"""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
