Cardea
import pandas as pd from cardea.data_loader import DataLoader from cardea.problem_definition import ProblemDefinition [docs]class DiagnosisPrediction (ProblemDefinition): """Defines the problem of diagnosis Prediction. Finding whether a patient will be diagnosed with a specifed diagnosis. Args: target_label_column_name (str): The target label of the prediction problem. target_entity (str): Name of the entity containing the target label. cutoff_time_label (str): The cutoff time label of the prediction problem. cutoff_entity (str): Name of the entity containing the cutoff time label. prediction_type (str): The type of the machine learning prediction. """ __name__ = 'diagnosis' updated_es = None target_label_column_name = 'diagnosis' target_entity = 'Encounter' cutoff_time_label = 'start' cutoff_entity = 'Period' prediction_type = 'classification' conn = 'period' [docs] def __init__(self, d): self.diagnosis = d [docs] def generate_cutoff_times(self, es): """Generates cutoff times for the prediction problem. Args: es (featuretools.EntitySet): An EntitySet with the loaded data. 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. Raises: ValueError: An error occurs if the cutoff variable does not exist. """ es = self.generate_target_label(es) if DataLoader().check_column_existence( es, self.cutoff_entity, self.cutoff_time_label): # check the existance of the cutoff label generated_cts = self.unify_cutoff_time_admission_time( es, self.cutoff_entity, self.cutoff_time_label) es = es.entity_from_dataframe(entity_id=self.cutoff_entity, dataframe=generated_cts, index='object_id') cutoff_times = es[self.cutoff_entity].df['ct'].to_frame() label = es[self.target_entity].df[self.conn].values instance_id = list(es[self.target_entity].df.index) cutoff_times = cutoff_times.reindex(index=label) cutoff_times = cutoff_times[cutoff_times.index.isin(label)] cutoff_times['instance_id'] = instance_id cutoff_times.columns = ['time', 'instance_id'] cutoff_times['label'] = list(es[self.target_entity].df[self.target_label_column_name]) cutoff_times['label'] = cutoff_times['label'] == self.diagnosis return(es, self.target_entity, cutoff_times) else: raise ValueError('Cutoff time label {} in table {} does not exist'.format( self.cutoff_time_label, self.target_entity)) def generate_target_label(self, es): """Generates target labels in the case of having missing label in the entityset. Args: es: fhir entityset. Returns: Updated entityset with the generated label. Raises: ValueError: An error occurs if the target label cannot be generated. """ generate_from = 'Period' if (self.check_target_label( es, self.target_entity, self.target_label_column_name)): if not DataLoader().check_for_missing_values(es, self.target_entity, self.target_label_column_name): entity_set_df = es[self.target_entity].df merging_coding = pd.merge(es['Coding'].df, es['CodeableConcept'].df, left_on='object_id', right_on='coding', how='left') merging_condtion = pd.merge(merging_coding, es['Condition'].df, left_on='object_id_y', right_on='code', how='left') merging_diagnosis = pd.merge( merging_condtion, es['Encounter_Diagnosis'].df, left_on='identifier', right_on='condition', how='left') merging_encouter = pd.merge(merging_diagnosis, es[self.target_entity].df, left_on='subject', right_on='identifier', how='left') merging_encouter['target'] = merging_encouter['code_x'] set(es[self.target_entity].df.identifier) entity_set_df[self.target_label_column_name] = list(merging_encouter['target']) es = es.entity_from_dataframe(entity_id=self.target_entity, dataframe=entity_set_df, index='identifier') return es else: raise ValueError( 'Can not generate target label {} in table {} beacuse end label in \ table {} contains missing value.'.format( self.target_label_column_name, self. target_entity, generate_from)) else: raise ValueError( 'Can not generate target label {} in table {}.'.format( self.target_label_column_name, self.target_entity))