Ensemble learning methods and heterogeneous graph network fusion: building drug-gene-disease triple association prediction models.

Abstract

The potential association data between drugs, genes, and diseases is sparse and complex. Existing models find it difficult to effectively handle the problem of heterogeneous relationships and multi-source data fusion simultaneously, resulting in limited accuracy and generalization of association prediction. To address this problem, we propose a fusion method of relational graph convolutional network (R-GCN) and eXtreme Gradient Boosting (XGBoost). First, a heterogeneous graph containing drug, gene, and disease nodes and their relationships is constructed. The features of different types of nodes are aggregated and represented by R-GCN to generate high-quality node embeddings. Then, the embedded features of the drug-gene-disease triples are input into the XGBoost model for training to achieve the association prediction task. The findings demonstrate that the model's area under the curve reaches 0.92, and the F1 score reaches 0.85, indicating strong predictive ability. This method solves the problem of association prediction in complex biological networks and brings new technological support for precision medicine.