Related papers: Improving the Efficiency of Genomic Selection

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…

We propose a nonparametric procedure to achieve fast inference in generative graphical models when the number of latent states is very large. The approach is based on iterative latent variable preselection, where we alternate between…

Background: Advances in high throughput sequencing technologies provide a huge number of genomes to be analyzed. Thus, computational methods play a crucial role in analyzing and extracting knowledge from the data generated. Investigating…

The expressive and computationally inexpensive bipartite Graph Neural Networks (GNN) have been shown to be an important component of deep learning based Mixed-Integer Linear Program (MILP) solvers. Recent works have demonstrated the…

Gene panel selection aims to identify the most informative genomic biomarkers in label-free genomic datasets. Traditional approaches, which rely on domain expertise, embedded machine learning models, or heuristic-based iterative…

Restricted Boltzmann Machines and Deep Belief Networks have been successfully used in probabilistic generative model applications such as image occlusion removal, pattern completion and motion synthesis. Generative inference in such…

We combine K-Nearest Neighbors (KNN) with genetic algorithm (GA) for photometric redshift estimation of quasars, short for GeneticKNN, which is a weighted KNN approach supported by GA. This approach has two improvements compared to KNN: one…

Complex, non-additive genetic interactions are common and can be critical in determining phenotypes. Genome-wide association studies (GWAS) and similar statistical studies of linkage data, however, assume additive models of gene…

Genomic Selection (GS) uses whole-genome information to predict crop phenotypes and accelerate breeding. Traditional GS methods, however, struggle with prediction accuracy for complex traits and large datasets. We propose DPCformer, a deep…

Background: Single-cell RNA sequencing (scRNA-seq) yields valuable insights about gene expression and gives critical information about complex tissue cellular composition. In the analysis of single-cell RNA sequencing, the annotations of…

In plant and animal breeding studies a distinction is made between the genetic value (additive + epistatic genetic effects) and the breeding value (additive genetic effects) of an individual since it is expected that some of the epistatic…

Graph Neural Networks (GNNs) have achieved remarkable success in various graph-based tasks (e.g., node classification or link prediction). Despite their triumphs, GNNs still face challenges such as long training and inference times,…

Learning ensembles by bagging can substantially improve the generalization performance of low-bias, high-variance estimators, including those evolved by Genetic Programming (GP). To be efficient, modern GP algorithms for evolving (bagging)…

Linear Mixed Models (LMMs) are important tools in statistical genetics. When used for feature selection, they allow to find a sparse set of genetic traits that best predict a continuous phenotype of interest, while simultaneously correcting…

In genome-wide association studies (GWAS), hundreds of thousands of genetic markers (SNPs) are tested for association with a trait or phenotype. Reported effects tend to be larger in magnitude than the true effects of these markers, the…

Unsupervised feature selection is an important method to reduce dimensions of high dimensional data without labels, which is benefit to avoid ``curse of dimensionality'' and improve the performance of subsequent machine learning tasks, like…

In this work, we propose a new deep learning model for Genomic Prediction (GP), which involves correlating genotypic data with phenotypic. The genotypes are typically fed as a sequence of characters to the 1D-Convolution Neural Network…

Symbolic regression (SR) aims to discover mathematical expressions from data, a task traditionally tackled using Genetic Programming (GP) through combinatorial search over symbolic structures. Latent Space Optimization (LSO) methods use…

Multivariate linear mixed models (mvLMMs) have been widely used in many areas of genetics, and have attracted considerable recent interest in genome-wide association studies (GWASs). However, fitting mvLMMs is computationally non-trivial,…

Natural selection at one site shapes patterns of genetic variation at linked sites. Quantifying the effects of 'linked selection' on levels of genetic diversity is key to making reliable inference about demography, building a null model in…