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In some fields of AI, machine learning and statistics, the validation of new methods and algorithms is often hindered by the scarcity of suitable real-world datasets. Researchers must often turn to simulated data, which yields limited information about the applicability of the proposed methods to real problems. As a step forward, we have constructed two devices that allow us to quickly and inexpensively produce large datasets from non-trivial but well-understood physical systems. The devices, which we call causal chambers, are computer-controlled laboratories that allow us to manipulate and measure an array of variables from these physical systems, providing a rich testbed for algorithms from a variety of fields. We illustrate potential applications through a series of case studies in fields such as causal discovery, out-of-distribution generalization, change point detection, independent component analysis, and symbolic regression. For applications to causal inference, the chambers allow us to carefully perform interventions. We also provide and empirically validate a causal model of each chamber, which can be used as ground truth for different tasks. All hardware and software is made open source, and the datasets are publicly available at causalchamber.org or through the Python package causalchamber., Comment: 38 pages, 17 figures

Statistics suffers from a fundamental problem, "the curse of endogeneity" -- the regression function, or more broadly the prediction risk minimizer with infinite data, may not be the target we wish to pursue. This is because when complex data are collected from multiple sources, the biases deviated from the interested (causal) association inherited in individuals or sub-populations are not expected to be canceled. Traditional remedies are of hindsight and restrictive in being tailored to prior knowledge like untestable cause-effect structures, resulting in methods that risk model misspecification and lack scalable applicability. This paper seeks to offer a purely data-driven and universally applicable method that only uses the heterogeneity of the biases in the data rather than following pre-offered commandments. Such an idea is formulated as a nonparametric invariance pursuit problem, whose goal is to unveil the invariant conditional expectation $m^\star(x)\equiv \mathbb{E}[Y^{(e)}|X_{S^\star}^{(e)}=x_{S^\star}]$ with unknown important variable set $S^\star$ across heterogeneous environments $e\in \mathcal{E}$. Under the structural causal model framework, $m^\star$ can be interpreted as certain data-driven causality in general. The paper contributes to proposing a novel framework, called Focused Adversarial Invariance Regularization (FAIR), formulated as a single minimax optimization program that can solve the general invariance pursuit problem. As illustrated by the unified non-asymptotic analysis, our adversarial estimation framework can attain provable sample-efficient estimation akin to standard regression under a minimal identification condition for various tasks and models. As an application, the FAIR-NN estimator realized by two Neural Network classes is highlighted as the first approach to attain statistically efficient estimation in general nonparametric invariance learning., Comment: 47 pages, 5 figures with appendix

Prediction models often fail if train and test data do not stem from the same distribution. Out-of-distribution (OOD) generalization to unseen, perturbed test data is a desirable but difficult-to-achieve property for prediction models and in general requires strong assumptions on the data generating process (DGP). In a causally inspired perspective on OOD generalization, the test data arise from a specific class of interventions on exogenous random variables of the DGP, called anchors. Anchor regression models, introduced by Rothenhäusler et al. (J R Stat Soc Ser B 83(2):215-246, 2021. 10.1111/rssb.12398), protect against distributional shifts in the test data by employing causal regularization. However, so far anchor regression has only been used with a squared-error loss which is inapplicable to common responses such as censored continuous or ordinal data. Here, we propose a distributional version of anchor regression which generalizes the method to potentially censored responses with at least an ordered sample space. To this end, we combine a flexible class of parametric transformation models for distributional regression with an appropriate causal regularizer under a more general notion of residuals. In an exemplary application and several simulation scenarios we demonstrate the extent to which OOD generalization is possible.

We present repliclust (from repli-cate and clust-er), a Python package for generating synthetic data sets with clusters. Our approach is based on data set archetypes, high-level geometric descriptions from which the user can create many different data sets, each possessing the desired geometric characteristics. The architecture of our software is modular and object-oriented, decomposing data generation into algorithms for placing cluster centers, sampling cluster shapes, selecting the number of data points for each cluster, and assigning probability distributions to clusters. The project webpage, repliclust.org, provides a concise user guide and thorough documentation., Comment: 21 pages, 11 figures

Rhabdomyosarcoma (RMS) is a group of pediatric cancers with features of developing skeletal muscle. The cellular hierarchy and mechanisms leading to developmental arrest remain elusive. Here, we combined single-cell RNA sequencing, mass cytometry, and high-content imaging to resolve intratumoral heterogeneity of patient-derived primary RMS cultures. We show that the aggressive alveolar RMS (aRMS) subtype contains plastic muscle stem-like cells and cycling progenitors that drive tumor growth, and a subpopulation of differentiated cells that lost its proliferative potential and correlates with better outcomes. While chemotherapy eliminates cycling progenitors, it enriches aRMS for muscle stem-like cells. We screened for drugs hijacking aRMS toward clinically favorable subpopulations and identified a combination of RAF and MEK inhibitors that potently induces myogenic differentiation and inhibits tumor growth. Overall, our work provides insights into the developmental states underlying aRMS aggressiveness, chemoresistance, and progression and identifies the RAS pathway as a promising therapeutic target.

In recent years, there has been a growing interest in statistical methods that exhibit robust performance under distribution changes between training and test data. While most of the related research focuses on point predictions with the squared error loss, this article turns the focus towards probabilistic predictions, which aim to comprehensively quantify the uncertainty of an outcome variable given covariates. Within a causality-inspired framework, we investigate the invariance and robustness of probabilistic predictions with respect to proper scoring rules. We show that arbitrary distribution shifts do not, in general, admit invariant and robust probabilistic predictions, in contrast to the setting of point prediction. We illustrate how to choose evaluation metrics and restrict the class of distribution shifts to allow for identifiability and invariance in the prototypical Gaussian heteroscedastic linear model. Motivated by these findings, we propose a method to yield invariant probabilistic predictions, called IPP, and study the consistency of the underlying parameters. Finally, we demonstrate the empirical performance of our proposed procedure on simulated as well as on single-cell data.

Classical machine learning methods may lead to poor prediction performance when the target distribution differs from the source populations. This paper utilizes data from multiple sources and introduces a group distributionally robust prediction model defined to optimize an adversarial reward about explained variance with respect to a class of target distributions. Compared to classical empirical risk minimization, the proposed robust prediction model improves the prediction accuracy for target populations with distribution shifts. We show that our group distributionally robust prediction model is a weighted average of the source populations' conditional outcome models. We leverage this key identification result to robustify arbitrary machine learning algorithms, including, for example, random forests and neural networks. We devise a novel bias-corrected estimator to estimate the optimal aggregation weight for general machine-learning algorithms and demonstrate its improvement in the convergence rate. Our proposal can be seen as a distributionally robust federated learning approach that is computationally efficient and easy to implement using arbitrary machine learning base algorithms, satisfies some privacy constraints, and has a nice interpretation of different sources' importance for predicting a given target covariate distribution. We demonstrate the performance of our proposed group distributionally robust method on simulated and real data with random forests and neural networks as base-learning algorithms.