Peer Review History
| Original SubmissionApril 13, 2025 |
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PONE-D-25-18876 Predicting In-Hospital Mortality in ICU Patients with lymphoma Mellitus Using Machine Learning Models PLOS ONE Dear Dr. Lan, 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 Aug 08 2025 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. Please include the following items when submitting your revised manuscript:
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If you are unable to adhere to our open data policy, please kindly revise your statement to explain your reasoning and we will seek the editor's input on an exemption. Please be assured that, once you have provided your new statement, the assessment of your exemption will not hold up the peer review process. 4. 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 move it to the Methods section and delete it from any other section. Please ensure that your ethics statement is included in your manuscript, as the ethics statement entered into the online submission form will not be published alongside your manuscript. [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? The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented. Reviewer #1: Partly Reviewer #2: Partly ********** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: No ********** 3. Have the authors made all data underlying the findings in their manuscript fully available? The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified. Reviewer #1: Yes Reviewer #2: No ********** 4. Is the manuscript presented in an intelligible fashion and written in standard English? PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here. Reviewer #1: Yes Reviewer #2: Yes ********** 5. Review Comments to the Author Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters) Reviewer #1: 1. Regarding the outcome measure, while the study designates "in-hospital mortality" as the primary endpoint, further clarification on the temporal boundary of this definition would enhance the clinical interpretability of results. Given that mortality at different time points in ICU patients carries distinct clinical implications (e.g., 7-day mortality reflecting acute intervention efficacy, 28-day mortality indicating comprehensive treatment outcomes, and long-term mortality associated with underlying disease progression), it is recommended to reference the standard definitions in comparable studies and supplement the methodological rationale for time frame delineation. 2. Potential collinearity exists among variables selected by Lasso regression (e.g., BUN and Cr as renal function markers, platelet count and PT in coagulation function). Although Lasso regularization mitigates this issue, adding a correlation matrix would strengthen the argument for model robustness. Additionally, incorporating SHAP dependence plots or interaction value analyses to explore nonlinear interactions between key variables (e.g., BUN and platelet count) could provide richer evidence for clinical interpretation of model prediction mechanisms. 3. While baseline characteristics acknowledge the impact of multiple comorbidities, integrating a standardized comorbidity index (e.g., Charlson Index) to quantify comorbidity burden would systemize the risk factor analysis. As different comorbidities contribute differently to mortality, supplementing correlation analyses between comorbidity indices and death outcomes would enhance the clinical relevance of findings. Reviewer #2: Its my pleasure to review the manuscript titled "Predicting In-Hospital Mortality in ICU Patients with lymphoma Mellitus Using Machine Learning Models". The study develops and validates ML models for predicting in-hospital mortality in ICU patients with presumed lymphoma. While the methodology is generally sound and addresses a clinically relevant problem, critical terminology errors undermine the foundation of the work. Significant revisions are required before consideration for PLOS ONE. The AUC of 0.7766 is modest, and clinical applicability needs stronger justification. ________________________________________ The major Issues of the research included: 1. "Lymphoma Mellitus" is incorrect and non-existent. "Mellitus" specifically refers to diabetes (e.g., Diabetes Mellitus). The correct term is simply "Lymphoma". 2. The introduction could better emphasize the specific challenges of predicting mortality in lymphoma patients compared to the general ICU population (e.g., unique complications like tumor lysis syndrome, immunosuppression-related infections, specific organ involvement). The gap regarding ML for this specific subgroup is adequately stated. 3. The exclusion of 10,054 patients due to "missing values for all variables" (Fig 1) is unusual and concerning. It suggests potential selection bias. Were these patients truly missing every single variable collected? Clarification or rephrasing is needed (e.g., "missing key predictor or outcome variables"). 4. The long timeframe (2008-2019) introduces potential confounding from evolving ICU practices and lymphoma treatments over 11 years. This isn't addressed. 5. MIMIC-IV, while large, is single-center data (Beth Israel Deaconess MC). Generalizability to other settings may be limited, appropriately noted as a limitation. 6. While LASSO identified predictors, the justification for the initial set of variables extracted from MIMIC-IV is somewhat brief. Were lymphoma-specific variables (e.g., disease stage, type [Hodgkin/Non-Hodgkin], recent chemotherapy, presence of tumor lysis syndrome, neutropenia) considered or available? These are highly relevant to mortality risk in lymphoma patients. 7. The models only use admission/early ICU data. Interventions during the ICU stay (e.g., mechanical ventilation, vasopressors, dialysis, specific lymphoma treatments) are not included as potential predictors or confounders, significantly limiting the model's potential clinical applicability for dynamic risk assessment. This is a major omission. 8. The P-values in Table 1 require context. With 1591 patients, very small differences can become statistically significant. Emphasis should be on clinically meaningful differences. Reporting effect sizes (e.g., mean difference, Cohen's d for continuous; odds ratio for categorical) alongside P-values would be beneficial. Some variables (e.g., platelets, BUN) show large and clinically meaningful differences. 9. Details on hyperparameter tuning for the ML models (especially complex ones like CatBoost, NN) are lacking. Was tuning performed? How? This impacts performance and reproducibility. 10. The best model's AUC (0.7766) is modest for a clinical prediction model. While potentially better than traditional scores (though direct comparison isn't rigorously made), an AUC <0.8 often indicates limited clinical utility for individual prediction. This needs careful interpretation and tempering of claims about "high predictive performance" or "significant outperforming". 11. The description of data splitting for training/validation is unclear. Was a strict hold-out test set used after feature selection (LASSO) and hyperparameter tuning? Or was everything done within cross-validation folds? Preventing data leakage is crucial; the methodology section needs clarification. 12. The class imbalance (21.5% mortality) is acknowledged but the specific techniques used to handle it during model training (e.g., class weighting, sampling methods) are not described. This can significantly impact model performance, especially for metrics like F1-score. 13. Table 1 Presentation: Mixing "mean (SD)" and "Median (IQR)" formats for continuous variables without a clear rationale based on distribution (e.g., normality) is inconsistent. Variables like platelets and BUN are correctly presented as median (IQR) as they are skewed, but others (e.g., heart rate) presented as mean (SD) should be checked for normality or also presented as median (IQR) for consistency. Statistical tests (presumably t-tests/Wilcoxon, Chi-square/Fisher) used for Table 1 are not explicitly named. 14. P-value Interpretation: Reliance on P-values <0.05 in Table 1 without adjustment for multiple comparisons (e.g., Bonferroni, FDR) risks false positives. Given the large number of comparisons, discussing clinically significant differences is more important than purely statistical significance. 15. Missing Data: While median/mode imputation is common, the potential bias introduced by imputing missing values (especially if not missing at random - MAR) isn't discussed. The extent of missingness per variable before imputation isn't reported. 16. The discussion existed several shortcomings. (1) Overstatement of Performance: The modest AUC (0.7766) is not sufficiently critically discussed. Claims of "outstanding performance" or "significantly outperforming traditional methods" are not fully supported by the data presented (no direct comparison to SOFA/APACHE scores is shown). The clinical utility of an AUC of 0.7766 needs realistic appraisal. (2) Lymphoma Specificity: The discussion doesn't deeply engage with why lymphoma might pose unique prediction challenges compared to other ICU populations, or how the identified predictors might relate specifically to lymphoma pathophysiology beyond general critical illness (e.g., tumor burden impacting BUN/platelets, chemotherapy effects). (3) SHAP Utility: While SHAP is highlighted, the discussion could better elaborate on the concrete clinical value of the individual risk assessments (SHAP waterfall plots) shown in Fig 6. How would this directly change management? (4) ********** 6. PLOS authors have the option to publish the peer review history of their article (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: Feng SHEN ********** [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.] While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/ . PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org . 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| Revision 1 |
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<p>Predicting In-Hospital Mortality in ICU Patients with lymphoma Using Machine Learning Models PONE-D-25-18876R1 Dear Dr. Lan, 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, Chiara Lazzeri Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: |
| Formally Accepted |
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PONE-D-25-18876R1 PLOS ONE Dear Dr. Lan, 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. Chiara Lazzeri Academic Editor PLOS ONE |
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