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  <front>
    <journal-meta>
      <journal-id journal-id-type="iso-abbrev">Pharmacophore</journal-id>
      <journal-id journal-id-type="publisher-id">pharmacophorejournal.com</journal-id>
      <journal-id journal-id-type="publisher-id">Pharmacophore</journal-id>
      <journal-title-group>
        <journal-title>Pharmacophore</journal-title>
      </journal-title-group>
      <issn pub-type="epub">2229-5402</issn>
    </journal-meta>
    <article-meta>
      <article-id pub-id-type="publisher-id">pharmacophorejournal.com-6924</article-id>
      <article-id pub-id-type="doi">10.51847/WvgrULwuFS</article-id>
      <article-categories>
        <subj-group subj-group-type="heading">
          <subject>Original research</subject>
        </subj-group>
      </article-categories>
      <title-group>
        <article-title>Every Molecular Prediction Needs an Evidence Passport Linking Confidence, Applicability, Provenance, and Experimental Consequence</article-title>
      </title-group>
                    <contrib-group>
                      <contrib contrib-type="author">
              <name>
                <surname>Yamamoto</surname>
                <given-names>Hiroshi</given-names>
              </name>
                              <xref rid="aff1" ref-type="aff">1</xref>
                                                            <xref rid="cor1" ref-type="corresp" />
                          </contrib>
                      <contrib contrib-type="author">
              <name>
                <surname>Greco</surname>
                <given-names>Francesca</given-names>
              </name>
                              <xref rid="aff2" ref-type="aff">2</xref>
                                        </contrib>
                      <contrib contrib-type="author">
              <name>
                <surname>Bianchi</surname>
                <given-names>Andrea</given-names>
              </name>
                              <xref rid="aff3" ref-type="aff">3</xref>
                                        </contrib>
                      <contrib contrib-type="author">
              <name>
                <surname>Nakamura</surname>
                <given-names>Ryota</given-names>
              </name>
                              <xref rid="aff1" ref-type="aff">1</xref>
                                        </contrib>
                  </contrib-group>
                  <aff id="aff1">
            <label>1</label>Department of Molecular Prediction and Evidence Passports, Graduate School of Pharmacy, Kyoto University, Kyoto, Japan.
          </aff>
                  <aff id="aff2">
            <label>2</label>Department of Confidence and Applicability Assessment, Faculty of Pharmacy, University of Bologna, Bologna, Italy.
          </aff>
                  <aff id="aff3">
            <label>3</label>Department of Provenance and Experimental Consequence Tracking, Faculty of Pharmaceutical Sciences, University of Milan, Milan, Italy.
          </aff>
                  <aff id="aff4">
            <label>4</label>Kabardino-Balkarian State University named after H.M. Berbekov, Kabardino-Balkarian Republic, Russia.
          </aff>
                  <aff id="aff5">
            <label>5</label>North Caucasus Federal University, Stavropol, Russia.
          </aff>
                          <author-notes>
            <corresp id="cor1">
              <bold>Address for correspondence:</bold> Prof. Wael Abu Dayyih, Department of
              Pharmaceutical Chemistry, Faculty of Pharmacy, Mutah University, Al-Karak 61710, Jordan.
                              E-mail: <email xlink:href="yamamoto.hiroshi@kyoto-u.ac.jp">yamamoto.hiroshi@kyoto-u.ac.jp</email>
                          </corresp>
          </author-notes>
                    <pub-date pub-type="epub">
        <day>28</day>
        <month>12</month>
        <year>2024</year>
      </pub-date>
      <volume>15</volume>
      <issue>6</issue>
      <fpage>66</fpage>
      <lpage>75</lpage>
      <permissions>
        <copyright-statement>
          Copyright: &#x000a9; 2026 Pharmacophore
        </copyright-statement>
        <copyright-year>2026</copyright-year>
        <license>
          <ali:license_ref xmlns:ali="http://www.niso.org/schemas/ali/1.0/"
            specific-use="textmining" content-type="ccbyncsalicense">
            https://creativecommons.org/licenses/by-nc-sa/4.0/</ali:license_ref>
          <license-p>This is an open access journal, and articles are distributed under the terms of
            the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 License, which allows
            others to remix, tweak, and build upon the work non-commercially, as long as appropriate
            credit is given and the new creations are licensed under the identical terms.</license-p>
        </license>
      </permissions>
      <abstract>
        <title>A<sc>BSTRACT</sc></title>
        <p>Molecular predictions increasingly influence which compounds are screened, synthesized, optimized, or advanced, yet the evidential conditions surrounding those predictions are often separated from the outputs that enter experimental workflows. A probability, rank, or predicted property can therefore travel farther than its calibration evidence, applicability limits, data provenance, model version, and intended use. This article develops a proposed molecular prediction evidence passport as an original prediction-governance construct for keeping those elements attached to a bounded prediction event. The approach synthesizes methodological insights from molecular machine learning, uncertainty quantification, biomedical data stewardship, reporting guidance, and pharmaceutical decision practice. The passport is defined as a versioned, machine-readable and human-interpretable record that identifies the prediction object; preserves model, code, representation, and data lineage; distinguishes model confidence from calibrated uncertainty; records applicability conditions and unresolved uncertainty sources; states the experimental decision the prediction may inform; and links subsequent experimental consequences back to the originating record. The central contribution is not another performance metric, but an architecture for preventing benchmark performance, explanation, plausibility, or organizational approval from being misread as experimental confirmation, mechanism, therapeutic value, or deployment readiness. The construct may support more inspectable handoffs across screening, optimization, and candidate selection, while enabling later audit of what was known, assumed, changed, and acted upon. Its value remains conditional on schema design, semantic interoperability, data quality, human oversight, and prospective evaluation. The passport is therefore presented as a testable governance proposal rather than a validated standard, regulatory artifact, or autonomous decision system.</p>
      </abstract>
      <kwd-group>
                <kwd>Molecular prediction</kwd>
                <kwd>Evidence provenance</kwd>
                <kwd>Applicability domain</kwd>
                <kwd>Uncertainty quantification</kwd>
                <kwd>Data lineage</kwd>
                <kwd>Experimental decision-making</kwd>
              </kwd-group>
    </article-meta>
  </front>
</article>