M2DMiners specifications

Information


Unique identifier OMICS_20555
Name M2DMiners
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages MATLAB
Computer skills Advanced
Stability Stable
Maintained Yes

Subtools


  • HDMP
  • Jiang’s method
  • MaxFlow
  • NCPMDA
  • RLSMDA
  • RWRMDA

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Documentation


Maintainers


  • person_outline Xiaojun Chen <>
  • person_outline Hua Yu <>

Publication for M2DMiners

M2DMiners in publications

 (20)
PMCID: 5915491
PMID: 29691434
DOI: 10.1038/s41598-018-24532-7

[…] some diseases without the known related mirna. many studies have shown that global network similarity can effectively improve prediction performance. in 2012, chen et al. introduced a method named rwrmda to predict mirna–disease association based on global network similarity. they predicted a pathogenetic mirna through a restarted random walk. firstly, they integrated the mirna–mirna […]

PMCID: 5905221
PMID: 29665774
DOI: 10.1186/s12859-018-2146-x

[…] while an auc value of 0.5 indicated a purely random performance. the performance comparison in terms of the loocv results is shown in fig. . in the loocv, the dcsmda (when b was set to 6), rlsmda, wbsmda and hglda achieved aucs of 0.8155, 0.7826, 0.7582 and 0.7621, respectively. dcsmda predicted potential mirna-disease associations without requiring known mirna-disease associations. […]

PMCID: 5686822
PMID: 29137601
DOI: 10.1186/s12859-017-1924-1

[…] their target genes as seed nodes, the method can identify additional mirnas involved in the disease phenotype. experiments indicated that rwrmtn outperformed two existing state-of-the-art methods: rwrmda, a network-based method that also uses a rwr on homogeneous (rather than heterogeneous) mirna networks, and rlsmda, a machine learning-based method. interestingly, we could relate […]

PMCID: 5670180
PMID: 29101378
DOI: 10.1038/s41598-017-15235-6

[…] association is added. to evaluate the prediction performance of deepmda, we adopted 5-fold cross-validation compared with other five state-of-the-art computational models (i.e., rlsmda, hgimda, ncpmda, pbmda, rknnmda). rwrmda was a representative approach in the domain and was often considered as a standard method to validate performance. hgimda was an improved version of rwrmda […]

PMCID: 5585369
PMID: 28874691
DOI: 10.1038/s41598-017-10065-y

[…] be easily compared with methods that are able to perform predictions with few or even no annotation. however, we can state that mirai, even optimized with ea, is outclassed by recent methods such as ncpmda that exhibits an auc score of 0.9173 (althought calculated with leave-one-out cross validation and not a 5-fold validation), or pbmda with an auc score of 0.9172. our method is also clearly […]


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M2DMiners institution(s)
Key Lab of Agricultural Biotechnology of Ningxia, Agricultural Biotechnology Center, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, Ningxia, China; State Key Laboratory of Plant Genomics, Institute of Genetic and Developmental Biology, Chinese Academy of Sciences, Beijing, China; Beijing Computing Center, Beijing Academy of Science and Technology, Beijing, China
M2DMiners funding source(s)
Supported by the National Natural Science Foundation of China (Grant No. 31460338).

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