Julie Josse

Clément Bénard, Jeffrey Näf, Julie Josse

Distributional Random Forest (DRF) is a flexible forest-based method to estimate the full conditional distribution of a multivariate output of interest given input variables. In this article, we introduce a variable importance algorithm for DRFs, based on the well-established drop and relearn principle and MMD distance. While traditional importance measures only detect variables with an influence on the output mean, our algorithm detects variables impacting the output distribution more generally. We show that the introduced importance measure is consistent, exhibits high empirical performance on both real and simulated data, and outperforms competitors. In particular, our algorithm is highly efficient to select variables through recursive feature elimination, and can therefore provide small sets of variables to build accurate estimates of conditional output distributions.

Rémi Khellaf, Aurélien Bellet, Julie Josse

We study Federated Causal Inference, an approach to estimate treatment effects from decentralized data across centers. We compare three classes of Average Treatment Effect (ATE) estimators derived from the Plug-in G-Formula, ranging from simple meta-analysis to one-shot and multi-shot federated learning, the latter leveraging the full data to learn the outcome model (albeit requiring more communication). Focusing on Randomized Controlled Trials (RCTs), we derive the asymptotic variance of these estimators for linear models. Our results provide practical guidance on selecting the appropriate estimator for various scenarios, including heterogeneity in sample sizes, covariate distributions, treatment assignment schemes, and center effects. We validate these findings with a simulation study.

Linus Bleistein, Aurélien Bellet, Julie Josse

We consider the problem of solving the optimal transport problem between two empirical distributions with missing values. Our main assumption is that the data is missing completely at random (MCAR), but we allow for heterogeneous missingness probabilities across features and across the two distributions. As a first contribution, we show that the Wasserstein distance between empirical Gaussian distributions and linear Monge maps between arbitrary distributions can be debiased without significantly affecting the sample complexity. Secondly, we show that entropic regularized optimal transport can be estimated efficiently and consistently using iterative singular value thresholding (ISVT). We propose a validation set-free hyperparameter selection strategy for ISVT that leverages our estimator of the Bures-Wasserstein distance, which could be of independent interest in general matrix completion problems. Finally, we validate our findings on a wide range of numerical applications.

Lena Stempfle, Arthur James, Julie Josse et al.

Inherently interpretable machine learning (IML) models offer valuable support for clinical decision-making but face challenges when features contain missing values. Traditional approaches, such as imputation or discarding incomplete records, are often impractical in scenarios where data is missing at test time. We surveyed 55 clinicians from 29 French trauma centers, collecting 20 complete responses to study their interaction with three IML models in a real-world clinical setting for predicting hemorrhagic shock with missing values. Our findings reveal that while clinicians recognize the value of interpretability and are familiar with common IML approaches, traditional imputation techniques often conflict with their intuition. Instead of imputing unobserved values, they rely on observed features combined with medical intuition and experience. As a result, methods that natively handle missing values are preferred. These findings underscore the need to integrate clinical reasoning into future IML models to enhance human-computer interaction.

Christophe Muller, Erwan Scornet, Julie Josse

Predicting a response with partially missing inputs remains a challenging task even in parametric models, since parameter estimation in itself is not sufficient to predict on partially observed inputs. Several works study prediction in linear models. In this paper, we focus on logistic models, which present their own difficulties. From a theoretical perspective, we prove that a Pattern-by-Pattern strategy (PbP), which learns one logistic model per missingness pattern, accurately approximates Bayes probabilities in various missing data scenarios (MCAR, MAR and MNAR). Empirically, we thoroughly compare various methods (constant and iterative imputations, complete case analysis, PbP, and an EM algorithm) across classification, probability estimation, calibration, and parameter inference. Our analysis provides a comprehensive view on the logistic regression with missing values. It reveals that mean imputation can be used as baseline for low sample sizes, and improved performance is obtained via nonlinear multiple iterative imputation techniques with the labels (MICE.RF.Y). For large sample sizes, PbP is the best method for Gaussian mixtures, and we recommend MICE.RF.Y in presence of nonlinear features.

Aude Sportisse, Matthieu Marbac, Fabien Laporte et al.

Model-based unsupervised learning, as any learning task, stalls as soon as missing data occurs. This is even more true when the missing data are informative, or said missing not at random (MNAR). In this paper, we propose model-based clustering algorithms designed to handle very general types of missing data, including MNAR data. To do so, we introduce a mixture model for different types of data (continuous, count, categorical and mixed) to jointly model the data distribution and the MNAR mechanism, remaining vigilant to the relative degrees of freedom of each. Several MNAR models are discussed, for which the cause of the missingness can depend on both the values of the missing variable themselves and on the class membership. However, we focus on a specific MNAR model, called MNARz, for which the missingness only depends on the class membership. We first underline its ease of estimation, by showing that the statistical inference can be carried out on the data matrix concatenated with the missing mask considering finally a standard MAR mechanism. Consequently, we propose to perform clustering using the Expectation Maximization algorithm, specially developed for this simplified reinterpretation. Finally, we assess the numerical performances of the proposed methods on synthetic data and on the real medical registry TraumaBase as well.

Marine Le Morvan, Julie Josse, Erwan Scornet et al.

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 is not 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.

Marine Le Morvan, Julie Josse, Thomas Moreau et al.

The presence of missing values makes supervised learning much more challenging. Indeed, previous work has shown that even when the response is a linear function of the complete data, the optimal predictor is a complex function of the observed entries and the missingness indicator. As a result, the computational or sample complexities of consistent approaches depend on the number of missing patterns, which can be exponential in the number of dimensions. In this work, we derive the analytical form of the optimal predictor under a linearity assumption and various missing data mechanisms including Missing at Random (MAR) and self-masking (Missing Not At Random). Based on a Neumann-series approximation of the optimal predictor, we propose a new principled architecture, named NeuMiss networks. Their originality and strength come from the use of a new type of non-linearity: the multiplication by the missingness indicator. We provide an upper bound on the Bayes risk of NeuMiss networks, and show that they have good predictive accuracy with both a number of parameters and a computational complexity independent of the number of missing data patterns. As a result they scale well to problems with many features, and remain statistically efficient for medium-sized samples. Moreover, we show that, contrary to procedures using EM or imputation, they are robust to the missing data mechanism, including difficult MNAR settings such as self-masking.

Pascaline Descloux, Claire Boyer, Julie Josse et al.

We propose Robust Lasso-Zero, an extension of the Lasso-Zero methodology, initially introduced for sparse linear models, to the sparse corruptions problem. We give theoretical guarantees on the sign recovery of the parameters for a slightly simplified version of the estimator, called Thresholded Justice Pursuit. The use of Robust Lasso-Zero is showcased for variable selection with missing values in the covariates. In addition to not requiring the specification of a model for the covariates, nor estimating their covariance matrix or the noise variance, the method has the great advantage of handling missing not-at random values without specifying a parametric model. Numerical experiments and a medical application underline the relevance of Robust Lasso-Zero in such a context with few available competitors. The method is easy to use and implemented in the R library lass0.

Imke Mayer, Julie Josse, Félix Raimundo et al.

Inferring causal effects of a treatment, intervention or policy from observational data is central to many applications. However, state-of-the-art methods for causal inference seldom consider the possibility that covariates have missing values, which is ubiquitous in many real-world analyses. Missing data greatly complicate causal inference procedures as they require an adapted unconfoundedness hypothesis which can be difficult to justify in practice. We circumvent this issue by considering latent confounders whose distribution is learned through variational autoencoders adapted to missing values. They can be used either as a pre-processing step prior to causal inference but we also suggest to embed them in a multiple imputation strategy to take into account the variability due to missing values. Numerical experiments demonstrate the effectiveness of the proposed methodology especially for non-linear models compared to competitors.

Boris Muzellec, Julie Josse, Claire Boyer et al.

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.

Julie Josse, Jacob M. Chen, Nicolas Prost et al.

In many application settings, the data have missing entries which make analysis challenging. An abundant literature addresses missing values in an inferential framework: estimating parameters and their variance from incomplete tables. Here, we consider supervised-learning settings: predicting a target when missing values appear in both training and testing data. We show the consistency of two approaches in prediction. A striking result is that the widely-used method of imputing with a constant, such as the mean prior to learning is consistent when missing values are not informative. This contrasts with inferential settings where mean imputation is pointed at for distorting the distribution of the data. That such a simple approach can be consistent is important in practice. We also show that a predictor suited for complete observations can predict optimally on incomplete data, through multiple imputation. Finally, to compare imputation with learning directly with a model that accounts for missing values, we analyze further decision trees. These can naturally tackle empirical risk minimization with missing values, due to their ability to handle the half-discrete nature of incomplete variables. After comparing theoretically and empirically different missing values strategies in trees, we recommend using the "missing incorporated in attribute" method as it can handle both non-informative and informative missing values.

Aude Sportisse, Claire Boyer, Julie Josse

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.

Geneviève Robin, Hoi-To Wai, Julie Josse et al.

Many applications of machine learning involve the analysis of large data frames-matrices collecting heterogeneous measurements (binary, numerical, counts, etc.) across samples-with missing values. Low-rank models, as studied by Udell et al. [30], are popular in this framework for tasks such as visualization, clustering and missing value imputation. Yet, available methods with statistical guarantees and efficient optimization do not allow explicit modeling of main additive effects such as row and column, or covariate effects. In this paper, we introduce a low-rank interaction and sparse additive effects (LORIS) model which combines matrix regression on a dictionary and low-rank design, to estimate main effects and interactions simultaneously. We provide statistical guarantees in the form of upper bounds on the estimation error of both components. Then, we introduce a mixed coordinate gradient descent (MCGD) method which provably converges sub-linearly to an optimal solution and is computationally efficient for large scale data sets. We show on simulated and survey data that the method has a clear advantage over current practices, which consist in dealing separately with additive effects in a preprocessing step.

Julie Josse, Stefan Wager

We develop a flexible framework for low-rank matrix estimation that allows us to transform noise models into regularization schemes via a simple bootstrap algorithm. Effectively, our procedure seeks an autoencoding basis for the observed matrix that is stable with respect to the specified noise model; we call the resulting procedure a stable autoencoder. In the simplest case, with an isotropic noise model, our method is equivalent to a classical singular value shrinkage estimator. For non-isotropic noise models, e.g., Poisson noise, the method does not reduce to singular value shrinkage, and instead yields new estimators that perform well in experiments. Moreover, by iterating our stable autoencoding scheme, we can automatically generate low-rank estimates without specifying the target rank as a tuning parameter.