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One way of investigating how genes affect human traits would be with a genome-wide association study (GWAS). Genetic markers, known as single-nucleotide polymorphism (SNP), are used in GWAS. This raises privacy and security concerns as…
Genome-wide association studies (GWAS) are commonly employed to study the genetic basis of complex traits and diseases, and a key question is how much heritability could be explained by all variants in GWAS. One widely used approach that…
In general, deep neural network (DNN) pruning methods fall into two categories: 1) Weight-based deterministic constraints, and 2) Probabilistic frameworks. While each approach has its merits and limitations there are a set of common…
We consider the problems of hypothesis testing and model comparison under a flexible Bayesian linear regression model whose formulation is closely connected with the linear mixed effect model and the parametric models for SNP set analysis…
Studying the effects of groups of Single Nucleotide Polymorphisms (SNPs), as in a gene, genetic pathway, or network, can provide novel insight into complex diseases, above that which can be gleaned from studying SNPs individually. Common…
We construct genomic predictors for heritable and extremely complex human quantitative traits (height, heel bone density, and educational attainment) using modern methods in high dimensional statistics (i.e., machine learning). Replication…
Genetic association studies, in particular the genome-wide association study design, have provided a wealth of novel insights into the aetiology of a wide range of human diseases and traits. The next challenge consists of understanding the…
Genetic association studies have been a popular approach for assessing the association between common Single Nucleotide Polymorphisms (SNPs) and complex diseases. However, other genomic data involved in the mechanism from SNPs to disease,…
Deep neural networks are typically trained by optimizing a loss function with an SGD variant, in conjunction with a decaying learning rate, until convergence. We show that simple averaging of multiple points along the trajectory of SGD,…
We show that the signal-processing paradigm known as compressed sensing (CS) is applicable to genome-wide association studies (GWAS) and genomic selection (GS). The aim of GWAS is to isolate trait-associated loci, whereas GS attempts to…
Genome-wide association studies (GWAS) suggests that a complex disease is typically affected by many genetic variants with small or moderate effects. Identification of these risk variants remains to be a very challenging problem.…
Copy number variants (CNVs) account for more polymorphic base pairs in the human genome than do single nucleotide polymorphisms (SNPs). CNVs encompass genes as well as noncoding DNA, making these polymorphisms good candidates for functional…
Interactions among multiple genes across the genome may contribute to the risks of many complex human diseases. Whole-genome single nucleotide polymorphisms (SNPs) data collected for many thousands of SNP markers from thousands of…
An important task of human genetics studies is to accurately predict disease risks in individuals based on genetic markers, which allows for identifying individuals at high disease risks, and facilitating their disease treatment and…
Background and objective: Diabetes is a chronic pathology which is affecting more and more people over the years. It gives rise to a large number of deaths each year. Furthermore, many people living with the disease do not realize the…
Deep learning models in medical imaging are susceptible to shortcut learning, relying on confounding metadata (e.g., scanner model) that is often encoded in image embeddings. The crucial question is whether the model actively utilizes this…
Since most analysis software for genome-wide association studies (GWAS) currently exploit only unrelated individuals, there is a need for efficient applications that can handle general pedigree data or mixtures of both population and…
Predicting protein secondary structure is a fundamental problem in protein structure prediction. Here we present a new supervised generative stochastic network (GSN) based method to predict local secondary structure with deep hierarchical…
The exploration of selected single nucleotide polymorphisms (SNPs) to identify genetic diversity between different sequencing population pools (Pool-seq) is a fundamental task in genetic research. As underlying sequence reads and their…
Motivated by empirical arguments that are well-known from the genome-wide association studies (GWAS) literature, we study the statistical properties of linear mixed models (LMMs) applied to GWAS. First, we study the sensitivity of LMMs to…