Prediction of MiRNA-disease Associations Based on PCA and Cascade Forest

Overview

Journal BMC Bioinformatics

Publisher Biomed Central

Specialty Biology

Date 2024 Dec 20

PMID 39701957

Authors

Chuanlei Zhang

Yubo Li

Yinglun Dong

Wei Chen

Changqing Yu

Affiliations

Soon will be listed here.

Abstract

Background: As a key non-coding RNA molecule, miRNA profoundly affects gene expression regulation and connects to the pathological processes of several kinds of human diseases. However, conventional experimental methods for validating miRNA-disease associations are laborious. Consequently, the development of efficient and reliable computational prediction models is crucial for the identification and validation of these associations.

Results: In this research, we developed the PCACFMDA method to predict the potential associations between miRNAs and diseases. To construct a multidimensional feature matrix, we consider the fusion similarities of miRNA and disease and miRNA-disease pairs. We then use principal component analysis(PCA) to reduce data complexity and extract low-dimensional features. Subsequently, a tuned cascade forest is used to mine the features and output prediction scores deeply. The results of the 5-fold cross-validation using the HMDD v2.0 database indicate that the PCACFMDA algorithm achieved an AUC of 98.56%. Additionally, we perform case studies on breast, esophageal and lung neoplasms. The findings revealed that the top 50 miRNAs most strongly linked to each disease have been validated.

Conclusions: Based on PCA and optimized cascade forests, we propose the PCACFMDA model for predicting undiscovered miRNA-disease associations. The experimental results demonstrate superior prediction performance and commendable stability. Consequently, the PCACFMDA is a potent instrument for in-depth exploration of miRNA-disease associations.

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