Search results for "Computation"
showing 10 items of 7362 documents
Extended differential geometric LARS for high-dimensional GLMs with general dispersion parameter
2018
A large class of modeling and prediction problems involves outcomes that belong to an exponential family distribution. Generalized linear models (GLMs) are a standard way of dealing with such situations. Even in high-dimensional feature spaces GLMs can be extended to deal with such situations. Penalized inference approaches, such as the $$\ell _1$$ or SCAD, or extensions of least angle regression, such as dgLARS, have been proposed to deal with GLMs with high-dimensional feature spaces. Although the theory underlying these methods is in principle generic, the implementation has remained restricted to dispersion-free models, such as the Poisson and logistic regression models. The aim of this…
Metagenomics reveals our incomplete knowledge of global diversity
2008
Metagenomic sequencing obtains huge amounts of sequences from environmental and clinical samples, thus providing a glimpse of the global prokaryotic diversity of both species and genes in these sources. The current trend in metagenomic analysis follows the so-called gene-centric approach, focused on describing the environments by the study of the functional roles of the proteins encoded in the sequenced genes. In this way, it is clear that metagenomic analysis relies heavily on the accurate knowledge of the universe of proteins stored in the databases. Nevertheless, it is known that some biases exist in the composition of databases (which are rich in sequences from common, cultivable and ea…
Using Statistical and Computer Models to Quantify Volcanic Hazards
2009
Risk assessment of rare natural hazards, such as large volcanic block and ash or pyroclastic flows, is addressed. Assessment is approached through a combination of computer modeling, statistical modeling, and extreme-event probability computation. A computer model of the natural hazard is used to provide the needed extrapolation to unseen parts of the hazard space. Statistical modeling of the available data is needed to determine the initializing distribution for exercising the computer model. In dealing with rare events, direct simulations involving the computer model are prohibitively expensive. The solution instead requires a combination of adaptive design of computer model approximation…
Robust estimation and inference for bivariate line-fitting in allometry.
2011
In allometry, bivariate techniques related to principal component analysis are often used in place of linear regression, and primary interest is in making inferences about the slope. We demonstrate that the current inferential methods are not robust to bivariate contamination, and consider four robust alternatives to the current methods -- a novel sandwich estimator approach, using robust covariance matrices derived via an influence function approach, Huber's M-estimator and the fast-and-robust bootstrap. Simulations demonstrate that Huber's M-estimators are highly efficient and robust against bivariate contamination, and when combined with the fast-and-robust bootstrap, we can make accurat…
Importance sampling type estimators based on approximate marginal Markov chain Monte Carlo
2020
We consider importance sampling (IS) type weighted estimators based on Markov chain Monte Carlo (MCMC) targeting an approximate marginal of the target distribution. In the context of Bayesian latent variable models, the MCMC typically operates on the hyperparameters, and the subsequent weighting may be based on IS or sequential Monte Carlo (SMC), but allows for multilevel techniques as well. The IS approach provides a natural alternative to delayed acceptance (DA) pseudo-marginal/particle MCMC, and has many advantages over DA, including a straightforward parallelisation and additional flexibility in MCMC implementation. We detail minimal conditions which ensure strong consistency of the sug…
Visualizing categorical data in ViSta
2003
The modules in the statistical package ViSta related to categorical data analysis are presented These modules are: visualization of frequency data with mosaic and bar plots, correspondence analysis, multiple correspondence analysis and loglinear analysis. All these methods are implemented in ViSta with a big emphasis on plots and graphical representations of data, as well as interactivity for the user with the system. These provide a system that has shown to be easy, useful, and powerful, both for novice and experienced users.
SeqEditor: an application for primer design and sequence analysis with or without GTF/GFF files
2021
[Motivation]: Sequence analyses oriented to investigate specific features, patterns and functions of protein and DNA/RNA sequences usually require tools based on graphic interfaces whose main characteristic is their intuitiveness and interactivity with the user’s expertise, especially when curation or primer design tasks are required. However, interface-based tools usually pose certain computational limitations when managing large sequences or complex datasets, such as genome and transcriptome assemblies. Having these requirments in mind we have developed SeqEditor an interactive software tool for nucleotide and protein sequences’ analysis.
Clustering of spatial point patterns
2006
Spatial point patterns arise as the natural sampling information in many problems. An ophthalmologic problem gave rise to the problem of detecting clusters of point patterns. A set of human corneal endothelium images is given. Each image is described by using a point pattern, the cell centroids. The main problem is to find groups of images corresponding with groups of spatial point patterns. This is interesting from a descriptive point of view and for clinical purposes. A new image can be compared with prototypes of each group and finally evaluated by the physician. Usual descriptors of spatial point patterns such as the empty-space function, the nearest distribution function or Ripley's K-…
A Knowledge Management and Decision Support Model for Enterprises
2011
We propose a novel knowledge management system (KMS) for enterprises. Our system exploits two different approaches for knowledge representation and reasoning: a document-based approach based on data-driven creation of a semantic space and an ontology-based model. Furthermore, we provide an expert system capable of supporting the enterprise decisional processes and a semantic engine which performs intelligent search on the enterprise knowledge bases. The decision support process exploits the Bayesian networks model to improve business planning process when performed under uncertainty. Copyright © 2011 Patrizia Ribino et al.
Prior-based Bayesian information criterion
2019
We present a new approach to model selection and Bayes factor determination, based on Laplace expansions (as in BIC), which we call Prior-based Bayes Information Criterion (PBIC). In this approach, the Laplace expansion is only done with the likelihood function, and then a suitable prior distribution is chosen to allow exact computation of the (approximate) marginal likelihood arising from the Laplace approximation and the prior. The result is a closed-form expression similar to BIC, but now involves a term arising from the prior distribution (which BIC ignores) and also incorporates the idea that different parameters can have different effective sample sizes (whereas BIC only allows one ov…