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I have a csv file, size around 50Mb. The data is 986132 by 3 matrix of the following form.

data={{a1,b1,1},{a1,b2,1},{a1,b3,1},{a1,b4,1},{a2,b1,1},{a2,b5,1},{a2,b6,1},{a3,b1,1},{a3,b2,1},{a3,b6,1},{a3,b7,1},...{a3012,b1423,1}}

The third column is always 1 and there is no pattern between a's and b's.

In the matrix form of data, I focus on the second column (b's) and want to remove all the rows that has b$i$ that appears less than a certain number. Say it's 10.

So, for example, if b10, b31, b412 each appears less than 10 times in data, I want remove all the rows that contain b11, b31 and b412.

How can I do this? I've tried to convert it to a pivot table and sort it by the number of each b, but my computer can't process it maybe because of the memory limitation..

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Make some fake data:

SeedRandom[10]; numOccurrences = 5;
data = Table[{RandomInteger[{0, 100}], RandomInteger[{1, 100}], 1}, 100];

Group the data by the value of b, then select only those values of b for which at least numOccurrences instances are present, then take the values of the resulting association and flatten them back into the desired shape:

Select[Length[#] >= numOccurrences &]@ GroupBy[#[[2]] &]@ data;
Values[%]~Flatten~1

(* Out: 
 {{83, 1, 1}, {33, 1, 1}, {27, 1, 1}, {12, 1, 1}, {74, 1, 1}}
*)
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To generate data (with a[i] instead of ai but the principle is unchanged):

SeedRandom[2020];
n = 20;
indexA = RandomInteger[{1, 4}, n];
indexB = RandomInteger[{1, 4}, n];
data = Table[{a[indexA[[i]]], b[indexB[[i]]], 1}, {i, n}]

(* {{a[1], b[4], 1}, {a[1], b[2], 1}, {a[1], b[2], 1}, {a[1], b[4], 
  1}, {a[4], b[4], 1}, {a[1], b[4], 1}, {a[3], b[2], 1}, {a[4], b[3], 
  1}, {a[4], b[1], 1}, {a[3], b[3], 1}, {a[1], b[3], 1}, {a[4], b[3], 
  1}, {a[4], b[1], 1}, {a[4], b[4], 1}, {a[4], b[4], 1}, {a[2], b[2], 
  1}, {a[1], b[4], 1}, {a[2], b[1], 1}, {a[4], b[3], 1}, {a[2], b[4], 
  1}} *)

Then, store variablesn that appear less than min times in the second colum, and select rows whose second value in not in the list of bad indices badB:

min = 5;
badB = Select[Tally[data[[All, 2]]], #[[2]] < min &][[All, 1]]
Select[data, MemberQ[badB, #[[2]]] == False &]

(* {{a[1], b[4], 1}, {a[1], b[4], 1}, {a[4], b[4], 1}, {a[1], b[4], 
1}, {a[4], b[4], 1}, {a[4], b[4], 1}, {a[1], b[4], 1}, {a[2], b[4], 
1}} *)
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ClearAll[pick]
pick = Pick[#, 
    Developer`ToPackedArray @ UnitStep[(Counts[#[[All, 2]]] /@ #[[All, 2]]) - #2], 1] &;

Using data from MarcoB's answer:

SeedRandom[10];
data = Table[{RandomInteger[{0, 100}], RandomInteger[{1, 100}], 1}, 100];
pick[data, 5]
 {{83, 1, 1}, {33, 1, 1}, {27, 1, 1}, {12, 1, 1}, {74, 1, 1}}

Note: This approach preserves the ordering of kept rows.

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