For small number of documents is quiet fast but not for large ...

Which means that your code almost certainly runs in some form of exponetial time. I don't see how compression will not help you in either the short term as the overhead of the compression/decompression will hurt you or the long term as I can't see how your fundamental algorithmic problem is addressed by compression. An algorithm is still On^2 with or without compression.

In broad terms compression will only speed up an application if it lets you pass data faster through a narrow bandwidth chokepoint where the time price of compression/decompression has a worthwhile payoff.

If you have already observed that your code grinds to a halt on large data sets you need to fix the fundamental why of that issue. If you explained your problem more clearly it is possible that you may get a useful solution. I am almost certain that compression is not the solution you need.

Cheers

tachyon