PONE-D-20-11239

A k-Mismatch String Matching for Generalized Edit Distance using Diagonal Skipping Method

PLOS ONE

Dear Dr. Kim,

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 all the points raised during the review process.

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We look forward to receiving your revised manuscript.

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Hans A Kestler

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: No

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: No

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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: The paper covers an interesting technical topic and provides an algorithm within the scope of the topic.

In its current state, I see some flaws of the paper.

- While most of the paper ist written in understandable English, it is clear through the whole paper that the writer is not a native English speaker. I recommend having the paper checked by a native speaker or someone with experience in writing English mauscripts.

- The description of the algorithm is hard to read, mainly because some terms are used before they are explained. Especially the term "arrow" is not defined explicitly. Also, the pseudocode states an implementation step, but the reader has to search for a more detailed description of this initialization.

- In the description of the distance D (beginning in line 75), the difference between x_i and X_i is unclear. Is X_i a string or a character? If it's a string, why is it indexed? If it's a character, why is it written with a capital letter (in contrast to lowercase letters in line 75).

- It appears the algorithm and the datasets used for the analysis are not publicly available.

- The analysis part misses a statistical analysis. This can lead to a misinterpretation of the data: Shorter average running times do not necessarily imply a more efficient algorithm. Also, comparing running times per se can lead to systematic errors in the analyis. E.g. one of the algorithms might have been implemented more efficiently, the computer hardware might be more beneficial for one of the compared programs (e.g. due to cache structure, compiler optimization etc.).

To sum up, I think that the paper needs some work but has potential.

Reviewer #2: The author scrupulously details the approach for reducing the execution time when calculating the generalized edit distance, considering, for example, similar shape characters or keyboard character positions. Through the accurate experimental analysis and the corresponding figures we can visualize how, by means of the proposed method, the execution time is reduced when complicate distance metrics are used. Furthermore the author introduces the disadvantage of using the skipping method when simple metrics are employed.

However some essential introductory notions are ambiguous and need to be better explained.

For example, at line 75, according to the used notation, the input strings X and Y appear to have length i and j respectively, but afterwards, starting from line 76, i and j are used as indices. Even more confusion can be created by considering line 87, where the input sequence X and pattern Y are denoted with subscripts i and j respectively.

Besides certain technical details should be expanded and clarified to ensure better understanding. For instance in Equation 1 the functions of substitution, deletion and insertion should be precisely defined.

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Reviewer #1: No

Reviewer #2: No

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PONE-D-20-11239R1

A k-Mismatch String Matching for Generalized Edit Distance using Diagonal Skipping Method

PLOS ONE

Dear Dr. Kim,

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 perform the remaining minor changes raised by the reviewer.

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

Please submit your revised manuscript by Mar 28 2021 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: http://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols

We look forward to receiving your revised manuscript.

Kind regards,

Hans A Kestler

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: (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: Yes

Reviewer #2: Yes

**********

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

Reviewer #1: Yes

Reviewer #2: 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 #2: 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 #2: No

**********

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: In the current version of the paper, my previous comments to the last version have been adequately addressed.

Reviewer #2: Numerous of the apported adjustments improved the readability and informativeness of the paper, nevertheless a careful review is necessary for a complete perception of the study.

- A further accurate copy edit for language usage and grammar is mandatory. In fact a frequent mistake, is the usage of the verb in the third person singular when not required, for example at lines 98, 410, 412, but may not be the only ones. Other repetitive misspellings are the quoted comma (for example line 257: '1,') and capital letter after comma (see line 16). There are also lexical inaccuracies as close statement repetitions (for instance 343-345 and 349-350) or unclear references (at 346-348 one does not promptly associate "these experiments" with "the diagonal skipping method").

- The distance (as defined in lines 76-77) is the minimum number of operations to convert the input string into the pattern, it follows that the operations are always applied on the input string and never on the pattern. Therefore in expression (1) should be correct D(X_α-1, Y_β) + insertion(y_β) and D(X_α, Y_β-1) + deletion(x_α). This statement is also confirmed by the explanation of the example in Fig 1 (b), lines 112-118. Moreover the example in lines 104-109 needs a better adapted description.

- It is suggested to revisit the notations used to represent strings, substrings, the respective lengths and the indices to identify any character in the string/substring. There are misconceptions when the subscript refers to the length of a string/substring and when it refers to any character of the string/substring. For instance at line 267 the content suggests that D[α][1] wants to indicate the whole second column in the two-dimensional array D, however 'α' defines the length of the input substring. Moreover according to the employed notation D[α][β] (line 269) identifies only the rightmost bottom cell of D, but here it is intended to identify any cell of D.

- Comparing the definition of ‘traversal’ specified in 120-121, its usage in the pseudocode and in lines 229-230, the difference between arrow and traversal is unsettled.

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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.

A k-Mismatch String Matching for Generalized Edit Distance using Diagonal Skipping Method

PONE-D-20-11239R2

Dear Dr. Kim,

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.

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Kind regards,

Hans A Kestler

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

Reviewers' comments: