Bovine Milk Fat Intervention in Early Life and Its Impact on Microbiota, Metabolites and Clinical Phenotype: A Multi-Omics Stacked Regularization Approach
Abstract
:1. Introduction
Contributions
- Novel application of the Manifold Mixing for Stacked Regularization framework;
- Extension of MMSR by using curvature-dependent domain partition and non-linear inter-manifold maps;
- Novel application of PPA;
- Exploration of the effect of milk-fat-containing formula on infant gut parameters using a multi-omics multivariate model.
2. Materials and Methods
2.1. Data Set
2.2. Metabolomics
2.3. Microbiota Composition
2.4. Software
2.5. Stacked Regularization
2.6. Manifold Mixing for Stacked Regularization
Algorithm 1: partition_curved_regions. |
Input:, q(queue), (curvature array), (list of curved subspaces), , Return:, q
|
2.7. Pairwise Permutation Algorithm
3. Results
3.1. IF Data Set Model Performance
3.2. Feature Importance
4. Discussion
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Appendix A
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Pereira, J.; Bresser, L.R.F.; Riel, N.v.; Looijesteijn, E.; Schoemaker, R.; Ulfman, L.H.; Jeurink, P.; Karaglani, E.; Manios, Y.; Brouwer, R.W.W.; et al. Bovine Milk Fat Intervention in Early Life and Its Impact on Microbiota, Metabolites and Clinical Phenotype: A Multi-Omics Stacked Regularization Approach. BioMedInformatics 2022, 2, 281-296. https://doi.org/10.3390/biomedinformatics2020018
Pereira J, Bresser LRF, Riel Nv, Looijesteijn E, Schoemaker R, Ulfman LH, Jeurink P, Karaglani E, Manios Y, Brouwer RWW, et al. Bovine Milk Fat Intervention in Early Life and Its Impact on Microbiota, Metabolites and Clinical Phenotype: A Multi-Omics Stacked Regularization Approach. BioMedInformatics. 2022; 2(2):281-296. https://doi.org/10.3390/biomedinformatics2020018
Chicago/Turabian StylePereira, João, Lucas R. F. Bresser, Natal van Riel, Ellen Looijesteijn, Ruud Schoemaker, Laurien H. Ulfman, Prescilla Jeurink, Eva Karaglani, Yannis Manios, Rutger W. W. Brouwer, and et al. 2022. "Bovine Milk Fat Intervention in Early Life and Its Impact on Microbiota, Metabolites and Clinical Phenotype: A Multi-Omics Stacked Regularization Approach" BioMedInformatics 2, no. 2: 281-296. https://doi.org/10.3390/biomedinformatics2020018