Compare between similar and dissimilar couples of instances I label couples of similar and dissimilar instances based on user behavior.
each instance has a lot of features.
I have few ways of labeling the couples.
I know want to evaluate which of the label methods produce the most homogeneous distribution in the groups or to tell if the two groups comes from the same distributions.

I am looking for a statistical measures mostly.
Any suggestions?
You can compute a similarity score between each couple of instances (diff in features) and then you can check if the distribution of the difference for each group (similar and dissimilar) is significantly different using the Kolmogorov-Smirnov test.