PONE-D-22-26132ARTIFICIAL DRAGONFLY ALGORITHM IN THE HOPFIELD NEURAL NETWORK FOR  BOOLEAN k SATISFIABILITY REPRESENTATIONPLOS ONE

Dear Dr. ABUBAKAR,

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.

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ACADEMIC EDITOR: Dear authors, please carefully revise proposed manuscript according to all reviewers' comments and my comments. Additionally, according to PLOSONE journal policy, please make sure that your source code is available. I suggest you to use the data archiving tool Zenodo and generate doi which will be included in the revised version of the manuscript. 

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Please submit your revised manuscript by May 04 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,

Nebojsa Bacanin

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.

2. Thank you for stating the following financial disclosure:

“The authors are thankful to the Deanship of Scientific Research at Najran University for funding this work under the Research Collaboration Funding program grant coder NU/RC/SERC/11/5 and they are thankful to the registrar Univeristi Tun Hussein Onn Malaysia.”

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.

3. Thank you for stating the following in the Acknowledgments/ Funding Section of your manuscript:

“The authors are thankful to the Deanship of Scientific Research at Najran University for funding this work under the Research Collaboration Funding program grant coder NU/RC/SERC/11/5 and they are thankful to the registrar Univeristi Tun Hussein Onn Malaysia.”

We note that you have provided funding information that is not currently declared in your Funding Statement. However, funding information should not appear in the Acknowledgments section or other areas of your manuscript. We will only publish funding information present in the Funding Statement section of the online submission form.

Please remove any funding-related text from the manuscript and let us know how you would like to update your Funding Statement. Currently, your Funding Statement reads as follows:

 “The authors are thankful to the Deanship of Scientific Research at Najran University for funding this work under the Research Collaboration Funding program grant coder NU/RC/SERC/11/5 and they are thankful to the registrar Univeristi Tun Hussein Onn Malaysia.”

Please include your amended statements within your cover letter; we will change the online submission form on your behalf.

4. Thank you for stating the following in the Competing Interests section:

“The authors are thankful to the Deanship of Scientific Research at Najran University for funding this work under the Research Collaboration Funding program grant coder NU/RC/SERC/11/5 and they are thankful to the registrar Univeristi Tun Hussein Onn Malaysia”

Please confirm that this does not alter your adherence to all PLOS ONE policies on sharing data and materials, by including the following statement: ""This does not alter our adherence to  PLOS ONE policies on sharing data and materials.” (as detailed online in our guide for authors http://journals.plos.org/plosone/s/competing-interests).  If there are restrictions on sharing of data and/or materials, please state these. Please note that we cannot proceed with consideration of your article until this information has been declared.

Please include your updated Competing Interests statement in your cover letter; we will change the online submission form on your behalf.

5. In your Data Availability statement, you have not specified where the minimal data set underlying the results described in your manuscript can be found. PLOS defines a study's minimal data set as the underlying data used to reach the conclusions drawn in the manuscript and any additional data required to replicate the reported study findings in their entirety. All PLOS journals require that the minimal data set be made fully available. For more information about our data policy, please see http://journals.plos.org/plosone/s/data-availability.

Upon re-submitting your revised manuscript, please upload your study’s minimal underlying data set as either Supporting Information files or to a stable, public repository and include the relevant URLs, DOIs, or accession numbers within your revised cover letter. For a list of acceptable repositories, please see http://journals.plos.org/plosone/s/data-availability#loc-recommended-repositories. Any potentially identifying patient information must be fully anonymized.

Important: If there are ethical or legal restrictions to sharing your data publicly, please explain these restrictions in detail. Please see our guidelines for more information on what we consider unacceptable restrictions to publicly sharing data: http://journals.plos.org/plosone/s/data-availability#loc-unacceptable-data-access-restrictions. Note that it is not acceptable for the authors to be the sole named individuals responsible for ensuring data access.

We will update your Data Availability statement to reflect the information you provide in your cover letter.

Additional Editor Comments:

Dear Authors,

please revise proposed manuscript thoroughly according to all reviewers' comments.

Additionally, please do the following:

- In introduction section you must clearly state what is beyond state-of-the-art in proposed study.

- Statistical tests must be conducted to validate that the improvements of proposed approach are statistically significant in terms of employed performance metrics.

- Figures qualities must be improved. For examples, figs 1 and 2 look like they were taken from other source as it is. If this is the case, please generated your own images.

- I would suggest including more methods in comparative analysis.

- In the conclusion section you should clearly state what are practical and theoretical implications, as well as limitations of proposed study.

- References must be updated with more recent and relevant ones.

All the best,

Nebojsa Bacanin

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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

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2. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: No

Reviewer #2: Yes

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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

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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

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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. Is there any particular reason why the entire text is highlighted in yellow? It made reading very hard.

2. Avoid using acronyms in the abstract.

3. Introduction is too long. Separate it into Introduction and Literature review, two distinctive sections.

4. Paragraphs are too long as well, consider breaking them in smaller units.

5. State the research question clearly in the Introduction.

6. List the main contributions clearly in the Introduction (they are present, but should be emphasized more, for example like a list).

7. The literature review could be expanded, consider adding the following references that deal with dragonfly algorithm, and also ANN optimization by metaheuristics:

https://www.sciencedirect.com/science/article/abs/pii/S2210537922000506

https://www.sciencedirect.com/science/article/abs/pii/S0003682X21002152

https://link.springer.com/chapter/10.1007/978-981-15-8530-2_63

https://link.springer.com/article/10.1007/s00521-022-06946-7

https://www.mdpi.com/1996-1073/16/3/1434

8. Make sure that each parameter in every equation has been explained in the text.

9. Overall quality of figures should be improved - especially flowchart (fig. 2).

10. Discuss more why you have selected dragonfly - as there are numerous other metaheuristics algorithms.

11. Discuss the limitations of the proposed method in more details.

12. Elaborate more on the simulation setup - also give the results in tabular form (not only by graphs and charts).

Reviewer #2: In this paper, a hybrid computational method combining the artificial dragonfly algorithm (ADA) with the Hopfield neural network techniques for optimal Exact k Satisfiability representation is presented.

Several issues in this paper need to be addressed before publication:

The paper requires some reorganization. In the Introduction section, it is important to provide a brief overview of the topic addressed in the paper, along with a concise description of the main contributions, which are currently listed but need to be explained in greater detail. Additionally, a new section entitled "Related Work" should be added to the paper, which will include a description of previously used methodologies and systems that are currently part of the Introduction section.

Furthermore, it is essential to enhance the quality of Figure 2. Additionally, Figure 6 contains typos that need to be corrected.

Regarding the evaluation, it is important to note that simulated datasets were used to establish the Exact kSAT logical clauses. However, further explanation is required to fully understand this process. Therefore, additional effort is needed to test and prove the set hypotheses on the available datasets.

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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

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[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.

PONE-D-22-26132R1ARTIFICIAL DRAGONFLY ALGORITHM IN THE HOPFIELD NEURAL NETWORK FOR  BOOLEAN k SATISFIABILITY REPRESENTATIONPLOS ONE

Dear Dr. ABUBAKAR,

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: 

Dear Authors,

thank you for improving your manuscript, however I still have some comments.

- Figure quality should be improved, e.g. x-axis titles are too large and they should be resized.

- There are many inconsistencies in titles numbering, e.g. "1. Materials and Methods 2.1 Exact k Satisfiability of a Boolean Formula".

- Please make sure that all notations in expressions are defined.

- Please conduct appropriate statistical analysis. 

- Conclusion should be extended to include practical and theoretical limitations of proposed study.

- Please make sure that you ad here with all PLOS ONE policies. 

Thanks.

Warmest,

AE

==============================

Please submit your revised manuscript by Jun 30 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,

Nebojsa Bacanin

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.

Additional Editor Comments:

Dear Authors,

thank you for improving your manuscript, however I still have some comments.

- Figure quality should be improved, e.g. x-axis titles are too large and they should be resized.

- There are many inconsistencies in titles numbering, e.g. "1. Materials and Methods 2.1 Exact k Satisfiability of a Boolean Formula".

- Please make sure that all notations in expressions are defined.

- Please conduct appropriate statistical analysis.

- Conclusion should be extended to include practical and theoretical limitations of proposed study.

- Please make sure that you ad here with all PLOS ONE policies.

Thanks.

Warmest,

AE

[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 #2: All comments have been addressed

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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 #2: Yes

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3. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: (No Response)

Reviewer #2: Yes

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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 #2: Yes

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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: Yes

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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 #2: All of the requirements were met by the authors. The new version of the manuscript meets the requirements for publication in this type of journal.

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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

**********

[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.

ARTIFICIAL DRAGONFLY ALGORITHM IN THE HOPFIELD NEURAL NETWORK FOR  BOOLEAN k SATISFIABILITY REPRESENTATION

PONE-D-22-26132R2

Dear Dr. ABUBAKAR,

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,

Nebojsa Bacanin

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

Dear Authors,

thank you for revising your manuscript.

Only one minor note: I think that the Tukey's HSD test analysis results should be in tabular form.

All the best,

AE

Reviewers' comments: