The list of reference ligands also serves as an additional input for optimization. An input list of reference ligands is used to define 𝐀 in Eq. 3. If no reference ligands are specified, the algorithm selects the ligand with the highest sum similarity to the rest of the set or cluster. The one or more reference ligands that are either specified or calculated by HiMap for each cluster are assigned a Given the complexity of the procedure for setting up a graph optimization, HiMap has an interactive mode to walk the user through the required inputs.