Source code for evalml.data_checks.sparsity_data_check

"""Data check that checks if there are any columns with sparsely populated values in the input."""

from evalml.data_checks import (
    DataCheck,
    DataCheckActionCode,
    DataCheckActionOption,
    DataCheckMessageCode,
    DataCheckWarning,
)
from evalml.problem_types import handle_problem_types, is_multiclass
from evalml.utils.woodwork_utils import infer_feature_types

warning_too_unique = "Input columns ({}) for {} problem type are too sparse."


[docs]class SparsityDataCheck(DataCheck): """Check if there are any columns with sparsely populated values in the input. Args: problem_type (str or ProblemTypes): The specific problem type to data check for. 'multiclass' or 'time series multiclass' is the only accepted problem type. threshold (float): The threshold value, or percentage of each column's unique values, below which, a column exhibits sparsity. Should be between 0 and 1. unique_count_threshold (int): The minimum number of times a unique value has to be present in a column to not be considered "sparse." Defaults to 10. """ def __init__(self, problem_type, threshold, unique_count_threshold=10): self.problem_type = handle_problem_types(problem_type) if not is_multiclass(self.problem_type): raise ValueError("Sparsity is only defined for multiclass problem types.") self.threshold = threshold if threshold < 0 or threshold > 1: raise ValueError("Threshold must be a float between 0 and 1, inclusive.") self.unique_count_threshold = unique_count_threshold if unique_count_threshold < 0 or not isinstance(unique_count_threshold, int): raise ValueError("Unique count threshold must be positive integer.")
[docs] def validate(self, X, y=None): """Calculate what percentage of each column's unique values exceed the count threshold and compare that percentage to the sparsity threshold stored in the class instance. Args: X (pd.DataFrame, np.ndarray): Features. y (pd.Series, np.ndarray): Ignored. Returns: dict: dict with a DataCheckWarning if there are any sparse columns. Examples: >>> import pandas as pd For multiclass problems, if a column doesn't have enough representation from unique values, it will be considered sparse. >>> df = pd.DataFrame({ ... "sparse": [float(x) for x in range(100)], ... "not_sparse": [float(1) for x in range(100)] ... }) ... >>> sparsity_check = SparsityDataCheck(problem_type="multiclass", threshold=0.5, unique_count_threshold=10) >>> assert sparsity_check.validate(df) == [ ... { ... "message": "Input columns ('sparse') for multiclass problem type are too sparse.", ... "data_check_name": "SparsityDataCheck", ... "level": "warning", ... "code": "TOO_SPARSE", ... "details": { ... "columns": ["sparse"], ... "sparsity_score": {"sparse": 0.0}, ... "rows": None ... }, ... "action_options": [ ... { ... "code": "DROP_COL", ... "data_check_name": "SparsityDataCheck", ... "parameters": {}, ... "metadata": {"columns": ["sparse"], "rows": None} ... } ... ] ... } ... ] ... >>> df["sparse"] = [float(x % 10) for x in range(100)] >>> sparsity_check = SparsityDataCheck(problem_type="multiclass", threshold=1, unique_count_threshold=5) >>> assert sparsity_check.validate(df) == [] ... >>> sparse_array = pd.Series([1, 1, 1, 2, 2, 3] * 3) >>> assert SparsityDataCheck.sparsity_score(sparse_array, count_threshold=5) == 0.6666666666666666 """ messages = [] X = infer_feature_types(X) res = X.apply( SparsityDataCheck.sparsity_score, count_threshold=self.unique_count_threshold, ) too_sparse_cols = [col for col in res.index[res < self.threshold]] if too_sparse_cols: messages.append( DataCheckWarning( message=warning_too_unique.format( (", ").join( ["'{}'".format(str(col)) for col in too_sparse_cols], ), self.problem_type, ), data_check_name=self.name, message_code=DataCheckMessageCode.TOO_SPARSE, details={ "columns": too_sparse_cols, "sparsity_score": { col: res.loc[col] for col in too_sparse_cols }, }, action_options=[ DataCheckActionOption( DataCheckActionCode.DROP_COL, data_check_name=self.name, metadata={"columns": too_sparse_cols}, ), ], ).to_dict(), ) return messages
[docs] @staticmethod def sparsity_score(col, count_threshold=10): """Calculate a sparsity score for the given value counts by calculating the percentage of unique values that exceed the count_threshold. Args: col (pd.Series): Feature values. count_threshold (int): The number of instances below which a value is considered sparse. Default is 10. Returns: (float): Sparsity score, or the percentage of the unique values that exceed count_threshold. """ counts = col.value_counts() score = sum(counts > count_threshold) / counts.size return score