Missing values in radionuclide diffusion datasets can undermine the predictive accuracy and robustness of the machine learning(ML)models.In this study,regression-based missing data imputation method using a light grad...Missing values in radionuclide diffusion datasets can undermine the predictive accuracy and robustness of the machine learning(ML)models.In this study,regression-based missing data imputation method using a light gradient boosting machine(LGBM)algorithm was employed to impute more than 60%of the missing data,establishing a radionuclide diffusion dataset containing 16 input features and 813 instances.The effective diffusion coefficient(D_(e))was predicted using ten ML models.The predictive accuracy of the ensemble meta-models,namely LGBM-extreme gradient boosting(XGB)and LGBM-categorical boosting(CatB),surpassed that of the other ML models,with R^(2)values of 0.94.The models were applied to predict the D_(e)values of EuEDTA^(−)and HCrO_(4)^(−)in saturated compacted bentonites at compactions ranging from 1200 to 1800 kg/m^(3),which were measured using a through-diffusion method.The generalization ability of the LGBM-XGB model surpassed that of LGB-CatB in predicting the D_(e)of HCrO_(4)^(−).Shapley additive explanations identified total porosity as the most significant influencing factor.Additionally,the partial dependence plot analysis technique yielded clearer results in the univariate correlation analysis.This study provides a regression imputation technique to refine radionuclide diffusion datasets,offering deeper insights into analyzing the diffusion mechanism of radionuclides and supporting the safety assessment of the geological disposal of high-level radioactive waste.展开更多
Imputation of missing data has long been an important topic and an essential application for intelligent transportation systems(ITS)in the real world.As a state-of-the-art generative model,the diffusion model has prov...Imputation of missing data has long been an important topic and an essential application for intelligent transportation systems(ITS)in the real world.As a state-of-the-art generative model,the diffusion model has proven highly successful in image generation,speech generation,time series modelling etc.and now opens a new avenue for traffic data imputation.In this paper,we propose a conditional diffusion model,called the implicit-explicit diffusion model,for traffic data imputation.This model exploits both the implicit and explicit feature of the data simultaneously.More specifically,we design two types of feature extraction modules,one to capture the implicit dependencies hidden in the raw data at multiple time scales and the other to obtain the long-term temporal dependencies of the time series.This approach not only inherits the advantages of the diffusion model for estimating missing data,but also takes into account the multiscale correlation inherent in traffic data.To illustrate the performance of the model,extensive experiments are conducted on three real-world time series datasets using different missing rates.The experimental results demonstrate that the model improves imputation accuracy and generalization capability.展开更多
Accurate traffic flow prediction(TFP)is vital for efficient and sustainable transportation management and the development of intelligent traffic systems.However,missing data in real-world traffic datasets poses a sign...Accurate traffic flow prediction(TFP)is vital for efficient and sustainable transportation management and the development of intelligent traffic systems.However,missing data in real-world traffic datasets poses a significant challenge to maintaining prediction precision.This study introduces REPTF-TMDI,a novel method that combines a Reduced Error Pruning Tree Forest(REPTree Forest)with a newly proposed Time-based Missing Data Imputation(TMDI)approach.The REP Tree Forest,an ensemble learning approach,is tailored for time-related traffic data to enhance predictive accuracy and support the evolution of sustainable urbanmobility solutions.Meanwhile,the TMDI approach exploits temporal patterns to estimate missing values reliably whenever empty fields are encountered.The proposed method was evaluated using hourly traffic flow data from a major U.S.roadway spanning 2012-2018,incorporating temporal features(e.g.,hour,day,month,year,weekday),holiday indicator,and weather conditions(temperature,rain,snow,and cloud coverage).Experimental results demonstrated that the REPTF-TMDI method outperformed conventional imputation techniques across various missing data ratios by achieving an average 11.76%improvement in terms of correlation coefficient(R).Furthermore,REPTree Forest achieved improvements of 68.62%in RMSE and 70.52%in MAE compared to existing state-of-the-art models.These findings highlight the method’s ability to significantly boost traffic flow prediction accuracy,even in the presence of missing data,thereby contributing to the broader objectives of sustainable urban transportation systems.展开更多
Handling missing data accurately is critical in clinical research, where data quality directly impacts decision-making and patient outcomes. While deep learning (DL) techniques for data imputation have gained attentio...Handling missing data accurately is critical in clinical research, where data quality directly impacts decision-making and patient outcomes. While deep learning (DL) techniques for data imputation have gained attention, challenges remain, especially when dealing with diverse data types. In this study, we introduce a novel data imputation method based on a modified convolutional neural network, specifically, a Deep Residual-Convolutional Neural Network (DRes-CNN) architecture designed to handle missing values across various datasets. Our approach demonstrates substantial improvements over existing imputation techniques by leveraging residual connections and optimized convolutional layers to capture complex data patterns. We evaluated the model on publicly available datasets, including Medical Information Mart for Intensive Care (MIMIC-III and MIMIC-IV), which contain critical care patient data, and the Beijing Multi-Site Air Quality dataset, which measures environmental air quality. The proposed DRes-CNN method achieved a root mean square error (RMSE) of 0.00006, highlighting its high accuracy and robustness. We also compared with Low Light-Convolutional Neural Network (LL-CNN) and U-Net methods, which had RMSE values of 0.00075 and 0.00073, respectively. This represented an improvement of approximately 92% over LL-CNN and 91% over U-Net. The results showed that this DRes-CNN-based imputation method outperforms current state-of-the-art models. These results established DRes-CNN as a reliable solution for addressing missing data.展开更多
The frequent missing values in radar-derived time-series tracks of aerial targets(RTT-AT)lead to significant challenges in subsequent data-driven tasks.However,the majority of imputation research focuses on random mis...The frequent missing values in radar-derived time-series tracks of aerial targets(RTT-AT)lead to significant challenges in subsequent data-driven tasks.However,the majority of imputation research focuses on random missing(RM)that differs significantly from common missing patterns of RTT-AT.The method for solving the RM may experience performance degradation or failure when applied to RTT-AT imputation.Conventional autoregressive deep learning methods are prone to error accumulation and long-term dependency loss.In this paper,a non-autoregressive imputation model that addresses the issue of missing value imputation for two common missing patterns in RTT-AT is proposed.Our model consists of two probabilistic sparse diagonal masking self-attention(PSDMSA)units and a weight fusion unit.It learns missing values by combining the representations outputted by the two units,aiming to minimize the difference between the missing values and their actual values.The PSDMSA units effectively capture temporal dependencies and attribute correlations between time steps,improving imputation quality.The weight fusion unit automatically updates the weights of the output representations from the two units to obtain a more accurate final representation.The experimental results indicate that,despite varying missing rates in the two missing patterns,our model consistently outperforms other methods in imputation performance and exhibits a low frequency of deviations in estimates for specific missing entries.Compared to the state-of-the-art autoregressive deep learning imputation model Bidirectional Recurrent Imputation for Time Series(BRITS),our proposed model reduces mean absolute error(MAE)by 31%~50%.Additionally,the model attains a training speed that is 4 to 8 times faster when compared to both BRITS and a standard Transformer model when trained on the same dataset.Finally,the findings from the ablation experiments demonstrate that the PSDMSA,the weight fusion unit,cascade network design,and imputation loss enhance imputation performance and confirm the efficacy of our design.展开更多
Missing data presents a significant challenge in statistical analysis and machine learning, often resulting in biased outcomes and diminished efficiency. This comprehensive review investigates various imputation techn...Missing data presents a significant challenge in statistical analysis and machine learning, often resulting in biased outcomes and diminished efficiency. This comprehensive review investigates various imputation techniques, categorizing them into three primary approaches: deterministic methods, probabilistic models, and machine learning algorithms. Traditional techniques, including mean or mode imputation, regression imputation, and last observation carried forward, are evaluated alongside more contemporary methods such as multiple imputation, expectation-maximization, and deep learning strategies. The strengths and limitations of each approach are outlined. Key considerations for selecting appropriate methods, based on data characteristics and research objectives, are discussed. The importance of evaluating imputation’s impact on subsequent analyses is emphasized. This synthesis of recent advancements and best practices provides researchers with a robust framework for effectively handling missing data, thereby improving the reliability of empirical findings across diverse disciplines.展开更多
Compositional data, such as relative information, is a crucial aspect of machine learning and other related fields. It is typically recorded as closed data or sums to a constant, like 100%. The statistical linear mode...Compositional data, such as relative information, is a crucial aspect of machine learning and other related fields. It is typically recorded as closed data or sums to a constant, like 100%. The statistical linear model is the most used technique for identifying hidden relationships between underlying random variables of interest. However, data quality is a significant challenge in machine learning, especially when missing data is present. The linear regression model is a commonly used statistical modeling technique used in various applications to find relationships between variables of interest. When estimating linear regression parameters which are useful for things like future prediction and partial effects analysis of independent variables, maximum likelihood estimation (MLE) is the method of choice. However, many datasets contain missing observations, which can lead to costly and time-consuming data recovery. To address this issue, the expectation-maximization (EM) algorithm has been suggested as a solution for situations including missing data. The EM algorithm repeatedly finds the best estimates of parameters in statistical models that depend on variables or data that have not been observed. This is called maximum likelihood or maximum a posteriori (MAP). Using the present estimate as input, the expectation (E) step constructs a log-likelihood function. Finding the parameters that maximize the anticipated log-likelihood, as determined in the E step, is the job of the maximization (M) phase. This study looked at how well the EM algorithm worked on a made-up compositional dataset with missing observations. It used both the robust least square version and ordinary least square regression techniques. The efficacy of the EM algorithm was compared with two alternative imputation techniques, k-Nearest Neighbor (k-NN) and mean imputation (), in terms of Aitchison distances and covariance.展开更多
Genotype imputation has become an indispensable part of genomic data analysis. In recent years, imputation based on a multi-breed reference population has received more attention, but the relevant studies are scarce i...Genotype imputation has become an indispensable part of genomic data analysis. In recent years, imputation based on a multi-breed reference population has received more attention, but the relevant studies are scarce in pigs. In this study, we used the Illumina Porcine SNP50 Bead Chip to investigate the variations of imputation accuracy with various influencing factors and compared the imputation performance of four commonly used imputation software programs. The results indicated that imputation accuracy increased as either the validation population marker density, reference population sample size, or minor allele frequency(MAF) increased. However, the imputation accuracy would have a certain extent of decrease when the pig reference population was a mixed group of multiple breeds or lines. Considering both imputation accuracy and running time, Beagle 4.1 and FImpute are excellent choices among the four software packages tested. This work visually presents the impacts of these influencing factors on imputation and provides a reference for formulating reasonable imputation strategies in actual pig breeding.展开更多
Based on the two-dimensional relation table,this paper studies the missing values in the sample data of land price of Shunde District of Foshan City.GeoDa software was used to eliminate the insignificant factors by st...Based on the two-dimensional relation table,this paper studies the missing values in the sample data of land price of Shunde District of Foshan City.GeoDa software was used to eliminate the insignificant factors by stepwise regression analysis;NORM software was adopted to construct the multiple imputation models;EM algorithm and the augmentation algorithm were applied to fit multiple linear regression equations to construct five different filling datasets.Statistical analysis is performed on the imputation data set in order to calculate the mean and variance of each data set,and the weight is determined according to the differences.Finally,comprehensive integration is implemented to achieve the imputation expression of missing values.The results showed that in the three missing cases where the PRICE variable was missing and the deletion rate was 5%,the PRICE variable was missing and the deletion rate was 10%,and the PRICE variable and the CBD variable were both missing.The new method compared to the traditional multiple filling methods of true value closer ratio is 75%to 25%,62.5%to 37.5%,100%to 0%.Therefore,the new method is obviously better than the traditional multiple imputation methods,and the missing value data estimated by the new method bears certain reference value.展开更多
How many imputations are sufficient in multiple imputations? The answer given by different researchers varies from as few as 2 - 3 to as many as hundreds. Perhaps no single number of imputations would fit all situatio...How many imputations are sufficient in multiple imputations? The answer given by different researchers varies from as few as 2 - 3 to as many as hundreds. Perhaps no single number of imputations would fit all situations. In this study, η, the minimally sufficient number of imputations, was determined based on the relationship between m, the number of imputations, and ω, the standard error of imputation variances using the 2012 National Ambulatory Medical Care Survey (NAMCS) Physician Workflow mail survey. Five variables of various value ranges, variances, and missing data percentages were tested. For all variables tested, ω decreased as m increased. The m value above which the cost of further increase in m would outweigh the benefit of reducing ω was recognized as the η. This method has a potential to be used by anyone to determine η that fits his or her own data situation.展开更多
Multiple imputations compensate for missing data and produce multiple datasets by regression model and are considered the solver of the old problem of univariate imputation. The univariate imputes data only from a spe...Multiple imputations compensate for missing data and produce multiple datasets by regression model and are considered the solver of the old problem of univariate imputation. The univariate imputes data only from a specific column where the data cell was missing. Multivariate imputation works simultaneously, with all variables in all columns, whether missing or observed. It has emerged as a principal method of solving missing data problems. All incomplete datasets analyzed before Multiple Imputation by Chained Equations <span style="font-family:Verdana;">(MICE) presented were misdiagnosed;results obtained were invalid and should</span><span style="font-family:Verdana;"> not be countable to yield reasonable conclusions. This article will highlight why multiple imputations and how the MICE work with a particular focus on the cyber-security dataset.</span><b> </b><span style="font-family:Verdana;">Removing missing data in any dataset and replac</span><span style="font-family:Verdana;">ing it is imperative in analyzing the data and creating prediction models. Therefore,</span><span style="font-family:Verdana;"> a good imputation technique should recover the missingness, which involves extracting the good features. However, the widely used univariate imputation method does not impute missingness reasonably if the values are too large and may thus lead to bias. Therefore, we aim to propose an alternative imputation method that is efficient and removes potential bias after removing the missingness.</span>展开更多
Background: Genome-wide association studies and genomic predictions are thought to be optimized by using whole-genome sequence(WGS) data. However, sequencing thousands of individuals of interest is expensive.Imputatio...Background: Genome-wide association studies and genomic predictions are thought to be optimized by using whole-genome sequence(WGS) data. However, sequencing thousands of individuals of interest is expensive.Imputation from SNP panels to WGS data is an attractive and less expensive approach to obtain WGS data. The aims of this study were to investigate the accuracy of imputation and to provide insight into the design and execution of genotype imputation.Results: We genotyped 450 chickens with a 600 K SNP array, and sequenced 24 key individuals by whole genome re-sequencing. Accuracy of imputation from putative 60 K and 600 K array data to WGS data was 0.620 and 0.812 for Beagle, and 0.810 and 0.914 for FImpute, respectively. By increasing the sequencing cost from 24 X to 144 X, the imputation accuracy increased from 0.525 to 0.698 for Beagle and from 0.654 to 0.823 for FImpute. With fixed sequence depth(12 X), increasing the number of sequenced animals from 1 to 24, improved accuracy from 0.421 to0.897 for FImpute and from 0.396 to 0.777 for Beagle. Using optimally selected key individuals resulted in a higher imputation accuracy compared with using randomly selected individuals as a reference population for resequencing. With fixed reference population size(24), imputation accuracy increased from 0.654 to 0.875 for FImpute and from 0.512 to 0.762 for Beagle as the sequencing depth increased from 1 X to 12 X. With a given total cost of genotyping, accuracy increased with the size of the reference population for FImpute, but the pattern was not valid for Beagle, which showed the highest accuracy at six fold coverage for the scenarios used in this study.Conclusions: In conclusion, we comprehensively investigated the impacts of several key factors on genotype imputation. Generally, increasing sequencing cost gave a higher imputation accuracy. But with a fixed sequencing cost, the optimal imputation enhance the performance of WGP and GWAS. An optimal imputation strategy should take size of reference population, imputation algorithms, marker density, and population structure of the target population and methods to select key individuals into consideration comprehensively. This work sheds additional light on how to design and execute genotype imputation for livestock populations.展开更多
Background:Genotyping by sequencing(GBS)still has problems with missing genotypes.Imputation is important for using GBS for genomic predictions,especially for low depths,due to the large number of missing genotypes.Mi...Background:Genotyping by sequencing(GBS)still has problems with missing genotypes.Imputation is important for using GBS for genomic predictions,especially for low depths,due to the large number of missing genotypes.Minor allele frequency(MAF)is widely used as a marker data editing criteria for genomic predictions.In this study,three imputation methods(Beagle,IMPUTE2 and FImpute software)based on four MAF editing criteria were investigated with regard to imputation accuracy of missing genotypes and accuracy of genomic predictions,based on simulated data of livestock population.Results:Four MAFs(no MAF limit,MAF≥0.001,MAF≥0.01 and MAF≥0.03)were used for editing marker data before imputation.Beagle,IMPUTE2 and FImpute software were applied to impute the original GBS.Additionally,IMPUTE2 also imputed the expected genotype dosage after genotype correction(GcIM).The reliability of genomic predictions was calculated using GBS and imputed GBS data.The results showed that imputation accuracies were the same for the three imputation methods,except for the data of sequencing read depth(depth)=2,where FImpute had a slightly lower imputation accuracy than Beagle and IMPUTE2.GcIM was observed to be the best for all of the imputations at depth=4,5 and 10,but the worst for depth=2.For genomic prediction,retaining more SNPs with no MAF limit resulted in higher reliability.As the depth increased to 10,the prediction reliabilities approached those using true genotypes in the GBS loci.Beagle and IMPUTE2 had the largest increases in prediction reliability of 5 percentage points,and FImpute gained 3 percentage points at depth=2.The best prediction was observed at depth=4,5 and 10 using GcIM,but the worst prediction was also observed using GcIM at depth=2.Conclusions:The current study showed that imputation accuracies were relatively low for GBS with low depths and high for GBS with high depths.Imputation resulted in larger gains in the reliability of genomic predictions for GBS with lower depths.These results suggest that the application of IMPUTE2,based on a corrected GBS(GcIM)to improve genomic predictions for higher depths,and FImpute software could be a good alternative for routine imputation.展开更多
The problem of missing values has long been studied by researchers working in areas of data science and bioinformatics,especially the analysis of gene expression data that facilitates an early detection of cancer.Many...The problem of missing values has long been studied by researchers working in areas of data science and bioinformatics,especially the analysis of gene expression data that facilitates an early detection of cancer.Many attempts show improvements made by excluding samples with missing information from the analysis process,while others have tried to fill the gaps with possible values.While the former is simple,the latter safeguards information loss.For that,a neighbour-based(KNN)approach has proven more effective than other global estimators.The paper extends this further by introducing a new summarizationmethod to theKNNmodel.It is the first study that applies the concept of ordered weighted averaging(OWA)operator to such a problem context.In particular,two variations of OWA aggregation are proposed and evaluated against their baseline and other neighbor-based models.Using different ratios of missing values from 1%-20%and a set of six published gene expression datasets,the experimental results suggest that newmethods usually provide more accurate estimates than those compared methods.Specific to the missing rates of 5%and 20%,the best NRMSE scores as averages across datasets is 0.65 and 0.69,while the highest measures obtained by existing techniques included in this study are 0.80 and 0.84,respectively.展开更多
Time series forecasting has become an important aspect of data analysis and has many real-world applications.However,undesirable missing values are often encountered,which may adversely affect many forecasting tasks.I...Time series forecasting has become an important aspect of data analysis and has many real-world applications.However,undesirable missing values are often encountered,which may adversely affect many forecasting tasks.In this study,we evaluate and compare the effects of imputationmethods for estimating missing values in a time series.Our approach does not include a simulation to generate pseudo-missing data,but instead perform imputation on actual missing data and measure the performance of the forecasting model created therefrom.In an experiment,therefore,several time series forecasting models are trained using different training datasets prepared using each imputation method.Subsequently,the performance of the imputation methods is evaluated by comparing the accuracy of the forecasting models.The results obtained from a total of four experimental cases show that the k-nearest neighbor technique is the most effective in reconstructing missing data and contributes positively to time series forecasting compared with other imputation methods.展开更多
Common variants explain little of the variance of most common disease, prompting large-scale sequencing studies to understand the contribution of rare variants to these diseases. Imputation of rare variants from genom...Common variants explain little of the variance of most common disease, prompting large-scale sequencing studies to understand the contribution of rare variants to these diseases. Imputation of rare variants from genome-wide genotypic arrays offers a cost-efficient strategy to achieve necessary sample sizes required for adequate statistical power. To estimate the performance of imputation of rare variants, we imputed 153 individuals, each of whom was genotyped on 3 different genotype arrays including 317k, 610k and 1 million single nucleotide polymorphisms （SNPs）, to two different reference panels： HapMap2 and 1000 Genomes pilot March 2010 release （1KGpilot） by using IMPUTE version 2. We found that more than 94% and 84% of all SNPs yield acceptable accuracy （info 〉 0.4） in HapMap2 and 1KGpilot-based imputation, respectively. For rare variants （minor allele frequency （MAF） 〈5%）, the proportion of well- imputed SNPs increased as the MAF increased from 0.3% to 5% across all 3 genome-wide association study （GWAS） datasets. The proportion of well-imputed SNPs was 69%, 60% and 49% for SNPs with a MAF from 0.3% to 5% for 1M, 610k and 317k, respectively. None of the very rare variants （MAF 〈 0.3%） were well imputed. We conclude that the imputation accuracy of rare variants increases with higher density of genome-wide genotyping arrays when the size of the reference panel is small. Variants with lower MAF are more difficult to impute. These findings have important implications in the design and replication of large-scale sequencing studies.展开更多
In analyzing data from clinical trials and longitudinal studies, the issue of missing values is always a fundamental challenge since the missing data could introduce bias and lead to erroneous statistical inferences. ...In analyzing data from clinical trials and longitudinal studies, the issue of missing values is always a fundamental challenge since the missing data could introduce bias and lead to erroneous statistical inferences. To deal with this challenge, several imputation methods have been developed in the literature to handle missing values where the most commonly used are complete case method, mean imputation method, last observation carried forward (LOCF) method, and multiple imputation (MI) method. In this paper, we conduct a simulation study to investigate the efficiency of these four typical imputation methods with longitudinal data setting under missing completely at random (MCAR). We categorize missingness with three cases from a lower percentage of 5% to a higher percentage of 30% and 50% missingness. With this simulation study, we make a conclusion that LOCF method has more bias than the other three methods in most situations. MI method has the least bias with the best coverage probability. Thus, we conclude that MI method is the most effective imputation method in our MCAR simulation study.展开更多
This research was an effort to select best imputation method for missing upper air temperature data over 24 standard pressure levels. We have implemented four imputation techniques like inverse distance weighting, Bil...This research was an effort to select best imputation method for missing upper air temperature data over 24 standard pressure levels. We have implemented four imputation techniques like inverse distance weighting, Bilinear, Natural and Nearest interpolation for missing data imputations. Performance indicators for these techniques were the root mean square error (RMSE), absolute mean error (AME), correlation coefficient and coefficient of determination ( R<sup>2</sup> ) adopted in this research. We randomly make 30% of total samples (total samples was 324) predictable from 70% remaining data. Although four interpolation methods seem good (producing <1 RMSE, AME) for imputations of air temperature data, but bilinear method was the most accurate with least errors for missing data imputations. RMSE for bilinear method remains <0.01 on all pressure levels except 1000 hPa where this value was 0.6. The low value of AME (<0.1) came at all pressure levels through bilinear imputations. Very strong correlation (>0.99) found between actual and predicted air temperature data through this method. The high value of the coefficient of determination (0.99) through bilinear interpolation method, tells us best fit to the surface. We have also found similar results for imputation with natural interpolation method in this research, but after investigating scatter plots over each month, imputations with this method seem to little obtuse in certain months than bilinear method.展开更多
Individual tree detection (ITD) and the area-based approach (ABA) are combined to generate tree-lists using airborne LiDAR data. ITD based on the Canopy Height Model (CHM) was applied for overstory trees, while ABA ba...Individual tree detection (ITD) and the area-based approach (ABA) are combined to generate tree-lists using airborne LiDAR data. ITD based on the Canopy Height Model (CHM) was applied for overstory trees, while ABA based on nearest neighbor (NN) imputation was applied for understory trees. Our approach is intended to compensate for the weakness of LiDAR data and ITD in estimating understory trees, keeping the strength of ITD in estimating overstory trees in tree-level. We investigated the effects of three parameters on the performance of our proposed approach: smoothing of CHM, resolution of CHM, and height cutoff (a specific height that classifies trees into overstory and understory). There was no single combination of those parameters that produced the best performance for estimating stems per ha, mean tree height, basal area, diameter distribution and height distribution. The trees in the lowest LiDAR height class yielded the largest relative bias and relative root mean squared error. Although ITD and ABA showed limited explanatory powers to estimate stems per hectare and basal area, there could be improvements from methods such as using LiDAR data with higher density, applying better algorithms for ITD and decreasing distortion of the structure of LiDAR data. Automating the procedure of finding optimal combinations of those parameters is essential to expedite forest management decisions across forest landscapes using remote sensing data.展开更多
基金supported by the National Natural Science Foundation of China(No.12475340 and 12375350)Special Branch project of South Taihu Lakethe Scientific Research Fund of Zhejiang Provincial Education Department(No.Y202456326).
文摘Missing values in radionuclide diffusion datasets can undermine the predictive accuracy and robustness of the machine learning(ML)models.In this study,regression-based missing data imputation method using a light gradient boosting machine(LGBM)algorithm was employed to impute more than 60%of the missing data,establishing a radionuclide diffusion dataset containing 16 input features and 813 instances.The effective diffusion coefficient(D_(e))was predicted using ten ML models.The predictive accuracy of the ensemble meta-models,namely LGBM-extreme gradient boosting(XGB)and LGBM-categorical boosting(CatB),surpassed that of the other ML models,with R^(2)values of 0.94.The models were applied to predict the D_(e)values of EuEDTA^(−)and HCrO_(4)^(−)in saturated compacted bentonites at compactions ranging from 1200 to 1800 kg/m^(3),which were measured using a through-diffusion method.The generalization ability of the LGBM-XGB model surpassed that of LGB-CatB in predicting the D_(e)of HCrO_(4)^(−).Shapley additive explanations identified total porosity as the most significant influencing factor.Additionally,the partial dependence plot analysis technique yielded clearer results in the univariate correlation analysis.This study provides a regression imputation technique to refine radionuclide diffusion datasets,offering deeper insights into analyzing the diffusion mechanism of radionuclides and supporting the safety assessment of the geological disposal of high-level radioactive waste.
基金partially supported by the National Natural Science Foundation of China(62271485)the SDHS Science and Technology Project(HS2023B044)
文摘Imputation of missing data has long been an important topic and an essential application for intelligent transportation systems(ITS)in the real world.As a state-of-the-art generative model,the diffusion model has proven highly successful in image generation,speech generation,time series modelling etc.and now opens a new avenue for traffic data imputation.In this paper,we propose a conditional diffusion model,called the implicit-explicit diffusion model,for traffic data imputation.This model exploits both the implicit and explicit feature of the data simultaneously.More specifically,we design two types of feature extraction modules,one to capture the implicit dependencies hidden in the raw data at multiple time scales and the other to obtain the long-term temporal dependencies of the time series.This approach not only inherits the advantages of the diffusion model for estimating missing data,but also takes into account the multiscale correlation inherent in traffic data.To illustrate the performance of the model,extensive experiments are conducted on three real-world time series datasets using different missing rates.The experimental results demonstrate that the model improves imputation accuracy and generalization capability.
文摘Accurate traffic flow prediction(TFP)is vital for efficient and sustainable transportation management and the development of intelligent traffic systems.However,missing data in real-world traffic datasets poses a significant challenge to maintaining prediction precision.This study introduces REPTF-TMDI,a novel method that combines a Reduced Error Pruning Tree Forest(REPTree Forest)with a newly proposed Time-based Missing Data Imputation(TMDI)approach.The REP Tree Forest,an ensemble learning approach,is tailored for time-related traffic data to enhance predictive accuracy and support the evolution of sustainable urbanmobility solutions.Meanwhile,the TMDI approach exploits temporal patterns to estimate missing values reliably whenever empty fields are encountered.The proposed method was evaluated using hourly traffic flow data from a major U.S.roadway spanning 2012-2018,incorporating temporal features(e.g.,hour,day,month,year,weekday),holiday indicator,and weather conditions(temperature,rain,snow,and cloud coverage).Experimental results demonstrated that the REPTF-TMDI method outperformed conventional imputation techniques across various missing data ratios by achieving an average 11.76%improvement in terms of correlation coefficient(R).Furthermore,REPTree Forest achieved improvements of 68.62%in RMSE and 70.52%in MAE compared to existing state-of-the-art models.These findings highlight the method’s ability to significantly boost traffic flow prediction accuracy,even in the presence of missing data,thereby contributing to the broader objectives of sustainable urban transportation systems.
基金supported by the Intelligent System Research Group(ISysRG)supported by Universitas Sriwijaya funded by the Competitive Research 2024.
文摘Handling missing data accurately is critical in clinical research, where data quality directly impacts decision-making and patient outcomes. While deep learning (DL) techniques for data imputation have gained attention, challenges remain, especially when dealing with diverse data types. In this study, we introduce a novel data imputation method based on a modified convolutional neural network, specifically, a Deep Residual-Convolutional Neural Network (DRes-CNN) architecture designed to handle missing values across various datasets. Our approach demonstrates substantial improvements over existing imputation techniques by leveraging residual connections and optimized convolutional layers to capture complex data patterns. We evaluated the model on publicly available datasets, including Medical Information Mart for Intensive Care (MIMIC-III and MIMIC-IV), which contain critical care patient data, and the Beijing Multi-Site Air Quality dataset, which measures environmental air quality. The proposed DRes-CNN method achieved a root mean square error (RMSE) of 0.00006, highlighting its high accuracy and robustness. We also compared with Low Light-Convolutional Neural Network (LL-CNN) and U-Net methods, which had RMSE values of 0.00075 and 0.00073, respectively. This represented an improvement of approximately 92% over LL-CNN and 91% over U-Net. The results showed that this DRes-CNN-based imputation method outperforms current state-of-the-art models. These results established DRes-CNN as a reliable solution for addressing missing data.
基金supported by Graduate Funded Project(No.JY2022A017).
文摘The frequent missing values in radar-derived time-series tracks of aerial targets(RTT-AT)lead to significant challenges in subsequent data-driven tasks.However,the majority of imputation research focuses on random missing(RM)that differs significantly from common missing patterns of RTT-AT.The method for solving the RM may experience performance degradation or failure when applied to RTT-AT imputation.Conventional autoregressive deep learning methods are prone to error accumulation and long-term dependency loss.In this paper,a non-autoregressive imputation model that addresses the issue of missing value imputation for two common missing patterns in RTT-AT is proposed.Our model consists of two probabilistic sparse diagonal masking self-attention(PSDMSA)units and a weight fusion unit.It learns missing values by combining the representations outputted by the two units,aiming to minimize the difference between the missing values and their actual values.The PSDMSA units effectively capture temporal dependencies and attribute correlations between time steps,improving imputation quality.The weight fusion unit automatically updates the weights of the output representations from the two units to obtain a more accurate final representation.The experimental results indicate that,despite varying missing rates in the two missing patterns,our model consistently outperforms other methods in imputation performance and exhibits a low frequency of deviations in estimates for specific missing entries.Compared to the state-of-the-art autoregressive deep learning imputation model Bidirectional Recurrent Imputation for Time Series(BRITS),our proposed model reduces mean absolute error(MAE)by 31%~50%.Additionally,the model attains a training speed that is 4 to 8 times faster when compared to both BRITS and a standard Transformer model when trained on the same dataset.Finally,the findings from the ablation experiments demonstrate that the PSDMSA,the weight fusion unit,cascade network design,and imputation loss enhance imputation performance and confirm the efficacy of our design.
文摘Missing data presents a significant challenge in statistical analysis and machine learning, often resulting in biased outcomes and diminished efficiency. This comprehensive review investigates various imputation techniques, categorizing them into three primary approaches: deterministic methods, probabilistic models, and machine learning algorithms. Traditional techniques, including mean or mode imputation, regression imputation, and last observation carried forward, are evaluated alongside more contemporary methods such as multiple imputation, expectation-maximization, and deep learning strategies. The strengths and limitations of each approach are outlined. Key considerations for selecting appropriate methods, based on data characteristics and research objectives, are discussed. The importance of evaluating imputation’s impact on subsequent analyses is emphasized. This synthesis of recent advancements and best practices provides researchers with a robust framework for effectively handling missing data, thereby improving the reliability of empirical findings across diverse disciplines.
文摘Compositional data, such as relative information, is a crucial aspect of machine learning and other related fields. It is typically recorded as closed data or sums to a constant, like 100%. The statistical linear model is the most used technique for identifying hidden relationships between underlying random variables of interest. However, data quality is a significant challenge in machine learning, especially when missing data is present. The linear regression model is a commonly used statistical modeling technique used in various applications to find relationships between variables of interest. When estimating linear regression parameters which are useful for things like future prediction and partial effects analysis of independent variables, maximum likelihood estimation (MLE) is the method of choice. However, many datasets contain missing observations, which can lead to costly and time-consuming data recovery. To address this issue, the expectation-maximization (EM) algorithm has been suggested as a solution for situations including missing data. The EM algorithm repeatedly finds the best estimates of parameters in statistical models that depend on variables or data that have not been observed. This is called maximum likelihood or maximum a posteriori (MAP). Using the present estimate as input, the expectation (E) step constructs a log-likelihood function. Finding the parameters that maximize the anticipated log-likelihood, as determined in the E step, is the job of the maximization (M) phase. This study looked at how well the EM algorithm worked on a made-up compositional dataset with missing observations. It used both the robust least square version and ordinary least square regression techniques. The efficacy of the EM algorithm was compared with two alternative imputation techniques, k-Nearest Neighbor (k-NN) and mean imputation (), in terms of Aitchison distances and covariance.
基金supported by the China Agriculture Research System of MOF and MARA(CARS-35)the National Natural Science Foundation of China(32072696,31790414 and 31601916)the Fundamental Research Funds for the Central Universities(2662019PY011)。
文摘Genotype imputation has become an indispensable part of genomic data analysis. In recent years, imputation based on a multi-breed reference population has received more attention, but the relevant studies are scarce in pigs. In this study, we used the Illumina Porcine SNP50 Bead Chip to investigate the variations of imputation accuracy with various influencing factors and compared the imputation performance of four commonly used imputation software programs. The results indicated that imputation accuracy increased as either the validation population marker density, reference population sample size, or minor allele frequency(MAF) increased. However, the imputation accuracy would have a certain extent of decrease when the pig reference population was a mixed group of multiple breeds or lines. Considering both imputation accuracy and running time, Beagle 4.1 and FImpute are excellent choices among the four software packages tested. This work visually presents the impacts of these influencing factors on imputation and provides a reference for formulating reasonable imputation strategies in actual pig breeding.
基金This research was financially supported by FDCT NO.005/2018/A1also supported by Guangdong Provincial Innovation and Entrepreneurship Training Program Project No.201713719017College Students Innovation Training Program held by Guangdong university of Science and Technology Nos.1711034,1711080,and No.1711088.
文摘Based on the two-dimensional relation table,this paper studies the missing values in the sample data of land price of Shunde District of Foshan City.GeoDa software was used to eliminate the insignificant factors by stepwise regression analysis;NORM software was adopted to construct the multiple imputation models;EM algorithm and the augmentation algorithm were applied to fit multiple linear regression equations to construct five different filling datasets.Statistical analysis is performed on the imputation data set in order to calculate the mean and variance of each data set,and the weight is determined according to the differences.Finally,comprehensive integration is implemented to achieve the imputation expression of missing values.The results showed that in the three missing cases where the PRICE variable was missing and the deletion rate was 5%,the PRICE variable was missing and the deletion rate was 10%,and the PRICE variable and the CBD variable were both missing.The new method compared to the traditional multiple filling methods of true value closer ratio is 75%to 25%,62.5%to 37.5%,100%to 0%.Therefore,the new method is obviously better than the traditional multiple imputation methods,and the missing value data estimated by the new method bears certain reference value.
文摘How many imputations are sufficient in multiple imputations? The answer given by different researchers varies from as few as 2 - 3 to as many as hundreds. Perhaps no single number of imputations would fit all situations. In this study, η, the minimally sufficient number of imputations, was determined based on the relationship between m, the number of imputations, and ω, the standard error of imputation variances using the 2012 National Ambulatory Medical Care Survey (NAMCS) Physician Workflow mail survey. Five variables of various value ranges, variances, and missing data percentages were tested. For all variables tested, ω decreased as m increased. The m value above which the cost of further increase in m would outweigh the benefit of reducing ω was recognized as the η. This method has a potential to be used by anyone to determine η that fits his or her own data situation.
文摘Multiple imputations compensate for missing data and produce multiple datasets by regression model and are considered the solver of the old problem of univariate imputation. The univariate imputes data only from a specific column where the data cell was missing. Multivariate imputation works simultaneously, with all variables in all columns, whether missing or observed. It has emerged as a principal method of solving missing data problems. All incomplete datasets analyzed before Multiple Imputation by Chained Equations <span style="font-family:Verdana;">(MICE) presented were misdiagnosed;results obtained were invalid and should</span><span style="font-family:Verdana;"> not be countable to yield reasonable conclusions. This article will highlight why multiple imputations and how the MICE work with a particular focus on the cyber-security dataset.</span><b> </b><span style="font-family:Verdana;">Removing missing data in any dataset and replac</span><span style="font-family:Verdana;">ing it is imperative in analyzing the data and creating prediction models. Therefore,</span><span style="font-family:Verdana;"> a good imputation technique should recover the missingness, which involves extracting the good features. However, the widely used univariate imputation method does not impute missingness reasonably if the values are too large and may thus lead to bias. Therefore, we aim to propose an alternative imputation method that is efficient and removes potential bias after removing the missingness.</span>
基金supported by the National Natural Science Foundation of China(31772556)the China Agricultural Research System(CARS-41-G03)+2 种基金the Science Innovation Project of Guangdong(2015A020209159)the Special Program for Applied Research on Super Computation of the NSFC Guangdong Joint Fund(the second phase)under Grant No.U1501501technical support from the National Supercomputer Center in Guangzhou
文摘Background: Genome-wide association studies and genomic predictions are thought to be optimized by using whole-genome sequence(WGS) data. However, sequencing thousands of individuals of interest is expensive.Imputation from SNP panels to WGS data is an attractive and less expensive approach to obtain WGS data. The aims of this study were to investigate the accuracy of imputation and to provide insight into the design and execution of genotype imputation.Results: We genotyped 450 chickens with a 600 K SNP array, and sequenced 24 key individuals by whole genome re-sequencing. Accuracy of imputation from putative 60 K and 600 K array data to WGS data was 0.620 and 0.812 for Beagle, and 0.810 and 0.914 for FImpute, respectively. By increasing the sequencing cost from 24 X to 144 X, the imputation accuracy increased from 0.525 to 0.698 for Beagle and from 0.654 to 0.823 for FImpute. With fixed sequence depth(12 X), increasing the number of sequenced animals from 1 to 24, improved accuracy from 0.421 to0.897 for FImpute and from 0.396 to 0.777 for Beagle. Using optimally selected key individuals resulted in a higher imputation accuracy compared with using randomly selected individuals as a reference population for resequencing. With fixed reference population size(24), imputation accuracy increased from 0.654 to 0.875 for FImpute and from 0.512 to 0.762 for Beagle as the sequencing depth increased from 1 X to 12 X. With a given total cost of genotyping, accuracy increased with the size of the reference population for FImpute, but the pattern was not valid for Beagle, which showed the highest accuracy at six fold coverage for the scenarios used in this study.Conclusions: In conclusion, we comprehensively investigated the impacts of several key factors on genotype imputation. Generally, increasing sequencing cost gave a higher imputation accuracy. But with a fixed sequencing cost, the optimal imputation enhance the performance of WGP and GWAS. An optimal imputation strategy should take size of reference population, imputation algorithms, marker density, and population structure of the target population and methods to select key individuals into consideration comprehensively. This work sheds additional light on how to design and execute genotype imputation for livestock populations.
基金This study was funded by the Genomic Selection in Animals and Plants(GenSAP)research project financed by the Danish Council of Strategic Research(Aarhus,Denmark).Xiao Wang received Ph.D.stipends from the Technical University of Denmark(DTU Bioinformatics and DTU Compute),Denmark,and the China Scholarship Council,China.
文摘Background:Genotyping by sequencing(GBS)still has problems with missing genotypes.Imputation is important for using GBS for genomic predictions,especially for low depths,due to the large number of missing genotypes.Minor allele frequency(MAF)is widely used as a marker data editing criteria for genomic predictions.In this study,three imputation methods(Beagle,IMPUTE2 and FImpute software)based on four MAF editing criteria were investigated with regard to imputation accuracy of missing genotypes and accuracy of genomic predictions,based on simulated data of livestock population.Results:Four MAFs(no MAF limit,MAF≥0.001,MAF≥0.01 and MAF≥0.03)were used for editing marker data before imputation.Beagle,IMPUTE2 and FImpute software were applied to impute the original GBS.Additionally,IMPUTE2 also imputed the expected genotype dosage after genotype correction(GcIM).The reliability of genomic predictions was calculated using GBS and imputed GBS data.The results showed that imputation accuracies were the same for the three imputation methods,except for the data of sequencing read depth(depth)=2,where FImpute had a slightly lower imputation accuracy than Beagle and IMPUTE2.GcIM was observed to be the best for all of the imputations at depth=4,5 and 10,but the worst for depth=2.For genomic prediction,retaining more SNPs with no MAF limit resulted in higher reliability.As the depth increased to 10,the prediction reliabilities approached those using true genotypes in the GBS loci.Beagle and IMPUTE2 had the largest increases in prediction reliability of 5 percentage points,and FImpute gained 3 percentage points at depth=2.The best prediction was observed at depth=4,5 and 10 using GcIM,but the worst prediction was also observed using GcIM at depth=2.Conclusions:The current study showed that imputation accuracies were relatively low for GBS with low depths and high for GBS with high depths.Imputation resulted in larger gains in the reliability of genomic predictions for GBS with lower depths.These results suggest that the application of IMPUTE2,based on a corrected GBS(GcIM)to improve genomic predictions for higher depths,and FImpute software could be a good alternative for routine imputation.
基金This work is funded by Newton Institutional Links 2020-21 project:623718881,jointly by British Council and National Research Council of Thailand(www.britishcouncil.org).The corresponding author is the project PI.
文摘The problem of missing values has long been studied by researchers working in areas of data science and bioinformatics,especially the analysis of gene expression data that facilitates an early detection of cancer.Many attempts show improvements made by excluding samples with missing information from the analysis process,while others have tried to fill the gaps with possible values.While the former is simple,the latter safeguards information loss.For that,a neighbour-based(KNN)approach has proven more effective than other global estimators.The paper extends this further by introducing a new summarizationmethod to theKNNmodel.It is the first study that applies the concept of ordered weighted averaging(OWA)operator to such a problem context.In particular,two variations of OWA aggregation are proposed and evaluated against their baseline and other neighbor-based models.Using different ratios of missing values from 1%-20%and a set of six published gene expression datasets,the experimental results suggest that newmethods usually provide more accurate estimates than those compared methods.Specific to the missing rates of 5%and 20%,the best NRMSE scores as averages across datasets is 0.65 and 0.69,while the highest measures obtained by existing techniques included in this study are 0.80 and 0.84,respectively.
基金This research was supported by Basic Science Research Program through the National Research Foundation of Korea(NRF)funded by the Ministry of Education(Grant Number 2020R1A6A1A03040583).
文摘Time series forecasting has become an important aspect of data analysis and has many real-world applications.However,undesirable missing values are often encountered,which may adversely affect many forecasting tasks.In this study,we evaluate and compare the effects of imputationmethods for estimating missing values in a time series.Our approach does not include a simulation to generate pseudo-missing data,but instead perform imputation on actual missing data and measure the performance of the forecasting model created therefrom.In an experiment,therefore,several time series forecasting models are trained using different training datasets prepared using each imputation method.Subsequently,the performance of the imputation methods is evaluated by comparing the accuracy of the forecasting models.The results obtained from a total of four experimental cases show that the k-nearest neighbor technique is the most effective in reconstructing missing data and contributes positively to time series forecasting compared with other imputation methods.
文摘Common variants explain little of the variance of most common disease, prompting large-scale sequencing studies to understand the contribution of rare variants to these diseases. Imputation of rare variants from genome-wide genotypic arrays offers a cost-efficient strategy to achieve necessary sample sizes required for adequate statistical power. To estimate the performance of imputation of rare variants, we imputed 153 individuals, each of whom was genotyped on 3 different genotype arrays including 317k, 610k and 1 million single nucleotide polymorphisms （SNPs）, to two different reference panels： HapMap2 and 1000 Genomes pilot March 2010 release （1KGpilot） by using IMPUTE version 2. We found that more than 94% and 84% of all SNPs yield acceptable accuracy （info 〉 0.4） in HapMap2 and 1KGpilot-based imputation, respectively. For rare variants （minor allele frequency （MAF） 〈5%）, the proportion of well- imputed SNPs increased as the MAF increased from 0.3% to 5% across all 3 genome-wide association study （GWAS） datasets. The proportion of well-imputed SNPs was 69%, 60% and 49% for SNPs with a MAF from 0.3% to 5% for 1M, 610k and 317k, respectively. None of the very rare variants （MAF 〈 0.3%） were well imputed. We conclude that the imputation accuracy of rare variants increases with higher density of genome-wide genotyping arrays when the size of the reference panel is small. Variants with lower MAF are more difficult to impute. These findings have important implications in the design and replication of large-scale sequencing studies.
文摘In analyzing data from clinical trials and longitudinal studies, the issue of missing values is always a fundamental challenge since the missing data could introduce bias and lead to erroneous statistical inferences. To deal with this challenge, several imputation methods have been developed in the literature to handle missing values where the most commonly used are complete case method, mean imputation method, last observation carried forward (LOCF) method, and multiple imputation (MI) method. In this paper, we conduct a simulation study to investigate the efficiency of these four typical imputation methods with longitudinal data setting under missing completely at random (MCAR). We categorize missingness with three cases from a lower percentage of 5% to a higher percentage of 30% and 50% missingness. With this simulation study, we make a conclusion that LOCF method has more bias than the other three methods in most situations. MI method has the least bias with the best coverage probability. Thus, we conclude that MI method is the most effective imputation method in our MCAR simulation study.
基金supported by the National Natural Science Foundation of China(Grant No.30800776)the State High-Tech Development Plan of China(Grant No.2008AA101002)the Recommend International Advanced Agricultural Science and Technology Plan of China(Grant No2011-G2A)
文摘This research was an effort to select best imputation method for missing upper air temperature data over 24 standard pressure levels. We have implemented four imputation techniques like inverse distance weighting, Bilinear, Natural and Nearest interpolation for missing data imputations. Performance indicators for these techniques were the root mean square error (RMSE), absolute mean error (AME), correlation coefficient and coefficient of determination ( R<sup>2</sup> ) adopted in this research. We randomly make 30% of total samples (total samples was 324) predictable from 70% remaining data. Although four interpolation methods seem good (producing <1 RMSE, AME) for imputations of air temperature data, but bilinear method was the most accurate with least errors for missing data imputations. RMSE for bilinear method remains <0.01 on all pressure levels except 1000 hPa where this value was 0.6. The low value of AME (<0.1) came at all pressure levels through bilinear imputations. Very strong correlation (>0.99) found between actual and predicted air temperature data through this method. The high value of the coefficient of determination (0.99) through bilinear interpolation method, tells us best fit to the surface. We have also found similar results for imputation with natural interpolation method in this research, but after investigating scatter plots over each month, imputations with this method seem to little obtuse in certain months than bilinear method.
文摘Individual tree detection (ITD) and the area-based approach (ABA) are combined to generate tree-lists using airborne LiDAR data. ITD based on the Canopy Height Model (CHM) was applied for overstory trees, while ABA based on nearest neighbor (NN) imputation was applied for understory trees. Our approach is intended to compensate for the weakness of LiDAR data and ITD in estimating understory trees, keeping the strength of ITD in estimating overstory trees in tree-level. We investigated the effects of three parameters on the performance of our proposed approach: smoothing of CHM, resolution of CHM, and height cutoff (a specific height that classifies trees into overstory and understory). There was no single combination of those parameters that produced the best performance for estimating stems per ha, mean tree height, basal area, diameter distribution and height distribution. The trees in the lowest LiDAR height class yielded the largest relative bias and relative root mean squared error. Although ITD and ABA showed limited explanatory powers to estimate stems per hectare and basal area, there could be improvements from methods such as using LiDAR data with higher density, applying better algorithms for ITD and decreasing distortion of the structure of LiDAR data. Automating the procedure of finding optimal combinations of those parameters is essential to expedite forest management decisions across forest landscapes using remote sensing data.
