I have unbalanced classes. Group1 N = 140 Group2 N = 35 Group3 N = 30

I ran the code on this data and all the Groups got classified as Group1. I thought that since group1 is the majority group this is not a surprise. Then i ran the same code but this time with SMOTE, now all groups are 140, and i still got the same results, where all the groups were classified in Group1. Then i balanced the class weights (W/O SMOTE), but still got the same results. This was confusing to me. What am i doing wrong? Can someone help me understand this please? or what can i do to improve the model? I tried 5 different classifiers (KNN, AdaBoost, SVC, RF, DT) and in 4 out of 6 i got the same result!

Here's the code:

#Splitting data to training and testing 
X_train, X_test, y_train, y_test = train_test_split (X, y, test_size = 0.1, random_state=42)

#Apply StandardScaler for feature scaling
sc = StandardScaler()
X_train_std = sc.fit_transform(X_train)
X_test_std = sc.transform (X_test)

sm = SMOTE(random_state=42)
X_balanced, y_balanced = sm.fit_sample(X_train_std, y_train)

pca = PCA(random_state=42)

#Classifier regularization (SVC).

svc = SVC(random_state=42, class_weight= 'balanced')
pipe_svc = Pipeline(steps=[('pca', pca), ('svc', svc)])

# Parameters of pipelines can be set using ‘__’ separated parameter names:
parameters_svc = [{'pca__n_components': [2, 5, 20, 30, 40, 50, 60, 70, 80, 90, 100, 140, 150]}, 
                   {'svc__C':[1, 10, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, 200, 250, 300, 400, 500], 
                    'svc__kernel':['rbf', 'linear','poly'], 
                    'svc__gamma': [0.05, 0.06, 0.07, 0.08, 0.09, 0.001, 0.002, 0.003, 0.004, 0.005, 0.006, 0.007, 
                                   0.008,0.009, 0.0001, 0.0002, 0.0003, 0.0004, 0.0005],
                    'svc__degree': [1, 2, 3, 4, 5, 6],
                    'svc__gamma': ['auto', 'scale']}]

clfsvc = GridSearchCV(pipe_svc, param_grid =parameters_svc, iid=False, cv=10,
clfsvc.fit(X_balanced, y_balanced)

# Plot the PCA spectrum (SVC)

fig1, (ax0, ax1) = plt.subplots(nrows=2, sharex=True, figsize=(6, 6)) #(I added 1 to fig)
ax0.plot(pca.explained_variance_ratio_, linewidth=2)
ax0.set_ylabel('PCA explained variance')

            linestyle=':', label='n_components chosen')

# For each number of components, find the best classifier results
results_svc = pd.DataFrame(clfsvc.cv_results_) #(Added _svc to all variable def)
components_col_svc = 'param_pca__n_components'
best_clfs_svc = results_svc.groupby(components_col_svc).apply(
    lambda g: g.nlargest(1, 'mean_test_score'))

best_clfs_svc.plot(x=components_col_svc, y='mean_test_score', yerr='std_test_score',
               legend=False, ax=ax1)
ax1.set_ylabel('Classification accuracy (val)')


#Predicting the test set results (SVC)
y_pred1 = clfsvc.predict(X_test)

# Model Accuracy, how often is the classifier correct?
Accuracyscore_svc = accuracy_score(y_test, y_pred1)

print("Accuracy for SVC on CV data: ", Accuracyscore_svc)

# Making the confusion matrix to describe the performance of a classifier
from sklearn.metrics import confusion_matrix
cm1 = confusion_matrix (y_test, y_pred1)

# Get accuracy score
accuracy1 = accuracy_score(y_test, y_pred1)
print('Accuracy1: %.2f%%' % (accuracy1 * 100.0))

#Checking shape after confusion matrix
print (X_test)
print (y_pred1)

print (cm1)
  • $\begingroup$ What is the loss function that you are using ? Is loss function sensitive to class-imbalance ? $\endgroup$ Commented Mar 10, 2019 at 6:36
  • $\begingroup$ squared_hinge, not sure if it is sensitive to class imbalance, but when I used SMOTE or balanced class weight, shouldn't the data that goes to SVC, not be affected by that? $\endgroup$ Commented Mar 10, 2019 at 6:44
  • $\begingroup$ Can you get more data ? 200 samples might not be enough for model to generalize. $\endgroup$ Commented Mar 10, 2019 at 6:51
  • $\begingroup$ That was the max i could get! Could you kindly suggest something that i could do with the existing data? I really appreciate some help! $\endgroup$ Commented Mar 10, 2019 at 6:53
  • $\begingroup$ How many features are there in data, how many of these are categorical ? $\endgroup$ Commented Mar 10, 2019 at 6:57

1 Answer 1


I found the reason finally. I was using the unstandardized X_test. Thanks.


previously i defined the y_pred like so;

y_pred = clf.predict (xtest) 

and then constructed the confusion matrix like so;

cm = confusion_matrix (y_test, y_pred)

However, i forgot that i previously changed xtest using standard scalar like so;

x_test_std = sc.transform (xtest)

and that the new x_test that should be used is xtest_std not x_test.

When i realized this and used the proper x_test_std, everything worked and made much more sense.

  • 1
    $\begingroup$ Welcome to the site! It's completely OK to answer your own question. But please add some more detail and in the form of an answer so that other people can benefit from it in future searches. $\endgroup$ Commented Mar 13, 2019 at 12:54
  • $\begingroup$ I edited my answer. $\endgroup$ Commented Mar 13, 2019 at 22:57
  • 1
    $\begingroup$ Great! Next you should pick yourself as having the correct answer, it's the green checkbox right below the answer counter. $\endgroup$ Commented Mar 13, 2019 at 23:10

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