Results 11  20
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224
Kernel measures of conditional dependence
 In Adv. NIPS
, 2008
"... We propose a new measure of conditional dependence of random variables, based on normalized crosscovariance operators on reproducing kernel Hilbert spaces. Unlike previous kernel dependence measures, the proposed criterion does not depend on the choice of kernel in the limit of infinite data, for a ..."
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Cited by 87 (46 self)
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We propose a new measure of conditional dependence of random variables, based on normalized crosscovariance operators on reproducing kernel Hilbert spaces. Unlike previous kernel dependence measures, the proposed criterion does not depend on the choice of kernel in the limit of infinite data, for a wide class of kernels. At the same time, it has a straightforward empirical estimate with good convergence behaviour. We discuss the theoretical properties of the measure, and demonstrate its application in experiments. 1
An Empirical Study of Speed and Communication in GloballyDistributed Software Development
 IEEE Transactions on Software Engineering
, 2003
"... Abstract—Global software development is rapidly becoming the norm for technology companies. Previous qualitative research suggests that distributed development may increase development cycle time for individual work items (modification requests). We use both data from the source code change manageme ..."
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Cited by 83 (15 self)
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Abstract—Global software development is rapidly becoming the norm for technology companies. Previous qualitative research suggests that distributed development may increase development cycle time for individual work items (modification requests). We use both data from the source code change management system and survey data to model the extent of delay in a distributed software development organization and explore several possible mechanisms for this delay. One key finding is that distributed work items appear to take about two and onehalf times as long to complete as similar items where all the work is colocated. The data strongly suggest a mechanism for the delay, i.e., that distributed work items involve more people than comparable samesite work items, and the number of people involved is strongly related to the calendar time to complete a work item. We replicate the analysis of change data in a different organization with a different product and different sites and confirm our main findings. We also report survey results showing differences between samesite and distributed social networks, testing several hypotheses about characteristics of distributed social networks that may be related to delay. We discuss implications of our findings for practices and collaboration technology that have the potential for dramatically speeding distributed software development. Index Terms—Global development, collaboration, delay, speed, awareness, informal communication. 1
An Alternative Markov Property for Chain Graphs
 Scand. J. Statist
, 1996
"... Graphical Markov models use graphs, either undirected, directed, or mixed, to represent possible dependences among statistical variables. Applications of undirected graphs (UDGs) include models for spatial dependence and image analysis, while acyclic directed graphs (ADGs), which are especially conv ..."
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Cited by 74 (5 self)
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Graphical Markov models use graphs, either undirected, directed, or mixed, to represent possible dependences among statistical variables. Applications of undirected graphs (UDGs) include models for spatial dependence and image analysis, while acyclic directed graphs (ADGs), which are especially convenient for statistical analysis, arise in such fields as genetics and psychometrics and as models for expert systems and Bayesian belief networks. Lauritzen, Wermuth, and Frydenberg (LWF) introduced a Markov property for chain graphs, which are mixed graphs that can be used to represent simultaneously both causal and associative dependencies and which include both UDGs and ADGs as special cases. In this paper an alternative Markov property (AMP) for chain graphs is introduced, which in some ways is a more direct extension of the ADG Markov property than is the LWF property for chain graph. 1 INTRODUCTION Graphical Markov models use graphs, either undirected, directed, or mixed, to represent...
Statistical strategies for avoiding false discoveries in metabolomics and related experiments
, 2006
"... Many metabolomics, and other highcontent or highthroughput, experiments are set up such that the primary aim is the discovery of biomarker metabolites that can discriminate, with a certain level of certainty, between nominally matched ‘case ’ and ‘control ’ samples. However, it is unfortunately ve ..."
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Cited by 60 (11 self)
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Many metabolomics, and other highcontent or highthroughput, experiments are set up such that the primary aim is the discovery of biomarker metabolites that can discriminate, with a certain level of certainty, between nominally matched ‘case ’ and ‘control ’ samples. However, it is unfortunately very easy to find markers that are apparently persuasive but that are in fact entirely spurious, and there are wellknown examples in the proteomics literature. The main types of danger are not entirely independent of each other, but include bias, inadequate sample size (especially relative to the number of metabolite variables and to the required statistical power to prove that a biomarker is discriminant), excessive false discovery rate due to multiple hypothesis testing, inappropriate choice of particular numerical methods, and overfitting (generally caused by the failure to perform adequate validation and crossvalidation). Many studies fail to take these into account, and thereby fail to discover anything of true significance (despite their claims). We summarise these problems, and provide pointers to a substantial existing literature that should assist in the improved design and evaluation of metabolomics experiments, thereby allowing robust scientific conclusions to be drawn from the available data. We provide a list of some of the simpler checks that might improve one’s confidence that a candidate biomarker is not simply a statistical artefact, and suggest a series of preferred tests and visualisation tools that can assist readers and authors in assessing papers. These tools can be applied to individual metabolites by using multiple univariate tests performed in parallel across all metabolite peaks. They may also be applied to the validation of multivariate models. We stress in
Sparse inverse covariance matrix estimation via linear programming
, 2010
"... This paper considers the problem of estimating a high dimensional inverse covariance matrix that can be well approximated by “sparse ” matrices. Taking advantage of the connection between multivariate linear regression and entries of the inverse covariance matrix, we propose an estimating procedure ..."
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Cited by 55 (4 self)
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This paper considers the problem of estimating a high dimensional inverse covariance matrix that can be well approximated by “sparse ” matrices. Taking advantage of the connection between multivariate linear regression and entries of the inverse covariance matrix, we propose an estimating procedure that can effectively exploit such “sparsity”. The proposed method can be computed using linear programming and therefore has the potential to be used in very high dimensional problems. Oracle inequalities are established for the estimation error in terms of several operator norms, showing that the method is adaptive to different types of sparsity of the problem.
Learning Bayesian Networks from Data: An Efficient Approach Based on Information Theory
, 1997
"... This paper addresses the problem of learning Bayesian network structures from data by using an information theoretic dependency analysis approach. Based on our threephase construction mechanism, two efficient algorithms have been developed. One of our algorithms deals with a special case where the ..."
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Cited by 49 (0 self)
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This paper addresses the problem of learning Bayesian network structures from data by using an information theoretic dependency analysis approach. Based on our threephase construction mechanism, two efficient algorithms have been developed. One of our algorithms deals with a special case where the node ordering is given, the algorithm only require ) ( 2 N O CI tests and is correct given that the underlying model is DAGFaithful [Spirtes et. al., 1996]. The other algorithm deals with the general case and requires ) ( 4 N O conditional independence (CI) tests. It is correct given that the underlying model is monotone DAGFaithful (see Section 4.4). A system based on these algorithms has been developed and distributed through the Internet. The empirical results show that our approach is efficient and reliable. 1 Introduction The Bayesian network is a powerful knowledge representation and reasoning tool under conditions of uncertainty. A Bayesian network is a directed acyclic graph ...
A robust procedure for gaussian graphical model search from microarray data with p larger than n
 Journal of Machine Learning Research
, 2006
"... Learning of largescale networks of interactions from microarray data is an important and challenging problem in bioinformatics. A widely used approach is to assume that the available data constitute a random sample from a multivariate distribution belonging to a Gaussian graphical model. As a conse ..."
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Cited by 45 (6 self)
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Learning of largescale networks of interactions from microarray data is an important and challenging problem in bioinformatics. A widely used approach is to assume that the available data constitute a random sample from a multivariate distribution belonging to a Gaussian graphical model. As a consequence, the prime objects of inference are fullorder partial correlations which are partial correlations between two variables given the remaining ones. In the context of microarray data the number of variables exceed the sample size and this precludes the application of traditional structure learning procedures because a sampling version of fullorder partial correlations does not exist. In this paper we consider limitedorder partial correlations, these are partial correlations computed on marginal distributions of manageable size, and provide a set of rules that allow one to assess the usefulness of these quantities to derive the independence structure of the underlying Gaussian graphical model. Furthermore, we introduce a novel structure learning procedure based on a quantity, obtained from limitedorder partial correlations, that we call the nonrejection rate. The applicability and usefulness of the procedure are demonstrated by both simulated and real data.
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 44 (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.
Expanding From Discrete To Continuous Estimation Of Distribution Algorithms: The IDEA
 In Parallel Problem Solving From Nature  PPSN VI
, 2000
"... . The direct application of statistics to stochastic optimization based on iterated density estimation has become more important and present in evolutionary computation over the last few years. The estimation of densities over selected samples and the sampling from the resulting distributions, i ..."
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Cited by 39 (9 self)
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. The direct application of statistics to stochastic optimization based on iterated density estimation has become more important and present in evolutionary computation over the last few years. The estimation of densities over selected samples and the sampling from the resulting distributions, is a combination of the recombination and mutation steps used in evolutionary algorithms. We introduce the framework named IDEA to formalize this notion. By combining continuous probability theory with techniques from existing algorithms, this framework allows us to dene new continuous evolutionary optimization algorithms. 1 Introduction Algorithms in evolutionary optimization guide their search through statistics based on a vector of samples, often called a population. By using this stochastic information, non{deterministic induction is performed in order to attempt to use the structure of the search space and thereby aid the search for the optimal solution. In order to perform induct...
Inference and Learning in Hybrid Bayesian Networks
, 1998
"... We survey the literature on methods for inference and learning in Bayesian Networks composed of discrete and continuous nodes, in which the continuous nodes have a multivariate Gaussian distribution, whose mean and variance depends on the values of the discrete nodes. We also briefly consider hybrid ..."
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Cited by 39 (3 self)
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We survey the literature on methods for inference and learning in Bayesian Networks composed of discrete and continuous nodes, in which the continuous nodes have a multivariate Gaussian distribution, whose mean and variance depends on the values of the discrete nodes. We also briefly consider hybrid Dynamic Bayesian Networks, an extension of switching Kalman filters. This report is meant to summarize what is known at a sufficient level of detail to enable someone to implement the algorithms, but without dwelling on formalities.