$distances{$key1}{$key2} = $value;

##</code><code>##

obj1 obj2 => 0.95
obj2 obj3 => 0.76
obj1 obj4 => 0.80
...

##</code><code>##

@subsets = (
{
    obj1  => "C1",
    obj2  => "C2",
    obj3  => "C3",
    obj4  => "C4",
    obj5  => "C5",
}
);

##</code><code>##

%used = (
{
    obj1  => "C1",
    obj2  => "C2",
    obj3  => "C3",
    obj4  => "C4",
    obj5  => "C5",
}
);

##</code><code>##

for ($i = 0; $i < 50; $i++) { #loop over array of hashes (each subset will have 50 keys)
    foreach my $key (keys $subsets[$i]) { #5 keys at each level
        my $max = 0;
        my @max;
        for my $key1 (keys %distances) {
            if $key !exists (keys %used) {
                $max = max (values %{$distances{$key1}});
                push @max, $max;
                # somehow retrieve the 2nd key
            }
        }
        my $maxmax = max @max;
        # $subsets[$i+1]{2nd_key_with_max_val} = "e.g. C1"
        # push %used with key and value
        @max = [];
    }
}