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477
Making the most of statistical analyses: Improving interpretation and presentation
 American Journal of Political Science
, 2000
"... Social scientists rarely take full advantage of the information available in their statistical results. As a consequence, they miss opportunities to present quantities that are of greatest substantive interest for their research and express the appropriate degree of certainty about these quantities. ..."
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Cited by 600 (26 self)
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Social scientists rarely take full advantage of the information available in their statistical results. As a consequence, they miss opportunities to present quantities that are of greatest substantive interest for their research and express the appropriate degree of certainty about these quantities. In this article, we offer an approach, built on the technique of statistical simulation, to extract the currently overlooked information from any statistical method and to interpret and present it in a readerfriendly manner. Using this technique requires some expertise,
General methods for monitoring convergence of iterative simulations
 J. Comput. Graph. Statist
, 1998
"... We generalize the method proposed by Gelman and Rubin (1992a) for monitoring the convergence of iterative simulations by comparing between and within variances of multiple chains, in order to obtain a family of tests for convergence. We review methods of inference from simulations in order to develo ..."
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Cited by 551 (8 self)
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We generalize the method proposed by Gelman and Rubin (1992a) for monitoring the convergence of iterative simulations by comparing between and within variances of multiple chains, in order to obtain a family of tests for convergence. We review methods of inference from simulations in order to develop convergencemonitoring summaries that are relevant for the purposes for which the simulations are used. We recommend applying a battery of tests for mixing based on the comparison of inferences from individual sequences and from the mixture of sequences. Finally, we discuss multivariate analogues, for assessing convergence of several parameters simultaneously.
Genomic control for association studies
, 1999
"... A dense set of single nucleotide polymorphisms (SNP) covering the genome and an efficient method to assess SNP genotypes are expected to be available in the near future. An outstanding question is how to use these technologies efficiently to identify genes affecting liability to complex disorders. ..."
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Cited by 480 (13 self)
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A dense set of single nucleotide polymorphisms (SNP) covering the genome and an efficient method to assess SNP genotypes are expected to be available in the near future. An outstanding question is how to use these technologies efficiently to identify genes affecting liability to complex disorders. To achieve this goal, we propose a statistical method that has several optimal properties: It can be used with casecontrol data and yet, like familybased designs, controls for population heterogeneity; it is insensitive to the usual violations of model assumptions, such as cases failing to be strictly independent; and, by using Bayesian outlier methods, it circumvents the need for Bonferroni correction for multiple tests, leading to better performance in many settings while still constraining risk for false positives. The performance of our genomic control method is quite good for plausible effects of liability genes, which bodes well for future genetic analyses of complex disorders.
Bayesian measures of model complexity and fit
 Journal of the Royal Statistical Society, Series B
, 2002
"... [Read before The Royal Statistical Society at a meeting organized by the Research ..."
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Cited by 466 (4 self)
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[Read before The Royal Statistical Society at a meeting organized by the Research
Mixed membership stochastic block models for relational data with application to proteinprotein interactions
 In Proceedings of the International Biometrics Society Annual Meeting
, 2006
"... We develop a model for examining data that consists of pairwise measurements, for example, presence or absence of links between pairs of objects. Examples include protein interactions and gene regulatory networks, collections of authorrecipient email, and social networks. Analyzing such data with p ..."
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Cited by 378 (52 self)
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We develop a model for examining data that consists of pairwise measurements, for example, presence or absence of links between pairs of objects. Examples include protein interactions and gene regulatory networks, collections of authorrecipient email, and social networks. Analyzing such data with probabilistic models requires special assumptions, since the usual independence or exchangeability assumptions no longer hold. We introduce a class of latent variable models for pairwise measurements: mixed membership stochastic blockmodels. Models in this class combine a global model of dense patches of connectivity (blockmodel) and a local model to instantiate nodespecific variability in the connections (mixed membership). We develop a general variational inference algorithm for fast approximate posterior inference. We demonstrate the advantages of mixed membership stochastic blockmodels with applications to social networks and protein interaction networks.
Bayesian Compressive Sensing
, 2007
"... The data of interest are assumed to be represented as Ndimensional real vectors, and these vectors are compressible in some linear basis B, implying that the signal can be reconstructed accurately using only a small number M ≪ N of basisfunction coefficients associated with B. Compressive sensing ..."
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Cited by 330 (24 self)
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The data of interest are assumed to be represented as Ndimensional real vectors, and these vectors are compressible in some linear basis B, implying that the signal can be reconstructed accurately using only a small number M ≪ N of basisfunction coefficients associated with B. Compressive sensing is a framework whereby one does not measure one of the aforementioned Ndimensional signals directly, but rather a set of related measurements, with the new measurements a linear combination of the original underlying Ndimensional signal. The number of required compressivesensing measurements is typically much smaller than N, offering the potential to simplify the sensing system. Let f denote the unknown underlying Ndimensional signal, and g a vector of compressivesensing measurements, then one may approximate f accurately by utilizing knowledge of the (underdetermined) linear relationship between f and g, in addition to knowledge of the fact that f is compressible in B. In this paper we employ a Bayesian formalism for estimating the underlying signal f based on compressivesensing measurements g. The proposed framework has the following properties: (i) in addition to estimating the underlying signal f, “error bars ” are also estimated, these giving a measure of confidence in the inverted signal; (ii) using knowledge of the error bars, a principled means is provided for determining when a sufficient
Improving Text Classification by Shrinkage in a Hierarchy of Classes
, 1998
"... When documents are organized in a large number of topic categories, the categories are often arranged in a hierarchy. The U.S. patent database and Yahoo are two examples. ..."
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Cited by 289 (6 self)
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When documents are organized in a large number of topic categories, the categories are often arranged in a hierarchy. The U.S. patent database and Yahoo are two examples.
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 ..."
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Cited by 265 (7 self)
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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.
Modeling Multilevel Data Structures
 AMERICAN JOURNAL OF POLITICAL SCIENCE
, 1997
"... Although integrating multiple levels of data into an analysis can often yield better inferences about the phenomenon under study, traditional methodologies used to combine multiple levels of data are problematic. In this paper, we discuss several methodologies under the rubric of multilevel analys ..."
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Cited by 152 (0 self)
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Although integrating multiple levels of data into an analysis can often yield better inferences about the phenomenon under study, traditional methodologies used to combine multiple levels of data are problematic. In this paper, we discuss several methodologies under the rubric of multilevel analysis. Multilevel methods, we argue, provide researchers, particularly researchers using comparative data, substantial leverage in overcoming the typical problems associated with either ignoring multiple levels of data, or problems associated with combining lowerlevel and higherlevel data (including overcoming implicit assumptions of fixed and constant effects). The paper discusses several variants of the multilevel model and provides an application of individuallevel support for European integration using comparative political data from Western Europe.
Information Extraction with HMMs and Shrinkage
 In Proceedings of the AAAI99 Workshop on Machine Learning for Information Extraction
, 1999
"... Hidden Markov models (HMMs) are a powerful probabilistic tool for modeling time series data, and have been applied with success to many languagerelated tasks such as part of speech tagging, speech recognition, text segmentation and topic detection. This paper describes the application of HMMs to an ..."
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Cited by 135 (3 self)
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Hidden Markov models (HMMs) are a powerful probabilistic tool for modeling time series data, and have been applied with success to many languagerelated tasks such as part of speech tagging, speech recognition, text segmentation and topic detection. This paper describes the application of HMMs to another language related taskinformation extractionthe problem of locating textual subsegments that answer a particular information need. In our work, the HMM state transition probabilities and word emission probabilities are learned from labeled training data. As in many machine learning problems, however, the lack of suÆcient labeled training data hinders the reliability of the model. The key contribution of this paper is the use of a statistical technique called \shrinkage" that signi cantly improves parameter estimation of the HMM emission probabilities in the face of sparse training data. In experiments on seminar announcements and Reuters acquisitions articles, shrinkage is shown to r...