<i>MedGraphNet</i>: Leveraging Multi-Relational Graph Neural Networks and Text Knowledge for Biomedical Predictions.

Genetic, molecular, and environmental factors influence diseases through complex interactions with genes, phenotypes, and drugs. Current methods often fail to integrate diverse multi-relational biological data meaningfully, limiting the discovery of novel risk genes and drugs. To address this, we present <i>MedGraphNet</i>, a multi-relational Graph Neural Network (GNN) model designed to infer relationships among drugs, genes, diseases, and phenotypes. <i>MedGraphNet</i> initializes nodes using informative embeddings from existing text knowledge, allowing for robust integration of various data types and improved generalizability. Our results demonstrate that <i>MedGraphNet</i> matches and often outperforms traditional single-relation approaches, particularly in scenarios with isolated or sparsely connected nodes. The model shows generalizability to external datasets, achieving high accuracy in identifying disease-gene associations and drug-phenotype relationships. Notably, <i>MedGraphNet</i> accurately inferred drug side effects without direct training on such data. Using Alzheimer's disease as a case study, <i>MedGraphNet</i> successfully identified relevant phenotypes, genes, and drugs, corroborated by existing literature. These findings demonstrate the potential of integrating multi-relational data with text knowledge to enhance biomedical predictions and drug repurposing for diseases. <i>MedGraphNet</i> code is available at https://github.com/vinash85/MedGraphNet.