Domain
Domain
Bases: BaseModel
Source code in bofire/data_models/domain/domain.py
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candidate_column_names
property
The columns in the candidate dataframe
Returns:
Type | Description |
---|---|
List[str]: List of columns in the candidate dataframe (input feature keys + input feature keys_pred, input feature keys_sd, input feature keys_des) |
constraints = Field(default_factory=lambda: Constraints())
class-attribute
instance-attribute
Representation of the optimization problem/domain
Attributes:
Name | Type | Description |
---|---|---|
inputs |
List[Input]
|
List of input features. Defaults to []. |
outputs |
List[Output]
|
List of output features. Defaults to []. |
constraints |
List[Constraint]
|
List of constraints. Defaults to []. |
experiment_column_names
property
The columns in the experimental dataframe
Returns:
Type | Description |
---|---|
List[str]: List of columns in the experiment dataframe (output feature keys + valid_output feature keys) |
aggregate_by_duplicates(experiments, prec, delimiter='-', method='mean')
Aggregate the dataframe by duplicate experiments
Duplicates are identified based on the experiments with the same input features. Continuous input features are rounded before identifying the duplicates. Aggregation is performed by taking the average of the involved output features.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
experiments
|
DataFrame
|
Dataframe containing experimental data |
required |
prec
|
int
|
Precision of the rounding of the continuous input features |
required |
delimiter
|
str
|
Delimiter used when combining the orig. labcodes to a new one. Defaults to "-". |
'-'
|
method
|
Literal['mean', 'median']
|
Which aggregation method to use. Defaults to "mean". |
'mean'
|
Returns:
Type | Description |
---|---|
Tuple[DataFrame, list]
|
Tuple[pd.DataFrame, list]: Dataframe holding the aggregated experiments, list of lists holding the labcodes of the duplicates |
Source code in bofire/data_models/domain/domain.py
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coerce_invalids(experiments)
Coerces all invalid output measurements to np.nan
Parameters:
Name | Type | Description | Default |
---|---|---|---|
experiments
|
DataFrame
|
Dataframe containing experimental data |
required |
Returns:
Type | Description |
---|---|
DataFrame
|
pd.DataFrame: coerced dataframe |
Source code in bofire/data_models/domain/domain.py
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describe_experiments(experiments)
Method to get a tabular overview of how many measurements and how many valid entries are included in the input data for each output feature
Parameters:
Name | Type | Description | Default |
---|---|---|---|
experiments
|
DataFrame
|
Dataframe with experimental data |
required |
Returns:
Type | Description |
---|---|
DataFrame
|
pd.DataFrame: Dataframe with counts how many measurements and how many valid entries are included in the input data for each output feature |
Source code in bofire/data_models/domain/domain.py
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get_nchoosek_combinations(exhaustive=False)
Get all possible NChooseK combinations
Parameters:
Name | Type | Description | Default |
---|---|---|---|
exhaustive
|
bool
|
if True all combinations are returned. Defaults to False. |
False
|
Returns:
Name | Type | Description |
---|---|---|
Tuple |
(used_features_list, unused_features_list)
|
used_features_list is a list of lists containing features used in each NChooseK combination. unused_features_list is a list of lists containing features unused in each NChooseK combination. |
Source code in bofire/data_models/domain/domain.py
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validate_candidates(candidates, only_inputs=False, tol=1e-05, raise_validation_error=True)
Method to check the validty of proposed candidates
Parameters:
Name | Type | Description | Default |
---|---|---|---|
candidates
|
DataFrame
|
Dataframe with suggested new experiments (candidates) |
required |
only_inputs
|
(bool, optional)
|
If True, only the input columns are validated. Defaults to False. |
False
|
tol
|
(float, optional)
|
tolerance parameter for constraints. A constraint is considered as not fulfilled if the violation is larger than tol. Defaults to 1e-6. |
1e-05
|
raise_validation_error
|
bool
|
If true an error will be raised if candidates violate constraints, otherwise only a warning will be displayed. Defaults to True. |
True
|
Raises:
Type | Description |
---|---|
ValueError
|
when a column is missing for a defined input feature |
ValueError
|
when a column is missing for a defined output feature |
ValueError
|
when a non-numerical value is proposed |
ValueError
|
when an additional column is found |
ConstraintNotFulfilledError
|
when the constraints are not fulfilled and |
Returns:
Type | Description |
---|---|
DataFrame
|
pd.DataFrame: dataframe with suggested experiments (candidates) |
Source code in bofire/data_models/domain/domain.py
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validate_constraints()
Validate that the constraints defined in the domain fit to the input features.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
v
|
List[Constraint]
|
List of constraints or empty if no constraints are defined |
required |
values
|
List[Input]
|
List of input features of the domain |
required |
Raises:
Type | Description |
---|---|
ValueError
|
Feature key in constraint is unknown. |
Returns:
Type | Description |
---|---|
List[Constraint]: List of constraints defined for the domain |
Source code in bofire/data_models/domain/domain.py
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validate_experiments(experiments, strict=False)
Checks the experimental data on validity
Parameters:
Name | Type | Description | Default |
---|---|---|---|
experiments
|
DataFrame
|
Dataframe with experimental data |
required |
strict
|
bool
|
Boolean to distinguish if the occurrence of fixed features in the dataset should be considered or not. Defaults to False. |
False
|
Raises:
Type | Description |
---|---|
ValueError
|
empty dataframe |
ValueError
|
the column for a specific feature is missing the provided data |
ValueError
|
there are labcodes with null value |
ValueError
|
there are labcodes with nan value |
ValueError
|
labcodes are not unique |
ValueError
|
the provided columns do no match to the defined domain |
ValueError
|
the provided columns do no match to the defined domain |
ValueError
|
Input with null values |
ValueError
|
Input with nan values |
Returns:
Type | Description |
---|---|
DataFrame
|
pd.DataFrame: The provided dataframe with experimental data |
Source code in bofire/data_models/domain/domain.py
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validate_unique_feature_keys()
Validates if provided input and output feature keys are unique
Parameters:
Name | Type | Description | Default |
---|---|---|---|
v
|
Outputs
|
List of all output features of the domain. |
required |
value
|
Dict[str, Inputs]
|
Dict containing a list of input features as single entry. |
required |
Raises:
Type | Description |
---|---|
ValueError
|
Feature keys are not unique. |
Returns:
Name | Type | Description |
---|---|---|
Outputs |
Keeps output features as given. |
Source code in bofire/data_models/domain/domain.py
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