Peer Review History
| Original SubmissionJanuary 25, 2026 |
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Dear Dr. bi, Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process. Please submit your revised manuscript by Apr 08 2026 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file.
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Kind regards, GV Narasimha Kumar Academic Editor PLOS One Journal Requirements: When submitting your revision, we need you to address these additional requirements. 1. Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming. The PLOS ONE style templates can be found at https://journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and 2. Please note that PLOS One has specific guidelines on code sharing for submissions in which author-generated code underpins the findings in the manuscript. In these cases, all author-generated code must be made available without restrictions upon publication of the work. Please review our guidelines at https://journals.plos.org/plosone/s/materials-and-software-sharing#loc-sharing-code and ensure that your code is shared in a way that follows best practice and facilitates reproducibility and reuse. 3. Please update your submission to use the PLOS LaTeX template. The template and more information on our requirements for LaTeX submissions can be found at http://journals.plos.org/plosone/s/latex. 4. Thank you for stating the following in the Acknowledgments Section of your manuscript: “This work is supported by the Anhui Provincial Health Science Research Fund (AHWJ2024BAb30015) and the Anhui Provincial Natural Science Research Fund for Higher Education Institutions (2023AH050568).” We note that you have provided funding information that is not currently declared in your Funding Statement. However, funding information should not appear in the Acknowledgments section or other areas of your manuscript. We will only publish funding information present in the Funding Statement section of the online submission form. Please remove any funding-related text from the manuscript and let us know how you would like to update your Funding Statement. Currently, your Funding Statement reads as follows: “The author(s) received no specific funding for this work.” Please include your amended statements within your cover letter; we will change the online submission form on your behalf. 5. We note that the grant information you provided in the ‘Funding Information’ and ‘Financial Disclosure’ sections do not match. When you resubmit, please ensure that you provide the correct grant numbers for the awards you received for your study in the ‘Funding Information’ section. 6. Thank you for stating the following financial disclosure: “This work is supported by the Anhui Provincial Health Science Research Fund (AHWJ2024BAb30015) and the Anhui Provincial Natural Science Research Fund for Higher Education Institutions (2023AH050568).” At this time, please address the following queries: a) Please clarify the sources of funding (financial or material support) for your study. List the grants or organizations that supported your study, including funding received from your institution. b) State what role the funders took in the study. If the funders had no role in your study, please state: “The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.” c) If any authors received a salary from any of your funders, please state which authors and which funders. d) If you did not receive any funding for this study, please state: “The authors received no specific funding for this work.” Please include your amended statements within your cover letter; we will change the online submission form on your behalf. 7. PLOS requires an ORCID iD for the corresponding author in Editorial Manager on papers submitted after December 6th, 2016. Please ensure that you have an ORCID iD and that it is validated in Editorial Manager. To do this, go to ‘Update my Information’ (in the upper left-hand corner of the main menu), and click on the Fetch/Validate link next to the ORCID field. This will take you to the ORCID site and allow you to create a new iD or authenticate a pre-existing iD in Editorial Manager. 8. We note that you have included the phrase “data not shown” in your manuscript. Unfortunately, this does not meet our data sharing requirements. PLOS does not permit references to inaccessible data. We require that authors provide all relevant data within the paper, Supporting Information files, or in an acceptable, public repository. Please add a citation to support this phrase or upload the data that corresponds with these findings to a stable repository (such as Figshare or Dryad) and provide and URLs, DOIs, or accession numbers that may be used to access these data. Or, if the data are not a core part of the research being presented in your study, we ask that you remove the phrase that refers to these data. 9. Your ethics statement should only appear in the Methods section of your manuscript. If your ethics statement is written in any section besides the Methods, please delete it from any other section. 10. Please include a separate caption for each figure in your manuscript. 11. If the reviewer comments include a recommendation to cite specific previously published works, please review and evaluate these publications to determine whether they are relevant and should be cited. There is no requirement to cite these works unless the editor has indicated otherwise. Additional Editor Comments: Dear Author, The manuscript covers a significant issue and utilizes numerous machine-learning models. As per the reviewers comments, significant improvements are needed before it can be fully evalauted. Reagrds, [Note: HTML markup is below. Please do not edit.] Reviewers' comments: Reviewer's Responses to Questions Comments to the Author 1. Is the manuscript technically sound, and do the data support the conclusions? Reviewer #1: Yes Reviewer #2: Yes ********** 2. Has the statistical analysis been performed appropriately and rigorously? -->?> Reviewer #1: N/A Reviewer #2: Yes ********** 3. Have the authors made all data underlying the findings in their manuscript fully available??> The PLOS Data policy Reviewer #1: Yes Reviewer #2: Yes ********** 4. Is the manuscript presented in an intelligible fashion and written in standard English??> Reviewer #1: Yes Reviewer #2: No ********** Reviewer #1: I recommend major revision. The manuscript has potential, but major concerns remain: (1) multiple Chinese labels in figures/tables in an English submission (basic reporting error), (2) unclear and overly tabular presentation of feature-engineering outputs, with insufficient clarity on cross-model common-feature selection criteria, (3) questionable placement/interpretation of one-way p-values and inconsistent data reporting, and (4) lack of external and prospective validation, which weakens generalizability claims. Substantial revision is needed before the manuscript can be properly evaluated. Reviewer #2: This manuscript presents a machine learning–based diagnostic model integrating serum Cystatin 4 (CST4) with routine laboratory indicators for early screening of gastrointestinal tumors. The topic is clinically relevant, particularly given the need for non-invasive and accessible screening strategies in resource-limited settings. The inclusion of calibration curves, SHAP analysis, and decision curve analysis strengthens the interpretability and clinical framing of the model. However, several methodological and design limitations reduce confidence in the robustness and generalizability of the findings. While the reported AUC of 0.85 for the SVM model is promising, important concerns remain regarding study design, validation strategy, and potential bias. I would clearly divide my opinion in two separate sections- Major comments- 1. The title focuses specifically on tumor markers and a diagnostic model based on serum CST4 combined with routine laboratory indicators. However, the Introduction section is largely framed around gastrointestinal malignant tumors in general, with substantial emphasis on cancer burden and prognosis rather than clearly leading into biomarker-based early screening. To improve readability and coherence, the authors should either: Revise the Introduction to more clearly focus on the limitations of current serum tumor markers and the rationale for integrating novel biomarkers (such as CST4) with routine laboratory indicators using machine learning approaches or Modify the title to better reflect the broader discussion of gastrointestinal malignancies and early detection challenges presented in the Introduction and discussion. 2. The study uses a retrospective case-control design comparing confirmed tumor patients with apparently healthy controls. This design may inflate diagnostic performance due to spectrum bias. In real-world screening, differentiation between cancer and benign gastrointestinal disease (e.g., gastritis, polyps, inflammatory conditions) is more clinically relevant than cancer vs healthy individuals. So I furthher suggest the authors should clarify whether controls were screened for subclinical GI pathology and discuss spectrum bias more explicitly. Future validation in a prospective screening cohort is strongly recommended. 3. The manuscript includes 344 participants (214 cases and 130 controls), and 11 machine learning algorithms were evaluated. However, no formal justification of sample size or power calculation is provided. Given the relatively small dataset and the number of candidate predictors (38 variables initially), there is a potential risk of model instability and overfitting. In diagnostic modeling studies, especially those involving machine learning, it is important to justify whether the sample size is adequate relative to the number of predictors and the modeling approach (e.g., events-per-variable considerations, learning curves, or simulation-based power analysis). 4. The manuscript suggests suitability for “large-scale screening” and emphasizes cost reduction compared to endoscopy. However: No cost-effectiveness analysis was conducted. Sensitivity (80.3%) may be insufficient for primary screening. Positive predictive value was not reported. Temper claims regarding large-scale screening and provide PPV/NPV estimates at plausible prevalence rates. Minor Comments 1. Clarify inconsistencies in software versions (Python 3.10 vs 3.9). 2. Provide more detail on missing data proportion and imputation impact. 3. Specify whether CST4 ELISA kits were validated for clinical diagnostic use. 4. Improve clarity regarding model hyperparameter tuning. 5. Language editing can be considered to improve fluency in the Discussion. I would like to congratulate the authorsn for carrying out this important study and I am hopeful to see the improved version of this manuscript in the revised version. Thank you. ********** what does this mean?). If published, this will include your full peer review and any attached files. If you choose “no”, your identity will remain anonymous but your review may still be made public. Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy Reviewer #1: No Reviewer #2: Yes: Pritam Goswami ********** [NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.] To ensure your figures meet our technical requirements, please review our figure guidelines: https://journals.plos.org/plosone/s/figures You may also use PLOS’s free figure tool, NAAS, to help you prepare publication quality figures: https://journals.plos.org/plosone/s/figures#loc-tools-for-figure-preparation. NAAS will assess whether your figures meet our technical requirements by comparing each figure against our figure specifications.
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| Revision 1 |
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Dear Dr. Shen, Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process. Please submit your revised manuscript by Jul 27 2026 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file.
If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter. If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: https://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols. Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols. As the corresponding author, your ORCID iD is verified in the submission system and will appear in the published article. PLOS supports the use of ORCID, and we encourage all coauthors to register for an ORCID iD and use it as well. Please encourage your coauthors to verify their ORCID iD within the submission system before final acceptance, as unverified ORCID iDs will not appear in the published article. Only the individual author can complete the verification step; PLOS staff cannot verify ORCID iDs on behalf of authors. We look forward to receiving your revised manuscript. Kind regards, GV Narasimha Kumar Academic Editor PLOS One Journal Requirements: 1. If the reviewer comments include a recommendation to cite specific previously published works, please review and evaluate these publications to determine whether they are relevant and should be cited. There is no requirement to cite these works unless the editor has indicated otherwise. 2. Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice. Additional Editor Comments: Dear Authors, The authors have addressed most of the queries as per the reviewers' comments; however, still significant justifications/changes are needed to meet the scientific rigour of the journal. The reviewers' comments are attached for compliance. Reagrds, [Note: HTML markup is below. Please do not edit.] Reviewers' comments: Reviewer's Responses to Questions Comments to the Author Reviewer #2: All comments have been addressed Reviewer #3: (No Response) Reviewer #4: (No Response) ********** 2. Is the manuscript technically sound, and do the data support the conclusions??> Reviewer #2: Yes Reviewer #3: Partly Reviewer #4: Yes ********** 3. Has the statistical analysis been performed appropriately and rigorously? -->?> Reviewer #2: Yes Reviewer #3: Yes Reviewer #4: No ********** 4. Have the authors made all data underlying the findings in their manuscript fully available??> The PLOS Data policy Reviewer #2: (No Response) Reviewer #3: Yes Reviewer #4: Yes ********** 5. Is the manuscript presented in an intelligible fashion and written in standard English??> Reviewer #2: Yes Reviewer #3: Yes Reviewer #4: Yes ********** Reviewer #2: The manuscript addresses an important and clinically relevant topic. The integration of serum CST4 with routine laboratory indicators and machine learning approaches is interesting and has potential translational value. The authors have made considerable efforts to improve the manuscript, and many of the previous concerns have been adequately addressed. Nevertheless, a few issues still merit attention before the manuscript is considered for publication. External Validation The authors appropriately acknowledge the lack of external validation as a limitation. However, this remains the major challenge for clinical implementation. The discussion would benefit from a stronger emphasis that the current findings are based on internal validation only and that prospective multicenter validation is essential before the model can be applied in routine practice. Spectrum Bias Although the control group was carefully characterized, the retrospective case–control design may still lead to an overestimation of diagnostic performance. It would be helpful if the authors explicitly mention that model performance in real-world screening populations may be lower than that observed in the present study. Sample Size Considerations The additional explanation regarding events-per-variable is appreciated. However, EPV criteria were originally developed for traditional regression models and may not fully capture sample-size requirements for modern machine-learning algorithms. A brief acknowledgment of this limitation would strengthen the manuscript. Specificity of the Model The reported sensitivity is impressive and supports the potential use of the model as a rule-out tool. However, the specificity remains relatively modest. The authors may consider discussing the clinical implications of false-positive results and the possibility of optimizing decision thresholds in future studies. Missing Data Imputation The manuscript now provides information on the proportion of missing data and the imputation strategy. For reproducibility, additional details regarding the random forest imputation procedure would be valuable, including whether imputation was performed separately within the training and testing datasets. Hyperparameter Optimization The revised description of hyperparameter tuning is helpful. Nevertheless, providing additional details such as the gamma parameter, search ranges, and the overall tuning strategy would further enhance reproducibility. Reporting of Diagnostic Metrics While confidence intervals are provided for the AUC, it would be beneficial to report confidence intervals for sensitivity, specificity, PPV, and NPV as well. This would allow readers to better assess the precision of the reported estimates. Minor Editorial Issue The short title appears to refer to breast cancer diagnosis, whereas the manuscript focuses on gastrointestinal tumors. This seems to be an inadvertent editing error and should be corrected before publication. Overall Recommendation Overall, this is a well-conducted and clinically meaningful study. The authors have responded constructively to reviewer comments and substantially improved the manuscript. Addressing the points outlined above would further strengthen the scientific rigor, transparency, and clinical relevance of the work. Reviewer #3: The authors state in their response that feature selection was performed exclusively on the training dataset to avoid data leakage. However, the Methods section indicates that the dataset was randomly split into training and test sets after initial feature selection on the full dataset. Could the authors clarify the exact sequence of feature selection and data partitioning? If feature selection was performed before train–test splitting, there is a risk of data leakage that may have led to optimistic estimates of model performance. The authors provide an events-per-variable (EPV) justification for sample size adequacy. However, EPV criteria were originally developed for traditional regression-based models and may not fully address sample size requirements for machine-learning algorithms such as SVM, Random Forest, XGBoost, and neural networks. Could the authors further justify the adequacy of the sample size in the context of machine-learning model development and validation? The manuscript states that the calibration curve deviation of less than 5% confirms the absence of significant overfitting. Calibration performance alone may not be sufficient to exclude overfitting. The authors are encouraged to moderate this statement and indicate that the findings suggest limited evidence of overfitting rather than definitively demonstrating its absence. The response regarding cost reduction remains largely qualitative. While the authors estimate potential savings from reduced endoscopy use, no formal cost-effectiveness or health-economic analysis was performed. This limitation should be more clearly acknowledged, and conclusions regarding economic benefits should remain cautious. In the Results section, the manuscript states that “Projected performance of the model in different prevalence scenarios is summarized in Table ??” Please verify and correct this apparent placeholder or formatting error before publication. The manuscript focuses on gastrointestinal tumors; however, the submission metadata contains the short title “Machine Learning-Based Integration of Serum CST4 and Routine Laboratory Markers for Breast Cancer Diagnosis.” Although this may represent a submission-system artifact, the authors should carefully verify that no residual references to breast cancer remain anywhere in the manuscript, supplementary materials, figures, or metadata. Reviewer #4: � The manuscript states “The entire feature selection process was performed exclusively on the training set” but later states “The dataset was randomly split into a training set after initial feature selection on the full dataset.” These statements are contradictory. Authors must clearly specify: 1. Was train-test split performed first? 2. Were imputation, feature selection, correlation filtering, and scaling conducted only within the training data? 3. Was the test set completely untouched until final evaluation? A workflow diagram is strongly recommended. � The model was developed and tested in a single-center retrospective cohort only. Internal validation alone cannot establish generalizability. Authors must clearly specify: 1. Explicitly label the model as internally validated only. 2. Remove wording suggesting clinical deployment. 3. Add TRIPOD-AI compliant discussion of external validation requirements. � The control group is substantially different from cases: Tumor group mean age: 62.1 years; Control group mean age: 50.9 years. Age itself becomes a strong discriminator. The model may partially distinguish "older cancer patients" from "younger controls" rather than cancer from non-cancer. Require 1. Age- and sex-matched analysis 2. Stratified analysis by age categories 3. Sensitivity analysis excluding age as a predictor Without this, diagnostic performance may be overestimated. � The authors use the traditional EPV approach. EPV is not an accepted justification for modern machine-learning models. For: SVM, XGBoost, Random Forest and Neural Networks. EPV calculations are insufficient. Authors should Justify sample size using modern prediction-model methodology; Report optimism correction; Provide learning curves or bootstrap validation. � The dataset contains: 214 tumor cases 130 controls (62% prevalence). The manuscript does not state: Whether class weighting was used. Whether resampling was performed. Whether threshold optimization was used. � Thirty-eight biomarkers were compared between groups. Numerous univariate tests were performed without multiplicity correction. Apply Benjamini-Hochberg FDR correction or Bonferroni adjustment and report adjusted p-values. � Table 1 lacks Age comparison, Sex comparison, Tumor stage distribution, Histological subtype distribution. Yet these are likely major confounders. Add a comprehensive baseline characteristics table. � Only AUC confidence intervals are reported. Missing a few requirements like 95% CIs for: Sensitivity, Specificity, PPV, NPV. These are essential. � PPV/NPV Calculations Need Clarification. ********** what does this mean?). If published, this will include your full peer review and any attached files. If you choose “no”, your identity will remain anonymous but your review may still be made public. Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy Reviewer #2: Yes: Pritam Goswami Reviewer #3: No Reviewer #4: No ********** [NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.] To ensure your figures meet our technical requirements, please review our figure guidelines: https://journals.plos.org/plosone/s/figures You may also use PLOS’s free figure tool, NAAS, to help you prepare publication quality figures: https://journals.plos.org/plosone/s/figures#loc-tools-for-figure-preparation. NAAS will assess whether your figures meet our technical requirements by comparing each figure against our figure specifications. |
| Revision 2 |
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<p>Serum Cystatin 4 Combined with Routine Clinical Laboratory Indicators: A Support Vector Machine Diagnostic Model for Early Screening of Gastrointestinal Tumors PONE-D-26-02453R2 Dear Dr. Shen, We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements. Within one week, you’ll receive an e-mail detailing the required amendments. When these have been addressed, you’ll receive a formal acceptance letter and your manuscript will be scheduled for publication. An invoice will be generated when your article is formally accepted. Please note, if your institution has a publishing partnership with PLOS and your article meets the relevant criteria, all or part of your publication costs will be covered. Please make sure your user information is up-to-date by logging into Editorial Manager at Editorial Manager® and clicking the ‘Update My Information' link at the top of the page. For questions related to billing, please contact billing support. If your institution or institutions have a press office, please notify them about your upcoming paper to help maximize its impact. If they’ll be preparing press materials, please inform our press team as soon as possible -- no later than 48 hours after receiving the formal acceptance. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org. Kind regards, GV Narasimha Kumar Academic Editor PLOS One Additional Editor Comments (optional): Dear Authors, Thank you addressing all the reviewers' and editorial comments, and now the manuscript is scientifically justified for publication in the journal. Reviewers' comments: |
| Formally Accepted |
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PONE-D-26-02453R2 PLOS One Dear Dr. Shen, I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS One. Congratulations! Your manuscript is now being handed over to our production team. At this stage, our production department will prepare your paper for publication. This includes ensuring the following: * All references, tables, and figures are properly cited * All relevant supporting information is included in the manuscript submission, * There are no issues that prevent the paper from being properly typeset You will receive further instructions from the production team, including instructions on how to review your proof when it is ready. Please keep in mind that we are working through a large volume of accepted articles, so please give us a few days to review your paper and let you know the next and final steps. Lastly, if your institution or institutions have a press office, please let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, please inform our press team within the next 48 hours. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org. You will receive an invoice from PLOS for your publication fee after your manuscript has reached the completed accept phase. If you receive an email requesting payment before acceptance or for any other service, this may be a phishing scheme. Learn how to identify phishing emails and protect your accounts at https://explore.plos.org/phishing. If we can help with anything else, please email us at customercare@plos.org. Thank you for submitting your work to PLOS One and supporting open access. Kind regards, PLOS ONE Editorial Office Staff on behalf of Dr. GV Narasimha Kumar Academic Editor PLOS One |
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