Results 1  10
of
39
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 ..."
Abstract

Cited by 201 (5 self)
 Add to MetaCart
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.
On Differential Variability of Expression Ratios: Improving . . .
 JOURNAL OF COMPUTATIONAL BIOLOGY
, 2001
"... We consider the problem of inferring fold changes in gene expression from cDNA microarray data. Standard procedures focus on the ratio of measured fluorescent intensities at each spot on the microarray, but to do so is to ignore the fact that the variation of such ratios is not constant. Estimates o ..."
Abstract

Cited by 165 (5 self)
 Add to MetaCart
We consider the problem of inferring fold changes in gene expression from cDNA microarray data. Standard procedures focus on the ratio of measured fluorescent intensities at each spot on the microarray, but to do so is to ignore the fact that the variation of such ratios is not constant. Estimates of gene expression changes are derived within a simple hierarchical model that accounts for measurement error and fluctuations in absolute gene expression levels. Significant gene expression changes are identified by deriving the posterior odds of change within a similar model. The methods are tested via simulation and are applied to a panel of Escherichia coli microarrays.
ModelBased Clustering and Data Transformations for Gene Expression Data
, 2001
"... Motivation: Clustering is a useful exploratory technique for the analysis of gene expression data. Many different heuristic clustering algorithms have been proposed in this context. Clustering algorithms based on probability models offer a principled alternative to heuristic algorithms. In particula ..."
Abstract

Cited by 124 (8 self)
 Add to MetaCart
Motivation: Clustering is a useful exploratory technique for the analysis of gene expression data. Many different heuristic clustering algorithms have been proposed in this context. Clustering algorithms based on probability models offer a principled alternative to heuristic algorithms. In particular, modelbased clustering assumes that the data is generated by a finite mixture of underlying probability distributions such as multivariate normal distributions. The issues of selecting a 'good' clustering method and determining the 'correct' number of clusters are reduced to model selection problems in the probability framework. Gaussian mixture models have been shown to be a powerful tool for clustering in many applications.
StabilityBased Validation of Clustering Solutions
, 2004
"... Data clustering describes a set of frequently employed techniques in exploratory data analysis to extract “natural” group structure in data. Such groupings need to be validated to separate the signal in the data from spurious structure. In this context, finding an appropriate number of clusters is a ..."
Abstract

Cited by 73 (6 self)
 Add to MetaCart
Data clustering describes a set of frequently employed techniques in exploratory data analysis to extract “natural” group structure in data. Such groupings need to be validated to separate the signal in the data from spurious structure. In this context, finding an appropriate number of clusters is a particularly important model selection question. We introduce a measure of cluster stability to assess the validity of a cluster model. This stability measure quantifies the reproducibility of clustering solutions on a second sample, and it can be interpreted as a classification risk with regard to class labels produced by a clustering algorithm. The preferred number of clusters is determined by minimizing this classification risk as a function of the number of clusters. Convincing results are achieved on simulated as well as gene expression data sets. Comparisons to other methods demonstrate the competitive performance of our method and its suitability as a general validation tool for clustering solutions in realworld problems.
Watermarking Relational Databases
 In 28th Int’l Conference on Very Large Databases, Hong Kong
, 2002
"... We enunciate the need for watermarking database relations to deter their piracy, identify the unique characteristics of relational data which pose new challenges for watermarking, and provide desirable properties of a watermarking system for relational data. A watermark can be applied to any d ..."
Abstract

Cited by 70 (4 self)
 Add to MetaCart
We enunciate the need for watermarking database relations to deter their piracy, identify the unique characteristics of relational data which pose new challenges for watermarking, and provide desirable properties of a watermarking system for relational data. A watermark can be applied to any database relation having attributes which are such that changes in a few of their values do not affect the applications.
Defining transcription modules using largescale gene expression data
 Bioinformatics
, 2004
"... Running title: Defining modules using largescale expression data Motivation: Largescale gene expression data comprising a variety of cellular conditions holds the promise of a global view on the transcription program. While conventional clustering algorithms have been successfully applied to small ..."
Abstract

Cited by 70 (2 self)
 Add to MetaCart
Running title: Defining modules using largescale expression data Motivation: Largescale gene expression data comprising a variety of cellular conditions holds the promise of a global view on the transcription program. While conventional clustering algorithms have been successfully applied to smaller datasets, the utility of many algorithms for the analysis of largescale data is limited by their inability to capture combinatorial and conditionspecific coregulation. In addition, there is an increasing need to integrate the rapidly accumulating body of other highthroughput biological data with the expression analysis. In a previous work, we introduced the Signature Algorithm, which overcomes the problems of conventional clustering and allows for intuitive integration of additional biological data. However, the applicability of this approach to global analyses is constrained by the comprehensiveness of relevant external data and by its lacking capability of capturing hierarchical organization of the transcription network. Methods: We present a novel method for the analysis of largescale expression data, which assigns genes into contextdependent and potentially overlapping regulatory units. We introduce
Data Analysis with Bayesian Networks: A Bootstrap Approach
, 1999
"... In recent years there has been significant progress in algorithms and methods for inducing Bayesian networks from data. However, in complex data analysis problems, we need to go beyond being satisfied with inducing networks with high scores. We need to provide confidence measures on features o ..."
Abstract

Cited by 48 (7 self)
 Add to MetaCart
In recent years there has been significant progress in algorithms and methods for inducing Bayesian networks from data. However, in complex data analysis problems, we need to go beyond being satisfied with inducing networks with high scores. We need to provide confidence measures on features of these networks: Is the existence of an edge between two nodes warranted? Is the Markov blanket of a given node robust? Can we say something about the ordering of the variables? We should be able to address these questions, even when the amount of data is not enough to induce a high scoring network. In this paper we propose Efron's Bootstrap as a computationally efficient approach for answering these questions. In addition, we propose to use these confidence measures to induce better structures from the data, and to detect the presence of latent variables.
Learning Module Networks
, 2003
"... Methods for learning Bayesian networks can discover dependency structure between observed variables. Although these methods are useful in many applications, they run into computational and statistical problems in domains that involve a large number of variables. In this paper, we ..."
Abstract

Cited by 44 (4 self)
 Add to MetaCart
Methods for learning Bayesian networks can discover dependency structure between observed variables. Although these methods are useful in many applications, they run into computational and statistical problems in domains that involve a large number of variables. In this paper, we
An empirical study of Principal Component Analysis for clustering gene expression data
, 2001
"... Motivation: There is a great need to develop analytical methodology to analyze and to exploit the information contained in gene expression data. Because of the large number of genes and the complexity of biological networks, clustering is a useful exploratory technique for analysis of gene expressio ..."
Abstract

Cited by 44 (4 self)
 Add to MetaCart
Motivation: There is a great need to develop analytical methodology to analyze and to exploit the information contained in gene expression data. Because of the large number of genes and the complexity of biological networks, clustering is a useful exploratory technique for analysis of gene expression data. Other classical techniques, such as principal component analysis (PCA), have also been applied to analyze gene expression data. Using different data analysis techniques and different clustering algorithms to analyze the same data set can lead to very different conclusions. Our goal is to study the effectiveness of principal components (PC's) in capturing cluster structure. In other words, we empirically compared the quality of clusters obtained from the original data set to the quality of clusters obtained from clustering the PC's using both real and synthetic gene expression data sets. Results: Our empirical study showed that clustering with the PC's instead of the original variables does not necessarily improve, and often degrade, cluster quality. In particular, the first few PC's (which contain most of the variation in the data) do not necessarily capture most of the cluster structure. We also showed that clustering with PC's has different impact on different algorithms and different similarity metrics. Overall, we would not recommend PCA before clustering except in special circumstances. Availability: The software is under development. Contact: kayee cs.washington.edu Supplementary information: http://www.cs.washington.edu/homes/kayee/pca 1
Linear regression and twoclass classification with gene expression data
 Bioinformatics
, 2003
"... Motivation: Using gene expression data to classify (or predict) tumor types has received much research attention recently. Due to some special features of gene expression data, several new methods have been proposed, including the weighted voting scheme of Golub et al., the compound covariate method ..."
Abstract

Cited by 31 (2 self)
 Add to MetaCart
Motivation: Using gene expression data to classify (or predict) tumor types has received much research attention recently. Due to some special features of gene expression data, several new methods have been proposed, including the weighted voting scheme of Golub et al., the compound covariate method of Hedenfalk et al. (originally proposed by Tukey), and the shrunken centroids method of Tibshirani et al. These methods look different and are more or less ad hoc. Results: We point out a close connection of the three methods with a linear regression model. Casting the classification problem in the general framework of linear regression naturally leads to new alternatives, such as partial least squares (PLS) methods and penalized PLS (PPLS) methods. Using two real data sets, we show the competitive performance of our new methods when compared with the other three methods. Contact: