What does `ValueError: cannot reindex from a duplicate axis` mean?

This error usually rises when you join / assign to a column when the index has duplicate values. Since you are assigning to a row, I suspect that there is a duplicate value in affinity_matrix.columns, perhaps not shown in your question.

As others have said, you've probably got duplicate values in your original index. To find them do this:

df[df.index.duplicated()]