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I am doing my PhD on a small field in engineering where even if the review process is double blinded you would know who is going to review your paper.

This incident that I am going to mention is very odd and this is the first time that happened to me since I switched my research area. I am currently struggling to get my work accepted in a conference knowing that I have already 10 papers published among them 2 journals and most of them I wrote them when I was doing my master (I am mentioning this to let you know that I have already a little experience with the review process)

There are two groups in our field who are doing the same work that we are doing but they are applying an existing approach naively whereas we came up with a big novelty.

So they rejected our paper twice: once for conference submission and another time when we submitted an extension of the same work to transactions since it got rejected for the conference so we thought that we could argue with the reviewers in a journal but it didn't even go through the pre-screening process and these reviewers gave same arguments.

"First reviewer reason from the first group: Your method is very effective and definitely you have tested your model with the training data"

"The other reviewer reason from the second group is pretty much the same: Your model is over-fitting or you are using the training data to test your model"

However we explicitly stated in our manuscript that we use a testing data that was collected separately and was not used for training the model.

On top of that they mentioned also things that prove they did not even bother to read the manuscript for instance one of them said that we should run an experiment that we have already included it in the paper with a big figure.

My advisor has emailed the Editor-in-Chief of the journal but as we have expected he didn't even read his email and he replied with one sentence mentioning that we can consider re-submitting the manuscript.

So I am wondering are there other means and ways to win such a battle when the scientific field which is supposed to be decent and fair turns to be unfair.

EDIT:

I forgot to mention that as opposed to the review policy which clearly states that reviewers are supposed to not know each others or read other reviewer's comments, one of them discussed the comments of another reviewer and he clearly referred to them in his comments.

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    Obviously if multiple reviewers misunderstand your work in exactly the same way, then you aren't doing a good enough job of explaining it well. So fix it and resubmit the manuscript, as the EiC suggested. (You might want to read this answer) – ff524 Nov 11 '16 at 4:18
  • @ff524: Thanks a lot for your reply but that's what we did when we resubmitted for the journal and we made sure to write everything explicitly and clearly but still they insisted. I used to think that these kind of things are very fair and I need to work harder on the manuscript to make it clear but this time they gave ridiculous scientific reason and we even thought the first time me and my advisor that the reviewer's PhD student did that given the comments. – user2987 Nov 11 '16 at 4:33
  • Convince the editor that they are wrong and he needs to find other reviewers. If you can't, then you need to find another journal. – Karl Nov 11 '16 at 5:27
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    Quoting Pete Clark: "the reviewers are always right, even when they aren't". If they got the wrong impression, your paper isn't clear enough and further readers may think the same and reject your paper as sloppy. – Davidmh Nov 11 '16 at 9:47
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    I disagree that it is obvious that OP isn't doing a good enough job of explaining their research. In most cases, this would be the likely explanation, but, having personally encountered what the OP describes, I'm not so sure that that is what is happening here. – Mad Jack Nov 11 '16 at 13:23
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You can complain to the editor, but you should not expect too much from it. Remember that reviewers work for free, so unless there are a lot of complaints about one reviewer, the editor will not take action because the reviewer would just stop reviewing for this journal. Moreover the editor, who quite often is also working for free, may not take your complaints seriously, or judge that your case is not important enough for him to invest some hours of work - remember that he has to read your article to judge your case.

So the easiest thing to do is to submit your paper somewhere else, there are plenty of possibilities. However, if it is rejected again, and you didn't aim at the best journals, you should think really hard about trying again. There are many articles that should not have been written.

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