• Journal of the Korean Data and Information Science Society
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• v.15 no.4
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• pp.945-955
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• 2004

'Complete-case analysis' is easy to carry out and it may be fine with small amount of missing data. However, this method is not recommended in general because the estimates are usually biased and not efficient. There are numerous alternatives to complete-case analysis. One alternative is the single imputation. Some of the most common single imputation methods are reviewed and the performances are compared by simulation studies.

• Journal of the Korean Data and Information Science Society
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• v.16 no.4
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• pp.1079-1086
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• 2005

Most discussions of single imputation methods and the EM algorithm concern point estimation of population quantities with missing values. A second concern is how to get standard errors of the point estimates obtained from the filled-in data by single imputation methods and EM algorithm. Now we focus on how to estimate standard errors with incorporating the additional uncertainty due to nonresponse. There are some approaches to account for the additional uncertainty. The general two possible approaches are considered. One is the jackknife method of resampling methods. The other is multiple imputation(MI). These two approaches are reviewed and compared through simulation studies.

• Journal of KIISE:Software and Applications
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• v.32 no.2
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• pp.99-107
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• 2005

In this paper, wc propose a now missing imputation method for minimizing loss of information linkage disequilibrium-based and haplotype-based imputation method, which estimate missing values of the data based on the specificity of Single Nucleotide Polymorphism(SNP) genotype data. Method for imputing data is needed to minimize the loss of information caused by experimental missing data. In general, missing imputation of biological data has used major allele imputation method. but this approach is not optima]. 1'his method has high error rates of missing values estimation since the characteristics of the genotype data are not considered not take into consideration the specific structure of the data. In this paper, we show the results of the comparative evaluation of our model methods and major imputation method for the estimation of missing values.

• 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.

• 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.

• Genomics & Informatics
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• v.15 no.3
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• pp.108-111
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• 2017

Recently developed computational methods allow the imputation of human leukocyte antigen (HLA) genes using intergenic single nucleotide polymorphism markers. To improve the imputation accuracy in HLA imputation, it is essential to increase the sample size and the diversity of alleles in the reference panel. Our software, MergeReference, helps achieve this goal by providing a streamlined pipeline for combining multiple reference panels into one.

• Genomics & Informatics
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• v.20 no.3
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• pp.34.1-34.11
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• 2022

Multilevel analysis is an appropriate and powerful tool for analyzing hierarchical structure data widely applied from public health to genomic data. In practice, however, we may lose the information on multiple nesting levels in the multilevel analysis since data may fail to capture all levels of hierarchy, or the top or intermediate levels of hierarchy are ignored in the analysis. In this study, we consider a multilevel linear mixed effect model (LMM) with single imputation that can involve all data hierarchy levels in the presence of missing top or intermediate-level clusters. We evaluate and compare the performance of a multilevel LMM with single imputation with other models ignoring the data hierarchy or missing intermediate-level clusters. To this end, we applied a multilevel LMM with single imputation and other models to hierarchically structured cohort data with some intermediate levels missing and to simulated data with various cluster sizes and missing rates of intermediate-level clusters. A thorough simulation study demonstrated that an LMM with single imputation estimates fixed coefficients and variance components of a multilevel model more accurately than other models ignoring data hierarchy or missing clusters in terms of mean squared error and coverage probability. In particular, when models ignoring data hierarchy or missing clusters were applied, the variance components of random effects were overestimated. We observed similar results from the analysis of hierarchically structured cohort data.

• The Korean Journal of Applied Statistics
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• v.31 no.4
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• pp.507-516
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• 2018

Widely used among the various single imputation methods is k-nearest neighbors (KNN) imputation due to its robustness even when a parametric model such as multivariate normality is not satisfied. We propose a weighted adaptive nearest neighbors imputation method that combines the adaptive nearest neighbors imputation method that accounts for the local features of the data in the KNN imputation method and weighted k-nearest neighbors method that are less sensitive to extreme value or outlier among k-nearest neighbors. We conducted a Monte Carlo simulation study to compare the performance of the proposed imputation method with previous imputation methods.

• Journal of Intelligence and Information Systems
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• v.9 no.2
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• pp.51-63
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• 2003

Collaborative filtering is one of the methodologies that are most widely used for recommendation system. It is based on a data matrix of each customer's preferences of products. There could be a lot of missing values in such preference data matrix. This incomplete data is one of the reasons to deteriorate the accuracy of recommendation system. There are several treatments to deal with the incomplete data problem such as case deletion and single imputation. Those approaches are simple and easy to implement but they may provide biased results. Multiple imputation method imputes m values for each missing value. It overcomes flaws of single imputation approaches through considering the uncertainty of missing values. The objective of this paper is to suggest multiple imputation-based collaborative filtering approach for recommendation system to improve the accuracy in prediction performance. The experimental works show that the proposed approach provides better performance than the traditional Collaborative filtering approach, especially in case that there are a lot of missing values in dataset used for recommendation system.