So I have a dataset of shape (430,17), that consists of 13 classes (imbalanced) and 17 features. The end goal is to create a NN which btw works when I import the imblanced dataset, however when i try to over-sample the minority classes using SMOTE in jupyter notebook, the classes do get balanced but also the shape changes.

from imblearn.over_sampling import SMOTE
from sklearn.preprocessing import OneHotEncoder
from imblearn.pipeline import Pipelineenter 

steps = [('onehot', OneHotEncoder()), ('smt', SMOTE())]
pipeline = Pipeline(steps=steps)

X_res, y_res = pipeline.fit_resample(X, y)

The y_res shape is (754,) from y shape which was (430,), so upsampling works, also by checking:

unique, counts = np.unique(y_res, return_counts=True)
print(np.asarray((unique, counts)).T)

the classes have been balanced. However, the X_res shape has now changed to (754, 5553), from X shape which was (430, 17). Then, if I fit these data in my NN it doesnt work of course since the input_dim has changed for my input layer.

My question is, did the SMOTE procedure add not only rows to balance the classes but also columns? Should't I got X_res with shape (754, 17)? and because I need these data for a NN they have to be arrays, or numpys, instead of pd.dataframes, which is also complicated to understand where that 5553 columns come from.

I am new in python and jupyter so I do not know how to solve this, and I would really appreciate any help :)


1 Answer 1


Your understanding is correct: data balancing techniques like SMOTE will only add/remove rows (data points) not columns (features). I suspect your extra dimensions are due to one-hot-encoding.

  • $\begingroup$ Alright, thank you for the reply, but then how can I do a mutliclass balance with SMOTE? without using steps = [('onehot', OneHotEncoder()), ('smt', SMOTE())] pipeline = Pipeline(steps=steps) $\endgroup$
    – rSar
    Dec 9, 2021 at 12:44
  • $\begingroup$ In SMOTE's fit_resample(X, y), you could keep the one-hot-encoding of the X values if you'd like but its not needed.. The y values can be scalar values (binary, or multi classed as is) or LabelEncoded vectors which is what I think you were going after. $\endgroup$
    – eliangius
    Dec 9, 2021 at 14:16

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