We considered hyperparameters affecting molecular representation and HNSW construction. For the molecular representation, we considered four fingerprint types: Morgan fingerprints with a radius of 2, Morgan fingerprints with a radius of 3, RDKit fingerprints, and MACCS keys. For each fingerprint, we considered five lengths: 128, 256, 512, 1024, and 2048 bits (except for MACCS keys, which always had a length of 166 bits). For HNSW construction, we considered various efConstruction and M parameters, which controlled the number of neighbor candidates and connected neighbors, respectively, when adding a new vector. We considered four efConstruction values: 100, 200, 300, and 400, and six M values: 2, 4, 8, 16, 32, and 64. These values were chosen according to reasonable ranges suggested by the authors of the hnswlib library.