Secure linear regression at speed of plaintext methods.
problem Secure multiparty linear regression and feature selection.
method Distributed algorithms combining geometric ideas.
result Efficient and secure genome-wide association studies.
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48 results for “genome-wide association”
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.
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…
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…
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…
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…
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 …
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.
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…
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.
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.
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…
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…
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.
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…
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.
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.
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 …
An approach for learning ancestral causal relationships in high dimensions, validated on human genome-wide data.
problem Learning ancestral causal relationships in high-dimensional biological data.
method Supervised learning approach with discrete indicators treated as labels, scalable to large problems.
result The approach is highly effective and scalable to the human genome-wide setting, robust to perturbations of input information.
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…
Improves normalizing flows by incorporating data dependencies.
problem Current normalizing flow learning assumes independent data, leading to errors.
method Proposes a likelihood objective with dependencies and efficient learning algorithm.
result Improves density estimation and data generation on real-world data.
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.
With the wealth of high-throughput sequencing data generated by recent large-scale consortia, predictive gene expression modelling has become an important tool for integrative analysis of transcriptomic and epigenetic data. However, sequencing data-sets are characteristically large, and previously modelling frameworks …
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…
Causal inference from observational data often assumes "ignorability," that all confounders are observed. This assumption is standard yet untestable. However, many scientific studies involve multiple causes, different variables whose effects are simultaneously of interest. We propose the deconfounder, an algorithm that…
New method accurately identifies causal genes from GWAS data.
problem Understanding the biological mechanisms behind genetic markers and phenotypes.
method Principled summary-based causal inference framework for GWAS data.
result Our method accurately identifies causal genes without individual-level data.
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.
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…
SAERMA combines deep learning and rule mining to identify SNP interactions.
problem Identifying significant SNPs and their interactions in complex diseases.
method Stacked Autoencoder Rule Mining Algorithm (SAERMA) integrating deep learning and association rule mining.
result Achieved high classification accuracy (77% AUC, 77% SE, 68% SP) with 100 units.
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.
Efficiently solves Elastic Net in high dimensions with Newton method.
problem Feature selection in high-dimensional data with non-negligible collinearity.
method Semi-smooth Newton Augmented Lagrangian Method.
result Significantly reduces computational cost compared to competitors.
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, …
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.
Progress in probabilistic generative models has accelerated, developing richer models with neural architectures, implicit densities, and with scalable algorithms for their Bayesian inference. However, there has been limited progress in models that capture causal relationships, for example, how individual genetic factor…
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) 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…
When performing regression on a dataset with variables, it is often of interest to go beyond using main linear effects and include interactions as products between individual variables. For small-scale problems, these interactions can be computed explicitly but this leads to a computational complexity of at least $…
We propose a method for simultaneously detecting shared and unshared communities in heterogeneous multilayer weighted and undirected networks. The multilayer network is assumed to follow a generative probabilistic model that takes into account the similarities and dissimilarities between the communities. We make use of…
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.
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.
Gene-Gene association for Imaging Genetics Data using Robust Kernel Canonical Correlation Analysisstat.ML
In genome-wide interaction studies, to detect gene-gene interactions, most methods are divided into two folds: single nucleotide polymorphisms (SNP) based and gene-based methods. Basically, the methods based on the gene are more effective than the methods based on a single SNP. Recent years, while the kernel canonical …
Volterra and polynomial regression models play a major role in nonlinear system identification and inference tasks. Exciting applications ranging from neuroscience to genome-wide association analysis build on these models with the additional requirement of parsimony. This requirement has high interpretative value, but …
Motivation: Analysis of relationships of drug structure to biological response is key to understanding off-target and unexpected drug effects, and for developing hypotheses on how to tailor drug thera-pies. New methods are required for integrated analyses of a large number of chemical features of drugs against the corr…
Machine learning has been gaining traction in recent years to meet the demand for tools that can efficiently analyze and make sense of the ever-growing databases of biomedical data in health care systems around the world. However, effectively using machine learning methods requires considerable domain expertise, which …
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…
In high-dimensional linear models, the sparsity assumption is typically made, stating that most of the parameters are equal to zero. Under the sparsity assumption, estimation and, recently, inference have been well studied. However, in practice, sparsity assumption is not checkable and more importantly is often violate…
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.