Maximum-likelihood methods in DIALS

Maximum Likelihood Methods in Molecular Phylogenetics

Least squares methods in maximum likelihood problems

It is well known that the GaussNewton algorithm for solving nonlinear least squares problems is a special case of the scoring algorithm for maximizing log likelihoods. What has received less attention is that the computation of the current correction in the scoring algorithm in both its line search and trust region forms can be cast as a linear least squares problem. This is an important observ...

Simple Maximum Likelihood Methods for the Optical

Recently a new method for obtaining restriction maps was developed by David Schwartz at NYU. Using this method restriction maps are created from uorescent images of individual molecules obtained using a microscope. For every individual observed molecule, image processing methods are used to generate a list of the approximate locations of the sites where the molecule is cut by the restriction en...

Maximum Likelihood Methods for Phylogenetic Inference

In this article, we provide an overview of maximum likelihood methods for phylogenetic inference. A brief introduction to general maximum likelihood estimation is provided. We define a phylogenetic likelihood, summarize how to compute this likelihood, and then discuss approaches used to maximize the phylogenetic likelihood function. We discuss a property of the maximum likelihood estimation, ca...

Maximum Likelihood Estimation of Parameters in Generalized Functional Linear Model

Sometimes, in practice, data are a function of another variable, which is called functional data. If the scalar response variable is categorical or discrete, and the covariates are functional, then a generalized functional linear model is used to analyze this type of data. In this paper, a truncated generalized functional linear model is studied and a maximum likelihood approach is used to esti...