The easiest thing is not to set the default, but apply the default while reading the value in the end, like my $ov = $overlap->{$a}{$b} // 0 (requires perl 5.10 or newer, but older versions than 5.12 aren't maintained anyway).
By the way a nicer way to write the inner loops is
my $last = @members - 1;
for my $i (0 .. $last) {
for my $j ($i + i .. $last) {
$overlap->{$members[$i]}{$members[$j]}++;
$overlap->{$members[$j]}{$members[$i]}++;
}
}
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