• Survey Research
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• v.11 no.1
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• pp.1-18
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• 2010

We compare various imputation methods for compensating wave nonresponse that are commonly adopted in many panel surveys. Unlike the cross-sectional survey, the panel survey is involved a time-effect in nonresponse in a sense that nonresponse may happen for some but not all waves. Thus, responses in neighboring waves can be used as powerful predictors for imputing wave nonresponse such as in longitudinal regression imputation, carry-over imputation, nearest neighborhood regression imputation and row-column imputation method. For comparison, we carry out a simulation study on a few income data from the Korean Welfare Panel Study based on two performance criteria: predictive accuracy and estimation accuracy. Our simulation shows that the ratio and row-column imputation methods are much more effective in terms of both criteria. Regression, longitudinal regression and carry-over imputation methods performed better in predictive accuracy, but less in estimation accuracy. On the other hand, nearest neighborhood, nearest neighbor regression and hot-deck imputation show higher performance in estimation accuracy but lower predictive accuracy. Finally, the mean imputation shows much lower performance in both criteria.

• Asian-Australasian Journal of Animal Sciences
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• v.29 no.4
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• pp.464-470
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• 2016

The objective of this study was to investigate the accuracy of imputation from low density (LDC) to moderate density SNP chips (MDC) in a Thai Holstein-Other multibreed dairy cattle population. Dairy cattle with complete pedigree information (n = 1,244) from 145 dairy farms were genotyped with GeneSeek GGP20K (n = 570), GGP26K (n = 540) and GGP80K (n = 134) chips. After checking for single nucleotide polymorphism (SNP) quality, 17,779 SNP markers in common between the GGP20K, GGP26K, and GGP80K were used to represent MDC. Animals were divided into two groups, a reference group (n = 912) and a test group (n = 332). The SNP markers chosen for the test group were those located in positions corresponding to GeneSeek GGP9K (n = 7,652). The LDC to MDC genotype imputation was carried out using three different software packages, namely Beagle 3.3 (population-based algorithm), FImpute 2.2 (combined family- and population-based algorithms) and Findhap 4 (combined family- and population-based algorithms). Imputation accuracies within and across chromosomes were calculated as ratios of correctly imputed SNP markers to overall imputed SNP markers. Imputation accuracy for the three software packages ranged from 76.79% to 93.94%. FImpute had higher imputation accuracy (93.94%) than Findhap (84.64%) and Beagle (76.79%). Imputation accuracies were similar and consistent across chromosomes for FImpute, but not for Findhap and Beagle. Most chromosomes that showed either high (73%) or low (80%) imputation accuracies were the same chromosomes that had above and below average linkage disequilibrium (LD; defined here as the correlation between pairs of adjacent SNP within chromosomes less than or equal to 1 Mb apart). Results indicated that FImpute was more suitable than Findhap and Beagle for genotype imputation in this Thai multibreed population. Perhaps additional increments in imputation accuracy could be achieved by increasing the completeness of pedigree information.

• Journal of Korean Institute of Industrial Engineers
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• v.38 no.4
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• pp.276-284
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• 2012

Classification algorithms generally assume that the data is complete. However, missing values are common in real data sets due to various reasons. In this paper, we propose to use locally linear reconstruction (LLR) for missing value imputation to improve the classification performance when missing values exist. We first investigate how much missing values degenerate the classification performance with regard to various missing ratios. Then, we compare the proposed missing value imputation (LLR) with three well-known single imputation methods over three different classifiers using eight data sets. The experimental results showed that (1) any imputation methods, although some of them are very simple, helped to improve the classification accuracy; (2) among the imputation methods, the proposed LLR imputation was the most effective over all missing ratios, and (3) when the missing ratio is relatively high, LLR was outstanding and its classification accuracy was as high as the classification accuracy derived from the compete data set.

• Communications for Statistical Applications and Methods
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• v.30 no.6
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• pp.577-587
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• 2023

Conventional categorical data imputation techniques, such as mode imputation, often encounter issues related to overestimation. If the variable has too many categories, multinomial logistic regression imputation method may be impossible due to computational limitations. To rectify these limitations, we propose a two-stage imputation method. During the first stage, we utilize the Boruta variable selection method on the complete dataset to identify significant variables for the target categorical variable. Then, in the second stage, we use the important variables for the target categorical variable for logistic regression to impute missing data in binary variables, polytomous regression to impute missing data in categorical variables, and predictive mean matching to impute missing data in quantitative variables. Through analysis of both asymmetric and non-normal simulated and real data, we demonstrate that the two-stage imputation method outperforms imputation methods lacking variable selection, as evidenced by accuracy measures. During the analysis of real survey data, we also demonstrate that our suggested two-stage imputation method surpasses the current imputation approach in terms of accuracy.

• Journal of Animal Science and Technology
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• v.63 no.6
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• pp.1232-1246
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• 2021

Recently, the cattle genome sequence has been completed, followed by developing a commercial single nucleotide polymorphism (SNP) chip panel in the animal genome industry. In order to increase statistical power for detecting quantitative trait locus (QTL), a number of animals should be genotyped. However, a high-density chip for many animals would be increasing the genotyping cost. Therefore, statistical inference of genotype imputation (low-density chip to high-density) will be useful in the animal industry. The purpose of this study is to investigate the effect of the reference population size and marker density on the imputation accuracy and to suggest the appropriate number of reference population sets for the imputation in Hanwoo cattle. A total of 3,821 Hanwoo cattle were divided into reference and validation populations. The reference sets consisted of 50k (38,916) marker data and different population sizes (500, 1,000, 1,500, 2,000, and 3,600). The validation sets consisted of four validation sets (Total 889) and the different marker density (5k [5,000], 10k [10,000], and 15k [15,000]). The accuracy of imputation was calculated by direct comparison of the true genotype and the imputed genotype. In conclusion, when the lowest marker density (5k) was used in the validation set, according to the reference population size, the imputation accuracy was 0.793 to 0.929. On the other hand, when the highest marker density (15k), according to the reference population size, the imputation accuracy was 0.904 to 0.967. Moreover, the reference population size should be more than 1,000 to obtain at least 88% imputation accuracy in Hanwoo cattle.

• Journal of Animal Science and Technology
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• v.58 no.1
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• pp.1.1-1.6
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• 2016

Background: Genotype imputation is an important process of predicting unknown genotypes, which uses reference population with dense genotypes to predict missing genotypes for both human and animal genetic variations at a low cost. Machine learning methods specially boosting methods have been used in genetic studies to explore the underlying genetic profile of disease and build models capable of predicting missing values of a marker. Methods: In this study strategies and factors affecting the imputation accuracy of parent-offspring trios compared from lower-density SNP panels (5 K) to high density (10 K) SNP panel using three different Boosting methods namely TotalBoost (TB), LogitBoost (LB) and AdaBoost (AB). The methods employed using simulated data to impute the un-typed SNPs in parent-offspring trios. Four different datasets of G1 (100 trios with 5 k SNPs), G2 (100 trios with 10 k SNPs), G3 (500 trios with 5 k SNPs), and G4 (500 trio with 10 k SNPs) were simulated. In four datasets all parents were genotyped completely, and offspring genotyped with a lower density panel. Results: Comparison of the three methods for imputation showed that the LB outperformed AB and TB for imputation accuracy. The time of computation were different between methods. The AB was the fastest algorithm. The higher SNP densities resulted the increase of the accuracy of imputation. Larger trios (i.e. 500) was better for performance of LB and TB. Conclusions: The conclusion is that the three methods do well in terms of imputation accuracy also the dense chip is recommended for imputation of parent-offspring trios.

• The Korean Journal of Applied Statistics
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• v.21 no.1
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• pp.95-107
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• 2008

Survey on the rural living indicators was the statistic approved from National Statistical Office and the survey executed by rural resources development institute. This study was used the raw data of survey on the rural living indicators in 2005. After editing procedure for raw data, we were studied 1,582 households which is acquired through elimination of case included nonresponses, and imputed a nonresponses of 15 item selected from 146 item. The imputation methods and efficiency of imputation for simulation was adapted differently from type of data. For continuous data, we imputed the nonresponses with mean imputation, regression imputation, adjusted grey-based k-NN imputation(DU, DW, WU, WW) and compared the results with RMSE. For categorical data, we imputed the nonresponses with mode method, probability imputation, conditional mode method, conditional probability method, hot-deck imputation, and compared the results with Accuracy. By the results, regression imputation and adjusted grey-based k-NN imputation appropriated for continuous data and hot-deck imputation appropriated for categorical data.

• Journal of the Korean Data and Information Science Society
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• v.14 no.2
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• pp.143-152
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• 2003

A data set having missing observations is often completed by using imputed values. In this paper, performances and accuracy of five imputation procedures are evaluated when missing values exist only on the response variable in the exponential regression model. Our simulation results show that adjusted exponential regression imputation procedure can be well used to compensate for missing data, in particular, compared to other imputation procedures. An illustrative example using real data is provided.

• 한국데이터정보과학회:학술대회논문집
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• 2003.05a
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• pp.135-144
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• 2003

A data set having missing observations is often completed by using imputed values. In this paper, performances and accuracy of five imputation procedures are evaluated when missing values exist only on the response variable in the exponential regression model. Our simulation results show that adjusted exponential regression imputation procedure can be well used to compensate for missing data, in particular, compared to other imputation procedures. An illustrative example using real data is provided.

• Proceedings of the Korean Statistical Society Conference
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• 2001.11a
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• pp.143-148
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• 2001

A dataset having missing observations is often completed by using imputed values. In this paper the performances and accuracy of complete case methods and four imputation procedures are evaluated when missing values exist only on the response variables in the Weibull regression model. Our simulation results show that compared to other imputation procedures, in particular, hotdeck and Weibull regression imputation procedure can be well used to compensate for missing data. In addition an illustrative real data is given.