Nasima Tamboli — October 29, 2021
Beginner Data Exploration Python

This article was published as a part of the Data Science Blogathon

Introduction

The problem of missing value is quite common in many real-life datasets. Missing value can bias the results of the machine learning models and/or reduce the accuracy of the model. This article describes what is missing data, how it is represented, and the different reasons for the missing data. Along with the different categories of missing data, it also details out different ways of handling missing values with examples.

The following topics are covered in this guide:

  1. What Is Missing Data (Missing Values)?
  2. How Missing Data/Values Are Represented In The Dataset?
  3. Why Is Data Missing From The Dataset?
  4. Types Of Missing Values
  5. Missing Completely At Random (MCAR)
  6. Missing At Random (MAR)
  7. Missing Not At Random (MNAR)
  8. Why Do We Need To Care About Handling Missing Data?
  9. How To Handle Missing Values?
  10. Checking for missing values
  11. Figure Out How To Handle The Missing Data
  12. Deleting the Missing values
  13. Deleting the Entire Row
  14. Deleting the Entire Column
  15. Imputing the Missing Value
  16. Replacing With Arbitrary Value
  17. Replacing With Mean
  18. Replacing With Mode
  19. Replacing With Median
  20. Replacing with Previous Value – Forward Fill
  21. Replacing with Next Value – Backward Fill
  22. Interpolation
  23. Imputing Missing Values For Categorical Features
  24. Impute the Most Frequent Value
  25. Impute the Value “missing”, which treats it as a Separate Category
  26. Imputation of Missing Values using sci-kit learn library
  27. Univariate Approach
  28. Multivariate Approach
  29. Nearest Neighbors Imputations (KNNImputer)
  30. Adding missing indicator to encode “missingness” as a feature
  31. EndNote

What is a Missing Value?

Missing data is defined as the values or data that is not stored (or not present) for some variable/s in the given dataset.
Below is a sample of the missing data from the Titanic dataset. You can see the columns ‘Age’ and ‘Cabin’ have some missing values.
missing values

Image 1

 

How is Missing Value Represented In The Dataset?

In the dataset, blank shows the missing values.

In Pandas, usually, missing values are represented by NaN.

It stands for Not a Number.

missing value in dataset

Image 2

The above image shows the first few records of the Titanic dataset extracted and displayed using Pandas.

Why Is Data Missing From The Dataset

There can be multiple reasons why certain values are missing from the data.

Reasons for the missing data from the dataset affect the approach of handling missing data. So it’s necessary to understand why the data could be missing.

Some of the reasons are listed below:

  • Past data might get corrupted due to improper maintenance.
  • Observations are not recorded for certain fields due to some reasons. There might be a failure in recording the values due to human error.
  • The user has not provided the values intentionally.

Types Of Missing Value

Formally the missing values are categorized as follows:

types od missing value

Image 3

Missing Completely At Random (MCAR)

In MCAR, the probability of data being missing is the same for all the observations.

In this case, there is no relationship between the missing data and any other values observed or unobserved (the data which is not recorded) within the given dataset.

That is, missing values are completely independent of other data. There is no pattern.

In the case of MCAR, the data could be missing due to human error, some system/equipment failure, loss of sample, or some unsatisfactory technicalities while recording the values.

For Example, suppose in a library there are some overdue books. Some values of overdue books in the computer system are missing. The reason might be a human error like the librarian forgot to type in the values. So, the missing values of overdue books are not related to any other variable/data in the system.

It should not be assumed as it’s a rare case. The advantage of such data is that the statistical analysis remains unbiased.

Missing At Random (MAR)

Missing at random (MAR) means that the reason for missing values can be explained by variables on which you have complete information as there is some relationship between the missing data and other values/data.

In this case, the data is not missing for all the observations. It is missing only within sub-samples of the data and there is some pattern in the missing values.

For example, if you check the survey data, you may find that all the people have answered their ‘Gender’ but ‘Age’ values are mostly missing for people who have answered their ‘Gender’ as ‘female’. (The reason being most of the females don’t want to reveal their age.)

So, the probability of data being missing depends only on the observed data.

In this case, the variables ‘Gender’ and ‘Age’ are related and the reason for missing values of the ‘Age’ variable can be explained by the ‘Gender’ variable but you can not predict the missing value itself.

Suppose a poll is taken for overdue books of a library. Gender and the number of overdue books are asked in the poll. Assume that most of the females answer the poll and men are less likely to answer. So why the data is missing can be explained by another factor that is gender.

In this case, the statistical analysis might result in bias.

Getting an unbiased estimate of the parameters can be done only by modeling the missing data.

Missing Not At Random (MNAR)

Missing values depend on the unobserved data.

If there is some structure/pattern in missing data and other observed data can not explain it, then it is Missing Not At Random (MNAR).

If the missing data does not fall under the MCAR or MAR then it can be categorized as MNAR.

It can happen due to the reluctance of people in providing the required information. A specific group of people may not answer some questions in a survey.

For example, suppose the name and the number of overdue books are asked in the poll for a library. So most of the people having no overdue books are likely to answer the poll. People having more overdue books are less likely to answer the poll.

So in this case, the missing value of the number of overdue books depends on the people who have more books overdue.

Another example, people having less income may refuse to share that information in a survey.

In the case of MNAR as well the statistical analysis might result in bias.

Why Do We Need To Care About Handling Missing Value?

It is important to handle the missing values appropriately.

  • Many machine learning algorithms fail if the dataset contains missing values. However, algorithms like K-nearest and Naive Bayes support data with missing values.
  • You may end up building a biased machine learning model which will lead to incorrect results if the missing values are not handled properly.
  • Missing data can lead to a lack of precision in the statistical analysis.

How To Handle Missing Value?

Let’s take an example of the Loan Prediction Practice Problem from Analytics Vidhya.

You can download the dataset from the following link.

(https://courses.analyticsvidhya.com/courses/loan-prediction-practice-problem-using-python)

Checking for missing values

The first step in handling missing values is to look at the data carefully and find out all the missing values.

The following code shows the total number of missing values in each column.

It also shows the total number of missing values in entire data set.

IN:
import pandas as pd
train_df = pd.read_csv("train.csv")
#Find the missing values from each column
train_df.isnull().sum()
OUT:
Loan_ID  0
Gender  13
Married  3
Dependents  15
Education  0
Self_Employed 32
ApplicantIncome  0
CoapplicantIncome  0
LoanAmount  22
Loan_Amount_Term  14
Credit_History  50
Property_Area  0
Loan_Status  0
dtype: int64

From the above output, we can see that there are 6 columns – Gender, Married, Dependents, Self_Employed, LoanAmount, Loan_Amount_Term and Credit_History having missing values.

IN:
#Find the total number of missing values from the entire dataset
train_df.isnull().sum().sum() 

OUT:
149

There are 149 missing values in total.

Figure Out How To Handle The Missing Data

Analyze each column with missing values carefully to understand the reasons behind the missing values as it is crucial to find out the strategy for handling the missing values.

There are 2 primary ways of handling missing values:

  1. Deleting the Missing values
  2. Imputing the Missing Values

Deleting the Missing value

Generally, this approach is not recommended. It is one of the quick and dirty techniques one can use to deal with missing values.

If the missing value is of the type Missing Not At Random (MNAR), then it should not be deleted.

If the missing value is of type Missing At Random (MAR) or Missing Completely At Random (MCAR) then it can be deleted.

The disadvantage of this method is one might end up deleting some useful data from the dataset.

There are 2 ways one can delete the missing values:

Deleting the entire row

If a row has many missing values then you can choose to drop the entire row.

If every row has some (column) value missing then you might end up deleting the whole data.

Code to drop the entire row is as follows:

IN:
df = train_df.dropna(axis=0)
df.isnull().sum()
OUT:
Loan_ID  0
Gender  0
Married  0
Dependents  0
Education  0
Self_Employed 0
ApplicantIncome  0
CoapplicantIncome  0
LoanAmount  0
Loan_Amount_Term  0
Credit_History  0
Property_Area  0
Loan_Status  0
dtype: int64

Deleting the entire column

If a certain column has many missing values then you can choose to drop the entire column.

Code to drop the entire column is as follows:

IN:
df = train_df.drop(['Dependents'],axis=1)
df.isnull().sum()

OUT:
Loan_ID  0
Gender  13
Married  3
Education  0
Self_Employed 32
ApplicantIncome  0
CoapplicantIncome  0
LoanAmount  22
Loan_Amount_Term  14
Credit_History  50
Property_Area  0
Loan_Status  0
dtype: int64

Imputing the Missing Value

There are different ways of replacing the missing values. You can use the python libraries Pandas and Sci-kit learn as follows:

Replacing With Arbitrary Value

If you can make an educated guess about the missing value then you can replace it with some arbitrary value using the following code.

Ex. In the following code, we are replacing the missing values of the ‘Dependents’ column with ‘0’.

IN:
#Replace the missing value with '0' using 'fiilna' method
train_df['Dependents'] = train_df['Dependents'].fillna(0)
train_df[‘Dependents'].isnull().sum()

OUT:
0

Replacing With Mean

This is the most common method of imputing missing values of numeric columns. If there are outliers then the mean will not be appropriate. In such cases, outliers need to be treated first.

You can use the ‘fillna’ method for imputing the columns ‘LoanAmount’ and ‘Credit_History’ with the mean of the respective column values.

IN:
#Replace the missing values for numerical columns with mean
train_df['LoanAmount'] = train_df['LoanAmount'].fillna(train_df['LoanAmount'].mean())
train_df['Credit_History'] = train_df[‘Credit_History'].fillna(train_df['Credit_History'].mean())

OUT:
Loan_ID  0
Gender  13
Married  3
Dependents  15
Education  0
Self_Employed 32
ApplicantIncome  0
CoapplicantIncome  0
LoanAmount 0
Loan_Amount_Term 0
Credit_History 0
Property_Area  0
Loan_Status  0
dtype: int64

Replacing With Mode

Mode is the most frequently occurring value. It is used in the case of categorical features.

You can use the ‘fillna’ method for imputing the categorical columns ‘Gender’, ‘Married’, and ‘Self_Employed’.

IN:

#Replace the missing values for categorical columns with mode
train_df['Gender'] = train_df['Gender'].fillna(train_df['Gender'].mode()[0])
train_df['Married'] = train_df['Married'].fillna(train_df['Married'].mode()[0])
train_df['Self_Employed'] = train_df[‘Self_Employed'].fillna(train_df['Self_Employed'].mode()[0])
train_df.isnull().sum()

OUT:
Loan_ID 0
Gender  0
Married 0
Dependents  0
Education 0
Self_Employed 0
ApplicantIncome 0
CoapplicantIncome 0
LoanAmount  0
Loan_Amount_Term  0
Credit_History  0
Property_Area 0
Loan_Status 0
dtype: int64

Replacing With Median

Median is the middlemost value. It’s better to use the median value for imputation in the case of outliers.

You can use ‘fillna’ method for imputing the column ‘Loan_Amount_Term’ with the median value.

train_df['Loan_Amount_Term']= train_df['Loan_Amount_Term'].fillna(train_df['Loan_Amount_Term'].median())

Replacing with previous value – Forward fill

In some cases, imputing the values with the previous value instead of mean, mode or median is more appropriate. This is called forward fill. It is mostly used in time series data.

You can use ‘fillna’ function with the parameter ‘method = ffill’

IN:
import pandas as pd
import numpy as np
test = pd.Series(range(6))
test.loc[2:4] = np.nan
test
OUT:
0 0.0
1 1.0
2 Nan
3 Nan
4 Nan
5 5.0
dtype: float64
IN:
# Forward-Fill
test.fillna(method=‘ffill')
OUT:
0 0.0
1 1.0
2 1.0
3 1.0
4 1.0
5 5.0
dtype: float64

Replacing with next value – Backward fill

In backward fill, the missing value is imputed using the next value.

IN:
# Backward-Fill
test.fillna(method=‘bfill')
OUT:
0 0.0
1 1.0
2 5.0
3 5.0
4 5.0
5 5.0
dtype: float64

Interpolation

Missing values can also be imputed using interpolation. Pandas interpolate method can be used to replace the missing values with different interpolation methods like ‘polynomial’, ‘linear’, ‘quadratic’. Default method is ‘linear’.

IN:
test.interpolate()
OUT:
0 0.0
1 1.0
2 2.0
3 3.0
4 4.0
5 5.0
dtype: float64

Imputing Missing Values For Categorical Features

There are two ways to impute missing values for categorical features as follows:

Impute the Most Frequent Value

We will make use of ‘SimpleImputer’ in this case and as this is a non-numeric column we can’t use mean or median but we can use most frequent value and constant.

IN:
import pandas as pd
import numpy as np
X = pd.DataFrame({'Shape':['square', 'square', 'oval', 'circle', np.nan]})
X
Shape
OUT:
0 square
1 square
2 oval
3 circle
4 NaN
IN:
from sklearn.impute import SimpleImputer
imputer = SimpleImputer(strategy='most_frequent')
imputer.fit_transform(X)
OUT:
array([['square'],
       ['square'],
       ['oval'],
       ['circle'],
       ['square']], dtype=object)

As you can see, the missing value is imputed with the most frequent value ’square’.

Impute the Value “missing”, which treats it as a Separate Category

IN:
imputer = SimpleImputer(strategy='constant', fill_value='missing')
imputer.fit_transform(X)
OUT:
array([['square'],
       ['square'],
       ['oval'],
       ['circle'],
       ['missing']], dtype=object)

In any of the above approaches, you will still need to OneHotEncode the data (or you can also use some other encoder of your choice). After One Hot Encoding, in case 1, instead of the values ‘square’, ‘oval’,’ circle’, you will get three feature columns. And in case 2, you will get four feature columns (4th one for the ‘missing’ category). So it’s like adding the missing indicator column in the data. There is another way to add a missing indicator column, which we will discuss further.

Imputation of Missing Value Using sci-kit learn Library

Univariate Approach

In a Univariate approach, only a single feature is taken into consideration. You can use the class SimpleImputer and replace the missing values with mean, mode, median or some constant value.

Let’s see an example:

IN:
import numpy as np
from sklearn.impute import SimpleImputer
imp = SimpleImputer(missing_values=np.nan, strategy='mean')
imp.fit([[1, 2], [np.nan, 3], [7, 6]])
OUT: SimpleImputer()
IN:
X = [[np.nan, 2], [6, np.nan], [7, 6]]
print(imp.transform(X))
OUT:
[[4.          2.        ]
 [6.          3.666...]
 [7.          6.        ]]

Multivariate Approach

In a multivariate approach, more than one feature is taken into consideration. There are two ways to impute missing values considering the multivariate approach. Using KNNImputer or IterativeImputer classes.

Let’s take an example of a titanic dataset.

Suppose the feature ‘age’ is well correlated with the feature ‘Fare’ such that people with lower fares are also younger and people with higher fares are also older.

In that case, it would make sense to impute low age for low fare values and high age for high fares values. So here we are taking multiple features into account by following a multivariate approach.

IN:
import pandas as pd
df = pd.read_csv('http://bit.ly/kaggletrain', nrows=6)
cols = ['SibSp', 'Fare', 'Age']
X = df[cols]
X
SibSp Fare Age
0 1 7.2500 22.0
1 1 71.2833 38.0
2 0 7.9250 26.0
3 1 53.1000 35.0
4 0 8.0500 35.0
5 0 8.4583 NaN

IN:
from sklearn.experimental import enable_iterative_imputer
from sklearn.impute import IterativeImputer
impute_it = IterativeImputer()
impute_it.fit_transform(X)
OUT:
array([[ 1.        ,  7.25      , 22.        ],
       [ 1.        , 71.2833    , 38.        ],
       [ 0.        ,  7.925     , 26.        ],
       [ 1.        , 53.1       , 35.        ],
       [ 0.        ,  8.05      , 35.        ],
       [ 0.        ,  8.4583    , 28.50639495]])

Let’s see how IterativeImputer works. For all rows, in which ‘Age’ is not missing sci-kit learn runs a regression model. It uses ‘Sib sp’ and ‘Fare’ as the features and ‘Age’ as the target. And then for all rows for which ‘Age’ is missing, it makes predictions for ‘Age’ by passing ‘Sib sp’ and ‘Fare’ to the training model. So it actually builds a regression model with two features and one target and then makes predictions on any places where there are missing values. And those predictions are the imputed values.

Nearest Neighbors Imputations (KNNImputer)

Missing values are imputed using the k-Nearest Neighbors approach where a Euclidean distance is used to find the nearest neighbors.

Let’s take the above example of the titanic dataset to see how it works.

IN:
from sklearn.impute import KNNImputer
impute_knn = KNNImputer(n_neighbors=2)
impute_knn.fit_transform(X)
OUT:
array([[ 1.    ,  7.25  , 22.    ],
       [ 1.    , 71.2833, 38.    ],
       [ 0.    ,  7.925 , 26.    ],
       [ 1.    , 53.1   , 35.    ],
       [ 0.    ,  8.05  , 35.    ],
       [ 0.    ,  8.4583, 30.5   ]])

In the above example, the n_neighbors=2. So sci-kit learn finds the two most similar rows measured by how close the ‘Sib sp’ and ‘Fare’ values are to the row which has missing values. In this case, the last row has a missing value. And the third row and the fifth row have the closest values for the other two features. So the average of the ‘Age’ feature from these two rows is taken as the imputed value.

Adding missing indicator to encode “missingness” as a feature

In some cases, while imputing missing values, you can preserve information about which values were missing and use that as a feature.
Because sometimes there may be a relationship between the reason for missing values (also called the “missingness”) and the target variable you are trying to predict.

Why do we need to do this?

Suppose you are predicting the presence of a disease and you can imagine a scenario in which a missing age is a good predictor of a disease because assume that we don’t have records for people in poverty. The age values are not missing at random. They are missing for people in poverty and poverty is a good predictor of disease. Thus, missing age or “missingness” is a good predictor of disease.

IN:
import pandas as pd
import numpy as np
X = pd.DataFrame({'Age':[20, 30, 10, np.nan, 10]})
X
Age
0 20.0
1 30.0
2 10.0
3 NaN
4 10.0

IN:
from sklearn.impute
import SimpleImputer
# impute the mean
imputer = SimpleImputer()
imputer.fit_transform(X)
OUT:
array([[20. ],
       [30. ],
       [10. ],
       [17.5],
       [10. ]])

IN:
imputer = SimpleImputer(add_indicator=True)
imputer.fit_transform(X)
OUT:
array([[20. ,  0. ],
       [30. ,  0. ],
       [10. ,  0. ],
       [17.5,  1. ],
       [10. ,  0. ]])

 

In the above example, the second column indicates whether the corresponding value in the first column was missing or not. ‘1’ indicates that the corresponding value was missing and ‘0’ indicates that the corresponding value was not missing.

If you don’t want to impute missing values but only want to have the indicator matrix then you can use the ‘MissingIndicator’ class from scikit learn.

End Notes

  • It is critical to reduce the potential bias in the machine learning models and get the precise statistical analysis of the data.
  • Handling missing values is one of the challenges of data analysis.
  • Understanding different categories of missing data help in making decisions on how to handle it.
  • We explored different categories of missing data and the different ways of handling it in this article.
  • Missing values handling is a gigantic topic. In any case, it’s very important to understand your data well and why it’s missing, talk to the experts if possible to figure out what’s going on with the data before blindly following any of the above methods.

References:

https://scikit-learn.org/stable/modules/impute.html

https://github.com/justmarkham/scikit-learn-tips

Image Source-

  1. Image 1 – https://analyticsindiamag.com/5-ways-handle-missing-values-machine-learning-datasets/
  2. Image 2 – https://medium.com/bycodegarage/a-comprehensive-guide-on-handling-missing-values-b1257a4866d1
  3. Image 3 – https://theblogmedia.com/appropriately-handling-missing-values-for-statistical-modelling-and-prediction/

The media shown in this article is not owned by Analytics Vidhya and are used at the Author’s discretion.

About the Author

Nasima Tamboli
Nasima Tamboli

Freelance Software Engineer Data Science Enthusiast and Content Writer Loves Coding E-mail: [email protected] LinkedIn:https://www.linkedin.com/in/nasima-tamboli

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