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134
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.
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 564 (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.
Efficient approximations for the marginal likelihood of Bayesian networks with hidden variables
 Machine Learning
, 1997
"... We discuss Bayesian methods for learning Bayesian networks when data sets are incomplete. In particular, we examine asymptotic approximations for the marginal likelihood of incomplete data given a Bayesian network. We consider the Laplace approximation and the less accurate but more efficient BIC/MD ..."
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Cited by 178 (10 self)
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We discuss Bayesian methods for learning Bayesian networks when data sets are incomplete. In particular, we examine asymptotic approximations for the marginal likelihood of incomplete data given a Bayesian network. We consider the Laplace approximation and the less accurate but more efficient BIC/MDL approximation. We also consider approximations proposed by Draper (1993) and Cheeseman and Stutz (1995). These approximations are as efficient as BIC/MDL, but their accuracy has not been studied in any depth. We compare the accuracy of these approximations under the assumption that the Laplace approximation is the most accurate. In experiments using synthetic data generated from discrete naiveBayes models having a hidden root node, we find that (1) the BIC/MDL measure is the least accurate, having a bias in favor of simple models, and (2) the Draper and CS measures are the most accurate. 1
A Guide to the Literature on Learning Probabilistic Networks From Data
, 1996
"... This literature review discusses different methods under the general rubric of learning Bayesian networks from data, and includes some overlapping work on more general probabilistic networks. Connections are drawn between the statistical, neural network, and uncertainty communities, and between the ..."
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Cited by 172 (0 self)
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This literature review discusses different methods under the general rubric of learning Bayesian networks from data, and includes some overlapping work on more general probabilistic networks. Connections are drawn between the statistical, neural network, and uncertainty communities, and between the different methodological communities, such as Bayesian, description length, and classical statistics. Basic concepts for learning and Bayesian networks are introduced and methods are then reviewed. Methods are discussed for learning parameters of a probabilistic network, for learning the structure, and for learning hidden variables. The presentation avoids formal definitions and theorems, as these are plentiful in the literature, and instead illustrates key concepts with simplified examples. Keywords Bayesian networks, graphical models, hidden variables, learning, learning structure, probabilistic networks, knowledge discovery. I. Introduction Probabilistic networks or probabilistic gra...
Probabilistic independence networks for hidden Markov probability models
, 1996
"... Graphical techniques for modeling the dependencies of random variables have been explored in a variety of different areas including statistics, statistical physics, artificial intelligence, speech recognition, image processing, and genetics. Formalisms for manipulating these models have been develop ..."
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Cited by 167 (12 self)
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Graphical techniques for modeling the dependencies of random variables have been explored in a variety of different areas including statistics, statistical physics, artificial intelligence, speech recognition, image processing, and genetics. Formalisms for manipulating these models have been developed relatively independently in these research communities. In this paper we explore hidden Markov models (HMMs) and related structures within the general framework of probabilistic independence networks (PINs). The paper contains a selfcontained review of the basic principles of PINs. It is shown that the wellknown forwardbackward (FB) and Viterbi algorithms for HMMs are special cases of more general inference algorithms for arbitrary PINs. Furthermore, the existence of inference and estimation algorithms for more general graphical models provides a set of analysis tools for HMM practitioners who wish to explore a richer class of HMM structures. Examples of relatively complex models to handle sensor fusion and coarticulation in speech recognition are introduced and treated within the graphical model framework to illustrate the advantages of the general approach.
Stochastic simulation algorithms for dynamic probabilistic networks
, 1995
"... Stochastic simulation algorithms such as likelihood weighting often give fast, accurate approximations to posterior probabilities in probabilistic networks, and are the methods of choice for very large networks. Unfortunately, the special characteristics of dynamic probabilistic networks (DPNs), whi ..."
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Cited by 151 (11 self)
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Stochastic simulation algorithms such as likelihood weighting often give fast, accurate approximations to posterior probabilities in probabilistic networks, and are the methods of choice for very large networks. Unfortunately, the special characteristics of dynamic probabilistic networks (DPNs), which are used to represent stochastic temporal processes, mean that standard simulation algorithms perform very poorly. In essence, the simulation trials diverge further and further from reality as the process is observed over time. In this paper, we present simulation algorithms that use the evidence observed at each time step to push the set of trials back towards reality. The first algorithm, "evidence reversal " (ER) restructures each time slice of the DPN so that the evidence nodes for the slice become ancestors of the state variables. The second algorithm, called "survival of the fittest " sampling (SOF), "repopulates " the set of trials at each time step using a stochastic reproduction rate weighted by the likelihood of the evidence according to each trial. We compare the performance of each algorithm with likelihood weighting on the original network, and also investigate the benefits of combining the ER and SOF methods. The ER/SOF combination appears to maintain bounded error independent of the number of time steps in the simulation.
Propagation of Probabilities, Means and Variances in Mixed Graphical Association Models
 Journal of the American Statistical Association
, 1992
"... A scheme is presented for modelling and local computation of exact probabilities, means and variances for mixed qualitative and quantitative variables. The models assume that the conditional distribution of the quantitative variables, given the qualitative, is multivariate Gaussian. The computationa ..."
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Cited by 143 (2 self)
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A scheme is presented for modelling and local computation of exact probabilities, means and variances for mixed qualitative and quantitative variables. The models assume that the conditional distribution of the quantitative variables, given the qualitative, is multivariate Gaussian. The computational architecture is set up by forming a tree of belief universes, and the calculations are then performed by local message passing between universes. The asymmetry between the quantitative and qualitative variables sets some additional limitations for the specification and propagation structure. Approximate methods when these are not appropriately fulfilled are sketched. Lauritzen and Spiegelhalter (1988) showed how to exploit the local structure in the specification of a discrete probability model for fast and efficient computation, thereby paving the way for exploiting probability based models as parts of realistic systems for planning and decision support. The technique was subsequently imp...
A characterization of Markov equivalence classes for acyclic digraphs
, 1995
"... Undirected graphs and acyclic digraphs (ADGs), as well as their mutual extension to chain graphs, are widely used to describe dependencies among variables in multivariate distributions. In particular, the likelihood functions of ADG models admit convenient recursive factorizations that often allow e ..."
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Cited by 92 (7 self)
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Undirected graphs and acyclic digraphs (ADGs), as well as their mutual extension to chain graphs, are widely used to describe dependencies among variables in multivariate distributions. In particular, the likelihood functions of ADG models admit convenient recursive factorizations that often allow explicit maximum likelihood estimates and that are well suited to building Bayesian networks for expert systems. Whereas the undirected graph associated with a dependence model is uniquely determined, there may, however, be many ADGs that determine the same dependence ( = Markov) model. Thus, the family of all ADGs with a given set of vertices is naturally partitioned into Markovequivalence classes, each class being associated with a unique statistical model. Statistical procedures, such as model selection or model averaging, that fail to take into account these equivalence classes, may incur substantial computational or other inefficiencies. Here it is shown that each Markovequivalence class is uniquely determined by a single chain graph, the essential graph, that is itself simultaneously Markov equivalent to all ADGs in the equivalence class. Essential graphs are characterized, a polynomialtime algorithm for their construction is given, and their applications to model selection and other statistical
Construction of Bayesian Network Structures From Data: A Brief Survey and an Efficient Algorithm
, 1995
"... Previous algorithms for the recovery of Bayesian belief network structures from data have been either highly dependent on conditional independence (CI) tests, or have required on ordering on the nodes to be supplied by the user. We present an algorithm that integrates these two approaches: CI tests ..."
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Cited by 77 (8 self)
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Previous algorithms for the recovery of Bayesian belief network structures from data have been either highly dependent on conditional independence (CI) tests, or have required on ordering on the nodes to be supplied by the user. We present an algorithm that integrates these two approaches: CI tests are used to generate an ordering on the nodes from the database, which is then used to recover the underlying Bayesian network structure using a nonCltestbased method. Results of the evaluation of the algorithm on a number of databases (e.g., ALARM, LED, and SOYBEAN) are presented. We also discuss some algorithm performance issues and open problems.