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I submitted an article to a journal, and it was rejected. The reviewers criticised some configuration values I used in my software. The comments were very helpful.

I have since improved the software, re-run the experiments, and extensively rewritten the article. I plan to submit it to the same journal. I suspect there's a good chance it will go to some of the same reviewers.

The controversial configuration parameters are no longer needed, and so are not mentioned in the article. I'm worried that if the reviewers saw the earlier version of the article, they may be confused by the "missing" parameters.

For this reason, I am tempted to include a note explaining the change. Is this a reasonable thing to do, or would it seem amateurish? Would it be better to just communicate this to the editor instead of including a note in the submission itself?

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    Usually journals don't allow a resubmission of a reject article, unless the editor invited you to resubmit. – Herman Toothrot Jan 3 '18 at 11:26
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    The concern about the article going to the same reviewers may also be valid even when switching to another venue. – O. R. Mapper Jan 3 '18 at 12:54
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    @Herman Which field is that? In my field it’s somewhat common to resubmit substantially revised articles to the same journal, even if no direct invitation for a resubmission was given (though you’d usually inquire informally with the handling editor beforehand). – Konrad Rudolph Jan 3 '18 at 15:02
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    As an aside, I have seen papers include acknowledgements of helpful input from anonymous reviewers. It sounds like that would be appropriate in this case. – Ergwun Jan 4 '18 at 0:43
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When resubmitting a paper after rejection, many journals require the authors to provide a detailed response to reviewers, whether or not the paper is going to be assessed by the same reviewers.

Therefore, instead of including a note to explain the change, include a complete response to reviewers, even though the journal you are submitting to does not require it. It would be useful even if the reviewers are not the same, because it's quite likely that new reviewers will receive the initial comments.

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    I would rather explain some of it in the cover letter, it's not a resubmission so it doesn't require a response to reviewers. – Herman Toothrot Jan 3 '18 at 11:25
  • @HermanToothroth As I said, some journals even in the case of new submission require that the authors address previous reviewers' remarks. Some publishers require that the authors comment on the reviewers' remarks even in the case of submission to a different journal belonging to the same publisher. Thus, in any case, it's better to prepare a response to the reviewers (given also the high probability that the paper is sent to the same reviewers). – Massimo Ortolano Jan 3 '18 at 18:41
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Even if you don't call it a resubmission, if its going back to the same journal, it is indeed a resubmission. Even after an extensive rewrite. This is a common occurrence.

I'm sure as part of the application they will ask if you have previously submitted this work to this journal and ask for the manuscript number. In doing so everyone will know its a resubmission. It will probably go back to the same editor who will obviously recognize the work. And probably back to the same group of reviewers.

This means that you include with it, a response to reviewers. If the comments no longer apply due to the rewrite, then simply state that as your response.

The hard part will be convincing the editor that your paper is worth another look. In your cover letter you tell them how helpful the reviewers comments were and that you made significant changes to the software and the manuscript text to address the concerns. If you ignore the fact that your work was previously reviewed they might just reject it based on that. You want to make it easy for them to accept your work, not hard.

Including a response to reviewers makes your submission stronger, not weaker.

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If this is not a resubmission you do not need to add any note. The paper should be self-standing and if these parameters are not used than there is no need to mentioned that they were in the previous model. The only parameters of interests are the ones being used, unless you are doing a comparative study or improving upon a previous model, in that case you would have to explain why you are not using these parameters. As long as you support all of your parameter choices you do not need to explain what you did before.

If you submit to the same journal after having received permission from the editor, than briefly state the main changes you have made, but again, the paper should be self standing.

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In case you do not resubmit to the same journal (in which case your cover letter could contain these notes), but rather to a different journal or to a conference (since you seem to be working on topics that intersect with computer science):

You can always add notes to the reviewers to your document. I have done so multiple times for conference submissions in CS, once even with adding a cover sheet to a conference submission requesting the reviewers to look in the appendix to see if some of their points of criticism are addressed. I've never received negative comments about this.

However, doing so risks a comment by the reviewer that the information in the notes is so essential that it should be in the paper. So this strategy only makes sense if you can give reasons that make it 100% clear that the content from the notes to the reviewers should not be in the paper.

The cover sheet mentioned above may look weird, but the first section in your appendix being titled "Notes to the Reviewers" should not. However, some conferences employ automatic length checking of the paper and take this appendix into account, so you can only use this strategy if your paper is short enough with the notes.

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