scholarly journals GSimp: A Gibbs sampler based left-censored missing value imputation approach for metabolomics studies

2017 ◽  
Author(s):  
Runmin Wei ◽  
Jingye Wang ◽  
Erik Jia ◽  
Tianlu Chen ◽  
Yan Ni ◽  
...  
Keyword(s):  
Gibbs Sampler ◽  
Real World ◽  
Missing Values ◽  
Statistical Analyses ◽  
Targeted Metabolomics ◽  
Missing Not At Random ◽  
Missing Value ◽  
Imputation Methods ◽  
Missing Value Imputation ◽  
Imputation Approach

AbstractLeft-censored missing values commonly exist in targeted metabolomics datasets and can be considered as missing not at random (MNAR). Improper data processing procedures for missing values will cause adverse impacts on subsequent statistical analyses. However, few imputation methods have been developed and applied to the situation of MNAR in the field of metabolomics. Thus, a practical left-censored missing value imputation method is urgently needed. We have developed an iterative Gibbs sampler based left-censored missing value imputation approach (GSimp). We compared GSimp with other three imputation methods on two real-world targeted metabolomics datasets and one simulation dataset using our imputation evaluation pipeline. The results show that GSimp outperforms other imputation methods in terms of imputation accuracy, observation distribution, univariate and multivariate analyses, and statistical sensitivity. The R code for GSimp, evaluation pipeline, vignette, real-world and simulated targeted metabolomics datasets are available at: https://github.com/WandeRum/GSimp.Author summaryMissing values caused by the limit of detection/quantification (LOD/LOQ) were widely observed in mass spectrometry (MS)-based targeted metabolomics studies and could be recognized as missing not at random (MNAR). MNAR leads to biased parameter estimations and jeopardizes following statistical analyses in different aspects, such as distorting sample distribution, impairing statistical power, etc. Although a wide range of missing value imputation methods was developed for –omics studies, a limited number of methods was designed appropriately for the situation of MNAR currently. To alleviate problems caused by MNAR and facilitate targeted metabolomics studies, we developed a Gibbs sampler based missing value imputation approach, called GSimp, which is public-accessible on GitHub. And we compared our method with existing approaches using an imputation evaluation pipeline on real-world and simulated metabolomics datasets to demonstrate the superiority of our method from different perspectives.

scholarly journals A data-driven missing value imputation approach for longitudinal datasets

2021 ◽  
Author(s):  
Caio Ribeiro ◽  
Alex A. Freitas
Keyword(s):  
Missing Data ◽  
Longitudinal Data ◽  
Missing Values ◽  
Error Rates ◽  
Imputation Method ◽  
Data Driven ◽  
Missing Value ◽  
Missing Value Imputation ◽  
Human Ageing ◽  
Imputation Approach

AbstractLongitudinal datasets of human ageing studies usually have a high volume of missing data, and one way to handle missing values in a dataset is to replace them with estimations. However, there are many methods to estimate missing values, and no single method is the best for all datasets. In this article, we propose a data-driven missing value imputation approach that performs a feature-wise selection of the best imputation method, using known information in the dataset to rank the five methods we selected, based on their estimation error rates. We evaluated the proposed approach in two sets of experiments: a classifier-independent scenario, where we compared the applicabilities and error rates of each imputation method; and a classifier-dependent scenario, where we compared the predictive accuracy of Random Forest classifiers generated with datasets prepared using each imputation method and a baseline approach of doing no imputation (letting the classification algorithm handle the missing values internally). Based on our results from both sets of experiments, we concluded that the proposed data-driven missing value imputation approach generally resulted in models with more accurate estimations for missing data and better performing classifiers, in longitudinal datasets of human ageing. We also observed that imputation methods devised specifically for longitudinal data had very accurate estimations. This reinforces the idea that using the temporal information intrinsic to longitudinal data is a worthwhile endeavour for machine learning applications, and that can be achieved through the proposed data-driven approach.

scholarly journals GSimp: A Gibbs sampler based left-censored missing value imputation approach for metabolomics studies

2018 ◽  
Vol 14 (1) ◽  
pp. e1005973 ◽  
Author(s):  
Runmin Wei ◽  
Jingye Wang ◽  
Erik Jia ◽  
Tianlu Chen ◽  
Yan Ni ◽  
...  
Keyword(s):  
Gibbs Sampler ◽  
Missing Value ◽  
Missing Value Imputation ◽  
Imputation Approach

scholarly journals Missing Value Imputation Approach for Mass Spectrometry-based Metabolomics Data

2017 ◽  
Author(s):  
Runmin Wei ◽  
Jingye Wang ◽  
Mingming Su ◽  
Erik Jia ◽  
Tianlu Chen ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Missing Values ◽  
Pearson Correlation ◽  
Imputation Accuracy ◽  
Metabolomics Data ◽  
Missing Value ◽  
Sample Distribution ◽  
Imputation Methods ◽  
Missing Value Imputation ◽  
Squared Error

AbstractIntroductionMissing values exist widely in mass-spectrometry (MS) based metabolomics data. Various methods have been applied for handling missing values, but the selection of methods can significantly affect following data analyses and interpretations. According to the definition, there are three types of missing values, missing completely at random (MCAR), missing at random (MAR), and missing not at random (MNAR).ObjectivesThe aim of this study was to comprehensively compare common imputation methods for different types of missing values using two separate metabolomics data sets (977 and 198 serum samples respectively) to propose a strategy to deal with missing values in metabolomics studies.MethodsImputation methods included zero, half minimum (HM), mean, median, random forest (RF), singular value decomposition (SVD), k-nearest neighbors (kNN), and quantile regression imputation of left-censored data (QRILC). Normalized root mean squared error (NRMSE) and NRMSE-based sum of ranks (SOR) were applied to evaluate the imputation accuracy for MCAR/MAR and MNAR correspondingly. Principal component analysis (PCA)/partial least squares (PLS)-Procrustes sum of squared error were used to evaluate the overall sample distribution. Student’s t-test followed by Pearson correlation analysis was conducted to evaluate the effect of imputation on univariate statistical analysis.ResultsOur findings demonstrated that RF imputation performed the best for MCAR/MAR and QRILC was the favored one for MNAR.ConclusionCombining with “modified 80% rule”, we proposed a comprehensive strategy and developed a public-accessible web-tool for missing value imputation in metabolomics data.

scholarly journals A New Heuristic Approach for Treating Missing Value: ABCimp

2019 ◽  
Vol 25 (6) ◽  
pp. 48-54
Author(s):  
Pinar Cihan ◽  
Zeynep Banu Ozger
Keyword(s):  
Statistical Methods ◽  
Real World ◽  
Artificial Bee Colony Algorithm ◽  
Artificial Bee Colony ◽  
Missing Values ◽  
Superior Performance ◽  
Classification Error ◽  
Missing Value ◽  
Imputation Methods ◽  
Bee Colony

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 %.

scholarly journals NAguideR: performing and prioritizing missing value imputations for consistent bottom-up proteomic analyses

2020 ◽  
Vol 48 (14) ◽  
pp. e83-e83 ◽  
Author(s):  
Shisheng Wang ◽  
Wenxue Li ◽  
Liqiang Hu ◽  
Jingqiu Cheng ◽  
Hao Yang ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Quantitative Proteomics ◽  
Missing Values ◽  
Protein Complexes ◽  
Label Free ◽  
Missing Value ◽  
Imputation Methods ◽  
Data Independent Acquisition ◽  
Low Performance ◽  
User Friendly

Abstract Mass spectrometry (MS)-based quantitative proteomics experiments frequently generate data with missing values, which may profoundly affect downstream analyses. A wide variety of imputation methods have been established to deal with the missing-value issue. To date, however, there is a scarcity of efficient, systematic, and easy-to-handle tools that are tailored for proteomics community. Herein, we developed a user-friendly and powerful stand-alone software, NAguideR, to enable implementation and evaluation of different missing value methods offered by 23 widely used missing-value imputation algorithms. NAguideR further evaluates data imputation results through classic computational criteria and, unprecedentedly, proteomic empirical criteria, such as quantitative consistency between different charge-states of the same peptide, different peptides belonging to the same proteins, and individual proteins participating protein complexes and functional interactions. We applied NAguideR into three label-free proteomic datasets featuring peptide-level, protein-level, and phosphoproteomic variables respectively, all generated by data independent acquisition mass spectrometry (DIA-MS) with substantial biological replicates. The results indicate that NAguideR is able to discriminate the optimal imputation methods that are facilitating DIA-MS experiments over those sub-optimal and low-performance algorithms. NAguideR further provides downloadable tables and figures supporting flexible data analysis and interpretation. NAguideR is freely available at http://www.omicsolution.org/wukong/NAguideR/ and the source code: https://github.com/wangshisheng/NAguideR/.

scholarly journals Comparison of missing value imputation methods for crop yield data

2006 ◽  
Vol 17 (4) ◽  
pp. 339-349 ◽  
Author(s):  
Ravindra S. Lokupitiya ◽  
Erandathie Lokupitiya ◽  
Keith Paustian
Keyword(s):  
Crop Yield ◽  
Yield Data ◽  
Missing Value ◽  
Imputation Methods ◽  
Missing Value Imputation

scholarly journals Outlier Removal in Model-Based Missing Value Imputation for Medical Datasets

2018 ◽  
Vol 2018 ◽  
pp. 1-9 ◽  
Author(s):  
Min-Wei Huang ◽  
Wei-Chao Lin ◽  
Chih-Fong Tsai
Keyword(s):  
Missing Values ◽  
Positive Impact ◽  
Numerical Data ◽  
Data Type ◽  
Mixed Data ◽  
Instance Selection ◽  
Missing Value ◽  
Missing Value Imputation ◽  
Noisy Information ◽  
Selection Algorithms

Many real-world medical datasets contain some proportion of missing (attribute) values. In general, missing value imputation can be performed to solve this problem, which is to provide estimations for the missing values by a reasoning process based on the (complete) observed data. However, if the observed data contain some noisy information or outliers, the estimations of the missing values may not be reliable or may even be quite different from the real values. The aim of this paper is to examine whether a combination of instance selection from the observed data and missing value imputation offers better performance than performing missing value imputation alone. In particular, three instance selection algorithms, DROP3, GA, and IB3, and three imputation algorithms, KNNI, MLP, and SVM, are used in order to find out the best combination. The experimental results show that that performing instance selection can have a positive impact on missing value imputation over the numerical data type of medical datasets, and specific combinations of instance selection and imputation methods can improve the imputation results over the mixed data type of medical datasets. However, instance selection does not have a definitely positive impact on the imputation result for categorical medical datasets.

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