<?xml version="1.0" encoding="UTF-8"?><!DOCTYPE article PUBLIC "-//NLM//DTD JATS (Z39.96) Journal Publishing DTD v1.2 20190208//EN" "http://jats.nlm.nih.gov/publishing/1.2/JATS-journalpublishing1.dtd"><article xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink" article-type="research-article" dtd-version="1.2" xml:lang="en">
    <front>
        <journal-meta>
            <journal-id journal-id-type="pmc">F1000Research</journal-id>
            <journal-title-group>
                <journal-title>F1000Research</journal-title>
            </journal-title-group>
            <issn pub-type="epub">2046-1402</issn>
            <publisher>
                <publisher-name>F1000 Research Limited</publisher-name>
                <publisher-loc>London, UK</publisher-loc>
            </publisher>
        </journal-meta>
        <article-meta>
            <article-id pub-id-type="doi">10.12688/f1000research.175934.1</article-id>
            <article-categories>
                <subj-group subj-group-type="heading">
                    <subject>Research Article</subject>
                </subj-group>
                <subj-group>
                    <subject>Articles</subject>
                </subj-group>
            </article-categories>
            <title-group>
                <article-title>Leveraging Artificial Intelligence (AI) based algorithm for Accurate Estrogen receptor (ER) and Progesterone receptor (PR) Analysis in breast cancer diagnostics: potential to be a crucial aid in routine workflow</article-title>
                <fn-group content-type="pub-status">
                    <fn>
                        <p>[version 1; peer review: 1 approved with reservations]</p>
                    </fn>
                </fn-group>
            </title-group>
            <contrib-group>
                <contrib contrib-type="author" corresp="yes">
                    <name>
                        <surname>Pai</surname>
                        <given-names>Kanthilatha</given-names>
                    </name>
                    <role content-type="http://credit.niso.org/">Conceptualization</role>
                    <role content-type="http://credit.niso.org/">Data Curation</role>
                    <role content-type="http://credit.niso.org/">Formal Analysis</role>
                    <role content-type="http://credit.niso.org/">Funding Acquisition</role>
                    <role content-type="http://credit.niso.org/">Investigation</role>
                    <role content-type="http://credit.niso.org/">Methodology</role>
                    <role content-type="http://credit.niso.org/">Project Administration</role>
                    <role content-type="http://credit.niso.org/">Resources</role>
                    <role content-type="http://credit.niso.org/">Software</role>
                    <role content-type="http://credit.niso.org/">Supervision</role>
                    <role content-type="http://credit.niso.org/">Validation</role>
                    <role content-type="http://credit.niso.org/">Visualization</role>
                    <role content-type="http://credit.niso.org/">Writing &#x2013; Original Draft Preparation</role>
                    <role content-type="http://credit.niso.org/">Writing &#x2013; Review &amp; Editing</role>
                    <uri content-type="orcid">https://orcid.org/0000-0002-6947-5552</uri>
                    <xref ref-type="corresp" rid="c1">a</xref>
                    <xref ref-type="aff" rid="a1">1</xref>
                </contrib>
                <contrib contrib-type="author" corresp="yes">
                    <name>
                        <surname>Singh</surname>
                        <given-names>Brij Mohan Kumar</given-names>
                    </name>
                    <role content-type="http://credit.niso.org/">Conceptualization</role>
                    <role content-type="http://credit.niso.org/">Data Curation</role>
                    <role content-type="http://credit.niso.org/">Formal Analysis</role>
                    <role content-type="http://credit.niso.org/">Funding Acquisition</role>
                    <role content-type="http://credit.niso.org/">Investigation</role>
                    <role content-type="http://credit.niso.org/">Methodology</role>
                    <role content-type="http://credit.niso.org/">Project Administration</role>
                    <role content-type="http://credit.niso.org/">Supervision</role>
                    <role content-type="http://credit.niso.org/">Validation</role>
                    <role content-type="http://credit.niso.org/">Visualization</role>
                    <role content-type="http://credit.niso.org/">Writing &#x2013; Original Draft Preparation</role>
                    <role content-type="http://credit.niso.org/">Writing &#x2013; Review &amp; Editing</role>
                    <xref ref-type="corresp" rid="c2">b</xref>
                    <xref ref-type="aff" rid="a1">1</xref>
                </contrib>
                <contrib contrib-type="author" corresp="no">
                    <name>
                        <surname>Udupa</surname>
                        <given-names>Chethana Babu</given-names>
                    </name>
                    <role content-type="http://credit.niso.org/">Formal Analysis</role>
                    <role content-type="http://credit.niso.org/">Investigation</role>
                    <role content-type="http://credit.niso.org/">Methodology</role>
                    <role content-type="http://credit.niso.org/">Project Administration</role>
                    <xref ref-type="aff" rid="a1">1</xref>
                </contrib>
                <contrib contrib-type="author" corresp="no">
                    <name>
                        <surname>Pai</surname>
                        <given-names>Madhavi</given-names>
                    </name>
                    <role content-type="http://credit.niso.org/">Formal Analysis</role>
                    <role content-type="http://credit.niso.org/">Investigation</role>
                    <role content-type="http://credit.niso.org/">Methodology</role>
                    <role content-type="http://credit.niso.org/">Project Administration</role>
                    <xref ref-type="aff" rid="a1">1</xref>
                </contrib>
                <contrib contrib-type="author" corresp="no">
                    <name>
                        <surname>Verma</surname>
                        <given-names>Vani</given-names>
                    </name>
                    <role content-type="http://credit.niso.org/">Formal Analysis</role>
                    <role content-type="http://credit.niso.org/">Investigation</role>
                    <role content-type="http://credit.niso.org/">Methodology</role>
                    <role content-type="http://credit.niso.org/">Project Administration</role>
                    <xref ref-type="aff" rid="a1">1</xref>
                </contrib>
                <contrib contrib-type="author" corresp="no">
                    <name>
                        <surname>Jha</surname>
                        <given-names>Sumit</given-names>
                    </name>
                    <role content-type="http://credit.niso.org/">Conceptualization</role>
                    <role content-type="http://credit.niso.org/">Data Curation</role>
                    <role content-type="http://credit.niso.org/">Formal Analysis</role>
                    <role content-type="http://credit.niso.org/">Investigation</role>
                    <role content-type="http://credit.niso.org/">Methodology</role>
                    <role content-type="http://credit.niso.org/">Project Administration</role>
                    <role content-type="http://credit.niso.org/">Resources</role>
                    <role content-type="http://credit.niso.org/">Software</role>
                    <role content-type="http://credit.niso.org/">Supervision</role>
                    <role content-type="http://credit.niso.org/">Validation</role>
                    <role content-type="http://credit.niso.org/">Writing &#x2013; Review &amp; Editing</role>
                    <xref ref-type="aff" rid="a2">2</xref>
                </contrib>
                <contrib contrib-type="author" corresp="no">
                    <name>
                        <surname>Aatre</surname>
                        <given-names>Kiran</given-names>
                    </name>
                    <role content-type="http://credit.niso.org/">Conceptualization</role>
                    <role content-type="http://credit.niso.org/">Funding Acquisition</role>
                    <role content-type="http://credit.niso.org/">Resources</role>
                    <role content-type="http://credit.niso.org/">Software</role>
                    <role content-type="http://credit.niso.org/">Supervision</role>
                    <role content-type="http://credit.niso.org/">Writing &#x2013; Review &amp; Editing</role>
                    <uri content-type="orcid">https://orcid.org/0000-0003-0423-5176</uri>
                    <xref ref-type="aff" rid="a2">2</xref>
                </contrib>
                <contrib contrib-type="author" corresp="no">
                    <name>
                        <surname>Mishra</surname>
                        <given-names>Purnendu</given-names>
                    </name>
                    <role content-type="http://credit.niso.org/">Formal Analysis</role>
                    <role content-type="http://credit.niso.org/">Investigation</role>
                    <role content-type="http://credit.niso.org/">Methodology</role>
                    <role content-type="http://credit.niso.org/">Project Administration</role>
                    <role content-type="http://credit.niso.org/">Resources</role>
                    <role content-type="http://credit.niso.org/">Software</role>
                    <role content-type="http://credit.niso.org/">Supervision</role>
                    <role content-type="http://credit.niso.org/">Validation</role>
                    <role content-type="http://credit.niso.org/">Visualization</role>
                    <xref ref-type="aff" rid="a2">2</xref>
                </contrib>
                <contrib contrib-type="author" corresp="no">
                    <name>
                        <surname>Godkhindi</surname>
                        <given-names>Vishwapriya Mahadev</given-names>
                    </name>
                    <role content-type="http://credit.niso.org/">Formal Analysis</role>
                    <role content-type="http://credit.niso.org/">Investigation</role>
                    <role content-type="http://credit.niso.org/">Methodology</role>
                    <role content-type="http://credit.niso.org/">Project Administration</role>
                    <xref ref-type="aff" rid="a3">3</xref>
                </contrib>
                <contrib contrib-type="author" corresp="no">
                    <name>
                        <surname>Sharma</surname>
                        <given-names>Swati</given-names>
                    </name>
                    <role content-type="http://credit.niso.org/">Formal Analysis</role>
                    <role content-type="http://credit.niso.org/">Investigation</role>
                    <role content-type="http://credit.niso.org/">Methodology</role>
                    <role content-type="http://credit.niso.org/">Project Administration</role>
                    <uri content-type="orcid">https://orcid.org/0000-0002-8098-8455</uri>
                    <xref ref-type="aff" rid="a1">1</xref>
                </contrib>
                <contrib contrib-type="author" corresp="no">
                    <name>
                        <surname>Singh</surname>
                        <given-names>Gursevak</given-names>
                    </name>
                    <role content-type="http://credit.niso.org/">Data Curation</role>
                    <role content-type="http://credit.niso.org/">Formal Analysis</role>
                    <role content-type="http://credit.niso.org/">Investigation</role>
                    <role content-type="http://credit.niso.org/">Methodology</role>
                    <role content-type="http://credit.niso.org/">Project Administration</role>
                    <role content-type="http://credit.niso.org/">Software</role>
                    <role content-type="http://credit.niso.org/">Supervision</role>
                    <role content-type="http://credit.niso.org/">Validation</role>
                    <role content-type="http://credit.niso.org/">Visualization</role>
                    <xref ref-type="aff" rid="a2">2</xref>
                </contrib>
                <contrib contrib-type="author" corresp="no">
                    <name>
                        <surname>Mathur</surname>
                        <given-names>Shubham</given-names>
                    </name>
                    <role content-type="http://credit.niso.org/">Formal Analysis</role>
                    <role content-type="http://credit.niso.org/">Investigation</role>
                    <role content-type="http://credit.niso.org/">Methodology</role>
                    <role content-type="http://credit.niso.org/">Project Administration</role>
                    <role content-type="http://credit.niso.org/">Software</role>
                    <role content-type="http://credit.niso.org/">Supervision</role>
                    <role content-type="http://credit.niso.org/">Validation</role>
                    <role content-type="http://credit.niso.org/">Visualization</role>
                    <xref ref-type="aff" rid="a2">2</xref>
                </contrib>
                <contrib contrib-type="author" corresp="no">
                    <name>
                        <surname>Modi</surname>
                        <given-names>Akash</given-names>
                    </name>
                    <role content-type="http://credit.niso.org/">Formal Analysis</role>
                    <role content-type="http://credit.niso.org/">Investigation</role>
                    <role content-type="http://credit.niso.org/">Methodology</role>
                    <role content-type="http://credit.niso.org/">Project Administration</role>
                    <role content-type="http://credit.niso.org/">Software</role>
                    <role content-type="http://credit.niso.org/">Supervision</role>
                    <role content-type="http://credit.niso.org/">Validation</role>
                    <role content-type="http://credit.niso.org/">Visualization</role>
                    <xref ref-type="aff" rid="a2">2</xref>
                </contrib>
                <contrib contrib-type="author" corresp="no">
                    <name>
                        <surname>Kumar</surname>
                        <given-names>Rajiv</given-names>
                    </name>
                    <role content-type="http://credit.niso.org/">Formal Analysis</role>
                    <role content-type="http://credit.niso.org/">Investigation</role>
                    <role content-type="http://credit.niso.org/">Methodology</role>
                    <role content-type="http://credit.niso.org/">Project Administration</role>
                    <role content-type="http://credit.niso.org/">Supervision</role>
                    <role content-type="http://credit.niso.org/">Validation</role>
                    <role content-type="http://credit.niso.org/">Visualization</role>
                    <xref ref-type="aff" rid="a2">2</xref>
                </contrib>
                <aff id="a1">
                    <label>1</label>Dept of Pathology, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India</aff>
                <aff id="a2">
                    <label>2</label>Applied Materials India, Bangalore, Karnataka, 560066, India</aff>
                <aff id="a3">
                    <label>3</label>Mangalore Institute of Oncology, Mangaluru, Karnataka, 576104, India</aff>
            </contrib-group>
            <author-notes>
                <corresp id="c1">
                    <label>a</label>
                    <email xlink:href="mailto:kl.pai@manipal.edu">kl.pai@manipal.edu</email>
                </corresp>
                <corresp id="c2">
                    <label>b</label>
                    <email xlink:href="mailto:brij.singh@manipal.edu">brij.singh@manipal.edu</email>
                </corresp>
                <fn fn-type="conflict">
                    <p>No competing interests were disclosed.</p>
                </fn>
            </author-notes>
            <pub-date pub-type="epub">
                <day>11</day>
                <month>5</month>
                <year>2026</year>
            </pub-date>
            <pub-date pub-type="collection">
                <year>2026</year>
            </pub-date>
            <volume>15</volume>
            <elocation-id>702</elocation-id>
            <history>
                <date date-type="accepted">
                    <day>27</day>
                    <month>4</month>
                    <year>2026</year>
                </date>
            </history>
            <permissions>
                <copyright-statement>Copyright: &#x00a9; 2026 Pai K et al.</copyright-statement>
                <copyright-year>2026</copyright-year>
                <license xlink:href="https://creativecommons.org/licenses/by/4.0/">
                    <license-p>This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.</license-p>
                </license>
            </permissions>
            <self-uri content-type="pdf" xlink:href="https://f1000research.com/articles/15-702/pdf"/>
            <abstract>
                <sec>
                    <title>Background</title>
                    <p>Scoring of estrogen receptor (ER) and progesterone receptor (PR) expression in breast cancer is critical for identifying patients who would benefit with hormonal therapy. Since manual scoring of immunohistochemistry (IHC) is influenced by pathologist experience, fatigue, inter-observer variability, and subjectivity, artificial intelligence (AI)&#x2013;based algorithms, trained on large datasets can aid to improve diagnostic accuracy.</p>
                </sec>
                <sec>
                    <title>Methodology</title>
                    <p>This study evaluated an AI-based algorithm for ER and PR IHC scoring in 297 ER and 293 PR cases of invasive breast carcinoma and compared the scores with that of pathologists (two senior and two junior) A pre-trained automated algorithm (Mimansa) identified region of interest and provided the scoreswhich was compared with the consensus score of pathologists-ground truth(GT).Concordance was evaluated using Cohen&#x2019;s kappa and F1 score.</p>
                </sec>
                <sec>
                    <title>Results</title>
                    <p>For ER IHC, GT scores included 169 strong positive, 31 low positive, and 98 negative cases. Agreement with GT was 99% and 98% for senior pathologists, 97% for the AI algorithm, and 95% and 93% for junior pathologists. The algorithm correctly classified all strong positive cases but showed discordance in 16 low-score cases, with four false negatives and ten false positives. Notably, it identified two true positive cases missed by all pathologists.</p>
                    <p>For PR IHC, agreement rates were 98% and 97% for senior pathologists, 92% for the algorithm, and 93% and 91% for junior pathologists. The algorithm achieved perfect accuracy in strong positive cases but produced 16 false negatives and eight false positives among low-score cases. Cohen&#x2019;s kappa values were 0.91 (ER) and 0.84 (PR).</p>
                </sec>
                <sec>
                    <title>Conclusion:</title>
                    <p>The AI algorithm demonstrated high concordance with expert consensus, performing comparably to senior pathologists and outperforming junior pathologists in several metrics. It shows promise as a supportive second-reader tool, particularly in low-positive cases where diagnostic errors may significantly impact patient management.</p>
                </sec>
            </abstract>
            <kwd-group kwd-group-type="author">
                <kwd>breast cancer</kwd>
                <kwd>biomarker expression</kwd>
                <kwd>Estrogen receptor</kwd>
                <kwd>Progesterone receptor</kwd>
                <kwd>algorithm</kwd>
                <kwd>manual</kwd>
            </kwd-group>
            <funding-group>
                <award-group id="fund-1">
                    <funding-source>Applied Materials, Bangalore</funding-source>
                    <award-id>MUIND10002256</award-id>
                </award-group>
                <funding-statement>Industry Grant (APPLIED MATERIALS INDIA) Grant No: MUIND 10002256 towards development of Artificial Intelligence based decision support system for breast cancer diagnosis </funding-statement>
                <funding-statement>
                    <italic>The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.</italic>
                </funding-statement>
            </funding-group>
        </article-meta>
    </front>
    <body>
        <sec id="sec5" sec-type="intro">
            <title>Introduction</title>
            <p>The presence and degree of Estrogen receptor (ER) and Progesterone receptor (PR) expression hold significant importance in both prognostic evaluation and selection of the most suitable treatment strategy in patients with breast cancer.
                <sup>
                    <xref ref-type="bibr" rid="ref1">1</xref>
                </sup> Studies highlight that positive receptor status often correlates with better outcomes and responsiveness to hormone therapy, improving survival rates.
                <sup>
                    <xref ref-type="bibr" rid="ref2">2</xref>
                </sup>
            </p>
            <p>Interpreting ER and PR expression in breast cancer poses challenges owing to its subjective nature, which is influenced by factors such as pathologist experience, training, and workload fatigue.
                <sup>
                    <xref ref-type="bibr" rid="ref3">3</xref>&#x2013;
                    <xref ref-type="bibr" rid="ref5">5</xref>
                </sup> Recent advancements suggest that Artificial Intelligence (AI) can enhance the accuracy and reproducibility of these assessments.
                <sup>
                    <xref ref-type="bibr" rid="ref5">5</xref>,
                    <xref ref-type="bibr" rid="ref6">6</xref>
                </sup> Studies show AI&#x2019;s potential in standardizing receptor quantification and improving diagnostic precision.
                <sup>
                    <xref ref-type="bibr" rid="ref7">7</xref>
                </sup>
            </p>
            <p>While there have been several studies reporting on the development of individual AI models for the assessment of Her2, ER/PR in breast cancer, which have demonstrated good accuracy and reliability, their adoption has been limited because of several factors such as cost, lack of validation, and integration into routine pathology workflows.
                <sup>
                    <xref ref-type="bibr" rid="ref8">8</xref>,
                    <xref ref-type="bibr" rid="ref9">9</xref>
                </sup>
            </p>
            <p>In this study, we conducted a comparative analysis of scores between the algorithm, junior, and senior pathologists in assessing the scores of ER and PR expressions in breast carcinoma to validate the performance of our in-house built algorithm (Mimansa) and its potential for incorporation into the workflow to improve diagnostic accuracy.</p>
        </sec>
        <sec id="sec6">
            <title>Materials and methods</title>
            <p>We conducted a comprehensive search of our pathology database to retrieve 300 surgical pathology cases to include all cases of invasive breast carcinoma of all types diagnosed from March 2020&#x2013;March 2021, and study period started from June 2021&#x00a0;after obtaining Institutional ethics committee approval. The study incorporated a mix of slides from trucut biopsy and resection specimens to validate the algorithm across different sample types.</p>
            <p>In our study, we obtained hematoxylin and eosin (H&amp;E)-stained slides and immunohistochemically (IHC) stained slides for ER and PR. We excluded slides of poor quality, those with bubbles, and those that faded. Ultimately, we included 297 ER IHC slides and 293 PR IHC slides, along with their corresponding H&amp;E slides, to ensure correlation and validation of the algorithm&#x2019;s performance.</p>
            <sec id="sec7">
                <title>Estrogen receptor (ER) and Progesterone receptor (PR) immunohistochemistry</title>
                <p>ER expression was assessed using formalin-fixed paraffin embedded (FFPE) tissue sections (ischemic time&#x00a0;&lt;&#x00a0;1&#x00a0;h and fixation time between 3 and 36&#x00a0;h) by immunohistochemistry (IHC) using an anti-ER antibody (clone EP1 mouse monoclonal antibody; Dako) and anti-PR (Clone PgR636 mouse monoclonal antibody; Dako), and staining was performed using an automated IHC stainer (Ventana Benchmark XT, Ventana Medical Systems Inc., Tucson, AZ, USA). ER and PR expression was scored using the Allred scoring system as shown in 
                    <xref ref-type="table" rid="T1">
Table 1</xref>.</p>
                <table-wrap id="T1" orientation="portrait" position="float">
                    <label>
Table 1. </label>
                    <caption>
                        <title>Allred score for ER and PR expression.</title>
                    </caption>
                    <table content-type="article-table" frame="hsides">
                        <thead>
                            <tr>
                                <th align="left" colspan="2" rowspan="1" valign="top">Percentage score</th>
                                <th align="left" colspan="2" rowspan="1" valign="top">Intensity score</th>
                            </tr>
                            <tr>
                                <th align="left" colspan="1" rowspan="1" valign="top">Score</th>
                                <th align="left" colspan="1" rowspan="1" valign="top">Percentage of stained cells</th>
                                <th align="left" colspan="1" rowspan="1" valign="top">Score</th>
                                <th align="left" colspan="1" rowspan="1" valign="top">Intensity of staining</th>
                            </tr>
                        </thead>
                        <tbody>
                            <tr>
                                <td align="left" colspan="1" rowspan="1" valign="top">
                                    <styled-content style="#0D0D0D" style-type="color">0</styled-content>
</td>
                                <td align="left" colspan="1" rowspan="1" valign="top">No cells are ER/PR Positive</td>
                                <td align="left" colspan="1" rowspan="1" valign="top">0</td>
                                <td align="left" colspan="1" rowspan="1" valign="top">Negative</td>
                            </tr>
                            <tr>
                                <td align="left" colspan="1" rowspan="1" valign="top">
                                    <styled-content style="#0D0D0D" style-type="color">1</styled-content>
</td>
                                <td align="left" colspan="1" rowspan="1" valign="top">&lt;1% cells are ER/PR Positive</td>
                                <td align="left" colspan="1" rowspan="1" valign="top">1</td>
                                <td align="left" colspan="1" rowspan="1" valign="top">Mild</td>
                            </tr>
                            <tr>
                                <td align="left" colspan="1" rowspan="1" valign="top">
                                    <styled-content style="#0D0D0D" style-type="color">2</styled-content>
</td>
                                <td align="left" colspan="1" rowspan="1" valign="top">1&#x2013;10% are ER/PR Positive</td>
                                <td align="left" colspan="1" rowspan="1" valign="top">2</td>
                                <td align="left" colspan="1" rowspan="1" valign="top">Moderate</td>
                            </tr>
                            <tr>
                                <td align="left" colspan="1" rowspan="1" valign="top">
                                    <styled-content style="#0D0D0D" style-type="color">3</styled-content>
</td>
                                <td align="left" colspan="1" rowspan="1" valign="top">11&#x2013;33% are ER/PR Positive</td>
                                <td align="left" colspan="1" rowspan="1" valign="top">3</td>
                                <td align="left" colspan="1" rowspan="1" valign="top">Strong</td>
                            </tr>
                            <tr>
                                <td align="left" colspan="1" rowspan="1" valign="top">
                                    <styled-content style="#0D0D0D" style-type="color">4</styled-content>
</td>
                                <td align="left" colspan="1" rowspan="1" valign="top">34&#x2013;66% are ER/PR Positive</td>
                                <td colspan="1" rowspan="1"/>
                                <td colspan="1" rowspan="1"/>
                            </tr>
                            <tr>
                                <td align="left" colspan="1" rowspan="1" valign="top">
                                    <styled-content style="#0D0D0D" style-type="color">5</styled-content>
</td>
                                <td align="left" colspan="1" rowspan="1" valign="top">67&#x2013;100% are ER/PR Positive</td>
                                <td colspan="1" rowspan="1"/>
                                <td colspan="1" rowspan="1"/>
                            </tr>
                        </tbody>
                    </table>
                    <table-wrap-foot>
                        <p>Allred Score&#x00a0;=&#x00a0;Percentage score&#x00a0;+&#x00a0;Intensity score.</p>
                    </table-wrap-foot>
                </table-wrap>
                <p>Algorithm development</p>
                <p>

                    <italic toggle="yes">Methodology</italic>
                </p>
                <p>In this paper, we present a fully automatic multi-class tissue segmentation in-house built algorithm (Mimansa) that classifies tumors as well as other tissue regions, such as acini, ducts, and DCIS, into fine-grained segmentation maps of histopathology images. The proposed model works with multiple stains of breast IHC, including and not limited to nuclear (ER, PR) stains. The model was built using 10 million patches extracted from 513 WSI from multiple data sources and multiple scanners to account for strain and scanner illumination variations.</p>
                <p>For the ground truth, because complete slide annotation is very difficult and time-consuming, a selective region-wise annotation technique was utilized. The pathologists selected 2&#x2013;3 mutually exclusive non-similar small regions and annotated them completely with multiple labels, including tumor, normal, stroma, acini, duct, blood vessels, and DCIS. Annotations for bad regions such as Folds, Artifacts, bubbles, and out-of-focus areas were also performed, and the patches were extracted from the annotated regions.</p>
                <p>

                    <italic toggle="yes">Class imbalance</italic>
                </p>
                <p>In clinical samples of WSI, tumor regions are far fewer than normal tissue regions and the background. Using filtration techniques, the non-tissue area and background were ignored. Because the majority of the annotated tissue regions were either Tumor or Normal/Stroma tissues, all additional regions (blood vessels, DCIS, acini, ducts, folds, skin, and Unknowns) were classified into a section called others. A data generator pipeline was introduced to ensure that all batches had a similar class distribution of 2:1:1 (tumor: normal: others). The algorithm also accounts for pixel-level imbalances of the dataset using a set of normalized dynamic weights.</p>
                <p>

                    <italic toggle="yes">Data augmentation and final model</italic>
                </p>
                <p>The images were adjusted for visual (brightness and contrast), color, and texture differences. Augmentation techniques were used to enhance the dataset.</p>
                <p>To compensate for the manually annotated dataset, the Phase-1 model learns basic nuances such as cell structures, background, regions to ignore, different tissue types, and staining colors. However, this model cannot be scaled to different data sources, scanner variations, and similar looking tissues such as DCIS and ACINIs, which look like tumors and have smaller FOV. In Phase-2, works on increasing augmentations and predictions. This allows for a tighter thresholding, thereby increasing the accuracy of the model.</p>
            </sec>
            <sec id="sec8">
                <title>Whole slide scanning and analysis</title>
                <p>The slides were scanned using Morpholens 6&#x00a0;T at 40X magnification and uploaded to a cloud-based platform. The in-house built-in algorithm (Mimansa) was run to score each case, providing the proportion of positively stained tumour cells for ER and PR and the intensity of positive cells to generate a total score according to the Allred scoring system (
                    <xref ref-type="fig" rid="f1">Figures 1</xref> and 
                    <xref ref-type="fig" rid="f2">2</xref>). Manual scoring of ER and PR IHC of the above slides was independently performed by four pathologists: two senior pathologists with over 15&#x00a0;years of experience in breast pathology (Sr Path 1, Sr Path 2) and two with less than three years of experience (Jr Path 1, Jr Path 2). The ER and PR scores were dichotomized, with ER/PR positivity recognized at an Allred Score cut-off of 3. Using this cut-off, scores of 0 to 2 were considered negative for ER/PR and not actionable, while scores of 3 to 8 were regarded as positive and suitable for hormonal therapy according to the American Society of Clinical Oncology/College of American Pathologists guidelines. Any discrepancy between the scores of pathologists resulting in an actionable outcome (cut-off score of 3) that would affect therapeutic decision was reviewed to obtain an initial consensus score. The algorithm was run on the digitized slides to obtain Allred scores for ER and PR similar to that of the pathologist&#x2019;s score. The algorithm score was compared with the initial (pathologist) consensus score, and any discordance was reviewed to obtain a final consensus score (ground truth). The study design is depicted in 
                    <xref ref-type="fig" rid="f3">Figure 3</xref>. ER and PR scores were further classified into three groups: 0&#x2013;2 as negative, 3&#x2013;5 as low positive and 6&#x2013;8 as strong positive. The agreement and reliability between the raters and the AI-based algorithm were statistically analyzed.</p>
                <fig fig-type="figure" id="f1" orientation="portrait" position="float">
                    <label>Figure 1. </label>
                    <caption>
                        <title>Photomicrograph shows identification of tumour regions (region of interest) and nuclei detection using multiple colours by algorithm.</title>
                        <p>This image is output generated by the algorithm, which was developed by training AI tool (Mimansa) by pathologists and software engineers who are listed as authors to detect and represent hormone receptor staining patterns.</p>
                    </caption>
                    <graphic id="gr1" orientation="portrait" position="float" xlink:href="https://f1000research-files.f1000.com/manuscripts/193957/b1708c38-a1f6-45e8-982a-fa55b8190f9e_figure1.gif"/>
                </fig>
                <fig fig-type="figure" id="f2" orientation="portrait" position="float">
                    <label>Figure 2. </label>
                    <caption>
                        <title>Photomicrograph shows IHC stained ER slide on left and corresponding detection and classification of nuclei as negative (green), weak positive (yellow), moderate positive (orange) and strong positive (red) by algorithm.</title>
                        <p>This image is output generated by the algorithm, which was developed by training AI tool (Mimansa) by pathologists and software engineers who are listed as authors to detect and represent hormone receptor staining patterns.</p>
                    </caption>
                    <graphic id="gr2" orientation="portrait" position="float" xlink:href="https://f1000research-files.f1000.com/manuscripts/193957/b1708c38-a1f6-45e8-982a-fa55b8190f9e_figure2.gif"/>
                </fig>
                <fig fig-type="figure" id="f3" orientation="portrait" position="float">
                    <label>Figure 3. </label>
                    <caption>
                        <title>Study design to evaluate the performance of AI based algorithm scores with pathologists&#x2019; score: The algorithm score was compared with the initial (pathologist) consensus score by pathologist&#x2019;s and any discordance was reviewed to obtain a final consensus score (ground truth).</title>
                        <p>The Google material design icons were used for the figures.</p>
                    </caption>
                    <graphic id="gr3" orientation="portrait" position="float" xlink:href="https://f1000research-files.f1000.com/manuscripts/193957/b1708c38-a1f6-45e8-982a-fa55b8190f9e_figure3.gif"/>
                </fig>
            </sec>
            <sec id="sec9">
                <title>Statistical analysis</title>
                <p>Data were analyzed using IBM-SPSS Statistics for Windows version 23.0 (Armonk, NY, IBM Corp). Categorical data were expressed in terms of proportions and percentages. Inter-rater reliability analysis was performed using Cohen&#x2019;s Kappa with significance testing and confidence intervals to see the agreement of the algorithm with ground truth for ER/PR scores across different score ranges as well as three groups: negative, low positive, and strong positive scores. Pearson&#x2019;s correlation coefficient was used to evaluate the agreement of scores generated by the algorithm and other raters, which included senior pathologists and junior pathologists with the ground truth (final consensus scores).</p>
            </sec>
        </sec>
        <sec id="sec10" sec-type="results">
            <title>Results</title>
            <p>The age of the patients ranged from 18 to 79&#x00a0;years. Trucut biopsies formed majority of cases (60.60%).</p>
            <p>The most common histopathological diagnosis was Invasive ductal carcinoma of no special type. Luminal type showing either ER and/or PR positivity accounted tor 82.15% of the cases. 
                <xref ref-type="table" rid="T2">
Table 2</xref> shows the pathological features of the 297 cases of breast carcinoma analysed in this study.</p>
            <table-wrap id="T2" orientation="portrait" position="float">
                <label>
Table 2. </label>
                <caption>
                    <title>Shows the demographic features of the cases included in the study (N&#x00a0;=&#x00a0;297).</title>
                </caption>
                <table content-type="article-table" frame="hsides">
                    <thead>
                        <tr>
                            <th align="left" colspan="2" rowspan="1" valign="top"/>
                            <th align="left" colspan="1" rowspan="1" valign="top">Number</th>
                            <th align="left" colspan="1" rowspan="1" valign="top">
Range/percentage</th>
                        </tr>
                    </thead>
                    <tbody>
                        <tr>
                            <td align="left" colspan="1" rowspan="1" valign="top">Age</td>
                            <td colspan="1" rowspan="1"/>
                            <td colspan="1" rowspan="1"/>
                            <td align="left" colspan="1" rowspan="1" valign="top">18&#x2013;79&#x00a0;years</td>
                        </tr>
                        <tr>
                            <td align="left" colspan="1" rowspan="2" valign="top">Specimen type</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">Trucut biopsy</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">180</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">60.60%</td>
                        </tr>
                        <tr>
                            <td align="left" colspan="1" rowspan="1" valign="top">Resection</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">117</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">39.39%</td>
                        </tr>
                        <tr>
                            <td align="left" colspan="1" rowspan="3" valign="top">Histological type</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">Invasive ductal carcinoma, NST</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">218</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">73.40%</td>
                        </tr>
                        <tr>
                            <td align="left" colspan="1" rowspan="1" valign="top">Invasive lobular carcinoma</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">21</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">7.07%</td>
                        </tr>
                        <tr>
                            <td align="left" colspan="1" rowspan="1" valign="top">Others</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">58</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">19.53%</td>
                        </tr>
                        <tr>
                            <td align="left" colspan="1" rowspan="6" valign="top">Molecular subtype</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">Luminal type (ER and or PR positive)</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">244</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">82.15%</td>
                        </tr>
                        <tr>
                            <td align="left" colspan="1" rowspan="1" valign="top">
                                <bold>Her 2 status</bold>
</td>
                            <td colspan="1" rowspan="1"/>
                            <td align="left" colspan="1" rowspan="1" valign="top"/>
                        </tr>
                        <tr>
                            <td align="left" colspan="1" rowspan="1" valign="top">Negative (0,1+)</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">237</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">79.80%</td>
                        </tr>
                        <tr>
                            <td align="left" colspan="1" rowspan="1" valign="top">Equivocal (2+)</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">25</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">8.42%</td>
                        </tr>
                        <tr>
                            <td align="left" colspan="1" rowspan="1" valign="top">Positive (3+)</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">35</td>
                            <td colspan="1" rowspan="1">11.78%</td>
                        </tr>
                        <tr>
                            <td align="left" colspan="1" rowspan="1" valign="top">Triple negative</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">53</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">17.85%</td>
                        </tr>
                    </tbody>
                </table>
            </table-wrap>
            <p>
                <xref ref-type="table" rid="T3">
Table 3</xref> reveals the performance of algorithm for ER and PR expression.and the reasons for mis-interpretation. There was concordance of 93.93% with ER expression, while slightly lower at 87.37% for PR expression scoring by algorithm when compared with ground truth. The reasons for misinterpretation are listed in 
                <xref ref-type="table" rid="T3">
Table 3</xref> and in 
                <xref ref-type="fig" rid="f4">Figure 4</xref>.</p>
            <table-wrap id="T3" orientation="portrait" position="float">
                <label>
Table 3. </label>
                <caption>
                    <title>Shows the agreement of ER and PR scores between algorithm and ground truth and the reason for mis-interpretation.</title>
                </caption>
                <table content-type="article-table" frame="hsides">
                    <thead>
                        <tr>
                            <th align="left" colspan="1" rowspan="2" valign="top">Comparison of algorithm scores with ground truth</th>
                            <th align="left" colspan="2" rowspan="1" valign="top">ER scores</th>
                            <th align="left" colspan="2" rowspan="1" valign="top">PR scores</th>
                            <th align="left" colspan="1" rowspan="2" valign="top">Reason for mis-Interpretation
</th>
                        </tr>
                        <tr>
                            <th align="left" colspan="1" rowspan="1" valign="top">Total No (297)</th>
                            <th align="left" colspan="1" rowspan="1" valign="top">Percentage</th>
                            <th align="left" colspan="1" rowspan="1" valign="top">Total No (293)</th>
                            <th align="left" colspan="1" rowspan="1" valign="top">
Percentage</th>
                        </tr>
                    </thead>
                    <tbody>
                        <tr>
                            <td align="left" colspan="1" rowspan="1" valign="top">Concordant</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">279</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">93.93%</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">256</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">87.37%</td>
                            <td colspan="1" rowspan="1"/>
                        </tr>
                        <tr>
                            <td align="left" colspan="1" rowspan="1" valign="top">Discordant (False positive)</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">09</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">3.03%</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">19</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">6.48%</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">
                                <p>

                                    <list list-type="bullet">
                                        <list-item>
                                            <label>&#x27a2;</label>
                                            <p>Positive staining of normal breast acini</p>
                                        </list-item>
                                        <list-item>
                                            <label>&#x27a2;</label>
                                            <p>Ductal carcinoma in situ positive, while invasive tumour negative</p>
                                        </list-item>
                                        <list-item>
                                            <label>&#x27a2;</label>
                                            <p>Tissue folds</p>
                                        </list-item>
                                        <list-item>
                                            <label>&#x27a2;</label>
                                            <p>Stain particles</p>
                                        </list-item>
                                        <list-item>
                                            <label>&#x27a2;</label>
                                            <p>Non- specific staining of stromal cells</p>
                                        </list-item>
                                        <list-item>
                                            <label>&#x27a2;</label>
                                            <p>Non- specific staining of cytoplasm of tumour cells</p>
                                        </list-item>
                                    </list>
                                </p>
</td>
                        </tr>
                        <tr>
                            <td align="left" colspan="1" rowspan="1" valign="top">Discordant (False negative)</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">07</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">2.35%</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">18</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">6.14%</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">&lt; 10% cells missed by algorithm</td>
                        </tr>
                        <tr>
                            <td align="left" colspan="1" rowspan="1" valign="top">Discordant (True positive)</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">02</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">0.67%</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">---</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">----</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">Review of 2 cases of ground truth score of 0 and positive by Algorithm was confirmed to be low positive (Score 3&#x2013;4). All the pathologists had missed few positive (&lt;10%) cells in their interpretation which was detected by algorithm</td>
                        </tr>
                    </tbody>
                </table>
            </table-wrap>
            <fig fig-type="figure" id="f4" orientation="portrait" position="float">
                <label>Figure 4. </label>
                <caption>
                    <title>Photomicrograph shows reasons for misinterpretation of ER/PR expression by algorithm giving false positive scores (marked with arrow) A) Positive staining in normal interspersed breast acini, while tumor cells are negative B) positive staining in stromal cells while tumor cells are negative C) Ductal in situ component positive while invasive tumor negative D) non- specific cytoplasmic staining while nuclei negative E) non-specific background staining F) brown stain particles while tumour cells negative.</title>
                </caption>
                <graphic id="gr4" orientation="portrait" position="float" xlink:href="https://f1000research-files.f1000.com/manuscripts/193957/b1708c38-a1f6-45e8-982a-fa55b8190f9e_figure4.gif"/>
            </fig>
            <p>There were no statistically significant differences in ER and PR scores between the trucut biopsy and resection specimens.</p>
            <p>
                <xref ref-type="table" rid="T4">
Tables 4</xref>&#x2013;
                <xref ref-type="table" rid="T6">6</xref> reveal Algorithm performance for different scores, low positive and strong positive scores as well as comparison with senior and junior pathologists for ER expression.</p>
            <table-wrap id="T4" orientation="portrait" position="float">
                <label>
Table 4. </label>
                <caption>
                    <title>Algorithm agreement with ground truth for Allred ER scores (0&#x2013;8) N&#x00a0;=&#x00a0;297.</title>
                </caption>
                <table content-type="article-table" frame="hsides">
                    <thead>
                        <tr>
                            <th align="left" colspan="1" rowspan="1" valign="top">ER</th>
                            <th align="left" colspan="1" rowspan="1" valign="top">Conditional</th>
                            <th align="left" colspan="1" rowspan="2" valign="top">Kappa</th>
                            <th align="left" colspan="3" rowspan="1" valign="top">Asymptotic</th>
                            <th align="left" colspan="2" rowspan="1" valign="top">Asymptotic 95% Confidence interval</th>
                        </tr>
                        <tr>
                            <th align="left" colspan="1" rowspan="1" valign="top">Scores</th>
                            <th align="left" colspan="1" rowspan="1" valign="top">Probability</th>
                            <th align="left" colspan="1" rowspan="1" valign="top">Standard error</th>
                            <th align="left" colspan="1" rowspan="1" valign="top">Z</th>
                            <th align="left" colspan="1" rowspan="1" valign="top">Sigma</th>
                            <th align="left" colspan="1" rowspan="1" valign="top">
Lower bound</th>
                            <th align="left" colspan="1" rowspan="1" valign="top">
Upper bound</th>
                        </tr>
                    </thead>
                    <tbody>
                        <tr>
                            <td align="left" colspan="1" rowspan="1" valign="top">0</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.879</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.821</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">&lt;015</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">54.803</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">&lt;001</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.792</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.850</td>
                        </tr>
                        <tr>
                            <td align="left" colspan="1" rowspan="1" valign="top">2</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.107</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.86</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">&lt;015</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">5.76</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">&lt;001</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.57</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.116</td>
                        </tr>
                        <tr>
                            <td align="left" colspan="1" rowspan="1" valign="top">3</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.355</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.325</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">&lt;015</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">21.671</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">&lt;001</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.295</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.354</td>
                        </tr>
                        <tr>
                            <td align="left" colspan="1" rowspan="1" valign="top">4</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.275</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.246</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">&lt;015</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">16.439</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">&lt;001</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.217</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.276</td>
                        </tr>
                        <tr>
                            <td align="left" colspan="1" rowspan="1" valign="top">5</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.302</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.275</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">&lt;015</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">18.362</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">&lt;001</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.246</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.304</td>
                        </tr>
                        <tr>
                            <td align="left" colspan="1" rowspan="1" valign="top">6</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.251</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.213</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">&lt;015</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">14.23</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">&lt;001</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.184</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.243</td>
                        </tr>
                        <tr>
                            <td align="left" colspan="1" rowspan="1" valign="top">7</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.277</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.181</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">&lt;015</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">12.106</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">&lt;001</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.152</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.211</td>
                        </tr>
                        <tr>
                            <td align="left" colspan="1" rowspan="1" valign="top">8</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.780</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.683</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">&lt;015</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">43.578</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">&lt;001</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.623</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.623</td>
                        </tr>
                    </tbody>
                </table>
            </table-wrap>
            <table-wrap id="T5" orientation="portrait" position="float">
                <label>
Table 5. </label>
                <caption>
                    <title>Algorithm performance in negative, low positive (3-5) and positive (5-8) groups with ground truth for ER expression, N&#x00a0;=&#x00a0;297.</title>
                </caption>
                <table content-type="article-table" frame="hsides">
                    <thead>
                        <tr>
                            <th align="left" colspan="1" rowspan="1" valign="top">ER</th>
                            <th align="left" colspan="1" rowspan="1" valign="top">Conditional</th>
                            <th align="left" colspan="1" rowspan="2" valign="top">Kappa</th>
                            <th align="left" colspan="3" rowspan="1" valign="top">Asymptotic</th>
                            <th align="left" colspan="2" rowspan="1" valign="top">Asymptotic 95% Confidence interval</th>
                        </tr>
                        <tr>
                            <th align="left" colspan="1" rowspan="1" valign="top">Scores</th>
                            <th align="left" colspan="1" rowspan="1" valign="top">Probability</th>
                            <th align="left" colspan="1" rowspan="1" valign="top">Standard error</th>
                            <th align="left" colspan="1" rowspan="1" valign="top">Z</th>
                            <th align="left" colspan="1" rowspan="1" valign="top">Sigma</th>
                            <th align="left" colspan="1" rowspan="1" valign="top">Lower bound</th>
                            <th align="left" colspan="1" rowspan="1" valign="top">Upper bound</th>
                        </tr>
                    </thead>
                    <tbody>
                        <tr>
                            <td align="left" colspan="1" rowspan="1" valign="top">Negative (0&#x2013;2)</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.929</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.891</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">&lt;015</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">59.454</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">&lt;001</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.861</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.920</td>
                        </tr>
                        <tr>
                            <td align="left" colspan="1" rowspan="1" valign="top">Low positive (3-5)</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.636</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.587</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">&lt;015</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">39.158</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">&lt;001</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.557</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.616</td>
                        </tr>
                        <tr>
                            <td align="left" colspan="1" rowspan="1" valign="top">Strong positive (6-8)</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.963</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.921</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">&lt;015</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">61.48</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">&lt;001</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.892</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.950</td>
                        </tr>
                    </tbody>
                </table>
            </table-wrap>
            <table-wrap id="T6" orientation="portrait" position="float">
                <label>
Table 6. </label>
                <caption>
                    <title>Shows the inter-item correlation matrix for ER scores, comparing the algorithm (AI) and various pathologists against the ground truth.</title>
                </caption>
                <table content-type="article-table" frame="hsides">
                    <thead>
                        <tr>
                            <th align="left" colspan="1" rowspan="1" valign="top"/>
                            <th align="left" colspan="1" rowspan="1" valign="top">Ground truth</th>
                            <th align="left" colspan="1" rowspan="1" valign="top">AI (algorithm)</th>
                            <th align="left" colspan="1" rowspan="1" valign="top">Sr Path1</th>
                            <th align="left" colspan="1" rowspan="1" valign="top">Sr Path 2</th>
                            <th align="left" colspan="1" rowspan="1" valign="top">Jr Path 1</th>
                            <th align="left" colspan="1" rowspan="1" valign="top">
Jr Path 2</th>
                        </tr>
                    </thead>
                    <tbody>
                        <tr>
                            <td align="left" colspan="1" rowspan="1" valign="top">Ground truth</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">1.000</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.937</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.992</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.976</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.966</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.958</td>
                        </tr>
                        <tr>
                            <td align="left" colspan="1" rowspan="1" valign="top">AI (algorithm)</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.937</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">1.000</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.933</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.921</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.918</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.912</td>
                        </tr>
                        <tr>
                            <td align="left" colspan="1" rowspan="1" valign="top">Sr Path 1</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.992</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.933</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">1.000</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.974</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.966</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.957</td>
                        </tr>
                        <tr>
                            <td align="left" colspan="1" rowspan="1" valign="top">Sr Path 2</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.976</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.921</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.974</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">1.000</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.963</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.952</td>
                        </tr>
                        <tr>
                            <td align="left" colspan="1" rowspan="1" valign="top">Jr Path 1</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.966</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.918</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.966</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.963</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">1.000</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.972</td>
                        </tr>
                        <tr>
                            <td align="left" colspan="1" rowspan="1" valign="top">Jr Path 2</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.958</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.912</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.957</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.952</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.972</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">1.000</td>
                        </tr>
                    </tbody>
                </table>
            </table-wrap>
            <p>For ER expression, the ground truth (GT) revealed 169 strong positive, 31 low positive, and 98 negative cases. Concordance with GT was highest among senior pathologists (99% and 98%), followed by the AI algorithm (97%), and slightly lower for junior pathologists (95% and 93%). The algorithm was particularly accurate in correctly classifying all strong positive cases; however, discordance was observed in 16 low-score cases, including four false negatives and ten false positives. Importantly, the algorithm correctly identified two true positive cases that were missed by all pathologists.</p>
            <p>
                <xref ref-type="table" rid="T7">
Tables 7</xref>&#x2013;
                <xref ref-type="table" rid="T9">9</xref> reveal Algorithm performance for different scores, low positive and strong positive scores as well as comparison with senior and junior pathologists for PR expression.</p>
            <table-wrap id="T7" orientation="portrait" position="float">
                <label>
Table 7. </label>
                <caption>
                    <title>Algorithm agreement with ground truth for All red PR scores (0&#x2013;8) N&#x00a0;=&#x00a0;293.</title>
                </caption>
                <table content-type="article-table" frame="hsides">
                    <thead>
                        <tr>
                            <th align="left" colspan="1" rowspan="1" valign="top">PR</th>
                            <th align="left" colspan="1" rowspan="1" valign="top">Conditional</th>
                            <th align="left" colspan="1" rowspan="2" valign="top">Kappa</th>
                            <th align="left" colspan="3" rowspan="1" valign="top">Asymptotic</th>
                            <th align="left" colspan="2" rowspan="1" valign="top">Asymptotic 95% Confidence interval</th>
                        </tr>
                        <tr>
                            <th align="left" colspan="1" rowspan="1" valign="top">Scores</th>
                            <th align="left" colspan="1" rowspan="1" valign="top">Probability</th>
                            <th align="left" colspan="1" rowspan="1" valign="top">Standard error</th>
                            <th align="left" colspan="1" rowspan="1" valign="top">Z</th>
                            <th align="left" colspan="1" rowspan="1" valign="top">Sigma</th>
                            <th align="left" colspan="1" rowspan="1" valign="top">Lower bound</th>
                            <th align="left" colspan="1" rowspan="1" valign="top">
Upper bound</th>
                        </tr>
                    </thead>
                    <tbody>
                        <tr>
                            <td align="left" colspan="1" rowspan="1" valign="top">0</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.875</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.776</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.015</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">51.474</td>
                            <td align="left" colspan="1" rowspan="1" valign="bottom">&lt;001</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.747</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.806</td>
                        </tr>
                        <tr>
                            <td align="left" colspan="1" rowspan="1" valign="top">2</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.131</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.104</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.015</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">6.913</td>
                            <td align="left" colspan="1" rowspan="1" valign="bottom">&lt;001</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.075</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.029</td>
                        </tr>
                        <tr>
                            <td align="left" colspan="1" rowspan="1" valign="top">3</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.274</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.237</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.015</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">15.718</td>
                            <td align="left" colspan="1" rowspan="1" valign="bottom">&lt;001</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.208</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.134</td>
                        </tr>
                        <tr>
                            <td align="left" colspan="1" rowspan="1" valign="top">4</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.362</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.313</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.015</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">20.726</td>
                            <td align="left" colspan="1" rowspan="1" valign="bottom">&lt;001</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.283</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.267</td>
                        </tr>
                        <tr>
                            <td align="left" colspan="1" rowspan="1" valign="top">5</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.319</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.276</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.015</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">18.326</td>
                            <td align="left" colspan="1" rowspan="1" valign="bottom">&lt;001</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.247</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.342</td>
                        </tr>
                        <tr>
                            <td align="left" colspan="1" rowspan="1" valign="top">6</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.347</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.302</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.015</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">20.024</td>
                            <td align="left" colspan="1" rowspan="1" valign="bottom">&lt;001</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.272</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.306</td>
                        </tr>
                        <tr>
                            <td align="left" colspan="1" rowspan="1" valign="top">7</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.297</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.240</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.015</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">15.904</td>
                            <td align="left" colspan="1" rowspan="1" valign="bottom">&lt;001</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.210</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.269</td>
                        </tr>
                        <tr>
                            <td align="left" colspan="1" rowspan="1" valign="top">8</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.768</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.703</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.015</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">46.584</td>
                            <td align="left" colspan="1" rowspan="1" valign="bottom">&lt;001</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.673</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.732</td>
                        </tr>
                    </tbody>
                </table>
            </table-wrap>
            <table-wrap id="T8" orientation="portrait" position="float">
                <label>
Table 8. </label>
                <caption>
                    <title>Algorithm performance in negative, low positive (3-5) and positive (5-8) groups with ground truth for PR expression N&#x00a0;=&#x00a0;293.</title>
                </caption>
                <table content-type="article-table" frame="hsides">
                    <thead>
                        <tr>
                            <th align="left" colspan="1" rowspan="1" valign="top">ER</th>
                            <th align="left" colspan="1" rowspan="1" valign="top">Conditional</th>
                            <th align="left" colspan="1" rowspan="2" valign="top">Kappa</th>
                            <th align="left" colspan="3" rowspan="1" valign="top">Asymptotic</th>
                            <th align="left" colspan="2" rowspan="1" valign="top">Asymptotic 95% Confidence interval</th>
                        </tr>
                        <tr>
                            <th align="left" colspan="1" rowspan="1" valign="top">Scores</th>
                            <th align="left" colspan="1" rowspan="1" valign="top">Probability</th>
                            <th align="left" colspan="1" rowspan="1" valign="top">Standard error</th>
                            <th align="left" colspan="1" rowspan="1" valign="top">Z</th>
                            <th align="left" colspan="1" rowspan="1" valign="top">Sigma</th>
                            <th align="left" colspan="1" rowspan="1" valign="top">Lower bound</th>
                            <th align="left" colspan="1" rowspan="1" valign="top">
Upper bound</th>
                        </tr>
                    </thead>
                    <tbody>
                        <tr>
                            <td align="left" colspan="1" rowspan="1" valign="top">Negative (0&#x2013;2)</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.910</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.829</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.015</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">54.648</td>
                            <td align="left" colspan="1" rowspan="1" valign="bottom">&lt;001</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.799</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.858</td>
                        </tr>
                        <tr>
                            <td align="left" colspan="1" rowspan="1" valign="top">Low positive (3-5)</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.618</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.534</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.015</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">35.199</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">&lt;001</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.504</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.563</td>
                        </tr>
                        <tr>
                            <td align="left" colspan="1" rowspan="1" valign="top">Strong positive (6-8)</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.906</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.856</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.015</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">56.477</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">&lt;001</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.827</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.886</td>
                        </tr>
                    </tbody>
                </table>
            </table-wrap>
            <table-wrap id="T9" orientation="portrait" position="float">
                <label>
Table 9. </label>
                <caption>
                    <title>Shows inter-item correlation matrix for PR scores, comparing the algorithm (AI) and various pathologists against the ground truth.</title>
                </caption>
                <table content-type="article-table" frame="hsides">
                    <thead>
                        <tr>
                            <th align="left" colspan="1" rowspan="1" valign="top"/>
                            <th align="left" colspan="1" rowspan="1" valign="top">Ground truth</th>
                            <th align="left" colspan="1" rowspan="1" valign="top">AI (algorithm)</th>
                            <th align="left" colspan="1" rowspan="1" valign="top">Sr Path 1</th>
                            <th align="left" colspan="1" rowspan="1" valign="top">Sr Path 2</th>
                            <th align="left" colspan="1" rowspan="1" valign="top">Jr Path 1</th>
                            <th align="left" colspan="1" rowspan="1" valign="top">
Jr Path 2</th>
                        </tr>
                    </thead>
                    <tbody>
                        <tr>
                            <td align="left" colspan="1" rowspan="1" valign="top">Ground truth</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">1.000</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.887</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.984</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.980</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.932</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.937</td>
                        </tr>
                        <tr>
                            <td align="left" colspan="1" rowspan="1" valign="top">AI (algorithm)</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.887</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">1.000</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.875</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.891</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.889</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.879</td>
                        </tr>
                        <tr>
                            <td align="left" colspan="1" rowspan="1" valign="top">Sr Path 1</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.984</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.875</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">1.000</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.964</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.921</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.931</td>
                        </tr>
                        <tr>
                            <td align="left" colspan="1" rowspan="1" valign="top">Sr Path 2</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.980</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.891</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.964</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">1.000</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.931</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.932</td>
                        </tr>
                        <tr>
                            <td align="left" colspan="1" rowspan="1" valign="top">Jr Path 1</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.932</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.889</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.921</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.931</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">1.000</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.937</td>
                        </tr>
                        <tr>
                            <td align="left" colspan="1" rowspan="1" valign="top">Jr Path 2</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.937</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.879</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.931</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.932</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">.937</td>
                            <td align="left" colspan="1" rowspan="1" valign="top">1.000</td>
                        </tr>
                    </tbody>
                </table>
            </table-wrap>
            <p>The above results for PR immunohistochemistry reveals 98% and 97% agreement for senior pathologists, 92% for the algorithm, and 93% and 91% for junior pathologists with ground truth. The algorithm for PR expression also achieved perfect concordance in strong positive cases but showed reduced performance in low-score cases, resulting in 16 false negatives and eight false positives. Cohen&#x2019;s kappa coefficients demonstrated excellent agreement for ER (&#x03ba;&#x00a0;=&#x00a0;0.91) and strong agreement for PR (&#x03ba;&#x00a0;=&#x00a0;0.84).</p>
        </sec>
        <sec id="sec11" sec-type="discussion">
            <title>Discussion</title>
            <p>Assessing estrogen receptor (ER) and progesterone receptor (PR) status by immunohistochemistry in breast cancer is essential, as it guides treatment decisions and predicts therapeutic responses.
                <sup>
                    <xref ref-type="bibr" rid="ref10">10</xref>&#x2013;
                    <xref ref-type="bibr" rid="ref12">12</xref>
                </sup> However, the reliability of assay results depends on both the consistency of assay performance and the accuracy of its interpretation.
                <sup>
                    <xref ref-type="bibr" rid="ref13">13</xref>
                </sup> Automated immune-stainers with high reproducibility, combined with whole slide digitalization and dedicated software helps in objective image quantification through color and intensity segmentation, allowing for unbiased scoring.
                <sup>
                    <xref ref-type="bibr" rid="ref5">5</xref>,
                    <xref ref-type="bibr" rid="ref14">14</xref>
                </sup>
            </p>
            <p>Several studies have validated the performance of automated scoring methods against manual assessment of estrogen receptor (ER) and progesterone receptor (PR) expression in breast cancer and have shown a strong correlation between automated image analysis and manual scoring techniques, suggesting that automated methods can serve as reliable alternatives.
                <sup>
                    <xref ref-type="bibr" rid="ref14">14</xref>&#x2013;
                    <xref ref-type="bibr" rid="ref16">16</xref>
                </sup> Some models were based on tissue microarrays, while others utilized whole slide images for analysis.
                <sup>
                    <xref ref-type="bibr" rid="ref14">14</xref>,
                    <xref ref-type="bibr" rid="ref17">17</xref>,
                    <xref ref-type="bibr" rid="ref18">18</xref>
                </sup> Some of the algorithms used required training and inputs from pathologists, while others have used algorithms that do not require supervision.
                <sup>
                    <xref ref-type="bibr" rid="ref19">19</xref>,
                    <xref ref-type="bibr" rid="ref20">20</xref>
                </sup> Automated or digital image analysis has several advantages, such as reducing the bias in sampling, reducing inter- and intra-reader variability, providing more consistent reporting, and significantly reducing pathologists&#x2019; workload.
                <sup>
                    <xref ref-type="bibr" rid="ref21">21</xref>
                </sup>
            </p>
            <p>In our study, we demonstrated that the algorithm developed (Mimansa) was able to detect the relevant tumor regions from WSI, quantify immunohistochemical expression, generate ER and PR scores, and effectively replicate the ER and PR scores produced by pathologist visual scoring. Our study showed good agreement of the AI algorithm in assessing ER and PR scores with the ground truth, which was slightly lower than that of pathologists. There was no statistically significant difference between the scores of senior and junior pathologists as well as the algorithm. The overall agreement between the ER score and ground truth was 93.93%, and the PR score was 87.37%. Similar results were noted in a study by Jung et al., which showed 93% concordance for ER expression (197 cases) and 89.4% (199 cases) for PR expression by the algorithm.
                <sup>
                    <xref ref-type="bibr" rid="ref22">22</xref>
                </sup> Shafi et al. observed 93.85 concordance for ER expression in their study on 97 cases
                <sup>
                    <xref ref-type="bibr" rid="ref23">23</xref>
                </sup> and the Pearson correlation coefficient (PCC) score in our study was 0.937 and 0.887 for ER and PR, respectively, which was similar to the study by Bankhead et al., which showed a PCC of 0.908 and 0.862 for ER and PR, respectively.
                <sup>
                    <xref ref-type="bibr" rid="ref24">24</xref>
                </sup> Sharangpani et al. found an agreement of 85% and 81% between the automatic determination of positivity/negativity of ER and PR-stained cells with manual scoring.
                <sup>
                    <xref ref-type="bibr" rid="ref15">15</xref>
                </sup> Gokhale et al. reported 95% concordance between automated and manual scoring, while Mofidi et al. demonstrated a highly significant correlation (r2&#x00a0;=&#x00a0;0.844) between digital and manual ones.
                <sup>
                    <xref ref-type="bibr" rid="ref7">7</xref>,
                    <xref ref-type="bibr" rid="ref14">14</xref>
                </sup>
            </p>
            <p>In our study, the algorithm demonstrated excellent agreement for negative (0&#x2013;2) and strong positive (6&#x2013;8) groups, with kappa values of .891 and .921 for ER expression and .829 and .856, respectively, for PR expression, and moderate agreement for the low positive (3&#x2013;5 scores) group with a kappa of .587 for ER expression and .534 or PR expression, suggesting the need for refinement of the algorithm to identify low positive (3&#x2013;5) scores. We identified reasons for the inaccuracies in this group with false-positive scores due to misinterpretation that occurred due to interspersed positive staining of normal breast acini, ductal carcinoma in situ component when the invasive component was negative, tissue folds with brown staining, stain artifact clumps on the tissue, non-specific staining of stromal cells, and cytoplasm of the cytoplasm of tumor cells. Shafi et al. also reported three cases of false-positive ER expression by DIA, which was mainly due to intermixed benign glands in the tumor area, ductal carcinoma in situ (DCIS) components, and tissue folding .21 However, these false-positive scores in our case could be mitigated by incorporating an option in the algorithm to manually exclude areas such as tissue folds, normal breast acini, etc. before re-running the analysis. Such misclassification errors occurring from poorly stained samples or samples of bad quality can be overcome by the ability of digital image analysis to reclassify or drop individual detected objects and recalculate the software provided results.
                <sup>
                    <xref ref-type="bibr" rid="ref25">25</xref>
                </sup>
            </p>
            <p>We noticed 7 false-negative cases for ER and 18 for PR, with the majority occurring in the low positive score range, highlighting the need for further refinement in this category. Conversely, the AI algorithm identified two true-positive ER cases that were missed by all the pathologists. This capability highlights the potential of the algorithm to significantly influence patient treatment decisions by detecting subtle positive findings that could otherwise be overlooked. This ability of the algorithm to detect critical diagnostic errors demonstrates its potential for improving diagnostic accuracy. Studies have shown improved intra- and interobserver agreement by providing pathologists with computer-aided IHC measurements during the visual scoring process. It is possible that the pathologist missed some positive cells because of the sheer size of the images.
                <sup>
                    <xref ref-type="bibr" rid="ref18">18</xref>
                </sup> Since consensus scoring by experts is impractical in routine practice, automated IHC measurements may provide a means to improve scores. Shafi et al. demonstrated increased efficiency in the ER assessment of breast cancer by integrating DIA in the workflow of pathologists.
                <sup>
                    <xref ref-type="bibr" rid="ref23">23</xref>
                </sup> AI analyzer could be used as an aid to pathologists as a &#x2018;second reader&#x2019; in harmonizing judgments that may diverge due to over- or underestimations.
                <sup>
                    <xref ref-type="bibr" rid="ref26">26</xref>
                </sup> Jung et al. suggested utilizing the AI analyzer as a tool for second opinions, where pathologists can maintain their original workflow, requiring reinterpretation in only a selected subset of cases (approximately 10% for ER and PR).
                <sup>
                    <xref ref-type="bibr" rid="ref22">22</xref>
                </sup>
            </p>
            <p>One of the drawbacks of the study was the scope of validation of the AI algorithm, which was primarily confined to enhancing the concordance of pathologist interpretations. Clinical validation, such as its impact on patient survival outcomes, was not performed.</p>
            <sec id="sec12" sec-type="conclusion">
                <title>Conclusion</title>
                <p>The algorithm showed good agreement in scoring ER and PR expressions with the ground truth, making it a reliable tool for aiding diagnostic decision-making. It can serve as a valuable support tool for pathologists and provide a second opinion, particularly in low-positive cases where human error might occur. Notably, the algorithm identified two cases in which patients could benefit from anti-estrogen treatment, highlighting its potential clinical impact.</p>
            </sec>
            <sec id="sec13">
                <title>Ethical considerations</title>
                <p>The study has been approved by the Kasturba Medical College and Kasturba Hospital Institutional Ethics Committee (IEC) (Ref: IEC No 05/2020 dated 18
                    <sup>th</sup> June 2020 and extension (Amendment) IEC No 186/2021, dated 10
                    <sup>th</sup> Feb 2021).</p>
            </sec>
        </sec>
        <sec id="sec14">
            <title>Consent</title>
            <p>As the study is retrospective does not involve any intervention of subjects and uses lab based coded data collection; Consent waived by the ethics committee.</p>
        </sec>
    </body>
    <back>
        <sec id="sec17" sec-type="data-availability">
            <title>Date availability statement</title>
            <p>The dataset supporting the findings of this study, including ER and PR scores generated by both algorithmic assessment and pathologists, is publicly available in the Fig share repository at 
                <ext-link ext-link-type="uri" xlink:href="https://doi.org/10.6084/m9.figshare.31313629">https://doi.org/10.6084/m9.figshare.31313629</ext-link>.
                <sup>
                    <xref ref-type="bibr" rid="ref27">27</xref>
                </sup>
            </p>
            <p>The dataset is licensed under a 
                <ext-link ext-link-type="uri" xlink:href="https://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution 4.0 International License (CC BY 4.0)</ext-link>.</p>
        </sec>
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    <sub-article article-type="reviewer-report" id="report486492">
        <front-stub>
            <article-id pub-id-type="doi">10.5256/f1000research.193957.r486492</article-id>
            <title-group>
                <article-title>Reviewer response for version 1</article-title>
            </title-group>
            <contrib-group>
                <contrib contrib-type="author">
                    <name>
                        <surname>Salh</surname>
                        <given-names>Chiman Haydar</given-names>
                    </name>
                    <xref ref-type="aff" rid="r486492a1">1</xref>
                    <role>Referee</role>
                </contrib>
                <aff id="r486492a1">
                    <label>1</label>Erbil Polytechnic University, Erbil, Iraq</aff>
            </contrib-group>
            <author-notes>
                <fn fn-type="conflict">
                    <p>
                        <bold>Competing interests: </bold>No competing interests were disclosed.</p>
                </fn>
            </author-notes>
            <pub-date pub-type="epub">
                <day>16</day>
                <month>6</month>
                <year>2026</year>
            </pub-date>
            <permissions>
                <copyright-statement>Copyright: &#x00a9; 2026 Salh CH</copyright-statement>
                <copyright-year>2026</copyright-year>
                <license xlink:href="https://creativecommons.org/licenses/by/4.0/">
                    <license-p>This is an open access peer review report distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.</license-p>
                </license>
            </permissions>
            <related-article ext-link-type="doi" id="relatedArticleReport486492" related-article-type="peer-reviewed-article" xlink:href="10.12688/f1000research.175934.1"/>
            <custom-meta-group>
                <custom-meta>
                    <meta-name>recommendation</meta-name>
                    <meta-value>approve-with-reservations</meta-value>
                </custom-meta>
            </custom-meta-group>
        </front-stub>
        <body>
            <p>The manuscript is well written, addresses an important clinical application of AI in digital pathology, and presents results that support the conclusions. The study demonstrates high concordance between the AI algorithm and expert pathologist assessment, indicating that the algorithm may serve as a valuable second-reader tool. The manuscript is suitable for indexing after minor revisions aimed at improving methodological transparency and reproducibility.</p>
            <p> </p>
            <p> The manuscript clearly demonstrates that the algorithm performs well in strongly positive and negative cases. The discussion appropriately acknowledges the reduced performance in low-positive cases and identifies potential causes of false-positive and false-negative classifications.</p>
            <p> </p>
            <p> While the overall methodology is described, the manuscript would benefit from additional technical details regarding the AI model architecture, training strategy, validation procedures, and performance optimization. Providing more information would improve reproducibility and allow independent evaluation of the algorithm.</p>
            <p> </p>
            <p> Consider including additional information regarding external validation on datasets from other institutions to assess generalizability.</p>
            <p> </p>
            <p> The discussion could further elaborate on how the identified sources of error (normal acini, DCIS, tissue folds, staining artefacts) may be addressed in future versions of the algorithm.</p>
            <p> </p>
            <p> A brief discussion of computational requirements and workflow integration in routine pathology laboratories would enhance the practical relevance of the study.</p>
            <p>Is the work clearly and accurately presented and does it cite the current literature?</p>
            <p>Partly</p>
            <p>If applicable, is the statistical analysis and its interpretation appropriate?</p>
            <p>Yes</p>
            <p>Are all the source data underlying the results available to ensure full reproducibility?</p>
            <p>Partly</p>
            <p>Is the study design appropriate and is the work technically sound?</p>
            <p>Yes</p>
            <p>Are the conclusions drawn adequately supported by the results?</p>
            <p>Yes</p>
            <p>Are sufficient details of methods and analysis provided to allow replication by others?</p>
            <p>Yes</p>
            <p>Reviewer Expertise:</p>
            <p>NA</p>
            <p>I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard, however I have significant reservations, as outlined above.</p>
        </body>
    </sub-article>
</article>
