arXiv subjects

Anton Rask Lundborg

Publications and source records attributed to Anton Rask Lundborg.

8 recordsLinked to original sources

arXiv2026

Perturbation-based Effect Measures for Compositional Data

Existing effect measures for compositional features are inadequate for many modern applications, for example, in microbiome research, since they display traits such as high-dimensionality and sparsity that can be poorly modelled with traditional parametric approaches. Further, assessing -- in an unbiased way -- how summary statistics of a composition (e.g., racial diversity) affect a response variable is not straightforward. We propose a framework based on hypothetical data perturbations which defines interpretable statistical functionals on the compositions themselves, which we call average perturbation effects. These effects naturally account for confounding that biases frequently used marginal dependence analyses. We show how average perturbation effects can be estimated efficiently by deriving a perturbation-dependent reparametrization and applying semiparametric estimation techniques. We analyze the proposed estimators empirically on simulated and semi-synthetic data and demonstrate advantages over existing techniques on data from New York schools and microbiome data.

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arXiv2026

Outcome-adapted Automatic Debiased Machine Learning

Parameters of interest in causal inference, such as treatment or policy effects, can often be expressed as linear functionals of an outcome regression function. Automatic debiased machine learning (AutoDML) is a unified framework for obtaining asymptotically normal estimators of such parameters, which requires estimation of both a regression function and a Riesz representer. Existing AutoDML neural network architectures, such as RieszNet and MADNet, use a shared intermediate covariate representation. However, it remains unclear whether this shared representation should be predictive of the Riesz representer or the outcome. We show that a shared representation of the covariates that preserves predictive power of the outcome while discarding information about the Riesz representer is asymptotically more efficient than the baseline AutoDML estimator that uses all covariates. Motivated by these results, we propose the outcome-adapted AutoDML estimator and establish its asymptotic behavior in a sample splitting framework. We provide a neural network implementation of the estimator that learns a sparse representation of the covariates that is predictive of the outcome but not predictive of the Riesz representer. We demonstrate the efficiency gains of our estimator over existing alternatives on synthetic data and achieve state-of-the-art estimation accuracy on the semi-synthetic IHDP benchmark dataset.

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arXiv2025

Efficient adjustment for complex covariates: Gaining efficiency with DOPE

Covariate adjustment is a ubiquitous method used to estimate the average treatment effect (ATE) from observational data. Assuming a known graphical structure of the data generating model, recent results give graphical criteria for optimal adjustment, which enables efficient estimation of the ATE. However, graphical approaches are challenging for high-dimensional and complex data, and it is not straightforward to specify a meaningful graphical model of non-Euclidean data such as texts. We propose a new framework that accommodates adjustment for any subset of information expressed by the covariates, and we show that the information that is minimally sufficient for prediction of the outcome given the treatment is also most efficient for adjustment. Based on our theoretical results, we propose the Debiased Outcome-adapted Propensity Estimator (DOPE) for efficient estimation of the ATE, and we provide asymptotic results for DOPE under general conditions. Compared to the augmented inverse propensity weighted (AIPW) estimator, DOPE can retain its efficiency even when the covariates are highly predictive of treatment. We illustrate this with a single-index model, and with an implementation of DOPE based on neural networks, we demonstrate its performance on simulated and real data. Our results show that DOPE provides an efficient and robust methodology for ATE estimation in various observational settings.

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arXiv2024

Algorithm-agnostic significance testing in supervised learning with multimodal data

Valid statistical inference is crucial for decision-making but difficult to obtain in supervised learning with multimodal data, e.g., combinations of clinical features, genomic data, and medical images. Multimodal data often warrants the use of black-box algorithms, for instance, random forests or neural networks, which impede the use of traditional variable significance tests. We address this problem by proposing the use of COvariance Measure Tests (COMETs), which are calibrated and powerful tests that can be combined with any sufficiently predictive supervised learning algorithm. We apply COMETs to several high-dimensional, multimodal data sets to illustrate (i) variable significance testing for finding relevant mutations modulating drug-activity, (ii) modality selection for predicting survival in liver cancer patients with multiomics data, and (iii) modality selection with clinical features and medical imaging data. In all applications, COMETs yield results consistent with domain knowledge without requiring data-driven pre-processing which may invalidate type I error control. These novel applications with high-dimensional multimodal data corroborate prior results on the power and robustness of COMETs for significance testing. COMETs are implemented in the comets R package available on CRAN and pycomets Python library available on GitHub. Source code for reproducing all results is available at https://github.com/LucasKook/comets. All data sets used in this work are openly available.

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arXiv2024

Model-based causal feature selection for general response types

Discovering causal relationships from observational data is a fundamental yet challenging task. Invariant causal prediction (ICP, Peters et al., 2016) is a method for causal feature selection which requires data from heterogeneous settings and exploits that causal models are invariant. ICP has been extended to general additive noise models and to nonparametric settings using conditional independence tests. However, the latter often suffer from low power (or poor type I error control) and additive noise models are not suitable for applications in which the response is not measured on a continuous scale, but reflects categories or counts. Here, we develop transformation-model (TRAM) based ICP, allowing for continuous, categorical, count-type, and uninformatively censored responses (these model classes, generally, do not allow for identifiability when there is no exogenous heterogeneity). As an invariance test, we propose TRAM-GCM based on the expected conditional covariance between environments and score residuals with uniform asymptotic level guarantees. For the special case of linear shift TRAMs, we also consider TRAM-Wald, which tests invariance based on the Wald statistic. We provide an open-source R package 'tramicp' and evaluate our approach on simulated data and in a case study investigating causal features of survival in critically ill patients.

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arXiv2024

The Projected Covariance Measure for assumption-lean variable significance testing

Testing the significance of a variable or group of variables $X$ for predicting a response $Y$, given additional covariates $Z$, is a ubiquitous task in statistics. A simple but common approach is to specify a linear model, and then test whether the regression coefficient for $X$ is non-zero. However, when the model is misspecified, the test may have poor power, for example when $X$ is involved in complex interactions, or lead to many false rejections. In this work we study the problem of testing the model-free null of conditional mean independence, i.e. that the conditional mean of $Y$ given $X$ and $Z$ does not depend on $X$. We propose a simple and general framework that can leverage flexible nonparametric or machine learning methods, such as additive models or random forests, to yield both robust error control and high power. The procedure involves using these methods to perform regressions, first to estimate a form of projection of $Y$ on $X$ and $Z$ using one half of the data, and then to estimate the expected conditional covariance between this projection and $Y$ on the remaining half of the data. While the approach is general, we show that a version of our procedure using spline regression achieves what we show is the minimax optimal rate in this nonparametric testing problem. Numerical experiments demonstrate the effectiveness of our approach both in terms of maintaining Type I error control, and power, compared to several existing approaches.

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arXiv2023

Confounder Selection: Objectives and Approaches

Confounder selection is perhaps the most important step in the design of observational studies. A number of criteria, often with different objectives and approaches, have been proposed, and their validity and practical value have been debated in the literature. Here, we provide a unified review of these criteria and the assumptions behind them. We list several objectives that confounder selection methods aim to achieve and discuss the amount of structural knowledge required by different approaches. Finally, we discuss limitations of the existing approaches and implications for practitioners.

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arXiv2022

Conditional Independence Testing in Hilbert Spaces with Applications to Functional Data Analysis

We study the problem of testing the null hypothesis that X and Y are conditionally independent given Z, where each of X, Y and Z may be functional random variables. This generalises testing the significance of X in a regression model of scalar response Y on functional regressors X and Z. We show however that even in the idealised setting where additionally (X, Y, Z) has a Gaussian distribution, the power of any test cannot exceed its size. Further modelling assumptions are needed and we argue that a convenient way of specifying these is based on choosing methods for regressing each of X and Y on Z. We propose a test statistic involving inner products of the resulting residuals that is simple to compute and calibrate: type I error is controlled uniformly when the in-sample prediction errors are sufficiently small. We show this requirement is met by ridge regression in functional linear model settings without requiring any eigen-spacing conditions or lower bounds on the eigenvalues of the covariance of the functional regressor. We apply our test in constructing confidence intervals for truncation points in truncated functional linear models and testing for edges in a functional graphical model for EEG data.

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