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132
Using Bayesian networks to analyze expression data
 Journal of Computational Biology
, 2000
"... 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 biologica ..."
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Cited by 912 (17 self)
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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 graphbased 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 cellcycle measurements of Spellman et al. (1998). Key words: gene expression, microarrays, Bayesian methods. 1.
Learning Bayesian belief networks: An approach based on the MDL principle
 Computational Intelligence
, 1994
"... A new approach for learning Bayesian belief networks from raw data is presented. The approach is based on Rissanen's Minimal Description Length (MDL) principle, which is particularly well suited for this task. Our approach does not require any prior assumptions about the distribution being lear ..."
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Cited by 226 (8 self)
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A new approach for learning Bayesian belief networks from raw data is presented. The approach is based on Rissanen's Minimal Description Length (MDL) principle, which is particularly well suited for this task. Our approach does not require any prior assumptions about the distribution being learned. In particular, our method can learn unrestricted multiplyconnected belief networks. Furthermore, unlike other approaches our method allows us to tradeo accuracy and complexity in the learned model. This is important since if the learned model is very complex (highly connected) it can be conceptually and computationally intractable. In such a case it would be preferable to use a simpler model even if it is less accurate. The MDL principle o ers a reasoned method for making this tradeo. We also show that our method generalizes previous approaches based on Kullback crossentropy. Experiments have been conducted to demonstrate the feasibility of the approach. Keywords: Knowledge Acquisition � Bayes Nets � Uncertainty Reasoning. 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 180 (12 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
Healthy, Wealthy, and Wise? Tests for Direct Causal Paths
 Journal of Econometrics
, 2001
"... This paper utilizes the Asset and Health Dynamics of the Oldest Old (AHEAD) Panel to test for the absence of causal links from socioeconomic status (SES) to health innovations and mortality, and from health conditions to innovations in wealth. We conclude that there is no direct causal link from ..."
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Cited by 102 (4 self)
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This paper utilizes the Asset and Health Dynamics of the Oldest Old (AHEAD) Panel to test for the absence of causal links from socioeconomic status (SES) to health innovations and mortality, and from health conditions to innovations in wealth. We conclude that there is no direct causal link from SES to mortality or to incidence of most sudden onset health conditions (accidents and some acute conditions), but there is an association of SES with incidence of gradual onset health conditions (mental conditions, and some degenerative and chronic conditions), due either to causal links or to persistent unobserved behavioral or genetic factors that have a common influence on both SES and innovations in health. We conclude that there is no direct causal link from health status to innovations in wealth.
ANCESTRAL GRAPH MARKOV MODELS
, 2002
"... This paper introduces a class of graphical independence models that is closed under marginalization and conditioning but that contains all DAG independence models. This class of graphs, called maximal ancestral graphs, has two attractive features: there is at most one edge between each pair of verti ..."
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Cited by 95 (18 self)
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This paper introduces a class of graphical independence models that is closed under marginalization and conditioning but that contains all DAG independence models. This class of graphs, called maximal ancestral graphs, has two attractive features: there is at most one edge between each pair of vertices; every missing edge corresponds to an independence relation. These features lead to a simple parameterization of the corresponding set of distributions in the Gaussian case.
Random Algorithms for the Loop Cutset Problem
 Journal of Artificial Intelligence Research
, 1999
"... We show how to find a minimum loop cutset in a Bayesian network with high probability. Finding such a loop cutset is the first step in Pearl's method of conditioning for inference. Our random algorithm for finding a loop cutset, called RepeatedWGuessI, outputs a minimum loop cutset, after ..."
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Cited by 84 (1 self)
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We show how to find a minimum loop cutset in a Bayesian network with high probability. Finding such a loop cutset is the first step in Pearl's method of conditioning for inference. Our random algorithm for finding a loop cutset, called RepeatedWGuessI, outputs a minimum loop cutset, after O(c \Delta 6 k kn) steps, with probability at least 1 \Gamma (1 \Gamma 1 6 k ) c6 k , where c ? 1 is a constant specified by the user, k is the size of a minimum weight loop cutset, and n is the number of vertices. We also show empirically that a variant of this algorithm, called WRA, often finds a loop cutset that is closer to the minimum loop cutset than the ones found by the best deterministic algorithms known. 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 71 (5 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,
Logical and algorithmic properties of conditional independence and graphical models
 THE ANNALS OF STATISTICS
, 1993
"... ..."
dseparation: From theorems to algorithms
 IN UNCERTAINTY IN ARTICIAL INTELLIGENCE 5
, 1990
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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 43 (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.