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.objective import Objective
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('CC(N(C)C)=O')
_______________________________________smiles_to_mordred_features - 0.2s, 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('CCCCOC(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 - 0.0s, 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('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('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 - 0.2s, 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(‘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
In this example, we maximize the yield of a reaction and define a corresponding objective.
objective = Objective(
mode="SINGLE", targets=[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 \
173 Butyornitrile Cesium acetate Di-tert-butylphenylphosphine
424 p-Xylene Cesium pivalate (t-Bu)PhCPhos
Temperature Concentration
173 90.0 0.153
424 90.0 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)
print("\n\nRecommended experiments with fake measured values: ")
print(recommendation)
Recommended experiments with fake measured values:
Solvent Base Ligand \
173 Butyornitrile Cesium acetate Di-tert-butylphenylphosphine
424 p-Xylene Cesium pivalate (t-Bu)PhCPhos
Temperature Concentration yield
173 90.0 0.153 16.303332
424 90.0 0.100 30.308258
campaign.add_measurements(recommendation)