scikit-learn / scikit-learn/scikit-learn
`SequentialFeatureSelector` is not passing pandas df to estimator/pipeline
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Description
Describe the bug
SequentialFeatureSelector cannot be used with a pipeline that expects a pandas dataframe (e.g. a one containing a ColumnTransformer) as an input.
At the same time the same pipeline can be used in cross_val_score.
Steps/Code to Reproduce
from sklearn.feature_selection import SequentialFeatureSelector
from sklearn.compose import ColumnTransformer
from sklearn.preprocessing import StandardScaler
from sklearn.compose import make_column_selector
from sklearn.pipeline import Pipeline
from sklearn.linear_model import LogisticRegression
from sklearn.model_selection import cross_val_score
import pandas as pd
import numpy as np
df = pd.DataFrame(data=np.random.rand(10,4), columns=["1","2", "3", "4"])
y = np.random.randint(0,2, size=(10,))
ct = ColumnTransformer(
transformers=[
("numerical", StandardScaler(), make_column_selector(pattern="1")),
],
remainder="passthrough",
)
pipeline = Pipeline([("ct", ct), ("lr", LogisticRegression())])
# this works
print("cross_val_score", cross_val_score(pipeline, df, y, cv=2))
sfs = SequentialFeatureSelector(pipeline, cv=2)
sfs.fit(df, y=y)
Expected Results
No error is thrown and the features are selected.
Actual Results
....sklearn/model_selection/_validation.py:372: FitFailedWarning:
2 fits failed out of a total of 2.
...
ValueError: make_column_selector can only be applied to pandas dataframes
Versions
System:
python: 3.9.5 (default, Nov 23 2021, 15:27:38) [GCC 9.3.0]
executable: /root/.cache/pypoetry/virtualenvs/science-yd9zGFjU-py3.9/bin/python
machine: Linux-5.13.0-35-generic-x86_64-with-glibc2.31
Python dependencies:
pip: 22.0.3
setuptools: 60.9.3
sklearn: 1.0.2
numpy: 1.19.5
scipy: 1.8.0
Cython: None
pandas: 1.4.1
matplotlib: 3.5.1
joblib: 1.1.0
threadpoolctl: 3.1.0
Built with OpenMP: True
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by running the provided SequentialFeatureSelector reproduction with the pandas DataFrame, ColumnTransformer, and pipeline. Trace where SequentialFeatureSelector prepares data for estimator fits and compare it with the working cross_val_score path. Done means the example completes without the pandas-dataframe error and selects features successfully.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- pandas, python
- Domain
- machine-learning
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100