Related papers: Deep Learning Classification of Polygenic Obesity …

Even though Deep Neural Networks (DNNs) are widely celebrated for their practical performance, they possess many intriguing properties related to depth that are difficult to explain both theoretically and intuitively. Understanding how…

Studying phenotype-gene association can uncover mechanism of diseases and develop efficient treatments. In complex disease where multiple phenotypes are available and correlated, analyzing and interpreting associated genes for each…

Large-scale supervised classification algorithms, especially those based on deep convolutional neural networks (DCNNs), require vast amounts of training data to achieve state-of-the-art performance. Decreasing this data requirement would…

Polygenic risk scores (PRS) developed from genome-wide association studies (GWAS) can be used for risk stratification by quantifying the genetic contribution to disease, and many clinical applications have been proposed. Bayesian methods…

This paper proposes a straightforward and cost-effective approach to assess whether a deep neural network (DNN) relies on the primary concepts of training samples or simply learns discriminative, yet simple and irrelevant features that can…

In the context of supervised learning of a function by a neural network, we claim and empirically verify that the neural network yields better results when the distribution of the data set focuses on regions where the function to learn is…

Deep neural network (DNN) models have achieved state-of-the-art predictive accuracy in a wide range of supervised learning applications. However, accurately quantifying the uncertainty in DNN predictions remains a challenging task. For…

In the past decade, Genome-Wide Association Studies (GWAS) have delivered an increasingly broad view of the genetic basis of human phenotypic variation. One of the major developments from GWAS is polygenic scores, a genetic predictor of an…

It is widely held that a substantial genetic component underlies Bipolar Disorder (BD) and other neuropsychiatric disease traits. Recent efforts have been aimed at understanding the genetic basis of disease susceptibility, with genome-wide…

Deep learning is a powerful tool for whole slide image (WSI) analysis. Typically, when performing supervised deep learning, a WSI is divided into small patches, trained and the outcomes are aggregated to estimate disease grade. However,…

Genetic investigations often involve the testing of vast numbers of related hypotheses simultaneously. To control the overall error rate, a substantial penalty is required, making it difficult to detect signals of moderate strength. To…

Childhood obesity remains a major public health challenge in the United States, strongly influenced by a combination of individual-level, household-level, and environmental-level risk factors. Traditional epidemiological studies typically…

Many forensic genetic trace samples are of too low quality to obtain short tandem repeat (STR) DNA profiles as the nuclear DNA they contain is highly degraded (e.g., telogen hairs). Instead, performing shotgun DNA sequencing of such samples…

Imputation using external reference panels is a widely used approach for increasing power in GWAS and meta-analysis. Existing HMM-based imputation approaches require individual-level genotypes. Here, we develop a new method for Gaussian…

A panel of large number of common Single Nucleotide Polymorphisms (SNPs) distributed across an entire porcine genome has been widely used to represent genetic variability of pig. With the advent of SNP-array technology, a genome-wide…

From a fresh data science perspective, this thesis discusses the prediction of coronary artery disease based on genetic variations at the DNA base pair level, called Single-Nucleotide Polymorphisms (SNPs), collected from the Ontario Heart…

Neural parameter allocation search (NPAS) automates parameter sharing by obtaining weights for a network given an arbitrary, fixed parameter budget. Prior work has two major drawbacks we aim to address. First, there is a disconnect in the…

Single-hidden layer feed forward neural networks (SLFNs) are widely used in pattern classification problems, but a huge bottleneck encountered is the slow speed and poor performance of the traditional iterative gradient-based learning…

Along with rich health-related metadata, medical images have been acquired for over 40,000 male and female UK Biobank participants, aged 44-82, since 2014. Phenotypes derived from these images, such as measurements of body composition from…

Single-cell RNA sequencing (scRNA-seq) technology provides high-throughput gene expression data to study the cellular heterogeneity and dynamics of complex organisms. Graph neural networks (GNNs) have been widely used for automatic cell…