# Multi-task genomic prediction using gated residual variable selection neural networks

## TL;DR

This paper introduces a new neural network model that combines genomic and pedigree data to improve prediction accuracy in genomics.

## Contribution

The novel GRVSNN framework integrates pedigree and genomic data for multi-task genomic prediction with improved accuracy and interpretability.

## Key findings

- GRVSNN outperforms traditional models with lower MSE and higher correlation in test data.
- The model selects fewer genetic markers and pedigree loadings, enhancing interpretability.

## Abstract

The recent development of high-throughput sequencing techniques provide massive data that can be used in genome-wide prediction (GWP). Although GWP is effective on its own, the incorporation of traditional polygenic pedigree information into GWP has been shown to further improve prediction accuracy. However, most of the methods developed in this field require that individuals with genomic information can be connected to the polygenic pedigree within a standard linear mixed model framework that involves calculation of computationally demanding matrix inverses of the combined pedigrees. The extension of this integrated approach to more flexible machine learning methods has been slow.

This study aims to enhance genomic prediction by implementing gated residual variable selection neural networks (GRVSNN) for multi-task genomic prediction. By integrating low-rank information from pedigree-based relationship matrices with genomic markers, we seek to improve predictive accuracy and interpretability compared to conventional regression and deep learning (DL) models. The prediction properties of the GRVSNN model are evaluated on several real-world datasets, including loblolly pine, mouse and pig.

The experimental results demonstrate that the GRVSNN model outperforms traditional tabular genomic prediction models, including Bayesian regression methods and LassoNet. Using genomic and pedigree information, GRVSNN achieves a lower mean squared error (MSE), and higher Pearson (r) and distance (dCor) correlation between predicted and true phenotypic values in the test data. Moreover, GRVSNN selects fewer genetic markers and pedigree loadings which improves interpretability.

The suggested GRVSNN framework provides a novel and computationally effective approach to improve genomic prediction accuracy by integrating information from traditional pedigrees with genomic data. The model’s ability to conduct multi-task predictions underscores its potential to enhance selection processes in agricultural species and predict multiple diseases in precision medicine.