is contained in the so-called 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 space---classical model selection

summing to one. It is usual to impose the condition that the non-diagonal elements of a rate matrix sum to one, but I will work with unnormalised rate matrices. For nucleotides, an arbitrary 12-parameter rate matrix, which I will call a non-time reversible, or NTR rate matrix, can be written as follows

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

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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

. In this paper classical matrix perturbation theory is approached from a probabilistic point of view. The perturbed quantity is approximated by a first-order perturbation expansion, in which the perturbation is assumed to be random. This permits the computation of statistics estimating

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

for automatically combining statistically significant alignments produced by BLAST into a position-specific score matrix, and searching the database using this matrix. The resulting Position-Specific Iterated BLAST (PSIBLAST) program runs at approximately the same speed per iteration as gapped BLAST, but in many

This article presents convenient reduced-form 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 credit-spread option

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