommend that with small to moderate samples, bootstrap methods (B. Efron & R. Tibshirani, 1993) be used to assess mediation. Bootstrap tests are powerful ..."
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Cited by 696 (4 self)
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Mediation is said to occur when a causal effect of some variable X on an outcome Y is explained by some intervening variable M. The authors recommend that with small to moderate samples, bootstrap methods (B. Efron & R. Tibshirani, 1993) be used to assess mediation. Bootstrap tests are powerful because they detect that the sampling distribution of the mediated effect is skewed away from 0. They argue that R. M. Baron and D. A. Kenny’s (1986) recommendation of first testing the X → Y association for statistical significance should not be a requirement when there is a priori belief that the effect size is small or suppression is a possibility. Empirical examples and computer setups for bootstrap analyses are provided. Mediation models of psychological processes are popular because they allow interesting associations to be decomposed into components that reveal possible causal mechanisms. These models are useful for theory development and testing as well as for the identification of possible points of intervention in applied work. Mediation is equally of interest to experimental psychologists as it is to those who study naturally occurring processes through nonexperimental studies. For example, social–cognitive psychologists are interested in showing that the effects of cognitive priming on attitude change are mediated by the accessibility of certain beliefs (Eagly & Chaiken, 1993). Developmental psychologists use longitudinal methods to study how parental unemployment can have adverse effects on child behavior through its intervening effect on quality of parenting (Conger et al., 1990). Mediation analysis is also used in organizational
The Nature of Theory in Information Systems
 MIS Quarterly
, 2006
"... The aim of this research essay is to examine the structural nature of theory in information systems. Despite the importance of theory, questions relating to its form and structure are neglected in comparison with questions relating to epistemology. The essay addresses issues of causality, explanatio ..."
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Cited by 289 (6 self)
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The aim of this research essay is to examine the structural nature of theory in information systems. Despite the importance of theory, questions relating to its form and structure are neglected in comparison with questions relating to epistemology. The essay addresses issues of causality, explanation, prediction and generalization that underlie an understanding of theory. A taxonomy is proposed that classifies information systems theories with respect to the manner in which four central goals are addressed: analysis, explanation, prediction and prescription. Five interrelated types of theory are distinguished: (i) theory for analysing; (ii) theory for explaining, (iii) theory for predicting; (iv) theory for explaining and predicting; and (v) theory for design and action. Examples illustrate the nature of each theory type. The applicability of the taxonomy is demonstrated by classifying a sample of journal articles. The paper contributes by showing that multiple views of theory exist and by exposing the assumptions underlying different viewpoints. In addition, it is suggested that the type of theory under development can influence the choice of an epistemological approach. Support is given for the legitimacy and value of each theory type. The building of integrated bodies of theory that encompass all theory types is advocated.
The Bayes Net Toolbox for MATLAB
 Computing Science and Statistics
, 2001
"... The Bayes Net Toolbox (BNT) is an opensource Matlab package for directed graphical models. BNT supports many kinds of nodes (probability distributions), exact and approximate inference, parameter and structure learning, and static and dynamic models. BNT is widely used in teaching and research: the ..."
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Cited by 250 (1 self)
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The Bayes Net Toolbox (BNT) is an opensource Matlab package for directed graphical models. BNT supports many kinds of nodes (probability distributions), exact and approximate inference, parameter and structure learning, and static and dynamic models. BNT is widely used in teaching and research: the web page has received over 28,000 hits since May 2000. In this paper, we discuss a broad spectrum of issues related to graphical models (directed and undirected), and describe, at a highlevel, how BNT was designed to cope with them all. We also compare BNT to other software packages for graphical models, and to the nascent OpenBayes effort.
Principles and practice in reporting structural equation analyses
 PSYCHOLOGICAL METHODS
, 2002
"... Principles for reporting analyses using structural equation modeling are reviewed, with the goal of supplying readers with complete and accurate information. It is recommended that every report give a detailed justification of the model used, along with plausible alternatives and an account of ident ..."
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Cited by 235 (1 self)
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Principles for reporting analyses using structural equation modeling are reviewed, with the goal of supplying readers with complete and accurate information. It is recommended that every report give a detailed justification of the model used, along with plausible alternatives and an account of identifiability. Nonnormality and missing data problems should also be addressed. A complete set of parameters and their standard errors is desirable, and it will often be convenient to supply the correlation matrix and discrepancies, as well as goodnessoffit indices, so that readers can exercise independent critical judgment. A survey of fairly representative studies compares recent practice with the principles of reporting recommended here.
Inferring Subnetworks from Perturbed Expression Profiles
, 2001
"... Genomewide 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 structur ..."
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Cited by 204 (14 self)
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Genomewide 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
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 201 (14 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
The maxmin hillclimbing Bayesian network structure learning algorithm
, 2006
"... We present a new algorithm for Bayesian network structure learning, called MaxMin HillClimbing (MMHC). The algorithm combines ideas from local learning, constraintbased, and searchandscore techniques in a principled and effective way. It first reconstructs the skeleton of a Bayesian network a ..."
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Cited by 156 (8 self)
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We present a new algorithm for Bayesian network structure learning, called MaxMin HillClimbing (MMHC). The algorithm combines ideas from local learning, constraintbased, and searchandscore techniques in a principled and effective way. It first reconstructs the skeleton of a Bayesian network and then performs a Bayesianscoring greedy hillclimbing search to orient the edges. In our extensive empirical evaluation MMHC outperforms on average and in terms of various metrics several prototypical and stateoftheart
Structure and Strength in Causal Induction
"... We present a framework for the rational analysis of elemental causal induction – learning about the existence of a relationship between a single cause and effect – based upon causal graphical models. This framework makes precise the distinction between causal structure and causal strength: the diffe ..."
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Cited by 156 (36 self)
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We present a framework for the rational analysis of elemental causal induction – learning about the existence of a relationship between a single cause and effect – based upon causal graphical models. This framework makes precise the distinction between causal structure and causal strength: the difference between asking whether a causal relationship exists and asking how strong that causal relationship might be. We show that two leading rational models of elemental causal induction, ∆P and causal power, both estimate causal strength, and introduce a new rational model, causal support, that assesses causal structure. Causal support predicts several key phenomena of causal induction that cannot be accounted for by other rational models, which we explore through a series of experiments. These phenomena include the complex interaction between ∆P and the baserate probability of the effect in the absence of the cause, sample size effects, inferences from incomplete contingency tables, and causal learning from rates. Causal support also provides a better account of a number of existing datasets than either ∆P or causal power.