ENGINEERING ISSN 2995-8067

Information Technology | Artiϐicial Intelligence | Data Engineering

Article Information Research Article

Submitted: December 08, 2023
Approved: January 22 2024 Enhancing Missing Values
Published: January 23, 2024

How to cite this article: Ayub H, Jamil H. Enhancing Missing Imputation through
Values Imputation through Transformer-Based Predictive
Modeling. IgMin Res. Jan 23, 2024; 2(1): 025-031. IgMin ID:
igmin140; DOI: 10.61927/igmin140; Available at:
Transformer-Based
Predictive Modeling
www.igminresearch.com/articles/pdf/igmin140.pdf

Copyright license: © 2024 Ayub H, et al. This is an open access

article distributed under the Creative Commons Attribution Hina Ayub1 and Harun Jamil2*
License, which permits unrestricted use, distribution, and
1
reproduction in any medium, provided the original work is Interdisciplinary Graduate Program in Advance Convergence Technology and Science, Jeju
properly cited. National University, Jeju, 63243, Republic of Korea
2
Department of Electronics Engineering, Jeju National University, Jeju, 63243, Jeju-do,
Republic of Korea

*Correspondence: Harun Jamil, Department of Electronics Engineering, Jeju National

University, Jeju, 63243, Jeju-do, Republic of Korea, Email: [email protected]

Abstract
This paper tackles the vital issue of missing value imputation in data preprocessing, where traditional techniques like zero, mean, and KNN imputation fall short
in capturing intricate data relationships. This often results in suboptimal outcomes, and discarding records with missing values leads to significant information loss.
Our innovative approach leverages advanced transformer models renowned for handling sequential data. The proposed predictive framework trains a transformer
model to predict missing values, yielding a marked improvement in imputation accuracy. Comparative analysis against traditional methods—zero, mean, and KNN
imputation—consistently favors our transformer model. Importantly, LSTM validation further underscores the superior performance of our approach. In hourly data,
our model achieves a remarkable R2 score of 0.96, surpassing KNN imputation by 0.195. For daily data, the R2 score of 0.806 outperforms KNN imputation by 0.015
and exhibits a notable superiority of 0.25 over mean imputation. Additionally, in monthly data, the proposed model’s R2 score of 0.796 excels, showcasing a significant
improvement of 0.1 over mean imputation. These compelling results highlight the proposed model’s ability to capture underlying patterns, offering valuable insights
for enhancing missing values imputation in data analyses.

Introduction a paradigm shift from rule-based imputation methods to a more

data-driven and adaptive approach [3]. By harnessing the power
In the ever-evolving data analysis landscape, the challenge of of self-attention mechanisms [4], the transformer model can
missing values within datasets is a formidable hurdle, impacting the effectively capture intricate relationships and dependencies across
reliability and efficacy of downstream applications [1]. Addressing different features, leading to more accurate predictions of missing
this challenge has spurred the development of various imputation values.
techniques, each attempting to reconcile the absence of data points
with meaningful estimations. Traditional methods, such as zero This innovative approach is particularly advantageous when
imputation, mean imputation, and K-Nearest Neighbors (KNN) dealing with large and complex datasets, where conventional
imputation, have long been employed. Yet, their efficacy is often imputation techniques may struggle to capture the nuanced
limited in capturing complex dataset’s intricate relationships and patterns inherent in the data. The transformer model’s ability to
patterns. consider global context and long-range dependencies ensures a
holistic understanding of the dataset, enhancing its capacity to
Recognizing the shortcomings of conventional approaches impute missing values in a manner that aligns with the underlying
and the imperative to preserve valuable information lost through structure of the information [5]. Statistical imputation techniques
record removal, this paper introduces an innovative method for employ conventional statistical methods, such as substituting
missing values imputation. The proposed approach leverages missing values with the mean of available data and utilizing
the capabilities of advanced transformer models, which have regression models [6-8].
exhibited exceptional performance in handling sequential data
and contextual information. The transformer model is trained In addressing missing data in short-term air pollutant
to predict missing values based on the inherent contextual monitoring with real-time PM2.5 monitors [9], univariate methods
dependencies within the dataset, offering a promising alternative like Markov, random, and mean imputations prove superior,
to traditional imputation techniques [2]. Moreover, the utilization especially beneficial in resource-limited contexts. Furthermore,
of transformer models in missing values imputation represents DACMI [10] addresses missing clinical data with a shared dataset,

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ISSN 2995-8067 DOI: 10.61927/igmin140

revealing that models like LightGBM and XGBoost, coupled with researchers and data scientists. Recent research [31] thoroughly
careful feature engineering, excel in imputation performance, compares seven data imputation methods for numeric datasets,
emphasizing the importance of balanced model complexity. In revealing kNN imputation’s consistent outperformance. This
scRNA-seq, vital for studying single-cell transcription, addressing contribution adds valuable insights to the ongoing discourse
high-dimensionality and dropout values is crucial. This study [11] on selecting optimal methods for handling missing data in data
evaluates advanced imputation methods, providing insights for mining tasks. Furthermore, we introduce an additional validation
selecting appropriate approaches in diverse data contexts and layer by subjecting the imputed data to scrutiny through Long
aiding downstream functional analysis. Both the Self-Organizing Short-Term Memory (LSTM) networks [32]. This not only assesses
Map (SOM) [12,13] and the MLP [14] represent additional ML the accuracy of imputation but also gauges the temporal coherence
techniques applied for the imputation of missing values. of the imputed values.

Furthermore, studies employing the regression approach By undertaking this exploration, we aim to contribute valuable
[15] implemented a novel method involving weighted quantile insights into the realm of missing values imputation, offering a
regression to estimate missing values within health data. In nuanced understanding of the capabilities of transformer-based
another article [16], the author introduced a comprehensive case models. The observed improvements in imputation accuracy,
regression approach for handling missing values, employing particularly validated through LSTM analysis, underscore the
functional principal components. Iterative regression is used for potential of our proposed approach to address the persistent
effective imputation in multivariate data [17]. Another method challenges associated with missing data. Through this work, we
Hot-deck imputation, matches missing values with complete aspire to provide a robust foundation for future advancements in
values on key variables [18]. Research is conducted on expectation data preprocessing and analysis methodologies. These are the key
minimization in handling missing data using a dataset analyzing contributions of the article:
the effects of feeding behaviors among drug-treated and untreated
• Introduced a novel missing values imputation approach
animals [19]. Recognizing the insufficiency of merely deleting or
using transformer models, deviating from traditional
discarding missing data [20], researchers often turn to employing
methods.
multiple imputations. Multiple imputation involves leveraging the
observed data distribution to estimate numerous values, reflecting • Leveraging self-attention mechanisms, the transformer-
the uncertainty surrounding the true value. This approach has based model provides a data-driven and adaptive solution
predominantly been utilized to address the constraints associated for capturing intricate data relationships.
with single imputation [21].
• Through a comprehensive comparative analysis, the
Moreover, another study [22] evaluates imputation methods for transformer model consistently outperforms traditional
incomplete water network data, focusing on small to medium-sized imputation techniques like zero, mean, and KNN.
utilities. Among the tested methods, IMPSEQ outperforms others
in imputing missing values in cast iron water mains data from the • The inclusion of LSTM validation adds a layer of scrutiny,
City of Calgary, offering insights for cost-effective water mains evaluating not only imputation accuracy but also the
renewal planning. The proposed one-hot encoding method by temporal coherence of imputed values.
[23] excels in addressing missing data for credit risk classification,
• The proposed model showcases robust performance across
demonstrating superior accuracy and computational efficiency,
diverse datasets, demonstrating its efficacy in preserving
especially in high missing-rate scenarios, when integrated with
data relationships and capturing variability.
the CART model. Another work [24] proposes a novel imputation
method for symbolic regression using Genetic Programming
Methodology
(GP) and weighted K-Nearest Neighbors (KNN). It outperforms
state-of-the-art methods in accuracy, symbolic regression, and Handling missing values in datasets is a crucial challenge,
imputation time on real-world datasets. Conventional techniques particularly when predicting these values based on available
for multiple imputations exhibit suboptimal performance when data. Figure 1 outlines a comprehensive process for predicting
confronted with high-dimensional data, prompting researchers to missing values using a transformer model. In the initial step, we
enhance these algorithms [25,26]. Likewise, indications exist that showcase an example dataset with missing values, highlighting
exercising caution is advisable when applying continuous-based the intricacies of the task. Moving to step two, we prepare the
approaches to impute categorical data, as it may introduce bias data for missing values imputation by segregating complete data
into the results [27]. for model training and reserving a test set for predicting missing
data. Before arranging the data, each data sequence is assigned
Motivated by the need for a comprehensive evaluation, we a unique identifier, ensuring traceability. Complete data features
conduct extensive experiments to compare the performance of our (f0, f3, f6, and f9) are repositioned on the right side in the third
transformer-based imputation against established methods. This step. Subsequently, in step four, all complete rows are relocated to
comparison extends beyond conventional imputation techniques, the top of the dataset.
encompassing zero [28], mean [29], and KNN imputations [30].
In the context of missing value imputation, it is noteworthy Step five reveals the division of the dataset into X-data and
that addressing missing values is a common concern among Y-data, forming the basis for training the model. In step six, we

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Figure 1: A detailed process of preparing data for the Transformer for missing values prediction.

select the complete X-Data and the target feature f1 from Y-Data, the subsequent step nine, the adeptly trained model takes on the
which contains missing data. Utilizing the train-test split on task of predicting missing values within the X-Data. The imputed
X-Data and Y-Data (f1), we generate X-Train, Y-Train, X-Test, and f1 feature is seamlessly integrated back into the X-Data, initiating
Y-Test. In step seven, the train data is prepared for our proposed a cascading effect as subsequent missing values are accurately
prediction model, providing a complete set for training the predicted. This iterative refinement persists until the entirety of
Transformer model. missing values is meticulously filled.

Advancing further, at step eight, the transformer undergoes In the culminating step, the dataset is meticulously organized,
comprehensive training using the entirety of the available data. In preserving its inherent structure by adhering to initially assigned

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IDs. This methodical approach not only ensures the seamless Table 1: A detailed comparative analysis of the Imputation techniques.
integration of imputed values but also maintains the overall Proposed
FE P Zero Mean Mode KNN
integrity and coherence of the dataset. In essence, our methodology Data Measure Imputation imputation Imputation Imputation
Model
Imputation
provides a structured and systematic solution, navigating the
R2 score 0.233 0.647 0.437 0.765 0.96
intricacies of missing value imputation using a transformer model. MAE 0.058 0.113 0.075 0.037 0.036
MSE 0.006 0.02 0.008 0.003 0.003
Proposed model validation Hourly
Data RMSE 0.077 0.141 0.089 0.055 0.055
MAPE 1.2 0.92 1.01 0.83 0.423
After the missing data imputation process finished using
R2 score 0.391 0.556 0.471 0.791 0.806
our suggested transformer-based prediction model, a thorough
MAE 0.066 0.051 0.059 0.048 0.028
validation was carried out. During the validation stage, we aimed
MSE 0.009 0.008 0.0073 0.004 0.003
to assess how well our suggested model performed in comparison Daily
RMSE 0.077 0.095 0.055 0.045 0.045
Data
to other widely used imputation techniques, such as zero, mean, MAPE 0.93 0.85 0.89 0.47 0.32
mode, and KNN imputation. We used these various imputation R2 score 0.251 0.696 0.698 0.419 0.796
methods to produce five sets of imputed data. We validated each MAE 0.023 0.051 0.029 0.038 0.025
imputation model using Long Short-Term Memory (LSTM) Monthly
MSE 0.001 0.003 0.002 0.004 0.001
networks to evaluate its effectiveness thoroughly. The LSTM Data RMSE 0.032 0.055 0.045 0.063 0.032
network was fed the imputed data from all five models, including MAPE 1.13 0.89 0.891 1.01 0.523

our suggested transformer-based imputation, as shown in Figure

2. Our objective was to conduct a comprehensive comparison and three datasets: hourly energy consumption data, daily energy
evaluation of the overall performance and forecast accuracy for each consumption data, and monthly energy consumption data; the R2
imputed dataset. Notably, the results consistently demonstrated score emerges as a critical metric for evaluating the effectiveness
the superior performance of our proposed transformer-based of various imputation methods. The proposed imputation model
prediction-based imputation model when pitted against other, yields a noteworthy R2 score of 0.96 in hourly data, showcasing a
less intricate imputation techniques. This underscores its robust substantial improvement of 0.195 over the next best method, KNN
predictive capabilities in effectively managing missing values imputation. This enhancement underscores the proposed model’s
within the dataset. ability to capture underlying patterns within the data, outshining
traditional techniques such as zero, mean, and mode imputation.
The validation procedure, when juxtaposed with conventional
Similarly, the proposed model’s R2 score of 0.806 in daily data
imputation techniques, serves as a testament to the resilience and
efficacy of our proposed model. The outcomes not only showcase its outperforms the KNN imputation by 0.015, demonstrating a
superiority but also affirm its ability to outperform fewer complex notable superiority of 0.25 over the mean imputation. Moving
alternatives. to monthly data, the proposed model’s R2 score of 0.796 excels,
showcasing a significant improvement of 0.1 over mean imputation
Results and analysis and an even more substantial gain of 0.359 over mode imputation.

Table 1 examines the imputation performance across Overall, these results consistently highlight the proposed

Figure 2: Validation process of the Imputed data using LSTM.

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model’s effectiveness in preserving data relationships and underscore the robustness of the proposed model in minimizing
capturing variability across diverse datasets, positioning it as a imputation errors. These comprehensive findings suggest that,
robust choice for imputing missing values when accurate modeling beyond R2 scores, the proposed imputation model consistently
of underlying data patterns is crucial. A visual analysis of the r2 excels across various error metrics, affirming its efficacy in
score for the selected imputation method is illustrated in Figure 3. accurately filling missing data and offering a comprehensive
solution for handling diverse datasets with absent values.
Beyond R2 scores, an in-depth analysis of other error metrics
further solidifies the superiority of the proposed imputation Critical discussion
model, as shown in Figure 4. In hourly consumption data, the
model’s Mean Absolute Error (MAE) of 0.036 is notably lower In this study, we have demonstrated the superior efficacy of
than that of other methods, reflecting its ability to predict missing transformer models over traditional methods like zero mean and
values with minimal deviation accurately. This trend continues in KNN imputation, particularly in handling accuracy and context
daily and monthly consumption data, where the proposed model in missing data. However, the performance of these models
consistently achieves the lowest MAE values, indicating superior varies with different data types and sizes, highlighting potential
imputation accuracy. Similarly, examining Mean Squared Error limitations in scalability and applicability to diverse datasets.
(MSE) and Root Mean Squared Error (RMSE) across all datasets, Comparative analysis suggests that while transformers excel in
the proposed model consistently outperforms alternative methods. interpreting sequential data, they may not be the most suitable
The observed reductions in MAE, MSE, and RMSE collectively choice for simpler or smaller datasets. The practical applications of

Figure 3: R2 score analysis for the selected imputation methods.

Figure 4: MAPE analysis for the selected imputation methods.

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How to cite this article: Ayub H, Jamil H. Enhancing Missing Values Imputation through Transformer-Based Predictive Modeling. IgMin Res. Jan 23, 2024; 2(1): 025-031. IgMin ID:
igmin140; DOI: 10.61927/igmin140; Available at: www.igminresearch.com/articles/pdf/igmin140.pdf

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