A Study of EM Algorithm as an Imputation Method: A Model-Based Simulation Study with Application to a Synthetic Compositional Data

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.

Missing Value Imputation for Radar-Derived Time-Series Tracks of Aerial Targets Based on Improved Self-Attention-Based Network

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.

Improved reservoir characterization by means of supervised machine learning and model-based seismic impedance inversion in the Penobscot field,Scotian Basin

The present research work attempted to delineate and characterize the reservoir facies from the Dawson Canyon Formation in the Penobscot field,Scotian Basin.An integrated study of instantaneous frequency,P-impedance,volume of clay and neutron-porosity attributes,and structural framework was done to unravel the Late Cretaceous depositional system and reservoir facies distribution patterns within the study area.Fault strikes were found in the EW and NEE-SWW directions indicating the dominant course of tectonic activities during the Late Cretaceous period in the region.P-impedance was estimated using model-based seismic inversion.Petrophysical properties such as the neutron porosity(NPHI)and volume of clay(VCL)were estimated using the multilayer perceptron neural network with high accuracy.Comparatively,a combination of low instantaneous frequency(15-30 Hz),moderate to high impedance(7000-9500 gm/cc*m/s),low neutron porosity(27%-40%)and low volume of clay(40%-60%),suggests fair-to-good sandstone development in the Dawson Canyon Formation.After calibration with the welllog data,it is found that further lowering in these attribute responses signifies the clean sandstone facies possibly containing hydrocarbons.The present study suggests that the shale lithofacies dominates the Late Cretaceous deposition(Dawson Canyon Formation)in the Penobscot field,Scotian Basin.Major faults and overlying shale facies provide structural and stratigraphic seals and act as a suitable hydrocarbon entrapment mechanism in the Dawson Canyon Formation's reservoirs.The present research advocates the integrated analysis of multi-attributes estimated using different methods to minimize the risk involved in hydrocarbon exploration.

Missing Data Imputation: A Comprehensive Review

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.

Model-Based Systems Engineering Approach to Design a Human Settlement to Better Serve Displaced People

The challenge of transitioning from temporary humanitarian settlements to more sustainable human settlements is due to a significant increase in the number of forcibly displaced people over recent decades, difficulties in providing social services that meet the required standards, and the prolongation of emergencies. Despite this challenging context, short-term considerations continue to guide their planning and management rather than more integrated, longer-term perspectives, thus preventing viable, sustainable development. Over the years, the design of humanitarian settlements has not been adapted to local contexts and perspectives, nor to the dynamics of urbanization and population growth and data. In addition, the current approach to temporary settlement harms the environment and can strain limited resources. Inefficient land use and ad hoc development models have compounded difficulties and generated new challenges. As a result, living conditions in settlements have deteriorated over the last few decades and continue to pose new challenges. The stakes are such that major shortcomings have emerged along the way, leading to disruption, budget overruns in a context marked by a steady decline in funding. However, some attempts have been made to shift towards more sustainable approaches, but these have mainly focused on vague, sector-oriented themes, failing to consider systematic and integration views. This study is a contribution in addressing these shortcomings by designing a model-driving solution, emphasizing an integrated system conceptualized as a system of systems. This paper proposes a new methodology for designing an integrated and sustainable human settlement model, based on Model-Based Systems Engineering and a Systems Modeling Language to provide valuable insights toward sustainable solutions for displaced populations aligning with the United Nations 2030 agenda for sustainable development.

Imputation from SNP chip to sequence: a case study in a Chinese indigenous chicken population

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.

Model-Based Degree Estimation of Unbalance and Misalignment in Flexible Coupling-rotor System

The condition of rotor system must be assessed in order to develop condition-based maintenance for rotating machinery. It is determined by multiple variables such as unbalance degree, misalignment degree, the amount of bending deformation of the shaft, occurrence of shaft crack of rotor system and so on. The estimation of the degrees of unbalance and misalignment in flexible coupling-rotor system is discussed. The model-based approach is employed to solve this problem. The models of the equivalent external loads for unbalance and misalignment are derived and analyzed. Then, the degrees of unbalance and misalignment are estimated by analyzing the components of the equivalent external loads of which the frequencies are equal to the 1 and 2 times running frequency respectively. The equivalent external loads are calculated according to the dynamic equation of the original rotor system and the differences between the dynamical responses in normal case and the vibrations when the degree of unbalance or misalignment or both changes. The denoise method based on bandpass filter is used to decrease the effect of noise on the estimation accuracy. The numerical examples are given to show that the proposed approach can estimate the degrees of unbalance and misalignment of the flexible coupling-rotor system accurately.

Comparative Study of Four Methods in Missing Value Imputations under Missing Completely at Random Mechanism

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.

Use of models in large-area forest surveys： comparing model-assisted, model-based and hybrid estimation

This paper focuses on the use of models for increasing the precision of estimators in large-area forest surveys. It is motivated by the increasing availability of remotely sensed data, which facilitates the development of models predicting the variables of interest in forest surveys. We present, review and compare three different estimation frameworks where models play a core role： model-assisted, model-based, and hybrid estimation. The first two are well known, whereas the third has only recently been introduced in forest surveys. Hybrid inference mixes design- based and model-based inference, since it relies on a probability sample of auxiliary data and a model predicting the target variable from the auxiliary data.We review studies on large-area forest surveys based on model-assisted, model- based, and hybrid estimation, and discuss advantages and disadvantages of the approaches. We conclude that no general recommendations can be made about whether model-assisted, model-based, or hybrid estimation should be preferred. The choice depends on the objective of the survey and the possibilities to acquire appropriate field and remotely sensed data. We also conclude that modelling approaches can only be successfully applied for estimating target variables such as growing stock volume or biomass, which are adequately related to commonly available remotely sensed data, and thus purely field based surveys remain important for several important forest parameters.

A comprehensive evaluation of factors affecting the accuracy of pig genotype imputation using a single or multi-breed reference population

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.

Comparisons of improved genomic predictions generated by different imputation methods for genotyping by sequencing data in livestock populations

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.

Experts' Knowledge Fusion in Model-Based Diagnosis Based on Bayes Networks

In previous researches on a model-based diagnostic system, the components are assumed mutually independent. Howerver , the assumption is not always the case because the information about whether a component is faulty or not usually influences our knowledge about other components. Some experts may draw such a conclusion that 'if component m 1 is faulty, then component m 2 may be faulty too'. How can we use this experts' knowledge to aid the diagnosis? Based on Kohlas's probabilistic assumption-based reasoning method, we use Bayes networks to solve this problem. We calculate the posterior fault probability of the components in the observation state. The result is reasonable and reflects the effectiveness of the experts' knowledge.

Improved KNN Imputation for Missing Values in Gene Expression Data

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.

Feedback Scheduling of Model-based Networked Control Systems with Flexible Workload

In this paper,a novel control structure called feedback scheduling of model-based networked control systems is proposed to cope with a flexible network load and resource constraints.The state update time is adjusted according to the real-time network congestion situation.State observer is used under the situation where the state of the controlled plant could not be acquired.The stability criterion of the proposed structure is proved with time-varying state update time.On the basis of the stability of the novel system structure,the compromise between the control performance and the network utilization is realized by using feedback scheduler. Examples are provided to show the advantage of the proposed control structure.

Optimized model-based control of main mine ventilation air flows with minimized energy consumption

In early 2018,the Boliden Garpenberg operation implemented an optimized control strategy as an addition to the existing ventilation on demand system.The purpose of the strategy is to further minimize energy use for main and booster fans,whilst also fulfilling airflow setpoints without violating constraints such as min/max differential pressure over fans and interaction of air between areas in mines.Using air flow measurements and a dynamical model of the ventilation system,a mine-wide coordination control of fans can be carried out.The numerical model is data driven and derived from historical operational data or step changes experiments.This makes both initial deployment and lifetime model maintenance,as the mine evolves,a comparably easy operation.The control has been proven to operate in a stable manner over long periods without having to re-calibrate the model.Results prove a 40%decrease in energy use for the fans involved and a greater controllability of air flow.Moreover,a 15%decrease of the total air flow into the mine will give additional proportional heating savings during winter periods.All in all,the multivariable controller shows a correlation between production in the mine and the ventilation system performance superior to all of its predecessors.

Missing Data Imputations for Upper Air Temperature at 24 Standard Pressure Levels over Pakistan Collected from Aqua Satellite

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 ( R2 ) 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.

Comparative Variance and Multiple Imputation Used for Missing Values in Land Price DataSet

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.

Missing Values Imputation Based on Iterative Learning

Databases for machine learning and data mining often have missing values. How to develop effective method for missing values imputation is a crucial important problem in the field of machine learning and data mining. In this paper, several methods for dealing with missing values in incomplete data are reviewed, and a new method for missing values imputation based on iterative learning is proposed. The proposed method is based on a basic assumption: There exist cause-effect connections among condition attribute values, and the missing values can be induced from known values. In the process of missing values imputation, a part of missing values are filled in at first and converted to known values, which are used for the next step of missing values imputation. The iterative learning process will go on until an incomplete data is entirely converted to a complete data. The paper also presents an example to illustrate the framework of iterative learning for missing values imputation.

Comparison of Missing Data Imputation Methods in Time Series Forecasting

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.