AMPFLDAP: Adaptive Message Passing and Feature Fusion on Heterogeneous Network for LncRNA-Disease Associations Prediction

• Published in: Interdisciplinary sciences : computational life sciences 2024-09, Vol.16 (3), p.608-622
• Main Authors: Su, Yansen, Liu, Jingjing, Wu, Qingwen, Gao, Zhen, Wang, Jing, Li, Haitao, Zheng, Chunhou
• Format: Article
• Language: English
• Subjects: Biomedical and Life Sciences; Computational Biology/Bioinformatics; Computational Science and Engineering; Computer Appl. in Life Sciences; Health Sciences; Life Sciences; Mathematical and Computational Physics; Medicine; Original Research Article; Statistics for Life Sciences; Theoretical; Theoretical and Computational Chemistry
• ISSN: 1913-2751; 1867-1462; 1867-1462
• DOI: 10.1007/s12539-024-00610-5

Exploration of the intricate connections between long noncoding RNA (lncRNA) and diseases, referred to as lncRNA-disease associations (LDAs), plays a pivotal and indispensable role in unraveling the underlying molecular mechanisms of diseases and devising practical treatment approaches. It is imperative to employ computational methods for predicting lncRNA-disease associations to circumvent the need for superfluous experimental endeavors. Graph-based learning models have gained substantial popularity in predicting these associations, primarily because of their capacity to leverage node attributes and relationships within the network. Nevertheless, there remains much room for enhancing the performance of these techniques by incorporating and harmonizing the node attributes more effectively. In this context, we introduce a novel model, i.e., Adaptive Message Passing and Feature Fusion (AMPFLDAP), for forecasting lncRNA-disease associations within a heterogeneous network. Firstly, we constructed a heterogeneous network involving lncRNA, microRNA (miRNA), and diseases based on established associations and employing Gaussian interaction profile kernel similarity as a measure. Then, an adaptive topological message passing mechanism is suggested to address the information aggregation for heterogeneous networks. The topological features of nodes in the heterogeneous network were extracted based on the adaptive topological message passing mechanism. Moreover, an attention mechanism is applied to integrate both topological and semantic information to achieve the multimodal features of biomolecules, which are further used to predict potential LDAs. The experimental results demonstrated that the performance of the proposed AMPFLDAP is superior to seven state-of-the-art methods. Furthermore, to validate its efficacy in practical scenarios, we conducted detailed case studies involving three distinct diseases, which conclusively demonstrated AMPFLDAP’s effectiveness in the prediction of LDAs.