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Niki Kilbertus

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22 papers

2 author rows

NeurIPS Conference 2025 Conference Paper

An Analysis of Causal Effect Estimation using Outcome Invariant Data Augmentation

Uzair Akbar
Niki Kilbertus
Hao Shen
Krikamol Muandet
Bo Dai

The technique of data augmentation (DA) is often used in machine learning for regularization purposes to better generalize under i. i. d. settings. In this work, we present a unifying framework with topics in causal inference to make a case for the use of DA beyond just the i. i. d. setting, but for generalization across interventions as well. Specifically, we argue that when the outcome generating mechanism is invariant to our choice of DA, then such augmentations can effectively be thought of as interventions on the treatment generating mechanism itself. This can potentially help to reduce bias in causal effect estimation arising from hidden confounders. In the presence of such unobserved confounding we typically make use of instrumental variables (IVs)—sources of treatment randomization that are conditionally independent of the outcome. However, IVs may not be as readily available as DA for many applications, which is the main motivation behind this work. By appropriately regularizing IV based estimators, we introduce the concept of IV-like (IVL) regression for mitigating confounding bias and improving predictive performance across interventions even when certain IV properties are relaxed. Finally, we cast parameterized DA as an IVL regression problem and show that when used in composition can simulate a worst-case application of such DA, further improving performance on causal estimation and generalization tasks beyond what simple DA may offer. This is shown both theoretically for the population case and via simulation experiments for the finite sample case using a simple linear example. We also present real data experiments to support our case.

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ICML Conference 2025 Conference Paper

Generative Intervention Models for Causal Perturbation Modeling

Nora Schneider
Lars Lorch
Niki Kilbertus
Bernhard Schölkopf
Andreas Krause 0001

We consider the problem of predicting perturbation effects via causal models. In many applications, it is a priori unknown which mechanisms of a system are modified by an external perturbation, even though the features of the perturbation are available. For example, in genomics, some properties of a drug may be known, but not their causal effects on the regulatory pathways of cells. We propose a generative intervention model (GIM) that learns to map these perturbation features to distributions over atomic interventions in a jointly-estimated causal model. Contrary to prior approaches, this enables us to predict the distribution shifts of unseen perturbation features while gaining insights about their mechanistic effects in the underlying data-generating process. On synthetic data and scRNA-seq drug perturbation data, GIMs achieve robust out-of-distribution predictions on par with unstructured approaches, while effectively inferring the underlying perturbation mechanisms, often better than other causal inference methods.

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ICML Conference 2025 Conference Paper

Learning Representations of Instruments for Partial Identification of Treatment Effects

Jonas Schweisthal
Dennis Frauen
Maresa Schröder
Konstantin Hess
Niki Kilbertus
Stefan Feuerriegel

Reliable estimation of treatment effects from observational data is important in many disciplines such as medicine. However, estimation is challenging when unconfoundedness as a standard assumption in the causal inference literature is violated. In this work, we leverage arbitrary (potentially high-dimensional) instruments to estimate bounds on the conditional average treatment effect (CATE). Our contributions are three-fold: (1) We propose a novel approach for partial identification through a mapping of instruments to a discrete representation space so that we yield valid bounds on the CATE. This is crucial for reliable decision-making in real-world applications. (2) We derive a two-step procedure that learns tight bounds using a tailored neural partitioning of the latent instrument space. As a result, we avoid instability issues due to numerical approximations or adversarial training. Furthermore, our procedure aims to reduce the estimation variance in finite-sample settings to yield more reliable estimates. (3) We show theoretically that our procedure obtains valid bounds while reducing estimation variance. We further perform extensive experiments to demonstrate the effectiveness across various settings. Overall, our procedure offers a novel path for practitioners to make use of potentially high-dimensional instruments (e. g. , as in Mendelian randomization).

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ICLR Conference 2025 Conference Paper

Signature Kernel Conditional Independence Tests in Causal Discovery for Stochastic Processes

Georg Manten
Cecilia Casolo
Emilio Ferrucci
Søren Wengel Mogensen
Cristopher Salvi
Niki Kilbertus

Inferring the causal structure underlying stochastic dynamical systems from observational data holds great promise in domains ranging from science and health to finance. Such processes can often be accurately modeled via stochastic differential equations (SDEs), which naturally imply causal relationships via `which variables enter the differential of which other variables'. In this paper, we develop conditional independence (CI) constraints on coordinate processes over selected intervals that are Markov with respect to the acyclic dependence graph (allowing self-loops) induced by a general SDE model. We then provide a sound and complete causal discovery algorithm, capable of handling both fully and partially observed data, and uniquely recovering the underlying or induced ancestral graph by exploiting time directionality assuming a CI oracle. Finally, to make our algorithm practically usable, we also propose a flexible, consistent signature kernel-based CI test to infer these constraints from data. We extensively benchmark the CI test in isolation and as part of our causal discovery algorithms, outperforming existing approaches in SDE models and beyond.

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AAAI Conference 2025 Conference Paper

Whole Genome Transformer for Gene Interaction Effects in Microbiome Habitat Specificity

Zhufeng Li
Sandeep Suresh Cranganore
Nicholas Youngblut
Niki Kilbertus

Leveraging the vast genetic diversity within microbiomes offers unparalleled insights into complex phenotypes, yet the task of accurately predicting and understanding such traits from genomic data remains challenging. We propose a framework taking advantage of existing large models for gene vectorization to predict habitat specificity from entire microbial genome sequences. Based on our model, we develop attribution techniques to elucidate gene interaction effects that drive microbial adaptation to diverse environments. We train and validate our approach on a large dataset of high quality microbiome genomes from different habitats. We not only demonstrate solid predictive performance, but also how sequence-level information of entire genomes allows us to identify gene associations underlying complex phenotypes. Our attribution recovers known important interaction networks and proposes new candidates for experimental follow up.

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TMLR Journal 2024 Journal Article

Learning Counterfactually Invariant Predictors

Francesco Quinzan
Cecilia Casolo
Krikamol Muandet
Yucen Luo
Niki Kilbertus

Notions of counterfactual invariance (CI) have proven essential for predictors that are fair, robust, and generalizable in the real world. We propose graphical criteria that yield a sufficient condition for a predictor to be counterfactually invariant in terms of a conditional independence in the observational distribution. In order to learn such predictors, we propose a model-agnostic framework, called Counterfactually Invariant Prediction (CIP), building on the Hilbert-Schmidt Conditional Independence Criterion (HSCIC), a kernel-based conditional dependence measure. Our experimental results demonstrate the effectiveness of CIP in enforcing counterfactual invariance across various simulated and real-world datasets including scalar and multi-variate settings.

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ICLR Conference 2024 Conference Paper

ODEFormer: Symbolic Regression of Dynamical Systems with Transformers

Stéphane d'Ascoli
Sören Becker
Philippe Schwaller
Alexander Mathis
Niki Kilbertus

We introduce ODEFormer, the first transformer able to infer multidimensional ordinary differential equation (ODE) systems in symbolic form from the observation of a single solution trajectory. We perform extensive evaluations on two datasets: (i) the existing ‘Strogatz’ dataset featuring two-dimensional systems; (ii) ODEBench, a collection of one- to four-dimensional systems that we carefully curated from the literature to provide a more holistic benchmark. ODEFormer consistently outperforms existing methods while displaying substantially improved robustness to noisy and irregularly sampled observations, as well as faster inference. We release our code, model and benchmark at https://github.com/sdascoli/odeformer.

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NeurIPS Conference 2024 Conference Paper

Targeted Sequential Indirect Experiment Design

Elisabeth Ailer
Niclas Dern
Jason Hartford
Niki Kilbertus

Scientific hypotheses typically concern specific aspects of complex, imperfectly understood or entirely unknown mechanisms, such as the effect of gene expression levels on phenotypes or how microbial communities influence environmental health. Such queries are inherently causal (rather than purely associational), but in many settings, experiments can not be conducted directly on the target variables of interest, but are indirect. Therefore, they perturb the target variable, but do not remove potential confounding factors. If, additionally, the resulting experimental measurements are high-dimensional and the studied mechanisms nonlinear, the query of interest is generally not identified. We develop an adaptive strategy to design indirect experiments that optimally inform a targeted query about the ground truth mechanism in terms of sequentially narrowing the gap between an upper and lower bound on the query. While the general formulation consists of a bi-level optimization procedure, we derive an efficiently estimable analytical kernel-based estimator of the bounds for the causal effect, a query of key interest, and demonstrate the efficacy of our approach in confounded, multivariate, nonlinear synthetic settings.

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ICLR Conference 2024 Conference Paper

Unbalancedness in Neural Monge Maps Improves Unpaired Domain Translation

Luca Eyring
Dominik Klein 0005
Théo Uscidda
Giovanni Palla
Niki Kilbertus
Zeynep Akata
Fabian J. Theis

In optimal transport (OT), a Monge map is known as a mapping that transports a source distribution to a target distribution in the most cost-efficient way. Recently, multiple neural estimators for Monge maps have been developed and applied in diverse unpaired domain translation tasks, e.g. in single-cell biology and computer vision. However, the classic OT framework enforces mass conservation, which makes it prone to outliers and limits its applicability in real-world scenarios. The latter can be particularly harmful in OT domain translation tasks, where the relative position of a sample within a distribution is explicitly taken into account. While unbalanced OT tackles this challenge in the discrete setting, its integration into neural Monge map estimators has received limited attention. We propose a theoretically grounded method to incorporate unbalancedness into any Monge map estimator. We improve existing estimators to model cell trajectories over time and to predict cellular responses to perturbations. Moreover, our approach seamlessly integrates with the OT flow matching (OT-FM) framework. While we show that OT-FM performs competitively in image translation, we further improve performance by incorporating unbalancedness (UOT-FM), which better preserves relevant features. We hence establish UOT-FM as a principled method for unpaired image translation.

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ICLR Conference 2023 Conference Paper

Modeling content creator incentives on algorithm-curated platforms

Jiri Hron
Karl Krauth
Michael I. Jordan
Niki Kilbertus
Sarah Dean

Content creators compete for user attention. Their reach crucially depends on algorithmic choices made by developers on online platforms. To maximize exposure, many creators adapt strategically, as evidenced by examples like the sprawling search engine optimization industry. This begets competition for the finite user attention pool. We formalize these dynamics in what we call an exposure game, a model of incentives induced by modern algorithms including factorization and (deep) two-tower architectures. We prove that seemingly innocuous algorithmic choices—e.g., non-negative vs. unconstrained factorization—significantly affect the existence and character of (Nash) equilibria in exposure games. We proffer use of creator behavior models like ours for an (ex-ante) pre-deployment audit. Such an audit can identify misalignment between desirable and incentivized content, and thus complement post-hoc measures like content filtering and moderation. To this end, we propose tools for numerically finding equilibria in exposure games, and illustrate results of an audit on the MovieLens and LastFM datasets. Among else, we find that the strategically produced content exhibits strong dependence between algorithmic exploration and content diversity, and between model expressivity and bias towards gender-based user and creator groups.

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ICML Conference 2023 Conference Paper

Predicting Ordinary Differential Equations with Transformers

Sören Becker
Michal Klein
Alexander Neitz
Giambattista Parascandolo
Niki Kilbertus

We develop a transformer-based sequence-to-sequence model that recovers scalar ordinary differential equations (ODEs) in symbolic form from irregularly sampled and noisy observations of a single solution trajectory. We demonstrate in extensive empirical evaluations that our model performs better or on par with existing methods in terms of accurate recovery across various settings. Moreover, our method is efficiently scalable: after one-time pretraining on a large set of ODEs, we can infer the governing law of a new observed solution in a few forward passes of the model.

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ICML Conference 2023 Conference Paper

Sequential Underspecified Instrument Selection for Cause-Effect Estimation

Elisabeth Ailer
Jason S. Hartford
Niki Kilbertus

Instrumental variable (IV) methods are used to estimate causal effects in settings with unobserved confounding, where we cannot directly experiment on the treatment variable. Instruments are variables which only affect the outcome indirectly via the treatment variable(s). Most IV applications focus on low-dimensional treatments and crucially require at least as many instruments as treatments. This assumption is restrictive: in the natural sciences we often seek to infer causal effects of high-dimensional treatments (e. g. , the effect of gene expressions or microbiota on health and disease), but can only run few experiments with a limited number of instruments (e. g. , drugs or antibiotics). In such under-specified problems, the full treatment effect is not identifiable in a single experiment even in the linear case. We show that one can still reliably recover the projection of the treatment effect onto the instrumented subspace and develop techniques to consistently combine such partial estimates from different sets of instruments. We then leverage our combined estimators in an algorithm that iteratively proposes the most informative instruments at each round of experimentation to maximize the overall information about the full causal effect.

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NeurIPS Conference 2023 Conference Paper

Stabilized Neural Differential Equations for Learning Dynamics with Explicit Constraints

Alistair White
Niki Kilbertus
Maximilian Gelbrecht
Niklas Boers

Many successful methods to learn dynamical systems from data have recently been introduced. However, ensuring that the inferred dynamics preserve known constraints, such as conservation laws or restrictions on the allowed system states, remains challenging. We propose stabilized neural differential equations (SNDEs), a method to enforce arbitrary manifold constraints for neural differential equations. Our approach is based on a stabilization term that, when added to the original dynamics, renders the constraint manifold provably asymptotically stable. Due to its simplicity, our method is compatible with all common neural differential equation (NDE) models and broadly applicable. In extensive empirical evaluations, we demonstrate that SNDEs outperform existing methods while broadening the types of constraints that can be incorporated into NDE training.

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NeurIPS Conference 2022 Conference Paper

Predicting Cellular Responses to Novel Drug Perturbations at a Single-Cell Resolution

Leon Hetzel
Simon Boehm
Niki Kilbertus
Stephan Günnemann
mohammad lotfollahi
Fabian Theis

Single-cell transcriptomics enabled the study of cellular heterogeneity in response to perturbations at the resolution of individual cells. However, scaling high-throughput screens (HTSs) to measure cellular responses for many drugs remains a challenge due to technical limitations and, more importantly, the cost of such multiplexed experiments. Thus, transferring information from routinely performed bulk RNA HTS is required to enrich single-cell data meaningfully. We introduce chemCPA, a new encoder-decoder architecture to study the perturbational effects of unseen drugs. We combine the model with an architecture surgery for transfer learning and demonstrate how training on existing bulk RNA HTS datasets can improve generalisation performance. Better generalisation reduces the need for extensive and costly screens at single-cell resolution. We envision that our proposed method will facilitate more efficient experiment designs through its ability to generate in-silico hypotheses, ultimately accelerating drug discovery.

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NeurIPS Conference 2022 Conference Paper

Sparsity in Continuous-Depth Neural Networks

Hananeh Aliee
Till Richter
Mikhail Solonin
Ignacio Ibarra
Fabian Theis
Niki Kilbertus

Neural Ordinary Differential Equations (NODEs) have proven successful in learning dynamical systems in terms of accurately recovering the observed trajectories. While different types of sparsity have been proposed to improve robustness, the generalization properties of NODEs for dynamical systems beyond the observed data are underexplored. We systematically study the influence of weight and feature sparsity on forecasting as well as on identifying the underlying dynamical laws. Besides assessing existing methods, we propose a regularization technique to sparsify ``input-output connections'' and extract relevant features during training. Moreover, we curate real-world datasets including human motion capture and human hematopoiesis single-cell RNA-seq data to realistically analyze different levels of out-of-distribution (OOD) generalization in forecasting and dynamics identification respectively. Our extensive empirical evaluation on these challenging benchmarks suggests that weight sparsity improves generalization in the presence of noise or irregular sampling. However, it does not prevent learning spurious feature dependencies in the inferred dynamics, rendering them impractical for predictions under interventions, or for inferring the true underlying dynamics. Instead, feature sparsity can indeed help with recovering sparse ground-truth dynamics compared to unregularized NODEs.

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NeurIPS Conference 2021 Conference Paper

On Component Interactions in Two-Stage Recommender Systems

Jiri Hron
Karl Krauth
Michael Jordan
Niki Kilbertus

Thanks to their scalability, two-stage recommenders are used by many of today's largest online platforms, including YouTube, LinkedIn, and Pinterest. These systems produce recommendations in two steps: (i) multiple nominators—tuned for low prediction latency—preselect a small subset of candidates from the whole item pool; (ii) a slower but more accurate ranker further narrows down the nominated items, and serves to the user. Despite their popularity, the literature on two-stage recommenders is relatively scarce, and the algorithms are often treated as mere sums of their parts. Such treatment presupposes that the two-stage performance is explained by the behavior of the individual components in isolation. This is not the case: using synthetic and real-world data, we demonstrate that interactions between the ranker and the nominators substantially affect the overall performance. Motivated by these findings, we derive a generalization lower bound which shows that independent nominator training can lead to performance on par with uniformly random recommendations. We find that careful design of item pools, each assigned to a different nominator, alleviates these issues. As manual search for a good pool allocation is difficult, we propose to learn one instead using a Mixture-of-Experts based approach. This significantly improves both precision and recall at $K$.

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ICML Conference 2021 Conference Paper

On Disentangled Representations Learned from Correlated Data

Frederik Träuble
Elliot Creager
Niki Kilbertus
Francesco Locatello
Andrea Dittadi
Anirudh Goyal
Bernhard Schölkopf
Stefan Bauer

The focus of disentanglement approaches has been on identifying independent factors of variation in data. However, the causal variables underlying real-world observations are often not statistically independent. In this work, we bridge the gap to real-world scenarios by analyzing the behavior of the most prominent disentanglement approaches on correlated data in a large-scale empirical study (including 4260 models). We show and quantify that systematically induced correlations in the dataset are being learned and reflected in the latent representations, which has implications for downstream applications of disentanglement such as fairness. We also demonstrate how to resolve these latent correlations, either using weak supervision during training or by post-hoc correcting a pre-trained model with a small number of labels.

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NeurIPS Conference 2020 Conference Paper

A Class of Algorithms for General Instrumental Variable Models

Niki Kilbertus
Matt J. Kusner
Ricardo Silva

Causal treatment effect estimation is a key problem that arises in a variety of real-world settings, from personalized medicine to governmental policy making. There has been a flurry of recent work in machine learning on estimating causal effects when one has access to an instrument. However, to achieve identifiability, they in general require one-size-fits-all assumptions such as an additive error model for the outcome. An alternative is partial identification, which provides bounds on the causal effect. Little exists in terms of bounding methods that can deal with the most general case, where the treatment itself can be continuous. Moreover, bounding methods generally do not allow for a continuum of assumptions on the shape of the causal effect that can smoothly trade off stronger background knowledge for more informative bounds. In this work, we provide a method for causal effect bounding in continuous distributions, leveraging recent advances in gradient-based methods for the optimization of computationally intractable objective functions. We demonstrate on a set of synthetic and real-world data that our bounds capture the causal effect when additive methods fail, providing a useful range of answers compatible with observation as opposed to relying on unwarranted structural assumptions.

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UAI Conference 2019 Conference Paper

The Sensitivity of Counterfactual Fairness to Unmeasured Confounding

Niki Kilbertus
Philip J. Ball
Matt J. Kusner
Adrian Weller
Ricardo Silva 0001

Causal approaches to fairness have seen substantial recent interest, both from the machine learning community and from wider parties interested in ethical prediction algorithms. In no small part, this has been due to the fact that causal models allow one to simultaneously leverage data and expert knowledge to remove discriminatory effects from predictions. However, one of the primary assumptions in causal modeling is that you know the causal graph. This introduces a new opportunity for bias, caused by misspecifying the causal model. One common way for misspecification to occur is via unmeasured confounding: the true causal effect between variables is partially described by unobserved quantities. In this work we design tools to assess the sensitivity of fairness measures to this confounding for the popular class of non-linear additive noise models (ANMs). Specifically, we give a procedure for computing the maximum difference between two counterfactually fair predictors, where one has become biased due to confounding. For the case of bivariate confounding our technique can be swiftly computed via a sequence of closed-form updates. For multivariate confounding we give an algorithm that can be efficiently solved via automatic differentiation. We demonstrate our new sensitivity analysis tools in real-world fairness scenarios to assess the bias arising from confounding.

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ICML Conference 2018 Conference Paper

Blind Justice: Fairness with Encrypted Sensitive Attributes

Niki Kilbertus
Adrià Gascón
Matt J. Kusner
Michael Veale
Krishna P. Gummadi
Adrian Weller

Recent work has explored how to train machine learning models which do not discriminate against any subgroup of the population as determined by sensitive attributes such as gender or race. To avoid disparate treatment, sensitive attributes should not be considered. On the other hand, in order to avoid disparate impact, sensitive attributes must be examined, e. g. , in order to learn a fair model, or to check if a given model is fair. We introduce methods from secure multi-party computation which allow us to avoid both. By encrypting sensitive attributes, we show how an outcome-based fair model may be learned, checked, or have its outputs verified and held to account, without users revealing their sensitive attributes.

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ICML Conference 2018 Conference Paper

Learning Independent Causal Mechanisms

Giambattista Parascandolo
Niki Kilbertus
Mateo Rojas-Carulla
Bernhard Schölkopf

Statistical learning relies upon data sampled from a distribution, and we usually do not care what actually generated it in the first place. From the point of view of causal modeling, the structure of each distribution is induced by physical mechanisms that give rise to dependences between observables. Mechanisms, however, can be meaningful autonomous modules of generative models that make sense beyond a particular entailed data distribution, lending themselves to transfer between problems. We develop an algorithm to recover a set of independent (inverse) mechanisms from a set of transformed data points. The approach is unsupervised and based on a set of experts that compete for data generated by the mechanisms, driving specialization. We analyze the proposed method in a series of experiments on image data. Each expert learns to map a subset of the transformed data back to a reference distribution. The learned mechanisms generalize to novel domains. We discuss implications for transfer learning and links to recent trends in generative modeling.

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NeurIPS Conference 2017 Conference Paper

Avoiding Discrimination through Causal Reasoning

Niki Kilbertus
Mateo Rojas Carulla
Giambattista Parascandolo
Moritz Hardt
Dominik Janzing
Bernhard Schölkopf

Recent work on fairness in machine learning has focused on various statistical discrimination criteria and how they trade off. Most of these criteria are observational: They depend only on the joint distribution of predictor, protected attribute, features, and outcome. While convenient to work with, observational criteria have severe inherent limitations that prevent them from resolving matters of fairness conclusively. Going beyond observational criteria, we frame the problem of discrimination based on protected attributes in the language of causal reasoning. This viewpoint shifts attention from "What is the right fairness criterion? " to "What do we want to assume about our model of the causal data generating process? " Through the lens of causality, we make several contributions. First, we crisply articulate why and when observational criteria fail, thus formalizing what was before a matter of opinion. Second, our approach exposes previously ignored subtleties and why they are fundamental to the problem. Finally, we put forward natural causal non-discrimination criteria and develop algorithms that satisfy them.

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