Consider data
which contains some nan below:
Column-1 Column-2 Column-3 Column-4 Column-5
0 NaN 15.0 63.0 8.0 40.0
1 60.0 51.0 NaN 54.0 31.0
2 15.0 17.0 55.0 80.0 NaN
3 54.0 43.0 70.0 16.0 73.0
4 94.0 31.0 94.0 29.0 53.0
5 99.0 52.0 77.0 91.0 58.0
6 84.0 19.0 36.0 NaN 97.0
7 41.0 91.0 62.0 67.0 68.0
8 44.0 38.0 27.0 53.0 37.0
9 58.0 NaN 63.0 57.0 28.0
10 66.0 68.0 89.0 36.0 47.0
11 7.0 81.0 5.0 99.0 16.0
12 43.0 55.0 64.0 88.0 NaN
13 8.0 90.0 91.0 44.0 4.0
14 29.0 52.0 94.0 71.0 47.0
15 22.0 21.0 68.0 61.0 38.0
16 76.0 36.0 70.0 99.0 50.0
17 38.0 31.0 66.0 79.0 99.0
18 94.0 22.0 92.0 39.0 58.0
I want to replace nan in the data
using sklearn.impute.IterativeImputer
. A friend helped me with the code below:
imp = IterativeImputer(missing_values=np.nan, sample_posterior=False,
max_iter=10, tol=0.001,
n_nearest_features=4, initial_strategy='median')
imp.fit(data)
imputed_data = pd.DataFrame(data=imp.transform(data),
columns=['Column-1', 'Column-2', 'Column-3', 'Column-4', 'Column-5'],
dtype='int')
The imputed_data
is:
Column-1 Column-2 Column-3 Column-4 Column-5
0 59 15 63 8 40
1 60 51 66 54 31
2 15 17 55 80 48
3 54 43 70 16 73
4 94 31 94 29 53
5 99 52 77 91 58
6 84 19 36 59 97
7 41 91 62 67 68
8 44 38 27 53 37
9 58 46 63 57 28
10 66 68 89 36 47
11 7 81 5 99 16
12 43 55 64 88 47
13 8 90 91 44 4
14 29 52 94 71 47
15 22 21 68 61 38
16 76 36 70 99 50
17 38 31 66 79 99
18 94 22 92 39 58
From the IterativeImputer
documentation , the default estimator is BayesianRidge()
. But if I use other estimators such as estimator=ExtraTreesRegressor(n_estimators=10, random_state=0)
like in the code below, it returns a warning message. The code:
imp = IterativeImputer(estimator=ExtraTreesRegressor(n_estimators=10, random_state=0), missing_values=np.nan, sample_posterior=False,
max_iter=10, tol=0.001,
n_nearest_features=4, initial_strategy='median')
imp.fit(data)
The message:
C:\Users\...\sklearn\impute\_iterative.py:599: ConvergenceWarning: [IterativeImputer] Early stopping criterion not reached. " reached.", ConvergenceWarning).
My question: is this a correct approach or should I do something to fix the warning message?
Thank you.
They are having the same issue here:
You are getting this error because of the parameters max_iter=10
& tol=0.001
set for IterativeImputer()
.
The stopping criterion ( abs(max(X_t - X_{t-1}))/abs(max(X[known_vals])) < tol
) is not met for 10 number of iterations( max_iter=10
).
Refer to the description of max_iter
in the parameters section of sklearn.impute.IterativeImputer
documentation .
One workaround to overcome this error is setting the max_iter
parameter value higher.
Have you tried to import ExtraTreesRegressor first. It should work fine.
from sklearn.ensemble import ExtraTreesRegressor.
Also check for the version of scikit learn. It should be 0.21.1 and above.
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