Missing Value Imputation Methods Research Articles

Trace Ratio Linear Discriminant Analysis for Medical Diagnosis: A Case Study of Dementia

Dementia is one of the most common neurological disorders among the elderly. Identifying those who are of high risk suffering dementia is important to the administration of early treatment in order to slow down the progression of dementia symptoms. However, to achieve accurate classification, significant amount of subject feature information are involved. Hence identification of demented subjects can be transformed into a pattern recognition problem with high-dimensional nonlinear datasets. In this paper, we introduce trace ratio linear discriminant analysis (TR-LDA) for dementia diagnosis. An improved ITR algorithm (iITR) is developed to solve the TR-LDA problem. This novel method can be integrated with advanced missing value imputation method and utilized for the analysis of the nonlinear datasets in many real-world medical diagnosis problems. Finally, extensive simulations are conducted to show the effectiveness of the proposed method. The results demonstrate that our method can achieve higher accuracies for identifying the demented patients than other state-of-art algorithms.

Locally linear reconstruction based missing value imputation for supervised learning

Most learning algorithms generally assume that data is complete so each attribute of all instances is filled with a valid value. However, missing values are very common in real datasets for various reasons. In this paper, we propose a new single imputation method based on locally linear reconstruction (LLR) that improves the prediction performance of supervised learning (classification & regression) with missing values. First, we investigate how missing values degrade the prediction performance with various missing ratios. Next, we compare the proposed missing value imputation method (LLR) with six well-known single imputation methods for five different learning algorithms based on 13 classification and nine regression datasets. The experimental results showed that (1) all imputation methods helped to improve the prediction accuracy, although some were very simple; (2) the proposed LLR imputation method enhanced the modeling performance more than all other imputation methods, irrespective of the learning algorithms and the missing ratios; and (3) LLR was outstanding when the missing ratio was relatively high and its prediction accuracy was similar to that of the complete dataset.

A missing value imputation method using a Bayesian network with weighted learning

AbstractWith the development of computer networks, it has become easy to have huge databases. Accordingly, it is becoming difficult for users to extract knowledge from such databases. In this paper we focus on data mining, especially classification. In real‐world data mining, the missing value problem occurs in cases such as speech containing noise, facial occlusion, and the like. When a test sample has missing values, a classification system cannot handle them. In previous studies, various imputation methods have been developed, with the objective of solving the missing value problem with numerous explanatory variables, even if some explanatory variables were ineffective for imputation. It has been said that the use of many variables degrades learning efficiency, and thus we believe that imputation methods should be developed considering the relations among explanatory variables. It is also effective to consider the relations between the test sample and each of the training samples. Therefore, we have proposed an imputation method using a Bayesian network with weighted learning. Experiments have confirmed that the proposed method imputes missed values with approximate values, and the classification system successfully classified test samples in which missed values were imputed by the proposed method, with better success than some conventional imputation methods. © 2012 Wiley Periodicals, Inc. Electron Comm Jpn, 95(12): 1–9, 2012; Published online in Wiley Online Library (wileyonlinelibrary.com). DOI 10.1002/ecj.11449

Comparison of missing value imputation methods in time series: the case of Turkish meteorological data

This study aims to compare several imputation methods to complete the missing values of spatio–temporal meteorological time series. To this end, six imputation methods are assessed with respect to various criteria including accuracy, robustness, precision, and efficiency for artificially created missing data in monthly total precipitation and mean temperature series obtained from the Turkish State Meteorological Service. Of these methods, simple arithmetic average, normal ratio (NR), and NR weighted with correlations comprise the simple ones, whereas multilayer perceptron type neural network and multiple imputation strategy adopted by Monte Carlo Markov Chain based on expectation–maximization (EM-MCMC) are computationally intensive ones. In addition, we propose a modification on the EM-MCMC method. Besides using a conventional accuracy measure based on squared errors, we also suggest the correlation dimension (CD) technique of nonlinear dynamic time series analysis which takes spatio–temporal dependencies into account for evaluating imputation performances. Depending on the detailed graphical and quantitative analysis, it can be said that although computational methods, particularly EM-MCMC method, are computationally inefficient, they seem favorable for imputation of meteorological time series with respect to different missingness periods considering both measures and both series studied. To conclude, using the EM-MCMC algorithm for imputing missing values before conducting any statistical analyses of meteorological data will definitely decrease the amount of uncertainty and give more robust results. Moreover, the CD measure can be suggested for the performance evaluation of missing data imputation particularly with computational methods since it gives more precise results in meteorological time series.

Missing Value Imputation Method by Using Bayesian Network with Weighted Learning

Missing Value Imputation Method by Using Bayesian Network with Weighted Learning

Missing data imputation for fuzzy rule-based classification systems

Fuzzy rule-based classification systems (FRBCSs) are known due to their ability to treat with low quality data and obtain good results in these scenarios. However, their application in problems with missing data are uncommon while in real-life data, information is frequently incomplete in data mining, caused by the presence of missing values in attributes. Several schemes have been studied to overcome the drawbacks produced by missing values in data mining tasks; one of the most well known is based on preprocessing, formerly known as imputation. In this work, we focus on FRBCSs considering 14 different approaches to missing attribute values treatment that are presented and analyzed. The analysis involves three different methods, in which we distinguish between Mamdani and TSK models. From the obtained results, the convenience of using imputation methods for FRBCSs with missing values is stated. The analysis suggests that each type behaves differently while the use of determined missing values imputation methods could improve the accuracy obtained for these methods. Thus, the use of particular imputation methods conditioned to the type of FRBCSs is required.

On the choice of the best imputation methods for missing values considering three groups of classification methods

In real-life data, information is frequently lost in data mining, caused by the presence of missing values in attributes. Several schemes have been studied to overcome the drawbacks produced by missing values in data mining tasks; one of the most well known is based on preprocessing, formerly known as imputation. In this work, we focus on a classification task with twenty-three classification methods and fourteen different imputation approaches to missing values treatment that are presented and analyzed. The analysis involves a group-based approach, in which we distinguish between three different categories of classification methods. Each category behaves differently, and the evidence obtained shows that the use of determined missing values imputation methods could improve the accuracy obtained for these methods. In this study, the convenience of using imputation methods for preprocessing data sets with missing values is stated. The analysis suggests that the use of particular imputation methods conditioned to the groups is required.

Evaluation of Three Simple Imputation Methods for Enhancing Preprocessing of Data with Missing Values

of the important stages of data mining is preprocessing, where the data is prepared for different mining tasks. Often, the real-world data tends to be incomplete, noisy, and inconsistent. It is very common that the data are not obtainable for every observation of every variable. So the presence of missing variables is obvious in the data set. A most important task when preprocessing the data is, to fill in missing values, smooth out noise and correct inconsistencies. This paper presents the missing value problem in data mining and evaluates some of the methods generally used for missing value imputation. In this work, three simple missing value imputation methods are implemented namely (1) Constant substitution, (2) Mean attribute value substitution and (3) Random attribute value substitution. The performance of the three missing value imputation algorithms were measured with respect to different rate or different percentage of missing values in the data set by using some known clustering methods. To evaluate the performance, the standard WDBC data set has been used.

KNN-DTW Based Missing Value Imputation for Microarray Time Series Data

Microarray technology provides an opportunity for scientists to analyze thousands of gene expression profiles simultaneously. However, microarray gene expression data often contain multiple missing expression values due to many reasons. Effective methods for missing value imputation in gene expression data are needed since many algorithms for gene analysis require a complete matrix of gene array values. Several algorithms are proposed to handle this problem, but they have various limitations. In this paper, we develop a novel method to impute missing values in microarray time-series data combining k-nearest neighbor (KNN) and dynamic time warping (DTW). We also analyze and implement several variants of DTW to further improve the efficiency and accuracy of our method. Experimental results show that our method is more accurate compared with existing missing value imputation methods on real microarray time series datasets.

Foreword of Special Issue on “E-Service and Applications”

Foreword of Special Issue on “E-Service and Applications”

Comparative analysis of missing value imputation methods to improve clustering and interpretation of microarray experiments

BackgroundMicroarray technologies produced large amount of data. In a previous study, we have shown the interest of k-Nearest Neighbour approach for restoring the missing gene expression values, and its positive impact of the gene clustering by hierarchical algorithm. Since, numerous replacement methods have been proposed to impute missing values (MVs) for microarray data. In this study, we have evaluated twelve different usable methods, and their influence on the quality of gene clustering. Interestingly we have used several datasets, both kinetic and non kinetic experiments from yeast and human.ResultsWe underline the excellent efficiency of approaches proposed and implemented by Bo and co-workers and especially one based on expected maximization (EM_array). These improvements have been observed also on the imputation of extreme values, the most difficult predictable values. We showed that the imputed MVs have still important effects on the stability of the gene clusters. The improvement on the clustering obtained by hierarchical clustering remains limited and, not sufficient to restore completely the correct gene associations. However, a common tendency can be found between the quality of the imputation method and the gene cluster stability. Even if the comparison between clustering algorithms is a complex task, we observed that k-means approach is more efficient to conserve gene associations.ConclusionsMore than 6.000.000 independent simulations have assessed the quality of 12 imputation methods on five very different biological datasets. Important improvements have so been done since our last study. The EM_array approach constitutes one efficient method for restoring the missing expression gene values, with a lower estimation error level. Nonetheless, the presence of MVs even at a low rate is a major factor of gene cluster instability. Our study highlights the need for a systematic assessment of imputation methods and so of dedicated benchmarks. A noticeable point is the specific influence of some biological dataset.

Dealing with missing values in large-scale studies: microarray data imputation and beyond

High-throughput biotechnologies, such as gene expression microarrays or mass-spectrometry-based proteomic assays, suffer from frequent missing values due to various experimental reasons. Since the missing data points can hinder downstream analyses, there exists a wide variety of ways in which to deal with missing values in large-scale data sets. Nowadays, it has become routine to estimate (or impute) the missing values prior to the actual data analysis. After nearly a decade since the publication of the first missing value imputation methods for gene expression microarray data, new imputation approaches are still being developed at an increasing rate. However, what is lagging behind is a systematic and objective evaluation of the strengths and weaknesses of the different approaches when faced with different types of data sets and experimental questions. In this review, the present strategies for missing value imputation and the measures for evaluating their performance are described. The imputation methods are first reviewed in the context of gene expression microarray data, since most of the methods have been developed for estimating gene expression levels; then, we turn to other large-scale data sets that also suffer from the problems posed by missing values, together with pointers to possible imputation approaches in these settings. Along with a description of the basic principles behind the different imputation approaches, the review tries to provide practical guidance for the users of high-throughput technologies on how to choose the imputation tool for their data and questions, and some additional research directions for the developers of imputation methodologies.

Comparison of missing value imputation methods for crop yield data

Most ecological data sets contain missing values, a fact which can cause problems in the analysis and limit the utility of resulting inference. However, ecological data also tend to be spatially correlated, which can aid in estimating and imputing missing values. We compared four existing methods of estimating missing values: regression, kernel smoothing, universal kriging, and multiple imputation. Data on crop yields from the National Agricultural Statistical Survey (NASS) and the Census of Agriculture (Ag Census) were the basis for our analysis. Our goal was to find the best method to impute missing values in the NASS datasets. For this comparison, we selected the NASS data for barley crop yield in 1997 as our reference dataset. We found in this case that multiple imputation and regression were superior to methods based on spatial correlation. Universal kriging was found to be the third best method. Kernel smoothing seemed to perform very poorly. Copyright © 2005 John Wiley & Sons, Ltd.

Support Vector Regression을 이용한 희소 데이터의 전처리

In various fields as web mining, bioinformatics, statistical data analysis, and so forth, very diversely missing values are found. These values make training data to be sparse. Largely, the missing values are replaced by predicted values using mean and mode. We can used the advanced missing value imputation methods as conditional mean, tree method, and Markov Chain Monte Carlo algorithm. But general imputation models have the property that their predictive accuracy is decreased according to increase the ratio of missing in training data. Moreover the number of available imputations is limited by increasing missing ratio. To settle this problem, we proposed statistical learning theory to preprocess for missing values. Our statistical learning theory is the support vector regression by Vapnik. The proposed method can be applied to sparsely training data. We verified the performance of our model using the data sets from UCI machine learning repository.