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What I should use? Note that MOPSO and NSGA-II are two different methodologies.

Although MOPSO had not been applied to P300-BCI systems studies, NSGA-II did.

or

Although MOPSO had not been applied to P300-BCI systems studies, NSGA-II had.

  • To my ear the most natural phrasing would be "NSGA-II was." Next, "NSGA-II had been." I can't defend that grammatically but it sounds fine to me, – Chaim May 12 '17 at 14:12
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In the first part of your sentence, we are dealing with a pluperfect passive. The positive form is "had been [past participle]" and the negative form is "had not been [past participle]".

The auxiliary verb here is "had".

Therefore, the correct answer should be "had":

Although MOPSO had not been applied to P300-BCI systems studies, NSGA-II had.

Here is the sentence with the implied part included:

Although MOPSO had not been applied to P300-BCI systems studies, NSGA-II had been applied to the P300-BCI systems studies.

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