scholarly journals Towards Efficiency in the Residual and Parametric Bootstrap Techniques

2016 ◽  
Vol 5 (5) ◽  
pp. 285
Author(s):  
Acha Chigozie K.
Keyword(s):  
Parametric Bootstrap ◽  
Bootstrap Techniques

scholarly journals Goodness-of-Fit Tests for Bivariate Time Series of Counts

Econometrics ◽  
2021 ◽  
Vol 9 (1) ◽  
pp. 10
Author(s):  
Šárka Hudecová ◽  
Marie Hušková ◽  
Simos G. Meintanis
Keyword(s):  
Goodness Of Fit ◽  
Probability Generating Function ◽  
Parametric Bootstrap ◽  
Real Data ◽  
Data Sets ◽  
Test Statistics ◽  
Finite Sample ◽  
Generalized Poisson ◽  
Goodness Of Fit Tests ◽  
Monte Carlo Experiments

This article considers goodness-of-fit tests for bivariate INAR and bivariate Poisson autoregression models. The test statistics are based on an L2-type distance between two estimators of the probability generating function of the observations: one being entirely nonparametric and the second one being semiparametric computed under the corresponding null hypothesis. The asymptotic distribution of the proposed tests statistics both under the null hypotheses as well as under alternatives is derived and consistency is proved. The case of testing bivariate generalized Poisson autoregression and extension of the methods to dimension higher than two are also discussed. The finite-sample performance of a parametric bootstrap version of the tests is illustrated via a series of Monte Carlo experiments. The article concludes with applications on real data sets and discussion.

Assessing the Impact of Secondary Structure and Solvent Accessibility on Protein Evolution

Genetics ◽  
1998 ◽  
Vol 149 (1) ◽  
pp. 445-458 ◽  
Author(s):  
Nick Goldman ◽  
Jeffrey L Thorne ◽  
David T Jones
Keyword(s):  
Amino Acid ◽  
Secondary Structure ◽  
Protein Evolution ◽  
Solvent Accessibility ◽  
Strong Association ◽  
Length Distribution ◽  
Parametric Bootstrap ◽  
Amino Acid Replacement ◽  
Physical Constraints ◽  
The Impact

Abstract Empirically derived models of amino acid replacement are employed to study the association between various physical features of proteins and evolution. The strengths of these associations are statistically evaluated by applying the models of protein evolution to 11 diverse sets of protein sequences. Parametric bootstrap tests indicate that the solvent accessibility status of a site has a particularly strong association with the process of amino acid replacement that it experiences. Significant association between secondary structure environment and the amino acid replacement process is also observed. Careful description of the length distribution of secondary structure elements and of the organization of secondary structure and solvent accessibility along a protein did not always significantly improve the fit of the evolutionary models to the data sets that were analyzed. As indicated by the strength of the association of both solvent accessibility and secondary structure with amino acid replacement, the process of protein evolution—both above and below the species level—will not be well understood until the physical constraints that affect protein evolution are identified and characterized.

scholarly journals The 3d $$ \mathcal{N} $$ = 6 bootstrap: from higher spins to strings to membranes

2021 ◽  
Vol 2021 (5) ◽  
Author(s):  
Damon J. Binder ◽  
Shai M. Chester ◽  
Max Jerdee ◽  
Silviu S. Pufu
Keyword(s):  
Block Decomposition ◽  
Point Function ◽  
Present Evidence ◽  
Bootstrap Techniques ◽  
Wide Range ◽  
Higher Spin ◽  
Tensor Multiplet ◽  
Higher Spins ◽  
M Theory ◽  
Chern Simons

Abstract We study the space of 3d $$ \mathcal{N} $$ N = 6 SCFTs by combining numerical bootstrap techniques with exact results derived using supersymmetric localization. First we derive the superconformal block decomposition of the four-point function of the stress tensor multiplet superconformal primary. We then use supersymmetric localization results for the $$ \mathcal{N} $$ N = 6 U(N)k × U(N + M)−k Chern-Simons-matter theories to determine two protected OPE coefficients for many values of N, M, k. These two exact inputs are combined with the numerical bootstrap to compute precise rigorous islands for a wide range of N, k at M = 0, so that we can non-perturbatively interpolate between SCFTs with M-theory duals at small k and string theory duals at large k. We also present evidence that the localization results for the U(1)2M × U (1 + M)−2M theory, which has a vector-like large-M limit dual to higher spin theory, saturates the bootstrap bounds for certain protected CFT data. The extremal functional allows us to then conjecturally reconstruct low-lying CFT data for this theory.

Spectral dynamic causal modelling of resting-state fMRI: an exploratory study relating effective brain connectivity in the default mode network to genetics

2020 ◽  
Vol 19 (3) ◽  
Author(s):  
Yunlong Nie ◽  
Eugene Opoku ◽  
Laila Yasmin ◽  
Yin Song ◽  
Jie Wang ◽  
...  
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Default Mode Network ◽  
Resting State ◽  
Brain Connectivity ◽  
Parametric Bootstrap ◽  
Imaging Genetics ◽  
Nucleotide Polymorphisms ◽  
Mixed Effect ◽  
Default Mode

AbstractWe conduct an imaging genetics study to explore how effective brain connectivity in the default mode network (DMN) may be related to genetics within the context of Alzheimer’s disease and mild cognitive impairment. We develop an analysis of longitudinal resting-state functional magnetic resonance imaging (rs-fMRI) and genetic data obtained from a sample of 111 subjects with a total of 319 rs-fMRI scans from the Alzheimer’s Disease Neuroimaging Initiative (ADNI) database. A Dynamic Causal Model (DCM) is fit to the rs-fMRI scans to estimate effective brain connectivity within the DMN and related to a set of single nucleotide polymorphisms (SNPs) contained in an empirical disease-constrained set which is obtained out-of-sample from 663 ADNI subjects having only genome-wide data. We relate longitudinal effective brain connectivity estimated using spectral DCM to SNPs using both linear mixed effect (LME) models as well as function-on-scalar regression (FSR). In both cases we implement a parametric bootstrap for testing SNP coefficients and make comparisons with p-values obtained from asymptotic null distributions. In both networks at an initial q-value threshold of 0.1 no effects are found. We report on exploratory patterns of associations with relatively high ranks that exhibit stability to the differing assumptions made by both FSR and LME.

scholarly journals Integration and Modularity of Quantitative Trait Locus Effects on Geometric Shape in the Mouse Mandible

Genetics ◽  
2004 ◽  
Vol 166 (4) ◽  
pp. 1909-1921
Author(s):  
Christian Peter Klingenberg ◽  
Larry J Leamy ◽  
James M Cheverud
Keyword(s):  
Quantitative Trait ◽  
Parametric Bootstrap ◽  
Interval Mapping ◽  
Procrustes Analysis ◽  
Bootstrap Test ◽  
Mandible Shape ◽  
Trait Locus ◽  
F2 Generation ◽  
Analysis Interval ◽  
Qtl Effects

Abstract The mouse mandible has long served as a model system for complex morphological structures. Here we use new methodology based on geometric morphometrics to test the hypothesis that the mandible consists of two main modules, the alveolar region and the ascending ramus, and that this modularity is reflected in the effects of quantitative trait loci (QTL). The shape of each mandible was analyzed by the positions of 16 morphological landmarks and these data were analyzed using Procrustes analysis. Interval mapping in the F2 generation from intercrosses of the LG/J and SM/J strains revealed 33 QTL affecting mandible shape. The QTL effects corresponded to a variety of shape changes, but ordination or a parametric bootstrap test of clustering did not reveal any distinct groups of QTL that would affect primarily one module or the other. The correlations of landmark positions between the two modules tended to be lower than the correlations between arbitrary subsets of landmarks, indicating that the modules were relatively independent of each other and confirming the hypothesized location of the boundary between them. While these results are in agreement with the hypothesis of modularity, they also underscore that modularity is a question of the relative degrees to which QTL contribute to different traits, rather than a question of discrete sets of QTL contributing to discrete sets of traits.

scholarly journals Parametric bootstrap estimators for hybrid inference in forest inventories

2017 ◽  
Vol 91 (3) ◽  
pp. 354-365 ◽  
Author(s):  
Mathieu Fortin ◽  
Rubén Manso ◽  
Robert Schneider
Keyword(s):  
Multiple Imputation ◽  
Nonlinear Models ◽  
Parametric Bootstrap ◽  
Simulation Studies ◽  
Variance Estimator ◽  
Resampling Methods ◽  
Forest Inventories ◽  
Point Estimator ◽  
Complex Models ◽  
High Level

Abstract In forestry, the variable of interest is not always directly available from forest inventories. Consequently, practitioners have to rely on models to obtain predictions of this variable of interest. This context leads to hybrid inference, which is based on both the probability design and the model. Unfortunately, the current analytical hybrid estimators for the variance of the point estimator are mainly based on linear or nonlinear models and their use is limited when the model reaches a high level of complexity. An alternative consists of using a variance estimator based on resampling methods (Rubin, D. B. (1987). Multiple imputation for nonresponse surveys. John Wiley & Sons, Hoboken, New Jersey, USA). However, it turns out that a parametric bootstrap (BS) estimator of the variance can be biased in contexts of hybrid inference. In this study, we designed and tested a corrected BS estimator for the variance of the point estimator, which can easily be implemented as long as all of the stochastic components of the model can be properly simulated. Like previous estimators, this corrected variance estimator also makes it possible to distinguish the contribution of the sampling and the model to the variance of the point estimator. The results of three simulation studies of increasing complexity showed no evidence of bias for this corrected variance estimator, which clearly outperformed the BS variance estimator used in previous studies. Since the implementation of this corrected variance estimator is not much more complicated, we recommend its use in contexts of hybrid inference based on complex models.

A New Method for Characterizing Replacement Rate Variation in Molecular Sequences: Application of the Fourier and Wavelet Models to Drosophila and Mammalian Proteins

Genetics ◽  
2000 ◽  
Vol 154 (1) ◽  
pp. 381-395
Author(s):  
Pavel Morozov ◽  
Tatyana Sitnikova ◽  
Gary Churchill ◽  
Francisco José Ayala ◽  
Andrey Rzhetsky
Keyword(s):  
Wavelet Transforms ◽  
Parametric Bootstrap ◽  
Real Data ◽  
New Method ◽  
Rate Variation ◽  
Discrete Wavelet ◽  
Data Sets ◽  
Ratio Test ◽  
Replacement Rate ◽  
New Models

Abstract We propose models for describing replacement rate variation in genes and proteins, in which the profile of relative replacement rates along the length of a given sequence is defined as a function of the site number. We consider here two types of functions, one derived from the cosine Fourier series, and the other from discrete wavelet transforms. The number of parameters used for characterizing the substitution rates along the sequences can be flexibly changed and in their most parameter-rich versions, both Fourier and wavelet models become equivalent to the unrestricted-rates model, in which each site of a sequence alignment evolves at a unique rate. When applied to a few real data sets, the new models appeared to fit data better than the discrete gamma model when compared with the Akaike information criterion and the likelihood-ratio test, although the parametric bootstrap version of the Cox test performed for one of the data sets indicated that the difference in likelihoods between the two models is not significant. The new models are applicable to testing biological hypotheses such as the statistical identity of rate variation profiles among homologous protein families. These models are also useful for determining regions in genes and proteins that evolve significantly faster or slower than the sequence average. We illustrate the application of the new method by analyzing human immunoglobulin and Drosophilid alcohol dehydrogenase sequences.

scholarly journals A Novel Method of Fault Detection and Identification in a Tightly Coupled, INS/GNSS-Integrated System

Sensors ◽  
2021 ◽  
Vol 21 (9) ◽  
pp. 2922
Author(s):  
Fan Zhang ◽  
Ye Wang ◽  
Yanbin Gao
Keyword(s):  
Fault Detection ◽  
Parametric Bootstrap ◽  
Integrated System ◽  
Range Data ◽  
Navigation Systems ◽  
Integrated Navigation ◽  
Multiple Faults ◽  
Detection And Identification ◽  
Fault Detection And Identification ◽  
Tightly Coupled

Fault detection and identification are vital for guaranteeing the precision and reliability of tightly coupled inertial navigation system (INS)/global navigation satellite system (GNSS)-integrated navigation systems. A variance shift outlier model (VSOM) was employed to detect faults in the raw pseudo-range data in this paper. The measurements were partially excluded or included in the estimation process depending on the size of the associated shift in the variance. As an objective measure, likelihood ratio and score test statistics were used to determine whether the measurements inflated variance and were deemed to be faulty. The VSOM is appealing because the down-weighting of faulty measurements with the proper weighting factors in the analysis automatically becomes part of the estimation procedure instead of deletion. A parametric bootstrap procedure for significance assessment and multiple testing to identify faults in the VSOM is proposed. The results show that VSOM was validated through field tests, and it works well when single or multiple faults exist in GNSS measurements.

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