Understanding and predicting COVID-19 clinical trial completion vs. cessation

Magdalyn E. Elkin; Xingquan Zhu

doi:10.1371/journal.pone.0253789

Peer Review History

Original SubmissionApril 6, 2021
4 May 2021 Decision Letter - Thippa Reddy Gadekallu, Editor Transfer Alert This paper was transferred from another journal. As a result, its full editorial history (including decision letters, peer reviews and author responses) may not be present. PONE-D-21-11234 Understanding and Predicting COVID-19 Clinical Trial Completion vs. Cessation PLOS ONE Dear Dr. Zhu, 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. Based on the comments received from the reviewers and my own observation, I suggest major revisions for the paper. Please submit your revised manuscript by Jun 18 2021 11:59PM. 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[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 ******** 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: No ****** 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. In Introduction section, the drawbacks of each conventional technique should be described clearly. 2. Introduction needs to explain the main contributions of the work more clearly. 3. The authors should emphasize the difference between other methods to clarify the position of this work further. 4. The Wide ranges of applications need to be addressed in Introductions 5. The objective of the research should be clearly defined in the last paragraph of the introduction section. 6. The authors can cite the following references. Analysis of dimensionality reduction techniques on big data. Deep learning and medical image processing for coronavirus (COVID-19) pandemic: A survey. An Incentive Based Approach for COVID-19 planning using Blockchain Technology. Reviewer #2: Please re structure the paper format 1. What are the limitations of the existing literature? 2. List out the main contributions of the current work. Visit this profile and cite couple of related papers: https://scholar.google.com/citations?user=dz4QKZIAAAAJ&hl=en 3. There are many typos and grammatical errors in the paper. The authors have to carefully proofread the paper to address them. 4. Summarize the related works section with a table. 5. Present a detailed analysis of the results obtained. 6. Discuss about the limitations and future scope of the present work. ****** 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. 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Revision 1
28 May 2021 Author Response The major changes of this revision are summarized as follows: • We added additional information to the Introduction section and ensured a clear statement of our study objective. • A new subsection Related Work was added to the Introduction to discuss related research and compare the existing research to our current study. • Table 1 was added in subsection Related Work to present a graphical summary and comparison between existing methods and proposed research. • We have added a subsection Contribution to the Introduction to summarize our current study's contribution. The main contributions of our study are as follows: o COVID-19 clinical trial benchmark: Our research delivers a COVID-19 benchmark for clinical trial completion vs. cessation study. The benchmark, including features and supporting documents, are published online for public access. o Clinical trial features: Our research proposes the most extensive set of features for clinical trial reports, including features to model trial administration, study information and design, eligibility, keywords, and drugs etc. In addition, our research also uses embedding features to model unstructured free texts in clinical trial reports for prediction. o Predictive modeling of COVID-19 trials: Our research is the first effort to model COVID-19 clinical trial completion vs. cessation. By using ensemble learning and sampling, our model achieves over 0.87 AUC scores and over 0.81 balanced accuracy for prediction, indicating high efficacy of using computational methods for COVID-19 clinical trial prediction. • In the revision, we introduced Friedman statistical tests to determine the statistical difference between ensemble classifiers tested over the different combinations of features. To give background information on the statistical test, a subsection Statistical Tests was added to the COVID-19 Clinical Trial Prediction section to explain the Friedman test and Nemenyi post hoc test. • Results from Friedman test and Nemenyi post hoc test are reported in COVID-19 Clinical Trial Prediction section. Figure 15 was added to show the critical difference diagrams for ensemble models' Balanced accuracy, F1, and AUC scores. • To simplify the results, we only display average performance comparisons between single models vs. ensemble models using all features. • The last paragraph of the result section presents an itemized list to clearly summarize the major findings from our experimental results. • We have gone carefully through the paper and fixed spelling and grammatical errors. In the revision summary, we provide detailed responses to all the comments from the reviewers. The text in italics is taken verbatim from the reviewers’ comments, and the roman text is our response. Attachments Attachment Submitted filename: COVID_19_Clinical_Trials_PLOS_One_Revision_Sumary___R1_.pdf https://doi.org/10.1371/journal.pone.0253789.r002
14 Jun 2021 Decision Letter - Thippa Reddy Gadekallu, Editor Understanding and Predicting COVID-19 Clinical Trial Completion vs. Cessation PONE-D-21-11234R1 Dear Dr. Zhu, 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, Thippa Reddy Gadekallu Academic Editor PLOS ONE Additional Editor Comments (optional): 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 #1: All comments have been addressed Reviewer #2: (No Response) ******** 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 #1: Yes Reviewer #2: (No Response) ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: (No Response) ****** 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 #1: Yes Reviewer #2: (No Response) ****** 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 #1: (No Response) Reviewer #2: (No Response) ****** 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 #1: I have gone the revised paper, the authors have addressed all my comments, paper can be accepted in the current form Reviewer #2: Author has submitted all the recommendations I am happy to accept the paper for publication. ****** 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 #1: No Reviewer #2: No https://doi.org/10.1371/journal.pone.0253789.r003
Formally Accepted
29 Jun 2021 Acceptance Letter - Thippa Reddy Gadekallu, Editor PONE-D-21-11234R1 Understanding and Predicting COVID-19 Clinical Trial Completion vs. Cessation Dear Dr. Zhu: 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 Dr. Thippa Reddy Gadekallu Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0253789.r004

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