Prediction of miRNA–Disease Associations by Cascade Forest Model Based on Stacked Autoencoder

• Published in: Molecules (Basel, Switzerland) Vol. 28; no. 13; p. 5013
• Main Authors: Hu, Xiang, Yin, Zhixiang, Zeng, Zhiliang, Peng, Yu
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 27.06.2023; MDPI
• Subjects: Ablation; Algorithms; Alzheimer's disease; Analysis; Bioinformatics; Breast cancer; Carcinoma, Hepatocellular; cascade forest; Case studies; Computational Biology - methods; Design; Graph representations; Humans; Liver cancer; Liver Neoplasms; Lung cancer; Lung Neoplasms - genetics; Machine learning; Methods; MicroRNA; MicroRNAs; MicroRNAs - genetics; miRNA–disease association; multi-source information; Neural networks; Performance evaluation; stacked autoencoder; Tumors; Taiwan; miRNA–disease association; stacked autoencoder; cascade forest; multi-source information
• ISSN: 1420-3049; 1420-3049
• DOI: 10.3390/molecules28135013

Numerous pieces of evidence have indicated that microRNA (miRNA) plays a crucial role in a series of significant biological processes and is closely related to complex disease. However, the traditional biological experimental methods used to verify disease-related miRNAs are inefficient and expensive. Thus, it is necessary to design some excellent approaches to improve efficiency. In this work, a novel method (CFSAEMDA) is proposed for the prediction of unknown miRNA–disease associations (MDAs). Specifically, we first capture the interactive features of miRNA and disease by integrating multi-source information. Then, the stacked autoencoder is applied for obtaining the underlying feature representation. Finally, the modified cascade forest model is employed to complete the final prediction. The experimental results present that the AUC value obtained by our method is 97.67%. The performance of CFSAEMDA is superior to several of the latest methods. In addition, case studies conducted on lung neoplasms, breast neoplasms and hepatocellular carcinoma further show that the CFSAEMDA method may be regarded as a utility approach to infer unknown disease–miRNA relationships.