False Discovery Rate

Causal discovery from observational data is a fundamental yet challenging task in scientific research. While existing approaches are primarily based on conditional independence tests, structure scores, or restrictive functional assumptions, we propose Decoupled Causal Discovery (DCD), a novel decoupling-based perspective that does not rely on these methodologies. DCD directly identifies the Markov boundary (MB) by decoupling non-target variables via weighting functions, such that only variables within the MB preserve dependence with the target under the decoupled distribution. Building on this, DCD iteratively constructs the Completed Partially Directed Acyclic Graph (CPDAG) by exploiting structural asymmetries within the MBs. We establish the theoretical identifiability, soundness, and completeness of DCD. Empirical evaluations demonstrate that DCD achieves strong performance, particularly excelling in challenging noise regimes.

Experimental design is commonly framed as choosing the experiment expected to provide the most information. Under partial identifiability however, persistent nuisance uncertainty can make the same observation carry different structural meanings. We introduce Resolution-Aware Experimental Design (RAED), which selects an experiment by the smallest expected nonempty structural candidate set achievable subject to false-exclusion control. We prove an exact cross-nuisance aliasing separation: an experiment can be preferred by structural and full-latent information gain, average classification, and nuisance-marginalized informativeness while having arbitrarily poorer valid structural resolution. RAED nevertheless preserves the expected ordering under a genuine composite Blackwell comparison. To make this criterion operational, we develop a learned score-based implementation with finite-sample nuisance-average and positive-tail calibration, and characterize a rare-tail sample-complexity obstruction. Under constrained sensing, two subsurface-flow benchmarks exhibit genuine RAED--expected-information-gain (EIG) experiment-selection disagreements, with the clearest and largest held-out resolution differences in WCA. In a fluvial benchmark, tail protection changes the selected physical experiment and replaces hard-region false exclusions primarily with explicit ambiguity. In a mechanistic methane-oxidation benchmark, a prospectively specified 5% false-exclusion tolerance also yields a nontrivial finite-sample population guarantee for tail-sensitive nuisance risk, with 95% joint confidence across all three structural families.

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.

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.

The problem of learning the graphical Markov blanket (MB) of a variable from data has applications in many areas such as structure learning for Bayesian networks and Markov random fields, causal discovery, and feature selection. However, a common assumption most methods make is that the conditional independencies in the distribution imply the same separation in the graphical structure -- also known as the faithfulness assumption. Unfortunately, this assumption can be violated by higher-order dependencies such as XOR and parity-type relations, and -- on finite samples -- by empirical violations that, in extreme cases, even induce spurious dependencies absent from the true distribution. Therefore, in this paper we propose a "k-order" relaxation of the faithfulness assumption that captures parity type relationships between k+2 variables. We then propose a proof of concept algorithm called k-order Markov blanket (kOMB) that uses this relaxation for MB discovery. Finally, we empirically show how kOMB can recover the MB of a variable under both true and empirical violations of faithfulness. Code available at: https://github.com/lklee9/k-order-Markov-blanket

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.

Motif discovery, the search for recurring patterns within a time series, is a core primitive of exploratory data analysis. A pattern, however, is defined by its duration, which analysts rarely know in advance. To resolve this unknown duration, an interval of window lengths is defined, and the accepted method is to try every length in that interval. Existing pan matrix profile (PMP) methods compute one z-normalized matrix profile per length, so $L$ lengths cost $L$ quadratic self-joins over the same series. We introduce Panache, to our knowledge the first one-pass streaming algorithm for z-normalized PMP motif discovery. It replaces the repeated self-joins with a single scan whose runtime is near-linear in the series length. The key observation is that mean-centering a subsequence changes only its DC Fourier coefficient, so the non-DC spectrum of every z-normalized subsequence can be maintained online by sliding-DFT recurrences and running statistics. This spectral state is the key under which similar subsequences collide in an occupancy-controlled hash directory and, through Parseval's theorem, yields a lower bound that rejects most colliding pairs before any exact computation. Panache computes every data-dependent parameter itself, leaving only a resource budget to tune. At the default budget, it recovers all top-20 pan-motifs against exact fixed-exclusion ground truth on 17 UCR configurations, and is faster than every CPU and GPU baseline benchmarked in this paper. On Wafer at five million samples over 51 lengths, Panache completes one pass in 2.9 minutes and emits the exact motifs in 6.0 minutes, against 7.95 hours for the fastest exact CPU baseline and 38.3 minutes for SCAMP on an H100 GPU.

On-the-fly category discovery requires deciding for each incoming test sample whether to assign it to an existing category or spawn a new one. Existing methods typically implement this decision through matching-based heuristics, such as radius- or hash-based rules. While effective in practice, these methods usually treat category birth implicitly as a fallback when no existing category matches confidently, rather than as an explicit alternative supported by its own statistical evidence. To address this, we propose DP-BOA, a posterior-predictive decision framework based on an online Dirichlet-process Gaussian mixture model with a Normal-Inverse-Wishart prior. During training, we use labeled data to calibrate a shared NIW prior over category Gaussians and warm-start the known-category posteriors. At test time, for each incoming sample, DP-BOA compares the posterior predictive evidence for assignment to existing categories against the evidence for spawning a new category induced by the DP prior, and then updates category statistics online after the decision. The method captures anisotropic category geometry and naturally adapts decision confidence as evidence accumulates. Across standard OCD benchmarks, DP-BOA consistently outperforms strong baselines and delivers particularly strong novel-class discovery performance while maintaining competitive known-class accuracy.

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.

Existing methods for testing deep neural networks (DNNs) primarily prioritize test inputs likely to reveal model faults under a fixed labeling budget. In practice, choosing that budget is difficult: too little testing misses failures, while too much incurs unnecessary labeling costs. This work studies the stopping problem in DNN testing. We formulate testing as a cost--benefit decision process in which labeling an input incurs cost $c$ and discovering a fault yields value $v$. Based on this formulation, we introduce \textit{AdaStop}, a framework that estimates the marginal fault discovery rate during testing and stops labeling when the estimated rate falls below the threshold $τ= c/v$. Experiments across multiple datasets, architectures, and selection strategies show that $65$--$84\%$ of faults can be discovered using only $9$--$31\%$ of the labeling budget.

Causal discovery with nonlinear mechanisms and latent confounders remains challenging. Existing methods often rely on either linear assumptions or causal sufficiency, limiting their applicability. We propose an MDL-based causal discovery framework that explicitly accounts for latent confounders while allowing flexible nonlinear mechanisms by minimizing the luckiness normalized maximum likelihood (LNML) code-length. The causal relationship between each variable pair is determined by selecting the shortest code-length of the causal model, and we introduce the notion of $Δ$-pseudo-collinearity to identify dependencies induced by latent confounders. Based on these ideas, we develop a greedy algorithm, termed Pseudo-Collinearity Guided Causal Discovery (PCG-CD). Experiments on synthetic and real-world datasets demonstrate that the proposed method accurately recovers directed causal relationships and effectively detects latent confounders.

Conditional functional dependencies (CFDs) are functional dependencies with a restricted scope: they specify the context in which a dependency holds and are useful for data-quality tasks, specifying complex integrity constraints, and extracting valuable insights from data. We study the CFD discovery problem, which is computationally demanding. We build on the state-of-the-art CFDFinder algorithm and introduce a set of algorithmic and engineering improvements, including a parallelization strategy, to produce ParCFDFinder. Our implementation is integrated into Desbordante - a high-performance open-source data profiler written in C++ that exposes a Python interface, enabling CFD discovery to be invoked from any Python program. Experimental results show that our enhancements speed up the algorithm by up to $318\times$ ($118\times$ on average) and reduce memory usage by up to $23\times$ ($14\times$ on average) compared with the existing Java-based implementation of Metanome. Integrating ParCFDFinder into Desbordante makes it possible, for the first time, to conveniently discover CFDs on datasets with hundreds of thousands of rows on a commodity machine within a reasonable time.

Conditional inference trees (CIT) and conditional inference forests (CIF) reduce split-selection bias by testing features before choosing split thresholds, but repeated permutation tests and threshold searches can make these methods computationally expensive. We study CIT and CIF as top-$k$ feature-ranking methods for downstream prediction using real-data benchmarks, runtime ablations, and synthetic feature-recovery experiments. At a fixed node, if the features and permutation budget do not depend on the node responses, Bonferroni-corrected $+1$ Monte Carlo permutation $p$-values control nodewise rejection under the complete permutation null. CIF ranks 4th among 17 classification methods on 22 datasets and 3rd among 18 regression methods on 8 datasets. With Bonferroni correction held fixed, the CIF runtime ablations indicate that adaptive stopping and the number of thresholds searched have the largest measured effect on runtime: turning off adaptive stopping and using exact threshold search increase fitting time by 4.0--8.4$\times$ and 1.9--10.8$\times$, respectively, while downstream score changes are at most 0.011. Sparse high-$p$ simulations indicate that forest feature sampling can leave informative features out of many split decisions. Overall, the results support CIF as a top-$k$ feature-ranking method in the evaluated downstream prediction benchmarks.

Feature rankings are widely used in supervised feature selection because they are simple, scalable and easy to interpret. Variables are first ranked by a relevance score, and a subset is then obtained by retaining the top-ranked variables. Although the first stage has been extensively studied, the second is often governed by an arbitrary cardinality, an empirical threshold or cross-validation, without a direct interpretation. This raises a basic question: given a feature ranking, when is there enough accumulated class-separation evidence to stop selecting features? This paper develops a distributional framework for transforming supervised feature rankings into class-independent subsets through an explicit risk-calibrated stopping rule. For each variable and each pair of classes, marginal separation is measured by the Bhattacharyya coefficient between the corresponding class-conditional distributions. The proposed method selects a single global subset shared by all classes by retaining the shortest prefix of a ranking whose residual product overlap falls below a prescribed threshold for every relevant class contrast. We derive binary and multiclass Bayes-risk bounds for the labelled product marginal problem, and obtain prior-dependent and prior-free calibrations of the residual-overlap threshold from a target all-pairs risk level. An empirical comparison on high-dimensional genomic datasets illustrates that the rule can reduce tens of thousands of variables to a few dozen while maintaining predictive performance statistically comparable to the all-features baseline. As the stopping rule only requires one-dimensional marginal overlap estimates and scans a precomputed ranking, it is well suited to very high-dimensional settings where exhaustive subset search is infeasible and interpretable truncation of feature rankings is essential.

Hybrid models combine trusted physics with data-driven correction, but a physical model is rarely wrong everywhere or in the same way. The key diagnostic question is local: where does the model fail, what missing mechanism explains the failure, and is the evidence statistically real? Existing sparse-discovery and discrepancy-learning methods usually fit one global correction, which can spread a local error into clean regimes, bias trusted physical parameters, and provide no calibrated significance for selected terms. We introduce LISDD, Localized, Identifiable Sparse Discovery of Discrepancy, a framework that localizes model error to an operating regime, identifies a sparse symbolic form for the missing mechanism, and certifies the discovery with an exact finite-sample test. LISDD fits the known physics on an automatically detected clean regime, flags discrepant regions with a calibrated residual-energy statistic, selects the local missing term by exhaustive holdout over a candidate library, and confirms significance with a sample-split $F$-test. A false-discovery-rate extension handles multiple discrepant regions with different missing mechanisms. In controlled experiments, LISDD keeps physical-parameter bias at 0.002 versus 0.43 for global-discrepancy and black-box baselines, raises localization $F_1$ from 0.44 to 0.80, recovers the correct symbolic form with probability one, attains exact detection, and controls the multi-region false-discovery rate while recovering every planted mechanism. The result is a calibrated diagnostic tool for grey-box building-energy models when a fixed physical law silently breaks in one operating regime.

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.

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.

Scientific discovery saturates when new hypotheses cease to provide independent information, even if the nominal hypothesis space remains large. We study hybrid discovery systems that combine structured local search with LLM-generated non-local proposals and pose the Search Compression Hypothesis: non-local exploration helps only when three geometric conditions co-occur: spectral compression, orthogonal escape from the explored span, and residual signal alignment with the target. We formalize these conditions, derive necessary conditions for hybrid advantage, and test the mechanism in controlled synthetic environments, large-scale A-share factor discovery, and symbolic-regression benchmarks; a public tabular operational sanity check tests the associated budget-allocation implication. Signal-planting and directed-versus-random experiments show that novelty alone is insufficient: random orthogonal jumps expand coverage but do not improve yield without predictive alignment. Across compression sweeps, real factor archives, and LLM-SRBench tasks, hybrid gains concentrate in weakly represented but target-bearing directions and vanish as the hypothesis space approaches full rank. The framework turns LLM-guided discovery from generic novelty search into a diagnostic procedure for deciding when directed non-local exploration is warranted.

Machine-learned anomaly detection is reshaping searches for new physics, but it has outrun the statistics used to interpret it. A raw anomaly score has no calibrated meaning, a model that scans many regions inflates the look-elsewhere effect, and the asymptotic significances the field relies on are blind to the background mismodelling that anomaly detectors are especially prone to. We propose a calibration layer, built on conformal prediction, that turns any anomaly score into a defensible significance with distribution-free, finite-sample guarantees. Conformal prediction converts scores into valid local p-values, weighted and Mondrian variants repair the sideband-to-signal-region exchangeability failures that resonant searches suffer, and a Gross-Vitells step carries the result through to a look-elsewhere-aware global significance. The layer does two things at once. It exposes miscalibration that the standard pipeline cannot see, and it corrects it without retraining the detector. On public LHC Olympics data, a classifier develops a substructure-mass correlation that makes sideband-calibrated background p-values anti-conservative. Taken at face value, this manufactures a $\sim 46σ$ excess from background sculpting alone, which the label-free weighted correction removes, restoring an honest null. When run as a blind wide-mass bump hunt, the standard asymptotic and unweighted procedures fabricate $\gtrsim10σ$ excesses and $\approx5σ$ excesses even in signal-free windows, while the conformal layer raises no false alarms and its global false-positive rate is verified on background-only pseudoexperiments. The result is an auditable, detector-agnostic path from an uncalibrated score to a trials-factor-aware significance, ready to be folded into experimental anomaly searches.

Open-ended scientific discovery asks agents to move beyond executing analyses for predefined questions. Across multiple rounds of exploration, a discovery agent must decide which phenomena warrant investigation while avoiding overinterpretation, where emerging claims exceed the evidential scope of the analyses. This creates an evidence-calibration problem: the exploration trajectory must be coupled with claim status so that evidence can guide both what to investigate next and what can be claimed. We introduce \textsc{StatefulDiscovery}, a discovery framework that externalizes investigation state and uses it to coordinate frontier selection, evidence acquisition, and claim adjudication. We evaluate \textsc{StatefulDiscovery} across 40 real-data discovery tasks. Compared with several baselines, \textsc{StatefulDiscovery} produces more claims overall judged to be both well-supported and high-value. Ablations indicate distinct roles for structured hypotheses, local adjudication, frontier control and persistent states. Together, these results suggest that explicit discovery state can couple exploration with evidence-calibrated claim formation. Our code is released at \href{https://github.com/SUSTech-GenAI/StatefulDiscovery.git}{https://github.com/SUSTech-GenAI/StatefulDiscovery.git}.

Raw numerical datasets remain less systematically examined in integrity screening than images, plagiarism, or summary-statistic inconsistencies. We developed the Fabrication-risk Digit Randomness Screening model (FDRS), a statistical and machine-learning framework for detecting non-random digit-pattern irregularities in numerical research data. FDRS integrates single- and joint-decimal-digit tests, Cramer's V, entropy metrics, Kullback-Leibler divergence, digit-preference indices, progressive subsampling, and semi-supervised risk scoring. It was evaluated using an instrument-derived enzymatic absorbance dataset (RawData, n=253) and a blinded manually simulated irregular dataset (ErrData, n=255). RawData showed no significant deviation in single third-decimal-digit analysis, whereas ErrData showed a significant deviation. In joint third-fourth decimal digit analysis, ErrData showed higher Cramer's V, lower normalized entropy, higher KL divergence, and a more persistent progressive-subsampling deviation signal. In internal validation, Elastic-net Logistic Regression achieved the highest AUC (0.98395) and lowest Brier score (0.048439), while Random Forest achieved the highest accuracy (0.926667) and balanced accuracy (0.935). RawData received a low ensemble risk score of 0.124627 and was classified as Grade 0; ErrData received a score of 0.740760 and was classified as Grade 3. External real-world benchmarks supported graded risk stratification: three datasets without identified public post-publication concerns were classified as Grade 0 or 1, whereas two datasets from publicly questioned or institutionally handled articles were classified as Grade 2 or 3. FDRS can prioritize raw numerical datasets for further review by integrating interpretable statistical and machine-learning features. It is an auxiliary digit-structure screening tool, not standalone evidence of fabrication or misconduct.

Background: Since 1990 many feature selection methods have been proposed across heterogeneous applications. To validate the usefulness of a new method, it needs to be compared against at least one baseline method from the existing literature on a feature selection task using at least one dataset. Recent developments in tabular Deep Learning (DL) and data valuation in Machine Learning (ML) suggest that the evaluation of new methods, algorithms, and models may be consciously or unconsciously biased. We hypothesise that a similar trend exists in feature selection (FS), particularly in filter feature selection (FFS). The aim of this study is therefore to examine FFS studies to identify factors that influence the evaluation and that might consist entry point for biases in order to recommend stronger principles for FFS evaluation. Methods: We analyse a sample of 28 high profile FFS studies published between 1994 and 2025. The analysis provides reflections on how to examine FFS studies, highlights lessons learned throughout the process, and gives five evidence-based recommendations for future FFS evaluation. Results: Multivariate Linear Regression analysis achieved a score of $R^2=0.33$. It means that 33% of the variance in the performance of new methods against chosen baselines (win rate) is explained by the number of datasets (#Datasets), the number of baselines (#Baselines), and the number of new methods (#NewMethods). Discussion: $R^2=0.33$ is considered medium explanation; which is promising given that this is the first such study. The medium explanation result is due to the fact that win rate is influenced by additional factors such as the maturity of the feature selection domain, the type of datasets and baselines, and the simplicity of the regression model used to explain the relationship.

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.

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.

Fraud detection in payment networks relies on labels generated through heterogeneous and imperfect observation processes, yet existing approaches treat fraud as a homogeneous binary variable. We show that this assumption is structurally incorrect and leads to provable inefficiency. We introduce an observation-mechanism taxonomy that partitions fraud into five classes, each defined by a distinct censorship and labeling pipeline. We prove that estimating fraud rates separately by class and aggregating strictly dominates pooled estimation, with the efficiency gap characterized as a Jensen penalty arising from heterogeneous observation rates. For each class, we derive the binding theoretical constraint on detection, including endogenous label corruption, structural non-observability, and feature non-informativeness. These results establish that fraud detection is fundamentally a collection of distinct estimation problems, each governed by its own observation structure and detection limit.

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 $\ell_{0}$-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.

Many novel unsupervised feature selection methods are proposed each year, yet their empirical evaluation is limited to supervised and unsupervised evaluation metrics computed on selected datasets, along with comparisons to existing methods. However, in the absence of an established evaluation baseline, it is difficult to determine the value added to the existing literature by each of these methods, and how effective their underlying approaches are. We propose using random feature selection as a baseline for evaluating the unsupervised feature selection methods. We empirically show that many of the state-of-the-art methods in unsupervised feature selection are outperformed by random feature selection in both performance and efficiency. Accordingly, we emphasize on the strict requirement of considering random feature selection as a baseline in the development process of novel unsupervised feature selection methods to ensure a consistent improvement over random feature selection.

Unsupervised anomaly detection is widely used in transaction fraud detection where labels are scarce. Isolation Forest (IF) is among the most popular classical methods due to its scalability and ease of deployment. We propose SilIF, an augmentation of Isolation Forest that adds a silhouette-based scoring layer computed in a representation space induced by the trees of the forest. For each point, we extract a vector of per-tree path lengths, cluster these "fingerprints" into structural groups, and compute a silhouette score that measures how well the point fits its assigned group versus the nearest alternative. The silhouette signal is combined with the base IF score via a single hyperparameter alpha. On the IEEE-CIS Fraud Detection benchmark (~590K transactions, 3.5% fraud), SilIF with alpha=1.0 improves over plain Isolation Forest by +0.0080 AUC-PR on average across five seeds, with SilIF winning on all five seeds (paired t-test p=0.046). We also report results on a synthetic credit-card dataset (Sparkov) where the silhouette augmentation does not improve over plain IF, and we characterize the conditions that distinguish the two outcomes. The paper presents SilIF as a tunable, easy-to-deploy enhancement to Isolation Forest with honest reporting of when it helps and when it does not. Code at https://github.com/venkat15vk/silif-anomaly-detection.

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.

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.

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.

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.

High-throughput gene perturbation experiments can test several genetic interventions in parallel, yet experimental budgets remain limited. A central goal is hit discovery: identifying as many perturbations as possible whose phenotypic effect exceeds a predefined threshold. Pure exploration strategies are statistically inefficient, wasting budget on low-value regions. Bayesian optimization methods offer a principled alternative but target a single global optimum, over-exploiting dominant modes while neglecting other high-value regions. We formalize hit discovery as a sequential experimental design problem and propose Probability-of-Hit, an acquisition function that directly targets threshold exceedance by ranking candidates according to their posterior probability of being a hit. We prove asymptotic optimality of this approach and demonstrate strong empirical performance on both synthetic benchmarks and real biological immunology datasets, including up to 6.4% improvement over baselines on the Schmidt IL-2 dataset.

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.

Gaussian process (GP) marginal likelihood scores and kernel conditional independence tests are theoretically appealing for nonlinear causal discovery but computationally prohibitive at scale. We present three complementary RFF-based methods forming a practical toolkit for score-based, constraint-based, and hybrid causal discovery. The Fourier Feature Marginal Likelihood (FFML) score approximates the exact GP marginal likelihood by replacing the $n x n$ kernel Gram matrix with a finite-dimensional feature representation, reducing cost to $O(nm^2 + m^3)$ while retaining the probabilistic interpretation and automatic complexity penalty of the exact score. FFML extends to mixed (continuous and discrete) parent sets via a product-kernel construction, with a Kronecker path for small discrete parent sets and a Hadamard-product path otherwise. The Tetrad Random Fourier Feature (TRFF) score is a complementary BIC-style alternative using penalized Student-t regression with random Fourier features. TRFF offers robustness to heavy-tailed noise and faster runtime than FFML. Empirically, TRFF and FFML exhibit a complementary precision-recall profile: TRFF achieves higher precision while FFML achieves better recall and lower SHD overall. The Fourier Feature Conditional Independence (FFCI) test is a fast nonparametric CI test for mixed data, using ridge residualization in feature space and a Frobenius-norm cross-covariance statistic approximated as a weighted sum of chi-squared variables. Empirically, BOSS+FFML achieves the lowest SHD on nonlinear data, while BOSS+TRFF offers the highest precision. When run through PC-Max, FFCI and RCIT exhibit complementary precision-recall profiles: RCIT is more precise while FFCI achieves better recall and substantially lower SHD, at approximately twice the runtime.

Statistical change point (CP) detection methods typically rely on likelihood-based inference and ignore contextual information about plausible CP locations beyond the observed sequence. Although informative priors provide a natural way to incorporate such information, general and computationally efficient methods for doing so are lacking, especially for multiple CP detection. To address this gap, we propose a prior-informed CP detection algorithm (Pi-Change) that incorporates prior information on CP locations through a time-varying penalty term. We prove that the proposed penalty can be embedded in the Pruned Exact Linear Time framework while preserving the dynamic programming recursion and pruning rule required for efficient multiple CP detection. Across simulation studies and three time-series applications, Pi-Change discourages spurious CPs unsupported by prior information, remains robust to prior misspecification, and improves detection accuracy. More broadly, Pi-Change extends multiple CP detection beyond purely data-driven fitting by incorporating partial prior knowledge in a computationally efficient and interpretable way. It is particularly useful when CPs arise from heterogeneous mechanisms or are associated with known external events, helping quantify the delay between an event and the resulting structural change.

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.

Feature selection (FS) is essential for biomarker discovery and clinical predictive modeling. Over the past decades, methodological literature on FS has become rich and mature, offering a wide spectrum of algorithmic approaches. However, much of this methodological progress has not fully translated into applied biomedical research. Moreover, challenges inherent in biomedical data, such as high-dimensional feature space, low sample size, multicollinearity, and missing values, make FS non-trivial. To help bridge this gap between methodological development and practical application, we propose ROOFS (RObust biOmarker Feature Selection), a Python package available at https://gitlab.inria.fr/compo/roofs, designed to help researchers in the choice of FS method adapted to their problem. ROOFS benchmarks multiple FS methods on the user's data and generates reports summarizing a comprehensive set of evaluation metrics, including downstream predictive performance estimated using optimism correction, stability, robustness of individual features, and true positive and false positive rates assessed on semi-synthetic data with a simulated outcome. We demonstrate the utility of ROOFS on data from the PIONeeR clinical trial, aimed at identifying predictors of resistance to anti-PD-(L)1 immunotherapy in lung cancer. Of the 34 FS methods gathered in ROOFS, we evaluated 23 in combination with 11 classifiers (253 models) and identified a filter based on the union of Benjamini-Hochberg false discovery rate-adjusted p-values from t-test and logistic regression as the optimal approach, outperforming other methods including widely used LASSO. We conclude that comprehensive benchmarking with ROOFS has the potential to improve the reproducibility of FS discoveries and increase the translational value of clinical models.

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.

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.