1. A method for generating weights for biometric tokens in probabilistic matching systems, comprising: analyzing biometric tokens of a reference data set, the reference data set comprising a plurality of biometric tokens for each of a plurality of distinct entities, the reference set further comprising a matched set of the tokens and an unmatched set of the tokens, by performing a pair-wise comparison of the tokens in the matched set and of the tokens in the unmatched set using a similarity scoring function; determining a plurality of scoring bins, based on similarity scores computed by the analyzing, wherein an upper and a lower boundary of each of the scoring bins is selected for separating the similarity scores; computing, for each of the scoring bins, a weight for the scoring bin, the weight for each bin computed in view of how many of the similarity scores from the matched set fall into the bin and how many of the similarity scores from the unmatched set fall into the bin; and using the weights for assessing subsequently-computed similarity scores from the similarity scoring function.