PONE-D-23-17033Network-based visualization of frequent sequencesPLOS ONE

Dear Dr. Bántay,

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 Sep 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.

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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,

Praveen Kumar Donta, Ph.D.

Academic Editor

PLOS ONE

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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: Partly

Reviewer #2: Yes

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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: Yes

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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: No

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. Please underscore the scientific value added to your paper in your abstract and introduction.

2. Some more recent schemes are also available; how do authors justify that the methods employed are appropriate?

3. The most recent papers need to be addressed in the related work sections.

4. what is the time complexity of proposed algorithms?

5. The motivation of the proposed method should be stated in the introduction.

6. The method proposed by the authors should be compared with the recent existing methods and explained to highlight the

advantages of the new method.

8. How much performance improved in terms of percentage? Please use the abstract to explain this precisely.

9. The language needs to be polished, some grammatical mistakes need to correct.

10. Some formatting errors exist. Correct the entire manuscript with proper formatting.

11. The results are not enough to show the efficiency of the proposed work, so, please extend the results parts to include further experiments.

12. Use high quality images for better visibility.

Reviewer #2: In this manuscript, authors aimed to extend excellent visualization-based by applying a network-based approach to frequent sequence pattern mining, seeking to fulfill the mentioned requirements as well as possible. Authors suggested to address the following comments and suggestions when preparing the revised version:

= Abstract: section needs to be re-drafted to be self-contained means it has to clearly show the hypothesis, methodology, techniques and tools used, and the results obtained.

= Keywords: Authors suggested to add some keywords by selecting relevant terms. Keywords play important role in the appearance of the manuscript in scholars search which will give it more hits and more citations.

= What assumptions authors made during the simulation phase of this research work? If there is any.

= Authors suggested to go through the following references and they MAY make use of them in updating the introduction and the related work sections:

- Ali Akbar Movassagh, Jafar A. Alzubi, Mehdi Gheisari, Mohamadtaghi Rahimi, Senthil kumar Mohan, Aaqif Afzaal Abbasi, Narjes Nabipour, “Artificial neural networks training algorithm integrating invasive weed optimization with diferential evolutionary model” Journal of Ambient Intelligence Humanized Computing, https://doi.org/10.1007/s12652-020-02623-6

- Omar A. Alzubi, Jafar A. Alzubi, Mohammed Alweshah, Issa Qiqieh, Sara Al-Shami, Manikandan Ramachandran, “An Optimal Pruning Algorithm of Classifier Ensembles: Dynamic Programming Approach” Neural Computing & Applications, 2020.

- Jafar A. Alzubi "Diversity Based Improved Bagging Algorithm" In Proceedings of the International Conference on Engineering & MIS 2015 (ICEMIS '15). Istanbul - Turkey.

- Jafar A. Alzubi, "Diversity-Based Boosting Algorithm". International Journal of Advanced Computer Science and Applications, Vol. 7, No. 5, 2016.

- O. A. Alzubi, J. A. Alzubi, S.Tedmori, H. Rashaideh, and O. Almomani "Consensus-Based Combining Method for Classifier Ensembles" The International Arab Journal of Information Technology, Vol. 15, No. 1, 2018.

= Conclusion: The conclusion should be abstracted so authors need to consider re-drafting it.

= Authors need to confirm that all acronyms are defined before being used for first time.

= Authors need to confirm that all mathematical notations are defined when being used for first time.

= Authors suggested to proofread the manuscript after addressing all comments to avoid any typo, grammatical, and lingual mistakes and errors.

= Authors advised to make sure that the format of all references is matching and complying with journal requirements and format.

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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.

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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: Shashank Singh

Reviewer #2: No

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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-23-17033R1Network-based visualization of frequent sequencesPLOS ONE

Dear Dr. Bántay,

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 27 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:

• 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,

Praveen Kumar Donta, Ph.D.

Academic Editor

PLOS ONE

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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

Reviewer #3: (No Response)

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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: Partly

Reviewer #2: Yes

Reviewer #3: Partly

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

Reviewer #1: Yes

Reviewer #2: N/A

Reviewer #3: I Don't Know

**********

4. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: No

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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: Yes

Reviewer #2: 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: The author has seamlessly incorporated all the comments. They carefully considered each suggestion and integrated it seamlessly into their revised manuscript.

Reviewer #2: Authors revised the manuscript according to reviewers comments and suggestions. Manuscript quality is enhanced and its scientific value increased. However, going through the manuscript one can easily spot few lingual and grammatical issues which needs to be addressed. so, authors suggested to get the manuscript proofread by an English native speaker to avoid such issues. Also, authors needs to double check the references style which has to meet with the journal one.

Reviewer #3: Authors revised the manuscript, mostly, according to reviewer comments. My comments for the manuscript:

1. CM-SPAM algorithm is used to first find the frequent sequential pattern in data that are then visualized with proposed three methods (NBVFS-WG, NBVFS-CM and NBVFS-TM). The topic is interesting and the problem is clearly stated. Authors claim that the “proposed visualization methods can significantly lower the time of information processing, for example, during the creation of machine learning models”. I did not find discussion about this claim in the results section. Similarly, lines 59-60: “without eliminating any relevant information during post-processing”. This line needs some more detail.

2. In abstract: Multiply or multiple?

3. Why CM-SPAM is used as there are other SPM algorithms too? In CM-SPAM, only minsup is the must parameter, other parameter such as min no of patterns, max number of patterns and gap are optional parameters. Authors should discuss why they used optional parameters. These are used to reduce he total number of discovered patterns? It is interesting that max gap of 2 is used. This will enforce the CM-SPAM to find patterns with some gaps and the order of events in the discovered patterns will change. I believe in the two datasets the order is important so why max gap of 2 is used? By the way add the reference for CM-SPAM.

Fournier-Viger, P., Gomariz, A., Campos, M., Thomas, R. (2014). Fast Vertical Mining of Sequential Patterns Using Co-occurrence Information. Proc. 18th Pacific-Asia Conference on Knowledge Discovery and Data Mining (PAKDD 2014), Part 1, Springer, LNAI, 8443. pp. 40-52.

4. Figures quality is very low. Should be replaced with high quality images.

5. Add the stats for the two datasets in a table form for easy understanding. Also add their references.

6. The data is converted to integer form to apply SPM algorithms. Right? If so then also explain the transformation process. Figures are hard to understand as it is hard to know which integers stands for which event or item.

7. This line: For example: the order of 306 actions is always 2 → 3 → 4 → 8; if actions 2,3 and 4 occur, it is almost 100% that 8 307 will occur as well. This kind of rules we can get with sequential rules. How authors are sure that 100% time, 8 will follow 2,3, and 4?

8. Ref [2] and [3] seems old. Authors can replace them recent references for the application of SPM. For example:

to extract hypernym relations from texts (Aldine et al. A 3-phase approach based on sequential mining and dependency parsing for enhancing hypernym patterns performance. The Knowledge Engineering Review, 36: E13, 2021.)

for genome analysis (Nawaz et al. Using artificial intelligence techniques for COVID-19 genome analysis. Applied Intelligence, 51: 3086-3103, 2021)

for tourist movement analysis (Cheng et al. A sequential pattern mining approach to tourist movement: The case of a mega event. Journal of Travel Research, 62(6): 1237-1256, 2023)

for workload prediction in cloud environment (M Amiri, L. Mohammad-Khanli and R. Mirandola. A sequential pattern mining model for application workload prediction in cloud environment. Journal of Network and Computer Applications, 105:21-62, 2018)

for mining discrete clinical data (Estiri, S. Vasey and S. N. Murphy. Transitive Sequential Pattern Mining for Discrete Clinical Data. In Proceedings of AIME, pp. 414-424, 2020)

for malware behavior analysis (Nawaz et al. MalSPM: Metamorphic malware behavior analysis and classification using sequential pattern mining. Computers & Security, 118: 102741, 2022)

9. It would be better if authors provide the GitHub link for the developed code

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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: Yes: Shashank Singh

Reviewer #2: No

Reviewer #3: 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-23-17033R2Network-based visualisation of frequent sequencesPLOS ONE

Dear Dr. Bántay,

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 Apr 08 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:

• 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,

Praveen Kumar Donta, Ph.D.

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.

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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: (No Response)

Reviewer #4: 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 #2: Yes

Reviewer #3: Yes

Reviewer #4: Yes

**********

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

Reviewer #2: N/A

Reviewer #3: I Don't Know

Reviewer #4: 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 #2: Yes

Reviewer #3: Yes

Reviewer #4: No

**********

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: Yes

Reviewer #4: 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 #2: The authors have appropriately addressed and corrected all the issues as per my previous comments. The related work has been enriched, and the indistinct description, as well as deficient analysis, have been improved and refined. More discussions have also been added. This paper has been comprehensively improved in terms of correctness, completeness, and readability to reach the standard for publication.

Reviewer #3: Authors properly addressed most of my previous concerns/suggestions.

Following previous comments needs revision from authors.

Comment 1. Authors did not provide justification for their claim that how the poposed

apptoach significantly reduce the computational time in information processing

Comment 3: Authors should provide the reason for why CM-SPAM is used and not other algorithms

such as CM-SPADE or TKS?

Comment 7: The pattern 2 3 4 and 8 occurs for which CM-SPAM generates the SUP.

100% occurences of such patterns means that support is equal to total number of records.

If it is the case then author can keep the line. Otherwise author can rewrite the line to remove

the 100% with SUP value.

Reviewer #4: Authors addressed all the comments and concerned carefully. The manuscript stands for the acceptance.

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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 #2: No

Reviewer #3: No

Reviewer #4: 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.

Network-based visualisation of frequent sequences

PONE-D-23-17033R3

Dear Dr. Bántay,

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.

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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,

Praveen Kumar Donta, Ph.D.

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

Reviewers' comments: