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Evaluation of penalized and machine learning methods for asthma disease prediction in the Korean Genome and Epidemiology Study (KoGES)
BackgroundGenome-wide association studies have successfully identified genetic variants associated with human disease. Various statistical approaches...
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Favoring the hierarchical constraint in penalized survival models for randomized trials in precision medicine
BackgroundThe research of biomarker-treatment interactions is commonly investigated in randomized clinical trials (RCT) for improving medicine...
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penalizedclr: an R package for penalized conditional logistic regression for integration of multiple omics layers
BackgroundThe matched case–control design, up until recently mostly pertinent to epidemiological studies, is becoming customary in biomedical...
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CNETML: maximum likelihood inference of phylogeny from copy number profiles of multiple samples
Phylogenetic trees based on copy number profiles from multiple samples of a patient are helpful to understand cancer evolution. Here, we develop a...
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Elements for Building Supervised Statistical Machine Learning Models
This chapter gives details of the linear multiple regression model including assumptions and some pros and cons, the maximum likelihood. Gradient...
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Accounting for grouped predictor variables or pathways in high-dimensional penalized Cox regression models
BackgroundThe standard lasso penalty and its extensions are commonly used to develop a regularized regression model while selecting candidate...
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Minimum Wasserstein Distance Estimator Under Finite Location-Scale Mixtures
When a population exhibits heterogeneity, we often model it via a finite mixture: decompose it into several different but homogeneous subpopulations....
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On Bayesian modeling of censored data in JAGS
BackgroundJust Another Gibbs Sampling (JAGS) is a convenient tool to draw posterior samples using Markov Chain Monte Carlo for Bayesian modeling....
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Small Animal PET Imaging: Towards an Imaging Analysis Approach for System Average Performance Conclusion
The purpose of this study is to present a novel small animal PET imaging system, which can be integrated with a small animal CT or MRI imaging in a...
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Bayesian and Classical Prediction Models for Categorical and Count Data
In this chapter, we explain, under a Bayesian framework, the fundamentals and practical issues for implementing genomic prediction models for...
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BEXCIS: Bayesian methods for estimating the degree of the skewness of X chromosome inactivation
BackgroundX chromosome inactivation (XCI) is an epigenetic phenomenon that one of two X chromosomes in females is transcriptionally silenced during...
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Assessing the relative performance of fast molecular dating methods for phylogenomic data
Advances in genome sequencing techniques produced a significant growth of phylogenomic datasets. This massive amount of data represents a...
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Robust variable selection with exponential squared loss for the partially linear varying coefficient spatial autoregressive model
The partially linear varying coefficient spatial autoregressive model is a semi-parametric spatial autoregressive model in which the coefficients of...
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Proteomics data analysis using multiple statistical approaches identified proteins and metabolic networks associated with sucrose accumulation in sugarcane
BackgroundSugarcane is the most important sugar crop, contributing > 80% of global sugar production. High sucrose content is a key target of...
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Bayesian variable selection for high-dimensional data with an ordinal response: identifying genes associated with prognostic risk group in acute myeloid leukemia
BackgroundAcute myeloid leukemia (AML) is a heterogeneous cancer of the blood, though specific recurring cytogenetic abnormalities in AML are...
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Cell Tree Rings: the structure of somatic evolution as a human aging timer
Biological age is typically estimated using biomarkers whose states have been observed to correlate with chronological age. A persistent limitation...
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The association between non-high-density lipoprotein cholesterol to high-density lipoprotein cholesterol ratio (NHHR) and suicidal ideation in adults: a population-based study in the United States
BackgroundThe ratio of non-high-density lipoprotein cholesterol (non-HDL-C) to high-density lipoprotein cholesterol (HDL-C) (NHHR) serves as a...
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Coinfection frequency in water flea populations is a mere reflection of parasite diversity
In nature, parasite species often coinfect the same host. Yet, it is not clear what drives the natural dynamics of coinfection prevalence. The...
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Geographic range size and speciation in honeyeaters
BackgroundDarwin and others proposed that a species’ geographic range size positively influences speciation likelihood, with the relationship...
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Introduction to Generalized Linear Mixed Models
Chapter 15 investigated linear mixed-effects models (LMMs). This chapter introduces generalized linear mixed...