FDR Control

FDR: False Discovery Rate

Latest papers 30

Oct 7, 2026stat.ML

Certified by Abstention: Distribution-Free Guarantees for Chain-of-Thought Verifiers at Small Calibration Budgets

Signals that predict whether a chain-of-thought (CoT) trace is correct are compared by AUC, but deploying one requires a threshold with a guarantee. We ask what distribution-free selective guarantees deliver for CoT verifiers at realistic calibration budgets of tens to a few hundred labelled problems, using seven open models, five verifier signals and 37,000 graded traces. The central observation is validity by abstention: an (α,δ)(α,δ)-valid procedure that issues a certificate with probability PfireP_{\rm fire} bounds the failure probability of an issued certificate only by δ/Pfireδ/P_{\rm fire}, so a certificate that rarely fires can be valid and wrong every time it is used. In a simulation with known risk the standard certificate fails in at most 0.3% of calibration draws but in up to 69% of those in which it fires. A certification floor and a lattice condition for Benjamini-Hochberg conformal selection explain why certificates abstain at these budgets, and the data bear them out: the standard certificate returns nothing or a large accepted set, and an unreadable residual-stream probe buys two to three times the coverage of the readable signals, an edge a cross-fitted reconstruction cannot recover linearly from the readable features. We then give a floor-started fixed-sequence certificate, valid without monotonicity assumptions, that covers more than the Bonferroni certificate on every model-signal pair and raises coverage at the non-vacuous target 0.75π00.75π_0 from 0.05 to 0.16, although the floor keeps absolute coverage small. Finally, a certificate cannot see what matters after deployment: under benchmark shift the error among accepted traces tracks the new task's base error, and under best-of-nn selection against the verifier it rises past the target while the empirical failure frequency stays below δδ, because abstention absorbs the failures.
Oct 5, 2026stat.ML

Valid Stopping in Adaptive Generator-Verifier Loops

Numerous agentic workflows are based on a generator-verifier loop: a generator proposes candidates, a cheap verifier scores them, and the workflow terminates when a proposal is verified as good enough. The verifier typically proxies a more costly ground-truth oracle, and as the generator searches adaptively against it, false acceptances may accumulate. Proposals can pass the proxy but fail under the costlier ground-truth check. We study when to stop these loops while controlling the false discovery rate of the accepted proposals. Our construction introduces tools of independent interest in distribution-free statistical testing and conformal risk control, including analysis of ee-values constructed through index betting and a novel conformal risk control procedure for non-monotone losses. We validate the approach in synthetic settings and on a protein-design benchmark.
Oct 1, 2026cs.LG

Evidence-Gated Research: Statistically Controlled Model Adoption in Adaptive Search

Adaptive model search is path dependent: once a challenger is adopted, it becomes the reference from which later candidates are generated. A statistically unsupported replacement can therefore alter hypotheses that have not yet been proposed. We introduce Evidence-Gated Research (EGR), a statistical adoption layer for moving-incumbent search. EGR freezes each challenger before decision evidence is revealed, builds anytime-valid evidence across a predeclared set of environments, routes evidence predictably toward unresolved components, composes a persistent candidate e-value, and passes that e-value to an online controller. Under explicit conditional-validity and predictability conditions, the resulting procedure controls false discovery rate for the declared all-environment adoption target even though earlier adoptions change later challengers. In a 5,000-trajectory closed-loop benchmark, development-only e-LOND attains persistent FDR 0.621, whereas no persistent false-adoption path is observed for the audited EGR variants in that finite run. In matched replay over 600 challenger--incumbent pairs, Stagewise EGR preserves fixed-anytime alternative crossing decisions while using 56.1% less decision evidence at the representative threshold. A three-environment public-data study and a 40,000-sample controlled neural benchmark reproduce the evidence-efficiency pattern. These results identify model replacement as a distinct statistical control point in adaptive model development.
Sep 30, 2026cs.CV

Mitigating Object Hallucination in Large Vision-Language Models via False Discovery Controlled Visual Data Splitting

Multiple object hallucination, where large vision-language models (LVLMs) generate objects not supported by the visual input, is a persistent challenge caused by visual uncertainty during decoding. Existing methods reduce hallucinations using contrastive signals, but they rely on heuristics and lack principled control of false positives at the image level. To address this, we propose False Discovery Rate-COntRol of HALlucination (CORAL), a training-free framework that models visual uncertainty using an uncertainty-aware visual data splitting strategy and leverages mirror statistics to quantify visual contrast during decoding. By computing mirror statistics from paired, symmetrically perturbed visual inputs, CORAL estimates spurious object predictions and sets a data-driven threshold to control the expected fraction of false discoveries per image, suppressing hallucinations while retaining high power for truly grounded objects. The framework is flexible, supports multiple LVLMs, and mitigates hallucinations without retraining or supervision. Extensive experiments on multiple benchmarks with several evaluation metrics demonstrate that CORAL consistently outperforms state-of-the-art methods, providing more reliable and robust hallucination control. Code is available at: https://changliu1993-cl.github.io/CORAL/
Sep 30, 2026stat.ME

Always-On Experimentation

Generative AI has dramatically accelerated the rate at which new treatments---from novel pharmaceuticals to online marketing campaigns---can be conceived and deployed. As a result, modern experimentation platforms often run continuously, with treatments added as they are ready and removed when they underperform. We formalize this "Always-On" experimental setting, in which treatments can be dynamically generated, added to, and removed from a running experiment, and study the statistical problem of deciding whether to accept or reject each treatment while controlling for the false discovery rate. We develop sequential tests that achieve time-uniform Type-I error control under arbitrary stopping times and "predictable" treatment schedules. Our approach builds on the testing-by-betting framework: we construct test supermartingales for testing the average treatment effect of each treatment, and show that the construction of these test supermartingales is growth-rate optimal in an almost-sure sense.
Sep 27, 2026stat.ML

Calibrated Derivative-Process Sensitivity for Gaussian-Process Variable Selection

Automatic relevance determination (ARD), the default tool for variable selection in Gaussian-process (GP) regression, ranks inputs by inverse lengthscales -- which measure how fast a function varies, not how much an input contributes to prediction -- and offers no calibrated rule for deciding which inputs to keep. The prediction-centred alternative, the derivative sensitivity νj=E[(∂f/∂xj)2]ν_j = \mathbb{E}[(\partial f/\partial x_j)^2], is available in closed form from a fitted GP, but turning it into a selection rule is harder than it looks: at a null input the estimator is a degenerate quadratic form, so Wald and Bernstein-von Mises cutoffs are anti-conservative, and the natural residual bootstrap is mis-scaled. We show that a studentized multiplier bootstrap of the GP derivative process repairs both, prove its validity through an invariance principle for quadratic forms, and obtain asymptotic family-wise and false-discovery-rate control across inputs. Over 100 replications the rule controls FDR wherever inputs are truly null, while uncalibrated derivative rankings breach the target by up to 2x and a Bernstein-von Mises cutoff by 2.2x; at matched FDR it loses no power; it holds under a Matérn kernel and input correlation up to 0.99; on real data with planted and authentic null inputs it admits 5-12x fewer spurious inputs; it costs 5-18% of the GP fit; and a block-averaged variant retains validity at cost linear in nn.
Sep 11, 2026cs.LG

Certified AI Triage of ICU Alarms

In the VTaC benchmark 71% of ventricular-tachycardia alarms are false, but silencing a real one can delay recognition of a dangerous arrhythmia. We reframe alarm reduction as three-way triage (retain, suppress, or defer) and bound the decision this analysis treats as harmful: among suppressed alarms, the fraction that were genuine stays below a user-set budget with 95% confidence, under i.i.d. event sampling. Alarms sharing a waveform record are dependent, so the clustered analysis is a sensitivity check. On the official split a 5% budget certifies in all three seeds, suppressing 74.8% of false alarms while silencing 1.5% of genuine ones, at AUROC 0.953 and Challenge Score 83.33, numerically comparable to the strongest of the eleven published systems. Our central finding measures what multiplicity costs: the correction charges for every candidate, so a finer grid can certify strictly less. Under held-out calibration the 885-cell grid we declared certifies 1 of 15 fold-runs, while choosing the grid on a separate selection partition certifies 8. We project the calibration volume each budget needs, making an uncertifiable budget a design parameter. Finally, adding a learned reliability dimension to the policy grid did not sharpen the certified frontier.
Sep 2, 2026cs.IR

GenCAR: Generative Counterfactual Alignment with Risk-Controlled Selection for Out-of-Distribution Recommendation

Serving useful recommendations under distribution shift is crucial for balancing utility and risk in out-of-distribution (OOD) recommendation. However, most existing OOD methods improve ranking or construct counterfactual candidates without controlling the proxy-label false discovery rate (FDR) of the served set. In this work, we formulate OOD serving as the αα-Valid Counterfactual Recommendation (αα-VCR) problem to retain candidate support learned from counterfactual supervision while controlling proxy-label FDR, and propose GenCAR, which couples preference-grounded counterfactual supervision with calibrated set selection. In particular, GenCAR fixes the stable-preference representation while intervening on the environmental factor, grounds offline large language model proposals through preference anchors and trust-radius filtering, and uses conformal pp-values for Benjamini--Hochberg selection. We theoretically bound conditional counterfactual approximation error and prove finite-sample, distribution-free control of proxy-label FDR under exchangeability and positive regression dependence, with a Benjamini--Yekutieli guarantee under arbitrary dependence. Extensive experiments audit realized proxy false discovery proportions and demonstrate that GenCAR consistently enhances OOD candidate recovery across diverse benchmarks.
Aug 6, 2026cs.AI

Innovation-Residual Auditing of Autonomous Analysis Agents: Localization, Detection Limits, Error Control, and Identifiability

Autonomous agents now carry out entire data analyses, selecting cohorts, joining tables, and fitting models with little step-by-step supervision. When such an analysis turns out to be wrong, someone must determine which operation caused it. A recent approach does this without any labelled mistakes, learning instead from analyses known to be sound and flagging operations that depart from what that model predicts; how reliable such audits are has not been studied. This paper supplies that analysis. The choice of score determines whether an error can be localized at all. If each operation is scored by how surprising it is given the operation immediately preceding it, then operations that merely inherit an earlier error are indistinguishable from correct ones, so one mistake produces one flag; scores computed against a longer reconstruction of the intended analysis instead spread a single mistake across many operations. We quantify how far they spread, and how to choose the comparison length when an error accumulates gradually rather than at once. We then give procedures that control the proportion of falsely flagged operations within a single audited analysis, requiring only that sound analyses be exchangeable rather than that the fitted model be correct, and we quantify how much the guarantees weaken when the model is imperfect or when the analysis was selected for review in a way that depends on its content. Finally we establish a limit on what any such audit can report: errors below a certain magnitude cannot be attributed at all, being indistinguishable from ordinary variation among sound analyses. This limit falls so slowly as more sound analyses are collected that at the representation sizes now in use a hundredfold increase reduces it by under two percent, so the dimension of the representation rather than the volume of training data is the binding constraint.
Aug 2, 2026stat.ML

Model-Agnostic FDR Control via Group Gaussian Mirror and Permutation SHAP

Most FDR-controlled feature selection methods are designed for coordinate-wise hypotheses, where each feature has a single weight or importance score. This abstraction fails in sequential and grouped models, where one original feature is represented by a block of sub-features, such as lags, recurrent states, or attention-based interactions. We propose a grouped-feature FDR control framework for such settings. For grouped linear models, we construct null-symmetric block-level mirror statistics with matrix-valued perturbations. For neural sequential models, we combine Permutation SHAP derivatives as model-agnostic block-level importance scores with kernel-based dependence measure. The framework is model-agnostic across network architectures, does not require specifying the covariate distribution, and reduces to Gaussian Mirror or Neural Gaussian Mirror when the block size is one. We prove FDR control for low- and high-dimensional grouped linear models and asymptotic symmetry of smoothed Permutation SHAP derivatives under fixed fitted nonlinear models. Experiments on simulated and real-world datasets show reliable FDR control and improved power under correlated grouped-feature signals.
Jul 25, 2026stat.ML

Robust Conformalized Selection with Noisy Responses

Conformalized selection has been widely applied to select high-quality candidates from large datasets with rigorous uncertainty quantification, such as reliable labeling, drug discovery, and the alignment of large language models. Nevertheless, existing methods assume clean responses on calibration data, an assumption that rarely holds in practice. In this paper, we formulate the above tasks as selecting candidates with true predicted labels or with responses exceeding certain values. We demonstrate that existing conformal selection methods fail to control the false discovery rate (FDR) or suffer from severe power loss under contaminated calibration data. To that end, we propose Robust Conformalized Selection (RCS), a unified framework for selective classification with valid FDR control under general label contamination. The key insight of RCS lies in a novel statistical reduction: by separately conditioning on different classes, we translate the intractable label noise into a localized covariate shift problem, which then enables a covariate-adjusted empirical-Bayes-type estimate of the number of false selections. Statistical properties such as the asymptotic FDR control, power optimality, and robustness of RCS are established. We further develop an instantiation of RCS under randomized response model, and also apply RCS to the task of selecting candidates with large response values. Extensive experiments on both simulated and real-world datasets demonstrate the effectiveness of RCS.
Jul 13, 2026math.ST

The Benjamini--Hochberg Procedure Can Fail to Control the FDR for Correlated Two-Sided Gaussian Tests

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 pp-values. We construct a factor model for which, at level α=0.01α=0.01, a rigorous interval-arithmetic certificate proves FDR>0.0104FDR>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.
Jul 6, 2026cs.CV

Shape Over Intensity: Directional Topological Encoding for False Positive Reduction in Intracranial Aneurysm Detection

Automated detection of intracranial aneurysms (IAs) from CT angiography (CTA) is severely hindered by high false-positive rates. Convolutional neural networks (CNNs) rely on local pixel intensities, causing systematic confusion between saccular aneurysms and vascular bifurcations - a problem especially acute for small lesions (<3 mm), where detection sensitivity falls below 60%. We propose a plug-and-play, topology-aware false-positive reduction framework evaluating the Smooth Euler Characteristic Transform (SECT) - a directional representation encoding global 3D vascular geometry independently of intensity - against persistence-based summaries (Persistence Images and Landscapes), tested on a stratified subset of the RSNA 2025 dataset. SECT achieves an AUC of 0.943, substantially outperforming direction-agnostic methods (AUC ~0.68), and exhibits a clinical performance inversion: it excels on the sub-3 mm cohort, maintaining 0.943 AUC and 78.5% sensitivity at 95% specificity. The representation is also scanner-agnostic, achieving 0.927 mean AUC under leave-one-scanner-out (LOGO) validation across four manufacturers. By capturing asymmetric geometric invariants rather than intensity profiles, SECT reliably resolves the primary structural confounder in IA detection, positioning it as a robust downstream filter for hybrid deep-learning diagnostic pipelines.
Jul 3, 2026stat.ML

Denoised Conformal Alignment for Reliable Selection of Conditional Average Treatment Effect Predictions

In selective deployment, practitioners act only on a model-chosen subset of individuals based on predicted conditional average treatment effects, but marginal conformal guarantees need not control reliability on that selected subset. We study reliable selection for black-box CATE predictors: selecting candidates whose CATE errors are below a tolerance while controlling the false discovery rate (FDR). Since CATE errors are unobservable, we construct doubly robust proxy errors from pseudo-outcomes; however, naive proxies can lose power under heteroskedasticity because variance overwhelms the reliability signal. We propose Denoised Conformal Alignment, which subtracts an estimated conditional variance component and combines conformal calibration with Benjamini--Hochberg selection. Our analysis shows that validity is governed by stability of proxy/oracle threshold labels, rather than pointwise perfection of the variance estimator. Experiments show substantially improved power while maintaining FDR control across challenging settings.
Jun 21, 2026stat.ML

Null-Calibrated Conformal Selection via Target-Membership Scores

Conformal selection aims to identify test candidates whose unknown responses fall in a target region while controlling the false discovery rate. Existing methods often inherit prediction-oriented nonconformity scores, such as residual or clipped residual scores, from conformal prediction. We argue that the natural score for selection is instead the target-membership probability. This score directly addresses the binary event being selected, and any monotone transform of it gives the Neyman--Pearson oracle ranking at a fixed null selection level. This distinction is irrelevant for mean-monotone targets, where conventional scores induce essentially the same ranking, but becomes important for interval-valued, variance-driven, multimodal, or multi-condition targets, where prediction-oriented scores can be misaligned with selection power. We study membership-score-based conformal selection and isolate one conformal calibration route, Null-Calibrated Conformal Selection (NCCS), which ranks test scores against confirmed non-target calibration examples. Under null exchangeability, NCCS yields finite-sample valid null p-values, which can be combined with BY under arbitrary dependence or with BH under standard positive-dependence conditions. Experiments support the score principle: membership scores match conventional scores on mean-monotone targets, substantially improve over mean-score selection on variance-driven targets, and, when calibrated by NCCS, trade power for finite-sample null validity in rare-target regimes where direct empirical-FDP thresholding can be anti-conservative.
Jun 13, 2026stat.ML

Finite Resources False Discovery Rate Control in Structured Hypothesis Spaces

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.
Jun 3, 2026stat.ML

Knockoffs-based False Discovery Rate Control and Simplification for Deep Neural Networks

The deep neural network is a widely used framework in machine learning that has been widely applied in various fields. However, deep neural networks often involve a large number of parameters and inputs, many of which may be irrelevant to the goal or true output. These parameters and input variables not only increase computational complexity, but also contribute to additional computational cost. One solution to this problem is knockoff methods, which have proven successful in controlling false discovery rates in high-dimensional regression. Building on the knockoff methods and using the regularised neural network, this paper proposes three variable screening methods under the condition of controlling false discovery rates: one layer filter, multiple layers filter, and variable weight aggregation filter. In comparison with existing algorithms, we find that our algorithms show satisfactory performance.
May 29, 2026stat.ME

A Distribution-Free Framework for Rewrite-Based Human-text Detection via Knockoff Filtering

We propose a distribution-free statistical framework that converts arbitrary rewrite-based detectors into detectors with finite-sample FDR guarantees without retraining. Our key observation is that rewrite-based detection implicitly constructs knockoff samples, enabling LLM-generated text detection to be formulated as a multiple hypothesis testing problem with knockoff structure. This perspective separates the design of detection statistics from the control of false discoveries, allowing existing rewrite detectors to inherit finite-sample false discovery rate (FDR) guarantees through a simple calibration procedure. We demonstrate reliable FDR control with meaningful detection power across three detection models, 19 domains, and four LLMs.
May 29, 2026cs.LG

Few-Shot Resampling for Scalable Statistically-Sound Data Mining

A key step in knowledge discovery is the evaluation of data mining results. In several applications, including pattern mining, graph analysis, and others, this step includes the evaluation of the statistical significance of the results, to avoid spurious discoveries due only to noise or random fluctuations in the data. While specialized procedures have been developed for some specific applications, resampling-based approaches are widely used, in particular for complex analyses where analytical results cannot be derived. However, current resampling-based approaches require the generation and analysis of thousands of resampled datasets, and are therefore impractical for large datasets or computationally intensive analyses. In this paper, we introduce FewRS, a simple and effective resampling-based approach to assess the statistical significance of data mining results with rigorous guarantees on the probability of false discoveries. Our approach can be used in every situation where resampling-based approaches are applied. FewRS builds on our derivation of a novel bound to the supremum deviation of test statistics representing the quality of data mining results. We prove that FewRS needs to generate and analyze an extremely small number of resampled datasets, leading to a highly scalable approach with wide applicability. We test our approach on common tasks such as pattern mining and network analysis. In all cases, our approach results in a reduction of up to two orders of magnitude in running time compared to the state of the art, while preserving high statistical power, enabling the statistical validation of data mining results on large-scale real-world datasets.
May 26, 2026stat.AP

Data-driven sparse identification of governing PDEs via knockoff filters and multi-criteria trade-offs

We propose KO-PDE-IDENT, a data-driven framework for identifying parsimonious partial differential equations (PDEs) with false discovery rate (FDR) control. PDE discovery from noisy observations is often hindered by extreme multicollinearity among candidate terms, which causes typical sparse-regression methods to select spurious terms. To address this problem, KO-PDE-IDENT initially mines a support set of potential candidate terms via model-X knockoff filters with finite-sample FDR control, then refines and ranks the surviving PDE alternatives. The framework integrates three components. First, knockoff feature statistics are constructed by coupling ℓ0\ell_{0}-constrained adaptive best-subset selection with SHapley Additive exPlanations (SHAP), yielding an effective and computationally efficient difference statistic. Second, a recursive feature elimination (RFE) procedure removes terms whose marginal contributions are dispensable and assesses statistical necessity through knockoff-perturbed hypothesis testing. Third, the final model selection is formulated as a multi-criteria decision-making (MCDM) problem, where the optimal governing equation is the alternative that best balances a wide range of criteria such as predictive accuracy, model complexity and coefficient uncertainty. We evaluate KO-PDE-IDENT on five canonical PDEs under severe noise corruption. Empirical results show that our framework can exactly recover the true PDE structure, eliminating false discoveries while retaining all true underlying terms, with low coefficient estimation error.
May 26, 2026stat.ME

Structure-Adaptive Conformal Inference for Large-Scale Out-of-Distribution Testing

This paper addresses structured out-of-distribution (OOD) testing in high-stakes machine learning applications. Traditional conformal methods rely on joint exchangeability, making it difficult to incorporate auxiliary information such as spatiotemporal or grouping structures. To overcome this limitation, we propose the structure-adaptive conformal q-value (SCQ), a significance index that integrates individual test evidence with structural patterns. We also develop pseudo-score-guided transductive automated model selection (P-TAMS), which adapts conformalized model selection to structured OOD testing across a toolbox of candidate models. Together, SCQ and P-TAMS form a unified framework under pairwise exchangeability, providing finite-sample error-rate control, improved power, and enhanced interpretability. Experiments on simulated and real data demonstrate that the proposed approach controls the false discovery rate and performs well across diverse settings.
May 20, 2026stat.ME

Everywhere Valid Bounds on False Discovery Proportions in Conformal Inference

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.
May 17, 2026stat.ME

Controlling False Discovery in Arbitrarily Structured Hypothesis Spaces via Reproducing Kernels

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.
May 13, 2026stat.ML

Conformal Anomaly Detection in Python: Moving Beyond Heuristic Thresholds with 'nonconform'

Most anomaly detection systems output scores rather than calibrated decisions, leaving practitioners to choose thresholds heuristically and without clear statistical interpretation. Conformal anomaly detection addresses this limitation by converting anomaly scores into calibrated p-values that are valid under the statistical assumption of data exchangeability, with a growing literature extending this idea beyond that setting. We present 'nonconform', a Python package for applying conformal anomaly detection within existing machine-learning workflows, and use it as the basis for an implementation-grounded introduction to the field. The package integrates with 'scikit-learn', 'pyod', and custom anomaly detectors, and provides a unified interface for calibration, p-value generation, and false discovery rate control. It supports several conformalization strategies, ranging from simple split-conformal calibration to more data-efficient and shift-aware extensions. Through a progression from foundational concepts to advanced conformalization strategies, complemented by code examples, the paper connects the statistical ideas behind conformal anomaly detection to their practical use in 'nonconform'. Empirical results demonstrate that the implemented methods enable statistically principled anomaly detection. Together, the package and exposition aim to make core conformal anomaly detection workflows more accessible and reproducible in experimental and production-oriented settings.
May 13, 2026stat.ML

A Regret Perspective on Online Multiple Testing

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 Weighted Regret\textit{Weighted Regret}. Under this metric, we prove the Duality of Regret Conservation\textit{Duality of Regret Conservation}: purely deterministic procedures ensuring strict FDR control inevitably incur an Ω(T)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(T)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.
May 7, 2026stat.ML

Decentralized Conformal Novelty Detection via Quantized Model Exchange

This work studies decentralized novelty detection with global false discovery rate (FDR) control across heterogeneous composite null distributions, without sharing the raw data due to privacy and bandwidth considerations. We propose a framework based on the exchange of quantized surrogate models, allowing independent agents to share low-precision representations of locally learned non-conformity score functions. We prove that evaluating data against these quantized composite scores preserves conditional exchangeability, providing rigorous finite-sample guarantees for global FDR control. Empirical studies on synthetic datasets confirm our theoretical results, demonstrating that the proposed approach maintains competitive statistical power while drastically reducing the communication cost.
Apr 13, 2026cs.LG

Beyond Fixed False Discovery Rates: Post-Hoc Conformal Selection with E-Variables

Conformal selection (CS) uses calibration data to identify test inputs whose unobserved outcomes are likely to satisfy a pre-specified minimal quality requirement, while controlling the false discovery rate (FDR). Existing methods fix the target FDR level before observing data, which prevents the user from adapting the balance between number of selected test inputs and FDR to downstream needs and constraints based on the available data. For example, in genomics or neuroimaging, researchers often inspect the distribution of test statistics, and decide how aggressively to pursue candidates based on observed evidence strength and available follow-up resources. To address this limitation, we introduce post-hoc CS (PH-CS), which generates a path of candidate selection sets, each paired with a data-driven false discovery proportion (FDP) estimate. PH-CS lets the user select any operating point on this path by maximizing a user-specified utility, arbitrarily balancing selection size and FDR. Building on conformal e-variables and the e-Benjamini-Hochberg (e-BH) procedure, PH-CS is proved to provide a finite-sample post-hoc reliability guarantee whereby the ratio between estimated FDP level and true FDP is, on average, upper bounded by 1, so that the average estimated FDP is, to first order, a valid upper bound on the true FDR. PH-CS is extended to control quality defined in terms of a general risk. Experiments on synthetic and real-world datasets demonstrate that, unlike CS, PH-CS can consistently satisfy user-imposed utility constraints while producing reliable FDP estimates and maintaining competitive FDR control.
Dec 4, 2025stat.ML

Provable FDR Control for Deep Feature Selection: Deep MLPs and Beyond

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 nn diverges faster than the latent dimension q∗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 B\mathbf{B}-right orthogonal invariance of the design matrix, and we discuss broader generalizations. We also present numerical experiments that underscore the theoretical findings.
Nov 10, 2025cs.SE

Structural Enforcement of Statistical Rigor in AI-Driven Discovery: A Functional Architecture

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.
Dec 1, 2023stat.ME

Multiple Testing of Linear Forms for Noisy Matrix Completion

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.