Autoencoder missing value imputation. This paper introduces a double autoencoder for imputation .

Autoencoder missing value imputation. However, the missing data influence the analysis and prediction results significantly. Dec 6, 2023 · Traditional methods for missing imputation face difficulties when operating in constrained environments characterized by short data collection periods and frequent consecutive missing. In detail, we generate 36 semi-synthetic scRNA-seq datasets with artificial zeros (whose original, non-missing values are known) by applying three Aug 1, 2024 · Our imputation method outperforms the comparison method. A recent deep-learning technique, variational autoencoders (VAEs), has been used for missing Abstract Missing data is a problem often found in real-world datasets and it can degrade the performance of most machine learning models. Jun 9, 2020 · On the MNIST and SVHN datasets we demonstrate improved marginal log-likelihood of observed data and better missing data imputation, compared to existing approaches. These models are able to learn a representation of the data with missing values and generate plausible new Oct 12, 2023 · Method: In this study, we propose a novel method that leverages the information from WGS data and reference metabolites to impute unknown metabolites. Difficulties mainly come from high May 21, 2025 · This project provides a scalable solution to fill missing values in large time-series datasets using a combination of Temporal Convolutional Networks (TCNs) and LSTM-based Denoising Autoencoders. This article proposes a new position-encoding denoising autoencoder (PE-DAE), which Apr 3, 2024 · 6. Our approach employs the Random Missing Value (RMV) algorithm to simulate missing data, enabling thorough testing and comparison of various imputation techniques. For training the model, I have only 113 days with complete data. e. Due to the ubiquitous presence of missing values in real-world datasets, an imputation algorithm can recover the missing values and provide users with a complete dataset that utilizes all the available observed information. The incomplete data obstruct the effective use of data and degrade the performance of data-driven models. Dec 1, 2020 · In paper [9], the autoencoder is trained with the data having no missing values for missing values prediction. Additionally, the learning process of missing value imputation models requires complete data, but there are limitations in securing complete vehicle communication data. This comprehensive review investigates various imputation techniques, cate-gorizing them into three primary approaches: deterministic methods, proba-bilistic models, and machine learning algorithms. One of the most common strategies to address this issue is to perform imputation, where the missing values are replaced by estimates. Considering the differences in attribute correlations among different sample Dec 14, 2020 · A maximum of 100 iterations was considered; -Denoising Autoencoder (DAE), which is an autoencoder trained with data containing additional noise, which in this context is the existence of missing Nov 5, 2018 · AutoImpute, which learns the inherent distribution of the input scRNA-seq data and imputes the missing values accordingly with minimal modification to the biologically silent genes. In this paper, Denoising Autoencoders are used to impute the missing traffic flow data. Usually, the implementations of this condition draw a random number from a uniform distribution and discard a value if that random number was below the desired missingness ratio. Jan 1, 2021 · The existence of missing values in real-world datasets increases the difficulty of data analysis. It is a challenging task to model incomplete data and reasonably impute missing values. Feb 27, 2020 · In this paper, we investigate a deep learning framework for missing imputation of smart meter data by leveraging a denoising autoencoder (DAE). Missing data in food composition databases (FCDB) significantly limits their usage. An ablation study shows on several UCI Machine Learning Repository datasets, the benefit of using this modified loss function and Jan 1, 2018 · Missing data values and differing sampling rates, particularly for important parameters such as particle size and stream composition, are a common problem in minerals processing plants. Their approach is based on a scaled-down transformer model [21] with self-supervised learning for computer vision using masked autoencoders (MAE). So what if an Autoencoder could learn the most salient features and then could reconstruct not only the input data but also the missing values? So the Denoising Autoencoder tries to undo the corruption done by the missing values. Abstract Missing data is a problem often found in real-world datasets and it can degrade the performance of most machine learning models. Denoising AutoEncoders (DAEs) were first Abstract. Method: In this study, we propose a novel method that leverages the Furthermore, observations with missing values may have a significant impact on predictive analysis, as well as on descriptive and inferential statistics. Mar 12, 2024 · Our approach utilizes a multi-view variational autoencoder to jointly model the burden score, polygenetic risk score (PGS), and linkage disequilibrium (LD) pruned single nucleotide polymorphisms (SNPs) for feature extraction and missing metabolomics data imputation. Results: We evaluate the performance of our method on empirical metabolomics datasets with missing values and demonstrate its superiority compared to conventional imputation techniques. All of my implementations are in Pytorch and can be found in my … Jul 14, 2024 · Autoencoder Imputation: Use autoencoders to learn a compressed representation of the data and impute missing values. Sep 3, 2018 · This implemented a denoising autoencoder with partial loss (DAPL) as a deep learning based alternative for imputating missing values especially for large datasets, that achieves comparable or better performance than conventional methods with less computational burden. Method: In this study, we propose a novel method that leverages the Feb 28, 2020 · Variational Auto Encoder with missing data In this post, I’m going to share my experiences flexibility of VAE with missing data. Instead of discarding missing values and related data, imputation approaches offer an alternative means of handling missing data. The DMDI method integrates a stacked denoising autoencoder with Gradient Boosting to improve imputation accuracy. A trend in these strategies is the use of generative models, one being Variational Autoencoders. An effective method to solve this problem is to impute the missing data in advance. Finance: Transaction records with missing metadata can be restored using learned relationships across merchant codes, amounts, and timestamps. Abstract Missing data presents a significant challenge in statistical analysis and machine learning, often resulting in biased outcomes and diminished efficiency. Over the years, several studies presented alternative imputation strategies to deal with the three missing Oct 18, 2024 · For imputation, Monae supports intra-modal imputation and cross-modal imputation in the scenario without paired information to save the high cost of generating paired multi-modality data. Data Imputation with Autoencoders Autoencoders may be used for data imputation. Our approach utilizes a multi-view variational autoencoder to jointly model the burden score, polygenetic risk score (PGS), and linkage disequilibrium (LD) pruned single nucleotide polymorphisms (SNPs) for feature extraction and missing Despite the recent development of smart metering devices, however, missing data still arise due to unexpected device power off, communication failure, measuring error, or other unknown reasons. Dec 14, 2020 · Missing data is a problem often found in real-world datasets and it can degrade the performance of most machine learning models. This study proposes a missing value imputation model based on adversarial autoencoder using spatiotemporal feature extraction to address these issues. Jan 7, 2025 · Comparing Autoencoder to Random Forest Imputation Random forest imputation is a widely used technique because it leverages the predictive power of decision tree ensembles to estimate missing values. Jan 1, 2022 · The computation of the average code from an autoencoder Improves the imputation of missing values. In this paper, we propose a joint optimization framework to mine attribute associations and category structures in incomplete datasets, aiming to impute missing values with a full understanding of the data structure. They observed how Autoencoder-based methods maintained or improved their results as the missingness rate increased. We propose the Multivariate Time-Series Imputation with Transformers (MTSIT), a novel Multi-View Variational Autoencoder for Missing Value Imputation in Untargeted Metabolomics We 1. Jun 20, 2020 · It has been demonstrated that modified denoising stacking autoencoders (MSDAEs) serve to implement high-performance missing value imputation schemes. Oct 1, 2024 · Specifically, SAE-Impute assesses sample correlations via subspace regression, predicts potential dropout values, and then leverages these predictions within an autoencoder framework for interpolation. This paper focuses on regression imputation and uses a tracking-removed autoencoder (TRAE) to construct the mutual fitting correlation on incomplete data. These models are able to learn a representation of the data with missing values and generate plausible new Sep 1, 2025 · Use Cases Where Autoencoder Imputation Shines Healthcare: EHRs often have sparse fields, and autoencoders can fill in vitals, diagnoses, or lab values based on latent patterns. Aug 31, 2020 · In this study, the missing value in three different real-world datasets was estimated by using denoising autoencoder (DAE), k-nearest neighbor (kNN) and multivariate imputation by chained Jan 27, 2025 · The authors concluded that their proposal, named Partial Multiple Imputation with VAE (PMIVAE), outperformed other imputation methods in most cases. Moreover, I will compare the results of a classification model with different proportions of missing values when using Denoising Abstract. Example: Use an autoencoder to impute missing values in a dataset with high Denoising Autoencoder implementation In our data, there are missing values, which can be considered as noise. (2021). Unsupervised imputation is often employed to replace the missing values with substitute values before supervised classification. This paper introduces a double autoencoder for imputation (Ae2I) that Nov 1, 2022 · Thus, in this paper, we propose a way to fully exploit the valuable transformer data, using a data imputation approach called the iterative denoising autoencoder (IDAE) method. The May 4, 2022 · Missing values are ubiquitous in industrial data sets because of multisampling rates, sensor faults, and transmission failures. On the other hand, complete MSDAE (CMSDAE) classifiers, which extend their inputs with target estimates from an auxiliary classifier and are layer by layer trained to recover both the observation and the target estimates, offer classification Dec 17, 2024 · In the context of missing data imputation, an autoencoder learns the underlying data representation and relationships, allowing it to reconstruct missing values effectively. Let’s see how data imputation with autoencoder works. We find that VAEs provide poor empirical coverage of missing data, with underestimation and overconfident imputations, particularly for more extreme missing data values. The integration of whole-genome sequencing (WGS) data with metabolomics data has emerged as a promising approach to enhance the accuracy of data imputation in metabolomics studies. The experimental results show that CWGAIN-GP achieves impressive performance in imputing continuous missing time series. Aug 6, 2020 · As missing values are frequently present in genomic data, practical methods to handle missing data are necessary for downstream analyses that require complete data sets. Jan 11, 2024 · Finally, We used three imputation accuracies on two real-world datasets, including experiments on imputation accuracy for eight comparison models, ablation study, and experiments on the effect of consecutive missing lengths. However, most imputation methods overlook the continuous imputation of missing values, significantly losing local information resources. Sep 30, 2022 · In this work, we investigate the ability of deep models, namely variational autoencoders (VAEs), to account for uncertainty in missing data through multiple imputation strategies. May 29, 2023 · For interpretability, Shapley values are used to prioritize input features for cross-modal imputation and known sample labels. Jan 25, 2024 · Incomplete instances with various missing attributes in many real-world applications have brought challenges to the classification tasks. Hence, it is imperative to handle missing data either by listwise deletion or by replacing the missing values with estimations from the observed data via imputation procedures. Numerous imputation algorithms have been proposed to deal with missing values, primarily based on supervised learning, that is, imputing the missing values by Implementation of imputation using different types of autoencoders described in paper. Several deep learning techniques have been used to address this issue, and one of them is the Autoencoder and its Denoising and Variational variants. The most common strategy of imputing missing values in a table is to study either the column-column relationship or the row-row relationship of the data table, then use the relationship to impute the missing values based on the non-missing values from other columns of the same row, or from the other rows of the same column. X 0 ∼ N (0, 1) X 1 ∼ N (1. Manufacturing & IoT: Sensor dropouts in time-series data can be This observation prompted our development of an open framework that would enable the rapid implementation of different autoencoder imputation methods on a dataset, comparing imputation performance and the sensitivity of a given predictive task relative to inferred missing values. The paper [10] proposes a theoretical model for missing data imputation where probability density function is used for neuron’s response in the first hidden layer. Few studies report results on the more challenging conditions Jul 1, 2024 · In [26], where transfer learning was introduced into missing value imputation, the model migrates temporal information from complete sequences to long-interval consecutive missing sequences and achieves excellent results in single time series imputation tasks but cannot handle multivariate time series data. Our study consists of three investigations. Our approach consists of a learning step and an imputation step. The proposed method imputes missing values of dissolved gas analysis (DGA) data, which is frequently lost, for various reasons. This python package contains implementation of Denoising Autoencoder, Multimodal Autoencoder, Variational Auto Oct 26, 2024 · Where traditional methods draw strength from being full information maximum likelihood procedures in which missing data can easily be dealt with, a FNN cannot handle missing input values naturally. Compared with prior work, ReMasker is both simple -- besides the missing values (i. Oct 1, 2023 · Missingness creates problems in data analyses and predictive modeling. This paper introduces a double autoencoder for imputation Nov 26, 2024 · Request PDF | Incomplete data modeling based on alternate update of clustering and autoencoder for missing value imputation | Missing values exist widely in real-world datasets, which restrict the Sep 1, 2022 · Missing data is a common problem in a wide range of fields that can arise as a result of different reasons: lack of analysis, mishandling samples, measurement error, etc. Accordingly, we develop a new deep learning model called MIssing Data Imputation denoising Autoencoder (MIDIA) that effectively imputes the MVs in a given dataset by exploring non-linear correlations between missing values and non-missing values. These models are able to learn a representation of the data with missing values and generate plausible new ones to Feb 1, 2023 · Abstract: We present ReMasker, a novel method for imputing missing values in tabular data by extending the masked autoencoding framework. Missing data imputation is used to avoid information loss (due to downsampling or discarding incomplete records). 6. However, the imputation of missing omics data is a non-trivial task. Many solutions have been proposed by relying on statistical or machine learning techniques. Jan 27, 2025 · We propose a Missing data Multiple Importance Sampling Variational Auto-Encoder (MMISVAE) method to effectively model incomplete data. com Sep 5, 2024 · To tackle the two limitations of current missing data imputation methods: the gap between training tasks and imputation tasks, and the inadequate extraction of correlations within SCADA data, this work proposes a data-driven framework named multiscale-attention masked autoencoder (MAMAE) for missing data imputation of wind turbines. This study proposes a method to estimate missing data using a masked-denoising autoencoder (Masked-DAE) with L2-norm regularization, which can handle various types of data, missing patterns, proportions, and distributions. Traditional techniques, in Jun 1, 2024 · Missing data is an issue that can negatively impact any task performed with the available data and it is often found in real-world domains such as healthcare. Oct 12, 2023 · Download Citation | Multi-View Variational Autoencoder for Missing Value Imputation in Untargeted Metabolomics | Background Missing data is a common challenge in mass spectrometry-based Feb 10, 2023 · Here, we conduct an empirical study to explore how to optimize the autoencoder design for imputing scRNA-seq data. Jan 1, 2020 · Despite the recent development of smart metering devices, however, missing data still arise due to unexpected device power off, communication failure, measuring error, or other unknown reasons. The occurrence of missing values in time series is a common phenomenon attributed to equipment malfunction during data acquisition and transmission errors. 3 − 0. In this work This paper proposes a modified Denoising AutoEncoder (mDAE) dedicated to imputing missing values in numerical tabular data. , naturally masked), we randomly ``re-mask'' another set of values, optimize the autoencoder by reconstructing this re-masked set, and apply the trained model to Jul 31, 2023 · To address the main problems in the classical autoencoder model used for missing value filling, a missing value filling model based on feature fusion enhanced autoencoder is developed, and a novel neural network hidden layer based on de-tracking neurons and radial basis function neurons are designed to collaboratively train to fill missing values. Oct 1, 2025 · This paper introduces Ae 2 I (Double Autoencoder for Imputation), a novel method that simultaneously and collaboratively leverages both row-wise and column-wise relationships to impute missing values. Here, the missing values are chosen independently at random. Missing values can also be estimated using extensively studied statistical and ML-based imputation algorithms. In this paper, we introduce the Long Short-Term Memory Network based Recurrent Autoencoder with Imputation Units and Temporal Attention Imputation Model (RATAI), tailored for multivariate time series. Dec 20, 2024 · Multivariate time series is ubiquitous in real-world applications, yet it often suffers from missing values that impede downstream analytical tasks. Specifically, we first design the input structure of hidden neurons in a dynamic way to enhance the Jan 16, 2023 · The most common strategy of imputing missing values in a table is to study either the column-column relationship or the row-row relationship of the data table, then use the relationship to impute the missing values based on the non-missing values from other columns of the same row, or from the other rows of the same column. In our earlier research, we Imputation on each dataset can be performed for two levels of corruption: light corruption, representing approximately 20% of records with a single missing value, or heavy corruption, with <10% of records complete, approximately 80% of records one or two missing values, and approximately 10% of records three or four missing values. One widely used practice is to delete the data with missing values directly, but this will undoubtedly cause the loss of information and thus affect the model’s accuracy. The method works by training a random forest model to predict the missing values of a feature using the other available features as inputs. Mar 2, 2021 · We present DeepMVI, a deep learning method for missing value imputation in multidimensional time-series datasets. The area of nutrition and food composition is no exception to the problem of missing values. It is tailored for environmental or sensor data, such as air quality datasets, with large gaps, irregular timestamps, and complex seasonal patterns. Department of Applied Computing, Michigan Technological University, 1400 Townsend Dr, Houghton, MI, 4993 , , I, Oct 5, 2018 · Missing data consists in the lack of information in a dataset and since it directly influences classification performance, neglecting it is not a valid option. Sep 25, 2023 · We present ReMasker, a new method of imputing missing values in tabular data by extending the masked autoencoding framework. Feb 27, 2020 · Despite the recent development of smart metering devices, however, missing data still arise due to unexpected device power off, communication failure, measuring error, or other unknown reasons. Missing values are a fundamental issue in many applications by constraining the application of different learning methods or by impairing the attained results. To validate the performance of SAE-Impute, we systematically conducted experiments on both simulated and real scRNA-seq datasets. , 2009) are artificial neural networks used to learn eficient representation of unlabeled data (encodings) and a decoding function that recreates the input data from the encoded representation. Jan 1, 2021 · In transportation engineering, spatio-temporal data including traffic flow, speed, and occupancy are collected from different kinds of sensors and used by transportation engineers for analysis. Commonly this problem is resolved by calculating Jan 16, 2019 · To infer the missing values, I try to model an denoising autoencoder but it doesn't provide good results. Missing data imputation has been an active research area in both statistics and machine learning fields for a few decades (Rubin, 1976). By learning the latent representations of both omics data, our method can effectively impute missing metabolomics values based on genomic information. In this paper, we introduce the denoising masked autoencoder (DMAE) model as a solution to improve the handling of missing data, even in such restrictive settings. Hence, motivated by the advent of deep learning, different solutions have also Sep 1, 2024 · Built on this approach, in this study, we propose a novel multi-scale variational autoencoder (MVAE) framework for imputing missing values in metabolomics data, leveraging genetic information from WGS data. One usually prefers missing-data imputation, which consists of filling missing entries with estimated values using the observed data. Aug 1, 2023 · Nowadays, the issue of MV imputation has become one of the research hotspots in the field of data quality, since the missing values (MVs) are prevalen… Missing values in the training data must be handled before training the machine learning (ML) model. In contrast to prior work, ReMasker is both {\em simple} -- besides the missing values (i. When to use Denoising Autoencoder as a method to impute missing values? In this project I will show you how to use Denoising Autoencoders to fill missing values. One of the remedies is imputation to fill the missing values based on observed values properly without undermining performance. May 4, 2024 · Due to various reasons, such as limitations in data collection and interruptions in network transmission, gathered data often contain missing values. Sep 1, 2024 · Built on this approach, in this study, we propose a novel multi-scale variational autoencoder (MVAE) framework for imputing missing values in metabolomics data, leveraging genetic information from WGS data. Existing state-of-the-art generative adversarial imputation methods face three main issues: limited applicability, neglect of latent categorical information that could reflect relationships among samples, and an inability to balance local and . This observation prompted our development of an open framework that would enable the rapid implementation of different autoencoder imputation methods on a dataset, comparing imputation performance and the sensitivity of a given predictive task relative to inferred missing values. Processing time series with missing segments is a fundamental challenge that puts obstacles to advanced analysis in various disciplines such as engineering, medicine, and economics. Missing data imputation is a very active research area (Van Buuren, 2018; Little & Rubin, 2019) with more than 150 implementations available according to Mayer et al. However, most of the imputation methods still have several limitations, including cannot restore the original distribution, handling various data missing patterns, and high Jan 11, 2024 · Finally, We used three imputation accuracies on two real-world datasets, including experiments on imputation accuracy for eight comparison models, ablation study, and experiments on the effect of consecutive missing lengths. This article proposes a new position-encoding denoising autoencoder (PE-DAE), which Nov 26, 2024 · Missing values exist widely in real-world datasets, which restrict the performance of data mining. In this paper, we propose an autoencoder (AE)-based multi-task learning (MTL) model and optimize missing values dynamically to classify incomplete datasets having interdependencies among attributes. AutoEncoders (AE) (Bengio et al. Jun 25, 2024 · We then assess the impact of missing values in the input genotypes on imputation accuracy and evaluate the effectiveness of our two-stage genotype imputation strategy against the missing values. Missing values are a common occurrence in industrial datasets, resulting from the multiple sampling rates, sensor malfunctions, and transmission errors, whose presence can significantly affect the accuracy of data-driven models. See full list on curiousily. Data The data is sampled as follows. 1. Oct 7, 2023 · One common problem in omics data analysis is missing values, which can arise due to various reasons, such as poor tissue quality and insufficient sample volumes. The Missing values in the training data must be handled before training the machine learning (ML) model. This model utilizes fuzzy clustering to partition the incomplete dataset into subclusters and then establishes a TRAE-based submodel for each subcluster to mine correlations between attributes. Several approaches based on statistics and machine learning techniques have been proposed for this By learning the latent representations of both omics data, our method can effectively impute missing metabolomics values based on genomic information. However, in most cases, the results are not yet satisfactory. The first investigation is the optimization of autoencoder design for imputation accuracy. State-of-the-art imputation techniques, including methods based on singular value decomposition and K-nearest neighbors, can be computationally expensive for large data sets and it is difficult to modify these algorithms to Jun 21, 2023 · Additionally, the learning process of missing value imputation models requires complete data, but there are limitations in securing complete vehicle communication data. However, the default loss function of this method gives the same importance to all data, while a more suitable solution should focus on the missing values. Data imputation is an established practice to resolve the issue, i. Missing data is an issue often addressed with imputation strategies that replace the missing values with plausible ones. estimating missing values from non-missing values in the dataset. 1 + 4 X 0, 1) X 2 ∼ N (2. This comprehensive review investigates various imputation techniques, categorizing them into three primary approaches: deterministic methods, probabilistic models, and machine learning algorithms. Jul 8, 2021 · The missingness pattern most often used in the literature on missing value imputation is MCAR. Feb 1, 2024 · Missing values are a common problem found in many real-world datasets, and cannot be avoided. Missing values are commonplace in decision support platforms that aggregate data over long time stretches from disparate sources, and reliable data analytics calls for careful handling of missing data. 5 X 0, 1) Nov 19, 2024 · This paper introduces a methodology based on Denoising AutoEncoder (DAE) for missing data imputation. , naturally masked), we randomly ``re-mask'' another set of values, optimize the autoencoder by reconstructing this re-masked set, and apply the trained model to predict the missing Jul 25, 2020 · However, those correlations are usually complex and thus difficult to identify. RATAI is designed to address certain Loss of information and bias in data analysis due to missing data are serious problems. Jul 2, 2024 · The imputation model for missing values draws inspiration from the work proposed by [11]. One strategy is imputing the missing values, and a wide variety of algorithms Dec 11, 2024 · Abstract Missing data presents a significant challenge in statistical analysis and ma-chine learning, often resulting in biased outcomes and diminished efficiency. The proposed methodology, called mDAE hereafter, results from a modification of the loss function and a straightforward procedure for choosing the hyper-parameters. Multi-scale variational autoencoder for imputation of missing values in untargeted metabolomics using whole-genome sequencing data Author: C Zhao, KJ Su, C Wu, X Cao, Q Sha, W Li, Z Luo et al. Oct 12, 2023 · Background: Missing data is a common challenge in mass spectrometry-based metabolomics, which can lead to biased and incomplete analyses. In this paper, we investigate a deep learning framework for missing imputation of smart meter data by leveraging a denoising autoencoder (DAE). Traditional techniques, including Feb 1, 2024 · In this section, we propose a category-based tracking-removed autoencoder to model incomplete data for missing value imputation. l0q6wu w7qq otofvaz gf koyfa sa xw uam ulrzv aa5