Search results for "Core"
showing 10 items of 1999 documents
Light Scattering Measurements of Hemoglobin Critical Fluctuation and the Energy Landscape For Polymerization
2010
We have developed a novel method for measuring light scattering to observe critical fluctuations in hemoglobin (Hb) solutions. A small rectangular cell (0.2 x 4.0 x 30 mm) is filled with 24 μL of Hb solution. An optical fiber with outer diameter of 125 μm (62.5 μm core) is sealed into the cell in contact with the solution, and light scattering is measured at 90°. The flat faces of the cell permit measuring absorbance spectra to ensure sample integrity. The scattering source is a 785 nm laser diode that delivers 1.5 mW to the sample. Scattered light is detected by a Hamamatsu GaAs(Cs) PMT via a LWD microscope objective. Measured scattered light intensity agrees (±10%) with scattered intensit…
Interval estimation for the breakpoint in segmented regression: a smoothed score-based approach
2017
Summary This paper is concerned with interval estimation for the breakpoint parameter in segmented regression. We present score-type confidence intervals derived from the score statistic itself and from the recently proposed gradient statistic. Due to lack of regularity conditions of the score, non-smoothness and non-monotonicity, naive application of the score-based statistics is unfeasible and we propose to exploit the smoothed score obtained via induced smoothing. We compare our proposals with the traditional methods based on the Wald and the likelihood ratio statistics via simulations and an analysis of a real dataset: results show that the smoothed score-like statistics perform in prac…
BGSA: a bit-parallel global sequence alignment toolkit for multi-core and many-core architectures
2018
Abstract Motivation Modern bioinformatics tools for analyzing large-scale NGS datasets often need to include fast implementations of core sequence alignment algorithms in order to achieve reasonable execution times. We address this need by presenting the BGSA toolkit for optimized implementations of popular bit-parallel global pairwise alignment algorithms on modern microprocessors. Results BGSA outperforms Edlib, SeqAn and BitPAl for pairwise edit distance computations and Parasail, SeqAn and BitPAl when using more general scoring schemes for pairwise alignments of a batch of sequence reads on both standard multi-core CPUs and Xeon Phi many-core CPUs. Furthermore, banded edit distance perf…
Automatic variable selection for exposure-driven propensity score matching with unmeasured confounders.
2020
Multivariable model building for propensity score modeling approaches is challenging. A common propensity score approach is exposure-driven propensity score matching, where the best model selection strategy is still unclear. In particular, the situation may require variable selection, while it is still unclear if variables included in the propensity score should be associated with the exposure and the outcome, with either the exposure or the outcome, with at least the exposure or with at least the outcome. Unmeasured confounders, complex correlation structures, and non-normal covariate distributions further complicate matters. We consider the performance of different modeling strategies in …
Sample size planning for survival prediction with focus on high-dimensional data
2011
Sample size planning should reflect the primary objective of a trial. If the primary objective is prediction, the sample size determination should focus on prediction accuracy instead of power. We present formulas for the determination of training set sample size for survival prediction. Sample size is chosen to control the difference between optimal and expected prediction error. Prediction is carried out by Cox proportional hazards models. The general approach considers censoring as well as low-dimensional and high-dimensional explanatory variables. For dimension reduction in the high-dimensional setting, a variable selection step is inserted. If not all informative variables are included…
On Rao Score and Pearson X2 Statistics in Generalized Linear Models
2005
The identity of the Rao score and PearsonX 2 statistics is well known in the areas where the latter was first introduced: goodness-of-fit in contingency tables and binary responses. We show in this paper that the same identity holds when the two statistics are used for testing goodness-of-fit of Generalized Linear Models. We also highlight the connections that exist between the two statistics when they are used for the comparison of nested models. Finally, we discuss some merits of these unifying results.
Adaptive reference-free compression of sequence quality scores
2014
Motivation: Rapid technological progress in DNA sequencing has stimulated interest in compressing the vast datasets that are now routinely produced. Relatively little attention has been paid to compressing the quality scores that are assigned to each sequence, even though these scores may be harder to compress than the sequences themselves. By aggregating a set of reads into a compressed index, we find that the majority of bases can be predicted from the sequence of bases that are adjacent to them and hence are likely to be less informative for variant calling or other applications. The quality scores for such bases are aggressively compressed, leaving a relatively small number at full reso…
A note on adjusted responses, fitted values and residuals in Generalized Linear Models
2014
Adjusted responses, adjusted fitted values and adjusted residuals are known to play in Generalized Linear Models the role played in Linear Models by observations, fitted values and ordinary residuals. We think this parallelism, which was widely recognized and used in the early literature on Generalized Linear Models, has been somewhat overlooked in more recent presentations. We revise this parallelism, systematizing and proving some results that are either scattered or not satisfactorily spelled out in the literature. In particular, we formally derive the asymptotic dispersion matrix of the (scaled) adjusted residuals, by proving that in Generalized Linear Models the fitted values are asym…
A differential-geometric approach to generalized linear models with grouped predictors
2016
We propose an extension of the differential-geometric least angle regression method to perform sparse group inference in a generalized linear model. An efficient algorithm is proposed to compute the solution curve. The proposed group differential-geometric least angle regression method has important properties that distinguish it from the group lasso. First, its solution curve is based on the invariance properties of a generalized linear model. Second, it adds groups of variables based on a group equiangularity condition, which is shown to be related to score statistics. An adaptive version, which includes weights based on the Kullback-Leibler divergence, improves its variable selection fea…
Premature conclusions about the signal‐to‐noise ratio in structural equation modeling research : A commentary on Yuan and Fang (2023)
2023
In a recent article published in this journal, Yuan and Fang (British Journal of Mathematical and Statistical Psychology, 2023) suggest comparing structural equation modeling (SEM), also known as covariance-based SEM (CB-SEM), estimated by normal-distribution-based maximum likelihood (NML), to regression analysis with (weighted) composites estimated by least squares (LS) in terms of their signal-to-noise ratio (SNR). They summarize their findings in the statement that “[c]ontrary to the common belief that CB-SEM is the preferred method for the analysis of observational data, this article shows that regression analysis via weighted composites yields parameter estimates with much smaller stan…