Relative error prediction via kernel regression smoothers

In this article, we introduce and study local constant and local linear nonparametric regression estimators when it is appropriate to assess performance in terms of mean squared relative error of prediction. We give asymptotic results for both boundary and non-boundary cases. These are special cases of more general asymptotic results that we provide concerning the estimation of the ratio of conditional expectations of two functions of the response variable. We also provide a good bandwidth selection method for the estimators. Examples of application, limited simulation results and discussion of related problems and approaches are also given

Pathway analysis of rare variants for the clustered phenotypes by using hierarchical structured components analysis

Backgrounds Recent large-scale genetic studies often involve clustered phenotypes such as repeated measurements. Compared to a series of univariate analyses of single phenotypes, an analysis of clustered phenotypes can be useful for substantially increasing statistical power to detect more genetic associations. Moreover, for the analysis of rare variants, incorporation of biological information can boost weak effects of the rare variants. Results Through simulation studies, we showed that the proposed method outperforms other method currently available for pathway-level analysis of clustered phenotypes. Moreover, a real data analysis using a large-scale whole exome sequencing dataset of 995 samples with metabolic syndrome-related phenotypes successfully identified the glyoxylate and dicarboxylate metabolism pathway that could not be identified by the univariate analyses of single phenotypes and other existing method. Conclusion In this paper, we introduced a novel pathway-level association test by combining hierarchical structured components analysis and penalized generalized estimating equations. The proposed method analyzes all pathways in a single unified model while considering their correlations. C/C++ implementation of PHARAOH-GEE is publicly available at http://statgen.snu.ac.kr/software/pharaoh-gee/.Publication costs are funded by the Korea Health Technology R&D Project through the Korea Health Industry Development Institute (KHIDI) grant (HI16C2037). Also, this work was supported by the Bio & Medical Technology Development Program of the National Research Foundation of Korea (NRF) grant (2013M3A9C4078158) and by grants of the Korea Health Technology R&D Project through the Korea Health Industry Development Institute (KHIDI), funded by the Ministry of Health & Welfare, Republic of Korea (grant number: HI16C2037, HI15C2165, HI16C2048)

Relative-error prediction

We derive the form of the best mean squared relative error predictor of Y given X. Some methods of estimating predictors with good relative error properties are proposed and studied via simulation. The methods are illustrated with an example in which county-level gasoline sales are predicted from county-level population.Prediction Power-of-the-mean model Relative error Relative least squares Variance function

Pathway-based approach using hierarchical components of rare variants to analyze multiple phenotypes

Abstract Background As one possible solution to the “missing heritability” problem, many methods have been proposed that apply pathway-based analyses, using rare variants that are detected by next generation sequencing technology. However, while a number of methods for pathway-based rare-variant analysis of multiple phenotypes have been proposed, no method considers a unified model that incorporate multiple pathways. Results Simulation studies successfully demonstrated advantages of multivariate analysis, compared to univariate analysis, and comparison studies showed the proposed approach to outperform existing methods. Moreover, real data analysis of six type 2 diabetes-related traits, using large-scale whole exome sequencing data, identified significant pathways that were not found by univariate analysis. Furthermore, strong relationships between the identified pathways, and their associated metabolic disorder risk factors, were found via literature search, and one of the identified pathway, was successfully replicated by an analysis with an independent dataset. Conclusions Herein, we present a powerful, pathway-based approach to investigate associations between multiple pathways and multiple phenotypes. By reflecting the natural hierarchy of biological behavior, and considering correlation between pathways and phenotypes, the proposed method is capable of analyzing multiple phenotypes and multiple pathways simultaneously

Bayesian Extended Redundancy Analysis: A Bayesian Approach to Component-based Regression with Dimension Reduction

Multivariate Behavioral Research55130-4

A Functional Analysis of Deception Detection of a Mock Crime using Infrared Thermal Imaging and the Concealed Information Test

The purpose of this study was to utilize thermal imaging and the Concealed Information Test to detect deception in participants who committed a mock crime. A functional analysis using a functional ANOVA and a functional discriminant analysis was conducted to decrease the variation in the physiological data collected through the thermal imaging camera. Participants chose between a non-crime mission (Innocent Condition: IC), or a mock crime (Guilty Condition: GC) of stealing a wallet in a computer lab. Temperature in the periorbital region of the face was measured while questioning participants regarding mock crime details. Results revealed that the GC showed significantly higher temperatures when responding to crime relevant items compared to irrelevant items, while the IC did not. The functional ANOVA supported the initial results that facial temperatures of the GC elevated when responding to crime relevant items, demonstrating an interaction between group (guilty/innocent) and relevance (relevant/irrelevant). The functional discriminant analysis revealed that answering crime relevant items can be used to discriminate guilty from innocent participants. These results suggest that measuring facial temperatures in the periorbital region while conducting the Concealed Information Test is able to differentiate the GC from the IC

Kernel-based hierarchical structural component models for pathway analysis

Motivation: Pathway analyses have led to more insight into the underlying biological functions related to the phenotype of interest in various types of omics data. Pathway-based statistical approaches have been actively developed, but most of them do not consider correlations among pathways. Because it is well known that there are quite a few biomarkers that overlap between pathways, these approaches may provide misleading results. In addition, most pathway-based approaches tend to assume that biomarkers within a pathway have linear associations with the phenotype of interest, even though the relationships are more complex. Results: To model complex effects including non-linear effects, we propose a new approach, Hierarchical structural CoMponent analysis using Kernel (HisCoM-Kernel). The proposed method models non-linear associations between biomarkers and phenotype by extending the kernel machine regression and analyzes entire pathways simultaneously by using the biomarker-pathway hierarchical structure. HisCoM-Kernel is a flexible model that can be applied to various omics data. It was successfully applied to three omics datasets generated by different technologies. Our simulation studies showed that HisCoM-Kernel provided higher statistical power than other existing pathway-based methods in all datasets. The application of HisCoM-Kernel to three types of omics dataset showed its superior performance compared to existing methods in identifying more biologically meaningful pathways, including those reported in previous studies.N