According to that metric, for two bits to be considered a match it is not enough that they are both nonzero, but they must have the same integer value. As such, the fraction of matching bits given two fingerprints of this type tends to be much lower compared to binary fingerprints. Second, it could be that MinHashing paths rather than circular fragments lead to more potential categorical values for each bit, reducing the number of bit matches when comparing two fingerprints. This would explain why MHFP has higher median pairwise Jaccard-Tanimoto similarity.