Integration strategies of multi-omics data for machine learning analysis
Schematic representation of the main strategies for multi-omics datasets integration. A) Early integration concatenates all omics datasets into a single matrix on which machine learning model can be applied. B) Mixed integration first independently transforms or maps each omics block into a new repr...
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| Vydané v: | Computational and structural biotechnology journal Ročník 19; s. 3735 - 3746 |
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| Hlavní autori: | , , , , |
| Médium: | Journal Article |
| Jazyk: | English |
| Vydavateľské údaje: |
Elsevier B.V
01.01.2021
Research Network of Computational and Structural Biotechnology Elsevier |
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| ISSN: | 2001-0370, 2001-0370 |
| On-line prístup: | Získať plný text |
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| Abstract | Schematic representation of the main strategies for multi-omics datasets integration. A) Early integration concatenates all omics datasets into a single matrix on which machine learning model can be applied. B) Mixed integration first independently transforms or maps each omics block into a new representation before combining them for downstream analysis. C) Intermediate integration simultaneously transforms the original datasets into common and omics-specific representations. D) Late integration analyses each omics separately and combines their final predictions. E) Hierarchical integration bases the integration of datasets on prior regulatory relationships between omics layers.
[Display omitted]
Increased availability of high-throughput technologies has generated an ever-growing number of omics data that seek to portray many different but complementary biological layers including genomics, epigenomics, transcriptomics, proteomics, and metabolomics. New insight from these data have been obtained by machine learning algorithms that have produced diagnostic and classification biomarkers. Most biomarkers obtained to date however only include one omic measurement at a time and thus do not take full advantage of recent multi-omics experiments that now capture the entire complexity of biological systems.
Multi-omics data integration strategies are needed to combine the complementary knowledge brought by each omics layer. We have summarized the most recent data integration methods/ frameworks into five different integration strategies: early, mixed, intermediate, late and hierarchical. In this mini-review, we focus on challenges and existing multi-omics integration strategies by paying special attention to machine learning applications. |
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| AbstractList | Increased availability of high-throughput technologies has generated an ever-growing number of omics data that seek to portray many different but complementary biological layers including genomics, epigenomics, transcriptomics, proteomics, and metabolomics. New insight from these data have been obtained by machine learning algorithms that have produced diagnostic and classification biomarkers. Most biomarkers obtained to date however only include one omic measurement at a time and thus do not take full advantage of recent multi-omics experiments that now capture the entire complexity of biological systems.Multi-omics data integration strategies are needed to combine the complementary knowledge brought by each omics layer. We have summarized the most recent data integration methods/ frameworks into five different integration strategies: early, mixed, intermediate, late and hierarchical. In this mini-review, we focus on challenges and existing multi-omics integration strategies by paying special attention to machine learning applications. Schematic representation of the main strategies for multi-omics datasets integration. A) Early integration concatenates all omics datasets into a single matrix on which machine learning model can be applied. B) Mixed integration first independently transforms or maps each omics block into a new representation before combining them for downstream analysis. C) Intermediate integration simultaneously transforms the original datasets into common and omics-specific representations. D) Late integration analyses each omics separately and combines their final predictions. E) Hierarchical integration bases the integration of datasets on prior regulatory relationships between omics layers. Increased availability of high-throughput technologies has generated an ever-growing number of omics data that seek to portray many different but complementary biological layers including genomics, epigenomics, transcriptomics, proteomics, and metabolomics. New insight from these data have been obtained by machine learning algorithms that have produced diagnostic and classification biomarkers. Most biomarkers obtained to date however only include one omic measurement at a time and thus do not take full advantage of recent multi-omics experiments that now capture the entire complexity of biological systems. Multi-omics data integration strategies are needed to combine the complementary knowledge brought by each omics layer. We have summarized the most recent data integration methods/ frameworks into five different integration strategies: early, mixed, intermediate, late and hierarchical. In this mini-review, we focus on challenges and existing multi-omics integration strategies by paying special attention to machine learning applications. Increased availability of high-throughput technologies has generated an ever-growing number of omics data that seek to portray many different but complementary biological layers including genomics, epigenomics, transcriptomics, proteomics, and metabolomics. New insight from these data have been obtained by machine learning algorithms that have produced diagnostic and classification biomarkers. Most biomarkers obtained to date however only include one omic measurement at a time and thus do not take full advantage of recent multi-omics experiments that now capture the entire complexity of biological systems. Multi-omics data integration strategies are needed to combine the complementary knowledge brought by each omics layer. We have summarized the most recent data integration methods/ frameworks into five different integration strategies: early, mixed, intermediate, late and hierarchical. In this mini-review, we focus on challenges and existing multi-omics integration strategies by paying special attention to machine learning applications.Increased availability of high-throughput technologies has generated an ever-growing number of omics data that seek to portray many different but complementary biological layers including genomics, epigenomics, transcriptomics, proteomics, and metabolomics. New insight from these data have been obtained by machine learning algorithms that have produced diagnostic and classification biomarkers. Most biomarkers obtained to date however only include one omic measurement at a time and thus do not take full advantage of recent multi-omics experiments that now capture the entire complexity of biological systems. Multi-omics data integration strategies are needed to combine the complementary knowledge brought by each omics layer. We have summarized the most recent data integration methods/ frameworks into five different integration strategies: early, mixed, intermediate, late and hierarchical. In this mini-review, we focus on challenges and existing multi-omics integration strategies by paying special attention to machine learning applications. Schematic representation of the main strategies for multi-omics datasets integration. A) Early integration concatenates all omics datasets into a single matrix on which machine learning model can be applied. B) Mixed integration first independently transforms or maps each omics block into a new representation before combining them for downstream analysis. C) Intermediate integration simultaneously transforms the original datasets into common and omics-specific representations. D) Late integration analyses each omics separately and combines their final predictions. E) Hierarchical integration bases the integration of datasets on prior regulatory relationships between omics layers. [Display omitted] Increased availability of high-throughput technologies has generated an ever-growing number of omics data that seek to portray many different but complementary biological layers including genomics, epigenomics, transcriptomics, proteomics, and metabolomics. New insight from these data have been obtained by machine learning algorithms that have produced diagnostic and classification biomarkers. Most biomarkers obtained to date however only include one omic measurement at a time and thus do not take full advantage of recent multi-omics experiments that now capture the entire complexity of biological systems. Multi-omics data integration strategies are needed to combine the complementary knowledge brought by each omics layer. We have summarized the most recent data integration methods/ frameworks into five different integration strategies: early, mixed, intermediate, late and hierarchical. In this mini-review, we focus on challenges and existing multi-omics integration strategies by paying special attention to machine learning applications. |
| Author | Périn, Olivier Picard, Milan Bodein, Antoine Droit, Arnaud Scott-Boyer, Marie-Pier |
| Author_xml | – sequence: 1 givenname: Milan orcidid: 0000-0002-2466-2012 surname: Picard fullname: Picard, Milan organization: Molecular Medicine Department, CHU de Québec Research Center, Université Laval, Québec, QC, Canada – sequence: 2 givenname: Marie-Pier surname: Scott-Boyer fullname: Scott-Boyer, Marie-Pier organization: Molecular Medicine Department, CHU de Québec Research Center, Université Laval, Québec, QC, Canada – sequence: 3 givenname: Antoine orcidid: 0000-0002-9843-504X surname: Bodein fullname: Bodein, Antoine organization: Molecular Medicine Department, CHU de Québec Research Center, Université Laval, Québec, QC, Canada – sequence: 4 givenname: Olivier surname: Périn fullname: Périn, Olivier organization: Digital Sciences Department, L'Oréal Advanced Research, Aulnay-sous-bois, France – sequence: 5 givenname: Arnaud surname: Droit fullname: Droit, Arnaud email: Arnaud.Droit@crchudequebec.ulaval.ca organization: Molecular Medicine Department, CHU de Québec Research Center, Université Laval, Québec, QC, Canada |
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| Snippet | Schematic representation of the main strategies for multi-omics datasets integration. A) Early integration concatenates all omics datasets into a single matrix... Increased availability of high-throughput technologies has generated an ever-growing number of omics data that seek to portray many different but complementary... |
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| SubjectTerms | biomarkers biotechnology Deep learning epigenetics genomics Integration strategy Machine learning metabolomics Multi-omics Multi-view multiomics Network proteomics Review transcriptomics |
| Title | Integration strategies of multi-omics data for machine learning analysis |
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