good. you can shorten your while loop a bit, though...

while (<>)
{
    $freq{$_}++ for split;
}
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your @array variable was merely a temp, used to glue two statements together. split defaults to a whitespace split on $_, which is what <> is filling. i've flipped around the for loop, as well.

also, i wouldn't be so destructive to the sorted array. instead of popping the value, how about selecting it, by

my $mode = $sorted_array[-1]; ## aren't negative indexes neat?
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~Particle *accelerates*