Conference paper Open Access

The need of standardised metadata to encode causal relationships: Towards safer data-driven machine learning biological solutions

Beatriz Garcia Santa Cruz; Carlos Vega; Frank Hertel


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  <identifier identifierType="DOI">10.5281/zenodo.5729350</identifier>
  <creators>
    <creator>
      <creatorName>Beatriz Garcia Santa Cruz</creatorName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0002-0939-4443</nameIdentifier>
    </creator>
    <creator>
      <creatorName>Carlos Vega</creatorName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0002-7979-9921</nameIdentifier>
    </creator>
    <creator>
      <creatorName>Frank Hertel</creatorName>
    </creator>
  </creators>
  <titles>
    <title>The need of standardised metadata to encode causal relationships: Towards safer data-driven machine learning biological solutions</title>
  </titles>
  <publisher>Zenodo</publisher>
  <publicationYear>2021</publicationYear>
  <subjects>
    <subject>confounders</subject>
    <subject>causality</subject>
    <subject>metadata</subject>
    <subject>machine learning</subject>
    <subject>systems biology</subject>
  </subjects>
  <dates>
    <date dateType="Issued">2021-11-16</date>
  </dates>
  <language>en</language>
  <resourceType resourceTypeGeneral="ConferencePaper"/>
  <alternateIdentifiers>
    <alternateIdentifier alternateIdentifierType="url">https://zenodo.org/record/5729350</alternateIdentifier>
  </alternateIdentifiers>
  <relatedIdentifiers>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsVersionOf">10.5281/zenodo.5729349</relatedIdentifier>
  </relatedIdentifiers>
  <version>Version presented at the Computational Intelligence Methods for Bioinformatics and Biostatistics 2021 (CIBB2021)</version>
  <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;In this paper, we discuss the importance of considering causal relations in the development of machine learning solutions to prevent factors hampering the robustness and generalisation capacity of the models, such as induced biases. This issue often arises when the algorithm decision is affected by confounding factors. In this work, we argue that the integration of causal relationships can identify potential confounders. We call for standardised meta-information practices as a crucial step for proper machine learning solutions development, validation, and data sharing. Such practices include detailing the dataset generation process, aiming for automatic integration of causal relationships.&amp;nbsp;&lt;/p&gt;

&lt;p&gt;&amp;nbsp;&lt;/p&gt;</description>
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