ANMDA: Anti-noise Based Computational Model for Predicting Potential MiRNA-disease Associations

Overview

Journal BMC Bioinformatics

Publisher Biomed Central

Specialty Biology

Date 2021 Jul 3

PMID 34215183

Citations 3

Authors

Xue-Jun Chen

Xin-Yun Hua

Zhen-Ran Jiang

Affiliations

Soon will be listed here.

Abstract

Background: A growing proportion of research has proved that microRNAs (miRNAs) can regulate the function of target genes and have close relations with various diseases. Developing computational methods to exploit more potential miRNA-disease associations can provide clues for further functional research.

Results: Inspired by the work of predecessors, we discover that the noise hiding in the data can affect the prediction performance and then propose an anti-noise algorithm (ANMDA) to predict potential miRNA-disease associations. Firstly, we calculate the similarity in miRNAs and diseases to construct features and obtain positive samples according to the Human MicroRNA Disease Database version 2.0 (HMDD v2.0). Then, we apply k-means on the undetected miRNA-disease associations and sample the negative examples equally from the k-cluster. Further, we construct several data subsets through sampling with replacement to feed on the light gradient boosting machine (LightGBM) method. Finally, the voting method is applied to predict potential miRNA-disease relationships. As a result, ANMDA can achieve an area under the receiver operating characteristic curve (AUROC) of 0.9373 ± 0.0005 in five-fold cross-validation, which is superior to several published methods. In addition, we analyze the predicted miRNA-disease associations with high probability and compare them with the data in HMDD v3.0 in the case study. The results show ANMDA is a novel and practical algorithm that can be used to infer potential miRNA-disease associations.

Conclusion: The results indicate the noise hiding in the data has an obvious impact on predicting potential miRNA-disease associations. We believe ANMDA can achieve better results from this task with more methods used in dealing with the data noise.

Citing Articles

Prediction of miRNA-disease associations based on PCA and cascade forest.

Zhang C, Li Y, Dong Y, Chen W, Yu C BMC Bioinformatics. 2024; 25(1):386.

PMID: 39701957 PMC: 11660965. DOI: 10.1186/s12859-024-05999-w.

Applying negative sample denoising and multi-view feature for lncRNA-disease association prediction.

Yao D, Zhang B, Li X, Zhan X, Zhan X, Zhang B Front Genet. 2024; 14:1332273.

PMID: 38264213 PMC: 10803626. DOI: 10.3389/fgene.2023.1332273.

A clustering-based sampling method for miRNA-disease association prediction.

Wei Z, Yao D, Zhan X, Zhang S Front Genet. 2022; 13:995535.

PMID: 36176298 PMC: 9513605. DOI: 10.3389/fgene.2022.995535.

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