mlim : Single and Multiple Imputation with Automated Machine Learning

GitHub dev CRAN version

mlim is the first missing data imputation software to implement automated machine learning for performing multiple imputation or single imputation of missing data. The software, which is currently implemented as an R package, brings the state-of-the-arts of machine learning to provide a versatile missing data solution for various data types (continuous, binary, multinomial, and ordinal). In a nutshell, mlim is expected to outperform any other available missing data imputation software on many grounds. For example, mlim is expected to deliver:

  1. Lower imputation error compared to other missing data imputation software.
  2. Higher imputation fairness, when the data suffers from severe class imbalance, unnormal destribution, or the variables (features) have interactions with one another.
  3. Faster imputation of big datasets because mlim excells in making an efficient use of available CPU cores and the runtime scales fairly well as the size of data becomes huge.

The high performance of mlim is mainly by fine-tuning an ELNET algorithm, which often outperforms any standard statistical procedure or untuned machine learning algorithm and generalizes very well. However, mlim is an active research project and hence, it comes with a set of experimental optimization toolkit for exploring the possibility of performing multiple imputation with industry-standard machine learning algorithms such as Deep Learning, Gradient Boosting Machine, Extreme Gradient Boosting, and Stacked Ensembles. These algorithms can be used for either imputing missing data or optimizing already imputed data, but are NOT used by default NOR recommended to all users. Advanced users who are interested in exploring the possibilities of imputing missing data with these algorithms are recommended to read the free handbook (see below). These algorithms, as noted, are experimental, and the author is intended to examine their effectiveness for academic research (at this point). If you are interested to collaborate, get in touch with the author.

NOTE: Prior to version 0.3.0, mlim did not use a stochastic procedure and thus, the multiple imputation algorithm was inflating the relationships between the imputed variables. A solution is implemented in version 0.3.0, which is automatically activated for multiple imputation and is currently under testing. You can investigate the code for stochastic = TRUE argument to see how this procedure is implemented. In stochastic multiple imputation, mlim uses the estimated RMSE of each continuous variable as an indication of standard error and replaces the imputed values with stochastic values drawn with a mean equal to the imputed value and SD equal to the RMSE. For factor variables, however, mlim draws a random value based on estimated probabilities of each factor level for each missing value. These two procedures are still under testing… Meanwhile, for a single imputation, mlim continues to be the top performer among other R packages that I have tested.

Fine-tuning missing data imputation

Simply put, for each variable in the dataset, mlim automatically fine-tunes a fast machine learning model, which results in significantly lower imputation error compared to classical statistical models or even untuned machine learning imputation software that use Random Forest or unsuperwised learning algorithms. Moreover, mlim is intended to give social scientists a powerful solution to their missing data problem, a tool that can automatically adopts to different variable types, that can appear at different rates, with unknown destributions and have high correlations or interactions with one another. But it is not just about higher accuracy! mlim also delivers fairer imputation, particularly for categorical and ordinal variables because it automatically balances the levels of the avriable, minimizing the bias resulting from class imbalance, which can often be seen in social science data and has been commonly ignored by missing data imputation software.

mlim outperforms other R packages for all variable types, continuous, binary (factor), multinomial (factor), and ordinal (ordered factor). The reason for this improved performance is that mlim:

Procedure: From preimputation to imputation and postimputation

When a dataframe with NAs is given to mlim, the NAs are replaced with plausible values (e.g. Mean and Mode) to prepare the dataset for the imputation, as shown in the flowchart below:

mlim follows three steps to optimize the missing data imputation. This procedure is optional, depending on the amount of computing resources available to you. In general, ELNET imputation already outperforms other available single and multiple imputation methods available in R. However, the imputation error can be further improved by training stronger algorithms such as GBM, XGB, DL, or even Ensemble, stacking several models on top of one another. For the majority of the users, the GBM or XGB (XGB is available only in Mac OSX and Linux) will significantly imprive the ELNET imputation, if long-enough time is provided to generate a lot of models to fine-tune them.

You do not necessarily need the post-imputation. Once you have reimputed the data with ELNET, you can stop there. ELNET is relatively a fast algorithm and it is easy to fine-tune it compared to GBM, XGB, DL, or Ensemble. In addition, ELNET generalizes nicely and is less prone to overfiting. In the flowchart below the procedure of mlim algorithm is drawn. When using mlim, you can use ELNET to impute a dataset with NA or optimize the imputed values of a dataset that is already imputed. If you wish to go the extra mile, you can use heavier algorithms as well to activate the postimputation procedure, but it is strictly optional and by default, mlim does not use postimputation.

Fast imputation with ELNET (without postimputation)

Below are some comparisons between different R packages for carrying out multiple imputations (bars with error) and single imputation. In these analyses, I only used the ELNET algorithm, which fine-tunes much faster than other algorithms (GBM, XGBoost, and DL). As it evident, ELNET already outperforms all other single and multiple imputation procedures available in R language. However, the performance of mlim can still be improved, by adding another algorithm, which activates the postimputation procedure.


mlim is under fast development. The package receive monthly updates on CRAN. Therefore, it is recommended that you install the GitHub version until version 0.1 is released. To install the latest development version from GitHub:


Or alternatively, install the latest stable version from CRAN:


Supported algorithms

mlim supports several algorithms:

ELNET is the default imputation algorithm. Among all of the above, ELNET is the simplest model, fastest to fine-tune, requires the least amount of RAM and CPU, and yet, it is the most stable one, which also makes it one of the most generalizable algorithms. By default, mlim uses only ELNET, however, you can add another algorithm to activate the post-imputation procedure.


But which one should you choose, assuming computation resources are not in question? Well, GBM is very liokely to outperform ELNET, if you specify a large enough max_models argument to well-tune the algorithm for imputing each feature. That basically means generating more than 100 models, at least. But you will enjoy a slight – yet probably statistically significant – improvement in the imputation accuracy. The option is there, for those who can use it, and to my knowledge, fine-tuning GBM with large enough number of models will be the most accurate imputation algorithm compared to any other procedure I know. But ELNET comes second and compared to its speed advantage, it is indeed charming!

Both of these algorithms offer one advantage over all the other machine learning missing data imputation methods such as kNN, K-Means, PCA, Random Forest, etc… Simply put, you do not need to specify any parameter yourself, everything is automatic and mlim searches for the optimal parameters for imputing each variable within each iteration. For all the aformentioned packages, some parameters need to be specified, which influence the imputation accuracy. Number of k for kNN, number of components for PCA, number of trees (and other parameters) for Random Forest, etc… This is why elnet outperform the other packages. You get a software that optimizes its models on its own.

Advantages and limitations

mlim fine-tunes models for imputation, a procedure that has never been implemented in other R packages. This procedure often yields much higher accuracy compared to other machine learning imputation methods or missing data imputation procedures because of using more accurate models that are fine-tuned for each feature in the dataset. The cost, however, is computational resources. If you have access to a very powerful machine, with a huge amount of RAM per CPU, then try GBM. If you specify a high enough number of models in each fine-tuning process, you are likely to get a more accurate imputation that ELNET. However, for personal machines and laptops, ELNET is generally recommended (see below). If your machine is not powerful enough, it is likely that the imputation crashes due to memory problems…. So, perhaps begin with ELNET, unless you are working with a powerful server. This is my general advice as long as mlim is in Beta version and under development.



iris ia a small dataset with 150 rows only. Let’s add 50% of artifitial missing data and compare several state-of-the-art machine learning missing data imputation procedures. ELNET comes up as a winner for a very simple reason! Because it was fine-tuned and all the rest were not. The larger the dataset and the higher the number of features, the difference between ELNET and the others becomes more vivid.

Single imputation

In a single imputation, the NAs are replaced with the most plausible values according the model. You do not get the diversity of the multiple imputation, but you still get an estimated imputation error based on 10-fold (or higher, if specified) cross-validation procedure for each variable (column) in the dataset. As shown below, mlim provides the mlim.error() function to summarize the imputation error for the entire dataset or each variable.

# Comparison of different R packages imputing iris dataset
# ===============================================================================
rm(list = ls())

# Add artifitial missing data
# ===============================================================================
irisNA <-, p = 0.5, stratify = TRUE, seed = 2022)

# Single imputation with mlim, giving it 180 seconds to fine-tune each imputation
# ===============================================================================
MLIM <- mlim(irisNA, m=1, seed = 2022, tuning_time = 180) 
print(MLIMerror <- mlim.error(MLIM, irisNA, iris))

# kNN Imputation with VIM
# ===============================================================================
kNN <- kNN(irisNA, imp_var=FALSE)
print(kNNerror <- mlim.error(kNN, irisNA, iris))

# Single imputation with MICE (for the sake of demonstration)
# ===============================================================================
MC <- mice(irisNA, m=1, maxit = 50, method = 'pmm', seed = 500)
print(MCerror <- mlim.error(MC, irisNA, iris))

# Random Forest Imputation with missForest
# ===============================================================================
RF <- missForest(irisNA)
print(RFerror <- mlim.error(RF$ximp, irisNA, iris))

Multiple imputation

mlim supports multiple imputation. All you need to do is to specify an integer higher than 1 for the value of m. For example, set m = 5 in the mlim function to impute 5 datasets. Then, mlim returns a list including 5 datasets. You can convert this list to a mids object using the mlim.mids() function and then follow up the analysis with the mids object the same way it is carried out by the mice R package. Here is an example:

# Comparison of different R packages imputing iris dataset
# ===============================================================================
rm(list = ls())

# Add artifitial missing data
# ===============================================================================
irisNA <-, p = 0.5, stratify = TRUE, seed = 2022)

# multiple imputation with mlim, giving it 180 seconds to fine-tune each imputation
# ===============================================================================
MLIM2 <- mlim(irisNA,  m = 5, seed = 2022, tuning_time = 180) 
print(MLIMerror2 <- mlim.error(MLIM2, irisNA, iris))
mids <- mlim.mids(MLIM2, dfNA)
fit <- with(data=mids, exp=glm(Species ~ Sepal.Length, family = "binomial"))
res <- mice::pool(fit)