The top 10 hypotheses presented following the HipHop (common feature hypotheses) calculation are internally scored and ranked. You can refer to Catalyst manual for details of these internal scoring. I believe you are asking about external scoring of the hypotheses. A typical procedure for such external scoring is as follows (extracted from page 1339 of Güner and Bowen, Curr Top Med Chem, 2013, 13(11), 1327-1342:

External scoring and validation of pharmacophore models: This will involve first building a 3D decoy database that is seeded with a number of known active ligands. The number of compounds and the ratio of seeded active ligands in the database is up to the researcher; nevertheless, one should be careful to register compounds into the decoy database that are relevant to the enzyme considered, and avoid registering compounds that are not relevant (e.g., cyclohexane as an inactive compound in the database will not provide any useful information to the researcher). Once the database is ready, use each of the pharmacophore models, which were selected in the previous two steps, as search queries to screen the 3D database. As the number of compounds (D) and the number of active compounds in the database (A) are known, and one can determine the number of known active compounds in the hit list (Ha), and the total number of compounds in the hit list (Ht), one can then calculate the GH-score for each pharmacophore model and prioritize the models for each training set based on this score [133, 134)] The combination of several diverse high scoring models for each training set will now constitute the battery of pharmacophore models selected for use in the profiler.

References cited above (133, 134) have a good description and validation of the GH-score:

[133] Raymond, J. W.; Willett, P. Effectiveness of graph-based and fingerprint-based similarity measures for virtual screening of 2D chemical structure databases. J Comp-aided Molec Des 2002, 16, 59–71.

[134] Edgar, S. J.; Holliday, J. D.; Willett, P. Effectiveness of retrieval in similarity searches of chemical databases: a review of performance measures. J Molec Graph Model 2000, 18, 343–357.

The original GH-score papers are at Chapter 11-12 of the Pharmacophore book:

Pharmacophore Perception, Development, and Use in Drug Design; Güner, O. F., Ed.; International University Line: La Jolla, CA, 2000.