2024/06/02 by Wenyu Xi, Juan Wang, Xi, Wen-Yu +7
Biochemistry, Genetics and Molecular Biology · #Artificial Intelligence (cs.AI) #Cancer-related molecular mechanisms research #Circular RNAs in diseases #FOS: Biological sciences #FOS: Computer and information sciences #Machine Learning (cs.LG) #Machine Learning in Bioinformatics #Quantitative Methods (q-bio.QM)
paper · pdf · doi:10.48550/arxiv.2406.03406
openalex publication_date 2024/06/02 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
The emerging research shows that lncRNA has crucial research value in a series of complex human diseases. Therefore, the accurate identification of lncRNA-disease associations (LDAs) is very important for the warning and treatment of diseases. However, most of the existing methods have limitations in identifying nonlinear LDAs, and it remains a huge challenge to predict new LDAs. In this paper, a deep learning model based on a heterogeneous network and convolutional neural network (CNN) is proposed for lncRNA-disease association prediction, named HCNNLDA. The heterogeneous network containing the lncRNA, disease, and miRNA nodes, is constructed firstly. The embedding matrix of a lncRNA-disease node pair is constructed according to various biological premises about lncRNAs, diseases, and miRNAs. Then, the low-dimensional feature representation is fully learned by the convolutional neural network. In the end, the XGBoot classifier model is trained to predict the potential LDAs. HCNNLDA obtains a high AUC value of 0.9752 and AUPR of 0.9740 under the 5-fold cross-validation. The experimental results show that the proposed model has better performance than that of several latest prediction models. Meanwhile, the effectiveness of HCNNLDA in identifying novel LDAs is further demonstrated by case studies of three diseases. To sum up, HCNNLDA is a feasible calculation model to predict LDAs.