MDHGI: Matrix Decomposition and Heterogeneous Graph Inference for miRNA-disease association prediction

PLoS Computational Biology
Xing ChenLi Huang

Abstract

Recently, a growing number of biological research and scientific experiments have demonstrated that microRNA (miRNA) affects the development of human complex diseases. Discovering miRNA-disease associations plays an increasingly vital role in devising diagnostic and therapeutic tools for diseases. However, since uncovering associations via experimental methods is expensive and time-consuming, novel and effective computational methods for association prediction are in demand. In this study, we developed a computational model of Matrix Decomposition and Heterogeneous Graph Inference for miRNA-disease association prediction (MDHGI) to discover new miRNA-disease associations by integrating the predicted association probability obtained from matrix decomposition through sparse learning method, the miRNA functional similarity, the disease semantic similarity, and the Gaussian interaction profile kernel similarity for diseases and miRNAs into a heterogeneous network. Compared with previous computational models based on heterogeneous networks, our model took full advantage of matrix decomposition before the construction of heterogeneous network, thereby improving the prediction accuracy. MDHGI obtained AUCs of 0.8945 and 0.8240 in the ...Continue Reading

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Citations

Apr 2, 2019·PLoS Computational Biology·Cheng LiangJiawei Luo
May 6, 2019·International Journal of Molecular Sciences·Xiaoyong PanYu-Dong Cai
Jul 23, 2019·PLoS Computational Biology·Xing ChenJun Yin
Aug 29, 2019·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Ping XuanYingying Song
Feb 29, 2020·International Journal of Molecular Sciences·Xing ChenNa-Na Guan
Aug 30, 2019·PloS One·Paweł WiczlingMagdalena Ratajska
Oct 1, 2019·Briefings in Bioinformatics·Pingjian DingChee-Keong Kwoh
Dec 28, 2019·Protein and Peptide Letters·Jia QuChun-Chun Wang
Apr 11, 2019·Protein and Peptide Letters·Yijie DingFei Guo
Sep 21, 2019·Protein and Peptide Letters·Cheng ShiHeng Zheng
Aug 25, 2020·Nucleic Acids Research·Lin NingDong Wang
Oct 3, 2020·Molecular Genetics and Genomics : MGG·Lin ZhongQi Zhao
Oct 26, 2018·Frontiers in Microbiology·Li-Hong PengYan Zhao
Mar 27, 2020·Frontiers in Bioengineering and Biotechnology·Junfeng ZhuQi Zhao
Jan 24, 2019·International Journal of Molecular Sciences·Chen ZhaoAleksander S Popel
Apr 12, 2019·Frontiers in Microbiology·Xiaoqing RuChunyu Wang

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Methods Mentioned

BETA
PCA

Software Mentioned

HGIMDA
MaxFlow
HDMP
RBMMMDA
MCMDA
MIDP
RWRMDA
RKNNMDA
MDHGI
MiRAI

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