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BRANEnet: Embedding Multilayer Networks for Omics Data Integration

surabhi Jagtap; Aurélie Pirayre; Frédérique Bidard; Laurent Duval; Fragkiskos D. Malliaros


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  <identifier identifierType="DOI">10.5281/zenodo.7007534</identifier>
  <creators>
    <creator>
      <creatorName>surabhi Jagtap</creatorName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0001-7599-5434</nameIdentifier>
      <affiliation>CentraleSupelec</affiliation>
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    <creator>
      <creatorName>Aurélie Pirayre</creatorName>
      <affiliation>IFP energies nouvelles</affiliation>
    </creator>
    <creator>
      <creatorName>Frédérique Bidard</creatorName>
      <affiliation>IFP energies nouvelles</affiliation>
    </creator>
    <creator>
      <creatorName>Laurent Duval</creatorName>
      <affiliation>IFP energies nouvelles</affiliation>
    </creator>
    <creator>
      <creatorName>Fragkiskos D. Malliaros</creatorName>
      <affiliation>CentraleSupelec</affiliation>
    </creator>
  </creators>
  <titles>
    <title>BRANEnet: Embedding Multilayer Networks for Omics Data Integration</title>
  </titles>
  <publisher>Zenodo</publisher>
  <publicationYear>2022</publicationYear>
  <subjects>
    <subject>multi-omics data</subject>
    <subject>multilayer network</subject>
    <subject>biological network integration</subject>
    <subject>graph representation learning</subject>
    <subject>regulatory network inference</subject>
  </subjects>
  <contributors>
    <contributor contributorType="ContactPerson">
      <contributorName>surabhi Jagtap</contributorName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0001-7599-5434</nameIdentifier>
      <affiliation>CentraleSupelec</affiliation>
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  <dates>
    <date dateType="Issued">2022-08-18</date>
  </dates>
  <resourceType resourceTypeGeneral="Software"/>
  <alternateIdentifiers>
    <alternateIdentifier alternateIdentifierType="url">https://zenodo.org/record/7007534</alternateIdentifier>
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    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsCitedBy" resourceTypeGeneral="Text">10.21203/rs.3.rs-1588328/v1</relatedIdentifier>
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  <rightsList>
    <rights rightsURI="https://creativecommons.org/licenses/by/4.0/legalcode">Creative Commons Attribution 4.0 International</rights>
    <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
  </rightsList>
  <descriptions>
    <description descriptionType="Abstract">&lt;p&gt;BRANEnet is&amp;nbsp;&amp;nbsp;a novel multi-omics integration framework for multilayer heterogeneous networks. In particular, it embeds graph-based information from multi-omics data in a lower-dimensional space.&amp;nbsp; To capture relevant context around each node of interest, it&amp;nbsp;leverages a properly chosen random walk-based Positive Pointwise Mutual Information (PPMI) matrix.&lt;/p&gt;

&lt;p&gt;&amp;nbsp;&lt;/p&gt;</description>
  </descriptions>
  <fundingReferences>
    <fundingReference>
      <funderName>Agence Nationale de la Recherche</funderName>
      <funderIdentifier funderIdentifierType="Crossref Funder ID">10.13039/501100001665</funderIdentifier>
      <awardNumber awardURI="info:eu-repo/grantAgreement/ANR//ANR-20-CE23-0009/">ANR-20-CE23-0009</awardNumber>
      <awardTitle>Scalable and robust representation learning on graphs</awardTitle>
    </fundingReference>
  </fundingReferences>
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