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228
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 1088 (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 graph-based 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 cell-cycle measurements of Spellman et al. (1998). Key words: gene expression, microarrays, Bayesian methods. 1.
Bayesian Network Classifiers
, 1997
"... Recent work in supervised learning has shown that a surprisingly simple Bayesian classifier with strong assumptions of independence among features, called naive Bayes, is competitive with state-of-the-art classifiers such as C4.5. This fact raises the question of whether a classifier with less restr ..."
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Cited by 796 (20 self)
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Recent work in supervised learning has shown that a surprisingly simple Bayesian classifier with strong assumptions of independence among features, called naive Bayes, is competitive with state-of-the-art classifiers such as C4.5. This fact raises the question of whether a classifier with less restrictive assumptions can perform even better. In this paper we evaluate approaches for inducing classifiers from data, based on the theory of learning Bayesian networks. These networks are factored representations of probability distributions that generalize the naive Bayesian classifier and explicitly represent statements about independence. Among these approaches we single out a method we call Tree Augmented Naive Bayes (TAN), which outperforms naive Bayes, yet at the same time maintains the computational simplicity (no search involved) and robustness that characterize naive Bayes. We experimentally tested these approaches, using problems from the University of California at Irvine repository, and compared them to C4.5, naive Bayes, and wrapper methods for feature selection.
Hierarchically Classifying Documents Using Very Few Words
, 1997
"... The proliferation of topic hierarchies for text documents has resulted in a need for tools that automatically classify new documents within such hierarchies. Existing classification schemes which ignore the hierarchical structure and treat the topics as separate classes are often inadequate in text ..."
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Cited by 521 (8 self)
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The proliferation of topic hierarchies for text documents has resulted in a need for tools that automatically classify new documents within such hierarchies. Existing classification schemes which ignore the hierarchical structure and treat the topics as separate classes are often inadequate in text classification where the there is a large number of classes and a huge number of relevant features needed to distinguish between them. We propose an approach that utilizes the hierarchical topic structure to decompose the classification task into a set of simpler problems, one at each node in the classification tree. As we show, each of these smaller problems can be solved accurately by focusing only on a very small set of features, those relevant to the task at hand. This set of relevant features varies widely throughout the hierarchy, so that, while the overall relevant feature set may be large, each classifier only examines a small subset. The use of reduced feature sets allows us to util...
Probabilistic Boolean networks: a rule-based uncertainty model for gene regulatory networks
, 2002
"... Motivation: Our goal is to construct a model for genetic regulatory networks such that the model class: (i ) incorporates rule-based dependencies between genes; (ii ) allows the systematic study of global network dynamics; (iii ) is able to cope with uncertainty, both in the data and the model selec ..."
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Cited by 391 (59 self)
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Motivation: Our goal is to construct a model for genetic regulatory networks such that the model class: (i ) incorporates rule-based dependencies between genes; (ii ) allows the systematic study of global network dynamics; (iii ) is able to cope with uncertainty, both in the data and the model selection; and (iv ) permits the quantification of the relative influence and sensitivity of genes in their interactions with other genes.
Learning Bayesian Networks With Local Structure
, 1996
"... . We examine a novel addition to the known methods for learning Bayesian networks from data that improves the quality of the learned networks. Our approach explicitly represents and learns the local structure in the conditional probability distributions (CPDs) that quantify these networks. This inc ..."
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Cited by 272 (12 self)
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. We examine a novel addition to the known methods for learning Bayesian networks from data that improves the quality of the learned networks. Our approach explicitly represents and learns the local structure in the conditional probability distributions (CPDs) that quantify these networks. This increases the space of possible models, enabling the representation of CPDs with a variable number of parameters. The resulting learning procedure induces models that better emulate the interactions present in the data. We describe the theoretical foundations and practical aspects of learning local structures and provide an empirical evaluation of the proposed learning procedure. This evaluation indicates that learning curves characterizing this procedure converge faster, in the number of training instances, than those of the standard procedure, which ignores the local structure of the CPDs. Our results also show that networks learned with local structures tend to be more complex (in terms of a...
Optimal Structure Identification with Greedy Search
, 2002
"... In this paper we prove the so-called "Meek Conjecture". In particular, we show that if a is an independence map of another DAG then there exists a finite sequence of edge additions and covered edge reversals in such that (1) after each edge modification and (2) after all mod ..."
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Cited by 249 (1 self)
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In this paper we prove the so-called "Meek Conjecture". In particular, we show that if a is an independence map of another DAG then there exists a finite sequence of edge additions and covered edge reversals in such that (1) after each edge modification and (2) after all modifications H.
Learning Bayesian network structure from massive datasets: the “sparse candidate” algorithm
- In Proceedings of the 15th Conference on Uncertainty in Artificial Intelligence (UAI
, 1999
"... Learning Bayesian networks is often cast as an optimization problem, where the computational task is to find a structure that maximizes a sta-tistically motivated score. By and large, existing learning tools address this optimization problem using standard heuristic search techniques. Since the sear ..."
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Cited by 247 (7 self)
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Learning Bayesian networks is often cast as an optimization problem, where the computational task is to find a structure that maximizes a sta-tistically motivated score. By and large, existing learning tools address this optimization problem using standard heuristic search techniques. Since the search space is extremely large, such search procedures can spend most of the time examining candidates that are extremely unreasonable. This problem becomes critical when we deal with data sets that are large either in the number of in-stances, or the number of attributes. In this paper, we introduce an algorithm that achieves faster learning by restricting the search space. This iterative algorithm restricts the par-ents of each variable to belong to a small sub-set of candidates. We then search for a network that satisfies these constraints. The learned net-work is then used for selecting better candidates for the next iteration. We evaluate this algorithm both on synthetic and real-life data. Our results show that it is significantly faster than alternative search procedures without loss of quality in the learned structures. 1
Learning Bayesian Networks is NP-Hard
, 1994
"... Algorithms for learning Bayesian networks from data have two components: a scoring metric and a search procedure. The scoring metric computes a score reflecting the goodness-of-fit of the structure to the data. The search procedure tries to identify network structures with high scores. Heckerman et ..."
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Cited by 194 (2 self)
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Algorithms for learning Bayesian networks from data have two components: a scoring metric and a search procedure. The scoring metric computes a score reflecting the goodness-of-fit of the structure to the data. The search procedure tries to identify network structures with high scores. Heckerman et al. (1994) introduced a Bayesian metric, called the BDe metric, that computes the relative posterior probability of a network structure given data. They show that the metric has a property desireable for inferring causal structure from data. In this paper, we show that the problem of deciding whether there is a Bayesian network---among those where each node has at most k parents---that has a relative posterior probability greater than a given constant is NP-complete, when the BDe metric is used. 1 Introduction Recently, many researchers have begun to investigate methods for learning Bayesian networks, including Bayesian methods [Cooper and Herskovits, 1991, Buntine, 1991, York 1992, Spiegel...
A Bayesian approach to learning Bayesian networks with local structure
- In Proceedings of Thirteenth Conference on Uncertainty in Artificial Intelligence
, 1997
"... Recently several researchers have investigated techniques for using data to learn Bayesian networks containing compact representations for the conditional probability distributions (CPDs) stored at each node. The majority of this work has concentrated on using decision-tree representations for the C ..."
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Cited by 191 (18 self)
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Recently several researchers have investigated techniques for using data to learn Bayesian networks containing compact representations for the conditional probability distributions (CPDs) stored at each node. The majority of this work has concentrated on using decision-tree representations for the CPDs. In addition, researchers typically apply non-Bayesian (or asymptotically Bayesian) scoring functions such as MDL to evaluate the goodness-of-fit of networks to the data. In this paper we investigate a Bayesian approach to learning Bayesian networks that contain the more general decision-graph representations of the CPDs. First, we describe how to evaluate the posterior probability— that is, the Bayesian score—of such a network, given a database of observed cases. Second, we describe various search spaces that can be used, in conjunction with a scoring function and a search procedure, to identify one or more high-scoring networks. Finally, we present an experimental evaluation of the search spaces, using a greedy algorithm and a Bayesian scoring function. 1
Learning Equivalence Classes Of Bayesian Network Structures
, 1996
"... Approaches to learning Bayesian networks from data typically combine a scoring metric with a heuristic search procedure. Given aBayesian network structure, many of the scoring metrics derived in the literature return a score for the entire equivalence class to which the structure belongs. When ..."
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Cited by 176 (1 self)
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Approaches to learning Bayesian networks from data typically combine a scoring metric with a heuristic search procedure. Given aBayesian network structure, many of the scoring metrics derived in the literature return a score for the entire equivalence class to which the structure belongs. When using such a metric, it is appropriate for the heuristic search algorithm to searchover equivalence classes of Bayesian networks as opposed to individual structures. We present the general formulation of a search space for which the states of the search correspond to equivalence classes of structures. Using this space, anyoneofanumber of heuristic searchalgorithms can easily be applied. We compare greedy search performance in the proposed search space to greedy search performance in a search space for which the states correspond to individual Bayesian network structures. 1
