Imputation Approach Research Articles

Comprehensive Evaluation of Advanced Imputation Methods for Proteomic Data Acquired via the Label-Free Approach

Mass-spectrometry-based proteomics frequently utilizes label-free quantification strategies due to their cost-effectiveness, methodological simplicity, and capability to identify large numbers of proteins within a single analytical run. Despite these advantages, the prevalence of missing values (MV), which can impact up to 50% of the data matrix, poses a significant challenge by reducing the accuracy, reproducibility, and interpretability of the results. Consequently, effective handling of missing values is crucial for reliable quantitative analysis in proteomic studies. This study systematically evaluated the performance of selected imputation methods for addressing missing values in proteomic dataset. Two protein identification algorithms, FragPipe and MaxQuant, were employed to generate datasets, enabling an assessment of their influence on im-putation efficacy. Ten imputation methods, representing three methodological categories—single-value (LOD, ND, SampMin), local-similarity (kNN, LLS, RF), and global-similarity approaches (LSA, BPCA, PPCA, SVD)—were analyzed. The study also investigated the impact of data logarithmization on imputation performance. The evaluation process was conducted in two stages. First, performance metrics including normalized root mean square error (NRMSE) and the area under the receiver operating characteristic (ROC) curve (AUC) were applied to datasets with artificially introduced missing values. The datasets were designed to mimic varying MV rates (10%, 25%, 50%) and proportions of values missing not at random (MNAR) (0%, 20%, 40%, 80%, 100%). This step enabled the assessment of data characteristics on the relative effectiveness of the imputation methods. Second, the imputation strategies were applied to real proteomic datasets containing natural missing values, focusing on the true-positive (TP) classification of proteins to evaluate their practical utility. The findings highlight that local-similarity-based methods, particularly random forest (RF) and local least-squares (LLS), consistently exhibit robust performance across varying MV scenarios. Furthermore, data logarithmization significantly enhances the effectiveness of global-similarity methods, suggesting it as a beneficial preprocessing step prior to imputation. The study underscores the importance of tailoring imputation strategies to the specific characteristics of the data to maximize the reliability of label-free quantitative proteomics. Interestingly, while the choice of protein identification algorithm (FragPipe vs. MaxQuant) had minimal influence on the overall imputation error, differences in the number of proteins classified as true positives revealed more nuanced effects, emphasizing the interplay between imputation strategies and downstream analysis outcomes. These findings provide a comprehensive framework for improving the accuracy and reproducibility of proteomic analyses through an informed selection of imputation approaches.

Uni-to-Multi Modal Knowledge Distillation for Bidirectional LiDAR-Camera Semantic Segmentation.

Combining LiDAR points and images for robust semantic segmentation has shown great potential. However, the heterogeneity between the two modalities (e.g. the density, the field of view) poses challenges in establishing a bijective mapping between each point and pixel. This modality alignment problem introduces new challenges in network design and data processing for cross-modal methods. Specifically, 1) points that are projected outside the image planes; 2) the complexity of maintaining geometric consistency limits the deployment of many data augmentation techniques. To address these challenges, we propose a cross-modal knowledge imputation and transition approach. First, we introduce a bidirectional feature fusion strategy that imputes missing image features and performs cross-modal fusion simultaneously. This allows us to generate reliable predictions even when images are missing. Second, we propose a Uni-to-Multi modal Knowledge Distillation (U2MKD) framework, leveraging the transfer of informative features from a single-modality teacher to a cross-modality student. This overcomes the issues of augmentation misalignment and enables us to train the student effectively. Extensive experiments on the nuScenes, Waymo, and SemanticKITTI datasets demonstrate the effectiveness of our approach. Notably, our method achieves an 8.3 mIoU gain over the LiDAR-only baseline on the nuScenes validation set and achieves state-of-the-art performance on the three datasets.

WBDI Approach for Univariate Time Series Imputation

WBDI Approach for Univariate Time Series Imputation

Imputation Methods for Missing Values in Estimation of Population Mean under Diagonal Systematic Sampling Scheme

In survey sampling, the use of auxiliary information to enhance estimators of population parameters under simple random sampling stratified random sampling and systematic sampling has been widely discussed. Similarly, some existing estimators were modified using regression imputation approach to obtain two imputation schemes and estimators that impute the responses non-respondents thereby eliminating difficulties in data presentation, compilation. The theoretical properties (estimators, biases and mean squared errors) of the proposed imputation scheme were derived so as to assess their robustness and efficiency. The theoretical findings were supported by simulation studies on population generated using four distributions namely; Beta, Gamma, Exponential and Uniform distributions. The averages of biases, MSEs and PREs of the estimators in comparison to the existing estimators were computed from the simulated data and the results showed that on average, the estimators of the proposed imputation scheme have minimum biases, minimum MSEs and higher PREs compared to the traditional unbiased estimators. These results imply that the estimators of the proposed schemes are more efficient and robust than the conventional unbiased estimators.

Data discretization impact on deep learning for missing value imputation of continuous data

In various fields of information examination, for example, AI, profoundly getting the hang of missing information is a typical issue. Missing qualities should be tended to since they can adversely affect the exactness and adequacy of prescient models. This research investigates how data discretization affects deep learning methods for filling the missing values in datasets with continuous features. They provide a unique method for imputing missing values using deep neural networks (DNNs) called extravagant expectation maximization-deep neural network (EEM-DNN). This approach discretizes continuous features into separate intervals initially. This is justified by treating the issue of missing value imputation as a classification work, with the missing values being considered a distinct class. A DNN, designed explicitly for imputation, is then trained using the discretized data. The expectation maximization concepts are incorporated into the network architecture, and as a result, the network iteratively improves its imputation predictions. They run comprehensive experiments on several datasets from different fields to gauge the efficacy of the suggested strategy. The effectiveness of EEM-DNN is compared to that of other imputation approaches, such as traditional imputation techniques and deep learning methods without data discretization. Our findings show that data discretization significantly enhances imputation accuracy. In terms of imputation accuracy and prediction performance on downstream tasks, the EEM-DNN method regularly performs better than alternative methods. It also examines if various discretization techniques affect the overall imputation process. They find that the trade-off between bias and variance in imputed data depends on the discretization method selected. This highlights the significance of choosing a suitable discretization approach depending on the unique properties of the dataset.

A novel MissForest-based missing values imputation approach with recursive feature elimination in medical applications

BackgroundMissing values in datasets present significant challenges for data analysis, particularly in the medical field where data accuracy is crucial for patient diagnosis and treatment. Although MissForest (MF) has demonstrated efficacy in imputation research and recursive feature elimination (RFE) has proven effective in feature selection, the potential for enhancing MF through RFE integration remains unexplored.MethodsThis study introduces a novel imputation method, “recursive feature elimination-MissForest” (RFE-MF), designed to enhance imputation quality by reducing the impact of irrelevant features. A comparative analysis is conducted between RFE-MF and four classical imputation methods: mean/mode, k-nearest neighbors (kNN), multiple imputation by chained equations (MICE), and MF. The comparison is carried out across ten medical datasets containing both numerical and mixed data types. Different missing data rates, ranging from 10 to 50%, are evaluated under the missing completely at random (MCAR) mechanism. The performance of each method is assessed using two evaluation metrics: normalized root mean squared error (NRMSE) and predictive fidelity criterion (PFC). Additionally, paired samples t-tests are employed to analyze the statistical significance of differences among the outcomes.ResultsThe findings indicate that RFE-MF demonstrates superior performance across the majority of datasets when compared to four classical imputation methods (mean/mode, kNN, MICE, and MF). Notably, RFE-MF consistently outperforms the original MF, irrespective of variable type (numerical or categorical). Mean/mode imputation exhibits consistent performance across various scenarios. Conversely, the efficacy of kNN imputation fluctuates in relation to varying missing data rates.ConclusionThis study demonstrates that RFE-MF holds promise as an effective imputation method for medical datasets, providing a novel approach to addressing missing data challenges in medical applications.

Implementation of PPCA Imputation, SMOTE-N Class Balancing in Hepatitis Classification Using Naïve Bayes

The availability of complete data in research is crucial, especially in the initial stages. The Hepatitis data used in this study encountered issues such as missing data and class imbalance, which hindered its optimal utilization. The method employed to address missing data was the PPCA imputation method. After filling in the missing data, the data was balanced using the SMOTE-N class balancing method and classified using Gaussian Naïve Bayes. The aim of this research was to compare the classification evaluation of hepatitis disease using Naive Bayes with the PPCA imputation approach and SMOTE-N class balancing. The best results from each scenario yielded an AUC value of 0.833 in the first scenario with an 80:20 data split for training and testing, and 0.875 in the second scenario with a 90:10 data split. The highest AUC value was obtained in the application of PPCA imputation with SMOTE-N class balancing using Naive Bayes classification. This demonstrates that the implementation of PPCA imputation with SMOTE-N class balancing has a better impact on the performance of Naïve Bayes classification.

Assessing the impact of missing data in youth overweight and obesity research: complete case analysis versus multiple imputation

ABSTRACT Youth overweight and obesity (OWOB) surveillance often uses body mass index (BMI) derived from self-reported height and weight, but these measures can suffer from high proportions of missing data. Complete case analysis (CCA) is the most common approach to handle missing data, but this approach can introduce bias if missing data are not missing completely at random. Using BMI and related covariate data from 36,546 female and 37,126 male youth aged 12–19 years who participated in the COMPASS study in 2018/19, where approximately 30% of BMI data were missing, results and inference were compared between CCA and multiple imputation (MI) approaches to examine associations with youth BMI. Results of regression joint models showed contrasting findings between MI and CCA, highlighting that appropriate methodological choices in the handling of missing data are essential in youth OWOB research and that choices can impact research inference and thereby associated policy and programming recommendations.

Comparing imputation approaches for immigration status in ED visits: Implications for using electronic medical records.

This study aimed to compare imputation approaches to identify the likely undocumented patient population in electronic health record (EHRs). EHR are a promising source of information on undocumented immigrants' medical needs and care utilization, but there is no verified way to identify immigration status in the data. Different approaches to approximating immigration status in EHR introduce unique biases, which in turn has major implications on our understanding of undocumented immigrant patients. We used a dataset of all emergency department (ED) visits from 2016 to 2019 in the Los Angeles Department of Health Services (LADHS) merged across patient medical records, demographic data, and claims data. We included all ED visits from our patient groups of interest and limited to patients at or over the age of 18 years at the time of their ED visit and excluded empty encounter records (n = 1,106,086 ED encounters). We created three patient groups: (1) US-born, (2) foreign-born documented, and (3) undocumented using two different imputation approaches: a logical approach versus statistical assignment. We compared predicted probabilities for two outcomes: an ED visit related to a behavioral health (BH) disorder and inpatient admission/transfer to another facility. Both approaches provide comparable estimates among the three patient groups for ED encounters for a BH disorder and inpatient admission/transfer to another facility. Undocumented immigrants are less likely to have a BH diagnosis in the ED and are less likely to be admitted or transferred compared to the US-born. Researchers should consider expanding EHR with administrative data when studying the undocumented patient population and may prefer a logical approach to estimate immigration status. Researchers who rely on payer status alone (i.e., restricted Medicaid) as a proxy for undocumented immigrants in EHR should consider how this may bias their results. As Medicaid expands for undocumented immigrants, statistical assignment may become the preferred method.

Estimating the impact of social distance policy in mitigating COVID-19 spread with factor-based imputation approach

AbstractWe identify the effectiveness of social distancing policies in reducing the transmission of the COVID-19 spread. We build a model that measures the relative frequency and geographic distribution of the virus growth rate and provides hypothetical infection distribution in the states that enacted the social distancing policies, where we control time-varying, observed and unobserved, state-level heterogeneities. Using panel data on infection and deaths in all US states from February 20 to April 20, 2020, we find that stay-at-home orders and other types of social distancing policies significantly reduced the growth rate of infection and deaths. We show that the effects are time varying and range from the weakest at the beginning of policy intervention to the strongest by the end of our sample period. We also found that social distancing policies were more effective in states with higher income, better education, more white people, more democratic voters, and higher CNN viewership.

ReMiND: Recovery of missing neuroimaging using diffusion models with application to Alzheimer’s disease

Abstract Missing data is a significant challenge in medical research. In longitudinal studies of Alzheimer’s disease (AD) where structural magnetic resonance imaging (MRI) is collected from individuals at multiple time points, participants may miss a study visit or drop out. Additionally, technical issues such as participant motion in the scanner may result in unusable imaging data at designated visits. Such missing data may hinder the development of high-quality imaging-based biomarkers. To address the problem of missing MRI data in studies of AD, we introduced a novel 3D diffusion model specifically designed for imputing missing structural MRI (Recovery of Missing Neuroimaging using Diffusion models (ReMiND)). The model generates a whole-brain image conditional on a single structural MRI observed at a past visit or conditional on one past and one future observed structural MRI relative to the missing observation. The performance of models was compared with two alternative imputation approaches: forward filling and image generation using variational autoencoders. Experimental results show that our method can generate 3D structural MRI with high similarity to ground-truth images at designated visits. Furthermore, images generated using ReMiND show relatively lower differences in volume estimation between the imputed and observed images compared to images generated by forward filling or autoencoders. Additionally, ReMiND provides more accurate estimated rates of atrophy over time in important anatomical brain regions than the two comparator methods. Our 3D diffusion model can impute missing structural MRI data at a single designated visit and outperforms alternative methods for imputing whole-brain images that are missing from longitudinal trajectories.

The association between tobacco use and COVID-19 diagnoses in three Nordic countries: a pooled analysis.

Previous research has suggested an unexpected negative association between smoking and susceptibility to COVID-19. This study, drawing on population-based data from three Nordic countries-Sweden, Norway, and Finland-aims to investigate this association further, capitalizing on diversity introduced by different containment measures. The objective of this research was to examine the association between cigarette smoking and snus (smokeless tobacco) use and the risk of confirmed COVID-19 infection. A pooled analysis integrating original data from 547,685 participants across three countries. We used a multiple imputation approach based on conditional probabilities to impute the systematically missing covariates. The associations between tobacco use and COVID-19 infection were assessed, controlling for potential confounding factors. Current cigarette smokers had a lower risk of a confirmed COVID-19 case, whereas there was an increased risk among snus users. Our sensitivity analysis confirmed that the associations between tobacco use and COVID-19 infection risk are robust, remaining consistent regardless of whether covariate imputation was applied. Findings support a negative association between smoking and SARS-CoV-2 infection, but not the hypothesis that nicotine may be protective against the risk of contracting SARS-CoV-2 infection.

Prognostic model for predicting Alzheimer’s disease conversion using functional connectome manifolds

BackgroundEarly detection of Alzheimer’s disease (AD) is essential for timely management and consideration of therapeutic options; therefore, detecting the risk of conversion from mild cognitive impairment (MCI) to AD is crucial during neurodegenerative progression. Existing neuroimaging studies have mostly focused on group differences between individuals with MCI (or AD) and cognitively normal (CN), discarding the temporal information of conversion time. Here, we aimed to develop a prognostic model for AD conversion using functional connectivity (FC) and Cox regression suitable for conversion event modeling.MethodsWe developed a prognostic model using a large-scale Alzheimer’s Disease Neuroimaging Initiative dataset, and it was validated using external data obtained from the Open Access Series of Imaging Studies. We considered individuals who were initially CN or had MCI but progressed to AD and those with MCI with no progression to AD during the five-year follow-up period. As the exact conversion time to AD is unknown, we inferred this information using imputation approaches. We generated cortex-wide principal FC gradients using manifold learning techniques and computed subcortical-weighted manifold degrees from baseline functional magnetic resonance imaging data. A penalized Cox regression model with an elastic net penalty was adopted to define a risk score predicting the risk of conversion to AD, using FC gradients and clinical factors as regressors.ResultsOur prognostic model predicted the conversion risk and confirmed the role of imaging-derived manifolds in the conversion risk. The brain regions that largely contributed to predicting AD conversion were the heteromodal association and visual cortices, as well as the caudate and hippocampus. Our risk score based on Cox regression was consistent with the expected disease trajectories and correlated with positron emission tomography tracer uptake and symptom severity, reinforcing its clinical usefulness. Our findings were validated using an independent dataset. The cross-sectional application of our model showed a higher risk for AD than that for MCI, which correlated with symptom severity scores in the validation dataset.ConclusionWe proposed a prognostic model predicting the risk of conversion to AD. The associated risk score may provide insights for early intervention in individuals at risk of AD conversion.

Low-Rank Tensor and Hybrid Smoothness Regularization-Based Approach for Traffic Data Imputation With Multimodal Missing

Low-Rank Tensor and Hybrid Smoothness Regularization-Based Approach for Traffic Data Imputation With Multimodal Missing

Multiple imputation of missing data in large studies with many variables: A fully conditional specification approach using partial least squares.

Multiple imputation (MI) is one of the most popular methods for handling missing data in psychological research. However, many imputation approaches are poorly equipped to handle a large number of variables, which are a common sight in studies that employ questionnaires to assess psychological constructs. In such a case, conventional imputation approaches often become unstable and require that the imputation model be simplified, for example, by removing variables or combining them into composite scores. In this article, we propose an alternative method that extends the fully conditional specification approach to MI with dimension reduction techniques such as partial least squares. To evaluate this approach, we conducted a series of simulation studies, in which we compared it with other approaches that were based on variable selection, composite scores, or dimension reduction through principal components analysis. Our findings indicate that this novel approach can provide accurate results even in challenging scenarios, where other approaches fail to do so. Finally, we also illustrate the use of this method in real data and discuss the implications of our findings for practice. (PsycInfo Database Record (c) 2024 APA, all rights reserved).

Enhanced prediction of agricultural CO2 emission using ensemble machine learning-based imputation approach

Enhanced prediction of agricultural CO2 emission using ensemble machine learning-based imputation approach

ScDTL: enhancing single-cell RNA-seq imputation through deep transfer learning with bulk cell information.

The increasing single-cell RNA sequencing (scRNA-seq) data enable researchers to explore cellular heterogeneity and gene expression profiles, offering a high-resolution view of the transcriptome at the single-cell level. However, the dropout events, which are often present in scRNA-seq data, remaining challenges for downstream analysis. Although a number of studies have been developed to recover single-cell expression profiles, their performance may be hindered due to not fully exploring the inherent relations between genes. To address the issue, we propose scDTL, a deep transfer learning based approach for scRNA-seq data imputation by harnessing the bulk RNA-sequencing information. We firstly employ a denoising autoencoder trained on bulk RNA-seq data as the initial imputation model, and then leverage a domain adaptation framework that transfers the knowledge learned by the bulk imputation model to scRNA-seq learning task. In addition, scDTL employs a parallel operation with a 1D U-Net denoising model to provide gene representations of varying granularity, capturing both coarse and fine features of the scRNA-seq data. Finally, we utilize a cross-channel attention mechanism to fuse the features learned from the transferred bulk imputation model and U-Net model. In the evaluation, we conduct extensive experiments to demonstrate that scDTL could outperform other state-of-the-art methods in the quantitative comparison and downstream analyses.

Systematically missing data in distributed data networks: multiple imputation when data cannot be pooled

Systematically missing data in distributed data networks presents practical and methodological challenges. Failure to handle it appropriately can bias statistical inference. Multiple imputations can be used to address systematic missingness. However, when data from different study sites cannot be pooled into a unified file, conventional imputation approaches become unavailable due to the absence of a basis for imputation. To address such challenges, we introduce an imputation method based on conditional quantiles – conditional quantile imputation (CQI) – which involves four steps: (i) estimating 99 quantiles for the systematically missing variable in studies with observed data; (ii) deriving a weighted average of regression coefficients across studies and transmitting it to sites with systematically missing data; (iii) imputing the systematically missing values based on observed data and the set of regression coefficients from step ii; and (iv) combining estimates of the substantive outcome model across imputations using Rubin's rules. We evaluate CQI in different simulation scenarios and illustrate it with an applied data example. We conclude that CQI can be a suitable approach for the imputation of systematically missing data when data from multiple studies cannot be pooled.

Autoencoder imputation of missing heterogeneous data for Alzheimer's disease classification

AbstractMissing Alzheimer's disease (AD) data is prevalent and poses significant challenges for AD diagnosis. Previous studies have explored various data imputation approaches on AD data, but the systematic evaluation of deep learning algorithms for imputing heterogeneous and comprehensive AD data is limited. This study investigates the efficacy of denoising autoencoder‐based imputation of missing key features of heterogeneous data that comprised tau‐PET, MRI, cognitive and functional assessments, genotype, sociodemographic, and medical history. The authors focused on extreme (≥40%) missing at random of key features which depend on AD progression; identified as the history of a mother having AD, APoE ε4 alleles, and clinical dementia rating. Along with features selected using traditional feature selection methods, latent features extracted from the denoising autoencoder are incorporated for subsequent classification. Using random forest classification with 10‐fold cross‐validation, robust AD predictive performance of imputed datasets (accuracy: 79%–85%; precision: 71%–85%) across missingness levels, and high recall values with 40% missingness are found. Further, the feature‐selected dataset using feature selection methods, including autoencoder, demonstrated higher classification score than that of the original complete dataset. These results highlight the effectiveness and robustness of autoencoder in imputing crucial information for reliable AD prediction in AI‐based clinical decision support systems.

Addressing the implementation challenge of risk prediction model due to missing risk factors: The submodel approximation approach.

Clinical prediction models have been widely acknowledged as informative tools providing evidence-based support for clinical decision making. However, prediction models are often underused in clinical practice due to many reasons including missing information upon real-time risk calculation in electronic health records (EHR) system. Existing literature to address this challenge focuses on statistical comparison of various approaches while overlooking the feasibility of their implementation in EHR. In this article, we propose a novel and feasible submodel approach to address this challenge for prediction models developed using the model approximation (also termed "preconditioning") method. The proposed submodel coefficients are equivalent to the corresponding original prediction model coefficients plus a correction factor. Comprehensive simulations were conducted to assess the performance of the proposed method and compared with the existing "one-step-sweep" approach as well as the imputation approach. In general, the simulation results show the preconditioning-based submodel approach is robust to various heterogeneity scenarios and is comparable to the imputation-based approach, while the "one-step-sweep" approach is less robust under certain heterogeneity scenarios. The proposed method was applied to facilitate real-time implementation of a prediction model to identify emergency department patients with acute heart failure who can be safely discharged home.