9 Popular Data Imputation Techniques In Machine Learning

9 Popular Data Imputation Techniques In Machine Learning

Data is the backbone of any analysis. However, it is not uncommon for datasets to have missing values due to various reasons such as data corruption, non-responses, or incomplete data collection. These missing values can significantly impact the accuracy and reliability of any analysis performed on the dataset. Therefore, it is crucial to fill in these gaps using data imputation techniques before any analysis is performed.

Data imputation techniques refer to the methods used to fill in missing data points in a dataset. These techniques vary in complexity, with some using simple statistical measures such as the mean or median to fill in the gaps, while others use more advanced machine learning algorithms to predict missing values based on the patterns in the available data.

9 Popular Data Imputation Techniques In Machine Learning

Click to Tweet

In this guide, we will explore the various data imputation techniques available, their strengths and limitations, and how to choose the most appropriate technique for your dataset. We will also provide practical examples and step-by-step guides on how to implement these techniques using popular programming languages such as Python.

Whether you are a data analyst or a data scientist, this guide will equip you with the necessary knowledge and skills to accurately and effectively complete your data puzzle by filling in the missing pieces.

What is Data Imputation

Data is an essential component of any analysis, but it is not uncommon for datasets to contain missing values. Missing data can arise for various reasons, such as data entry errors, participant non-response, or technical malfunctions. 

These missing values can lead to biased or inefficient estimates, compromising the accuracy of statistical analysis. One way to address this issue is through data imputation techniques, which allow us to estimate missing values based on the available data.

The goal of data imputation is to replace missing data with plausible values, based on the available information in the dataset. This process allows us to retain as much information as possible from the incomplete data and provides us with a more complete dataset for analysis.

Data imputation techniques can be divided into two categories: 

  1. Single Imputation

    • Single imputation involves replacing each missing value with a single estimated value, whereas multiple imputation creates several imputed datasets by imputing missing values multiple times. 

  2. Multiple Imputation

Types Of Missing Data

Types Of Missing Data

Primarily, we categorize missing data into three segments: 

  1. Missing Completely at Random (MCAR), 

  2. Missing at Random (MAR), 

  3. Missing Not at Random (MNAR).

Grasping the nuances of each category is crucial, as it aids in selecting the right technique to address the data gaps so we can select the best data imputation technique.

MCAR - Missing Completely at Random

Here, every variable and observation holds an equal likelihood of being absent. Picture a child playing with multi-colored Lego blocks to construct a building. Each block symbolizes distinct data elements, such as shape and hue. 

During the play, the child might misplace some blocks. These misplaced blocks equate to absent data, akin to the child's inability to recall the specifics of the lost Lego. This lapse occurs without any pattern, leaving the rest of the data unaffected.

MAR - Missing at Random

In the MAR scenario, the chances of a data point going missing hinge on the values of that specific variable or other associated variables in the dataset. This indicates a varied likelihood of data absence across observations and variables. 

For instance, in a data community survey, those data scientists who aren't proactive about learning might be unaware of the latest algorithms or tools. Consequently, they might sidestep certain questions. The absence of their responses correlates with their learning habits.

MNAR- Missing Not at Random

MNAR stands out as the most challenging type of absent data. It comes into play when the other two categories (MCAR and MAR) don't. 

Under MNAR, different values within the same variable possess distinct probabilities of going missing, and the underlying reasons might remain elusive. 

Take, for instance, a survey centered on marital relationships. Couples in strained relationships might be reticent about answering specific questions, possibly due to discomfort or embarrassment.

Importance Of Using Data Imputation In Machine Learning

The necessity for data imputation arises because the absence of data can result in:

1. Dataset Skewness: Extensive missing data can skew the variable distribution, thereby altering the perceived significance of distinct categories within the dataset.

2. Incompatibility with ML Libraries: Most machine learning tools, with SkLearn being a prime example, might falter with incomplete data. These libraries don't always inherently manage missing values, leading to potential errors during operations.

3. Model Accuracy Concerns: A dataset riddled with missing entries can introduce bias. This bias, in turn, can compromise the integrity and accuracy of the resulting analytical model.

4. Preservation of Data Integrity: Often, there's a need to retain the entirety of a dataset, especially if each data point holds significant value. For datasets that aren't vast, discarding even a small portion can disproportionately influence the eventual analytical model.

Having established the significance of data imputation, our next focus will be on understanding the diverse techniques and approaches used in the imputation process.

Popular Data Imputation Techniques

There are various data imputation techniques available, and selecting the appropriate one is crucial to maintain the data's accuracy and integrity.

Popular Data Imputation Techniques

Below are popular data imputation techniques, we are going to discuss about each of this technique in the coming sections.

  • Mean Imputation

  • Mode Imputation

  • Next or Previous Value 

  • Maximum or Minimum Value

  • Hot Deck Imputation

  • Cold Deck Imputation

  • Regression Imputation

  • K-nearest Neighbor (KNN) Imputation

  • Multiple Imputation

Mean Imputation Technique

Mean imputation is a common and simple technique for filling in missing data. It involves replacing missing values with the mean value of the non-missing values in the same feature/column.

While this technique is easy to implement, it can lead to biased and imprecise estimates, especially if there is a high percentage of missing values.

Mode Imputation Technique

Mode imputation is similar to mean imputation, but instead of using the mean value, it uses the most frequent value in the same feature/column to impute the missing values. This technique is useful for imputing categorical data.

Next or Previous Value

One of the simpler methods for imputing missing values in time series or sequential data is to use the previous (or next) observed value.

This technique is often referred to as 'forward fill' or 'backward fill' in pandas, where you either propagate the previous value forward ('forward fill') or use the subsequent value to fill the missing one ('backward fill'). While it is straightforward and quick, it's best suited for data where observations have temporal or sequential correlations.

Maximum or Minimum Value

Another approach to handling missing values is to replace them with the maximum or minimum value of the dataset or feature. This method might be helpful when trying to emphasize extreme values, especially in datasets where outliers or extreme values have significant meaning.

However, this method can potentially distort the distribution of the dataset and may not be suitable for every scenario.

Hot Deck Imputation Technique

Hot deck imputation is a method that replaces missing values with a randomly selected value from a non-missing value in the same feature/column. 

The values in the dataset are grouped into categories based on similar attributes, and each category forms a "deck." The missing values are then replaced with randomly selected values from the same deck.

Cold Deck Imputation Technique

Cold deck imputation is similar to hot deck imputation, but instead of randomly selecting values from the same deck, it selects values from a different dataset or historical record.

Regression Imputation Technique

Regression imputation is a more advanced technique that involves using a regression model to predict missing values based on the non-missing values in the same dataset.

This technique can lead to more accurate imputation, but it requires more computational resources and assumes that the data follows a linear pattern.

K-Nearest Neighbor (KNN) Imputation Technique

KNN imputation is a non-parametric technique that involves finding the K nearest neighbors of each missing value based on the similarity of their non-missing values. The missing values are then imputed using the average of the K nearest neighbors. 

This technique can handle non-linear relationships between variables and is useful for datasets with a small percentage of missing values.

Multiple Imputation Technique

Multiple imputation is a technique that involves creating multiple imputed datasets, each with different imputed values based on different models and assumptions. The datasets are then analyzed separately, and the results are combined to provide more accurate and reliable estimates. 

This technique can handle complex missing data patterns and provides uncertainty estimates. However, it requires more computational resources and can be difficult to implement.

How to Choose the Right Imputation Technique

Choosing the right imputation technique is crucial for accurate analysis and reliable results. There are several factors to consider when selecting an appropriate imputation technique, including the nature of the data, the missingness pattern, the analysis goals, and the potential impact of imputation on the results.

How to Choose the Right Imputation Technique

Understanding these factors can help in making an informed decision and selecting the most suitable imputation technique.

Understanding the Data

It's crucial to comprehend the data thoroughly before selecting an imputation technique. Understanding the variables, their distributions, and how they interact with one another is part of this. 

Different imputation methods can affect the statistical properties of the data differently and are better suited for particular types of data. For instance, regression imputation may be more appropriate for variables with a strong linear relationship to other variables than mean imputation for variables with a normal distribution. 

Before choosing an imputation technique, it is crucial to comprehend the data and its characteristics. 

Evaluating the Missingness Pattern

When selecting an imputation technique, the pattern of the missing data is also crucial. The best imputation technique can be chosen by being aware of the causes of missing data and the patterns that they follow. 

Simple imputation techniques, such as mean imputation or regression imputation, may be appropriate, for instance, if the missing data occurs randomly and is unlikely to be related to the other variables.

However, more complex imputation methods, such as K-nearest neighbor (KNN) imputation, may be needed if the missing data is connected to other variables.

Considering the Analysis Goals

The analysis goals should also be taken into consideration when selecting an imputation technique. The goal of the analysis will determine which variables are important and how missing data affects the analysis.

For example, if the analysis goal is to identify the relationship between two variables, imputation techniques that preserve this relationship should be used.

Assessing the Impact of Imputation

Finally, it is important to assess the impact of imputation on the analysis. Imputation can affect the distribution and statistical properties of the data, and these changes may have a significant impact on the results of the analysis. 

Therefore, it is important to evaluate the impact of imputation on the analysis results and ensure that the results are robust to the imputation technique used. This can be done by comparing the results of the analysis with and without imputation and evaluating the sensitivity of the results to different imputation techniques.

Implementing Data Imputation Techniques In Python

Data imputation is a critical step in the data analysis process, and Python provides a range of libraries that can be used to impute missing values. In this section, we will provide an overview of some popular Python libraries for data imputation and walk through an example of how to use these libraries to impute missing data.

For data imputation, Python has a number of libraries, including scikit-learn, Keras, and fancyimpute. Popular machine learning library Scikit-learn offers a number of imputation methods, including mean imputation, median imputation, and KNN imputation.

Implementing Data Imputation Techniques In Python

A variety of tools are offered by the deep learning library Keras for handling missing data in deep learning models. A third-party library called fancyimpute offers a variety of imputation methods, including iterative imputation and matrix factorization.

Loading and Preprocessing Data

Before imputing missing data, it is important to first load and preprocess the data. This involves handling missing data, removing irrelevant features, and converting categorical variables into numerical variables. In Python, we can use libraries such as Pandas and NumPy to load and preprocess data.

Applying data Imputation Techniques to Missing Data

We can use data imputation techniques to fill in the gaps left by missing data after the data has been loaded and preprocessed. The amount of missing data, the type of data, and the objectives of the analysis all play a role in the choice of imputation technique.

To apply data imputation methods, we can use Python libraries like scikit-learn and fancyimpute.

Evaluating the Imputed Data

The quality of the imputed data must be assessed after data imputation techniques have been used. This entails determining whether the imputed data has any bias and whether it has the same distribution as the original data as well as whether it is consistent with the observed data.

To visualize and assess the imputed data, we can use Python libraries like Pandas and Matplotlib.

Data Imputation Implementation In Python

Let’s put all of these topics together into a Python code

  • Output
    MSE on test set (imputed using mean strategy): 2854.40
  • MSE on test set (imputed using median strategy): 2787.43
  • MSE on test set (imputed using KNN imputation): 2717.12
Data Imputation Implementation In Python

This code demonstrates the use of SimpleImputer for imputing missing values using mean and median strategies, and KNNImputer for imputing missing values using K-nearest neighbor imputation. 

The code loads the diabetes dataset from sklearn, introduces some missing values, splits the data into training and testing sets, applies the imputation techniques to the missing data, trains a linear regression model on the imputed data, and evaluates the model's performance using mean squared error (MSE) on the test set.

Best Practices To Follow While Applying Data Imputation

Data imputation is the process of replacing missing data values with plausible estimates. Handling missing data is a common problem in many fields, including healthcare, finance, and social sciences. 

However, imputation methods must be chosen carefully to avoid over-imputation, the introduction of biases, and loss of accuracy

Handling Missing Data Before Imputation

It's crucial to resolve any potential data issues before imputing any missing values. This may entail performing duplicate and inconsistency checks as well as looking for any patterns or trends in the missing data. It's also crucial to think about whether the missing data is absent at random or if a systematic cause can be found.

Avoiding Over-Imputation

When too many missing values are imputed, the result is over-imputation, which produces skewed or incorrect data. It's crucial to take into account the potential effects of imputing missing values on the entire data set in order to prevent over-imputation. Additionally, it's crucial to employ imputation methods that are suitable for the particular kind of data being imputed.

Handling Outliers and Extreme Values

Imputation techniques can be significantly impacted by outliers and extreme values. Prior to imputation, it's crucial to think about how these values will be handled. Outliers and extreme values may need to be eliminated or treated differently from the rest of the data depending on the imputation technique used.

Sensitivity Analysis and Reporting

It's important to perform sensitivity analyses to assess the robustness of the imputed data. This can involve comparing the results of multiple imputation techniques or varying the assumptions used in the imputation process. 

Additionally, it's important to report the details of the imputation process, including the specific techniques used and any decisions made during the imputation process. This will allow others to evaluate the validity of the imputed data and replicate the imputation process if necessary.


Data imputation is an important task in the data cleaning process. In this article, we discussed some of the best practices for data imputation, including handling missing data before imputation, avoiding over-imputation, handling outliers and extreme values, and sensitivity analysis and reporting. 

These practices can help ensure that the imputed data is as accurate and reliable as possible, and can improve the performance of downstream analyses.

The techniques for data imputation will advance along with methods for data collection and analysis. New imputation techniques that are better suited to handling missing data in various dataset types may be the subject of future research. 

Research may also concentrate on improving the transparency and reproducibility of data imputation techniques as well as methods for assessing the reliability and accuracy of imputed data. Overall, the advancement of research in a variety of fields will depend on the creation of fresh and improved data imputation techniques.

Frequently Asked Questions (FAQs) On Data Imputation Techniques

1. What is Data Imputation?

Data imputation refers to the process of replacing missing or incomplete data with substituted values to create a complete dataset.

2. Why is Data Imputation Necessary in Machine Learning?

Missing data can skew results, reduce the statistical power of models, and lead to biased parameter estimates. Imputing missing values helps in achieving better and more consistent results.

3. What is Mean Imputation?

Mean imputation involves replacing missing values with the mean of the available data. It's simple but may not always be the most accurate, especially if the data isn’t normally distributed.

4. How does Median Imputation Differ from Mean Imputation?

Median imputation uses the median (the middle value) instead of the mean. It's especially useful for data with outliers or non-normal distributions.

5. What is Mode Imputation?

Mode imputation replaces missing values with the mode (most frequent value) of the data. It's particularly suitable for categorical data.

6. Can I Use Linear Regression for Data Imputation?

Yes, linear regression can predict missing values based on other related variables in the dataset. However, it assumes a linear relationship between variables.

7. What is K-Nearest Neighbors (KNN) Imputation?

KNN imputation identifies 'k' samples in the dataset that are similar to the observation with the missing value and fills in the missing value based on these 'k' nearest neighbors.

8. How Does Multiple Imputation Work?

Multiple imputation creates several imputed datasets, analyzes each separately, and averages the results to produce a single estimation. It accounts for the uncertainty of missing values better than single imputation methods.

9. What is Stochastic Regression Imputation?

It's like linear regression imputation but adds a random error term to account for variability, making imputations more realistic.

10. Are there Advanced Techniques like Deep Learning for Imputation?

 Yes, deep learning techniques such as autoencoders can be used for imputing missing values, especially in complex datasets with non-linear relationships.

11. Is Imputation Always Recommended for Missing Data?

 Not always. Sometimes it may be better to omit observations with missing data, especially if the proportion of missing data is minimal or if the data is missing non-randomly.

12. How Do I Choose the Best Imputation Technique for My Data?

 The choice depends on the nature of your data (e.g., continuous vs. categorical), the amount of data missing, the relationship between variables, and the desired complexity of the imputation method.

Recommended Courses

Machine Learning Courses

Machine Learning Course

Rating: 4.5/5

Deep Learning Courses

Deep Learning Course

Rating: 4/5

Natural Language Processing Course

NLP Course

Rating: 4/5

Follow us:


I hope you like this post. If you have any questions ? or want me to write an article on a specific topic? then feel free to comment below.


Leave a Reply

Your email address will not be published. Required fields are marked *