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Wednesday 12 August

Statistical Methodology

Efficient Response-Adaptive Randomization for Multi-arm Trials with Prioritized Composite Endpoints

The efficient randomized-adaptive design attains the minimal possible variance of the allocation proportion for any pre-specified target and has been extended from two to several treatment arms, but both versions target a single response. Confirmatory trials increasingly rely on several prioritized endpoints, typically efficacy followed by safety, that cannot be reduced to one summary without losing information. The efficient randomized-adaptive design is extended here to targets driven by the net treatment benefit of generalized pairwise comparisons, allowing any number of arms and endpoints of mixed type, including censored time-to-event outcomes. Strong consistency, a law of the iterated logarithm, and asymptotic normality of the allocation proportions are established by combining a sequential Hájek projection for the net benefit with the martingale technique used for the original design, and the design is shown to attain the semiparametric efficiency bound within the class of designs that track a smooth function of the net benefit. In simulations calibrated to a three-arm phase III melanoma trial, the proposed design concentrates allocation on the superior treatment more efficiently than designs driven by a single endpoint, while preserving type I error and power. A redesign of the trial illustrates the practical benefit, and the approach is discussed in relation to current regulatory thinking on adaptive designs for confirmatory trials.
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Statistical Methodology · Cross-listed from econ.EM

Coarsening Latent-Class Probabilities: Directional Distortion and Coverage Loss

Outcomes are regressed on a calibrated probability vector for unobserved class membership. Under a structural conditional mean excluding the score and conditional calibration, the observed-data model reduces to a partially linear regression. The probability vector is a Berkson-type surrogate for membership, so the effect vector $\tau$ is identified without attenuation. In practice the vector is often coarsened to a hard label - an argmax, a confidence threshold - and that label need not retain the Berkson property. For any coarsening the plug-in estimator converges to $\mathcal{A}\tau$, where $\mathcal{A}-I$ is determined by the regression of the discarded part of the score on the retained part. Coarsening therefore leaves $\tau$ undistorted exactly when that regression vanishes, and otherwise distorts some contrasts far more than others. The same operator determines the bias that drives coverage loss. Where that bias is of the order of the standard error, the Wald interval has limiting coverage $\Phi(z-\nu)-\Phi(-z-\nu)$, with $\nu$ their ratio. A fixed bias sends coverage to zero. Operator, standard error, and - through the uncoarsened estimator - the bias are estimable from observed data, so the implied coverage can be approximated before the interval is reported. Simulations show severe coverage loss after argmax coarsening. Three real-data audits exhibit the direction-specific distortion.
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Statistical Methodology

Analytically Corrected Bayesian Modularization for Local Item Calibration

The continuous calibration of pilot items embedded in operational assessments is challenging when pilot samples are small and adaptively routed. We formalize a Bayesian modularization framework for local item calibration that blocks feedback from pilot responses to the operational latent scale: Plausible Values are drawn from the operational posterior, and each pilot item is calibrated by its own local logistic regression. This construction is computationally scalable, protects operational trait estimates from malfunctioning pilot items, and admits Firth's penalized likelihood for sparse routed samples. Because treating imputed traits as fixed predictors induces attenuation, we derive closed-form disattenuation mappings that recover the generating item parameters under normal-ogive, posterior-normality, homoscedasticity, and joint-normality approximations. The resulting Modular Local Calibration (MLC) estimator reaches the target of marginal-likelihood calibration without per-item numerical integration. A multivariate delta-method covariance combined with Rubin's-rules pooling propagates operational item-parameter uncertainty into the focal item standard errors. Monte Carlo simulations for the unidimensional 2PL show that corrected MLC substantially reduces attenuation bias and yields nominal-to-conservative interval coverage in the studied conditions, including under restricted-range MAR routing.
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Tuesday 11 August

Statistical Methodology

Joint Conditional Maximum Likelihood Estimation of Beta Regression for Panel Data with Higher-Order Autoregressive Errors

Existing panel beta regression estimators do not accommodate higher-order autoregressive dependence within a joint likelihood framework. We develop such an estimator: a joint conditional maximum-likelihood beta-AR(k) model extended from a single time series to panel data, and extend it to panel inference through two new covariance estimators - a generalization of Beck-Katz panel-corrected standard errors (PCSE) and a Driscoll-Kraay-style alternative (DK) - to account for the cross-panel dependence the extension introduces. The estimator is evaluated by Monte Carlo simulation spanning AR(1)-AR(3) error structures, three panel sizes, and five series lengths, under both independent panels and genuine cross-panel dependence, against an uncorrected baseline. PCSE generally exhibited superior Type I error control and coverage relative to DK, at a power cost that was modest and partly illusory given DK's own miscalibration. Under genuine cross-panel dependence, the uncorrected estimator's Type I error was severe and did not diminish with additional data, while both corrections resolved it, with PCSE again preferred. An illustrative multi-site disease management example is provided, along with a Stata implementation (xtbetark).
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Statistical Methodology

When Unpaired Sets Support Shared-Corruption Calibration: Moment Geometry and Two-Sample Precision

Collections of diverse observations often share one acquisition, processing, geometric, or channel corruption, while only an unpaired clean reference set is available. For a prescribed low-dimensional correction shared across observations, the observed and clean reference sets support inference only through the response of fixed moments. We formulate this problem as two-sample moment calibration and report a rank-aware information state combining local rank, scaled moment sensitivity, source-separated covariance, and a moment compatibility residual. Full rank gives local moment identifiability, whereas kernel directions remain unresolved to first order. A unified linearization separates observed-set and reference-set uncertainty. Under covariance weighting, the weakest scaled singular value determines worst-direction asymptotic amplification. For an orientation-preserving planar-similarity correction shared across observations, ensemble centroids and a nonzero third-order complex moment yield closed-form global population identification of translation, rotation, and isotropic scale under matched-population and no-clipping assumptions. Controlled validation tests the predicted $N^{-1}$ and $\sigma_{\min}^{-2}$ laws, Gaussian efficiency, and interval coverage. Bounded applications report color corrected-output quality, channel magnitude-response calibration, and a separate paired geometric de-beautification result. The framework therefore reports missing or weak information instead of treating every fitted correction as identified.
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All authors Shuheng Cao, Zhenhao Zhang, Ruiqi Chen, Renjie Cao, Siyu Zhang, Zhaoxiang Feng, Lingwei Dang, Haoyang Wu

Statistical Methodology

Exact Conditional Confidence Intervals for Cramér's V: Near-Nominal and Tight Where the Guaranteed Interval Is Wide and the Software Interval Does Not Cover

Cramér's V, the effect size reported beside almost every chi-square test, is almost never accompanied by a confidence interval, because the interval is a hard nuisance-parameter problem: infinitely many tables share one effect-size value. The two intervals an analyst can reach for are unsatisfactory. The projection of a joint confidence region onto the effect size is guaranteed for every table but wide, over-covering at essentially 1.000 on larger tables; the noncentral inversion the software prints, and the bootstrap, are narrow but do not cover (median coverage 0.31 on this study's grid). This paper supplies an interval that is both valid and informative. Conditioning on the observed margins makes the exact conditional distribution of the Pearson statistic under a non-null association computable with no asymptotics and no Monte Carlo; inverting it yields a near-nominal confidence interval for Cramér's V that is a third to a half the width of the projection, the advantage growing with table size. The one price, stated plainly, is a change of estimand to the effect size at the observed margins; the mid-p default undercovers small effects, where a conservative variant or the projection remains the fallback.
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Statistical Methodology

An Exact Noise Floor for Contingency-Table Effect Sizes: A Per-Table Reporting Gate, and How Often It Would Change Reported Magnitudes

Cramer's V and the other chi-square-family effect sizes are positive under exact independence, so a reported value can be smaller than what the same statistic produces on a table with no association at all. The upward bias is classical (Tschuprow 1925; Bartlett 1937; corrected by Bergsma 2013), and reporting the boundary value, the critical effect size, beside the observed one has been recommended in general form (Perugini et al. 2025); we claim neither. Our contribution is two things a general recommendation does not supply. First, an exact per-table reporting gate: the noise floor V_0.95, the value the effect size reaches by chance 5% of the time under independence, computed from the exact margin-conditional law rather than the asymptotic critical value. The asymptotic floor miscalibrates where reporting is riskiest: on heterogeneous tables its false-alarm rate reaches 0.10 against a 0.05 target, while the exact floor holds nominal. Second, a measurement: across 4,129 real two-way tables from 291 public datasets, 21.8% of labeled effects (cluster-robust 95% CI 17 to 27%) sit on tables with no significant association. We recommend reporting V_0.95, in exact form on sparse or heterogeneous tables, beside every association measure and at the design stage.
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2609.26128 · 11 Aug · 27 pages, 6 figures. Under review at Journal of Applied Statistics. Reproducible code, data, and the derivation companion are openly archived on Zenodo: https://doi.org/10.5281/zenodo.21664321. Part of a contingency-table effect-size series (companions on the point estimate, the confidence interval, and the exact conditional distribution engine)

Statistical Methodology

Time-Varying Multi-Seasonal ARMA Models

We propose an ARMA model that allows for multiple seasonal periods and time varying parameters in both regular and seasonal components, building upon previous work for pure AR processes and the conditional likelihood. The model is parameterized to ensure stability and invertibility at each time point. The parameter evolution is governed by dynamic shrinkage processes, enabling extended periods of essentially constant parameters, gradual changes, and abrupt shifts. The model includes a stochastic volatility component to account for potentially heterogeneous noise, also modeled by a dynamic shrinkage process. A Gibbs sampler is developed using the exact likelihood, with separate updating steps for the latent errors and the unobserved pre-sample history of the process. The time-varying AR and MA parameters are sampled jointly using a fast posterior sampler based on the extended Kalman filter. The model and the efficiency of the Gibbs sampler are evaluated using simulated and real data. A case study on monthly air passenger data in the US during 1990-2024 reveals significant changes in seasonality during the Covid-19 pandemic.
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Statistical Methodology

Estimating the perturbed utility route choice model with trip-level data

We provide an estimator for the perturbed utility route choice (PURC) model that works with data at the level of individual trips. The estimator is a nested fixed-point algorithm that combines an upper bias-corrected linear regression problem with a lower individual-level perturbed utility maximization problem. We establish the statistical properties of the microPURC estimator and confirm these results with an experiment using simulated data. Finally, we demonstrate the estimator in practice using a large real-world dataset.
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All authors Mogens Fosgerau, Nikolaj Nielsen, Thomas Rasmussen, Rui Yao

Statistical Methodology

Semiparametric efficient estimation of the Cox regression coefficient when there can be ties

The Cox model and the Cox regression coefficient are widely used in applied work, although the corresponding statistical theory is principally developed in the continuous case where there can be no tied failure times. In this work, we derive the efficiency bound of the Cox regression coefficient in the Cox model, without imposing continuity or discreteness assumptions on the failure distribution. Then, under a technical assumption that the population failure mass points belong to an unknown finite set, we show that the “exact” estimator in \citet{cox1972regression} is asymptotically efficient. Next, we propose an asymptotically equivalent estimator which solves the efficient score which has lower computational complexity than the exact Cox score. The development employs recently introduced martingale theory, and throughout examples of the general theory are given for both the absolutely continuous case and the discrete case.
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Statistical Methodology

Graphical Models for Multivariate Count Data

The classical multinomial, negative multinomial, hypergeometric, and negative hypergeometric distributions are naturally organized by two features of the sampling scheme: sampling with or without replacement and stopping after a fixed number of draws or a fixed number of failures. We complete the graphical analogue of this scheme for decomposable graphs by adding graphical hypergeometric and graphical negative hypergeometric distributions to the previously introduced graphical multinomial and graphical negative multinomial models in Danielewska et al. (2025). The resulting four families provide a unified parametric framework for graphical modeling of multivariate count data, in which dependence and admissible configurations are encoded by a graph. They interpolate between products of univariate distributions for the empty graph and the corresponding classical multivariate distributions for the complete graph, while retaining explicit Markov factorizations and tractable sampling representations. We further develop a unified Bayesian hierarchy based on graphical Dirichlet-type distributions, obtaining explicit posterior and predictive laws. The framework is particularly natural for count data arising under exclusion or incompatibility constraints. We discuss several such applications and illustrate its practical potential using Rydberg-atom excitation data.
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Statistical Methodology

Every pooling rule has its world: matching probability combination rules to situations and stakes

Systems often need to combine two numerical assessments of the same yes/no question. The appropriate formula depends on what the numbers represent and on how the sources are related. Averaging is correct when one of several alternative interpretations applies; multiplying odds is correct when probability reports are based on conditionally independent evidence and a common prior; and probabilities of alternative successful derivations require their dependence or shared evidence to be taken into account. We state the assumptions behind several common combination rules and derive the corresponding combined probabilities. Two groups of Monte Carlo experiments address different questions. First, controlled generating mechanisms verify that the derived rule recovers the correct probability in the situations for which its assumptions hold. Second, the same mechanisms measure the consequences of using a mismatched rule, using logarithmic score and threshold decisions with different costs. Distinct pooling rules can produce the same binary decision at threshold 1/2 while assigning substantially different probabilities, so binary accuracy alone can conceal important differences. We also give probabilistic interpretations of conflicting-evidence rules and show that, for overlapping derivations, retaining the identities of shared uncertain premises permits direct calculation of the probability that at least one derivation is available. Pairwise combination of proof probabilities loses information when there are three or more derivations.
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Statistical Methodology · Cross-listed from q-bio.GN

CosMAP: Contrastive Manifold Approximation and Projection for Dimensionality Reduction of Omics and Genealogical Data

Omics datasets, particularly single-cell RNA sequencing data, are high-dimensional, sparse, noisy, and dominated by zero values, making faithful low-dimensional representation challenging. Existing dimensionality-reduction methods may distort local neighbourhoods, global organization, or the cohesion of meaningful populations, with similar limitations arising in genealogical data. We introduce Contrastive Manifold Approximation and Projection (CosMAP), a graph-based unsupervised dimensionality-reduction method for producing faithful and interpretable embeddings. CosMAP extends the graph-based framework of UMAP by combining cosine-similarity neighbourhoods with temperature-normalized contrastive affinities, which are optimized in the embedding space using an attractive–repulsive objective. It further employs a two-phase refinement strategy: an intermediate higher-dimensional representation is first learned and then used to reconstruct the neighbourhood graph and initialize the final low-dimensional embedding. We evaluate CosMAP on MNIST and USPS handwritten-digit datasets, mouse retina and cortex single-cell RNA-sequencing datasets, and a large genealogical kinship dataset derived from BALSAC-CARTaGENE. Compared with state-of-the-art dimensionality-reduction methods, CosMAP produces more coherent visual representations, improves neighbourhood preservation, and provides clearer global organization of digit classes, biological cell populations, and regional genealogical patterns. These results indicate that CosMAP offers a robust framework for exploratory analysis of complex, sparse, high-dimensional data. The implementation is publicly available at https://github.com/FenosoaRandrianjatovo/CosMAP-dr.
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All authors Fenosoa Randrianjatovo, Maya Saleh, Simon Girard, Amadou Barry

Statistical Methodology

Bayesian inference on beta diversity via feature allocation models with imperfect detection

Beta diversity quantifies variation in species composition across ecological communities and is fundamental for understanding biodiversity patterns across space and environmental gradients. Statistical inference on beta diversity is challenging: species occurrence data are high dimensional, many species remain unobserved despite extensive sampling, and surveys are subject to imperfect detection. Existing approaches are typically based on empirical dissimilarity indices with limited uncertainty quantification or on models that rely on unrealistic exchangeability and perfect detection assumptions. We introduce a new class of Bayesian feature allocation models for partially exchangeable species occurrence data with imperfect detection. The framework combines latent feature allocation models with occupancy-based detection mechanisms, allowing heterogeneous species compositions across sites, explicitly accounting for false negatives, and accommodating the discovery of previously unobserved species. We develop coherent probabilistic inference for species sharing and beta diversity, deriving explicit posterior and predictive distributions for between-community heterogeneity, including the number of shared species across sites and the number expected under future sampling. These analytical results yield interpretable posterior summaries of compositional heterogeneity and facilitate scalable inference in high-dimensional biodiversity studies. Simulation studies and an application to global fungal biodiversity data demonstrate improved inference on species sharing and between-community diversity.
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Statistical Methodology

Detection coherence of tests

There exist tests calibrated under a null narrower than the one implied by their test statistic – the detection-null set. The part of the detection-null set not in the null is the test's blind spot. A framework for assessing detection coherence – whether a test's blind spot is empty – is introduced, built on new concepts of calibration statistic, detector, detection functional, detection-null set, and blind spot. It is demonstrated that the Wilcoxon–Mann–Whitney, Kruskal–Wallis, Friedman, and logrank tests are detection incoherent as unrestricted tests. Detection incoherent tests may become coherent under restrictions that make the blind spot empty, though domain restriction is not a reliable route to coherence in practice, since the boundary of the coherence-restoring domain is unknown and unverifiable. The Kolmogorov–Smirnov and Zaremba tests, and the Maximum Mean Discrepancy test with a characteristic kernel, are shown to be universally detection coherent. Due to the blind spot, a detection incoherent test misses discoveries when non-rejecting and yields spurious discoveries when rejecting, in both cases regardless of sample size. Detection incoherent tests should be abandoned.
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2608.11177 · 11 Aug · The detection functionals of the KW and logrank tests are indexed by the sample allocation, following the discovery by Brunner, Konietschke, Bathke and Pauly (2021) of dependence of consistency regions on allocation; incoherence is now demonstrated at every allocation

Statistical Methodology

Goodness-of-Fit Tests and Calibration Machine-Learning Algorithms for Logistic Regression with Sparse Data

Assessing the goodness-of-fit of a logistic regression model is a critical prerequisite before the model is used for inference. However, goodness-of-fit (GOF) tests such as the chi-square and deviance tests often give invalid results when the data are "sparse" – a common issue with continuous predictors like age or weight, where the asymptotic distributional assumptions are not satisfied. This thesis studies classical GOF tests for binary logistic regression under both grouped and sparse data, comparing about 30 statistical tests and machine-learning calibration algorithms. These span the classical chi-square and Hosmer-Lemeshow variants, standardized Pearson statistics, covariate-space partitioning, smoothing-based methods, and contemporary calibration machine-learning and bootstrap procedures. At a fixed size, the GiViTI calibration test (2016), McCullagh (1989), Osius-Rojek (1992), le Cessie (1995) and Stute-Zhu (2002) proved empirically powerful, balancing correct identification of bad models (high empirical power) against not raising false alarms on good models (correct empirical Type I error). Relying on formal methods alone is insufficient: visual diagnostics such as calibration plots are a vital exploratory step for detecting model deficiencies that formal tests often overlook. An application to real data (the Low Birth Weight dataset) shows that many of these tests fail to give valid conclusions when exposed to the complexities of actual datasets. The main conclusion is that model assessment requires a combination of several powerful statistical tests alongside careful visual inspection of model calibration.
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Statistical Methodology

Resampling simplicial depth

The simplicial depth (SD) is a commonly used indicator of the centrality of points $x\in\mathbb{R}^d$ with respect to distributions $P$ on $\mathbb{R}^d$. Asymptotic theory for the sample SD is based on its representation as a $U$-statistic, which can be either non-degenerate or degenerate. For $d=2$, we prove under mild conditions that this $U$-statistic is degenerate with rate $n$ if and only if $x$ is a center of symmetry of $P$. Otherwise, the asymptotic distribution of SD is non-degenerate with rate $\sqrt{n}$. Because the location of the center of symmetry of $P$ is usually unknown, these two modes of behavior complicate the estimation of the sample distribution of SD at $x$. We propose a two-step adaptive subsampling procedure for estimating that distribution. First, an estimator $\widehat \gamma$ of a parameter $\gamma\in\{1/2, 1\}$ characterizing the correct rate of convergence $n^\gamma$ of SD is constructed based on subsampling. Our estimator uses a bias correction suitable for $U$-statistics. Second, $\widehat \gamma$ is employed for approximating the distribution of the sample SD. We prove the consistency of this subsampling approach and illustrate its usefulness (i) in the construction of confidence intervals for SD, and (ii) in an SD-based supervised classification task
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Statistical Methodology · Cross-listed from stat.OT

Generative AI use in Statistical Research: A Literature Review and Code Generation Case Study

Generative artificial intelligence (GenAI) is a large language model (LLM) that has the ability to generate media based on user-provided prompts. Given the demonstrated capabilities of models such as ChatGPT in information synthesis and programming, there is growing interest in their potential role within the research process. However, little work has evaluated recent GenAI models for research tasks in the domain of statistical research. This case study examines GenAI as a tool for developing a literature review and translating methodology from academic papers into code, for the topic of dynamic treatment regime (DTR) estimation via the dynamic weighted ordinary least squares (dWOLS) approach. Specifically, we utilize ChatGPT-5 and ScholarAI (Sept-Nov 2025 release) in the processes of identifying relevant sources for the literature review, creating summaries of papers, identifying gaps in research, and R code generation to implement methodology. Our findings show that current GenAI models lack the depth and contextual understanding required to accomplish these tasks without careful prompting and supervision of a knowledgeable researcher. Nonetheless, GenAI has potential to increase efficiency of tasks which take advantage of its search and summarization abilities, as well as basic code debugging and algorithm formation. We demonstrate that under a knowledgeable guide, GenAI can function as a research tool, but not as a substitute for methodological expertise.
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Statistical Methodology · Cross-listed from stat.AP

Early Pregnancy Treatment Decisions: Designing Perinatal Pharmacoepidemiology Studies using Real-World Data

Research on the use of medications during pregnancy has two primary goals: to detect signals that medications may be harmful to a pregnant individual or fetus, and to support better treatment of pregnant people who require pharmacotherapy. Target trial emulation has been proposed as an approach to estimate the effects of interventions in real world data, with recent extensions to the pregnancy setting. This approach focuses on aligning eligibility and treatment initiation with start of follow up, which is particularly desirable given methodological challenges specific to pregnancy, such as right and left censoring and truncation, competing events, differences in gestational length, and varying etiologically susceptible periods. While previous work on target trial emulation in pregnancy has focused on initiation versus non-initiation of point treatments such as vaccines or antibiotics, this paper focuses on research questions regarding changes to pregestational treatment regimes, and aims to highlight opportunities and approaches to designing studies that align with relevant time points during early pregnancy at which treatment decisions occur in clinical practice. Using the example of treatment for type 2 diabetes mellitus, we review methods for identifying pregnancy episodes in routinely collected healthcare data, introduce possible time zero candidates, and discuss analytic approaches that minimize potential bias due to selection and immortal person time.
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All authors Mollie E. Wood, Robert W. Platt, Jennifer A. Hutcheon, Jacqueline M. Cohen, Chase D. Latour, Andrea V. Margulis, Lucia C. Petito, Sonia M. Grandi

Statistical Methodology

A parametric framework for assessing and estimating sufficient follow-up time in cure models

Reliable estimation of cure fractions depends critically on adequate follow-up. Classical procedures for assessing follow-up sufficiency are primarily inferential, whereas a separate body of literature estimates time to cure using excess-hazard, conditional cure-probability, or residual-survival definitions. These two approaches remain largely disconnected: assessing the adequacy of observed follow-up does not generally quantify the additional follow-up required under an explicit tolerance, whereas estimating time to cure does not itself provide a formal inferential assessment of the available follow-up. We develop a unified parametric framework that combines the Parametric Follow-up Sufficiency Test, which compares the terminal Kaplan-Meier estimate with the cure fraction estimated from a parametric mixture cure model, with two complementary tolerance-based formulations: the Plateau Distance Criterion on the population survival scale and the Residual Survival Criterion on the susceptible survival scale. We derive closed-form expressions for both criteria under the Weibull mixture cure model and establish that they yield identical minimum follow-up times under an appropriate transformation of their tolerance parameters. We evaluate the finite-sample performance of the framework through Monte Carlo simulations across sample sizes, cure fractions, and administrative censoring scenarios. Applications to prostate cancer and triple-negative breast cancer data illustrate how the framework assesses available follow-up, estimates additional observation time under prespecified tolerances, and identifies settings in which follow-up is already adequate.
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All authors Luiz Silva-Resende, Dionisio Alves-Neto, Danilo Alvares, Vera Tomazella

Statistical Methodology

Finite-sample correction for the covariate-adjusted log-rank test

The covariate-adjusted log-rank test is a novel method for covariate adjustment in randomized trials with time-to-event endpoints, offering guaranteed efficiency gains compared to the standard log-rank test. However, it has been noted that, in small samples, this method may lead to type I error rate inflation. This issue is particularly pronounced in trials with imbalanced allocation and settings where the number of adjustment covariates is large relative to the sample size. We propose a finite-sample correction for the denominator of the covariate-adjusted log-rank test statistic that accounts for the loss of the residual degrees of freedom as well as the uncertainty in the unknown regression coefficients. In simulations, we show that applying this correction leads to a substantial reduction in the type I error rate inflation across multiple scenarios.
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Statistical Methodology

Endogeneity-Aware Cognitive Diagnostic Model for Multidomain Ordinal Assessments

Multidomain assessment batteries generate ordinal item responses that are often summarized through latent attribute profiles. Conventional cognitive diagnostic models (CDMs) provide interpretable measurement models for such profiles, but they typically do not represent directed dependence among latent attributes from distinct domains. We propose an endogeneity-aware cognitive diagnostic model (EACDM) for multivariate ordinal assessments. The model combines a block-structured diagnostic measurement component, in which item groups are linked to domain-specific binary attributes through a block-diagonal Q-matrix, with a logistic structural component, in which one attribute block is regressed on another block and subject-level covariates while accounting for latent classification uncertainty. This formulation yields a parsimonious framework for studying endogenous relationships among diagnostic attributes without collapsing domain-specific measurement structure. We establish identifiability conditions for the Q-matrix, effective loadings, latent-profile probabilities, and structural coefficients, and develop a Markov chain Monte Carlo algorithm for joint estimation of the measurement and structural components. Simulation studies demonstrate accurate recovery of item parameters, latent structures, and structural coefficients for the proposed EACDM, whereas conventional CDMs can fail to recover the ground truth when endogeneity is present. We apply the proposed method to Parkinson's disease data to examine how non-motor latent traits relate to motor impairment profiles.
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Statistical Methodology

Optimal Stratification of a Sampling Frame: A Comparative Study of Classical, Quantum, and Quantum-Inspired Approaches

Optimal stratification aggregates strata into a small number of final strata to minimise total sample size required to meet target precision constraints. This combinatorial objective, reformulated as a within-cluster dispersion surrogate, can be expressed as a quadratic unconstrained binary optimisation (QUBO) problem. This paper reports a comparative case study of four solvers for that surrogate, run under heterogeneous free-tier constraints on an identical twenty-stratum frame from the swissmunicipalities dataset: a D-Wave-formulated QUBO, solved here by simulated annealing (QPU access unavailable); a gate-based quantum processor (IBM Quantum, running QAOA); a photonic entropy-quantum-computing device (QCi Dirac-3); and a classical GPU-based Ising machine as control (Fixstars Amplify AE). Solvers differ in hardware, computational budget, iteration count, and, for IBM, the encoding itself, so the comparison is a case study rather than a controlled experiment. Against a genetic-algorithm benchmark of 129 sample units, the best-known QUBO solution (objective 501.0) maps, after Bethel-Chromy evaluation, to a sample size of 160, a gap of roughly 24%, tied to the best solution found rather than a certified optimum. IBM and Dirac-3 fall further short, at 262 and 286; the IBM result is consistent with SWAP-routing degradation on a sparse qubit lattice, though not isolated from other causes, while Dirac-3, despite genuine optimisation, settles short of what a free GPU reaches in seconds. The paper concludes that a classical genetic algorithm remains, at the scale tested, the method of choice for optimal stratification, reflecting (a) limits of the dispersion surrogate versus the true Bethel-Chromy objective, not encodable as a low-degree polynomial, and (b) solver- and platform-specific limits in the IBM and Dirac-3 runs. These findings do not establish global optimality for either result.
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Statistical Methodology

When Is a General Factor Distinguishable? Non-Proportionality, Stable Structure, and the Bifactor Decision

Whether an added general dimension is necessary beyond correlated first-order factors is a property of population covariance, not an estimator. A bifactor structure is covariance-equivalent to correlated factors when general and group loadings are proportional within every cluster. When every cluster violates proportionality, at least three indicators per cluster and mild conditions rule out exact reproduction by a K-factor model with diagonal uniquenesses. Mixed configurations remain only partly characterized, motivating graded distinguishability. We develop a two-step procedure that delivers a stable first-order structure only when it persists across direct wider-count comparisons, then compares oblique and bifactor representations conditionally on delivery. A preliminary simulation study provides tentative design evidence. A major study develops three non-nested persistence profiles, designates .80/r2 as the practical default, and evaluates the frozen family on held-out replications from the same generators. Within the studied scenarios, anchor-only persistence outperforms anchor-zero, minimum congruence modestly outperforms maximum RMSD, and depth four adds no precision at the fixed .70 cutoff. Held-out results also expose stable-yet-wrong delivery under a weak core and show that the conditional comparison is highly accurate after correct recovery. Four empirical applications illustrate agreement, adjacent-count uncertainty, and non-delivery. Persistence, not count alone, carries the structural decision.
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Statistical Methodology

Win-Ratio Regression for Prioritized Composite Outcomes in Observational Studies: Doubly Robust and Efficient Estimation with Future-Score Correction

Prioritized pairwise outcomes are useful when clinical events follow a natural hierarchy, but censoring before pair resolution complicates estimation. We develop a win-ratio regression framework for this setting by defining a complete-data target over follow-up and deriving an estimating equation for the observed data. The central idea is future-score correction (FC): when censoring prevents later pairwise comparisons from being observed, the method replaces the remaining score with its conditional expectation given the observed history. This correction recovers pairwise information beyond that provided by inverse censoring weights alone. Additionally, we incorporate treatment weighting and baseline outcome augmentation to address baseline confounding. Together, these components yield double robustness for treatment assignment and censoring. Inference is obtained from U-statistic theory. Under standard regularity conditions, the AIPW-FC estimator is asymptotically normal and efficient when all nuisance functions are correctly specified. Simulations with 30%, 50%, and 65% censoring show that efficiency gains from future-score correction increase with the censoring rate, with relative efficiency reaching 1.50 under 65% censoring and near-nominal coverage for AIPW-FC. An application to OneFlorida electronic health record data illustrates the method for a composite outcome that prioritizes death over hospitalization.
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All authors Zhuochao Huang, Lucy Shao, Yi Guo, Ying Lu, Xin M. Tu, Changyong Feng, Tuo Lin

Statistical Methodology

Survey-robust uncertainty quantification in generalised additive models for location, scale, and shape

Conventional mean-only regression models are often too restrictive for the analysis of complex survey data, where interest frequently extends beyond the conditional mean to other aspects of the response distribution. Generalised additive models for location, scale and shape (GAMLSS) provide a flexible framework by allowing all distributional parameters to depend on covariates. However, existing model-based and model-robust standard errors fail to account for complex survey designs and can substantially underestimate the variability of regression parameter estimates. We propose a linearisation-based sandwich variance estimator that incorporates the survey design while remaining computationally efficient. Using a simulation study based on synthetic survey data, we demonstrate that the proposed estimator provides accurate standard error estimates and reliable confidence interval coverage for all distributional parameters, while offering a computationally efficient alternative to replication-based methods. We further illustrate the practical utility of the approach through a re-analysis of data from the 2019/20 Rwanda Demographic and Health Survey (DHS).
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Statistical Methodology

Duality and Error for Predictively Oriented Inference

Predictively oriented (PrO) inference quantifies uncertainty by selecting a distribution over model parameters to optimize a scoring rule applied to the induced predictive distribution, together with a divergence penalty from a reference distribution. By applying the scoring rule after averaging model densities, PrO inference targets predictive performance, accounting for model misspecification. We focus on the logarithmic score with general $\phi$-divergence regularization. Our contributions are twofold. First, we derive a finite-dimensional dual formulation of PrO inference. For $n$ observations, the dual problem has $n+1$ variables. We establish zero-duality-gap criteria and optimality conditions that relate the primal and dual solutions. When primal and dual solutions exist, these conditions yield a semi-analytical representation of the PrO posterior and certificates for assessing the accuracy of numerical solutions. For Kullback–Leibler regularization, the posterior has an exponential form. Second, we derive a finite-sample excess predictive-risk bound for approximate PrO posteriors that separates sampling fluctuation, approximation under a divergence budget, regularization, and numerical optimization error. The result applies even when the benchmark predictive risk is not attained by any probability distribution over the model parameters having finite divergence from the reference distribution. We use an exactly solvable categorical example to show that predictive-risk convergence can imply convergence to a unique predictive distribution even though the parameter distributions have no weak limit on the original parameter space. The example also shows that different $\phi$-divergences can require different regularization schedules. We conclude with a misspecified Gaussian location-mixture example that illustrates the dual computation, primal recovery, and numerical accuracy checks.
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All authors Aurya Javeed, Drew P. Kouri, Teresa Portone, Rebekah White

Statistical Methodology

Conditional validity of prediction-powered inference for spatially dependent finite populations

Prediction-powered inference (PPI) combines full-frame predictions with a small labelled sample to estimate finite-population regression coefficients. We establish conditions for the conditional validity of existing calibrated residual-regression PPI estimators under nonuniform label acquisition and spatially dependent prediction errors. Approximate calibration can leave a population-specific displacement: the projection of prediction errors onto coefficient-specific calibration defects. We characterize its role in conditional inference through the noncentrality of a fixed-candidate Wald region. The relevant target-weight function is the coefficient loading divided by acquisition intensity. When mean-approximation error does not dominate, directional covariance control yields a wider sufficient recovery regime than a total residual-energy bound. A bounded spectral-basis theorem gives conditional coverage under directional covariance, tail and nondegeneracy conditions, with Gaussian and bounded non-Gaussian spatial examples. The analysis accounts for estimation of the one-step augmentation and permits same-label selection from a fixed finite library with a common first-order influence vector. A periodic Fourier construction attains the stochastic directional-gap order within a restricted dictionary class. Constructed and real-record-set experiments illustrate why mean calibration need not protect a slope. The results concern descriptive census projection coefficients under the stated sampling and field conditions.
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Statistical Methodology

Expert-Guided g-computation with Large Language Models for Estimating Causal Effects on Timings: Applications to Hospital Quality Improvement

Hospital quality improvement (QI) programs routinely face multiple candidate interventions to optimize hospital flow, but existing methods struggle to estimate and rank the causal effects of such interventions. This work focuses on one of the most standard hospital metrics, the average length of stay (LOS), and its causal estimand, the average time saved. To characterize this causal effect, qualitative approaches rely on expert judgment to map patient trajectories, making them susceptible to cognitive biases; quantitative approaches rely on data-driven models, which fail when interventions are hypothetical with no historical data or have complex causal mechanisms that require clinical reasoning rather than data alone. We propose expert-guided g-computation, or egg-computation, which combines the complementary strengths of both approaches by connecting the Gantt charts commonly used to map patient trajectories with the causal DAG literature. We introduce a causal model over Gantt charts and establish identification using a variant of g-computation that seeks expert input only for components unidentifiable from data. To make egg-computation practical, we develop an LLM-assisted pipeline that reliably scales up expert reasoning. In simulations, egg-computation outperforms conventional causal inference methods when patients have diverse causal structures and intervention mechanisms. In a study of eleven candidate QI interventions at an urban safety-net hospital, the LLM pipeline generated graphs and time-saving estimates highly concordant with those of human experts. Beyond healthcare, egg-computation is a broadly applicable framework for estimating the average time saved for candidate interventions whose causal mechanisms can be represented using Gantt charts.
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All authors Patrick Vossler, Jialin Ouyang, F. Richard Guo, Anran Huang, Ali Shojaie, Lucas Zier, Fan Xia, Jean Feng

Statistical Methodology · Cross-listed from econ.EM

A Multinomial Probit Model for Asymmetric Choice Responses

Standard multinomial probit (MNP) models specify symmetric latent utility distributions, implying that choice probabilities respond symmetrically to positive and negative covariate shifts of the same magnitude. This restriction is often implausible in empirical choice settings and can lead to misleading elasticity and substitution predictions. We propose a skewed multinomial probit (SMNP) model that captures asymmetric choice responses by specifying a multivariate skew-normal distribution for the latent utilities. The model preserves the flexible substitution patterns of the MNP framework, introduces alternative-specific skewness parameters, and nests the standard MNP model when skewness is zero. Introducing skewness creates identification and computational challenges because the skewness parameters interact with the MNP scale normalization and disrupt the conditional Gaussian updating structure used in Bayesian MNP estimation. We address these challenges through a covariance reparameterization that enforces identification and positive definiteness by construction, interpretable priors on the identified parameter space, and a double data-augmentation scheme that yields a Metropolis-Hastings within Gibbs sampler. Numerical experiments and applications to consumer choice data show that SMNP recovers asymmetric choice responses, improves probabilistic prediction, and produces economically meaningful differences in price elasticities and substitution patterns.
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