Peer Review History
Original SubmissionSeptember 6, 2023 |
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PONE-D-23-26242Application of Machine Learning to Predict Cognitive Deficits in HIV using Auditory and Demographic FactorsPLOS ONE Dear Dr. Niemczak, 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 18 2024 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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If the figure is no longer to be included as part of the submission please remove all reference to it within the text. 8. Please include captions for your Supporting Information files at the end of your manuscript, and update any in-text citations to match accordingly. Please see our Supporting Information guidelines for more information: http://journals.plos.org/plosone/s/supporting-information. [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: No Reviewer #2: Yes Reviewer #3: Yes ********** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: No Reviewer #2: Yes Reviewer #3: 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: No Reviewer #2: No 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: In this work, the authors try to predict cognitive deficits in HIV using auditory measurements and demographic factors. The methodology, results and conclusions presented by the authors are unsatisfactory, incoherent and do not meet the standards of a well conducted experimentation and study. This work is highly incremental i.e applying stock machine learning techniques to understand the predictive capability of auditory signals beyond demographic factors. The authors start by setting the objective of predicting neuro-cognitive deficits in patients living with HIV using auditory tests and demographic factors. However, the experiments conducted and results presented do not seem to provide any added value to the research field. In Table 2, the authors compare the performance of different machine learning methods for their task showing very modest gains that does not demonstrate the importance of those small gains in the overall objective. Also, it is unclear how this prediction relates to predicting cognitive deficits in PLWH vs healthy populations. In Figure 2, the shapely values for some of the variables are very different between gaussian naive bayes and kernel naive bayes methods which brings doubt in the model predictions. There has been no comment or further investigation provided on this observed phenomenon. Overall, the manuscript provides little added value and is not suitable for publication. The results are unsatisfactory, not adequately substantiated with evidence, does not address the key questions in the objective and is incoherent in several ways described above. Reviewer #2: Summary: The paper uses machine learning (ML) algorithms to predict cognitive deficits with auditory and demographic data. In 5 of 7 ML algorithms under testing, auditory data help improves the prediction performance over models only based on demographic data. Naive Bayes based models are the best performing models (ROC-AUC around 0.9), based on which the most important features for cognitive deficits are identified. Both the statistical analysis and interpretations look good. Please see the comments below: Major: In 2.1 Data collection - Cognitive Data Collection, does the cognitive impairment indicator variable (MoCA score<26) the only response variable this study focus on? Is the "two sample" in T-test and the "classification error" in Bhattacharyya algorithm based on the binary variable derived from MoCA score (<26)? The data collection was during 2017-2022, which include the sars-cov-2 pandemic period. Can the authors comments on if the data collection procedures before and after the pandemic was changed or not, if the visiting intervals of the subjects was also impacted? If yes, how would these factors influence the data and results? e.g. due to the pandemic, it is possible a subject has multiple visits before pandemic and 1 visit after pandemic, where the time interval of visits before pandemic are short while the one after the pandemic is much longer. The data of that after-pandemic single visit tends to have higher influence on the slope than the other visits before pandemic. Can the authors discuss more about why Naive Bayes models are performing better than the others? And does the strong assumption of naive bayes hold in this study? It seems the auditory variable trajectories are useful to predict cognitive function. Can the authors comment on is it interesting to predict the cognitive function trajectory instead of the final cognitive function? Ensemble model represents a large class of models, which one is tested in this paper? As is indicated in discussion, the HIV status is not a significant predictor for cognitive function. I think is makes more sense to not highlight HIV in title and abstract. After reading the title and abstract, my expectation was that there would be a section talking about how auditory and demographic factors can be used to predict cognitive deficits specifically caused by HIV. Minor: Typo "2.63 Data Collection" -> "2.1 Data Collection" In supplementary figure 1, it seems from N=557 to N=478, there are some additional exclusion criteria but the second paragraph of "2.1 Data Collection - Subjects" did not mention it. In supplementary figure 1, typo "Exlusionary" -> "Exclusionary" In supplementary figure 2, the feature names on y axis are missing. In Table 3, can the authors describe how was the p-values was calculated? Reviewer #3: The publication is well written; there is not really a lot of 'new research' with respect to machine learning, but this is an interesting use case. Under "main outcomes" the "area under the curve" should specify the AUC is for the receiver operational characteristic (ROC) curve, and the other metrics should be cited too (F1 and Yourdon). There are many references that describe problems or issues with the AUC measure, particularly for imbalanced data sets such as this one. Precision / recall curves would be a good complimentary measure too. The main reason for this issue is that the work is pretty straight forward but does show some level of utility, so gaining more insight into how well the concept might work would be useful. For this reason, I would also like to see the confusion matrices from the supplement inserted and worked into the main text as well, for this is often the best way to see the impact of selected thresholds (which translate ROC curves and PR curves into 'real world' impact). ********** 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. 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Revision 1 |
Machine Learning for Predicting Cognitive Deficits using Auditory and Demographic Factors PONE-D-23-26242R1 Dear Dr. Niemczak, 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. If you have any questions relating to publication charges, 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, Billy Morara Tsima, MD MSc 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 #2: All comments have been addressed Reviewer #3: 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 #3: (No Response) ********** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #2: Yes Reviewer #3: (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 #2: No Reviewer #3: (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 #2: Yes Reviewer #3: (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 #2: The revisions look good. All the questions have been answered well. I recommend accepting it for publication. Reviewer #3: (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 #2: No Reviewer #3: No ********** |
Formally Accepted |
PONE-D-23-26242R1 PLOS ONE Dear Dr. Niemczak, 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 If revisions are needed, the production department will contact you directly to resolve them. If no revisions are needed, you will receive an email when the publication date has been set. At this time, we do not offer pre-publication proofs to authors during production of the accepted work. Please keep in mind that we are working through a large volume of accepted articles, so please give us a few weeks 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. 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. Billy Morara Tsima Academic Editor PLOS ONE |
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