Abstract: Methods and systems are provided to classify or identify a target molecule or its properties from regions of molecular surface of the target molecule. In an implementation, the system identifies patches of the surface, generates a respective latent space ID and a respective real space ID for each of the patches, uses the latent space IDs and the real space IDs to identify at least one candidate item that includes a surface resembling a surface region of the target molecule, wherein the surface region comprises multiple patches in the plurality of surface patches of the target molecule, and uses the at least one candidate item to determine an identification or a classification of the target molecule.