Basic example for using BayBE¶
This example shows how to create a campaign and how to use it. It is intended to be used as a first point of interaction with campaign after having read the corresponding user guide.
Necessary imports for this example¶
from baybe import Campaign
from baybe.objectives import SingleTargetObjective
from baybe.parameters import NumericalDiscreteParameter, SubstanceParameter
from baybe.searchspace import SearchSpace
from baybe.targets import NumericalTarget
from baybe.utils.dataframe import add_fake_results
Setup¶
This example presents the optimization of a direct Arylation reaction in a discrete space. For this, we require data for solvents, ligands and bases.
dict_solvent = {
"DMAc": r"CC(N(C)C)=O",
"Butyornitrile": r"CCCC#N",
"Butyl Ester": r"CCCCOC(C)=O",
"p-Xylene": r"CC1=CC=C(C)C=C1",
}
dict_base = {
"Potassium acetate": r"O=C([O-])C.[K+]",
"Potassium pivalate": r"O=C([O-])C(C)(C)C.[K+]",
"Cesium acetate": r"O=C([O-])C.[Cs+]",
"Cesium pivalate": r"O=C([O-])C(C)(C)C.[Cs+]",
}
dict_ligand = {
"BrettPhos": r"CC(C)C1=CC(C(C)C)=C(C(C(C)C)=C1)C2=C(P(C3CCCCC3)C4CCCCC4)C(OC)="
"CC=C2OC",
"Di-tert-butylphenylphosphine": r"CC(C)(C)P(C1=CC=CC=C1)C(C)(C)C",
"(t-Bu)PhCPhos": r"CN(C)C1=CC=CC(N(C)C)=C1C2=CC=CC=C2P(C(C)(C)C)C3=CC=CC=C3",
}
We define the chemical substances parameters using the dictionaries defined previously.
Here, we use "MORDRED" encoding, but others are available.
We proceed to define numerical discrete parameters temperature and concentration
and create the search space.
solvent = SubstanceParameter("Solvent", data=dict_solvent, encoding="MORDRED")
base = SubstanceParameter("Base", data=dict_base, encoding="MORDRED")
ligand = SubstanceParameter("Ligand", data=dict_ligand, encoding="MORDRED")
temperature = NumericalDiscreteParameter(
"Temperature", values=[90, 105, 120], tolerance=2
)
concentration = NumericalDiscreteParameter(
"Concentration", values=[0.057, 0.1, 0.153], tolerance=0.005
)
parameters = [solvent, base, ligand, temperature, concentration]
searchspace = SearchSpace.from_product(parameters=parameters)
________________________________________________________________________________
[Memory] Calling baybe.utils.chemistry._smiles_to_mordred_features...
_smiles_to_mordred_features('O=C([O-])C.[Cs+]')
_______________________________________smiles_to_mordred_features - 0.0s, 0.0min
________________________________________________________________________________
[Memory] Calling baybe.utils.chemistry._smiles_to_mordred_features...
_smiles_to_mordred_features('O=C([O-])C(C)(C)C.[Cs+]')
_______________________________________smiles_to_mordred_features - 0.0s, 0.0min
________________________________________________________________________________
[Memory] Calling baybe.utils.chemistry._smiles_to_mordred_features...
_smiles_to_mordred_features('O=C([O-])C.[K+]')
_______________________________________smiles_to_mordred_features - 0.0s, 0.0min
________________________________________________________________________________
[Memory] Calling baybe.utils.chemistry._smiles_to_mordred_features...
_smiles_to_mordred_features('O=C([O-])C(C)(C)C.[K+]')
_______________________________________smiles_to_mordred_features - 0.0s, 0.0min
________________________________________________________________________________
[Memory] Calling baybe.utils.chemistry._smiles_to_mordred_features...
_smiles_to_mordred_features(‘CN(C)C1=CC=CC(N(C)C)=C1C2=CC=CC=C2P(C(C)(C)C)C3=CC=CC=C3’) _______________________________________smiles_to_mordred_features - 0.2s, 0.0min ________________________________________________________________________________ [Memory] Calling baybe.utils.chemistry._smiles_to_mordred_features… _smiles_to_mordred_features(‘CC(C)C1=CC(C(C)C)=C(C(C(C)C)=C1)C2=C(P(C3CCCCC3)C4CCCCC 4)C(OC)=CC=C2OC’)
_______________________________________smiles_to_mordred_features - 0.3s, 0.0min
________________________________________________________________________________
[Memory] Calling baybe.utils.chemistry._smiles_to_mordred_features...
_smiles_to_mordred_features('CC(C)(C)P(C1=CC=CC=C1)C(C)(C)C')
_______________________________________smiles_to_mordred_features - 0.1s, 0.0min
________________________________________________________________________________
[Memory] Calling baybe.utils.chemistry._smiles_to_mordred_features...
_smiles_to_mordred_features('CCCCOC(C)=O')
_______________________________________smiles_to_mordred_features - 0.1s, 0.0min
________________________________________________________________________________
[Memory] Calling baybe.utils.chemistry._smiles_to_mordred_features...
_smiles_to_mordred_features('CCCC#N')
_______________________________________smiles_to_mordred_features - 0.0s, 0.0min
________________________________________________________________________________
[Memory] Calling baybe.utils.chemistry._smiles_to_mordred_features...
_smiles_to_mordred_features('CC(N(C)C)=O')
_______________________________________smiles_to_mordred_features - 0.0s, 0.0min
________________________________________________________________________________
[Memory] Calling baybe.utils.chemistry._smiles_to_mordred_features...
_smiles_to_mordred_features('CC1=CC=C(C)C=C1')
_______________________________________smiles_to_mordred_features - 0.1s, 0.0min
In this example, we maximize the yield of a reaction and define a corresponding objective.
objective = SingleTargetObjective(target=NumericalTarget(name="yield", mode="MAX"))
We now finally create the campaign using the objects configure previously.
campaign = Campaign(
searchspace=searchspace,
objective=objective,
)
Getting a recommendation and adding measurements¶
We use the recommend() function of the campaign for getting measurements.
recommendation = campaign.recommend(batch_size=2)
print("\n\nRecommended measurements with batch_size = 2: ")
print(recommendation)
Recommended measurements with batch_size = 2:
Solvent Base Ligand Temperature \
357 p-Xylene Cesium pivalate Di-tert-butylphenylphosphine 120.0
187 Butyl Ester Cesium pivalate BrettPhos 120.0
Concentration
357 0.057
187 0.100
Adding target values is done by creating a new column in the recommendation
dataframe named after the target.
In this example, we use the add_fake_results() utility to create fake results.
We then update the campaign by adding the measurements.
add_fake_results(recommendation, campaign.targets)
print("\n\nRecommended experiments with fake measured values: ")
print(recommendation)
Recommended experiments with fake measured values:
Solvent Base Ligand Temperature \
357 p-Xylene Cesium pivalate Di-tert-butylphenylphosphine 120.0
187 Butyl Ester Cesium pivalate BrettPhos 120.0
Concentration yield
357 0.057 31.359262
187 0.100 20.929889
campaign.add_measurements(recommendation)