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Probabilistic Inference Using Markov Chain Monte Carlo Methods
, 1993
"... Probabilistic inference is an attractive approach to uncertain reasoning and empirical learning in artificial intelligence. Computational difficulties arise, however, because probabilistic models with the necessary realism and flexibility lead to complex distributions over highdimensional spaces. R ..."
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Cited by 738 (24 self)
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Probabilistic inference is an attractive approach to uncertain reasoning and empirical learning in artificial intelligence. Computational difficulties arise, however, because probabilistic models with the necessary realism and flexibility lead to complex distributions over highdimensional spaces. Related problems in other fields have been tackled using Monte Carlo methods based on sampling using Markov chains, providing a rich array of techniques that can be applied to problems in artificial intelligence. The "Metropolis algorithm" has been used to solve difficult problems in statistical physics for over forty years, and, in the last few years, the related method of "Gibbs sampling" has been applied to problems of statistical inference. Concurrently, an alternative method for solving problems in statistical physics by means of dynamical simulation has been developed as well, and has recently been unified with the Metropolis algorithm to produce the "hybrid Monte Carlo" method. In computer science, Markov chain sampling is the basis of the heuristic optimization technique of "simulated annealing", and has recently been used in randomized algorithms for approximate counting of large sets. In this review, I outline the role of probabilistic inference in artificial intelligence, present the theory of Markov chains, and describe various Markov chain Monte Carlo algorithms, along with a number of supporting techniques. I try to present a comprehensive picture of the range of methods that have been developed, including techniques from the varied literature that have not yet seen wide application in artificial intelligence, but which appear relevant. As illustrative examples, I use the problems of probabilistic inference in expert systems, discovery of latent classes from data, and Bayesian learning for neural networks.
Stacked generalization
 Neural Networks
, 1992
"... Abstract: This paper introduces stacked generalization, a scheme for minimizing the generalization error rate of one or more generalizers. Stacked generalization works by deducing the biases of the generalizer(s) with respect to a provided learning set. This deduction proceeds by generalizing in a s ..."
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Cited by 714 (8 self)
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Abstract: This paper introduces stacked generalization, a scheme for minimizing the generalization error rate of one or more generalizers. Stacked generalization works by deducing the biases of the generalizer(s) with respect to a provided learning set. This deduction proceeds by generalizing in a second space whose inputs are (for example) the guesses of the original generalizers when taught with part of the learning set and trying to guess the rest of it, and whose output is (for example) the correct guess. When used with multiple generalizers, stacked generalization can be seen as a more sophisticated version of crossvalidation, exploiting a strategy more sophisticated than crossvalidation’s crude winnertakesall for combining the individual generalizers. When used with a single generalizer, stacked generalization is a scheme for estimating (and then correcting for) the error of a generalizer which has been trained on a particular learning set and then asked a particular question. After introducing stacked generalization and justifying its use, this paper presents two numerical experiments. The first demonstrates how stacked generalization improves upon a set of separate generalizers for the NETtalk task of translating text to phonemes. The second demonstrates how stacked generalization improves the performance of a single surfacefitter. With the other experimental evidence in the literature, the usual arguments supporting crossvalidation, and the abstract justifications presented in this paper, the conclusion is that for almost any realworld generalization problem one should use some version of stacked generalization to minimize the generalization error rate. This paper ends by discussing some of the variations of stacked generalization, and how it touches on other fields like chaos theory. Key Words: generalization and induction, combining generalizers, learning set preprocessing, crossvalidation, error estimation and correction.
Spectrum estimation and harmonic analysis
, 1982
"... AbstmctIn the choice of an eduutor for the spectnrm of a ation ..."
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Cited by 438 (3 self)
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AbstmctIn the choice of an eduutor for the spectnrm of a ation
Power laws, Pareto distributions and Zipf’s law
"... Many of the things that scientists measure have a typical size or “scale”—a typical value around which individual measurements are centred. A simple example would be the heights of human beings. Most adult human beings are about 180cm tall. There is some variation around this figure, notably dependi ..."
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Cited by 391 (0 self)
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Many of the things that scientists measure have a typical size or “scale”—a typical value around which individual measurements are centred. A simple example would be the heights of human beings. Most adult human beings are about 180cm tall. There is some variation around this figure, notably depending on sex, but we never see people who are 10cm tall, or 500cm. To make this observation more quantitative, one can plot a histogram of people’s heights, as I have done in Fig. 1a. The figure shows the heights in centimetres of adult men in the United States measured between 1959 and 1962, and indeed the distribution is relatively narrow and peaked around 180cm. Another telling observation is the ratio of the heights of the tallest and shortest people.
How to Fit a Response Time Distribution
"... Among the most valuable tools in behavioral science is statistically fitting mathematical models of cognition to data, response time distributions in particular. However, techniques for fitting distributions vary widely and little is known about the efficacy of different techniques. In this article, ..."
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Cited by 82 (1 self)
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Among the most valuable tools in behavioral science is statistically fitting mathematical models of cognition to data, response time distributions in particular. However, techniques for fitting distributions vary widely and little is known about the efficacy of different techniques. In this article, we assessed several fitting techniques by simulating six widely cited models of response time and using the fitting procedures to recover model parameters. The techniques include the maximization of likelihood and leastsquares fits of the theoretical distributions to different empirical estimates of the simulated distributions. A running example was used to illustrate the different estimation and fitting procedures. The simulation studies revealed that empirical density estimates are biased even for very large sample sizes. Some fitting techniques yielded more accurate and less variable parameter estimates than others. Methods that involved leastsquares fits to density estimates generally yielded very poor parameter estimates. How to Fit a Response Time Distribution The importance of considering the entire response time (RT) distribution in testing formal models of cognition is now widely appreciated. Fitting a model to mean RT alone can mask important details of the data that examination of the entire distribution would reveal, such as the behavior of fast and slow responses across the conditions of an experiment (e.g., Heathcote, Popiel & Mewhort, 1991), the extent of facilitation between perceptual channels (Miller, 1982), and the effects of practice on RT quantiles (Logan, 1992). Techniques for testing hypotheses based on the RT distribution have been developed (Townsend, 1990). In addition, the RT distribution provides an important meeting ground between theory and da...
Using electrostatic potentials to predict DNAbinding sites on DNAbinding proteins
 Nucleic Acids Res
, 2003
"... A method to detect DNAbinding sites on the surface of a protein structure is important for functional annotation. This work describes the analysis of residue patches on the surface of DNAbinding proteins and the development of a method of predicting DNAbinding sites using a single feature of th ..."
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Cited by 68 (2 self)
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A method to detect DNAbinding sites on the surface of a protein structure is important for functional annotation. This work describes the analysis of residue patches on the surface of DNAbinding proteins and the development of a method of predicting DNAbinding sites using a single feature of these surface patches. Surface patches and the DNAbinding sites were initially analysed for accessibility, electrostatic potential, residue propensity, hydrophobicity and residue conservation. From this, it was observed that the DNAbinding sites were, in general, amongst the top 10 % of patches with the largest positive electrostatic scores. This knowledge led to the development of a prediction method in which patches of surface residues were selected such that they excluded residues with negative electrostatic scores. This method was used to make predictions for a data set of 56 nonhomologous DNAbinding proteins. Correct predictions made for 68 % of the data set.
ConstrainedRealization MonteCarlo method for Hypothesis Testing
 Physica D
"... : We compare two theoretically distinct approaches to generating artificial (or "surrogate") data for testing hypotheses about a given data set. The first and more straightforward approach is to fit a single "best" model to the original data, and then to generate surrogate data s ..."
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Cited by 53 (1 self)
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: We compare two theoretically distinct approaches to generating artificial (or "surrogate") data for testing hypotheses about a given data set. The first and more straightforward approach is to fit a single "best" model to the original data, and then to generate surrogate data sets that are "typical realizations" of that model. The second approach concentrates not on the model but directly on the original data; it attempts to constrain the surrogate data sets so that they exactly agree with the original data for a specified set of sample statistics. Examples of these two approaches are provided for two simple cases: a test for deviations from a gaussian distribution, and a test for serial dependence in a time series. Additionally, we consider tests for nonlinearity in time series based on a Fourier transform (FT) method and on more conventional autoregressive movingaverage (ARMA) fits to the data. The comparative performance of hypothesis testing schemes based on these two approaches...
What is Special About Spatial Data? Alternative Perspectives on Spatial Data Analysis
, 1989
"... The analysis of spatial data has always played a central role in the quantitative scientific tradition in geography. Recently, there have appeared a considerable number of publications devoted to presenting research results and to assessing the state of the art. ..."
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Cited by 50 (3 self)
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The analysis of spatial data has always played a central role in the quantitative scientific tradition in geography. Recently, there have appeared a considerable number of publications devoted to presenting research results and to assessing the state of the art.
Sensitivity analysis of a land surface scheme using multicriteria methods
 J. Geophys. Res
, 1999
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Prototype Selection for Composite Nearest Neighbor Classifiers
, 1997
"... Combining the predictions of a set of classifiers has been shown to be an effective way to create composite classifiers that are more accurate than any of the component classifiers. Increased accuracy has been shown in a variety of realworld applications, ranging from protein sequence identificatio ..."
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Cited by 30 (1 self)
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Combining the predictions of a set of classifiers has been shown to be an effective way to create composite classifiers that are more accurate than any of the component classifiers. Increased accuracy has been shown in a variety of realworld applications, ranging from protein sequence identification to determining the fat content of ground meat. Despite such individual successes, the answers are not known to fundamental questions about classifier combination, such as "Can classifiers from any given model class be combined to create a composite classifier with higher accuracy?" or "Is it possible to increase the accuracy of a given classifier by combining its predictions with those of only a small number o...