Comparisons between AutoML systems at short time budgets -- tens of seconds rather than hours -- are common in tool READMEs and workshop papers, and they are easy to get wrong. We report a case study in which a simple AutoML engine, Orcetra, appeared to beat FLAML and AutoGluon on 513 OpenML datasets, winning 57.1% of them at a nominal 60-second budget and 78.4% of datasets against FLAML alone at 30 seconds. Both margins came from protocol defects that a results table cannot show. The search loop scored every candidate on the test split and reported the best, making the headline metric a maximum over dozens of noisy estimates while the baselines selected on training data and touched the test set once; and the budget was checked before launching a candidate but never enforced during one, so the system consumed a median of 120 s against a 60-second budget, 2.24x the wall-clock AutoGluon used. Re-running with selection moved to a validation split, the deadline enforced externally and every framework pinned to an equal share of the machine, Orcetra's win rate on the re-run subset falls from 59.4% to 34.3% and no pairwise difference against either competitor remains significant. Recording both estimands inside a single search lets us attribute the collapse: the selection rule accounts for 4.8 percentage points and unequal compute for most of the rest. The same traces give the selection bias as a function of budget, measured rather than assumed: it grows with $K$ but reaches only 0.27 accuracy points, about five times below the $σ\sqrt{2\ln K}$ bound a marginal-standard-error argument predicts, because candidates scored on shared test rows cancel most of the noise. We close with a checklist for short-budget comparisons. Code, per-dataset results and the scripts that regenerate every number and figure in the paper are released with it.
Design campaigns in chemistry, materials science, and machine learning share a bottleneck: determining how good a candidate truly is requires an expensive evaluation - an experiment, a first-principles simulation, or a full training run. Machine-learning surrogates that predict these outcomes are increasingly used not only to propose candidates but to grade them, and even to feed their own predictions back into the search as though they were measurements. Through mathematical analysis validated on three exhaustively ground-truthed design tasks, we establish when this practice is safe, what any certificate of safety must cost, and when the substitution provably pays. Predictive accuracy cannot anchor trust: near-perfect R^2 is compatible with worst-possible selections, and screening N candidates inflates the over-prediction at the selected candidate by a quantifiable "selection tax" with matching upper and lower bounds. Safety follows instead from an architectural rule - predictions may propose and train without restriction, but every certified conclusion must rest on true evaluations - which is sufficient with no assumptions on the surrogate, and necessary, since admitting predictions into certification with the standing of measurements opens a deterministic self-confirmation failure mode. We derive the minimal criterion under which a model may act as an oracle (rank preservation, not accuracy), show that trust must be purchased through selection-aware audits that are optimal in query complexity, and prove a dichotomy fixing when audited surrogates cut certified evaluation cost. Across 432 surrogate fits over six task-regime conditions, the audit statistic tracks deployed search performance at Spearman rank correlation 0.80-0.99, while the rank correlation of R^2 with deployed regret falls as low as 0.33; audited screening reduces certified oracle cost by a measured factor of 25.
Discovering the direct causes and effects of a target variable from observational data is a fundamental problem in causal discovery, with broad applications in domains such as gene regulatory analysis and biomedical research. Existing causal discovery methods either learn a global causal structure, which incurs substantial computational cost, or assume the absence of latent variables and selection bias, assumptions that are often violated in real-world settings. Motivated by these challenges, we study local causal structure learning in the presence of latent variables and selection bias. Specifically, we first characterize a local region that enables target-specific causal discovery without recovering the entire global structure. We then establish a theoretical bridge between causal information learned from the observed distribution induced on this local region and the corresponding information in the global causal structure. Building on these foundations, we propose LoCaLS, a local causal structure learning algorithm that is sound and complete under standard assumptions and identifies the same direct causes and effects of a target variable as those identifiable by global causal discovery methods, while allowing for latent variables and selection bias. Extensive experiments on random and real-world structures demonstrate that the proposed method consistently achieves higher structural accuracy than existing local methods while requiring substantially less computational effort than state-of-the-art global methods. Furthermore, applications to two real-world gene expression datasets reveal biologically plausible target-specific causal structures, demonstrating its practical applicability in large-scale biological data analysis.
Training data for machine learning is routinely collected by a selection process the model never sees: loans are observed only when granted, outcomes only when a test was ordered. The standard fixes -- importance weighting, covariate-shift correction, MAR imputation -- assume selection is ignorable given observables. Econometrics solved the harder case in 1979: Heckman's two-equation model jointly fits a probit selection equation and an outcome equation linked through correlated errors, and the inverse-Mills-ratio term corrects for selection on unobservables, where importance weighting is structurally helpless. We instantiate this for deep epistemic uncertainty: a deep outcome network, a linear selection head, and a joint bivariate-normal likelihood over all units, ensembled for predictive variance. In a controlled generator where sampling probability depends on an unobservable correlated (rho up to 0.9) with the outcome noise, deep ensembles, MC dropout, and GP baselines are overconfident exactly where data was avoided: coverage of nominal-90% intervals falls to 64.4% at rho=0.9, and importance weighting with oracle propensities does not fix it (43.1%) -- reweighting corrects the covariate distribution, not the conditional bias E[y|x,selected] != E[y|x]. The Heckman correction restores coverage (88.9%) when the selection equation has an instrument -- a variable affecting selection but not the outcome -- and degrades measurably without one (40.3%); we chart this honesty curve rather than hide it. On real tabular data with induced MNAR selection, the corrected intervals are the best-calibrated (lowest region-ECE) non-oracle method in selected-against regions; baselines matching its raw coverage do so only by over-widening everywhere. Our estimators reproduce classic Stata output to seven digits. We state which identification regime a practitioner is in, and release the code.
Retail intelligence often relies on monitoring popular, high-velocity products, potentially biasing economic indicators by ignoring the "long tail" of niche items. This simulation study investigates selection bias in inflation estimation and compares correction methods across diverse data-generating processes. Through 400 Monte Carlo replications spanning four scenarios--aligned step functions, smooth gradients, misaligned breaks, and polynomial relationships--we test the robustness of Inverse Probability Weighting (IPW) with five specifications against stratification with varying strata counts. Our findings reveal fundamental limits of weighting methods in retail long-tail contexts: stratification achieves superior performance in three of four scenarios, maintaining sub-0.04pp median error even when boundaries deliberately misalign with population breaks (116x advantage over IPW). However, IPW with spline propensity models wins under smooth polynomial relationships (median error 0.007pp vs. 0.013pp), demonstrating context-dependency. Critically, even an oracle IPW specification with perfect structural knowledge achieves 6.06pp error compared to stratification's 0.008pp in step-function scenarios. This reflects violation of the Positivity Assumption--a fundamental causal inference requirement--rather than IPW methodological inferiority. When selection probabilities differ dramatically (90% vs. 1%), weighting methods operate outside their theoretical design envelope. These results demonstrate that stratification provides a safer engineering choice in retail long-tail distributions with severe positivity violations.
Praharsh Nanavati, Jilles Vreeken, David Kaltenpothcs.LG
Causal discovery methods commonly assume that all data is independently and identically distributed (i.i.d.) and that there are no unmeasured variables affecting the system. In practice, these assumptions are often violated, leading to inaccurate inference. In this paper, we study how to identify hidden confounding and selection biases from causal mechanism shifts. In particular, we show that structural biases lead to dependent mechanism shifts. That is, by considering for which variables the mechanisms change given data from different environments, we can tell which variables are unbiased, which are subject to hidden confounding, and which are undergoing selection bias. We formalize this into an empirically testable criterion based on mutual information, and show under which conditions it identifies structural biases. To tell which nodes are subject to what kind of bias, we introduce the StruBI algorithm. Experiments on synthetic and real-world data show that StruBI works well in practice, accurately recovering affected variable sets and types of biases, outperforming the state-of-the-art by a wide margin.
Understanding how a prediction model will perform in a new environment before deployment is essential to preventing harm when algorithms inform decision-making. Two common sources of model performance degradation are (i) covariate shift, where the target covariate distribution differs from the source, and (ii) selective labels, where the observability of outcomes depends on historical decisions. We study pre-deployment model evaluation under the joint presence of covariate shift and labeling of outcomes selectively based on observed features. In particular, we present a double machine learning procedure for estimating the target risk of an arbitrary black-box prediction model under a general loss function. We show identification of this estimand under standard assumptions and derive a bias-corrected estimator based on the influence function of the target risk. Finally, we evaluate our estimator through experiments using the eICU electronic health records database, showing that it tracks the true target risk more accurately than methods that address either selective labels or covariate shift alone, as well as baselines that combine standard plug-in approaches.
Understanding potential selection in data is crucial for causal discovery; we argue that "selection" in common narratives takes two forms, which we term static and evolutionary selection, respectively. Static selection refers to a one-shot filtering process where observed data consist of a subset of the population of interest, as in survey volunteer bias. Evolutionary selection, in contrast, operates through repeated rounds of differential fitness in reproduction, where observed data constitute the latest generation shaped by a historical trajectory, as in immune adaptation, antibiotic resistance, and social norm emergence. Existing methods largely conflate these two forms and rely on an identical graphical model of selection. We show that this model is valid for static settings but fails to characterize data under evolution, yielding false discovery results. To address this, we introduce a new model that specifically characterizes evolutionary selection, and develop a sound and complete procedure for identifying such models from data across one or multiple environments or generations. Experimental results validate the method's ability to uncover the relevant mechanisms underlying evolution from data.
Recommender systems often rely on observational user--item interaction data, which is prone to selection bias due to users' selective interactions with items. Inverse propensity weighting and doubly robust estimators effectively mitigate selection bias under observed confounding, but are unreliable in the presence of hidden confounders. Existing approaches relying on randomized controlled trials (RCTs) or global sensitivity bounds are constrained in practice: RCTs demand costly experimental data, while global sensitivity bounds presume a uniformly bounded effect of unmeasured confounders on propensities through sensitivity analysis, thereby neglecting heterogeneity across user--item interactions. To overcome this limitation, we propose a novel framework, which estimates user--item level sensitivity bounds, thereby substantially relaxing the homogeneity assumption inherent in global sensitivity bounds named Personalized Unobserved-Confounding-aware Interaction Deconfounder (PUID). To ensure both robustness and predictive accuracy, we further develop an adversarial optimization strategy and propose a benchmark-guided variant (BPUID) that incorporates pre-trained models as stabilizing references. Extensive experiments on three real-world datasets demonstrate that our approach significantly outperforms global methods under hidden confounding, without requiring RCT data.
Federated learning (FL) trains a shared model from updates contributed by distributed clients, often implicitly assuming that contributing clients are representative of the target population. In practice, this representativeness assumption can fail at two distinct stages, inducing selection bias. First, eligibility rules such as device constraints, software requirements, or user consent determine which clients are ever enrolled and reachable for training, inducing \emph{enrollment bias}. Second, among enrolled clients, user and system factors such as battery state, network status, and local time determine which clients participate in each communication round, inducing \emph{participation bias}. Although existing work has largely addressed round-level participation bias, it has paid far less attention to population-level enrollment bias, which can induce a persistent mismatch between the training objective and the target-population objective. We formalize FL under a two-stage selection model and derive \textsc{FedIPW}, an inverse-probability-weighted aggregation scheme that recovers the target-population mean update under standard ignorability and positivity assumptions. Because client-level covariates are often unavailable for non-enrolled clients, we also introduce a limited-information aggregate-calibration extension that uses known target-population summaries to reweight the enrolled sample, partially correcting enrollment bias. We further provide an algorithm-agnostic optimization analysis under residual weighting error and show that incomplete selection correction can induce a non-vanishing bias floor. Finally, experiments on synthetic federated logistic regression validate the predicted objective mismatch and show that enrollment correction reduces target-population error under two-stage selection.