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MHMDA : Human Micro...
MHMDA : Human Microbe-Disease Association Prediction by Matrix Completion and Multi-Source Information
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- Wu, Chuanyan (författare)
- Lund University,Lunds universitet,Genomik, diabetes och endokrinologi,Forskargrupper vid Lunds universitet,Genomics, Diabetes and Endocrinology,Lund University Research Groups,Shandong University
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- Gao, Rui (författare)
- Shandong University
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- Zhang, Yusen (författare)
- Shandong University
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(creator_code:org_t)
- 2019
- 2019
- Engelska 7 s.
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Ingår i: IEEE Access. - 2169-3536. ; 7, s. 106687-106693
- Relaterad länk:
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http://dx.doi.org/10... (free)
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visa fler...
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https://lup.lub.lu.s...
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https://doi.org/10.1...
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Abstract
Ämnesord
Stäng
- Microbes are vital in human health. It is helpful to promote diagnostic and treatment of human disease and drug development by identifying microbe-disease associations. However, knowledge in this area still needs to be further improved. In this paper, a new computational model using matrix completion to predict human microbe-disease associations (mHMDA, Fig. 1) is developed. First, we extract the disease feature by Gaussian kernel-based similarity and symptom-based similarity. Meanwhile, the microbe feature is computed by Gaussian kernel-based similarity. As treating potential association as the missing elements of a matrix, the matrix completion is adopted to get the potential microbe-disease associations. Leave-one-out cross-validation (LOOCV) is carried out which get the AUC (The area under ROC curve) of 0.928 showing the effectiveness of mHMDA. Furthermore, 5-fold CV get the AUCs of 0.8838 ± 0.0044 (mean ± standard deviation). Moreover, through the four case studies (asthma, inflammatory bowel disease (IBD), type 2 diabetes (T2D), and type 1 diabetes (T1D)), we find that nine, ten, nine, and eight of top-ten inferred microorganisms for the four diseases are previously verified by experiments. All these results indicate the effectiveness of mHMDA. mHMDA might be helpful to infer the disease-related microorganisms.
Ämnesord
- MEDICIN OCH HÄLSOVETENSKAP -- Medicinsk bioteknologi -- Biomedicinsk laboratorievetenskap/teknologi (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Medical Biotechnology -- Biomedical Laboratory Science/Technology (hsv//eng)
Nyckelord
- matrix completion
- microbe-disease association prediction
- Microbial community
Publikations- och innehållstyp
- art (ämneskategori)
- ref (ämneskategori)
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