• # ppmlhdfe

• Referenced in 1 article [sw37489]
• techniques we introduce for accelerating HDFE-IRLS estimation specifically. ppmlhdfe also implements a novel ... check for the existence of (pseudo) maximum likelihood estimates...
• # latentnet

• Referenced in 18 articles [sw10550]
• modeling networks based on positing the existence of an latent space of characteristics ... Carlo algorithm. It can also compute maximum likelihood estimates for the latent position model...
• # Medlda

• Referenced in 11 articles [sw11723]
• data. However, existing supervised topic models predominantly employ likelihood-driven objective functions for learning ... corpus. In this paper, we propose the maximum entropy discrimination latent Dirichlet allocation (MedLDA) model ... applied for jointly max-margin and maximum likelihood learning of directed or undirected topic models ... variational methods for posterior inference and parameter estimation are derived and extensive empirical studies...
• # PoMo

• Referenced in 7 articles [sw35039]
• estimation. Here, we present a simple maximum likelihood approach that accounts for ancestral variation ... that we have recently shown to efficiently estimate mutation rates and fixation biases from within ... extend this model to perform efficient estimation of species trees. We test the performance ... sorting using simulations and compare it with existing methods both in accuracy and computational speed...
• # Rate4Site

• Referenced in 7 articles [sw35756]
• proteins of known three-dimensional (3D) structure exist, with yet unknown function. In light ... Rate4Site estimates the rate of evolution of amino acid sites using the maximum likelihood...
• # MEGA4

• Referenced in 7 articles [sw07695]
• MEGA software, which expands on the existing facilities for editing DNA sequence data from autosequencers ... manual sequence alignment, analyzing sequence alignments to estimate evolutionary distances, inferring phylogenetic trees, and testing ... generated. Another new feature is the Maximum Composite Likelihood (MCL) method for estimating evolutionary distances...
• # COMODE

• Referenced in 3 articles [sw36145]
• model are estimated by maximum likelihood using a nonlinear constraint optimization method. Likelihood-based cross ... performance of COMODE is compared with existing motif detection methods on simulated data that incorporate...
• # CodonTest

• Referenced in 1 article [sw37906]
• frequencies and branch lengths are estimated using standard maximum likelihood optimization procedures. We apply ... alignments and show improved model fit over existing models of codon evolution. Our results suggest...
• # BEAGLE

• Referenced in 4 articles [sw12586]
• approaches such as Bayesian inference and maximum likelihood estimation. Yet, for large data sets ... specialized library for phylogenetic calculation would allow existing software packages to make more effective...

• Referenced in 1 article [sw23503]
• research fields. However, currently only few estimators exist for individuals that are admixed, i.e. have ... from more than one population, and these estimators fail in some situations. RESULTS: We present ... software tool, RelateAdmix, for obtaining maximum likelihood estimates of pairwise relatedness from genetic data between...
• # roc

• Referenced in 2 articles [sw37359]
• Parametric maximum likelihood methods for fitting of the ROC curve provide direct estimates ... provide estimates of the area under the ROC curve, but do not directly estimate ... curve are com- monly used, although ambiguity exists about their behavior under diverse study conditions...
• # SemRegex

• Referenced in 1 article [sw36206]
• model using a syntax-based objective: maximum likelihood estimation (MLE). Such syntax-based approaches ... expressions from natural language. Different from the existing syntax-based approaches, SemRegex trains the model...
• # AprilCal

• Referenced in 1 article [sw37886]
• parameters in the camera model. Existing toolboxes ask users to capture images of a calibration ... their choosing, after which the maximum-likelihood calibration is computed using all images ... computes the stability of the focal length estimates for initializing the calibration, and another that...
• # GW-SEM

• Referenced in 1 article [sw37731]
• using a Diagonally Weighted Least Squares (DWLS) estimator for four common SEMs: a one-factor ... with the more traditional Full Information Maximum Likelihood parameters and p-values. We also present ... power analyses and a comparison with and existing multivariate GWAS software package...
• # pyMEF

• Referenced in 2 articles [sw07455]
• include Dirichlet process mixtures and $k$-maximum likelihood estimators. Most of the methods, including expectation ... compute. On the other hand, kernel density estimation yields large models which are computationally cheap ... simplification of the kernel density estimator. The simplification is a clustering method based ... exponential families. Unlike most of the other existing tools, this library allows...
• # DACTAL

• Referenced in 1 article [sw29613]
• sequences are challenging for existing methods, the estimation of substantially larger phylogenies poses a problem ... phylogeny estimation that produces trees from unaligned sequence datasets without ever needing to estimate ... decomposes the taxon set into overlapping subsets, estimates trees on each subset, and then combines ... compare DACTAL to SATé and maximum likelihood trees on estimated alignments using simulated and real...
• # strel2

• Referenced in 0 articles [sw37620]
• population-based datasets. strel2 implements the maximum-likelihood estimation approach developed by Estève ... user to obtain interval- and covariate-specific estimates of the quantities of interest. Although alternative ... more powerful commands for relative survival exist, strel2 is a simple tool that is particularly...