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Learning the Kernel Matrix with SemiDefinite Programming
, 2002
"... Kernelbased learning algorithms work by embedding the data into a Euclidean space, and then searching for linear relations among the embedded data points. The embedding is performed implicitly, by specifying the inner products between each pair of points in the embedding space. This information ..."
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Cited by 780 (22 self)
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is contained in the socalled kernel matrix, a symmetric and positive definite matrix that encodes the relative positions of all points. Specifying this matrix amounts to specifying the geometry of the embedding space and inducing a notion of similarity in the input spaceclassical model selection
Rate Matrix Prior (Draft)
, 2008
"... My convention is to have row vectors (of state frequencies) on the left acted on by transition matrices on the right. This seems to be the convention for Markov chains, although the opposite convention is generally more common. Rate matrices have rows summing to zero; transition matrices have rows s ..."
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summing to one. It is usual to impose the condition that the nondiagonal elements of a rate matrix sum to one, but I will work with unnormalised rate matrices. For nucleotides, an arbitrary 12parameter rate matrix, which I will call a nontime reversible, or NTR rate matrix, can be written as follows
The control of the false discovery rate in multiple testing under dependency
 Annals of Statistics
, 2001
"... Benjamini and Hochberg suggest that the false discovery rate may be the appropriate error rate to control in many applied multiple testing problems. A simple procedure was given there as an FDR controlling procedure for independent test statistics and was shown to be much more powerful than comparab ..."
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Cited by 1058 (16 self)
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Benjamini and Hochberg suggest that the false discovery rate may be the appropriate error rate to control in many applied multiple testing problems. A simple procedure was given there as an FDR controlling procedure for independent test statistics and was shown to be much more powerful than
Maximum Likelihood Phylogenetic Estimation from DNA Sequences with Variable Rates over Sites: Approximate Methods
 J. Mol. Evol
, 1994
"... Two approximate methods are proposed for maximum likelihood phylogenetic estimation, which allow variable rates of substitution across nucleotide sites. Three data sets with quite different characteristics were analyzed to examine empirically the performance of these methods. The first, called ..."
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Cited by 540 (28 self)
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Two approximate methods are proposed for maximum likelihood phylogenetic estimation, which allow variable rates of substitution across nucleotide sites. Three data sets with quite different characteristics were analyzed to examine empirically the performance of these methods. The first, called
Stochastic Perturbation Theory
, 1988
"... . In this paper classical matrix perturbation theory is approached from a probabilistic point of view. The perturbed quantity is approximated by a firstorder perturbation expansion, in which the perturbation is assumed to be random. This permits the computation of statistics estimating the variatio ..."
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Cited by 886 (35 self)
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. In this paper classical matrix perturbation theory is approached from a probabilistic point of view. The perturbed quantity is approximated by a firstorder perturbation expansion, in which the perturbation is assumed to be random. This permits the computation of statistics estimating
High dimensional graphs and variable selection with the Lasso
 ANNALS OF STATISTICS
, 2006
"... The pattern of zero entries in the inverse covariance matrix of a multivariate normal distribution corresponds to conditional independence restrictions between variables. Covariance selection aims at estimating those structural zeros from data. We show that neighborhood selection with the Lasso is a ..."
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Cited by 751 (23 self)
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The pattern of zero entries in the inverse covariance matrix of a multivariate normal distribution corresponds to conditional independence restrictions between variables. Covariance selection aims at estimating those structural zeros from data. We show that neighborhood selection with the Lasso
Gapped Blast and PsiBlast: a new generation of protein database search programs
 NUCLEIC ACIDS RESEARCH
, 1997
"... The BLAST programs are widely used tools for searching protein and DNA databases for sequence similarities. For protein comparisons, a variety of definitional, algorithmic and statistical refinements described here permits the execution time of the BLAST programs to be decreased substantially while ..."
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Cited by 8393 (85 self)
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for automatically combining statistically significant alignments produced by BLAST into a positionspecific score matrix, and searching the database using this matrix. The resulting PositionSpecific Iterated BLAST (PSIBLAST) program runs at approximately the same speed per iteration as gapped BLAST, but in many
Modeling Term Structures of Defaultable Bonds
, 1999
"... This article presents convenient reducedform models of the valuation of contingent claims subject to default risk, focusing on applications to the term structure of interest rates for corporate or sovereign bonds. Examples include the valuation of a creditspread option ..."
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Cited by 651 (34 self)
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This article presents convenient reducedform models of the valuation of contingent claims subject to default risk, focusing on applications to the term structure of interest rates for corporate or sovereign bonds. Examples include the valuation of a creditspread option
Sorting networks and their applications
, 1968
"... To achieve high throughput rates today's computers perform several operations simultaneously. Not only are I/O operations performed concurrently with computing, but also, in multiprocessors, several computing ..."
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Cited by 660 (0 self)
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To achieve high throughput rates today's computers perform several operations simultaneously. Not only are I/O operations performed concurrently with computing, but also, in multiprocessors, several computing
Results 1  10
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1,057,393