def select_problem(self, selection, parameter=None):
"""Select a prediction problem and extract information.
Update the select_problem attribute and generate the cutoff times,
the target entity and update the entityset.
Args:
selection: Name of the chosen prediction problem.
data: Entityset representation of the data.
parameters: A variable to change the default parameters, if any.
Returns:
The updated version of the entityset and cutoff time label.
"""
# problem selection
if selection == 'LengthOfStay':
self.chosen_problem = LengthOfStay()
elif selection == 'MortalityPrediction':
self.chosen_problem = MortalityPrediction()
elif selection == 'MissedAppointmentProblemDefinition':
self.chosen_problem = MissedAppointmentProblemDefinition()
elif selection == 'ProlongedLengthOfStay' and parameter:
self.chosen_problem = ProlongedLengthOfStay(parameter)
elif selection == 'ProlongedLengthOfStay':
self.chosen_problem = ProlongedLengthOfStay()
elif selection == 'Readmission' and parameter:
self.chosen_problem = Readmission(parameter)
elif selection == 'Readmission':
self.chosen_problem = Readmission()
elif selection == 'DiagnosisPrediction' and parameter:
self.chosen_problem = DiagnosisPrediction(parameter)
elif selection == 'DiagnosisPrediction':
raise ValueError('unspecified diagnosis code')
else:
raise ValueError('{} is not a defined problem'.format(selection))
# target label calculation
self.es, self.target_entity, cutoff = self.chosen_problem.generate_cutoff_times(
self.es)
return cutoff
class Cardea():
"""An interface class that ties the end-to-end system together.
Args:
es_loader (EntitySetLoader):
An entityset loader.
featurization (Featurization):
A featurization class.
modeler (Modeler):
A modeling class.
problems (list):
A list of currently available prediction problems.
chosen_problem (str):
The selected prediction problem or regression.
es (featuretools.EntitySet):
The loaded entityset.
target_entity (str):
The target entity for featurization.
"""
def __init__(self):
self.es_loader = EntitySetLoader()
self.featurization = Featurization()
self.es = None
self.chosen_problem = None
self.target_entity = None
self.modeler = None
def load_entityset(self, data, fhir=True):
"""Returns an entityset loaded with .csv files in data.
Load the given dataset into an entityset. The dataset
must be in FHIR or MIMIC structure format.
Args:
data (str):
A directory of all .csv files that should be loaded. To load demo dataset,
pass the name of the dataset "kaggle" or "mimic".
fhir (bool):
An indicator of whether to use FHIR or MIMIC schema.
Returns:
featuretools.EntitySet:
An entityset with loaded data.
"""
demo = ['kaggle', 'mimic']
if not os.path.exists(data) and data in demo:
data = self.download_demo(data)
if fhir:
self.es = self.es_loader.load_data_entityset(data)
else:
self.es = load_mimic_data(data)
@staticmethod
def download_demo(name, data_path=DATA_PATH):
data_path = os.path.join(data_path, name)
os.makedirs(data_path, exist_ok=True)
url = S3_URL.format(BUCKET, '{}.zip'.format(name))
compressed = ZipFile(BytesIO(urlopen(url).read()))
LOGGER.info('Downloading dataset %s from %s', name, url)
for file in compressed.namelist():
filename = os.path.join(data_path, file)
csv_file = compressed.open(file)
data = pd.read_csv(csv_file, dtype=str)
data.to_csv(filename, index=False)
return data_path
def list_problems(self):
"""Returns a list of the currently available problems.
Returns:
list:
A list of the available problems.
"""
problems = set([])
for attribute_string in dir(cardea.problem_definition):
attribute = getattr(cardea.problem_definition, attribute_string)
if isclass(attribute):
if attribute.__name__ and attribute.__name__ != 'ProblemDefinition':
problems.add(attribute.__name__)
return problems
def select_problem(self, selection, parameter=None):
"""Select a prediction problem and extract information.
Update the select_problem attribute and generate the cutoff times,
the target entity and update the entityset.
Args:
selection (str):
Name of the chosen prediction problem.
parameters (dict):
Variables to change the default parameters, if any.
Returns:
featuretools.EntitySet, str, pandas.DataFrame:
* An updated EntitySet if a new column is generated.
* A string indicating the selected target entity.
* A dataframe of cutoff times and their target labels.
"""
LOGGER.info("Selecting %s prediction problem", selection)
# problem selection
if selection == 'LengthOfStay':
self.chosen_problem = LengthOfStay()
elif selection == 'MortalityPrediction':
self.chosen_problem = MortalityPrediction()
elif selection == 'MissedAppointment':
self.chosen_problem = MissedAppointment()
elif selection == 'ProlongedLengthOfStay' and parameter:
self.chosen_problem = ProlongedLengthOfStay(parameter)
elif selection == 'ProlongedLengthOfStay':
self.chosen_problem = ProlongedLengthOfStay()
elif selection == 'Readmission' and parameter:
self.chosen_problem = Readmission(parameter)
elif selection == 'Readmission':
self.chosen_problem = Readmission()
elif selection == 'DiagnosisPrediction' and parameter:
self.chosen_problem = DiagnosisPrediction(parameter)
elif selection == 'DiagnosisPrediction':
raise ValueError('unspecified diagnosis code')
else:
raise ValueError('{} is not a defined problem'.format(selection))
# target label calculation
self.es, self.target_entity, cutoff = self.chosen_problem.generate_cutoff_times(self.es)
# set default pipeline
if self.chosen_problem.prediction_type == "classification":
pipeline = "Random Forest"
else:
pipeline = "Random Forest Regressor"
self.modeler = Modeler(pipeline, self.chosen_problem.prediction_type)
return cutoff
def list_feature_primitives(self):
"""Returns built-in primitive in Featuretools.
Returns:
pandas.DataFrame:
A dataframe that lists and describes each built-in primitives.
"""
return ft.list_primitives()
def generate_features(self, cutoff):
"""Returns a the calculated feature matrix.
Args:
es (featuretools.EntitySet):
An entityset that holds data.
cutoff (pandas.DataFrame):
A dataframe that indicates cutoff time for each instance.
Returns:
pandas.DataFrame, list:
* The generated feature matrix.
* List of feature definitions in the feature matrix.
"""
fm_encoded, _ = self.featurization.generate_feature_matrix(
self.es, self.target_entity, cutoff)
fm_encoded = fm_encoded.reset_index(drop=True)
return fm_encoded
def select_pipeline(self, pipeline):
"""Select a pipeline.
Args:
pipeline (MLPipeline or str):
A pipeline instance or the name/path of a pipeline.
"""
LOGGER.info("Selecting %s pipeline", pipeline)
self.modeler = Modeler(pipeline, self.chosen_problem.prediction_type)
def train_test_split(self, X, y, test_size, shuffle):
"""Split the training dataset and the testing dataset.
Args:
X (pandas.DataFrame or ndarray):
Inputs to the pipeline.
y (pandas.Series or ndarray):
Target values.
test_size (float):
The proportion of the dataset to include in the test dataset.
shuffle (bool):
Whether or not to shuffle the data before splitting.
Returns:
list:
List containing the train-test split of the inputs and targets.
"""
return self.modeler.train_test_split(X, y, test_size, shuffle)
def fit(self, X, y, tune=False, max_evals=10, scoring=None, verbose=False):
"""Train the cardea pipeline.
Args:
X (pandas.DataFrame or ndarray):
Inputs to the pipeline.
y (pandas.Series ndarray):
Target values.
tune (bool):
Whether to optimize hyper-parameters of the pipelines.
max_evals (int):
Maximum number of hyper-parameter optimization iterations.
scoring (str):
The name of the scoring function used in the hyper-parameter optimization.
verbose (bool):
Whether to log information during processing.
"""
self.modeler.fit(X, y, tune, max_evals, scoring, verbose)
def predict(self, X):
"""Get predictions from the cardea pipeline.
Args:
X (pandas.DataFrame or ndarray):
Inputs to the pipeline.
Returns:
ndarray:
Predictions to the input data.
"""
return self.modeler.predict(X)
def fit_predict(self, X, y, tune=False, max_evals=10, scoring=None, verbose=False):
"""Train a cardea pipeline then make predictions.
Args:
X (pandas.DataFrame or ndarray):
Inputs to the pipeline.
y (pandas.Series or ndarray):
Target values.
tune (bool):
Whether to optimize hyper-parameters of the pipelines.
max_evals (int):
Maximum number of hyper-parameter optimization iterations.
scoring (str):
The name of the scoring function used in the hyper-parameter optimization.
verbose (bool):
Whether to log information during processing.
Returns:
ndarray:
Predictions to the input data.
"""
return self.modeler.fit_predict(X, y, tune, max_evals, scoring, verbose)
def evaluate(self, X, y, test_size=0.2, shuffle=True, tune=False, max_evals=10, scoring=None,
metrics=None, verbose=False):
"""Evaluate the cardea pipeline.
Args:
X (pandas.DataFrame or ndarray):
Inputs to the pipeline.
y (pandas.Series or ndarray):
Target values.
test_size (float):
The proportion of the dataset to include in the test dataset.
shuffle (bool):
Whether or not to shuffle the data before splitting.
tune (bool):
Whether to optimize hyper-parameters of the pipelines.
max_evals (int):
Maximum number of hyper-parameter optimization iterations.
scoring (str):
The name of the scoring function used in the hyper-parameter optimization.
metrics (list):
A list of scoring function names. The scoring functions should be consistent
with the problem type.
verbose (bool):
Whether to log information during processing.
"""
return self.modeler.evaluate(
X, y, test_size, shuffle, tune, max_evals, scoring, metrics, verbose)
def save(self, path):
"""Save this object using pickle.
Args:
path (str):
Path to the file where the serialization of
this object will be stored.
"""
os.makedirs(os.path.dirname(path), exist_ok=True)
with open(path, 'wb') as pickle_file:
pickle.dump(self, pickle_file)
@classmethod
def load(cls, path: str):
"""Load an Orion instance from a pickle file.
Args:
path (str):
Path to the file where the instance has been
previously serialized.
Returns:
Cardea:
A Cardea instance
Raises:
ValueError:
If the serialized object is not an Cardea instance.
"""
with open(path, 'rb') as pickle_file:
cardea = pickle.load(pickle_file)
if not isinstance(cardea, cls):
raise ValueError('Serialized object is not a Cardea instance')
return cardea
class Cardea():
"""An interface class that ties the end-to-end system together.
Attributes:
es_loader: An entityset loader.
featurization: A featurization class.
modeler: A modeling class.
problems: A list of currently available prediction problems.
chosen_problem: The selected prediction problem or regression.
es: The loaded entityset.
target_entity: The target entity for featurization.
"""
def __init__(self):
self.es_loader = EntitySetLoader()
self.featurization = Featurization()
self.modeler = Modeler()
self.es = None
self.chosen_problem = None
self.target_entity = None
def load_data_entityset(self, folder_path=None):
"""Returns an entityset loaded with .csv files in folder_path.
Load the given dataset within the folder path into an entityset. The dataset
must be in a FHIR structure format. If no folder_path is not passed, the
function will automatically load kaggle's missed appointment dataset.
Args:
folder_path: A directory of all .csv files that should be loaded.
Returns:
An entityset with loaded data.
"""
if folder_path:
self.es = self.es_loader.load_data_entityset(folder_path)
else:
csv_s3 = "https://s3.amazonaws.com/dai-cardea/"
kaggle = [
'Address', 'Appointment_Participant', 'Appointment',
'CodeableConcept', 'Coding', 'Identifier', 'Observation',
'Patient', 'Reference'
]
fhir = {
resource: pd.read_csv(csv_s3 + resource + ".csv")
for resource in kaggle
}
self.es = self.es_loader.load_df_entityset(fhir)
def list_problems(self):
"""Returns a list of the currently available problems.
Returns:
A set of the available problems.
"""
problems = set([])
for attribute_string in dir(cardea.problem_definition):
attribute = getattr(cardea.problem_definition, attribute_string)
if isclass(attribute):
if attribute.__name__ and attribute.__name__ != 'ProblemDefinition':
problems.add(attribute.__name__)
return problems
def select_problem(self, selection, parameter=None):
"""Select a prediction problem and extract information.
Update the select_problem attribute and generate the cutoff times,
the target entity and update the entityset.
Args:
selection: Name of the chosen prediction problem.
data: Entityset representation of the data.
parameters: A variable to change the default parameters, if any.
Returns:
The updated version of the entityset and cutoff time label.
"""
# problem selection
if selection == 'LengthOfStay':
self.chosen_problem = LengthOfStay()
elif selection == 'MortalityPrediction':
self.chosen_problem = MortalityPrediction()
elif selection == 'MissedAppointmentProblemDefinition':
self.chosen_problem = MissedAppointmentProblemDefinition()
elif selection == 'ProlongedLengthOfStay' and parameter:
self.chosen_problem = ProlongedLengthOfStay(parameter)
elif selection == 'ProlongedLengthOfStay':
self.chosen_problem = ProlongedLengthOfStay()
elif selection == 'Readmission' and parameter:
self.chosen_problem = Readmission(parameter)
elif selection == 'Readmission':
self.chosen_problem = Readmission()
elif selection == 'DiagnosisPrediction' and parameter:
self.chosen_problem = DiagnosisPrediction(parameter)
elif selection == 'DiagnosisPrediction':
raise ValueError('unspecified diagnosis code')
else:
raise ValueError('{} is not a defined problem'.format(selection))
# target label calculation
self.es, self.target_entity, cutoff = self.chosen_problem.generate_cutoff_times(
self.es)
return cutoff
def list_feature_primitives(self):
"""Returns built-in primitive in Featuretools.
Returns:
A pandas dataframe that lists and describes each built-in primitives.
"""
return ft.list_primitives()
def generate_features(self, cutoff):
"""Returns a the calculated feature matrix.
Args:
es: A featuretools entityset that holds data.
cutoff: A pandas dataframe that indicates cutoff_time for each instance.
Returns:
Encoded feature_matrix, encoded features.
"""
fm_encoded, _ = self.featurization.generate_feature_matrix(
self.es, self.target_entity, cutoff)
fm_encoded = fm_encoded.reset_index(drop=True)
return fm_encoded
def execute_model(self,
feature_matrix,
target,
primitives,
optimize=False,
hyperparameters=None):
"""Executes and predict all the pipelines.
This method executes the given pipeline and returns a list for all the pipelines
with the result of each fold with its associated predicted values and actual values.
Args:
data_frame: A dataframe, which encapsulates all the records of that entity.
primitives_list: A list of the primitives within a pipeline.
optimize: A boolean value which indicates whether to optimize the model or not.
hyperparameters: A dictionary of hyperparameters for each primitives.
Returns:
A list for all the executed pipelines and its result.
"""
return self.modeler.execute_pipeline(
data_frame=feature_matrix,
target=target,
primitives_list=primitives,
problem_type=self.chosen_problem.prediction_type,
optimize=False,
hyperparameters=None)
def convert_to_json(dic):
"""Converts a given dictionary to json format.
Args:
dict: A dictionary of values to be coverted.
Returns:
A string in json format.
"""
return json.dumps(dic)
def convert_from_json(string):
"""Converts a given json string to dictionary format.
Args:
json: A dictionary of values to be coverted.
Returns:
A parsed dictionary.
"""
return json.loads(string)
def select_problem(self, selection, parameter=None):
"""Select a prediction problem and extract information.
Update the select_problem attribute and generate the cutoff times,
the target entity and update the entityset.
Args:
selection (str):
Name of the chosen prediction problem.
parameters (dict):
Variables to change the default parameters, if any.
Returns:
featuretools.EntitySet, str, pandas.DataFrame:
* An updated EntitySet if a new column is generated.
* A string indicating the selected target entity.
* A dataframe of cutoff times and their target labels.
"""
LOGGER.info("Selecting %s prediction problem", selection)
# problem selection
if selection == 'LengthOfStay':
self.chosen_problem = LengthOfStay()
elif selection == 'MortalityPrediction':
self.chosen_problem = MortalityPrediction()
elif selection == 'MissedAppointment':
self.chosen_problem = MissedAppointment()
elif selection == 'ProlongedLengthOfStay' and parameter:
self.chosen_problem = ProlongedLengthOfStay(parameter)
elif selection == 'ProlongedLengthOfStay':
self.chosen_problem = ProlongedLengthOfStay()
elif selection == 'Readmission' and parameter:
self.chosen_problem = Readmission(parameter)
elif selection == 'Readmission':
self.chosen_problem = Readmission()
elif selection == 'DiagnosisPrediction' and parameter:
self.chosen_problem = DiagnosisPrediction(parameter)
elif selection == 'DiagnosisPrediction':
raise ValueError('unspecified diagnosis code')
else:
raise ValueError('{} is not a defined problem'.format(selection))
# target label calculation
self.es, self.target_entity, cutoff = self.chosen_problem.generate_cutoff_times(self.es)
# set default pipeline
if self.chosen_problem.prediction_type == "classification":
pipeline = "Random Forest"
else:
pipeline = "Random Forest Regressor"
self.modeler = Modeler(pipeline, self.chosen_problem.prediction_type)
return cutoff