Peer Review History
| Original SubmissionDecember 19, 2024 |
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PONE-D-24-58388Diffusion-based skin disease data augmentation with detailed feature preservation and severity controlPLOS ONE Dear Dr. Kim, 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 Jun 13 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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Kind regards, Zeheng Wang Academic Editor PLOS ONE Journal Requirements: 1. When submitting your revision, we need you to address these additional requirements. 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 https://journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf 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, we expect all author-generated code to 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. 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. 4. Thank you for stating in your Funding Statement: This research was supported by the MSIT(Ministry of Science and ICT), Korea, under the ITRC(Information Technology Research Center) support program(IITP-2024-RS-2023-00258639) supervised by the IITP(Institute for Information \& Communications Technology Planning \& Evaluation). And, the present research has been conducted by the Research Grant of Kwangwoon University in 2024. Please provide an amended statement that declares *all* the funding or sources of support (whether external or internal to your organization) received during this study, as detailed online in our guide for authors at http://journals.plos.org/plosone/s/submit-now. Please also include the statement “There was no additional external funding received for this study.” in your updated Funding Statement. Please include your amended Funding Statement within your cover letter. We will change the online submission form on your behalf. 5. Please note that your Data Availability Statement is currently missing the repository name. If your manuscript is accepted for publication, you will be asked to provide these details on a very short timeline. We therefore suggest that you provide this information now, though we will not hold up the peer review process if you are unable. [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: Yes Reviewer #2: Partly Reviewer #3: Yes ********** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: No Reviewer #3: Yes ********** 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: Yes Reviewer #3: 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 Reviewer #3: 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: The paper “Diffusion-based skin disease data augmentation with detailed feature preservation and severity control” proposes a skin disease data augmentation technique based on a diffusion model, which solves the problem of data scarcity in skin disease diagnosis research through an improved stable diffusion model. In the study, an 8-channel variational autoencoder (VAE) module was introduced to enhance the model's representation ability in latent space, and multi-level embeddings techniques were used to preserve the detailed features of skin lesion areas. In addition, by combining pre trained segmentation and repair models with interpolation techniques, synthetic image generation of different disease severity levels has been achieved. In the classification experiment combining real and synthetic images, the average classification accuracy increased from 87% to 90%, verifying the effectiveness of this technology in alleviating the problem of medical data scarcity and improving diagnostic accuracy. Both the EFA Net model and the Diffusion based data augmentation model adopt innovative architectural designs to enhance performance. EFAM Net enhances feature extraction and fusion capabilities by introducing Attention Residual Learning ConvNeXt (ARLC) blocks, Parallel ConvNeXt (PCNXt) blocks, and Multi scale Efficient Attention Feature Fusion (MEAFF) blocks, particularly in multi-scale feature fusion and attention mechanisms, achieving high accuracy in skin lesion classification tasks. The Diffusion based model improves the Stable Diffusion model by using an 8-channel Variational Autoencoder (VAE) and multi-level embedding techniques, effectively enhancing the quality of image generation and detail preservation. At the same time, it controls the severity of diseases through segmentation masks and interpolation techniques, providing high-quality synthetic images for skin lesion data enhancement. The EFAM Net model focuses on the classification task of skin lesion images, enhancing feature extraction and fusion capabilities by designing ARLC blocks, PCNXt blocks, and MEAFF blocks. It performs particularly well in handling complex skin lesion features and can achieve classification accuracy of over 93% on multiple public datasets. The Diffusion based model focuses on solving the problem of scarce data on skin lesions. By improving the Stable Diffusion model and using 8-channel VAE and multi-level embedding techniques to generate high-quality composite images, and controlling the severity of the disease through segmentation masks and interpolation techniques, it performs well in image generation quality and detail preservation, significantly improving the effectiveness of composite data in classification tasks. Need to provide source code and dataset in a link. However, the shortcomings of this paper include: 1. Insufficient diversity of synthesized images: In some cases, synthesized images may overly emphasize certain details and features (such as hair areas or specific color information), resulting in images that are not natural enough and affecting the diversity and authenticity of synthesized data 2. Limitations of normal image generation: When generating normal skin areas, if there are significant differences between the lesion area and the surrounding background, it may result in the inability to generate completely realistic normal images, limiting the application of the model in certain scenarios. 3. Limitations of evaluation indicators: Although commonly used indicators such as FID and IS are used to evaluate the quality of synthesized images, these indicators show certain limitations in medical image synthesis tasks and cannot fully reflect the actual contribution of generated data to downstream diagnostic tasks. References: Ji, Z., Wang, X., Liu, C., et al. (2024). "EFAM-Net: A Multi-Class Skin Lesion Classification Model Utilizing Enhanced Feature Fusion and Attention Mechanisms." IEEE Access, 12, 143029-143041. DOI: 10.1109/ACCESS.2024.3468612 Reviewer #2: This paper presents a synthetic data augmentation strategy designed to enhance skin disease lesion diagnostic models. The authors employ an innovative technique utilizing multi-level CLIP embeddings, effectively capturing realistic lesion details for fine-grained control over realistic synthetic variations. Additionally, they use latent space manipulation as a clever means to simulate varying lesion severity levels. Their method demonstrates improved classification accuracy across multiple models; however, the observed improvements are modest (3%). Furthermore, the manuscript currently contains certain ambiguities in its description and methodology that should be clarified to strengthen the overall narrative and reproducibility. The following summarizes the Reviewer’s comments/concerns: - The introduction does not sufficiently motivate the clinical importance of skin disease diagnosis. The authors could strengthen this section by briefly discussing the prevalence and diagnostic challenges of skin diseases, highlighting current diagnostic methods and their limitations, and incorporating relevant examples from recent literature to clearly position their synthetic data augmentation approach. - The study uses a dataset of dermoscopy images but only provides class names. The authors should include brief clinical descriptions and key morphological characteristics of each class to enhance clarity and provide better context. - The authors should clarify how the 5-scale CLIP embeddings are derived, as the current explanation lacks detail. While ELITE is referenced, a brief description within the relevant section would improve completeness and accessibility for readers unfamiliar with the method. - The authors should provide more details on the inference process of their latent diffusion model. While Stable Diffusion is originally designed for text-to-image generation, this work leverages multi-level CLIP embeddings to preserve fine-grained details. Is this the sole conditioning mechanism, or are additional factors, such as class labels, incorporated? - The authors briefly mention DDIM in the related works section, however it is not mentioned again. It should be explicitly mentioned that DDIM is used during inference. - Latent space manipulation assumes the generated lesion corresponds to the highest severity level, but this may not always be the case. Could the authors clarify how severity levels are defined in the latent space and whether any constraints or validation steps ensure a consistent and accurate progression of severity? - The 8-channel VAE is evaluated using LPIPS and MS-SSIM for reconstruction, but its impact on the latent space is not assessed. Increasing VAE channels enlarges the latent representation and UNet, potentially improving performance but at a higher computational cost. An alternative is increasing input resolution while maintaining the same downsampling ratio, expanding the latent space without modifying the architecture. An ablation study comparing these approaches would be necessary to better justify the choice of an 8-channel VAE. - The proposed LDM is compared against Stable Diffusion as a baseline, but it is unclear how it was adapted to align with the study's objectives. The authors should provide more details on any modifications made, including changes to conditioning mechanisms and training procedures to ensure a fair and meaningful comparison. - The classification performance evaluation focuses on relatively shallow networks. Is there a reason deeper or transformer-based models were not considered? Given their improved feature extraction capabilities, could they bridge the 3% gap even without synthetic data augmentation? A complete justification and explanation is necessary Minor Issues: ● \mathcal{} should be used to properly format variables. ● Starting sentences with “And” should be avoided for better readability. ● LPIPS and MS-SSIM are both missing citations. Reviewer #3: 1. The model’s performance is validated exclusively on the HAM10000 dataset, which may not capture the full variability of skin conditions across populations and imaging conditions. If possible, broader validation on diverse datasets may help to establish generalizability. 2. The study lacks comprehensive ablation experiments to evaluate the individual impact of architectural choices (e.g., multi-level embeddings, adapter layers). This omission limits the interpretability and reproducibility of the work. 3. The background section would benefit from the addition of other relevant medical literature, such as "Advancing Precision Medicine: VAE Enhanced Predictions of Pancreatic Cancer Patient Survival in Local Hospital", to strengthen its persuasiveness. ********** 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: No Reviewer #3: 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.] 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. Please note that Supporting Information files do not need this step. |
| Revision 1 |
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PONE-D-24-58388R1Diffusion-based skin disease data augmentation with fine-grained detail preservation and interpolation for data diversityPLOS ONE Dear Dr. Yoo, 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 Sep 05 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:
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. We look forward to receiving your revised manuscript. Kind regards, Zeheng Wang Academic Editor PLOS ONE Journal Requirements: 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. 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. [Note: HTML markup is below. Please do not edit.] Reviewers' comments: Reviewer's Responses to Questions Comments to the Author 1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation. Reviewer #2: All comments have been addressed Reviewer #4: All comments have been addressed Reviewer #5: All comments have been addressed ********** 2. 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 #2: Yes Reviewer #4: Yes Reviewer #5: Yes ********** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #2: Yes Reviewer #4: Yes Reviewer #5: Yes ********** 4. 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 #2: (No Response) Reviewer #4: Yes Reviewer #5: Yes ********** 5. 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 #2: Yes Reviewer #4: Yes Reviewer #5: Yes ********** 6. 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 #2: The authors have addressed most of the major concerns in this revised manuscript. They have added additional implementation details, an ablation study, and more experiments for downstream classification on deeper transformer-based architectures. A minor remaining concern is the use of the term 'proxy severity level.' While an improvement over 'severity control,' the term 'proxy' implies an indirect measure that has been validated to correlate with the ground truth. As the authors rightly acknowledge, the proposed latent space interpolation method does not capture the multifaceted nature of clinical severity and has not been validated as such. I recommend replacing all instances of 'proxy severity level' with a more accurate and defensible term, such as the one used in the rebuttal: 'latent space interpolation for enhanced data diversity.' Reviewer #4: (No Response) Reviewer #5: This manuscript presents an innovative diffusion-based data augmentation method designed to improve the diversity and quality of synthetic dermoscopic images for skin disease classification. By enhancing the Stable Diffusion framework with an 8-channel variational autoencoder and multi-level CLIP visual embeddings, the authors aim to better preserve fine-grained lesion details. Additionally, they introduce a proxy severity interpolation strategy to simulate varying lesion intensities. The study is technically sound, and the authors have made meaningful revisions in response to previous reviewer comments, including improvements to the clinical motivation, dataset descriptions, and method transparency. Despite these strengths, several key concerns remain. First, the notion of “proxy severity” lacks sufficient empirical support. While the authors acknowledge that the interpolation does not represent clinically validated severity levels, no evaluation—either quantitative or by domain experts—is provided to demonstrate the interpretability or utility of these interpolated images. This weakens the claim that the generated data can aid in simulating disease progression or augmenting rare severity classes. Second, the study is limited to a single dataset (HAM10000), which restricts its generalizability. Although the authors discuss the limitations of existing public datasets, even a small-scale test on a secondary dataset (e.g., PH2 or ISIC) would help establish broader relevance. Additionally, while multiple classifier backbones are tested, the evaluation primarily focuses on shallow models. It remains unclear whether performance improvements would persist with more powerful architectures that could compensate for limited data without augmentation. The ablation study adds value but does not fully isolate the contributions of each component, such as adapter layers or class-conditioning strategies. Furthermore, the choice to expand VAE channels rather than image resolution is justified based on computational constraints, yet no comparative results are shown. More concrete evidence on the trade-offs between spatial resolution and latent dimensionality would be useful. Evaluation metrics are another concern. The continued reliance on FID and IS—despite acknowledging their limitations in medical imaging—underscores the need for more appropriate alternatives. Even a basic human visual assessment or task-based evaluation (e.g., classification accuracy using only synthetic images) would strengthen the argument that these images are diagnostically useful. ********** 7. 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 #2: No Reviewer #4: No Reviewer #5: 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.] 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. Please note that Supporting Information files do not need this step. |
| Revision 2 |
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Diffusion-based skin disease data augmentation with fine-grained detail preservation and interpolation for data diversity PONE-D-24-58388R2 Dear Dr. Yoo, 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, Zeheng Wang Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: |
| Formally Accepted |
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PONE-D-24-58388R2 PLOS ONE Dear Dr. Yoo, 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. Zeheng Wang Academic Editor PLOS ONE |
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