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46
Alignmentfree sequence comparisona review
 Bioinformatics
, 2003
"... Motivation: Genetic recombination and, in particular, genetic shuffling are at odds with sequence comparison by alignment, which assumes conservation of contiguity between homologous segments. A variety of theoretical foundations are being used to derive alignmentfree methods that overcome this lim ..."
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Cited by 43 (5 self)
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Motivation: Genetic recombination and, in particular, genetic shuffling are at odds with sequence comparison by alignment, which assumes conservation of contiguity between homologous segments. A variety of theoretical foundations are being used to derive alignmentfree methods that overcome this limitation. The formulation of alternative metrics for dissimilarity between sequences and their algorithmic implementations are reviewed. Results: The overwhelming majority of work on alignmentfree sequence has taken place in the past two decades, with most reports published in the past 5 years. Two main categories of methods have been proposed—methods based on word (oligomer) frequency, and methods that do not require resolving the sequence with fixed word length segments. The first category is based on the statistics of word frequency, on the distances defined in a Cartesian space defined by the frequency vectors, and on the information content of frequency distribution. The second category includes the use of Kolmogorov complexity and Chaos Theory. Despite their low visibility, alignmentfree metrics are in fact already widely used as preselection filters for alignmentbased querying of large applications. Recent work is furthering their usage as a scaleindependent methodology that is capable of recognizing homology when loss of contiguity is beyond the possibility of alignment. Availability: Most of the alignmentfree algorithms reviewed were implemented in MATLAB code and are available
A Primal Sketch of the Cortex Mean Curvature: a morphogenesis based approach to study the variability of the folding patterns
 IEEE Trans. Med. Imaging
, 2003
"... In this paper, we propose a new representation of the cortical surface that may be used to study the cortex folding process and to recover some putative stable anatomical landmarks called sulcal roots usually burried in the depth of adult brains. This representation is a primal sketch derived from a ..."
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Cited by 26 (2 self)
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In this paper, we propose a new representation of the cortical surface that may be used to study the cortex folding process and to recover some putative stable anatomical landmarks called sulcal roots usually burried in the depth of adult brains. This representation is a primal sketch derived from a scale space computed for the mean curvature of the cortical surface. This scalespace stems from a diffusion equation geodesic to the cortical surface. The primal sketch is made up of objects defined from mean curvature minima and saddle points. The resulting sketch aims first at highlighting significant elementary cortical folds, second at representing the fold merging process during brain growth. The relevance of the framework is illustrated by the study of central sulcus sulcal roots from antenatal to adult age. Some results are proposed for ten different brains. Some preliminary results are also provided for superior temporal sulcus.
Numerically Stable Generation of Correlation Matrices and Their Factors
 BIT
, 2000
"... . Correlation matricessymmetric positive semidefinite matrices with unit diagonal are important in statistics and in numerical linear algebra. For simulation and testing it is desirable to be able to generate random correlation matrices with specified eigenvalues (which must be nonnegative an ..."
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Cited by 21 (3 self)
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. Correlation matricessymmetric positive semidefinite matrices with unit diagonal are important in statistics and in numerical linear algebra. For simulation and testing it is desirable to be able to generate random correlation matrices with specified eigenvalues (which must be nonnegative and sum to the dimension of the matrix). A popular algorithm of Bendel and Mickey takes a matrix having the specified eigenvalues and uses a finite sequence of Given rotations to introduce 1s on the diagonal. We give improved formulae for computing the rotations and prove that the resulting algorithm is numerically stable. We show by example that the formulae originally proposed, which are used in certain existing Fortran implementations, can lead to serious instability. We also show how to modify the algorithm to generate a rectangular matrix with columns of unit 2norm. Such a matrix represents a correlation matrix in factored form, which can be preferable to representing the matrix itself, ...
Projection pursuit for exploratory supervised classification
 Journal of Computational and Graphical Statistics
, 2004
"... ABSTRACT In highdimensional data, one often seeks a few interesting lowdimensional projections which reveal important aspects of the data. Projection pursuit is a procedure for searching highdimensional data for interesting lowdimensional projections via the optimization of a criterion function ..."
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Cited by 15 (4 self)
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ABSTRACT In highdimensional data, one often seeks a few interesting lowdimensional projections which reveal important aspects of the data. Projection pursuit is a procedure for searching highdimensional data for interesting lowdimensional projections via the optimization of a criterion function called the projection pursuit index. Very few projection pursuit indices incorporate class or group information in the calculation, and hence can be adequately applied to supervised classification problems. We introduce new indices derived from linear discriminant analysis that can be used for exploratory supervised classification.
A dynamical model of general intelligence: the positive manifold of intelligence by mutualism. Psychological Review
, 2006
"... Scores on cognitive tasks used in intelligence tests correlate positively with each other, that is, they display a positive manifold of correlations. The positive manifold is often explained by positing a dominant latent variable, the g factor, associated with a single quantitative cognitive or biol ..."
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Cited by 10 (0 self)
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Scores on cognitive tasks used in intelligence tests correlate positively with each other, that is, they display a positive manifold of correlations. The positive manifold is often explained by positing a dominant latent variable, the g factor, associated with a single quantitative cognitive or biological process or capacity. In this article, a new explanation of the positive manifold based on a dynamical model is proposed, in which reciprocal causation or mutualism plays a central role. It is shown that the positive manifold emerges purely by positive beneficial interactions between cognitive processes during development. A single underlying g factor plays no role in the model. The model offers explanations of important findings in intelligence research, such as the hierarchical factor structure of intelligence, the low predictability of intelligence from early childhood performance, the integration/differentiation effect, the increase in heritability of g, and the Jensen effect, and is consistent with current explanations of the Flynn effect.
Diagnosability Analysis of MultiStation Manufacturing Processes
 Journal of Dynamic Systems, Measurement, and Control
, 2002
"... Variation propagation in a multistation manufacturing process (MMP) is described by the theory of ‘‘Stream of Variation.’ ’ Given that the measurements are obtained via certain sensor distribution scheme, the problem of whether the stream of variation of an MMP is diagnosable is of great interest t ..."
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Cited by 9 (5 self)
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Variation propagation in a multistation manufacturing process (MMP) is described by the theory of ‘‘Stream of Variation.’ ’ Given that the measurements are obtained via certain sensor distribution scheme, the problem of whether the stream of variation of an MMP is diagnosable is of great interest to both academia and industry. We present a comprehensive study of the diagnosability of MMPs in this paper. It is based on the state space model and is parallel to the concept of observability in control theory. Analogous to the observability matrix and index, the diagnosability matrix and index are first defined and then derived for MMP systems. The result of diagnosability study is applied to the evaluation of sensor distribution strategy. It can also be used as the basis to develop an optimal sensor distribution algorithm. An example of a threestation assembly process with multifixture layouts is presented to illustrate the methodology. �DOI: 10.1115/1.1435645� 1
Optimal sensor distribution for variation diagnosis in multistation manufacturing processes
, 2003
"... Abstract—This paper presents a methodology for optimal allocation of sensors in a multistation assembly process for the purpose of diagnosing in a timely manner variation sources that are responsible for product quality defects. A sensor system distributed in such a way can help manufacturers improv ..."
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Cited by 9 (5 self)
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Abstract—This paper presents a methodology for optimal allocation of sensors in a multistation assembly process for the purpose of diagnosing in a timely manner variation sources that are responsible for product quality defects. A sensor system distributed in such a way can help manufacturers improve product quality while, at the same time, reducing process downtime. Traditional approaches in sensor optimization fall into two categories: multistation sensor allocation for the purpose of product inspection (rather than diagnosis); and allocation of sensors for the purpose of variation diagnosis but at a single measurement station. In our approach, sensing information from different measurement stations is integrated into a statespace model and the effectiveness of a distributed sensor system is quantified by a diagnosability index. This index is further studied in terms of variation transmissibility between stations as well as variation detectability at individual stations. Based on an understanding of the mechanism of variation propagation, we develop a backwardpropagation strategy to determine the locations of measurement stations and the minimum number of sensors needed to achieve full diagnosability. An assembly example illustrates the methodology. Index Terms—Diagnosability, diagnosis of variation sources, multistation assembly process, sensor distribution.
Spatiotemporal EEG/MEG source analysis based on a parametric noise covariance model
 IEEE Transactions on Biomedical Engineering
, 2002
"... c○2000 IEEE. Personal use of this material is permitted. However, permission to reprint/republish this material for advertising or promotional purposes or for creating new collective works for resale or redistribution to servers or lists, or to reuse any copyrighted component of this work in other w ..."
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Cited by 8 (3 self)
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c○2000 IEEE. Personal use of this material is permitted. However, permission to reprint/republish this material for advertising or promotional purposes or for creating new collective works for resale or redistribution to servers or lists, or to reuse any copyrighted component of this work in other works must be obtained from the IEEE.
Feature Significance for Multivariate Kernel Density Estimation
"... Multivariate kernel density estimation provides information about structure in data. Feature significance is a technique for deciding whether features – such as local extrema – are statistically significant. This paper proposes a framework for feature significance in ddimensional data which combine ..."
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Cited by 8 (1 self)
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Multivariate kernel density estimation provides information about structure in data. Feature significance is a technique for deciding whether features – such as local extrema – are statistically significant. This paper proposes a framework for feature significance in ddimensional data which combines kernel density derivative estimators and hypothesis tests for modal regions. For the gradient and curvature estimators distributional properties are given, and pointwise test statistics are derived. The hypothesis tests extend the twodimensional feature significance ideas of Godtliebsen et al. (2002). The theoretical framework is complemented by novel visualisation for threedimensional data. Applications to real data sets show that tests based on the kernel curvature estimators perform well in identifying modal regions. These results can be enhanced by corresponding tests with kernel gradient estimators.
Model selection in electromagnetic source analysis with an application to VEF’s
 IEEE Transactions on Biomedical Engineering
, 2002
"... Abstract — In electromagnetic source analysis it is necessary to determine how many sources are required to describe the EEG or MEG adequately. Model selection procedures (MSP’s, or goodness of fit procedures) give an estimate of the required number of sources. Existing and new MSP’s are evaluated i ..."
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Cited by 7 (4 self)
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Abstract — In electromagnetic source analysis it is necessary to determine how many sources are required to describe the EEG or MEG adequately. Model selection procedures (MSP’s, or goodness of fit procedures) give an estimate of the required number of sources. Existing and new MSP’s are evaluated in different source and noise settings: two sources which are close or distant, and noise which is uncorrelated or correlated. The commonly used MSP residual variance is seen to be ineffective, that is it often selects too many sources. Alternatives like the adjusted Hotelling’s test, Bayes information criterion, and the Wald test on source amplitudes are seen to be effective. The adjusted Hotelling’s test is recommended if a conservative approach is taken, and MSP’s such as Bayes information criterion or the Wald test on source amplitudes are recommended if a more liberal approach is desirable. The MSP’s are applied to empirical data (visual evoked fields). I.