Interpretable, non-mechanistic forecasting using empirical dynamic modeling and interactive visualization

Lee Mason; Amy Berrington de Gonzalez; Montserrat Garcia-Closas; Stephen J. Chanock; Blànaid Hicks; Jonas S. Almeida

doi:10.1371/journal.pone.0277149

Peer Review History

Original SubmissionOctober 19, 2022
23 Jan 2023 Decision Letter - Zakariya Yahya Algamal, Editor PONE-D-22-28854Interpretable, non-mechanistic forecasting using empirical dynamic modeling and interactive visualizationPLOS ONE Dear Dr. Mason, 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 Mar 09 2023 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: A rebuttal 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. 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, Zakariya Yahya Algamal, PhD 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 https://journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf 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. 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: Yes ******** 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: Yes ****** 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. Abstract should be rewritten correctly with more details about proposed and used methods. 2. Methods section doesn't have sufficient details and basic equations about proposed methods. 3. In results section, statistical error measurements should be used for comparing the accuracy of result and inserted into tables. 4. Conclusions should be rewritten in more appropriate contents. Reviewer #2: The authors provided a web-application as a tool to produce the interpretations of non-mechanistic forecasts using Empirical Dynamic Modelling and interactive visualization. This tool is based on empirical dynamic modelling (EDM), a simple and intuitive non-mechanistic technique with four interactive plots. They made this tool available online for researchers and more details. Results, discussions and the statistical method used have been introduced. The manuscript is technical without theoretical contribution. Novelty resides in providing a web-application. In my opinion, the manuscript is interesting idea and scientifically coherent. It tackles an important issue. The state of the literature in the background is comprehensive and the related work is adequately cited. However, I find : Difficulty in following all the information in the manuscript due to the presentation is not very clear to me. The proposed tool should represent by an algorithm. It is not easy to understand the methodology of the tool through textual narration. I encourage the authors to spend more time in the section on Methods to present the details through a mathematical framework, as well as, for the mathematical notations. The authors full name in the reference should be included. For example, in reference (11) there are missing authors' names. Finally, the details of interactive visualization are not presented as well. ****** 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 ******** [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. Attachments Attachment Submitted filename: revew2.pdf https://doi.org/10.1371/journal.pone.0277149.r001
Revision 1
23 Feb 2023 Author Response Dear Dr. Algamal, Thank you for inviting us to re-submit our work to PLOS ONE. We would also like to thank you and the reviewers for taking the time to consider our manuscript and provide helpful feedback. We are very grateful for the insightful comments raised by the reviewers, and we hope that the revised manuscript is suitable for publication in your journal. Below, we have listed the suggestions and the changes we made in response: • “Difficulty in following all the information in the manuscript due to the presentation is not very clear to me.” (Reviewer 2) We have updated several parts of the manuscript to improve clarity, especially the methods and results sections. • “The proposed tool should represent by an algorithm. It is not easy to understand the methodology of the tool through textual narration.” (Reviewer 2) • “I encourage the authors to spend more time in the section on Methods to present the details through a mathematical framework, as well as, for the mathematical notations.” (Reviewer 2) • “Methods section doesn't have sufficient details and basic equations about proposed methods.” (Reviewer 1) In the methods section, we have moved many of the inline equations to their own lines, and updated the surrounding narration to clarify the role each equation plays in the tool. • “Finally, the details of interactive visualization are not presented as well.” (Reviewer 2) A very helpful comment, and we agree completely that a specific account of the interactive plots was missing in the original manuscript. To remedy this, we have re-written and expanded much of the results section, specifically to include more details of the interaction. • “The authors full name in the reference should be included. For example, in reference (11) there are missing authors' names.” (Reviewer 2) The references in our report are in the Vancouver style, as suggested by the PLOS ONE guidelines. The Vancouver style has a unique way of representing authors name where their last name is followed by their initials, without periods between the initials (e.g. for me it would be Mason LK). We (myself and another co-author) were unfamiliar with this style prior to submission but we have re-checked the references and we believe they adhere to this style. Regarding reference (11) in particular, the name “Pe’er G” perhaps appears abbreviated, but that is the spelling listed on the paper. • “Abstract should be rewritten correctly with more details about proposed and used methods.” (Reviewer 1) We have re-written the abstract to include a specific reference to the methods used (empirical dynamic modelling) and the methods proposed (the interactive dashboard and the shaded forecasting area based on kernel density estimation). • “In results section, statistical error measurements should be used for comparing the accuracy of result and inserted into tables.” (Reviewer 1) In the results section, we have now included a link to a notebook which compares the accuracy of the kernel density estimation method to some basic benchmarks. We have also included a tabular form of these comparisons (for the default data) in Supporting Information S1; this is also referenced in the results section. • Conclusions should be rewritten in more appropriate contents. (Reviewer 1) We have rewritten the conclusion paragraph so that it relates better to the rest of the manuscript. Once again, we’d like to thank the reviewers for these helpful comments. We are delighted to have to resubmit this paper with the suggested changes. We look forward to hearing your response. Sincerely, Lee Mason Division of Cancer Epidemiology and Genetics, National Cancer Institute 9609 Medical Center Drive, Rockville, Maryland 20850 Email: masonlk@nih.gov Attachments Attachment Submitted filename: Response To Reviewers.docx https://doi.org/10.1371/journal.pone.0277149.r002
16 Mar 2023 Decision Letter - Zakariya Yahya Algamal, Editor Interpretable, non-mechanistic forecasting using empirical dynamic modeling and interactive visualization PONE-D-22-28854R1 Dear Dr. Mason, 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 for payment will follow shortly after the formal acceptance. To ensure an efficient process, please log into Editorial Manager at http://www.editorialmanager.com/pone/, click the 'Update My Information' link at the top of the page, and double check that your user information is up-to-date. If you have any billing related questions, please contact our Author Billing department directly at authorbilling@plos.org. 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, Zakariya Yahya Algamal, PhD Academic Editor PLOS ONE Additional Editor Comments (optional): The authors have adequately addressed all the comments raised in a previous round of review. 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 ******** 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 ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #2: 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: 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 ****** 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 methods used in the study are appropriate and well-described. The discussion section provides an in-depth interpretation of the results. ****** 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 ******** https://doi.org/10.1371/journal.pone.0277149.r003
Formally Accepted
23 Mar 2023 Acceptance Letter - Zakariya Yahya Algamal, Editor PONE-D-22-28854R1 Interpretable, non-mechanistic forecasting using empirical dynamic modeling and interactive visualization Dear Dr. Mason: I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now with our production department. 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. If we can help with anything else, please email us at plosone@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 Professor Zakariya Yahya Algamal Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0277149.r004

Open letter on the publication of peer review reports

PLOS recognizes the benefits of transparency in the peer review process. Therefore, we enable the publication of all of the content of peer review and author responses alongside final, published articles. Reviewers remain anonymous, unless they choose to reveal their names.

We encourage other journals to join us in this initiative. We hope that our action inspires the community, including researchers, research funders, and research institutions, to recognize the benefits of published peer review reports for all parts of the research system.

Learn more at ASAPbio .