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I want to use a clustering algorithm for a data set that each row/record has 3 features/columns. All the features are integers.

First, I have tried DBSCAN method because it is a method that I know well. I have used the NearestNeighbors algorithm to choose eps and minpts values. The problem is that even if I choose a big N value, the N neighbors for many records are 0, because many records are the same. I don't want to delete these duplicate records.

Is there a particular clustering method for this scenario?

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