Association between urinary polycyclic aromatic hydrocarbons and risk of metabolic associated fatty liver disease.

OBJECTIVE: To investigate the effect of urinary PAHs on MAFLD. METHODS: The study included 3,136 adults from the National Health and Nutrition Examination Survey (NHANES) conducted between 2009 and 2016. Among them, 1,056 participants were diagnosed with MAFLD and were designated as the case group. The analysis of the relationship between monohydroxy metabolites of seven PAHs in urine and MAFLD was carried out using logistic regression and Bayesian kernel regression (BKMR) models. RESULTS: In single-pollutant models, the concentration of 2-hydroxynaphthalene (2-OHNAP) was positively correlated with MAFLD (OR = 1.47, 95% CI 1.18, 1.84), whereas 3-hydroxyfluorene (3-OHFLU) and 1-hydroxypyrene (1-OHPYR) demonstrated a negative correlation with MAFLD (OR = 0.59, 95% CI 0.48 0.73; OR = 0.70, 95% CI 0.55, 0.89). Conversely, in multi-pollutant models, 2-OHNAP, 2-hydroxyfluorene (2-OHFLU), 2-hydroxyphenanthrene, and 3-hydroxyphenanthrene (2&3-OHPHE) displayed positive correlations with MAFLD (OR = 6.17, 95% CI 3.15, 12.07; OR = 2.59, 95% CI 1.37, 4.89). However, 3-OHFLU and 1-OHPYR continued to exhibit negative correlations with MAFLD (OR = 0.09, 95% CI 0.05, 0.15; OR = 0.62, 95% CI 0.43, 0.88). Notably, the BKMR analysis mixtures approach did not indicate a significant joint effect of multiple PAHs on MAFLD, but identified interactions between 3-OHFLU and 2-OHFLU, 1-OHPYR and 2-OHFLU, and 1-OHPYR and 3-OHFLU. CONCLUSION: No significant association was found between mixed PAHs exposure and the risk of MAFLD. However, interactions were observed between 3-OHFLU and 2-OHFLU. Both 2-OHFLU and 2&3-OHPHE exposure are significant risk factors for MAFLD, whereas 3-OHFLU is a key protective factor for the disease.

Adaptive orthogonal directional total variation with kernel regression for CT image denoising.

BACKGROUND: Low-dose computed tomography (CT) has been successful in reducing radiation exposure for patients. However, the use of reconstructions from sparse angle sampling in low-dose CT often leads to severe streak artifacts in the reconstructed images. OBJECTIVE: In order to address this issue and preserve image edge details, this study proposes an adaptive orthogonal directional total variation method with kernel regression. METHODS: The CT reconstructed images are initially processed through kernel regression to obtain the N-term Taylor series, which serves as a local representation of the regression function. By expanding the series to the second order, we obtain the desired estimate of the regression function and localized information on the first and second derivatives. To mitigate the noise impact on these derivatives, kernel regression is performed again to update the first and second derivatives. Subsequently, the original reconstructed image, its local approximation, and the updated derivatives are summed using a weighting scheme to derive the image used for calculating orientation information. For further removal of stripe artifacts, the study introduces the adaptive orthogonal directional total variation (AODTV) method, which denoises along both the edge direction and the normal direction, guided by the previously obtained orientation. RESULTS: Both simulation and real experiments have obtained good results. The results of two real experiments show that the proposed method has obtained PSNR values of 34.5408 dB and 29.4634 dB, which are 1.2392-5.9333 dB and 2.828-6.7995 dB higher than the contrast denoising algorithm, respectively, indicating that the proposed method has good denoising performance. CONCLUSIONS: The study demonstrates the effectiveness of the method in eliminating strip artifacts and preserving the fine details of the images.

Flexible joint modeling of mean and dispersion for the directional tuning of neuronal spike counts.

The study of how the number of spikes in a middle temporal visual area (MT/V5) neuron is tuned to the direction of a visual stimulus has attracted considerable attention over the years, but recent studies suggest that the variability of the number of spikes might also be influenced by the directional stimulus. This entails that Poisson regression models are not adequate for this type of data, as the observations usually present over/underdispersion (or both) with respect to the Poisson distribution. This paper makes use of the double exponential family and presents a flexible model to estimate, jointly, the mean and dispersion functions, accounting for the effect of a circular covariate. The empirical performance of the proposal is explored via simulations and an application to a neurological data set is shown.

Associating somatic mutation with clinical outcomes through kernel regression and optimal transport.

Somatic mutations in cancer patients are inherently sparse and potentially high dimensional. Cancer patients may share the same set of deregulated biological processes perturbed by different sets of somatically mutated genes. Therefore, when assessing the associations between somatic mutations and clinical outcomes, gene-by-gene analysis is often under-powered because it does not capture the complex disease mechanisms shared across cancer patients. Rather than testing genes one by one, an intuitive approach is to aggregate somatic mutation data of multiple genes to assess their joint association with clinical outcomes. The challenge is how to aggregate such information. Building on the optimal transport method, we propose a principled approach to estimate the similarity of somatic mutation profiles of multiple genes between tumor samples, while accounting for gene-gene similarities defined by gene annotations or empirical mutational patterns. Using such similarities, we can assess the associations between somatic mutations and clinical outcomes by kernel regression. We have applied our method to analyze somatic mutation data of 17 cancer types and identified at least five cancer types, where somatic mutations are associated with overall survival, progression-free interval, or cytolytic activity.

Multiple kernel fusion: A novel approach for lake water depth modeling.

Multiple kernel fusion (MKF) refers to the task of combining multiple sources of information in the Hilbert space for improved performance. Very often the combined kernel is formed as a linear composition of multiple base kernels where the combination weights are learned from the data. As the first application of an MKF approach in hydrological modeling, lake water depth as one of the pivot factors in the reservoir analysis is simulated by considering different hydro-meteorological variables. The role of each individual input parameter is initially investigated by applying a kernel regression approach. We then illustrate the utility of an MKF formalism which learns kernel combination of weights to yield an optimal composition for kernel regression. A set of 40-year data collected from 27 groundwater and streamflow stations and 7 meteorological stations for precipitation and evaporation parameters in the vicinity of Lake Urmia are utilized for model development. Both visual and quantitative statistical performance criteria illustrate a superior performance for the MKF approach compared to kernel ridge regression (KRR), the support vector regression (SVR), back propagation neural network (BPNN) and auto regressive (AR) models. More specifically, while each individual input parameter fails to provide an accurate prediction for lake water depth modeling, an optimal combination of all input parameters incorporating the groundwater level, streamflow, precipitation and evaporation via a multiple kernel learning approach enhances the predictive performance of the model accuracy in the multiple scenarios. The promising results (RMSE = 0.098 m; R2 = 0.987; NSE = 0.986) may motivate the application of a MKF approach towards solving alternative and complex hydrological problems.

Distance-Metric Learning for Personalized Survival Analysis.

Personalized time-to-event or survival prediction with right-censored outcomes is a pervasive challenge in healthcare research. Although various supervised machine learning methods, such as random survival forests or neural networks, have been adapted to handle such outcomes effectively, they do not provide explanations for their predictions, lacking interpretability. In this paper, an alternative method for survival prediction by weighted nearest neighbors is proposed. Fitting this model to data entails optimizing the weights by learning a metric. An individual prediction of this method can be explained by providing the user with the most influential data points for this prediction, i.e., the closest data points and their weights. The strengths and weaknesses in terms of predictive performance are highlighted on simulated data and an application of the method on two different real-world datasets of breast cancer patients shows its competitiveness with established methods.

Trans-ethnic meta-analysis of rare variants in sequencing association studies.

Trans-ethnic meta-analysis is a powerful tool for detecting novel loci in genetic association studies. However, in the presence of heterogeneity among different populations, existing gene-/region-based rare variants meta-analysis methods may be unsatisfactory because they do not consider genetic similarity or dissimilarity among different populations. In response, we propose a score test under the modified random effects model for gene-/region-based rare variants associations. We adapt the kernel regression framework to construct the model and incorporate genetic similarities across populations into modeling the heterogeneity structure of the genetic effect coefficients. We use a resampling-based copula method to approximate asymptotic distribution of the test statistic, enabling efficient estimation of p-values. Simulation studies show that our proposed method controls type I error rates and increases power over existing approaches in the presence of heterogeneity. We illustrate our method by analyzing T2D-GENES consortium exome sequence data to explore rare variant associations with several traits.

Improving non-invasive hemoglobin measurement accuracy using nonparametric models.

Uncontrolled hemorrhage is a leading cause of preventable death among patients with trauma. Early recognition of hemorrhage can aid in the decision to administer blood transfusion and improve patient outcomes. To provide real-time measurement and continuous monitoring of hemoglobin concentration, the non-invasive and continuous hemoglobin (SpHb) measurement device has drawn extensive attention in clinical practice. However, the accuracy of such a device varies in different scenarios, so the use is not yet widely accepted. This article focuses on using statistical nonparametric models to improve the accuracy of SpHb measurement device by considering measurement bias among instantaneous measurements and individual evolution trends. In the proposed method, the robust locally estimated scatterplot smoothing (LOESS) method and the Kernel regression model are considered to address those issues. Overall performance of the proposed method was evaluated by cross-validation, which showed a substantial improvement in accuracy with an 11.3% reduction of standard deviation, 23.7% reduction of mean absolute error, and 28% reduction of mean absolute percentage error compared to the original measurements. The effects of patient demographics and initial medical condition were analyzed and deemed to not have a significant effect on accuracy. Because of its high accuracy, the proposed method is highly promising to be considered to support transfusion decision-making and continuous monitoring of hemoglobin concentration. The method also has promise for similar advancement of other diagnostic devices in healthcare.

Meta-MultiSKAT: Multiple phenotype meta-analysis for region-based association test.

The power of genetic association analyses can be increased by jointly meta-analyzing multiple correlated phenotypes. Here, we develop a meta-analysis framework, Meta-MultiSKAT, that uses summary statistics to test for association between multiple continuous phenotypes and variants in a region of interest. Our approach models the heterogeneity of effects between studies through a kernel matrix and performs a variance component test for association. Using a genotype kernel, our approach can test for rare-variants and the combined effects of both common and rare-variants. To achieve robust power, within Meta-MultiSKAT, we developed fast and accurate omnibus tests combining different models of genetic effects, functional genomic annotations, multiple correlated phenotypes, and heterogeneity across studies. In addition, Meta-MultiSKAT accommodates situations where studies do not share exactly the same set of phenotypes or have differing correlation patterns among the phenotypes. Simulation studies confirm that Meta-MultiSKAT can maintain the type-I error rate at the exome-wide level of 2.5 × 10-6 . Further simulations under different models of association show that Meta-MultiSKAT can improve the power of detection from 23% to 38% on average over single phenotype-based meta-analysis approaches. We demonstrate the utility and improved power of Meta-MultiSKAT in the meta-analyses of four white blood cell subtype traits from the Michigan Genomics Initiative (MGI) and SardiNIA studies.

Monte Carlo methods for nonparametric regression with heteroscedastic measurement error.

Nonparametric regression is a fundamental problem in statistics but challenging when the independent variable is measured with error. Among the first approaches was an extension of deconvoluting kernel density estimators for homescedastic measurement error. The main contribution of this article is to propose a new simulation-based nonparametric regression estimator for the heteroscedastic measurement error case. Similar to some earlier proposals, our estimator is built on principles underlying deconvoluting kernel density estimators. However, the proposed estimation procedure uses Monte Carlo methods for estimating nonlinear functions of a normal mean, which is different than any previous estimator. We show that the estimator has desirable operating characteristics in both large and small samples and apply the method to a study of benzene exposure in Chinese factory workers.

Order-restricted inference for means with missing values.

Missing values appear very often in many applications, but the problem of missing values has not received much attention in testing order-restricted alternatives. Under the missing at random (MAR) assumption, we impute the missing values nonparametrically using kernel regression. For data with imputation, the classical likelihood ratio test designed for testing the order-restricted means is no longer applicable since the likelihood does not exist. This article proposes a novel method for constructing test statistics for assessing means with an increasing order or a decreasing order based on jackknife empirical likelihood (JEL) ratio. It is shown that the JEL ratio statistic evaluated under the null hypothesis converges to a chi-bar-square distribution, whose weights depend on missing probabilities and nonparametric imputation. Simulation study shows that the proposed test performs well under various missing scenarios and is robust for normally and nonnormally distributed data. The proposed method is applied to an Alzheimer's disease neuroimaging initiative data set for finding a biomarker for the diagnosis of the Alzheimer's disease.

GPU-accelerated Kernel Regression Reconstruction for Freehand 3D Ultrasound Imaging.

Volume reconstruction method plays an important role in improving reconstructed volumetric image quality for freehand three-dimensional (3D) ultrasound imaging. By utilizing the capability of programmable graphics processing unit (GPU), we can achieve a real-time incremental volume reconstruction at a speed of 25-50 frames per second (fps). After incremental reconstruction and visualization, hole-filling is performed on GPU to fill remaining empty voxels. However, traditional pixel nearest neighbor-based hole-filling fails to reconstruct volume with high image quality. On the contrary, the kernel regression provides an accurate volume reconstruction method for 3D ultrasound imaging but with the cost of heavy computational complexity. In this paper, a GPU-based fast kernel regression method is proposed for high-quality volume after the incremental reconstruction of freehand ultrasound. The experimental results show that improved image quality for speckle reduction and details preservation can be obtained with the parameter setting of kernel window size of [Formula: see text] and kernel bandwidth of 1.0. The computational performance of the proposed GPU-based method can be over 200 times faster than that on central processing unit (CPU), and the volume with size of 50 million voxels in our experiment can be reconstructed within 10 seconds.

A novel random effect model for GWAS meta-analysis and its application to trans-ethnic meta-analysis.

Meta-analysis of trans-ethnic genome-wide association studies (GWAS) has proven to be a practical and profitable approach for identifying loci that contribute to the risk of complex diseases. However, the expected genetic effect heterogeneity cannot easily be accommodated through existing fixed-effects and random-effects methods. In response, we propose a novel random effect model for trans-ethnic meta-analysis with flexible modeling of the expected genetic effect heterogeneity across diverse populations. Specifically, we adopt a modified random effect model from the kernel regression framework, in which genetic effect coefficients are random variables whose correlation structure reflects the genetic distances across ancestry groups. In addition, we use the adaptive variance component test to achieve robust power regardless of the degree of genetic effect heterogeneity. Simulation studies show that our proposed method has well-calibrated type I error rates at very stringent significance levels and can improve power over the traditional meta-analysis methods. We reanalyzed the published type 2 diabetes GWAS meta-analysis (Consortium et al., 2014) and successfully identified one additional SNP that clearly exhibits genetic effect heterogeneity across different ancestry groups. Furthermore, our proposed method provides scalable computing time for genome-wide datasets, in which an analysis of one million SNPs would require less than 3 hours.

Empirical Likelihood for Estimating Equations with Nonignorably Missing Data.

We develop an empirical likelihood (EL) inference on parameters in generalized estimating equations with nonignorably missing response data. We consider an exponential tilting model for the nonignorably missing mechanism, and propose modified estimating equations by imputing missing data through a kernel regression method. We establish some asymptotic properties of the EL estimators of the unknown parameters under different scenarios. With the use of auxiliary information, the EL estimators are statistically more efficient. Simulation studies are used to assess the finite sample performance of our proposed EL estimators. We apply our EL estimators to investigate a data set on earnings obtained from the New York Social Indicators Survey.

Incorporating the neutrosophic framework into kernel regression for predictive mean estimation.

In traditional statistics, all research endeavors revolve around utilizing precise, crisp data for the predictive estimation of population mean in survey sampling, when the supplementary information is accessible. However, these types of estimates often suffer from bias. The major aim is to uncover the most accurate estimates for the unknown value of the population mean while minimizing the mean square error (MSE). We have employed the neutrosophic approach, which is the extension of classical statistics that deals with the uncertain, vague, and indeterminate information, and proposed a neutrosophic predictive estimator of finite population mean using the kernel regression. The proposed estimator does not yield a single numerical value but instead provides an interval range within which the population parameter is likely to exist. This approach enhances the efficiency of the estimators by offering an estimated interval that encompasses the unknown value of the population mean with the least possible mean squared error (MSE). The simulation-based efficiency of the proposed estimator is discussed using the Sine, Bump and real-time temperature data set of Islamabad by using symmetric (Gaussian) kernel. The proposed non-parametric neutrosophic estimator has shown more effective results under the various bandwidth selectors than the adapted neutrosophic estimators.

Machine Learning-Assisted Determination of C6H14 Mole Fraction From Molecular Emissions of Laser-Induced Hexane-Air Plasmas.

Laser-induced plasmas of materials containing hydrocarbons present strong carbon molecular emission features. Using these emissions to build models relating changes in spectral features to a physical parameter of the system, such as hydrocarbon content, can be difficult because of the dynamic complexity of the spectral features and temperature disequilibrium between molecular species. This study presents machine learning models trained to quantify the mole fraction of hexane in hexane-air plasmas from CN Violet and C2 Swan spectral features. Ensemble regression methods provide the most accurate predictions with root mean squared error on the order 10-2. Artificial neural network regressions produce predictions with superlative sensitivity, exhibiting detection limits as low as 0.008. These foundational models can be further refined with more advanced data to quantify the presence of carbon species in complex plasma environments, such as high-speed reacting flows.

Kernel Continuum Regression.

The continuum regression technique provides an appealing regression framework connecting ordinary least squares, partial least squares and principal component regression in one family. It offers some insight on the underlying regression model for a given application. Moreover, it helps to provide deep understanding of various regression techniques. Despite the useful framework, however, the current development on continuum regression is only for linear regression. In many applications, nonlinear regression is necessary. The extension of continuum regression from linear models to nonlinear models using kernel learning is considered. The proposed kernel continuum regression technique is quite general and can handle very flexible regression model estimation. An efficient algorithm is developed for fast implementation. Numerical examples have demonstrated the usefulness of the proposed technique.

Optimization of breeding program design through stochastic simulation with kernel regression.

In recent years, breeding programs have increased significantly in size and complexity, with various highly interdependent parameters and many contrasting breeding goals. As a result, resource allocation in these programs has become more complex, and deriving an optimal breeding strategy has become increasingly challenging. To address this, a common practice is to reduce the optimization problem to a set of scenarios that differ only in a few parameters and can therefore be analyzed in detail. The goal of this article is to provide a framework for the numerical optimization of breeding programs that goes beyond the simple comparison of scenarios. For this, we first determine the space of potential breeding programs only limited by basic constraints like the budget and housing capacities. Subsequently, the goal is to identify the optimal breeding program by finding the parametrization that maximizes the target function by combining different breeding goals. To assess the value of the target function for a parametrization, we propose using stochastic simulations and the subsequent use of a kernel regression method to cope with the stochasticity of simulation outcomes. This procedure is performed iteratively to narrow down the most promising areas of the search space and perform more and more simulations in these areas of interest. In a simplified example applied to a dairy cattle program, our proposed framework has shown its ability to identify an optimal breeding strategy that aligns with a target function aiming at genetic gain and genetic diversity conservation limited by budget constraints.

Adaptive Supervised Learning on Data Streams in Reproducing Kernel Hilbert Spaces with Data Sparsity Constraint.

Data are generated at an unprecedented rate and scale these days across many disciplines. The field of streaming data analysis has emerged as a result of new data collection and storage technologies in various areas, such as air pollution monitoring, detection of traffic congestion, disease surveillance, and recommendation systems. In this paper, we consider the problem of model estimation for data streams in reproducing kernel Hilbert spaces. We propose an adaptive supervised learning method with a data sparsity constraint that uses limited storage spaces and can handle non-stationary models. We demonstrate the competitive performance of the proposed method using simulations and analysis of the bike sharing dataset.

Biserial targeted feature projection based radial kernel regressive deep belief neural learning for covid-19 prediction.

Coronavirus disease 2019 (COVID-19) is a highly infectious viral disease caused by the novel SARS-CoV-2 virus. Different prediction techniques have been developed to predict the coronavirus disease's existence in patients. However, the accurate prediction was not improved and time consumption was not minimized. In order to address these existing problems, a novel technique called Biserial Targeted Feature Projection-based Radial Kernel Regressive Deep Belief Neural Learning (BTFP-RKRDBNL) is introduced to perform accurate disease prediction with lesser time consumption. The BTFP-RKRDBNL techniques perform disease prediction with the help of different layers such as two visible layers namely input and layer and two hidden layers. Initially, the features and data are collected from the dataset and transmitted to the input layer. The Point Biserial Correlative Target feature projection is used to select relevant features and other irrelevant features are removed with minimizing the disease prediction time. Then the relevant features are sent to the hidden layer 2. Next, Radial Kernel Regression is applied to analyze the training features and testing disease features to identify the disease with higher accuracy and a lesser false positive rate. Experimental analysis is planned to measure the prediction accuracy, sensitivity, and specificity, and prediction time for different numbers of patients. The result illustrates that the method increases the prediction accuracy, sensitivity, and specificity by 10, 6, and 21% and reduces the prediction time by 10% as compared to state-of-the-art works.