Conditional probabilistic graphical models provide a powerful framework for structured regression in spatio-temporal datasets with complex correlation patterns. However, in real-life applications a large fraction of observations is often missing, which can severely limit the representational power of these models. In this paper we propose a Marginalized Gaussian Conditional Random Fields (m-GCRF) structured regression model for dealing with missing labels in partially observed temporal attributed graphs. This method is aimed at learning with both labeled and unlabeled parts and effectively predicting future values in a graph. The method is even capable of learning from nodes for which the response variable is never observed in history, which poses problems for many state-of-the-art models that can handle missing data. The proposed model is characterized for various missingness mechanisms on 500 synthetic graphs. The benefits of the new method are also demonstrated on a challenging application for predicting precipitation based on partial observations of climate variables in a temporal graph that spans the entire continental US. We also show that the method can be useful for optimizing the costs of data collection in climate applications via active reduction of the number of weather stations to consider. In experiments on these real-world and synthetic datasets we show that the proposed model is consistently more accurate than alternative semi-supervised structured models, as well as models that either use imputation to deal with missing values or simply ignore them altogether.
One of the standard ways of handling missing values is imputing values based on some predictive model, and then applying the analysis on a fully observed dataset. To exploit the graph structure, previous studies have proposed imputation of missing values based on the exponential random graph model @cite_11 . The limitation of such an approach is that it is slow, as it requires Gibbs sampling, and so it cannot handle large graphs. Imputation of missing values can also be accomplished using matrix (or tensor) factorization methods. These methods can impute missing values with high accuracy even when large percentages (up to 95 , imputation-based methods use only point estimates of the missing values, effectively ignoring the prediction uncertainty when learning with imputed values. Techniques known as Multiple Imputation (MI) try to correct for this drawback, by sampling from the posterior distribution of missing values. On the other hand, these techniques can be less effective when a larger fraction of data is missing @cite_4 , and can be computationally very demanding.
@cite_4 @cite_11
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The predictive analysis of longitudinal social surveys is highly sensitive to the effects of missing data in temporal observations. Such high sensitivity to missing values raises the need for accurate data imputation, because without it a large fraction of collected data could not be used properly. Previous studies focused on the treatment of missing data in longitudinal social networks due to non-respondents and dealt with the problem largely by imputing missing links in isolation or analyzing the imputation effects on network statistics. We propose to account for changing network topology and interdependence between actors' links and attributes to construct a unified approach for imputation of links and attributes in longitudinal social surveys. The new method, based on an exponential random graph model, is evaluated experimentally for five scenarios of missing data models utilizing synthetic and real life datasets with 20 ---60 of nodes missing. The obtained results outperformed all alternatives, four of which were link imputation methods and two node attribute imputation methods. We further discuss the applicability and scalability of our approach to real life problems and compare our model with the latest advancements in the field. Our findings suggest that the proposed method can be used as a viable imputation tool in longitudinal studies. 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. Missing numerical values are prevalent, e.g., owing to unreliable sensor reading, collection and transmission among heterogeneous sources. Unlike categorized data imputation over a limited domain, the numerical values suffer from two issues: (1) sparsity problem, the incomplete tuple may not have sufficient complete neighbors sharing the same similar values for imputation, owing to the (almost) infinite domain; (2) heterogeneity problem, different tuples may not fit the same (regression) model. In this study, enlightened by the conditional dependencies that hold conditionally over certain tuples rather than the whole relation, we propose to learn a regression model individually for each complete tuple together with its neighbors. Our IIM, Imputation via Individual Models, thus no longer relies on sharing similar values among the k complete neighbors for imputation, but utilizes their regression results by the aforesaid learned individual (not necessary the same) models. Remarkably, we show that some existing methods are indeed special cases of our IIM, under the extreme settings of the number l of learning neighbors considered in individual learning. In this sense, a proper number l of neighbors is essential to learn the individual models (avoid over-fitting or under-fitting). We propose to adaptively learn individual models over various number l of neighbors for different complete tuples. By devising efficient incremental computation, the time complexity of learning a model reduces from linear to constant. Experiments on real data demonstrate that our IIM with adaptive learning achieves higher imputation accuracy than the existing approaches. Missing values are a common problem in many real world databases. Inadequate handing of missing data can lead to serious problems in data analysis. A common way to cope with this problem is to use imputation methods to fill missing values with plausible values. This paper proposes GPMI, a multiple imputation method that uses genetic programming as a regression method to estimate missing values. Experiments on eight datasets with six levels of missing values compare GPMI with seven other popular and advanced imputation methods on two measures: the prediction accuracy and the classification accuracy. The results show that, in most cases, GPMI not only achieves better prediction accuracy, but also better classification accuracy than the other imputation methods. We propose a novel method for imputing missing data by adapting the well-known Generative Adversarial Nets (GAN) framework. Accordingly, we call our method Generative Adversarial Imputation Nets (GAIN). The generator (G) observes some components of a real data vector, imputes the missing components conditioned on what is actually observed, and outputs a completed vector. The discriminator (D) then takes a completed vector and attempts to determine which components were actually observed and which were imputed. To ensure that D forces G to learn the desired distribution, we provide D with some additional information in the form of a hint vector. The hint reveals to D partial information about the missingness of the original sample, which is used by D to focus its attention on the imputation quality of particular components. This hint ensures that G does in fact learn to generate according to the true data distribution. We tested our method on various datasets and found that GAIN significantly outperforms state-of-the-art imputation methods. Missing values are a common problem when applying classification algorithms to real-world medical data. This is especially true for trauma patients, where the emergent nature of the cases makes it difficult to collect all of the relevant data for each patient. Standard methods for handling missingness first learn a model to estimate missing data values, and subsequently train and evaluate a classifier using data imputed with this model. Recently, several proposed methods have demonstrated the benefits of jointly estimating the imputation model and classifier parameters. However, these methods make assumptions that limit their utility with many real-world medical datasets. For example, the assumption that data elements are missing at random is often invalid.We address this situation by exploring a novel approach for jointly learning the imputation model and classifier. Unlike previous algorithms, our approach makes no assumptions about the missingness of the data, can be used with arbitrary probabilistic data models and classification loss functions, and can be used when both the training and testing data have missing values. We investigate the utility of this approach on the prediction of several patient outcomes in a large national registry of trauma patients, and find that it significantly outperforms standard sequential methods. A novel algorithm based on random forests with surrogate splits is proposed to address the classification problem of incomplete data without imputation.The algorithm allows each tree to cast a vote even the voting process is interrupted by missing attributes.Experimental results on various acknowledged datasets show that the proposed method is robust and efficient. Random forests (RF) is known as an efficient algorithm in classification, however it depends on the integrity of datasets. Conventional methods in dealing with missing values usually employ estimation and imputation approaches whose efficiency is tied to the assumptions of data features. Recently, algorithm of surrogate decisions in RF was developed and this paper proposes a random forests algorithm with modified surrogate splits (Adjusted Weight Voting Random Forest, AWVRF) which is able to address the incomplete data without imputation.Differing from the present surrogate method, in AWVRF algorithm, when the primary splitting attribute and the surrogate attributes of an internal node are all missing, the undergoing instance is allowed to exit at the current node with a vote. Then the weight of the vote is adjusted by the strength of the involved attributes and the final decision is made by weighted voting. AWVRF does not comprise imputation step, thus it is independent of data features.AWVRF is compared with the methods of mean imputation, LeoFill, knnimpute, BPCAfill and conventional RF with surrogate decisions (surrRF) using 50 times repeated 5-fold cross validation on 10 acknowledged datasets. In a total of 22 experiment settings, the method of AWVRF harvests the highest accuracy in 14 settings and the largest AUC in 7 settings, exhibiting its superiority over other methods. Compared with surrRF, AWVRF is significantly more efficient and remain good discrimination of prediction. Experimental results show that the present AWVRF algorithm can successfully handle the classification task for incomplete data. Missing data is a significant problem impacting all domains. State-of-the-art framework for minimizing missing data bias is multiple imputation, for which the choice of an imputation model remains nontrivial. We propose a multiple imputation model based on overcomplete deep denoising autoencoders. Our proposed model is capable of handling different data types, missingness patterns, missingness proportions and distributions. Evaluation on several real life datasets show our proposed model significantly outperforms current state-of-the-art methods under varying conditions while simultaneously improving end of the line analytics. This paper proposes to utilize information within incomplete instances (instances with missing values) when estimating missing values. Accordingly, a simple and efficient nonparametric iterative imputation algorithm, called the NIIA method, is designed for iteratively imputing missing target values. The NIIA method imputes each missing value several times until the algorithm converges. In the first iteration, all the complete instances are used to estimate missing values. The information within incomplete instances is utilized since the second imputation iteration. We conduct some experiments for evaluating the efficiency, and demonstrate: (1) the utilization of information within incomplete instances is of benefit to easily capture the distribution of a dataset; and (2) the NIIA method outperforms the existing methods in accuracy, and this advantage is clearly highlighted when datasets have a high missing ratio. Missing and corrupted data are ubiquitous in many science and engineering domains. We analyze the information-theoretic limits of recovering sparse vectors under various models of corrupted and missing data. In particular, consider a high-dimensional linear regression model y = X β∗ + є, where y Є Rn is the response vector, X Є RnXp is a random design matrix with p ≫ n and rows distributed i.i.d. as Ν(0, Σ x ), β∗ є Rp is the unknown regression vector, and є ∼ Ν(0,σ2єΙ) is independent additive noise. Whereas a traditional approach assumes that the covariates X are fully observed, we assume only that a corrupted version Z is observed. Our main contribution is to establish minimax rates of convergence for estimating β∗ in squared l 2 -loss, assuming β∗ is k-sparse. Our upper and lower bounds in both additive noise and missing data cases scale as k log(p k) n, with prefactors depending only on the corruption and or missing pattern of the data. Missing data analyses have received considerable recent attention in the methodological literature, and two “modern” methods, multiple imputation and maximum likelihood estimation, are recommended. The goals of this article are to (a) provide an overview of missing-data theory, maximum likelihood estimation, and multiple imputation; (b) conduct a methodological review of missing-data reporting practices in 23 applied research journals; and (c) provide a demonstration of multiple imputation and maximum likelihood estimation using the Longitudinal Study of American Youth data. The results indicated that explicit discussions of missing data increased substantially between 1999 and 2003, but the use of maximum likelihood estimation or multiple imputation was rare; the studies relied almost exclusively on listwise and pairwise deletion. Preface.PART I: OVERVIEW AND BASIC APPROACHES.Introduction.Missing Data in Experiments.Complete-Case and Available-Case Analysis, Including Weighting Methods.Single Imputation Methods.Estimation of Imputation Uncertainty.PART II: LIKELIHOOD-BASED APPROACHES TO THE ANALYSIS OF MISSING DATA.Theory of Inference Based on the Likelihood Function.Methods Based on Factoring the Likelihood, Ignoring the Missing-Data Mechanism.Maximum Likelihood for General Patterns of Missing Data: Introduction and Theory with Ignorable Nonresponse.Large-Sample Inference Based on Maximum Likelihood Estimates.Bayes and Multiple Imputation.PART III: LIKELIHOOD-BASED APPROACHES TO THE ANALYSIS OF MISSING DATA: APPLICATIONS TO SOME COMMON MODELS.Multivariate Normal Examples, Ignoring the Missing-Data Mechanism.Models for Robust Estimation.Models for Partially Classified Contingency Tables, Ignoring the Missing-Data Mechanism.Mixed Normal and Nonnormal Data with Missing Values, Ignoring the Missing-Data Mechanism.Nonignorable Missing-Data Models.References.Author Index.Subject Index. In this paper, we propose a novel method for image inpainting based on a Deep Convolutional Generative Adversarial Network (DCGAN). We define a loss function consisting of two parts: (1) a contextual loss that preserves similarity between the input corrupted image and the recovered image, and (2) a perceptual loss that ensures a perceptually realistic output image. Given a corrupted image with missing values, we use back-propagation on this loss to map the corrupted image to a smaller latent space. The mapped vector is then passed through the generative model to predict the missing content. The proposed framework is evaluated on the CelebA and SVHN datasets for two challenging inpainting tasks with random 80 corruption and large blocky corruption. Experiments show that our method can successfully predict semantic information in the missing region and achieve pixel-level photorealism, which is impossible by almost all existing methods. Recovering low-rank and sparse matrices from incomplete or corrupted observations is an important problem in statistics, machine learning, computer vision, as well as signal and image processing. In theory, this problem can be solved by the natural convex joint mixed relaxations (i.e., l 1 -norm and trace norm) under certain conditions. However, all current provable algorithms suffer from superlinear per-iteration cost, which severely limits their applicability to large-scale problems. In this paper, we propose a scalable, provable and structured robust bilinear factorization (RBF) method to recover low-rank and sparse matrices from missing and grossly corrupted data, i.e., robust matrix completion (RMC), or incomplete and grossly corrupted measurements, i.e., compressive principal component pursuit (CPCP). Specifically, we first present two small-scale matrix trace norm regularized bilinear factorization models for RMC and CPCP problems, in which repetitively calculating SVD of a large-scale matrix is replaced by updating two much smaller factor matrices. Then, we apply the alternating direction method of multipliers (ADMM) to efficiently solve the RMC problems. Finally, we provide the convergence analysis of our algorithm, and extend it to address general CPCP problems. Experimental results verified both the efficiency and effectiveness of our method compared with the state-of-the-art methods. Imputing missing values in high dimensional time-series is a difficult problem. This paper presents a strategy for training energy-based graphical models for imputation directly, bypassing difficulties probabilistic approaches would face. The training strategy is inspired by recent work on optimization-based learning (Domke, 2012) and allows complex neural models with convolutional and recurrent structures to be trained for imputation tasks. In this work, we use this training strategy to derive learning rules for three substantially different neural architectures. Inference in these models is done by either truncated gradient descent or variational mean-field iterations. In our experiments, we found that the training methods outperform the Contrastive Divergence learning algorithm. Moreover, the training methods can easily handle missing values in the training data itself during learning. We demonstrate the performance of this learning scheme and the three models we introduce on one artificial and two real-world data sets. The past decade has seen a noticeable shift in missing data handling techniques that assume a missing at random (MAR) mechanism, where the propensity for missing data on an outcome is related to other analysis variables. Although MAR is often reasonable, there are situations where this assumption is unlikely to hold, leading to biased parameter estimates. One such example is a longitudinal study of substance use where participants with the highest frequency of use also have the highest likelihood of attrition, even after controlling for other correlates of missingness. There is a large body of literature on missing not at random (MNAR) analysis models for longitudinal data, particularly in the field of biostatistics. Because these methods allow for a relationship between the outcome variable and the propensity for missing data, they require a weaker assumption about the missing data mechanism. This article describes 2 classic MNAR modeling approaches for longitudinal data: the selection model and the pattern mixture model. To date, these models have been slow to migrate to the social sciences, in part because they required complicated custom computer programs. These models are now quite easy to estimate in popular structural equation modeling programs, particularly Mplus. The purpose of this article is to describe these MNAR modeling frameworks and to illustrate their application on a real data set. Despite their potential advantages, MNAR-based analyses are not without problems and also rely on untestable assumptions. This article offers practical advice for implementing and choosing among different longitudinal models. The simplest approach to dealing with missing data is to restrict the analysis to complete cases, i.e. individuals with no missing values. This can induce bias, however. Inverse probability weighting (IPW) is a commonly used method to correct this bias. It is also used to adjust for unequal sampling fractions in sample surveys. This article is a review of the use of IPW in epidemiological research. We describe how the bias in the complete-case analysis arises and how IPW can remove it. IPW is compared with multiple imputation (MI) and we explain why, despite MI generally being more efficient, IPW may sometimes be preferred. We discuss the choice of missingness model and methods such as weight truncation, weight stabilisation and augmented IPW. The use of IPW is illustrated on data from the 1958 British Birth Cohort. Suppose an n x d design matrix in a linear regression problem is given, but the response for each point is hidden unless explicitly requested. The goal is to sample only a small number k << n of the responses, and then produce a weight vector whose sum of squares loss over all points is at most 1+epsilon times the minimum. When k is very small (e.g., k=d), jointly sampling diverse subsets of points is crucial. One such method called "volume sampling" has a unique and desirable property that the weight vector it produces is an unbiased estimate of the optimum. It is therefore natural to ask if this method offers the optimal unbiased estimate in terms of the number of responses k needed to achieve a 1+epsilon loss approximation. Surprisingly we show that volume sampling can have poor behavior when we require a very accurate approximation -- indeed worse than some i.i.d. sampling techniques whose estimates are biased, such as leverage score sampling. We then develop a new rescaled variant of volume sampling that produces an unbiased estimate which avoids this bad behavior and has at least as good a tail bound as leverage score sampling: sample size k=O(d log d + d epsilon) suffices to guarantee total loss at most 1+epsilon times the minimum with high probability. Thus, we improve on the best previously known sample size for an unbiased estimator, k=O(d^2 epsilon). Our rescaling procedure leads to a new efficient algorithm for volume sampling which is based on a "determinantal rejection sampling" technique with potentially broader applications to determinantal point processes. Other contributions include introducing the combinatorics needed for rescaled volume sampling and developing tail bounds for sums of dependent random matrices which arise in the process. In a companion paper we described what intuitively would seem to be the most general possible way to generate Coarsening at Random mechanisms, a sequential procedure called randomized monotone coarsening. Counter-examples showed that CAR mechanisms exist which cannot be represented in this way. Here, we further develop these results in two directions. Firstly, we consider what happens when data is coarsened at random in two or more phases. We show that the resulting coarsening mechanism is not CAR anymore, but under suitable assumptions is identified and can provide interesting alternative analysis of data under a non-CAR model. Secondly, we look at sequential mechanisms for generating MAR data, missing components of a multivariate random vector. Randomised monotone missingness schemes, in which one variable at a time is observed and depending on its value, another variable is chosen or the procedure is terminated, supply in our opinion the broadest class of physically interpretable MAR mechanisms. We show that every randomised monotone missingness scheme can be represented by a Markov monotone missingness scheme, in which the choice of which variable to observe next only depends on the set of previously observed variables and their values, not on the sequence in which they were measured. We also show that MAR mechanisms exist which cannot be represented sequentially. A statistical approach to a posteriori blockmodeling for graphs is proposed. The model assumes that the vertices of the graph are partitioned into two unknown blocks and that the probability of an edge between two vertices depends only on the blocks to which they belong. Statistical procedures are derived for estimating the probabilities of edges and for predicting the block structure from observations of the edge pattern only. ML estimators can be computed using the EM algorithm, but this strategy is practical only for small graphs. A Bayesian estimator, based on Gibbs sampling, is proposed. This estimator is practical also for large graphs. When ML estimators are used, the block structure can be predicted based on predictive likelihood. When Gibbs sampling is used, the block structure can be predicted from posterior predictive probabilities. A side result is that when the number of vertices tends to infinity while the probabilities remain constant, the block structure can be recovered correctly with probability tending to 1. (Less)