Handling missing values is a common challenge in biostatistical analyses, typically addressed by imputation methods. We propose a novel, fast, and easy-to-use imputation method called missing value imputation with adversarial random forests (MissARF), based on generative machine learning, that provides both single and multiple imputation. MissARF employs adversarial random forest (ARF) for density estimation and data synthesis. To impute a missing value of an observation, we condition on the non-missing values and sample from the estimated conditional distribution generated by ARF. Our experiments demonstrate that MissARF performs comparably to state-of-the-art single and multiple imputation methods in terms of imputation quality and fast runtime with no additional costs for multiple imputation.

In recent times, a considerable number of research studies have been carried out to address the issue of Missing Value Imputation (MVI). MVI aims to provide a primary solution for datasets that have one or more missing attribute values. The advancements in Artificial Intelligence (AI) drive the development of new and improved machine learning (ML) algorithms and methods. The advancements in ML have opened up significant opportunities for effectively imputing these missing values. The main objective of this article is to conduct a comprehensive and rigorous review, as well as analysis, of the state-of-the-art ML applications in MVI methods. This analysis seeks to enhance researchers' understanding of the subject and facilitate the development of robust and impactful interventions in data preprocessing for Data Analytics. The review is performed following the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) technique. More than 100 articles published between 2014 and 2023 are critically reviewed, considering the methods and findings. Furthermore, the latest literature is examined to scrutinize the trends in MVI methods and their evaluation. The accomplishments and limitations of the existing literature are discussed in detail. The survey concludes by identifying the current gaps in research and providing suggestions for future research directions and emerging trends in related fields of interest.

Multivariate time series data suffer from the problem of missing values, which hinders the application of many analytical methods. To achieve the accurate imputation of these missing values, exploiting inter-correlation by employing the relationships between sequences (i.e., a network) is as important as the use of temporal dependency, since a sequence normally correlates with other sequences. Moreover, exploiting an adequate network depending on time is also necessary since the network varies over time. However, in real-world scenarios, we normally know neither the network structure nor when the network changes beforehand. Here, we propose a missing value imputation method for multivariate time series, namely MissNet, that is designed to exploit temporal dependency with a state-space model and inter-correlation by switching sparse networks. The network encodes conditional independence between features, which helps us understand the important relationships for imputation visually. Our algorithm, which scales linearly with reference to the length of the data, alternatively infers networks and fills in missing values using the networks while discovering the switching of the networks. Extensive experiments demonstrate that MissNet outperforms the state-of-the-art algorithms for multivariate time series imputation and provides interpretable results.

Background: Missing data is a common challenge in mass spectrometry-based metabolomics, which can lead to biased and incomplete analyses. 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. Method: In this study, we propose a novel method that leverages the information from WGS data and reference metabolites to impute unknown metabolites. 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. By learning the latent representations of both omics data, our method can effectively impute missing metabolomics values based on genomic information. Results: We evaluate the performance of our method on empirical metabolomics datasets with missing values and demonstrate its superiority compared to conventional imputation techniques. Using 35 template metabolites derived burden scores, PGS and LD-pruned SNPs, the proposed methods achieved r2-scores > 0.01 for 71.55% of metabolites. Conclusion: The integration of WGS data in metabolomics imputation not only improves data completeness but also enhances downstream analyses, paving the way for more comprehensive and accurate investigations of metabolic pathways and disease associations. Our findings offer valuable insights into the potential benefits of utilizing WGS data for metabolomics data imputation and underscore the importance of leveraging multi-modal data integration in precision medicine research.

While training a Machine Learning model the quality of the model is directly proportional to the quality of data. However, in some cases, there are a lot of missing values in the dataset affecting the quality of prediction in the long run. Several methods can be used to fill the missing values and Datawig is one of the most efficient ones. Datawig is a Deep Learning library developed by AWS Labs and is primarily used for "Missing Value Imputation". The library uses "mxnet" as a backend to train the model and generate the predictions.

We present DeepMVI, a deep learning method for missing value imputation in multidimensional time-series datasets. 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. One strategy is imputing the missing values, and a wide variety of algorithms exist spanning simple interpolation, matrix factorization methods like SVD, statistical models like Kalman filters, and recent deep learning methods. We show that often these provide worse results on aggregate analytics compared to just excluding the missing data. DeepMVI uses a neural network to combine fine-grained and coarse-grained patterns along a time series, and trends from related series across categorical dimensions. After failing with off-the-shelf neural architectures, we design our own network that includes a temporal transformer with a novel convolutional window feature, and kernel regression with learned embeddings. The parameters and their training are designed carefully to generalize across different placements of missing blocks and data characteristics. Experiments across nine real datasets, four different missing scenarios, comparing seven existing methods show that DeepMVI is significantly more accurate, reducing error by more than 50% in more than half the cases, compared to the best existing method. Although slower than simpler matrix factorization methods, we justify the increased time overheads by showing that DeepMVI is the only option that provided overall more accurate analytics than dropping missing values.

Missing values widely exist in many real-world datasets, which hinders the performing of advanced data analytics. Properly filling these missing values is crucial but challenging, especially when the missing rate is high. Many approaches have been proposed for missing value imputation (MVI), but they are mostly heuristics-based, lacking a principled foundation and do not perform satisfactorily in practice. In this paper, we propose a probabilistic framework based on deep generative models for MVI. Under this framework, imputing the missing entries amounts to seeking a fixed-point solution between two conditional distributions defined on the missing entries and latent variables respectively. These distributions are parameterized by deep neural networks (DNNs) which possess high approximation power and can capture the nonlinear relationships between missing entries and the observed values. The learning of weight parameters of DNNs is performed by maximizing an approximation of the log-likelihood of observed values. We conducted extensive evaluation on 13 datasets and compared with 11 baselines methods, where our methods largely outperforms the baselines.

Unfortunately, real-world datasets often include only samples of observed values mixed with many missing or unknown elements. Missing values may occur due to human impatience, human error during data entry, data loss, faulty sensory equipment, changes in data collection methods, inability to decipher handwriting, privacy issues, legal requirements, and a variety of other practical factors. Thus, improvements to methods for imputing missing values can have far-reaching impact on improving the effectiveness of existing learning algorithms for operating on real-world data. We present a method for imputation called Unsupervised Backpropagation (UBP), which trains a multilayer perceptron (MLP) to fit to the manifold represented by the known features in a dataset. We demonstrate this algorithm with the task of imputing missing values, and we show that it is significantly more effective than other methods for imputation. Backpropagation has long been a popular method for training neural networks (Rumelhart et al., 1986; Werbos, 1990).