Predicting congenital syphilis cases: A performance evaluation of different machine learning models

Igor Vitor Teixeira; Morgana Thalita da Silva Leite; Flávio Leandro de Morais Melo; Élisson da Silva Rocha; Sara Sadok; Ana Sofia Pessoa da Costa Carrarine; Marília Santana; Cristina Pinheiro Rodrigues; Ana Maria de Lima Oliveira; Keduly Vieira Gadelha; Cleber Matos de Morais; Judith Kelner; Patricia Takako Endo

doi:10.1371/journal.pone.0276150

Peer Review History

Original SubmissionSeptember 29, 2022
18 Nov 2022 Decision Letter - Anwar P.P. Abdul Majeed, Editor PONE-D-22-27034Predicting congenital syphilis cases: a performance evaluation of different machine learning modelsPLOS ONE Dear Dr. Endo, 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 Jan 02 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. 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If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references.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 If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice.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: Yes ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: 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 ****** 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 ****** 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 was written fairly well, however several issues need to be addressed to consider as a good technical paper. Abstract The number of dataset is not defined here as well as the technique of feature selection. The results defined was in general, without including statistical results. Result and Discussion The result obtain from the study is too low compared to reference [7]. ****** 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 ******** [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". 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Revision 1
5 Dec 2022 Author Response Reviewer #1: The paper was written fairly well, however several issues need to be addressed to consider as a good technical paper. Dear reviewer, we do appreciate your comments and suggestions to improve our work. We have addressed them properly. Abstract The number of dataset is not defined here as well as the technique of feature selection. In Section Data set, we described the number of data set and tables as follow: "We used nine tables with anonymized data provided by the PMCP, extracted from their information system, named SIS-MC. These tables contain clinical and sociodemographic data regarding antenatal care, pregnant women's outcomes, and their children, from the cities served by the PMCP in the State of Pernambuco, Brazil, between the years of 2013 and 2021 [...]". "Fig 1 illustrates the data pre-processing methodology designed to unify the nine tables provided by the PMCP into an unified dataset [...]". In the Section Data set, we updated Fig 1 to illustrate the unification of the multiple tables into a unique data set, called a unified data set. We also updated the URL of the pre-processed data set publicly available at Data Mendeley. In Section SFA models, we said: "In order to automatically find the best subset of attributes (feature selection) and the best model configuration (hyperparameter optimization), in a given search space, two techniques were applied: (i) SFA and(ii) grid search, respectively. For each combination of the grid search technique (Table 3 presents the hyperparameters used in the grid search), two flavors of the SFA technique were performed (SFS and SBS)." In Section Hyper-parameter optimization and feature selection techniques, we have described both techniques: "The SFS flavor starts with an empty subset of attributes; with each iteration, a new attribute is added, thereby selecting the attributes that increase the model's performance. On the other hand, the SBS flavor begins with a subset including all the attributes of the data set; with each iteration, different combinations of attributes are evaluated, and the attribute with the least impact on model performance is removed." The results defined was in general, without including statistical results. As we did not make repetitions in our experiments, we can not include statistical results in this current work. In total, we had 126 models that were trained using AWS resources and took too long to be finished (more than 5 months). Therefore, due to the time needed to retrain the models and understanding the relevance of this question, we have added statistical analysis as future work. Result and Discussion The result obtain from the study is too low compared to reference [7]. We did not understand this point. Our reference [7] is an nationwide epidemiological bulletin from the Brazilian Ministry of Health. We are not able to compare results, as our dataset is restricted to specific samples in only one state (Pernambuco) and [7] does not have prediction results. Attachments Attachment Submitted filename: Plos one syphilis reviewer.pdf https://doi.org/10.1371/journal.pone.0276150.r002
5 Feb 2023 Decision Letter - Anwar P.P. Abdul Majeed, Editor PONE-D-22-27034R1Predicting congenital syphilis cases: a performance evaluation of different machine learning modelsPLOS ONE Dear Dr. Endo, 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 22 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, Anwar P.P. Abdul Majeed Academic Editor PLOS ONE Journal Requirements: 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 #1: (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 ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: N/A ****** 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 ****** 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: 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 #1: The paper was written fairly well, however there is some issue need to be addressed to consider as a good technical paper. The author state that table 3 in refer to "the hyperparameters used in the grid search", however in the manuscript table 3 caption is "Baseline characteristics of the data set.". Please make an amendment for this table caption ****** 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 ******** [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. https://doi.org/10.1371/journal.pone.0276150.r003
Revision 2
14 Feb 2023 Author Response Reviewer #1: The author state that table 3 in refer to "the hyperparameters used in the grid search", however in the manuscript table 3 caption is "Baseline characteristics of the data set.". Please make an amendment for this table caption Dear reviewer, we do appreciate your comment and suggestions to improve our work. The overall baseline characteristics of the pre-processed data set related to the pregnant women assisted by the PMCP are presented in Table 3; and Table 4 presents the hyperparameters used in the grid search. Attachments Attachment Submitted filename: Plos one syphilis reviewer 2.pdf https://doi.org/10.1371/journal.pone.0276150.r004
28 Mar 2023 Decision Letter - Anwar P.P. Abdul Majeed, Editor Predicting congenital syphilis cases: a performance evaluation of different machine learning models PONE-D-22-27034R2 Dear Dr. Endo, 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, Anwar P.P. Abdul Majeed 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 ******** 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 ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: No ****** 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 ****** 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: 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 #1: (No Response) ****** 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 ******** https://doi.org/10.1371/journal.pone.0276150.r005
Formally Accepted
22 May 2023 Acceptance Letter - Anwar P.P. Abdul Majeed, Editor PONE-D-22-27034R2 Predicting congenital syphilis cases: a performance evaluation of different machine learning models Dear Dr. Endo: 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. Anwar P.P. Abdul Majeed Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0276150.r006

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