A genome-wide association study (GWAS) correlates marker variation with trait variation in a sample of individuals. Each study subject is genotyped at a multitude of SNPs (single nucleotide polymorphisms) spanning the genome. Here we assume that subjects are unrelated and collected at random and that trait values are n…
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48 results for “genome wide association studies (GWAS)”
Differentially-Private Logistic Regression for Detecting Multiple-SNP Association in GWAS Databasesstat.ML
Following the publication of an attack on genome-wide association studies (GWAS) data proposed by Homer et al., considerable attention has been given to developing methods for releasing GWAS data in a privacy-preserving way. Here, we develop an end-to-end differentially private method for solving regression problems wi…
The Informed Elastic Net for Fast Grouped Variable Selection and FDR Control in Genomics Researchstat.ME
IEN speeds up T-Rex+GVS for fast, efficient GWAS.
problem Efficiently selecting groups of genetic variants in large-scale genomics studies.
method Informed Elastic Net (IEN) as a faster base selector for T-Rex+GVS.
result IEN reduces computation time while maintaining high TPR and FDR control.
Deep models improve GWAS by identifying genetic interactions.
problem Missing non-linear interaction effects in GWAS.
method Gradient-based DeepLIFT technique to interpret deep models.
result Known and novel genetic risk factors identified.
SEISM tests neural network features for regulatory genomics.
problem Testing neural network features for regulatory genomics.
method Selective inference procedure for sequence motifs.
result Sampling under specific parameters characterizes composite null hypothesis.
Extracting Epistatic Interactions in Type 2 Diabetes Genome-Wide Data Using Stacked Autoencodercs.LG
2 Diabetes is a leading worldwide public health concern, and its increasing prevalence has significant health and economic importance in all nations. The condition is a multifactorial disorder with a complex aetiology. The genetic determinants remain largely elusive, with only a handful of identified candidate genes. G…
Genome-wide association studies (GWA studies or GWAS) investigate the relationships between genetic variants such as single-nucleotide polymorphisms (SNPs) and individual traits. Recently, incorporating biological priors together with machine learning methods in GWA studies has attracted increasing attention. However, …
Genome-wide association studies (GWAS) have emerged as a rich source of genetic clues into disease biology, and they have revealed strong genetic correlations among many diseases and traits. Some of these genetic correlations may reflect causal relationships. We developed a method to quantify causal relationships betwe…
A computationally simple genome-wide association study (GWAS) algorithm for estimating the main and epistatic effects of markers or single nucleotide polymorphisms (SNPs) is proposed. It is based on the intuitive assumption that changes of alleles corresponding to important SNPs in a pair of individuals lead to large d…
Develops methods for GWAS of high dimensional phenotypes using summary statistics.
problem Lack of methods to model pleiotropy in multi-phenotype GWAS.
method Bayesian inference model using summary statistics, fast computation, and biologically informed priors.
result Demonstrates utility in metabolite GWAS with interpretable pathway-level inference.
One of the most important challenges in the analysis of high-throughput genetic data is the development of efficient computational methods to identify statistically significant Single Nucleotide Polymorphisms (SNPs). Genome-wide association studies (GWAS) use single-locus analysis where each SNP is independently tested…
Summary statistics of genome-wide association studies (GWAS) teach causal relationship between millions of genetic markers and tens and thousands of phenotypes. However, underlying biological mechanisms are yet to be elucidated. We can achieve necessary interpretation of GWAS in a causal mediation framework, looking to…
Common complex diseases are likely influenced by the interplay of hundreds, or even thousands, of genetic variants. Converging evidence shows that genetic variants with low marginal effects (LME) play an important role in disease development. Despite their potential significance, discovering LME genetic variants and as…
Federated learning improves bioinformatics by sharing data legally.
problem Lack of access to diverse data in bioinformatics.
method Combines data from multiple institutions legally.
result Federated learning accelerates clinical discovery and robust exploration.
Genome-wide association studies (GWAS) offer new opportunities to identify genetic risk factors for Alzheimer's disease (AD). Recently, collaborative efforts across different institutions emerged that enhance the power of many existing techniques on individual institution data. However, a major barrier to collaborative…
Constrained least squares regression is an essential tool for high-dimensional data analysis. Given a partition of input variables, this paper considers a particular class of nonconvex constraint functions that encourage the linear model to select a small number of variables from a small number of groups …
Genome-wide association studies (GWAS) have achieved great success in the genetic study of Alzheimer's disease (AD). Collaborative imaging genetics studies across different research institutions show the effectiveness of detecting genetic risk factors. However, the high dimensionality of GWAS data poses significant cha…
MASSIVE: Tractable and Robust Bayesian Learning of Many-Dimensional Instrumental Variable Modelsstat.ML
Bayesian method for robust causal inference using many-dimensional instrumental variables.
problem Intractable model space and uncertainty in selecting valid instrumental variables.
method Bayesian model averaging over promising instrumental variable models with weaker assumptions.
result Efficient and robust causal effect estimation in many-dimensional data.
We consider multi-response and multitask regression models, where the parameter matrix to be estimated is expected to have an unknown grouping structure. The groupings can be along tasks, or features, or both, the last one indicating a bi-cluster or "checkerboard" structure. Discovering this grouping structure along wi…
Enhances FDR control in variable selection using neural networks.
problem Balancing rigorous error control with statistical power in high-dimensional variable selection.
method Learning-augmented T-Rex Selector framework with a neural network trained on synthetic datasets.
result Achieves superior detection of true variables compared to existing approaches.
T-Rex selector selects variables fast and controls FDR in high-dimensional data.
problem Variable selection in high-dimensional data with FDR control.
method Fused solutions of early terminated random experiments.
result FDR control at target level with high variable selection power.
Advances of modern sensing and sequencing technologies generate a deluge of high dimensional space-temporal physiological and next-generation sequencing (NGS) data. Physiological traits are observed either as continuous random functions, or on a dense grid and referred to as function-valued traits. Both physiological a…
ParKCa combines multiple causal inference methods to infer new causes from known and unknown factors.
problem Causal inference from observational data when randomized experiments are not feasible.
method ParKCa uses a stacking approach to combine results from multiple causal inference methods.
result ParKCa infers more causes than existing methods in real-world and simulated datasets.
New methods improve genetic studies of complex diseases.
problem Improving genetic studies of complex diseases using high-dimensional clinical data.
method Evaluation of unsupervised disentangled representation learning methods (autoencoders, VAE, beta-VAE, FactorVAE) for genetic association studies.
result FactorVAEs and beta-VAEs outperform standard VAEs and non-variational autoencoders in genetic studies of asthma and COPD.
Genome-wide association studies (GWASs) aim to detect genetic risk factors for complex human diseases by identifying disease-associated single-nucleotide polymorphisms (SNPs). The traditional SNP-wise approach along with multiple testing adjustment is over-conservative and lack of power in many GWASs. In this article, …
In statistical genetics an important task involves building predictive models for the genotype-phenotype relationships and thus attribute a proportion of the total phenotypic variance to the variation in genotypes. Numerous models have been proposed to incorporate additive genetic effects into models for prediction or …
We detail distributed algorithms for scalable, secure multiparty linear regression and feature selection at essentially the same speed as plaintext regression. While the core geometric ideas are simple, the recognition of their broad utility when combined is novel. Our scheme opens the door to efficient and secure geno…
Generates new human genomic sequences for LAI training.
problem Lack of accessible reference data sets for LAI.
method Class-conditional VAE-GAN to generate realistic sequences.
result Generated sequences improve LAI method performance.
As an increasing number of genome-wide association studies reveal the limitations of attempting to explain phenotypic heritability by single genetic loci, there is growing interest for associating complex phenotypes with sets of genetic loci. While several methods for multi-locus mapping have been proposed, it is often…
With different genomes available, unsupervised learning algorithms are essential in learning genome-wide biological insights. Especially, the functional characterization of different genomes is essential for us to understand lives. In this book chapter, we review the state-of-the-art unsupervised learning algorithms fo…
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 tests show that these predictors capture, respectively, 40, 20, and 9 perc…
Viral sequence classification is an important task in pathogen detection, epidemiological surveys and evolutionary studies. Statistical learning methods are widely used to classify and identify viral sequences in samples from environments. These methods face several challenges associated with the nature and properties …
Genome-wide association studies have proven to be essential for understanding the genetic basis of disease. However, many complex traits---personality traits, facial features, disease subtyping---are inherently high-dimensional, impeding simple approaches to association mapping. We developed a nonparametric Bayesian re…
Proposes a two-stage method for testing variable interactions with FDR control.
problem Testing pairwise interactions in high-dimensional data with dependence.
method Two-stage testing procedure with FDR control using Cramér type moderate deviation technique.
result The proposed method controls FDR and has comparable or improved statistical power.
A plethora of natural, artificial and social systems exist which do not belong to the Boltzmann-Gibbs (BG) statistical-mechanical world, based on the standard additive entropy and its associated exponential BG factor. Frequent behaviors in such complex systems have been shown to be closely related to -stati…
regularized logistic regression has now become a workhorse of data mining and bioinformatics: it is widely used for many classification problems, particularly ones with many features. However, regularization typically selects too many features and that so-called false positives are unavoidable. In this pape…
LEARNER improves low-rank matrix estimation using source population data.
problem Improving low-rank matrix estimation in target populations with diverse data sources.
method LEARNER uses similarity in latent spaces between source and target populations to enhance estimation.
result LEARNER often outperforms benchmark methods, especially with higher signal-to-noise ratios in the source population.
Locally epistatic genomic relationship matrices for genomic association, prediction and selectionstat.AP
As the amount and complexity of genetic information increases it is necessary that we explore some efficient ways of handling these data. This study takes the "divide and conquer" approach for analyzing high dimensional genomic data. Our aims include reducing the dimensionality of the problem that has to be dealt one a…
The analysis of cancer genomic data has long suffered "the curse of dimensionality". Sample sizes for most cancer genomic studies are a few hundreds at most while there are tens of thousands of genomic features studied. Various methods have been proposed to leverage prior biological knowledge, such as pathways, to more…
Paper proposes dp-VAE for preserving spatial context in gene expression data.
problem Inaccessibility of spatial context in single-cell gene expression data.
method Generic representation learning and transfer learning framework with a distance-preserving regularizer.
result dp-VAE effectively reconstructs and imputes spatial context from gene expression data.
We introduce the C++ application and R package ranger. The software is a fast implementation of random forests for high dimensional data. Ensembles of classification, regression and survival trees are supported. We describe the implementation, provide examples, validate the package with a reference implementation, and …
Proposes using MLP for predicting optimal penalty in changepoint detection.
problem Predicting optimal penalty for changepoints in sequences.
method Uses a multilayer perceptron (MLP) with ReLU activation function to predict penalty.
result Improves accuracy and F1 score compared to existing models.
Genomic models learn DNA sequences to predict functions.
problem Understanding complex genetic interactions.
method Training LLMs on DNA sequences to predict functions.
result gLMs can predict functions of DNA elements.
Understanding functional organization of genetic information is a major challenge in modern biology. Following the initial publication of the human genome sequence in 2001, advances in high-throughput measurement technologies and efficient sharing of research material through community databases have opened up new view…
Fast and cheaper next generation sequencing technologies will generate unprecedentedly massive and highly-dimensional genomic and epigenomic variation data. In the near future, a routine part of medical record will include the sequenced genomes. A fundamental question is how to efficiently extract genomic and epigenomi…
New method reduces memory usage for high-dimensional variable selection.
problem Scalability issues in high-dimensional variable selection, especially in genomics.
method Adaptive sampling of null features to eliminate dummy matrix materialization.
result Reduces memory and runtime by several orders of magnitude while preserving FDR control.
In this paper we propose network methodology to infer prognostic cancer biomarkers based on the epigenetic pattern DNA methylation. Epigenetic processes such as DNA methylation reflect environmental risk factors, and are increasingly recognised for their fundamental role in diseases such as cancer. DNA methylation is a…
Proposes spBART for risk prediction using epigenetic signatures and covariates.
problem Complex high-dimensional epigenetic data and low-dimensional covariates for risk prediction.
method Semi-parametric Bayesian Additive Regression Trees (spBART) with cross-validation for variable selection.
result Achieves strong out-of-sample discrimination (AUC = 0.96) in held-out validation set.