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64
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 731 (16 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.
Being Bayesian about network structure
 Machine Learning
, 2000
"... Abstract. In many multivariate domains, we are interested in analyzing the dependency structure of the underlying distribution, e.g., whether two variables are in direct interaction. We can represent dependency structures using Bayesian network models. To analyze a given data set, Bayesian model sel ..."
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Cited by 202 (5 self)
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Abstract. In many multivariate domains, we are interested in analyzing the dependency structure of the underlying distribution, e.g., whether two variables are in direct interaction. We can represent dependency structures using Bayesian network models. To analyze a given data set, Bayesian model selection attempts to find the most likely (MAP) model, and uses its structure to answer these questions. However, when the amount of available data is modest, there might be many models that have nonnegligible posterior. Thus, we want compute the Bayesian posterior of a feature, i.e., the total posterior probability of all models that contain it. In this paper, we propose a new approach for this task. We first show how to efficiently compute a sum over the exponential number of networks that are consistent with a fixed order over network variables. This allows us to compute, for a given order, both the marginal probability of the data and the posterior of a feature. We then use this result as the basis for an algorithm that approximates the Bayesian posterior of a feature. Our approach uses a Markov Chain Monte Carlo (MCMC) method, but over orders rather than over network structures. The space of orders is smaller and more regular than the space of structures, and has much a smoother posterior “landscape”. We present empirical results on synthetic and reallife datasets that compare our approach to full model averaging (when possible), to MCMC over network structures, and to a nonBayesian bootstrap approach.
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 157 (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
A theory of causal learning in children: Causal maps and Bayes nets
 PSYCHOLOGICAL REVIEW
, 2004
"... The authors outline a cognitive and computational account of causal learning in children. They propose that children use specialized cognitive systems that allow them to recover an accurate “causal map ” of the world: an abstract, coherent, learned representation of the causal relations among events ..."
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Cited by 157 (33 self)
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The authors outline a cognitive and computational account of causal learning in children. They propose that children use specialized cognitive systems that allow them to recover an accurate “causal map ” of the world: an abstract, coherent, learned representation of the causal relations among events. This kind of knowledge can be perspicuously understood in terms of the formalism of directed graphical causal models, or Bayes nets. Children’s causal learning and inference may involve computations similar to those for learning causal Bayes nets and for predicting with them. Experimental results suggest that 2to 4yearold children construct new causal maps and that their learning is consistent with the Bayes net formalism.
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 only a st ..."
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Cited by 88 (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...
Comparing Bayesian Network Classifiers
, 1999
"... In this paper, we empirically evaluate algorithms for learning four types of Bayesian network (BN) classifiers  NaïveBayes, tree augmented NaïveBayes, BN augmented NaïveBayes and general BNs, where the latter two are learned using two variants of a conditionalindependence (CI) based BNlearnin ..."
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Cited by 78 (6 self)
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In this paper, we empirically evaluate algorithms for learning four types of Bayesian network (BN) classifiers  NaïveBayes, tree augmented NaïveBayes, BN augmented NaïveBayes and general BNs, where the latter two are learned using two variants of a conditionalindependence (CI) based BNlearning algorithm. Experimental results show the obtained classifiers, learned using the CI based algorithms, are competitive with (or superior to) the best known classifiers, based on both Bayesian networks and other formalisms; and that the computational time for learning and using these classifiers is relatively small. Moreover, these results also suggest a way to learn yet more effective classifiers; we demonstrate empirically that this new algorithm does work as expected. Collectively, these results argue that BN classifiers deserve more attention in machine learning and data mining communities. 1 INTRODUCTION Many tasks  including fault diagnosis, pattern recognition and forecasting  c...
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 59 (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,
Learning Bayesian Belief Network Classifiers: Algorithms and System
 Proceedings of 14 th Biennial conference of the
, 2001
"... This paper investigates the methods for learning predictive classifiers based on Bayesian belief networks (BN)  primarily unrestricted Bayesian networks and Bayesian multinets. We present our algorithms for learning these classifiers, and discuss how these methods address the overfitting proble ..."
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Cited by 59 (4 self)
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This paper investigates the methods for learning predictive classifiers based on Bayesian belief networks (BN)  primarily unrestricted Bayesian networks and Bayesian multinets. We present our algorithms for learning these classifiers, and discuss how these methods address the overfitting problem and provide a natural method for feature subset selection. Using a set of standard classification problems, we empirically evaluate the performance of various BNbased classifiers. The results show that the proposed BN and Bayes multinet classifiers are competitive with (or superior to) the best known classifiers, based on both BN and other formalisms; and that the computational time for learning and using these classifiers is relatively small. These results argue that BN based classifiers deserve more attention in the data mining community. 1 In t roduct i on Many tasks  including fault diagnosis, pattern recognition and forecasting  can be viewed as classification, as each r...
Active Learning for Structure in Bayesian Networks
 IN INTERNATIONAL JOINT CONFERENCE ON ARTIFICIAL INTELLIGENCE
, 2001
"... The task of causal structure discovery from empirical data is a fundamental problem in many areas. Experimental data is crucial for accomplishing this task. However, experiments are typically expensive, and must be selected with great care. This paper ..."
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Cited by 56 (2 self)
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The task of causal structure discovery from empirical data is a fundamental problem in many areas. Experimental data is crucial for accomplishing this task. However, experiments are typically expensive, and must be selected with great care. This paper
Exact Bayesian structure discovery in Bayesian networks
 J. of Machine Learning Research
, 2004
"... We consider a Bayesian method for learning the Bayesian network structure from complete data. Recently, Koivisto and Sood (2004) presented an algorithm that for any single edge computes its marginal posterior probability in O(n2 n) time, where n is the number of attributes; the number of parents per ..."
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Cited by 55 (8 self)
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We consider a Bayesian method for learning the Bayesian network structure from complete data. Recently, Koivisto and Sood (2004) presented an algorithm that for any single edge computes its marginal posterior probability in O(n2 n) time, where n is the number of attributes; the number of parents per attribute is bounded by a constant. In this paper we show that the posterior probabilities for all the n(n−1) potential edges can be computed in O(n2 n) total time. This result is achieved by a forward–backward technique and fast Möbius transform algorithms, which are of independent interest. The resulting speedup by a factor of about n 2 allows us to experimentally study the statistical power of learning moderatesize networks. We report results from a simulation study that covers data sets with 20 to 10,000 records over 5 to 25 discrete attributes. 1