No, the first sentence is ungrammatical because it is a dependent clause without a main clause. I'm not absolutely certain what it wants to say, but my best guess, given the paucity of information in the words you've provided, is that it should probably read something like this:
Because their methods yield category counts that are up to 95% accurate, which is acceptably high, and our method generates comparable results (Fig. 5), we compare only those sets with category counts that are less than ##%[You will have to provide a number here] accurate.
Use "because" instead of "since": the former is unambiguous. Be specific by providing concrete numbers for acceptable accuracy: 95% is good, but what is unacceptably low?. Eliminate unnecessary words. Say things as simply and clearly as possible.
If' I've misunderstood what this sentence wants to say, it's probably because there's insufficient context. I'm just guessing at what everything might mean. It's all so abstract.