AutoGGN: A Gene Graph Network AutoML Tool for Multi-Omics Research

Abstract Omics data can be used to identify biological characteristics from genetic to phenotypic levels during the life span of a living being, while molecular interaction networks have a fundamental impact on life activities. Integrating omics data and molecular interaction networks will help researchers delve into comprehensive information hidden in the data. Here, we propose a new multimodal method — AutoGGN — to integrate multi-omics data with molecular interaction networks based on graph convolutional neural networks (GCNs). We evaluated AutoGGN using three classification tasks: single-cell embryonic developmental stage classification, pan-cancer type classification, and breast cancer subtyping. On all three tasks, AutoGGN showed better performance than other methods. This means AutoGGN has the potential to extract insights more effectively by means of integrating molecular interaction networks with multi-omics data. Additionally, in order to provide a better understanding of how our model makes predictions, we utilized the SHAP module and identified the key genes contributing to the classification, providing insight for the design of downstream biological experiments.