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Article: BMCMDA: a novel model for predicting human microbe-disease associations via binary matrix completion

TitleBMCMDA: a novel model for predicting human microbe-disease associations via binary matrix completion
Authors
KeywordsMachine learning
Matrix completion
Microbe-disease association
Prediction
Issue Date2018
PublisherBioMed Central Ltd. The Journal's web site is located at http://www.biomedcentral.com/bmcbioinformatics/
Citation
BMC Bioinformatics, 2018, v. 19, p. 169-176 How to Cite?
AbstractBackground: Human Microbiome Project reveals the significant mutualistic influence between human body and microbes living in it. Such an influence lead to an interesting phenomenon that many noninfectious diseases are closely associated with diverse microbes. However, the identification of microbe-noninfectious disease associations (MDAs) is still a challenging task, because of both the high cost and the limitation of microbe cultivation. Thus, there is a need to develop fast approaches to screen potential MDAs. The growing number of validated MDAs enables us to meet the demand in a new insight. Computational approaches, especially machine learning, are promising to predict MDA candidates rapidly among a large number of microbe-disease pairs with the advantage of no limitation on microbe cultivation. Nevertheless, a few computational efforts at predicting MDAs are made so far. Results: In this paper, grouping a set of MDAs into a binary MDA matrix, we propose a novel predictive approach (BMCMDA) based on Binary Matrix Completion to predict potential MDAs. The proposed BMCMDA assumes that the incomplete observed MDA matrix is the summation of a latent parameterizing matrix and a noising matrix. It also assumes that the independently occurring subscripts of observed entries in the MDA matrix follows a binomial model. Adopting a standard mean-zero Gaussian distribution for the nosing matrix, we model the relationship between the parameterizing matrix and the MDA matrix under the observed microbe-disease pairs as a probit regression. With the recovered parameterizing matrix, BMCMDA deduces how likely a microbe would be associated with a particular disease. In the experiment under leave-one-out cross-validation, it exhibits the inspiring performance (AUC=0.906, AUPR =0.526) and demonstrates its superiority by ~7% and ~5% improvements in terms of AUC and AUPR respectively in the comparison with the pioneering approach KATZHMDA. Conclusions: Our BMCMDA provides an effective approach for predicting MDAs and can be also extended to other similar predicting tasks of binary relationship (e.g. protein-protein interaction, drug-target interaction).
Persistent Identifierhttp://hdl.handle.net/10722/262032
ISSN
2023 Impact Factor: 2.9
2023 SCImago Journal Rankings: 1.005
ISI Accession Number ID

 

DC FieldValueLanguage
dc.contributor.authorShi, JY-
dc.contributor.authorHuang, H-
dc.contributor.authorZhang, YN-
dc.contributor.authorCao, JB-
dc.contributor.authorYiu, SM-
dc.date.accessioned2018-09-28T04:52:16Z-
dc.date.available2018-09-28T04:52:16Z-
dc.date.issued2018-
dc.identifier.citationBMC Bioinformatics, 2018, v. 19, p. 169-176-
dc.identifier.issn1471-2105-
dc.identifier.urihttp://hdl.handle.net/10722/262032-
dc.description.abstractBackground: Human Microbiome Project reveals the significant mutualistic influence between human body and microbes living in it. Such an influence lead to an interesting phenomenon that many noninfectious diseases are closely associated with diverse microbes. However, the identification of microbe-noninfectious disease associations (MDAs) is still a challenging task, because of both the high cost and the limitation of microbe cultivation. Thus, there is a need to develop fast approaches to screen potential MDAs. The growing number of validated MDAs enables us to meet the demand in a new insight. Computational approaches, especially machine learning, are promising to predict MDA candidates rapidly among a large number of microbe-disease pairs with the advantage of no limitation on microbe cultivation. Nevertheless, a few computational efforts at predicting MDAs are made so far. Results: In this paper, grouping a set of MDAs into a binary MDA matrix, we propose a novel predictive approach (BMCMDA) based on Binary Matrix Completion to predict potential MDAs. The proposed BMCMDA assumes that the incomplete observed MDA matrix is the summation of a latent parameterizing matrix and a noising matrix. It also assumes that the independently occurring subscripts of observed entries in the MDA matrix follows a binomial model. Adopting a standard mean-zero Gaussian distribution for the nosing matrix, we model the relationship between the parameterizing matrix and the MDA matrix under the observed microbe-disease pairs as a probit regression. With the recovered parameterizing matrix, BMCMDA deduces how likely a microbe would be associated with a particular disease. In the experiment under leave-one-out cross-validation, it exhibits the inspiring performance (AUC=0.906, AUPR =0.526) and demonstrates its superiority by ~7% and ~5% improvements in terms of AUC and AUPR respectively in the comparison with the pioneering approach KATZHMDA. Conclusions: Our BMCMDA provides an effective approach for predicting MDAs and can be also extended to other similar predicting tasks of binary relationship (e.g. protein-protein interaction, drug-target interaction).-
dc.languageeng-
dc.publisherBioMed Central Ltd. The Journal's web site is located at http://www.biomedcentral.com/bmcbioinformatics/-
dc.relation.ispartofBMC Bioinformatics-
dc.rightsBMC Bioinformatics. Copyright © BioMed Central Ltd.-
dc.rightsThis work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.-
dc.subjectMachine learning-
dc.subjectMatrix completion-
dc.subjectMicrobe-disease association-
dc.subjectPrediction-
dc.titleBMCMDA: a novel model for predicting human microbe-disease associations via binary matrix completion-
dc.typeArticle-
dc.identifier.emailYiu, SM: smyiu@cs.hku.hk-
dc.identifier.authorityYiu, SM=rp00207-
dc.description.naturepublished_or_final_version-
dc.identifier.doi10.1186/s12859-018-2274-3-
dc.identifier.pmid30367598-
dc.identifier.scopuseid_2-s2.0-85051591654-
dc.identifier.hkuros292123-
dc.identifier.volume19-
dc.identifier.spage169-
dc.identifier.epage176-
dc.identifier.isiWOS:000442105800002-
dc.publisher.placeUnited Kingdom-
dc.identifier.issnl1471-2105-

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