Does the Missing Data Imputation Method Affect the Composition and Performance of Prognostic Models?


Mohammad Reza Baneshi 1 , * , AR Talei 2

1 Department of Biostatistics, Research Center for Modelling in Health, Kerman University of Medical Sciences, Kerman, Iran

2 Shahid Faghihi Hospital, Shiraz University of Medical Sciences, Shiraz, Iran

How to Cite: Baneshi M R, Talei A. Does the Missing Data Imputation Method Affect the Composition and Performance of Prognostic Models?, Iran Red Crescent Med J. 2012 ; 14(1):e95930.


Iranian Red Crescent Medical Journal: 14 (1); e95930
Published Online: January 31, 2012
Article Type: Research Article
Received: July 02, 2019
Accepted: January 31, 2012


Background: We already showed the superiority of imputation of missing data (via Multivariable Imputation via Chained Equations (MICE) method) over exclusion of them; however, the methodology of MICE is complicated. Furthermore, easier imputation methods are available. The aim of this study was to compare them in terms of model composition and performance.


Methods: Three hundreds and ten breast cancer patients were recruited. Four approaches were applied to impute missing data. First we adopted an ad hoc method in which missing data for each variable was replaced by the median of observed values. Then 3 likelihood-based approaches were used. In the regression imputation, a regression model compared the variable with missing data to the rest of the variables. The regression equation was used to fill the missing data. The Expectation Maximum (E-M) algorithm was implemented in which missing data and regression parameters were estimated iteratively until convergence of regression parameters. Finally, the MICE method was applied. Models developed were compared in terms of variables significantly contributed to the multifactorial analysis, sensitivity and specificity.


Results: All candidate variables significantly contributed to the MICE model. However, grade of disease lost its effect in other three models. The MICE model showed the best performance followed by E-M model.


Conclusion: Among imputation methods, final models were not the same, in terms of composition and performance. Therefore, modern imputation methods are recommended to recover the information.

© 2012, Author(s). This is an open-access article distributed under the terms of the Creative Commons Attribution-NonCommercial 4.0 International License ( which permits copy and redistribute the material just in noncommercial usages, provided the original work is properly cited.


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