Passing empty strings as components about edbo HOT 4 CLOSED

Glad to hear you have been finding EDBO useful. One way to handle your problem would be to one-hot-encode the ligands and include no ligand as an option. This is what that would look like if you used BO_express:

from edbo.bro import BO_express

# (1) Define a dictionary of components
reaction_components={
    'ligand': ['None','ligand1', 'ligand2', 'ligand3'],
    'concentration':[0.1, 0.2, 0.3]}

# (2) Define a dictionary of desired encodings
encoding={'ligand':'ohe',
          'concentration':'numeric'}

# (3) Instatiate BO_express
bo = BO_express(reaction_components=reaction_components,
                encoding=encoding,
                batch_size=10,
                acquisition_function='EI',
                target='yield')

from edbo.

I see, thanks for the swift reply!

Just a quick follow-up: would it be at all possible to use 'resolve' to do the same thing and setting all chemical descriptors for the 'None' ligand to 0?
It seems that when I try using 'resolve' while including 'None' (or, of course, any chemical not included in the NIH database) the edbo bot is spawned and when choosing to one-hot-encode the unknown component, all other components are also one-hot-encoded.

from edbo.

No problem! Indeed, the resolve method will only work for valid chemical names. In this case I think you may be better off with one-hot-encoding. However, If you would like to utilize a custom encoding I would suggest checking out the less automated but more flexible class edbo.bro.BO (https://b-shields.github.io/edbo/bro.html). BO will optimize over any numerical space you pass as the domain. You just have to specify it as a pandas DataFrame (e.g., generate one using a loop or load a CSV with pandas.read_csv).

from edbo.

Great, i'll check it out! Thanks for the help!

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