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Hidden Markov models in computational biology: applications to protein modeling
 JOURNAL OF MOLECULAR BIOLOGY
, 1994
"... Hidden.Markov Models (HMMs) are applied t.0 the problems of statistical modeling, database searching and multiple sequence alignment of protein families and protein domains. These methods are demonstrated the on globin family, the protein kinase catalytic domain, and the EFhand calcium binding moti ..."
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Cited by 656 (39 self)
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Hidden.Markov Models (HMMs) are applied t.0 the problems of statistical modeling, database searching and multiple sequence alignment of protein families and protein domains. These methods are demonstrated the on globin family, the protein kinase catalytic domain, and the EFhand calcium binding motif. In each case the parameters of an HMM are estimated from a training set of unaligned sequences. After the HMM is built, it is used to obtain a multiple alignment of all the training sequences. It is also used to search the. SWISSPROT 22 database for other sequences. that are members of the given protein family, or contain the given domain. The Hi " produces multiple alignments of good quality that agree closely with the alignments produced by programs that incorporate threedimensional structural information. When employed in discrimination tests (by examining how closely the sequences in a database fit the globin, kinase and EFhand HMMs), the '\ HMM is able to distinguish members of these families from nonmembers with a high degree of accuracy. Both the HMM and PROFILESEARCH (a technique used to search for relationships between a protein sequence and multiply aligned sequences) perform better in these tests than PROSITE (a dictionary of sites and patterns in proteins). The HMM appecvs to have a slight advantage over PROFILESEARCH in terms of lower rates of false
Learning lowlevel vision
 International Journal of Computer Vision
, 2000
"... We show a learningbased method for lowlevel vision problems. We setup a Markov network of patches of the image and the underlying scene. A factorization approximation allows us to easily learn the parameters of the Markov network from synthetic examples of image/scene pairs, and to e ciently prop ..."
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Cited by 586 (31 self)
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We show a learningbased method for lowlevel vision problems. We setup a Markov network of patches of the image and the underlying scene. A factorization approximation allows us to easily learn the parameters of the Markov network from synthetic examples of image/scene pairs, and to e ciently propagate image information. Monte Carlo simulations justify this approximation. We apply this to the \superresolution &quot; problem (estimating high frequency details from a lowresolution image), showing good results. For the motion estimation problem, we show resolution of the aperture problem and llingin arising from application of the same probabilistic machinery.
A Bayesian Framework for the Analysis of Microarray Expression Data: Regularized tTest and Statistical Inferences of Gene Changes
 Bioinformatics
, 2001
"... Motivation: DNA microarrays are now capable of providing genomewide patterns of gene expression across many different conditions. The first level of analysis of these patterns requires determining whether observed differences in expression are significant or not. Current methods are unsatisfactory ..."
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Cited by 485 (6 self)
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Motivation: DNA microarrays are now capable of providing genomewide patterns of gene expression across many different conditions. The first level of analysis of these patterns requires determining whether observed differences in expression are significant or not. Current methods are unsatisfactory due to the lack of a systematic framework that can accommodate noise, variability, and low replication often typical of microarray data. Results: We develop a Bayesian probabilistic framework for microarray data analysis. At the simplest level, we model logexpression values by independent normal distributions, parameterized by corresponding means and variances with hierarchical prior distributions. We derive point estimates for both parameters and hyperparameters, and regularized expressions for the variance of each gene by combining the empirical variance with a local background variance associated with neighboring genes. An additional hyperparameter, inversely related to the number of empirical observations, determines the strength of the background variance. Simulations show that these point estimates, combined with a ttest, provide a systematic inference approach that compares favorably with simple ttest or fold methods, and partly compensate for the lack of replication. Availability: The approach is implemented in a software called CyberT accessible through a Web interface at www.genomics.uci.edu/software.html. The code is available as Open Source and is written in the freely available statistical language R. and Department of Biological Chemistry, College of Medicine, University of California, Irvine. To whom all correspondence should be addressed. Contact: pfbaldi@ics.uci.edu, tdlong@uci.edu. 1
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 457 (12 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.
Predictive regressions
 Journal of Financial Economics
, 1999
"... When a rate of return is regressed on a lagged stochastic regressor, such as a dividend yield, the regression disturbance is correlated with the regressor's innovation. The OLS estimator's "nitesample properties, derived here, can depart substantially from the standard regression set ..."
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Cited by 452 (19 self)
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When a rate of return is regressed on a lagged stochastic regressor, such as a dividend yield, the regression disturbance is correlated with the regressor's innovation. The OLS estimator's "nitesample properties, derived here, can depart substantially from the standard regression setting. Bayesian posterior distributions for the regression parameters are obtained under speci"cations that di!er with respect to (i) prior beliefs about the autocorrelation of the regressor and (ii) whether the initial observation of the regressor is speci"ed as "xed or stochastic. The posteriors di!er across such speci"cations, and asset allocations in the presence of estimation risk exhibit sensitivity to those
InformationBased Objective Functions for Active Data Selection
 Neural Computation
"... Learning can be made more efficient if we can actively select particularly salient data points. Within a Bayesian learning framework, objective functions are discussed which measure the expected informativeness of candidate measurements. Three alternative specifications of what we want to gain infor ..."
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Cited by 429 (5 self)
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Learning can be made more efficient if we can actively select particularly salient data points. Within a Bayesian learning framework, objective functions are discussed which measure the expected informativeness of candidate measurements. Three alternative specifications of what we want to gain information about lead to three different criteria for data selection. All these criteria depend on the assumption that the hypothesis space is correct, which may prove to be their main weakness. 1 Introduction Theories for data modelling often assume that the data is provided by a source that we do not control. However, there are two scenarios in which we are able to actively select training data. In the first, data measurements are relatively expensive or slow, and we want to know where to look next so as to learn as much as possible. According to Jaynes (1986), Bayesian reasoning was first applied to this problem two centuries ago by Laplace, who in consequence made more important discoveries...
Active perception
 Proc IEEE, 76:9961005
, 1988
"... Most past and present work in machine perception has involved extensive static analysis of passively sampled data. However, it should be axiomatic that perception is not passive, but active. Perceptual activity is exploratory, probing, searching; percepts do not simply fall onto sensors as rain fall ..."
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Cited by 425 (12 self)
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Most past and present work in machine perception has involved extensive static analysis of passively sampled data. However, it should be axiomatic that perception is not passive, but active. Perceptual activity is exploratory, probing, searching; percepts do not simply fall onto sensors as rain falls onto ground. We do not just see, we look. And in the course,
Using simulation methods for Bayesian econometric models: Inference, development and communication
 Econometric Review
, 1999
"... This paper surveys the fundamental principles of subjective Bayesian inference in econometrics and the implementation of those principles using posterior simulation methods. The emphasis is on the combination of models and the development of predictive distributions. Moving beyond conditioning on a ..."
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Cited by 356 (19 self)
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This paper surveys the fundamental principles of subjective Bayesian inference in econometrics and the implementation of those principles using posterior simulation methods. The emphasis is on the combination of models and the development of predictive distributions. Moving beyond conditioning on a fixed number of completely specified models, the paper introduces subjective Bayesian tools for formal comparison of these models with as yet incompletely specified models. The paper then shows how posterior simulators can facilitate communication between investigators (for example, econometricians) on the one hand and remote clients (for example, decision makers) on the other, enabling clients to vary the prior distributions and functions of interest employed by investigators. A theme of the paper is the practicality of subjective Bayesian methods. To this end, the paper describes publicly available software for Bayesian inference, model development, and communication and provides illustrations using two simple econometric models. *This paper was originally prepared for the Australasian meetings of the Econometric Society in Melbourne, Australia,
The adaptive nature of human categorization
 Psychological Review
, 1991
"... A rational model of human categorization behavior is presented that assumes that categorization reflects the derivation of optimal estimates of the probability of unseen features of objects. A Bayesian analysis is performed of what optimal estimations would be if categories formed a disjoint partiti ..."
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Cited by 337 (2 self)
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A rational model of human categorization behavior is presented that assumes that categorization reflects the derivation of optimal estimates of the probability of unseen features of objects. A Bayesian analysis is performed of what optimal estimations would be if categories formed a disjoint partitioning of the object space and if features were independently displayed within a category. This Bayesian analysis is placed within an incremental categorization algorithm. The resulting rational model accounts for effects of central tendency of categories, effects of specific instances, learning of linearly nonseparable categories, effects of category labels, extraction of basic level categories, baserate effects, probability matching in categorization, and trialbytrial learning functions. Although the rational model considers just I level of categorization, it is shown how predictions can be enhanced by considering higher and lower levels. Considering prediction at the lower, individual level allows integration of this rational analysis of categorization with the earlier rational analysis of memory (Anderson & Milson, 1989). Anderson (1990) presented a rational analysis ot 6 human cognition. The term rational derives from similar &quot;rationalman&quot; analyses in economics. Rational analyses in other fields are sometimes called adaptationist analyses. Basically, they are efforts to explain the behavior in some domain on the assumption that the behavior is optimized with respect to some criteria of adaptive importance. This article begins with a general characterization ofhow one develops a rational theory of a particular cognitive phenomenon. Then I present the basic theory of categorization developed in Anderson (1990) and review the applications from that book. Since the writing of the book, the theory has been greatly extended and applied to many new phenomena. Most of this article describes these new developments and applications. A Rational Analysis Several theorists have promoted the idea that psychologists might understand human behavior by assuming it is adapted to the environment (e.g., Brunswik, 1956; Campbell, 1974; Gib