A hybrid feature extraction framework combining PCA and mutual information for gene expression based lung cancer classification

Syed Naseer Ahmad Shah; Kaartik Issar; Rafat Parveen

doi:10.1371/journal.pone.0342160

Peer Review History

Original SubmissionOctober 8, 2025
26 Dec 2025 Decision Letter - Suyan Tian, Editor Dear Dr. Shah, 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. A letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'. A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'. An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled 'Manuscript'. 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. 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There is no requirement to cite these works unless the editor has indicated otherwise. Additional Editor Comments: Please refine the methods section. Currently, the corresponding section is too long. Please split the results and dicussion into two sperate sections, and in the discussion section the current findings, the strengths and limitations of this study should be provided in detail. [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 ******** 2. Has the statistical analysis been performed appropriately and rigorously? -->?> Reviewer #1: Yes ****** 3. Have the authors made all data underlying the findings in their manuscript fully available??> The PLOS Data policy Reviewer #1: Yes ****** 4. Is the manuscript presented in an intelligible fashion and written in standard English??> Reviewer #1: Yes ****** Reviewer #1: The article is well written by the authors. The abstract needs to be modified. A flow diagram or schematic diagram of the work may be included. The Need for LASSO and its significance can be explained. Why PCA-MI is chosen for analysis instead of KL Divergence? MCC, Kappa and Dice coefficient may be included. The conclusion may be modified. ****** 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 ******** [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. https://doi.org/10.1371/journal.pone.0342160.r001
Revision 1
5 Jan 2026 Author Response 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: Yes Response: Dear reviewer thanks for the Acknowledgement. 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Response: Dear Reviewer, we are thankful for the appreciation for are statistical rigor. 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 Response: Dear Reviewer thanks for your appreciation ________________________________________ 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 Response: We thank the reviewer for this positive assessment. We have carefully proofread the revised version to correct any remaining typographical and grammatical errors. 5. Review Comments to the Author Reviewer #1 Comment: The article is well written by the authors. Response: Dear Reviewer thank you for the positive evaluation of our manuscript. Reviewer #1 Comment: The abstract needs to be modified. Response: Dear Reviewer, Thank you for this suggestion. The abstract has been revised to improve clarity and to better reflect the objectives, methodology, key results, and conclusions of the study. Reviewer #1 Comment: A flow diagram or schematic diagram of the work may be included. Response: Dear Reviewer, we thank you for the suggestion. A stepwise schematic diagram illustrating the complete workflow of the proposed methodology has been included in the manuscript (Figure 2) to enhance clarity and readability. Reviewer #1 Comment: The need for LASSO and its significance can be explained. Response: Dear Reviewer, Thank you for this valuable comment. We have added a detailed explanation of the motivation for using LASSO, highlighting its role in feature selection, dimensionality reduction, and prevention of overfitting in the revised manuscript in section 3.4 Comparative Analysis with Individual Feature Extraction Techniques. Reviewer #1 Comment: Why PCA-MI is chosen for analysis instead of KL Divergence? Response: Dear Reviewer, The rationale for selecting PCA-MI over KL Divergence has now been clearly explained in the revised manuscript, emphasizing the components preserved from PCA were ranked further by the MI scores that they achieved, which is an essential step in moving toward further tuning the features toward classification. (Refer Section 3.3) Reviewer #1 Comment: MCC, Kappa, and Dice coefficient may be included. Response: Dear Reviewer, we appreciate this suggestion. The Matthews Correlation Coefficient (MCC), Cohen’s Kappa, and Dice coefficient have now been included as additional performance evaluation metrics to provide a more comprehensive assessment of the model. (Refer section 4.4) Reviewer #1 Comment: The conclusion may be modified. Response: Dear Reviewer, Thank you for this comment. The Conclusion section has been revised to more clearly summarize the main findings, highlight the significance of the proposed approach, and outline potential future research directions. Attachments Attachment Submitted filename: Response to Reviewers.pdf https://doi.org/10.1371/journal.pone.0342160.r002
19 Jan 2026 Decision Letter - Suyan Tian, Editor A Hybrid Feature Extraction Framework Combining PCA and Mutual Information for Gene Expression based Lung Cancer Classification. PONE-D-25-54472R1 Dear Dr. Shah, 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, Suyan Tian Academic Editor PLOS One Additional Editor Comments (optional): Reviewers' comments: Reviewer's Responses to Questions Comments to the Author Reviewer #1: All comments have been addressed ******** 2. Is the manuscript technically sound, and do the data support the conclusions??> Reviewer #1: Yes ****** 3. Has the statistical analysis been performed appropriately and rigorously? -->?> Reviewer #1: Yes ****** 4. Have the authors made all data underlying the findings in their manuscript fully available??> The PLOS Data policy Reviewer #1: Yes ****** 5. Is the manuscript presented in an intelligible fashion and written in standard English??> Reviewer #1: Yes ****** Reviewer #1: All the corrections are included in the paper. Hence the manuscript does not need further review. The paper is well organized and well presented. ****** 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 ******** https://doi.org/10.1371/journal.pone.0342160.r003
Formally Accepted
Acceptance Letter - Suyan Tian, Editor PONE-D-25-54472R1 PLOS One Dear Dr. Shah, 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. Suyan Tian Academic Editor PLOS One https://doi.org/10.1371/journal.pone.0342160.r004

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