Hierarchical Negative Sampling Based Graph Contrastive Learning Approach for Drug-Disease Association Prediction

• Published in: IEEE journal of biomedical and health informatics 2024-05, Vol.28 (5), p.3146-3157
• Main Authors: Wang, Yuanxu, Song, Jinmiao, Dai, Qiguo, Duan, Xiaodong
• Format: Article
• Language: English
• Subjects: Aggregation; Algorithms; Artificial neural networks; Computational Biology - methods; Contrastive learning; Cost function; Disease; Disease - classification; Diseases; Drug development; Drug Repositioning - methods; drug-disease assoc- iations; Drugs; Entropy (Information theory); Feature extraction; graph neural networks; Graphs; Heterogeneous networks; Humans; Information processing; Machine Learning; Matrix decomposition; Molecular biophysics; negative sampling method; Pharmaceutical Preparations; Predictions; Proteins; Representations; Sampling; Sampling methods; Sampling techniques; Search algorithms
• ISSN: 2168-2194; 2168-2208; 2168-2208
• DOI: 10.1109/JBHI.2024.3360437

Predicting potential drug-disease associations (RDAs) plays a pivotal role in elucidating therapeutic strategies for diseases and facilitating drug repositioning, making it of paramount importance. However, existing methods are constrained and rely heavily on limited domain-specific knowledge, impeding their ability to effectively predict candidate associations between drugs and diseases. Moreover, the simplistic definition of unknown information pertaining to drug-disease relationships as negative samples presents inherent limitations. To overcome these challenges, we introduce a novel hierarchical negative sampling-based graph contrastive model, termed HSGCLRDA, which aims to forecast latent associations between drugs and diseases. In this study, HSGCLRDA integrates the association information as well as similarity between drugs, diseases and proteins. Meanwhile, the model constructs a drug-disease-protein heterogeneous network. Subsequently, employing a hierarchical structural sampling technique, we establish reliable negative drug-disease samples utilizing PageRank algorithms. Utilizing meta-path aggregation within the heterogeneous network, we derive low-dimensional representations for drugs and diseases, thereby constructing global and local feature graphs that capture their interactions comprehensively. To obtain representation information, we adopt a self-supervised graph contrastive approach that leverages graph convolutional networks (GCNs) and second-order GCNs to extract feature graph information. Furthermore, we integrate a contrastive cost function derived from the cross-entropy cost function, facilitating holistic model optimization. Experimental results obtained from benchmark datasets not only showcase the superior performance of HSGCLRDA compared to various baseline methods in predicting RDAs but also emphasize its practical utility in identifying novel potential diseases associated with existing drugs through meticulous case studies.