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11,431
A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood
, 2003
"... The increase in the number of large data sets and the complexity of current probabilistic sequence evolution models necessitates fast and reliable phylogeny reconstruction methods. We describe a new approach, based on the maximumlikelihood principle, which clearly satisfies these requirements. The ..."
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Cited by 2109 (30 self)
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The increase in the number of large data sets and the complexity of current probabilistic sequence evolution models necessitates fast and reliable phylogeny reconstruction methods. We describe a new approach, based on the maximumlikelihood principle, which clearly satisfies these requirements. The core of this method is a simple hillclimbing algorithm that adjusts tree topology and branch lengths simultaneously. This algorithm starts from an initial tree built by a fast distancebased method and modifies this tree to improve its likelihood at each iteration. Due to this simultaneous adjustment of the topology and branch lengths, only a few iterations are sufficient to reach an optimum. We used extensive and realistic computer simulations to show that the topological accuracy of this new method is at least as high as that of the existing maximumlikelihood programs and much higher than the performance of distancebased and parsimony approaches. The reduction of computing time is dramatic in comparison with other maximumlikelihood packages, while the likelihood maximization ability tends to be higher. For example, only 12 min were required on a standard personal computer to analyze a data set consisting of 500 rbcL sequences with 1,428 base pairs from plant plastids, thus reaching a speed of the same order as some popular distancebased and parsimony algorithms. This new method is implemented in the PHYML program, which is freely available on our web page:
Realtime human pose recognition in parts from single depth images
 In In CVPR, 2011. 3
"... We propose a new method to quickly and accurately predict 3D positions of body joints from a single depth image, using no temporal information. We take an object recognition approach, designing an intermediate body parts representation that maps the difficult pose estimation problem into a simpler p ..."
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Cited by 550 (19 self)
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We propose a new method to quickly and accurately predict 3D positions of body joints from a single depth image, using no temporal information. We take an object recognition approach, designing an intermediate body parts representation that maps the difficult pose estimation problem into a simpler perpixel classification problem. Our large and highly varied training dataset allows the classifier to estimate body parts invariant to pose, body shape, clothing, etc. Finally we generate confidencescored 3D proposals of several body joints by reprojecting the classification result and finding local modes. The system runs at 200 frames per second on consumer hardware. Our evaluation shows high accuracy on both synthetic and real test sets, and investigates the effect of several training parameters. We achieve state of the art accuracy in our comparison with related work and demonstrate improved generalization over exact wholeskeleton nearest neighbor matching. 1.
Bayes Factors
, 1995
"... In a 1935 paper, and in his book Theory of Probability, Jeffreys developed a methodology for quantifying the evidence in favor of a scientific theory. The centerpiece was a number, now called the Bayes factor, which is the posterior odds of the null hypothesis when the prior probability on the null ..."
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Cited by 1766 (74 self)
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In a 1935 paper, and in his book Theory of Probability, Jeffreys developed a methodology for quantifying the evidence in favor of a scientific theory. The centerpiece was a number, now called the Bayes factor, which is the posterior odds of the null hypothesis when the prior probability on the null is onehalf. Although there has been much discussion of Bayesian hypothesis testing in the context of criticism of P values, less attention has been given to the Bayes factor as a practical tool of applied statistics. In this paper we review and discuss the uses of Bayes factors in the context of five scientific applications in genetics, sports, ecology, sociology and psychology.
SemiSupervised Learning Literature Survey
, 2006
"... We review the literature on semisupervised learning, which is an area in machine learning and more generally, artificial intelligence. There has been a whole
spectrum of interesting ideas on how to learn from both labeled and unlabeled data, i.e. semisupervised learning. This document is a chapter ..."
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Cited by 757 (8 self)
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We review the literature on semisupervised learning, which is an area in machine learning and more generally, artificial intelligence. There has been a whole
spectrum of interesting ideas on how to learn from both labeled and unlabeled data, i.e. semisupervised learning. This document is a chapter excerpt from the author’s
doctoral thesis (Zhu, 2005). However the author plans to update the online version frequently to incorporate the latest development in the field. Please obtain the latest
version at http://www.cs.wisc.edu/~jerryzhu/pub/ssl_survey.pdf
Graphical models, exponential families, and variational inference
, 2008
"... The formalism of probabilistic graphical models provides a unifying framework for capturing complex dependencies among random variables, and building largescale multivariate statistical models. Graphical models have become a focus of research in many statistical, computational and mathematical fiel ..."
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Cited by 800 (26 self)
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The formalism of probabilistic graphical models provides a unifying framework for capturing complex dependencies among random variables, and building largescale multivariate statistical models. Graphical models have become a focus of research in many statistical, computational and mathematical fields, including bioinformatics, communication theory, statistical physics, combinatorial optimization, signal and image processing, information retrieval and statistical machine learning. Many problems that arise in specific instances — including the key problems of computing marginals and modes of probability distributions — are best studied in the general setting. Working with exponential family representations, and exploiting the conjugate duality between the cumulant function and the entropy for exponential families, we develop general variational representations of the problems of computing likelihoods, marginal probabilities and most probable configurations. We describe how a wide varietyof algorithms — among them sumproduct, cluster variational methods, expectationpropagation, mean field methods, maxproduct and linear programming relaxation, as well as conic programming relaxations — can all be understood in terms of exact or approximate forms of these variational representations. The variational approach provides a complementary alternative to Markov chain Monte Carlo as a general source of approximation methods for inference in largescale statistical models.
The Ensemble Kalman Filter: theoretical formulation And Practical Implementation
, 2003
"... The purpose of this paper is to provide a comprehensive presentation and interpretation of the Ensemble Kalman Filter (EnKF) and its numerical implementation. The EnKF has a large user group, and numerous publications have discussed applications and theoretical aspects of it. This paper reviews the ..."
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Cited by 482 (4 self)
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The purpose of this paper is to provide a comprehensive presentation and interpretation of the Ensemble Kalman Filter (EnKF) and its numerical implementation. The EnKF has a large user group, and numerous publications have discussed applications and theoretical aspects of it. This paper reviews
Markov chain monte carlo convergence diagnostics
 JASA
, 1996
"... A critical issue for users of Markov Chain Monte Carlo (MCMC) methods in applications is how to determine when it is safe to stop sampling and use the samples to estimate characteristics of the distribution of interest. Research into methods of computing theoretical convergence bounds holds promise ..."
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Cited by 367 (6 self)
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A critical issue for users of Markov Chain Monte Carlo (MCMC) methods in applications is how to determine when it is safe to stop sampling and use the samples to estimate characteristics of the distribution of interest. Research into methods of computing theoretical convergence bounds holds promise
Duplicate record detection: A survey
 TRANSACTIONS ON KNOWLEDGE AND DATA ENGINEERING
, 2007
"... Often, in the real world, entities have two or more representations in databases. Duplicate records do not share a common key and/or they contain errors that make duplicate matching a dif cult task. Errors are introduced as the result of transcription errors, incomplete information, lack of standard ..."
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Cited by 427 (11 self)
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Often, in the real world, entities have two or more representations in databases. Duplicate records do not share a common key and/or they contain errors that make duplicate matching a dif cult task. Errors are introduced as the result of transcription errors, incomplete information, lack of standard formats or any combination of these factors. In this article, we present a thorough analysis of the literature on duplicate record detection. We cover similarity metrics that are commonly used to detect similar eld entries, and we present an extensive set of duplicate detection algorithms that can detect approximately duplicate records in a database. We also cover multiple techniques for improving the ef ciency and scalability of approximate duplicate detection algorithms. We conclude with a coverage of existing tools and with a brief discussion of the big open problems in the area.
WinBUGS  a Bayesian modelling framework: concepts, structure, and extensibility
 Statistics and Computing
, 2000
"... WinBUGS is a fully extensible modular framework for constructing and analysing Bayesian full probability models. Models may be specified either textually via the BUGS language or pictorially using a graphical interface called DoodleBUGS. WinBUGS processes the model specification and constructs an ob ..."
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Cited by 394 (5 self)
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an objectoriented representation of the model. The software offers a userinterface, based on dialogue boxes and menu commands, through which the model may then be analysed using Markov chain Monte Carlo techniques. In this paper we discuss how and why various modern computing concepts, such as object
Results 1  10
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