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When determining a fragment, could a portion of the structure be used redundantly? For example a benzene ring evaluated independently as well as with any attached substructures)

While the hierarchical organisation of the model allows for sub and super-fragments to be stored, only the largest model fragment will be used in the prediction (for example, a toluene fragment would be used and not the smaller benzene ring). This allows for the most relevant context of the fragment to be considered by effectively looking at the most ‘local’ model (hypothesis) which will be comprised of the most similar training compounds. To use both would risk biasing the model towards overlapping fragments for which we have the most information and is one of the key advantages of a hierarchical model over a simpler flat ‘fingerprint’ based statistical approaches.

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