Multiple Hypothesis Testing

Many two-sample tests for populations of persistence diagrams assess global differences without identifying the regions of the birth-death plane that contribute to them. We study simultaneous inference for local mean contrasts when the number of available diagrams is fixed. They are differences in expected weighted feature mass within $\ell_\infty$ neighborhoods at several centers and radii. We estimate these contrasts using additive landmark responses. A Gaussian multiplier bootstrap calibrates simultaneous confidence intervals while allowing unequal group covariances. The neighborhoods whose intervals exclude zero form a map with approximate family-wise error control, and selecting a subset of original intervals for display preserves their joint coverage guarantee. On the simultaneous coverage event, every reported neighborhood lies within twice its radius of the support of the mean-measure difference. A geometric result gives sufficient radius conditions for a displaced feature to produce a nonzero contrast. A comparison of sufficient detection thresholds quantifies the tradeoff between reducing the number of tested coordinates and reserving observations for an independent pilot. In simulations with 40 to 120 diagrams per class, the bands achieved 94%-98% simultaneous coverage under both the strict null and equal means with unequal covariances. In the latter setting, a permutation maximum and the pooled-t implementation of the two-stage persistence-image test of Moon and Lazar rejected in up to 32% and 26% of runs, respectively. In the fixed-budget simulations, spending a third of the observations on a pilot to choose landmarks or radii located changes less often than a prespecified grid at a single radius. On the MUTAG benchmark, the localized region concentrates on rings of fused-ring systems, an exploratory reading.

LLM leaderboard gains can reflect selection among privately evaluated model variants, yet neither the number of variants nor their dependence is public. We ask how many hidden variants a published margin can support while retaining statistical evidence of a provider's advantage over a fixed comparator. For a fixed candidate family under a Gaussian margin model, we derive a sensitivity curve that reports this maximum count as a function of a lower bound on within-family correlation. The relevant correlation must match the score used for ranking and the sampling model: in a controlled family, pooled item correlation is 0.90, whereas composite-score correlation is 0.46 under item resampling and 0.92 when MMLU subjects are resampled. An item-based audit of 394 adjacent-rank claims on the Open LLM Leaderboard finds that 391 lack statistical support even before accounting for selection. Among claims that pass the uncorrected test, certification can depend on assumptions about the hidden family's correlation. The resulting curves make these assumptions explicit without estimating the unobserved search size.

Agent evaluations often use one benchmark to choose a workflow and then search for task types where its advantage weakens, so both conclusions are selected from the same data. We introduce Selection-Aware Semantic Stress Testing (\SASST{}), which learns a task reweighting from pre-execution features on discovery tasks and evaluates the same paired comparison on separate confirmation tasks. The protocol checks support and stability, uses joint bounds for all planned claims, and can return no claim. We prove conditional asymptotic validity under stated cluster assumptions. A forty-cluster audit finds Gaussian undercoverage and conservative Bonferroni $t$ bounds. In one 480-episode $τ$-bench study, a $3.75$ point discovery gain vanished on confirmation. A second-model study likewise confirmed neither a workflow benefit nor a stable stress rule.

Detecting a change in a multivariate series answers only the first of two questions; the operational question is which coordinates changed. Existing answers are incomplete. Block-level procedures certify predefined groups of coordinates under an additive union bound, high-dimensional variable-selection methods return interpretable rankings without error guarantees, and the post-detection inference literature controls error along the time axis rather than across coordinates. We propose ARM (Attribution by Rank Maxima), a wrapper that accepts a changepoint located by an arbitrary detector and returns the set of coordinates certified to have changed, each carrying a location or scale type label. ARM scores each coordinate by a max-over-splits rank statistic. Because this statistic dominates the corresponding statistic at the estimated split, the resulting certificate is invariant to the manner, and to the accuracy, of the changepoint estimate. Three finite-sample guarantees follow from within-coordinate ranks alone: per-coordinate validity under any detector; exact family-wise error control through a Westfall--Young joint permutation that preserves cross-coordinate dependence, with a fully distribution-free Holm fallback; and false discovery rate control under arbitrary coordinate dependence in high dimensions through Benjamini--Yekutieli and e-BH. In simulations, naive per-coordinate testing at the estimated changepoint inflates its family-wise error beyond $0.66$ as the dimension grows, whereas ARM maintains the nominal level while retaining validity under heavy tails, power in high dimensions, and accurate type labels. On five financial series surrounding the 2008 collapse, ARM attributes a scale change to every asset class and excludes injected control coordinates.

We study aggregation of statistical evidence under unknown and potentially complex dependence using group-invariance. Building on permutation-based constructions that treat transformed datasets as exchangeable units, we aggregate evidence across statistics for each transformed dataset and calibrate the resulting aggregates across transformations. We develop a finite-sample power and adaptivity theory for this framework, together with extensions to sequential and data-dependent aggregation that preserve validity. For single-batch aggregation, which uses one collection of transformed datasets for both standardization and calibration, we show that the critical values uniformly improve on deterministic calibrations valid under arbitrary dependence, including Bonferroni correction, while adapting to the unknown dependence structure. We also introduce a sequential alpha-spending version that permits early rejection when evidence is strong, and a two-batch extension that separates standardization from calibration to accommodate learned aggregation rules and reduce computation. Applications to adaptive nonparametric testing and conformal prediction illustrate how these results sharpen existing aggregation methods.

We show that the Benjamini--Hochberg procedure can fail to control the false discovery rate (FDR) at its nominal level for correlated two-sided Gaussian $p$-values. We construct a factor model for which, at level $α=0.01$, a rigorous interval-arithmetic certificate proves $FDR>0.0104$ for all sufficiently large numbers of hypotheses. This disproves a conjecture widely believed to be true for twenty years. Monte Carlo experiments are consistent with the theoretical result. The proof was obtained by GPT-5.6 Pro and carefully checked by the author.

Scientific discovery relies on large-scale hypothesis testing. However, the capacity to identify true discoveries while controlling false discovery faces major challenges: obtaining relevant reference data (the null distribution) is resource-intensive, leaving finite-data uncertainty, and the procedure should account for the inherent structure in the hypothesis space, when such structure exists. Here, we present a framework for controlling the false discovery rate both when each hypothesis is evidenced only by a finite count of null draws, leaving its p-value uncertain, and when the hypothesis space carries arbitrary structure, requiring only that the structure be represented through a suitable reproducing kernel. We present two decision rules that are both robust to structural mis-specification, yet offer a distinct trade-off between exact FDR control and statistical power. The first rule guarantees exact FDR control; the second maximizes power by adapting mirror-statistic control into count space, utilizing an analytical framework to assess FDR control when exact mirror symmetry is relaxed. Furthermore, the tractability gained by the RKHS framework allows us to directly investigate finite-data uncertainties, which we leverage to suggest a policy for the efficient allocation of null distribution samples.

Knowing how often a language model fails does not explain where its errors concentrate. When auditors examine many explanations, the strongest observed pattern may arise by chance. We introduce Janus, a procedure for checking proposed error patterns before reporting them. Janus starts with a fixed list of yes/no properties of the examples being evaluated, such as whether the input is long. For each property, it compares the model's error rates on examples with that property and those without it. To see how large a difference can arise by chance, it repeats this calculation after shuffling the yes/no labels across examples without changing the group sizes. These shuffled properties are called decoys. A pattern is reported only if the size of its error difference meets a threshold set using decoys. On separate held-out examples, the same group must still have the higher error rate and the difference must meet a minimum, which was chosen in advance. In a controlled experiment, where the model must find a code in documents containing tables of staff, projects, and renewal codes, Janus confirms five related patterns of higher error rates on tasks requiring more lookups across tables. It also confirms a sixth pattern: lower error rates on examples with the needed information at the ends of the tables. In our samples from the MuSiQue and LongBench v2 public benchmarks, SliceLine finds groups with high error rates, while Janus reports no confirmed error patterns for the example properties we chose to test. For comparison, we use standard tests that shuffle errors and account for testing many candidates. With the same holdout check, they confirm two to six controlled patterns, depending on the test and threshold, and none on either benchmark. In simulations with no real error patterns, Janus reports false patterns more often than Benjamini-Hochberg, depending on the decoy count.

Self-evolving agents improve by repeatedly proposing changes to their own prompts, skills, or workflows and keeping those that score higher on a small held-out set. Almost all effort has gone into the proposer that generates candidates; we argue the weak point is the acceptor, the rule that decides whether to commit a change. Applied hundreds of times against the same noisy dev estimate, the ubiquitous "keep it if the score went up" rule is uncontrolled adaptive multiple testing: the agent effectively p-hacks itself, accumulating false commits that make it churn and drift rather than improve. We recast committing as a sequential hypothesis test and propose PACE (Paired Anytime-valid Commit Evaluation), a training-free, anytime-valid commit gate. Each candidate is compared to the incumbent on identical instances and committed only when a testing-by-betting e-process accumulates decisive evidence, stopping early to save evaluations and controlling each candidate's false-commit probability at a user-set level even under optional stopping (a per-decision guarantee). On Qwen2.5 agents (0.5B-3B) self-evolving at the prompt level on GSM8K, SVAMP, and ARC-Challenge, greedy acceptance commits 30-42% false and 10-33% harmful edits when a genuine improvement is hidden among noisy proposals, while PACE commits the real one and essentially nothing else, matching greedy's held-out accuracy at sharply lower variance and about 18% lower evaluation cost. With no real gain available, greedy commits 13-21 spurious self-modifications per run (72-100% false) and degrades the most fragile agent by 4.9 points, while PACE holds at baseline. Reliability of self-evolution depends on the acceptor, not only on the proposer.

Benchmark data contamination has become a central challenge in LLM evaluation: when evaluation examples appear in the training data of one or more audited models, reported performance can be inflated and cross-model comparisons become unreliable. A broad line of training-data detection work designs scores to quantify how strongly a model memorizes a given data point, but these score-based methods lack theoretical guarantees. Recent conformal approaches provide provable false-identification control for a single model; however, applying them separately to each model can produce model-specific benchmarks, undermining fair comparison across models. In this work, we formalize multi-model benchmark decontamination as a joint selection problem and propose Joint Envelope Conformal Selection (JECS), a conformal procedure that enables global contamination rate (GCR) control under stated assumptions. Specifically, JECS computes per-model conformal p-values, aggregates them by the per-item maximum, and reconstructs a conservative envelope of the max-p null distribution from right-tail observations above a data-driven threshold. By applying the adaptive Benjamini-Hochberg (BH) procedure to the envelope-rescaled values, we select a benchmark with provable GCR control. Extensive experiments across various models and benchmarks demonstrate that JECS achieves higher power than the max-p baseline while consistently maintaining the target GCR control.

Modern applications of conformal inference to multiple testing problems, such as outlier detection and candidate selection, often involve selecting test samples whose conformal p-values fall below a threshold. The quality of such methods is often measured by the false discovery proportion (FDP), defined as the fraction of incorrect selections. Existing approaches typically control the expected value of the FDP, using methods such as the Benjamini-Hochberg procedure. This approach fails to provide high-probability bounds on the realized false discovery proportion and invalidates statistical guarantees if the rejection threshold is selected after inspecting the data. This paper establishes finite-sample, distribution-free upper bounds on the FDP that hold simultaneously over all possible rejection thresholds, enabling arbitrary post hoc selection of the threshold. Simultaneous validity is achieved by constructing a high-probability envelope for the empirical distribution function of null conformal p-values by sampling from their joint distribution. Furthermore, our framework allows practitioners to modulate the envelope's shape, thereby producing tight bounds in rejection regions of primary interest. We use this flexible approach to derive simultaneous FDP upper bounds for both outlier detection and conformal selection. We demonstrate through synthetic and real-data experiments that the resulting bounds are both valid and substantially less conservative than those derived from existing approaches.

Large-scale hypothesis testing is central to modern science, where controlling the False Discovery Rate (FDR) has become the standard approach to managing false positives across many simultaneous tests. Hypotheses rarely exist in isolation; they often exhibit structure through proximity, connectivity, or hierarchy. This structure represents both a challenge and an opportunity: while classical methods treat these dependencies as obstacles requiring conservative correction, leveraging them can substantially increase discovery power. Here, we reframe structured FDR control as a regularized learning problem. By optimizing within a suitable Reproducing Kernel Hilbert Space (RKHS), we introduce a framework that unifies continuous domains, graphs, and hierarchies under a single algorithm through kernel choice alone. This formulation enables smooth solutions in place of the piecewise-constant fits of prior methods, principled likelihood-based hyperparameter selection rather than heuristic tuning, and inference at unobserved locations which in turn supports sample-efficient experimental design. Building on this estimator, we provide two decision rules which we prove to control the FDR. We validate our method on two sources: spatial locations derived from high-dimensional real-world datasets, and a differential gene expression task utilizing protein-protein interaction graphs.

Online Multiple Testing (OMT), a fundamental pillar of sequential statistical inference, traditionally evaluates the False Discovery Rate (FDR) and statistical power in isolation, obscuring the highly asymmetric costs of false positives and false negatives in modern automated pipelines. To unify this evaluation, we introduce $\textit{Weighted Regret}$. Under this metric, we prove the $\textit{Duality of Regret Conservation}$: purely deterministic procedures ensuring strict FDR control inevitably incur an $Ω(T)$ linear regret penalty, as threshold depletion during signal-sparse cold starts forces massive false negatives. Tailored for exogenous testing streams, we propose Decoupled-OMT (DOMT) as a baseline-agnostic meta-wrapper. By incorporating a history-decoupled, strictly non-negative random perturbation, DOMT rescues purely deterministic baselines from severe threshold depletion. Crucially, it preserves exact asymptotic safety in stationary environments and rigorously bounds finite-sample error inflation during cold-starts. Guaranteeing zero additional false negatives, it yields an order-optimal $Ω(\sqrt{T})$ regret reduction in bursty environments, with a derived ``Cold-Start Tax'' characterizing the exact phase transition of algorithmic superiority. Experiments validate that DOMT consistently curtails empirical weighted regret, achieving an order-optimal sublinear mitigation of threshold depletion to navigate the non-stationary Pareto frontier.

Prediction sets provide a theoretically grounded framework for quantifying uncertainty in machine learning models. Adapting them to structured generation tasks, in particular, large language model (LLM) based code generation, remains a challenging problem. An existing attempt proposes PAC prediction sets but is limited by its strong monotonicity assumption on risk and single-label classification framework, which severely limits the space of candidate programs and cannot accommodate the multiple valid outputs inherent to code generation. To address these limitations, we propose an approach RisCoSet that leverages multiple hypothesis testing to construct risk-controlling predictions for LLM-based code generation. Given a trained code generation model, we produce a prediction set represented by a partial program, which is guaranteed to contain a correct solution with high confidence. Extensive experiments on three LLMs demonstrate the effectiveness of the proposed method. For instance, compared with the state-of-the-art, our method can significantly reduce the code removal by up to 24.5%, at the same level of risk.

Feature selection is a classical problem in statistics and machine learning, and it continues to remain an extremely challenging problem especially in the context of unknown non-linear relationships with dependent features. On the other hand, Shapley values are a classic solution concept from cooperative game theory that is widely used for feature attribution in general non-linear models with highly-dependent features. However, Shapley values are not naturally suited for feature selection since they tend to capture both direct effects from each feature to the response and indirect effects through other features. In this paper, we combine the advantages of Shapley values and adapt them to feature selection by proposing \emph{MinShap}, a modification of the Shapley value framework along with a suite of other related algorithms. In particular for MinShap, instead of taking the average marginal contributions over permutations of features, considers the minimum marginal contribution across permutations. We provide a theoretical foundation motivated by the faithfulness assumption in DAG (directed acyclic graphical models), a guarantee for the Type I error of MinShap, and show through numerical simulations and real data experiments that MinShap tends to outperform state-of-the-art feature selection algorithms such as LOCO, GCM and Lasso in terms of both accuracy and stability. We also introduce a suite of algorithms related to MinShap by using the multiple testing/p-value perspective that improves performance in lower-sample settings and provide supporting theoretical guarantees.

We develop a flexible feature selection framework based on deep neural networks that approximately controls the false discovery rate (FDR), a measure of Type-I error. The method applies to architectures whose first layer is fully connected. From the second layer onward, it accommodates multilayer perceptrons (MLPs) of arbitrary width and depth, convolutional and recurrent networks, attention mechanisms, residual connections, and dropout. The procedure also accommodates stochastic gradient descent with data-independent initializations and learning rates. To the best of our knowledge, this is the first work to provide a theoretical guarantee of FDR control for feature selection within such a general deep learning setting. Our analysis is built upon a multi-index data-generating model and an asymptotic regime in which the feature dimension $n$ diverges faster than the latent dimension $q^{*}$, while the sample size, the number of training iterations, the network depth, and hidden layer widths are left unrestricted. Under this setting, we show that each coordinate of the gradient-based feature-importance vector admits a marginal normal approximation, thereby supporting the validity of asymptotic FDR control. As a theoretical limitation, we assume $\mathbf{B}$-right orthogonal invariance of the design matrix, and we discuss broader generalizations. We also present numerical experiments that underscore the theoretical findings.

We study the problem of selecting the best heterogeneous treatment effect (HTE) estimator from a collection of candidates in settings where the treatment effect is fundamentally unobserved. We cast estimator selection as a multiple testing problem and introduce a ground-truth-free procedure based on a cross-fitted, exponentially weighted test statistic. A key component of our method is a two-way sample splitting scheme that decouples nuisance estimation from weight learning and ensures the stability required for valid inference. Leveraging a stability-based central limit theorem, we establish asymptotic familywise error rate control under mild regularity conditions. Empirically, our procedure provides reliable error control while substantially reducing false selections compared with commonly used methods across ACIC 2016, IHDP, and Twins benchmarks, demonstrating that our method is feasible and powerful even without ground-truth treatment effects.

AI-Scientist systems risk manufacturing spurious discoveries through uncontrolled multiple testing. We present a functional architecture that enforces statistical rigor at two levels: a Haskell embedded domain-specific language (the Research monad) that makes it impossible to test a hypothesis without updating the error budget, and a declarative scaffold, backed by an OS-level sandbox, that makes validation data physically absent from the environment in which LLM-generated code runs. We ground the design in a machine-checked Lean4 formalization of LORD++ online false-discovery-rate (FDR) control: we derive its error budget and prove both marginal and full FDR control, then close the gap to the implementation by verifying the budget's wealth invariant over IEEE754 arithmetic in SPARK/Ada. To our knowledge this is the first verified chain from theorem to floating-point implementation for an online FDR procedure. In simulation, the architecture holds the false discovery rate near 1% against a 5% target, where a naive approach reaches 41%. In end-to-end case studies, a valid test avoids the false discoveries a flawed one produces, yet still finds real effects when the data allow. An adversarial evaluation confirms that generated code cannot read the held-out data even when given its exact path.

Social scientists are increasingly turning to unstructured datasets to unlock new empirical insights, e.g., estimating descriptive statistics of or causal effects on quantitative measures derived from text, audio, or video data. In many settings, unsupervised analysis is of primary interest, in that the researcher does not want to (or cannot) manually pre-specify all important aspects of the unstructured data to measure; they are interested in "discovery." This paper proposes a general and flexible framework for pursuing such discovery from unstructured data in a statistically principled way. The framework leverages recent methods from the literature on AI interpretability to map unstructured data points to high-dimensional, sparse, and interpretable "concept embeddings"; computes statistics from these concept embeddings for testing interpretable, concept-by-concept hypotheses; performs selective inference on these hypotheses using algorithms validated by new results in high-dimensional central limit theory, producing a selected set ("discoveries"); and both generates and evaluates human-interpretable natural language descriptions of these discoveries. The proposed framework has few researcher degrees of freedom, is robust to data snooping and other post-selection inference concerns, and facilitates fast and inexpensive sensitivity analysis and replication. Applications to recent descriptive and causal analyses of unstructured data in empirical economics are explored.

Many important tasks of large-scale recommender systems can be naturally cast as testing multiple linear forms for noisy matrix completion. These problems, however, present unique challenges because of the subtle bias-and-variance tradeoff of and an intricate dependence among the estimated entries induced by the low-rank structure. In this paper, we develop a general approach to overcome these difficulties by introducing new statistics for individual tests with sharp asymptotics both marginally and jointly, and utilizing them to control the false discovery rate (FDR) via a data splitting and symmetric aggregation scheme. We show that valid FDR control can be achieved with guaranteed power under nearly optimal sample size requirements using the proposed methodology. Extensive numerical simulations and real data examples are also presented to further illustrate its practical merits.