I am trying to use GridSearchCV
with multiple scoring metrics, one of which, the adjusted R2. The latter, as far I am concerned, is not implemented in scikit-learn
. I would like to confirm whether my approach is the correct one to implement the adjusted R2.
Using the scores implemented in scikit-learn
(in the example below MAE and R2), I can do something like shown below (in this dummy example I am ignoring good practices, like feature scaling and a suitable number of iterations for SVR):
import numpy as np
from sklearn.svm import SVR
from sklearn.metrics import make_scorer
from sklearn.model_selection import GridSearchCV
from sklearn.metrics import r2_score, mean_absolute_error
#generate input
X = np.random.normal(75, 10, (1000, 2))
y = np.random.normal(200, 20, 1000)
#perform grid search
params = {"degree": [2, 3], "max_iter": [10]}
grid = GridSearchCV(SVR(), param_grid=params,
scoring={"MAE": "neg_mean_absolute_error", "R2": "r2"}, refit="R2")
grid.fit(X, y)
The example above will report the MAE and R2 for each cross-validated partition and will refit the best parameters based on the best R2. Following this example, I have attempted to do the same using a custom scorer:
def adj_r2(true, pred, p=2):
'''p is the number of independent variables and n is the sample size'''
n = true.size
return 1 - ((1 - r2_score(true, pred)) * (n - 1))/(n-p-1)
scorer=make_scorer(adj_r2)
grid = GridSearchCV(SVR(), param_grid=params,
scoring={"MAE": "neg_mean_absolute_error", "adj R2": scorer}, refit="adj R2")
grid.fit(X, y)
#print(grid.cv_results_)
The code above appears to generate values for the "adj R2" scorer. I have two questions:
GridSearchCV
.Firstly, adjusted R2 score is not available in sklearn so far because the API of scoring functions just takes y_true
and y_pred
. Hence, measuring the dimensions of X is out of question.
We can do a work around for SearchCV
s.
The scorer needs to have a signature of (estimator, X, y)
. This has been delivered in the make_scorer
here.
I have provided a more simplified version of that here for wrapping the r2 scorer.
def adj_r2(estimator, X, y_true):
n, p = X.shape
pred = estimator.predict(X)
return 1 - ((1 - r2_score(y_true, pred)) * (n - 1))/(n-p-1)
grid = GridSearchCV(SVR(), param_grid=params,
scoring={"MAE": "neg_mean_absolute_error",
"adj R2": adj_r2}, refit="adj R2")
grid.fit(X, y)