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Missing data is a crucial issue when applying machine learning algorithms to real-world datasets. Starting from the simple assumption that two batches extracted randomly from the same dataset should share the same distribution, we leverage optimal transport distances to quantify that criterion and turn it into a loss function to impute missing data values. We propose practical methods to minimize these losses using end-to-end learning, that can exploit or not parametric assumptions on the underlying distributions of values. We evaluate our methods on datasets from the UCI repository, in MCAR, MAR and MNAR settings. These experiments show that OT-based methods match or out-perform state-of-the-art imputation methods, even for high percentages of missing values.
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Missing data imputation can help improve the performance of prediction models in situations where missing data hide useful information. This paper compares methods for imputing missing categorical data for supervised classification tasks. We experiment on two machine learning benchmark datasets with missing categorical data, comparing classifiers trained on non-imputed (i.e., one-hot encoded) or imputed data with different levels of additional missing-data perturbation. We show imputation methods can increase predictive accuracy in the presence of missing-data perturbation, which can actually improve prediction accuracy by regularizing the classifier. We achieve the state-of-the-art on the Adult dataset with missing-data perturbation and k-nearest-neighbors (k-NN) imputation.
Several statistical models are given in the form of unnormalized densities, and calculation of the normalization constant is intractable. We propose estimation methods for such unnormalized models with missing data. The key concept is to combine imputation techniques with estimators for unnormalized models including noise contrastive estimation and score matching. In addition, we derive asymptotic distributions of the proposed estimators and construct confidence intervals. Simulation results with truncated Gaussian graphical models and the application to real data of wind direction reveal that the proposed methods effectively enable statistical inference with unnormalized models from missing data.
Missing values challenge data analysis because many supervised and unsupervised learning methods cannot be applied directly to incomplete data. Matrix completion based on low-rank assumptions are very powerful solution for dealing with missing values. However, existing methods do not consider the case of informative missing values which are widely encountered in practice. This paper proposes matrix completion methods to recover Missing Not At Random (MNAR) data. Our first contribution is to suggest a model-based estimation strategy by modelling the missing mechanism distribution. An EM algorithm is then implemented, involving a Fast Iterative Soft-Thresholding Algorithm (FISTA). Our second contribution is to suggest a computationally efficient surrogate estimation by implicitly taking into account the joint distribution of the data and the missing mechanism: the data matrix is concatenated with the mask coding for the missing values; a low-rank structure for exponential family is assumed on this new matrix, in order to encode links between variables and missing mechanisms. The methodology that has the great advantage of handling different missing value mechanisms is robust to model specification errors.The performances of our methods are assessed on the real data collected from a trauma registry (TraumaBase ) containing clinical information about over twenty thousand severely traumatized patients in France. The aim is then to predict if the doctors should administrate tranexomic acid to patients with traumatic brain injury, that would limit excessive bleeding.
How to learn a good predictor on data with missing values? Most efforts focus on first imputing as well as possible and second learning on the completed data to predict the outcome. Yet, this widespread practice has no theoretical grounding. Here we show that for almost all imputation functions, an impute-then-regress procedure with a powerful learner is Bayes optimal. This result holds for all missing-values mechanisms, in contrast with the classic statistical results that require missing-at-random settings to use imputation in probabilistic modeling. Moreover, it implies that perfect conditional imputation may not be needed for good prediction asymptotically. In fact, we show that on perfectly imputed data the best regression function will generally be discontinuous, which makes it hard to learn. Crafting instead the imputation so as to leave the regression function unchanged simply shifts the problem to learning discontinuous imputations. Rather, we suggest that it is easier to learn imputation and regression jointly. We propose such a procedure, adapting NeuMiss, a neural network capturing the conditional links across observed and unobserved variables whatever the missing-value pattern. Experiments confirm that joint imputation and regression through NeuMiss is better than various two step procedures in our experiments with finite number of samples.
Optimal transport is a machine learning problem with applications including distribution comparison, feature selection, and generative adversarial networks. In this paper, we propose feature-robust optimal transport (FROT) for high-dimensional data, which solves high-dimensional OT problems using feature selection to avoid the curse of dimensionality. Specifically, we find a transport plan with discriminative features. To this end, we formulate the FROT problem as a min--max optimization problem. We then propose a convex formulation of the FROT problem and solve it using a Frank--Wolfe-based optimization algorithm, whereby the subproblem can be efficiently solved using the Sinkhorn algorithm. Since FROT finds the transport plan from selected features, it is robust to noise features. To show the effectiveness of FROT, we propose using the FROT algorithm for the layer selection problem in deep neural networks for semantic correspondence. By conducting synthetic and benchmark experiments, we demonstrate that the proposed method can find a strong correspondence by determining important layers. We show that the FROT algorithm achieves state-of-the-art performance in real-world semantic correspondence datasets.
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