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Zhang, Shengkai, Li Gong, Qi Zeng, Wenhao Li, Feng Xiao, and Jintao Lei. "Imputation of GPS Coordinate Time Series Using missForest." Remote Sensing 13, no. 12 (June 12, 2021): 2312. http://dx.doi.org/10.3390/rs13122312.
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The global positioning system (GPS) can provide the daily coordinate time series to help geodesy and geophysical studies. However, due to logistics and malfunctioning, missing values are often “seen” in GPS time series, especially in polar regions. Acquiring a consistent and complete time series is the prerequisite for accurate and reliable statical analysis. Previous imputation studies focused on the temporal relationship of time series, and only a few studies used spatial relationships and/or were based on machine learning methods. In this study, we impute 20 Greenland GPS time series using missForest, which is a new machine learning method for data imputation. The imputation performance of missForest and that of four traditional methods are assessed, and the methods’ impacts on principal component analysis (PCA) are investigated. Results show that missForest can impute more than a 30-day gap, and its imputed time series has the least influence on PCA. When the gap size is 30 days, the mean absolute value of the imputed and true values for missForest is 2.71 mm. The normalized root mean squared error is 0.065, and the distance of the first principal component is 0.013. missForest outperforms the other compared methods. missForest can effectively restore the information of GPS time series and improve the results of related statistical processes, such as PCA analysis.
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Lenz, Michael, Andreas Schulz, Thomas Koeck, Steffen Rapp, Markus Nagler, Madeleine Sauer, Lisa Eggebrecht, et al. "Missing value imputation in proximity extension assay-based targeted proteomics data." PLOS ONE 15, no. 12 (December 14, 2020): e0243487. http://dx.doi.org/10.1371/journal.pone.0243487.
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Targeted proteomics utilizing antibody-based proximity extension assays provides sensitive and highly specific quantifications of plasma protein levels. Multivariate analysis of this data is hampered by frequent missing values (random or left censored), calling for imputation approaches. While appropriate missing-value imputation methods exist, benchmarks of their performance in targeted proteomics data are lacking. Here, we assessed the performance of two methods for imputation of values missing completely at random, the previously top-benchmarked ‘missForest’ and the recently published ‘GSimp’ method. Evaluation was accomplished by comparing imputed with remeasured relative concentrations of 91 inflammation related circulating proteins in 86 samples from a cohort of 645 patients with venous thromboembolism. The median Pearson correlation between imputed and remeasured protein expression values was 69.0% for missForest and 71.6% for GSimp (p = 5.8e-4). Imputation with missForest resulted in stronger reduction of variance compared to GSimp (median relative variance of 25.3% vs. 68.6%, p = 2.4e-16) and undesired larger bias in downstream analyses. Irrespective of the imputation method used, the 91 imputed proteins revealed large variations in imputation accuracy, driven by differences in signal to noise ratio and information overlap between proteins. In summary, GSimp outperformed missForest, while both methods show good overall imputation accuracy with large variations between proteins.
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Alsaber, Ahmad R., Jiazhu Pan, and Adeeba Al-Hurban . "Handling Complex Missing Data Using Random Forest Approach for an Air Quality Monitoring Dataset: A Case Study of Kuwait Environmental Data (2012 to 2018)." International Journal of Environmental Research and Public Health 18, no. 3 (February 2, 2021): 1333. http://dx.doi.org/10.3390/ijerph18031333.
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In environmental research, missing data are often a challenge for statistical modeling. This paper addressed some advanced techniques to deal with missing values in a data set measuring air quality using a multiple imputation (MI) approach. MCAR, MAR, and NMAR missing data techniques are applied to the data set. Five missing data levels are considered: 5%, 10%, 20%, 30%, and 40%. The imputation method used in this paper is an iterative imputation method, missForest, which is related to the random forest approach. Air quality data sets were gathered from five monitoring stations in Kuwait, aggregated to a daily basis. Logarithm transformation was carried out for all pollutant data, in order to normalize their distributions and to minimize skewness. We found high levels of missing values for NO2 (18.4%), CO (18.5%), PM10 (57.4%), SO2 (19.0%), and O3 (18.2%) data. Climatological data (i.e., air temperature, relative humidity, wind direction, and wind speed) were used as control variables for better estimation. The results show that the MAR technique had the lowest RMSE and MAE. We conclude that MI using the missForest approach has a high level of accuracy in estimating missing values. MissForest had the lowest imputation error (RMSE and MAE) among the other imputation methods and, thus, can be considered to be appropriate for analyzing air quality data.
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Misztal, Małgorzata Aleksandra. "Comparison of Selected Multiple Imputation Methods for Continuous Variables – Preliminary Simulation Study Results." Acta Universitatis Lodziensis. Folia Oeconomica 6, no. 339 (February 13, 2019): 73–98. http://dx.doi.org/10.18778/0208-6018.339.05.
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The problem of incomplete data and its implications for drawing valid conclusions from statistical analyses is not related to any particular scientific domain, it arises in economics, sociology, education, behavioural sciences or medicine. Almost all standard statistical methods presume that every object has information on every variable to be included in the analysis and the typical approach to missing data is simply to delete them. However, this leads to ineffective and biased analysis results and is not recommended in the literature. The state of the art technique for handling missing data is multiple imputation. In the paper, some selected multiple imputation methods were taken into account. Special attention was paid to using principal components analysis (PCA) as an imputation method. The goal of the study was to assess the quality of PCA‑based imputations as compared to two other multiple imputation techniques: multivariate imputation by chained equations (MICE) and missForest. The comparison was made by artificially simulating different proportions (10–50%) and mechanisms of missing data using 10 complete data sets from the UCI repository of machine learning databases. Then, missing values were imputed with the use of MICE, missForest and the PCA‑based method (MIPCA). The normalised root mean square error (NRMSE) was calculated as a measure of imputation accuracy. On the basis of the conducted analyses, missForest can be recommended as a multiple imputation method providing the lowest rates of imputation errors for all types of missingness. PCA‑based imputation does not perform well in terms of accuracy.
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Stekhoven, D. J., and P. Buhlmann. "MissForest--non-parametric missing value imputation for mixed-type data." Bioinformatics 28, no. 1 (October 28, 2011): 112–18. http://dx.doi.org/10.1093/bioinformatics/btr597.
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Dogo, Eustace M., Nnamdi I. Nwulu, Bhekisipho Twala, and Clinton Aigbavboa. "Accessing Imbalance Learning Using Dynamic Selection Approach in Water Quality Anomaly Detection." Symmetry 13, no. 5 (May 7, 2021): 818. http://dx.doi.org/10.3390/sym13050818.
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Automatic anomaly detection monitoring plays a vital role in water utilities’ distribution systems to reduce the risk posed by unclean water to consumers. One of the major problems with anomaly detection is imbalanced datasets. Dynamic selection techniques combined with ensemble models have proven to be effective for imbalanced datasets classification tasks. In this paper, water quality anomaly detection is formulated as a classification problem in the presences of class imbalance. To tackle this problem, considering the asymmetry dataset distribution between the majority and minority classes, the performance of sixteen previously proposed single and static ensemble classification methods embedded with resampling strategies are first optimised and compared. After that, six dynamic selection techniques, namely, Modified Class Rank (Rank), Local Class Accuracy (LCA), Overall-Local Accuracy (OLA), K-Nearest Oracles Eliminate (KNORA-E), K-Nearest Oracles Union (KNORA-U) and Meta-Learning for Dynamic Ensemble Selection (META-DES) in combination with homogeneous and heterogeneous ensemble models and three SMOTE-based resampling algorithms (SMOTE, SMOTE+ENN and SMOTE+Tomek Links), and one missing data method (missForest) are proposed and evaluated. A binary real-world drinking-water quality anomaly detection dataset is utilised to evaluate the models. The experimental results obtained reveal all the models benefitting from the combined optimisation of both the classifiers and resampling methods. Considering the three performance measures (balanced accuracy, F-score and G-mean), the result also shows that the dynamic classifier selection (DCS) techniques, in particular, the missForest+SMOTE+RANK and missForest+SMOTE+OLA models based on homogeneous ensemble-bagging with decision tree as the base classifier, exhibited better performances in terms of balanced accuracy and G-mean, while the Bg+mF+SMENN+LCA model based on homogeneous ensemble-bagging with random forest has a better overall F1-measure in comparison to the other models.
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Mari, Carlo, and Cristiano Baldassari. "Ensemble Methods for Jump-Diffusion Models of Power Prices." Energies 14, no. 8 (April 9, 2021): 2084. http://dx.doi.org/10.3390/en14082084.
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We propose a machine learning-based methodology which makes use of ensemble methods with the aims (i) of treating missing data in time series with irregular observation times and detecting anomalies in the observed time behavior; (ii) of defining suitable models of the system dynamics. We applied this methodology to US wholesale electricity price time series that are characterized by missing data, high and stochastic volatility, jumps and pronounced spikes. For missing data, we provide a repair approach based on the missForest algorithm, an imputation algorithm which is completely agnostic about the data distribution. To identify anomalies, i.e., turbulent movements of power prices in which jumps and spikes are observed, we took into account the no-gap reconstructed electricity price time series, and then we detected anomalous regions using the isolation forest algorithm, an anomaly detection method that isolates anomalies instead of profiling normal data points as in the most common techniques. After removing anomalies, the additional gaps will be newly filled by the missForest imputation algorithm. In this way, a complete and clean time series describing the stable dynamics of power prices can be obtained. The decoupling between the stable motion and the turbulent motion allows us to define suitable jump-diffusion models of power prices and to provide an estimation procedure that uses the full information contained in both the stable and the turbulent dynamics.
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Mostafa, Samih M. "Towards improving machine learning algorithms accuracy by benefiting from similarities between cases." Journal of Intelligent & Fuzzy Systems 40, no. 1 (January 4, 2021): 947–72. http://dx.doi.org/10.3233/jifs-201077.
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Data preprocessing is a necessary core in data mining. Preprocessing involves handling missing values, outlier and noise removal, data normalization, etc. The problem with existing methods which handle missing values is that they deal with the whole data ignoring the characteristics of the data (e.g., similarities and differences between cases). This paper focuses on handling the missing values using machine learning methods taking into account the characteristics of the data. The proposed preprocessing method clusters the data, then imputes the missing values in each cluster depending on the data belong to this cluster rather than the whole data. The author performed a comparative study of the proposed method and ten popular imputation methods namely mean, median, mode, KNN, IterativeImputer, IterativeSVD, Softimpute, Mice, Forimp, and Missforest. The experiments were done on four datasets with different number of clusters, sizes, and shapes. The empirical study showed better effectiveness from the point of view of imputation time, Root Mean Square Error (RMSE), Mean Absolute Error (MAE), and coefficient of determination (R2 score) (i.e., the similarity of the original removed value to the imputed one).
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Choi, Jeonghun, and Seung Jun Lee. "A Sensor Fault-Tolerant Accident Diagnosis System." Sensors 20, no. 20 (October 15, 2020): 5839. http://dx.doi.org/10.3390/s20205839.
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Emergency situations in nuclear power plants are accompanied by an automatic reactor shutdown, which gives a big task burden to the plant operators under highly stressful conditions. Diagnosis of the occurred accident is an essential sequence for optimum mitigations; however, it is also a critical source of error because the results of accident identification determine the task flow connected to all subsequent tasks. To support accident identification in nuclear power plants, recurrent neural network (RNN)-based approaches have recently shown outstanding performances. Despite the achievements though, the robustness of RNN models is not promising because wrong inputs have been shown to degrade the performance of RNNs to a greater extent than other methods in some applications. In this research, an accident diagnosis system that is tolerant to sensor faults is developed based on an existing RNN model and tested with anticipated sensor errors. To find the optimum strategy to mitigate sensor error, Missforest, selected from among various imputation methods, and gated recurrent unit with decay (GRUD), developed for multivariate time series imputation based on the RNN model, are compared to examine the extent that they recover the diagnosis accuracies within a given threshold.
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Alsaber, A., A. Al-Herz, J. Pan, K. Saleh, A. Al-Awadhi, W. Al-Kandari, E. Hasan, et al. "THU0556 MISSING DATA AND MULTIPLE IMPUTATION IN RHEUMATOID ARTHRITIS REGISTRIES USING SEQUENTIAL RANDOM FOREST METHOD." Annals of the Rheumatic Diseases 79, Suppl 1 (June 2020): 519.1–519. http://dx.doi.org/10.1136/annrheumdis-2020-eular.4838.
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Background:Missing data in clinical epidemiological researches violate the intention to treat principle,reduce statistical power and can induce bias if they are related to patient’s response to treatment. In multiple imputation (MI), covariates are included in the imputation equation to predict the values of missing data.Objectives:To find the best approach to estimate and impute the missing values in Kuwait Registry for Rheumatic Diseases (KRRD) patients data.Methods:A number of methods were implemented for dealing with missing data. These includedMultivariate imputation by chained equations(MICE),K-Nearest Neighbors(KNN),Bayesian Principal Component Analysis(BPCA),EM with Bootstrapping(Amelia II),Sequential Random Forest(MissForest) and mean imputation. Choosing the best imputation method wasjudged by the minimum scores ofRoot Mean Square Error(RMSE),Mean Absolute Error(MAE) andKolmogorov–Smirnov D test statistic(KS) between the imputed datapoints and the original datapoints that were subsequently sat to missing.Results:A total of 1,685 rheumatoid arthritis (RA) patients and 10,613 hospital visits were included in the registry. Among them, we found a number of variables that had missing values exceeding 5% of the total values. These included duration of RA (13.0%), smoking history (26.3%), rheumatoid factor (7.93%), anti-citrullinated peptide antibodies (20.5%), anti-nuclear antibodies (20.4%), sicca symptoms (19.2%), family history of a rheumatic disease (28.5%), steroid therapy (5.94%), ESR (5.16%), CRP (22.9%) and SDAI (38.0%), The results showed that among the methods used, MissForest gave the highest level of accuracy to estimate the missing values. It had the least imputation errors for both continuous and categorical variables at each frequency of missingness and it had the smallest prediction differences when the models used imputed laboratory values. In both data sets, MICE had the second least imputation errors and prediction differences, followed by KNN and mean imputation.Conclusion:MissForest is a highly accurate method of imputation for missing data in KRRD and outperforms other common imputation techniques in terms of imputation error and maintenance of predictive ability with imputed values in clinical predictive models. This approach can be used in registries to improve the accuracy of data, including the ones for rheumatoid arthritis patients.References:[1]Junninen, H.; Niska, H.; Tuppurainen, K.; Ruuskanen, J.; Kolehmainen, M. Methods for imputation ofmissing values in air quality data sets.Atmospheric Environment2004,38, 2895–2907.[2]Norazian, M.N.; Shukri, Y.A.; Azam, R.N.; Al Bakri, A.M.M. Estimation of missing values in air pollutiondata using single imputation techniques.ScienceAsia2008,34, 341–345.[3]Plaia, A.; Bondi, A. Single imputation method of missing values in environmental pollution data sets.Atmospheric Environment2006,40, 7316–7330.[4]Kabir, G.; Tesfamariam, S.; Hemsing, J.; Sadiq, R. Handling incomplete and missing data in water networkdatabase using imputation methods.Sustainable and Resilient Infrastructure2019, pp. 1–13.[5]Di Zio, M.; Guarnera, U.; Luzi, O. Imputation through finite Gaussian mixture models.ComputationalStatistics & Data Analysis2007,51, 5305–5316.Disclosure of Interests:None declared
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Cihan, Pinar, and Zeynep Banu Ozger. "A New Heuristic Approach for Treating Missing Value: ABCimp." Elektronika ir Elektrotechnika 25, no. 6 (December 6, 2019): 48–54. http://dx.doi.org/10.5755/j01.eie.25.6.24826.
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Missing values in datasets present an important problem for traditional and modern statistical methods. Many statistical methods have been developed to analyze the complete datasets. However, most of the real world datasets contain missing values. Therefore, in recent years, many methods have been developed to overcome the missing value problem. Heuristic methods have become popular in this field due to their superior performance in many other optimization problems. This paper introduces an Artificial Bee Colony algorithm based new approach for missing value imputation in the four real-world discrete datasets. At the proposed Artificial Bee Colony Imputation (ABCimp) method, Bayesian Optimization is integrated into the Artificial Bee Colony algorithm. The performance of the proposed technique is compared with other well-known six methods, which are Mean, Median, k Nearest Neighbor (k-NN), Multivariate Equation by Chained Equation (MICE), Singular Value Decomposition (SVD), and MissForest (MF). The classification error and root mean square error are used as the evaluation criteria of the imputation methods performance and the Naive Bayes algorithm is used as the classifier. The empirical results show that state-of-the-art ABCimp performs better than the other most popular imputation methods at the variable missing rates ranging from 3 % to 15 %.
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Dong, Weinan, Daniel Yee Tak Fong, Jin-sun Yoon, Eric Yuk Fai Wan, Laura Elizabeth Bedford, Eric Ho Man Tang, and Cindy Lo Kuen Lam. "Generative adversarial networks for imputing missing data for big data clinical research." BMC Medical Research Methodology 21, no. 1 (April 20, 2021). http://dx.doi.org/10.1186/s12874-021-01272-3.
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Abstract Background Missing data is a pervasive problem in clinical research. Generative adversarial imputation nets (GAIN), a novel machine learning data imputation approach, has the potential to substitute missing data accurately and efficiently but has not yet been evaluated in empirical big clinical datasets. Objectives This study aimed to evaluate the accuracy of GAIN in imputing missing values in large real-world clinical datasets with mixed-type variables. The computation efficiency of GAIN was also evaluated. The performance of GAIN was compared with other commonly used methods, MICE and missForest. Methods Two real world clinical datasets were used. The first was that of a cohort study on the long-term outcomes of patients with diabetes (50,000 complete cases), and the second was of a cohort study on the effectiveness of a risk assessment and management programme for patients with hypertension (10,000 complete cases). Missing data (missing at random) to independent variables were simulated at different missingness rates (20, 50%). The normalized root mean square error (NRMSE) between imputed values and real values for continuous variables and the proportion of falsely classified (PFC) for categorical variables were used to measure imputation accuracy. Computation time per imputation for each method was recorded. The differences in accuracy of different imputation methods were compared using ANOVA or non-parametric test. Results Both missForest and GAIN were more accurate than MICE. GAIN showed similar accuracy as missForest when the simulated missingness rate was 20%, but was more accurate when the simulated missingness rate was 50%. GAIN was the most accurate for the imputation of skewed continuous and imbalanced categorical variables at both missingness rates. GAIN had a much higher computation speed (32 min on PC) comparing to that of missForest (1300 min) when the sample size is 50,000. Conclusion GAIN showed better accuracy as an imputation method for missing data in large real-world clinical datasets compared to MICE and missForest, and was more resistant to high missingness rate (50%). The high computation speed is an added advantage of GAIN in big clinical data research. It holds potential as an accurate and efficient method for missing data imputation in future big data clinical research. Trial registration ClinicalTrials.gov ID: NCT03299010; Unique Protocol ID: HKUCTR-2232
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Guo, Chao-Yu, Ying-Chen Yang, and Yi-Hau Chen. "The Optimal Machine Learning-Based Missing Data Imputation for the Cox Proportional Hazard Model." Frontiers in Public Health 9 (July 5, 2021). http://dx.doi.org/10.3389/fpubh.2021.680054.
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An adequate imputation of missing data would significantly preserve the statistical power and avoid erroneous conclusions. In the era of big data, machine learning is a great tool to infer the missing values. The root means square error (RMSE) and the proportion of falsely classified entries (PFC) are two standard statistics to evaluate imputation accuracy. However, the Cox proportional hazards model using various types requires deliberate study, and the validity under different missing mechanisms is unknown. In this research, we propose supervised and unsupervised imputations and examine four machine learning-based imputation strategies. We conducted a simulation study under various scenarios with several parameters, such as sample size, missing rate, and different missing mechanisms. The results revealed the type-I errors according to different imputation techniques in the survival data. The simulation results show that the non-parametric “missForest” based on the unsupervised imputation is the only robust method without inflated type-I errors under all missing mechanisms. In contrast, other methods are not valid to test when the missing pattern is informative. Statistical analysis, which is improperly conducted, with missing data may lead to erroneous conclusions. This research provides a clear guideline for a valid survival analysis using the Cox proportional hazard model with machine learning-based imputations.
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Lin, Xihui, and Paul C. Boutros. "Optimization and expansion of non-negative matrix factorization." BMC Bioinformatics 21, no. 1 (January 6, 2020). http://dx.doi.org/10.1186/s12859-019-3312-5.
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Abstract Background Non-negative matrix factorization (NMF) is a technique widely used in various fields, including artificial intelligence (AI), signal processing and bioinformatics. However existing algorithms and R packages cannot be applied to large matrices due to their slow convergence or to matrices with missing entries. Besides, most NMF research focuses only on blind decompositions: decomposition without utilizing prior knowledge. Finally, the lack of well-validated methodology for choosing the rank hyperparameters also raises concern on derived results. Results We adopt the idea of sequential coordinate-wise descent to NMF to increase the convergence rate. We demonstrate that NMF can handle missing values naturally and this property leads to a novel method to determine the rank hyperparameter. Further, we demonstrate some novel applications of NMF and show how to use masking to inject prior knowledge and desirable properties to achieve a more meaningful decomposition. Conclusions We show through complexity analysis and experiments that our implementation converges faster than well-known methods. We also show that using NMF for tumour content deconvolution can achieve results similar to existing methods like ISOpure. Our proposed missing value imputation is more accurate than conventional methods like multiple imputation and comparable to missForest while achieving significantly better computational efficiency. Finally, we argue that the suggested rank tuning method based on missing value imputation is theoretically superior to existing methods. All algorithms are implemented in the R package NNLM, which is freely available on CRAN and Github.
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S, Hong, Sun Y, Li H, and Lynn HS. "A Note on the Required Sample Size of Model-Based Dose-Finding Methods for Molecularly Targeted Agents." Austin Biometrics and Biostatistics 6, no. 1 (March 3, 2021). http://dx.doi.org/10.26420/austinbiomandbiostat.2021.1037.
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Random forest has proven to be a successful machine learning method, but it also can be time-consuming for handling large datasets, especially for doing iterative tasks. Machine learning iterative imputation methods have been well accepted by researchers for imputing missing data, but such methods can be more time-consuming than standard imputation methods. To overcome this drawback, different parallel computing strategies have been proposed but their impact on imputation results and subsequent statistical analyses are relatively unknown. Newly proposed random forest implementations, such as ranger and randomForestSRC, have provided alternatives for easier parallelization, but their validity for doing iterative imputation are still unclear. Using random-forest imputation algorithm missForest as an example, this study examines two parallelized methods using newly proposed random forest implementations in comparison with the two parallel strategies (variable-wise distributed computation and model-wise distributed computation) using language-level parallelization from the software package. Results from the simulation experiments showed that the parallel strategies could influence both the imputation process and the final imputation results differently. Different parallel strategies can improve computational speed to a variable extent, and based on simulations, ranger can provide performance boost for datasets of different sizes with reasonable accuracy. Specifically, even though different strategies can produce similar normalized root mean squared prediction errors, the variable-wise distributed strategy led to additional biases when estimating the mean and inter-correlation of the covariates and their regression coefficients. And parallelization by randomForestSRC can lead to changes in both prediction errors and estimates.