Managing imbalanced Data Sets with SMOTE in Python

Posted on July 1, 2019 Updated on March 11, 2020

When working with data sets for machine learning, lots of these data sets and examples we see have approximately the same number of case records for each of the possible predicted values. In this kind of scenario we are trying to perform some kind of classification, where the machine learning model looks to build a model based on the input data set against a target variable. It is this target variable that contains the value to be predicted. In most cases this target variable (or feature) will contain binary values or equivalent in categorical form such as Yes and No, or A and B, etc or may contain a small number of other possible values (e.g. A, B, C, D).

For the classification algorithm to perform optimally and be able to predict the possible value for a new case record, it will need to see enough case records for each of the possible values. What this means, it would be good to have approximately the same number of records for each value (there are many ways to overcome this and these are outside the score of this post). But most data sets, and those that you will encounter in real life work scenarios, are never balanced, as in having a 50-50 split. What we typically encounter might be a 90-10, 98-2, etc type of split. These data sets are said to be imbalanced.

The image above gives examples of two approaches for creating a balanced data set. The first is under-sampling. This involves reducing the class that contains the majority of the case records and reducing it to match the number of case records in the minor class. The problems with this include, the resulting data set is too small to be meaningful, the case records removed could contain important records and scenarios that the model will need to know about.

The second example is creating a balanced data set by increasing the number of records in the minority class. There are a few approaches to creating this. The first approach is to create duplicate records, from the minor class, until such time as the number of case records are approximately the same for each class. This is the simplest approach. The second approach is to create synthetic records that are statistically equivalent of the original data set. A commonly technique used for this is called SMOTE, Synthetic Minority Oversampling Technique. SMOTE uses a nearest neighbors algorithm to generate new and synthetic data we can use for training our model. But one of the issues with SMOTE is that it will not create sample records outside the bounds of the original data set. As you can image this would be very difficult to do.

The following examples will illustrate how to perform Under-Sampling and Over-Sampling (duplication and using SMOTE) in Python using functions from Pandas, Imbalanced-Learn and Sci-Kit Learn libraries.

NOTE: The Imbalanced-Learn library (e.g. SMOTE)requires the data to be in numeric format, as it statistical calculations are performed on these. The python function get_dummies was used as a quick and simple to generate the numeric values. Although this is perhaps not the best method to use in a real project. With the other sampling functions can process data sets with a sting and numeric.

Data Set:  Is the Portuaguese Banking data set and is available on the UCI Data Set Repository, and many other sites. Here are some basics with that data set.

import warnings

import pandas as pd
import numpy as np
import matplotlib.pyplot as plt
get_ipython().magic('matplotlib inline')

bank_file = ".../bank-additional-full.csv"

# import dataset
df = pd.read_csv(bank_file, sep=';',)

# get basic details of df (num records, num features)
df.shape

df['y'].value_counts() # dataset is imbalanced with majority of class label as "no".

no     36548
yes     4640
Name: y, dtype: int64

#print bar chart
df.y.value_counts().plot(kind='bar', title='Count (target)');

Example 1a – Down/Under sampling the majority class y=1 (using random sampling)

count_class_0, count_class_1 = df.y.value_counts()

# Divide by class
df_class_0 = df[df['y'] == 0] #majority class
df_class_1 = df[df['y'] == 1] #minority class

# Sample Majority class (y=0, to have same number of records as minority calls (y=1)
df_class_0_under = df_class_0.sample(count_class_1)
# join the dataframes containing y=1 and y=0
df_test_under = pd.concat([df_class_0_under, df_class_1])

print('Random under-sampling:')
print(df_test_under.y.value_counts())
print("Num records = ", df_test_under.shape[0])

df_test_under.y.value_counts().plot(kind='bar', title='Count (target)');

Random under-sampling:
1    4640
0    4640
Name: y, dtype: int64
Num records =  9280

Example 1b – Down/Under sampling the majority class y=1 using imblearn

from imblearn.under_sampling import RandomUnderSampler

X = df_new.drop('y', axis=1)
Y = df_new['y']

rus = RandomUnderSampler(random_state=42, replacement=True)
X_rus, Y_rus = rus.fit_resample(X, Y)

df_rus = pd.concat([pd.DataFrame(X_rus), pd.DataFrame(Y_rus, columns=['y'])], axis=1)

print('imblearn over-sampling:')
print(df_rus.y.value_counts())
print("Num records = ", df_rus.shape[0])

df_rus.y.value_counts().plot(kind='bar', title='Count (target)');

[same results as Example 1a]

Example 1c – Down/Under sampling the majority class y=1 using Sci-Kit Learn

from sklearn.utils import resample

print("Original Data distribution")
print(df['y'].value_counts())

# Down Sample Majority class
down_sample = resample(df[df['y']==0],
replace = True, # sample with replacement
n_samples = df[df['y']==1].shape[0], # to match minority class
random_state=42) # reproducible results

# Combine majority class with upsampled minority class
train_downsample = pd.concat([df[df['y']==1], down_sample])

# Display new class counts
print('Sci-Kit Learn : resample : Down Sampled data set')
print(train_downsample['y'].value_counts())
print("Num records = ", train_downsample.shape[0])
train_downsample.y.value_counts().plot(kind='bar', title='Count (target)');

[same results as Example 1a]

Example 2 a – Over sampling the minority call y=0 (using random sampling)

df_class_1_over = df_class_1.sample(count_class_0, replace=True)
df_test_over = pd.concat([df_class_0, df_class_1_over], axis=0)

print('Random over-sampling:')
print(df_test_over.y.value_counts())

df_test_over.y.value_counts().plot(kind='bar', title='Count (target)');

Random over-sampling:
1    36548
0    36548
Name: y, dtype: int64

Example 2b – Over sampling the minority call y=0 using SMOTE

from imblearn.over_sampling import SMOTE

print(df_new.y.value_counts())
X = df_new.drop('y', axis=1)
Y = df_new['y']

sm = SMOTE(random_state=42)
X_res, Y_res = sm.fit_resample(X, Y)

df_smote_over = pd.concat([pd.DataFrame(X_res), pd.DataFrame(Y_res, columns=['y'])], axis=1)

print('SMOTE over-sampling:')
print(df_smote_over.y.value_counts())

df_smote_over.y.value_counts().plot(kind='bar', title='Count (target)');

[same results as Example 2a]

Example 2c – Over sampling the minority call y=0 using Sci-Kit Learn

from sklearn.utils import resample

print("Original Data distribution")
print(df['y'].value_counts())

# Upsample minority class
train_positive_upsample = resample(df[df['y']==1],
replace = True, # sample with replacement
n_samples = train_zero.shape[0], # to match majority class
random_state=42) # reproducible results

# Combine majority class with upsampled minority class
train_upsample = pd.concat([train_negative, train_positive_upsample])

# Display new class counts
print('Sci-Kit Learn : resample : Up Sampled data set')
print(train_upsample['y'].value_counts())
train_upsample.y.value_counts().plot(kind='bar', title='Count (target)');

[same results as Example 2a]