Generating weights for biometric tokens in probabilistic matching systems is disclosed, where these weights are generated from computations performed on matched sets and unmatched sets of a reference data set. In an embodiment, scores from a similarity scoring function are distributed among bins, and a weight is computed for each bin as the log of (the matched set ratio/the unmatched set ratio), where the ratios are computed as the number of scores in a particular bin as compared to the total size of the set. The weights may then be used subsequently with scores computed by the scoring function to assess confidence of a computed similarity score, and are directed toward making the output of the probabilistic matching system more data-driven and more accurate.