https://orcid.org/0000-0002-7634-8279
Peer Review History
| Original SubmissionMay 22, 2024 |
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PONE-D-24-19155Functional analysis within latent states: A novel framework for analysing functional time series dataPLOS ONE Dear Dr. Forbes, 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 Oct 06 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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Kind regards, Yu Zhou 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 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. Thank you for stating the following financial disclosure: "Full list of funders: Australian Research Council Centre of Excellence for Mathematical and Statistical Frontiers, CE140100049, KM Statistical Society of Australia, PhD Scholarship, OF Queensland University of Technology, PhD Scholarship, OF International Biometrics Society, PhD Scholarship, OF" Please state what role the funders took in the study. If the funders had no role, please state: ""The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript."" If this statement is not correct you must amend it as needed. Please include this amended Role of Funder statement in your cover letter; we will change the online submission form on your behalf. 4. Please ensure that you refer to Figure 6 in your text as, if accepted, production will need this reference to link the reader to the figure. 5. 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. 6. Please update your submission to use the PLOS LaTeX template. The template and more information on our requirements for LaTeX submissions can be found at http://journals.plos.org/plosone/s/latex. [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: N/A ********** 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: PONE-D-24-19155 Review Functional analysis within latent states: A novel framework for analysing functional time series data The authors propose a nested approach to analyse EEG signals from a single electrode, Cz, using functional data analysis versions of HMM and PCA, in a large dataset, N = 503, of early adolescents aged 9–15. The paper is well written, although sometimes repetitive and with occasional claims without substantiation. Although I question the wisdom of naming a method flawless, the approach is methodologically sound and should find its way eventually into mainstream neuroimaging. However, there are several points which need to be addressed before accepting the paper, and some recommendations that would make the paper and method more attractive to the neuroimaging community. Comment 1 - major The authors describe the results but provide no interpretation with respect to neuroscience. How, for example, do these findings align or not with EEG results from other studies with children (e.g. ADHD) or adults (HMM analysis)? How are the canonical frequency bands related to psychopathy and cognition, and do the findings in this paper agree or challenge previous findings? Without some interpretation of the results, the paper may end up being considered interesting but irrelevant for many neuroscience researchers who are faced with a multitude of different methods to apply to their data. Comment 2 - major The authors choose to analyse the EEG signals from Cz (supplementary motor area and sensorimotor cortex, motor coordination, planning and execution) but regress the results against psychopathology and cognitive measures, the latter which are associated with prefrontal and frontal cortex. Re-running the analysis with Fp1/Fp2 would provide a higher level of credibility of the results, or alternativey, providing an explanation why Cz would capture signals related to prefrontal/frontal activity. Comment 3 - minor Abstract - The flawless framework offers superior flexibility and nuance. This is unsubstantiated and unnecessary. Comment 4 – minor Page 3 Ref 11 – date is missing in the reference. Ref 15 is a preprint and does not represent ‘common practice’ in EEG research. Comment 5 – minor Page 4 HMM … latent states – remove ‘dominant modes’ as these are relevant for FPCA. Comment 6 – minor Page 5 and others The use of ‘longitudinal’ is incorrect. The method can be applied to any time-varying functional data. Comment 7 – minor Page 5 ‘In this work… using regression of clustering approaches’. There is no methodology outlined in the paper for regression of clustering approaches. Comment 8 – minor Page 6 – repetition – remove ‘building a biobank’ Comment 9 – minor Page 7 and page 32 ‘predominantly allocated to each latent state’. ‘…mainly… This implies that individuals were allocated to multiple dominant states which I do not believe was the case. Comment 10 – minor Page 10 ‘clinical relevance’ – I believe this should be clinical utility i.e. it is easy to measure in the clinic. ‘choosing high quality measures’ – unsubstantiated. Comment 11 – minor Page 13 – Repetition – suggest removing ‘Differing from a …’ Comment 12 – minor Page 14 – ‘Visual identification’ and ‘averaged’. The method would be more robust if you could find an algorithmic way to distinguish the centroids. What are the implications of averaging the centroids for initiation? Comment 13 – minor Page 15 – What criteria did you use to ‘assess’ the scree plots? Also ‘on inspection’ – for what? Comment 14 – minor Page 16 and elsewhere – Reference to section 3.1 etc. which do not exist. Comment 15 – minor Page 17 – Table 1 EHQ is not defined, and the order of the abbreviations does not follow the order in the table. ‘FOOOF performance….’ What is this and why is it here? Comment 16 – minor Page 18 and elsewhere – Figure 2 in the text should be Figure 3, etc for all subsequent figures. Comment 18 – major Page 19 – Section ‘Comparing Psychopathology….’ And Figure 5. I would like to see ANOVAs on the psycho and cognitive measures across the 4 dominant state groups. The statements on contrasts among the groups is not statistically substantiated. Comment 19 – minor Page 23 and elsewhere - ‘individuals with higher scores...’ What scores – do the authors mean the FPCA weightings? Comment 20 – minor Page 26-31 – I would suggest putting Table 3 and 4 together so that readers can compare the regression results across State1 and State 3 dominance groups. Comment 21 – major Page 26 – I would suggest putting a brief summary of the results at the start of the section ‘Bayesian Regression…’ highlighting that FHMM dynamics were statistically associated with NIH Flanker in the State 1 group, and YSR Ext, YSR Int, SCARED SR, and NIH Pattern in the State 3 group. With the additional FPCA analysis, individual weightings were statistically associated with NIH Pattern, NIH Card, NIH Flanker and NIH List in the State 1 group, and weightings in the State 3 group were statistically associated with YSR Ext, YSR Int, SCARED SR, and NIH Flanker. These findings and the insights they provide should be discussed in the discussion section. Comment 22 – minor Page 32 – repetition – remove second paragraph of the discussion. Comment 23 – major Page 33 - ‘These regresions….’ This is a description of the results which should eb interpreted in the context of previous findings in EEG. ‘…FDA methods can offer…’ – the reference to support the claim comes from 2014 – and the claim is exaggerated. Comment 24 – minor Page 34 – ‘…decreased interpretability...’ – this is a critique of alternative methods, but the method in this paper lacks interpretation! Comment 25 – minor Page 35 – ‘… well validated’. Again, this statement is unsubstantiated. What type of validation are you referring to? Where are the citations for the validation? Inconsistency – dimension reduction, dimensional reduction – dimensionality reduction is more commonly used in neuroscience. ‘… significantly enhance our understanding…’ The results are descriptive – maybe contribute to the understanding otherwise the statement is an exaggeration. Reviewer #2: The manuscript titled “Functional analysis within latent states: A novel framework for analysing functional time series data” proposes a novel method “flawless” based on functional data analysis (FDA) of time series data. The proposed framework uses functional principal component analysis (FPCA) and functional hidden Markov model (fHMM) to identify latent states in EEG signals. The authors explore the relationship between the latent states and measures of psychopathology and cognitive function provided alongwith the EEG data. The authors approach to predict the latent states and their association with behavorial measures is interesting and of wide interest to the community. However I have some reservations about the manuscript mainly pertaining to the efficacy and presentation of the method. In the introduction section of the manuscript, there are hardly any mention of fda based methods for exploring brain signals. Specifically, authors should include previous work in EEG signals based of FDA, FPCA and its variants. The authors should also include studies on EEG classification using HMM latent states. Finally, the literature review should also include latest methods and results using the EEG data from Healthy Brain Network the authors use in the study. The literature review section in the manuscript in general needs to be re-written. The FDA portion of the method section is poorly written and requires more details. Given that this is primarily a method paper, the authors should elaborate on how a time series data is converted to a functional data and mention the assumptions and constraints underlying the functional data obtained from a time series. The authors should also specially mention that FDA works on only single channel and hence spatio-temporal latent states or signal analysis could not be performed with the proposed method. A pseudo code of the algorithm along with the framework as given in Figure 1 will also help the readers to better understand the steps involved in flawless and make it easier to implement. I have the most reservation on the results sections. Although the authors mention in the abstract that “compared to traditional multivariate statistical methods, the flawless framework superior flexibility and nuance”, but I find no demonstration of the author’s claim. Although the proposed algorithm looks promising, the authors failed to show its superior performance as the flawless is not compared with any other method. The authors must demonstrate that indeed flawless performance is better than traditional methods by comparing it with traditional methods and demonstrating the results. The authors could demonstrate the method’s performance when using the same algorithm but using time series data instead of functional data. Since the authors are using EEG data from a public database, they have to additionally demonstrate the superior performance of the proposed method when compared with other recent methods used on the same data. Finally, along with comparisons with traditional multivariate methods, the authors should also compare with recent FDA based methods. Overall the manuscript is interesting the manuscript is interesting and proposed framework looks efficient. However the manuscript needs improvement in the literature review section in the Introduction and the results using proposed methods needs to be compared with other state-of-the-art methods. ********** 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: Yes: Fran Hancock 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. |
| Revision 1 |
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PONE-D-24-19155R1Functional analysis within latent states: A novel framework for analysing functional time series dataPLOS ONE Dear Dr. Forbes, 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. ============================== ACADEMIC EDITOR: Kindly address the pending comments. ============================== Please submit your revised manuscript by May 15 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, 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: All comments have been addressed Reviewer #3: (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: (No Response) Reviewer #3: Yes ********** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: (No Response) Reviewer #3: 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 #1: (No Response) Reviewer #3: 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: (No Response) Reviewer #3: 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) 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 #1: Yes: Fran Hancock 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.
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| Revision 2 |
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Functional analysis within latent states: A novel framework for analysing functional time series data PONE-D-24-19155R2 Dear Dr. Forbes, 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, Hilary Izuchukwu Okagbue, Ph.D 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 #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 #1: Yes Reviewer #3: Yes ********** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #3: 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 #1: Yes Reviewer #3: 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 Reviewer #3: 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) 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 #1: Yes: Fran Hancock Reviewer #3: No ********** |
| Formally Accepted |
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PONE-D-24-19155R2 PLOS ONE Dear Dr. Forbes, 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. 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 Hilary Izuchukwu Okagbue Academic Editor PLOS ONE |
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