I do like this general approach, however the OP is talking about a significant sized file of 500 MB. Depending upon the data of course, your HoH (hash of hash) structure could consume quite a bit more memory than the actual file size in MB.

{
  head1 => { val1 => 2, val2 => 1, val3 => 1, val6 => 1 },
  head2 => { val2 => 1, val4 => 2, val7 => 2 },
  head3 => { val3 => 2, val5 => 3 },
}
[download]

I came up with a representation (at this post) where the column values only occur once as hash keys and the value of each hash key is an array describing whether a value: appears or doesn't appear at all in column, whether a value only appears once in a column, whether a value occurs more than once in a column.

We both interpreted "unique" to mean different things.
I see you think that means: "don't repeat yourself after having said something once".
I thought it meant: "don't say anything at all if you would repeat yourself".

My data structure:

{
  val1 => [-1],   # val1 occurs more than once in col 1
  val2 => [2, 1], # val2 occurs once in col 1 and once in col 2
  val3 => [-3, 1], #val3 occurs more than once in col 3
                   #but only one time in col1
  val4 => [-2],
  val5 => [-3],
  val6 => [1],
  val7 => [-2], #val7 is mentioned at least twice in col2
}
[download]

Of course I could generate your same output from my data structure because I know the columns where the term appeared more than once.

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