A system for finding similar molecules to a query molecule includes a GCN, a PFS vector extractor, a compensated vector comparator (CVC) and a candidate vector selector. The GCN has been trained to output a molecular property vector from an input query or input candidate molecular vectors, respectively, The GCN transforms query atomic feature set (AFS) vectors and candidate AFS vectors into query property feature set (PFS) embedding vectors and candidate PFS embedding vectors. The PFS vector extractor extracts query PFS embedding vectors and candidate PFS embedding vectors from hidden layers of the trained GCN. The compensated vector comparator (CVC) calculates a compensated similarity metric (CSM) for at least one pair of query PFS embedding vector and one candidate PFS embedding vector. The candidate vector selector selects only such candidate molecular vectors.
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