AI4EVER: A Graphical Deep Learning Platform for GWAS-Informed Genomic Prediction
Summary: The potential of deep learning (DL) in genomic selection (GS) is constrained by the significant technical expertise required to design and implement neural networks. While DL has revolutionized fields like language processing and structural biology, its application in GS has not yet consistently outperformed traditional models like mixed linear models. The key to unlocking DL’s power in GS lies in the exploration of network architectures tailored to genomic data, a process that demands intensive programming and poses a barrier for many researchers. To overcome this challenge, we developed Artificial Intelligence for Efficient and Versatile Evaluation and Representation (AI4EVER), a freely available graphical software platform that enables users to explore and apply machine learning (ML) models without any coding. AI4EVER integrates a graphical user interface (GUI) with a Python-based ML backend. The platform currently supports five models: Ridge Regression, Random Forest, Gradient Boosted Decision Trees, Multi-Layer Perceptron, and a customizable Keras-based neural network that can simultaneously predict multiple traits in a single model. A key feature of AI4EVER is optional incorporation of genome-wide association study (GWAS) results (p-values) as feature weights during model training, enabling biologically informed DL workflows. The platform further provides real-time visualization of model performance metrics and automated feature-importance outputs to enhance interpretability. AI4EVER also separates model training and prediction workflows, allowing trained models to be reused for independent prediction datasets. Using a representative maize dataset, we demonstrate that AI4EVER enables access to advanced AI, empowers genomic researchers to accelerate data-driven decision-making in breeding programs, ultimately lowering the barrier to artificial intelligence-enabled genetic improvement in crops and animals and human health management.
