Statistical Computation
FunctionalCalibration: an R package for estimation in aggregated functional data model
Alex Rodrigo dos Santos Sousa and Vitor Ribas Perrone
Aggregated functional data arise in a variety of applications where only linear combinations of latent functional components are observed. A prominent example is found in chemometrics through the Beer-Lambert law. This paper introduces the FunctionalCalibration package for R, which provides tools for estimating constituent curves from aggregated functional observations under additive error models. The package implements calibration methods based on B-spline and wavelet basis expansions, allowing the recovery of smooth as well as locally irregular component functions. In addition, it includes simulation tools, visualization functions, and procedures for estimating weights in prediction problems. The package is illustrated through simulated and real
datasets, demonstrating its flexibility and practical applicability in functional calibration problems.
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Machine Learning (Statistics) · Cross-listed from cs.LG
The Order Is The Message
Jordan LeDoux
In a controlled experiment on modular arithmetic ($p = 9973$), varying only example ordering while holding all else constant, two fixed-ordering strategies achieve 99.5% test accuracy by epochs 487 and 659 respectively from a training set comprising 0.3% of the input space, well below established sample complexity lower bounds for this task under IID ordering. The IID baseline achieves 0.30% after 5{,}000 epochs from identical data. An adversarially structured ordering suppresses learning entirely. The generalizing model reliably constructs a
Fourier representation whose fundamental frequency is the
Fourier dual of the ordering structure, encoding information present in no individual training example, with the same fundamental emerging across all seeds tested regardless of initialization or training set composition. We discuss implications for training efficiency, the reinterpretation of grokking, and the safety risks of a channel that evades all content-level
auditing.
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Machine Learning (Statistics) · Cross-listed from cs.CG
Persistence-based topological optimization: a survey
Mathieu Carriere, Yuichi Ike, Théo Lacombe et al. (+1 more)
Computational
topology provides a tool, persistent homology, to extract quantitative descriptors from structured objects (images, graphs, point clouds, etc). These descriptors can then be involved in optimization problems, typically as a way to incorporate topological priors or to regularize machine learning models. This is usually achieved by minimizing adequate, topologically-informed losses based on these descriptors, which, in turn, naturally raises theoretical and practical questions about the possibility of optimizing such loss functions using gradient-based
algorithms. This has been an active research field in the topological data analysis community over the last decade, and various techniques have been developed to enable optimization of persistence-based loss functions with gradient descent schemes. This survey presents the current state of this field, covering its theoretical foundations, the algorithmic aspects, and showcasing practical uses in several applications. It includes a detailed introduction to persistence theory and, as such, aims at being accessible to mathematicians and data scientists newcomers to the field. It is accompanied by an open-source library which implements the different approaches covered in this survey, providing a convenient playground for researchers to get familiar with the field.
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All authors Mathieu Carriere, Yuichi Ike, Théo Lacombe, Naoki Nishikawa
Machine Learning (Statistics) · Cross-listed from cs.LG
Manifold Generalization Provably Proceeds Memorization in Diffusion Models
Zebang Shen, Ya-Ping Hsieh and Niao He
Diffusion models often generate novel samples even when the learned score is only coarse – a phenomenon not accounted for by the standard view of
diffusion training as density estimation. In this paper, we show that, under the
manifold hypothesis, this behavior can instead be explained by coarse scores capturing the geometry of the data while discarding the fine-scale distributional structure of the population measure~$\mu_{\scriptscriptstyle\mathrm{data}}$. Concretely, whereas estimating the full data distribution $\mu_{\scriptscriptstyle\mathrm{data}}$ supported on a $k$-dimensional
manifold is known to require the classical minimax rate $\tilde{\mathcal{O}}(N^{-1/k})$, we prove that
diffusion models trained with coarse scores can exploit the regularity of the
manifold support and attain a near-parametric rate toward a different target distribution. This target distribution has density uniformly comparable to that of~$\mu_{\scriptscriptstyle\mathrm{data}}$ throughout any $\tilde{\mathcal{O}}\bigl(N^{-\beta/(4k)}\bigr)$-neighborhood of the
manifold, where $\beta$ denotes the
manifold regularity. Our guarantees therefore depend only on the smoothness of the underlying support, and are especially favorable when the data density itself is irregular, for instance non-differentiable. In particular, when the
manifold is sufficiently smooth, we obtain that generalization – formalized as the ability to generate novel, high-fidelity samples – occurs at a statistical rate strictly faster than that required to estimate the full population distribution~$\mu_{\scriptscriptstyle\mathrm{data}}$.
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Statistical Methodology
Root Finding and Metamodeling for Rapid and Robust Computer Model Calibration
Yongseok Jeon and Sara Shashaani
We concern computer model calibration problem where the goal is to find the parameters that minimize the discrepancy between the multivariate real-world and computer model outputs. We propose to solve an approximation using signed residuals that enables a root finding approach and an accelerated search. We characterize the distance of the solutions to the approximation from the solutions of the original problem for the strongly-convex objective functions, showing that it depends on variability of the signed residuals across output dimensions, as wells as their variance and covariance. We develop a metamodel-based root finding framework under kriging and
stochastic kriging that is augmented with a sequential search space reduction. We derive three new acquisition functions for finding roots of the approximate problem along with their derivatives usable by first-order solvers. Compared to kriging,
stochastic kriging accounts for observational noise, promoting more robust solutions. We also analyze the case where a root may not exist. Our analysis of the asymptotic behavior in this context show that, since existence of roots in the approximation problem may not be known a priori, using new acquisition functions will not compromise the outcome. Numerical experiments on data-driven and physics-based examples demonstrate significant computational gains over standard calibration approaches.
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Machine Learning (Statistics) · Cross-listed from cs.LG
Probabilistic Geometric Alignment via Bayesian Latent Transport for Domain-Adaptive Foundation Models
Aueaphum Aueawatthanaphisut and Kuepon Auewattanapisut
Adapting large-scale foundation models to new domains with limited supervision remains a fundamental challenge due to latent distribution mismatch, unstable optimization dynamics, and miscalibrated uncertainty propagation. This paper introduces an uncertainty-aware probabilistic latent transport framework that formulates domain adaptation as a
stochastic geometric alignment problem in representation space. A
Bayesian transport operator is proposed to redistribute latent probability mass along Wasserstein-type geodesic trajectories, while a PAC-
Bayesian regularization mechanism constrains posterior model complexity to mitigate catastrophic overfitting. The proposed formulation yields theoretical guarantees on convergence stability, loss landscape smoothness, and sample efficiency under distributional shift. Empirical analyses demonstrate substantial reduction in latent
manifold discrepancy, accelerated transport energy decay, and improved covariance calibration compared with deterministic fine-tuning and
adversarial domain adaptation baselines. Furthermore, bounded posterior uncertainty
evolution indicates enhanced probabilistic reliability during cross-domain transfer. By establishing a principled connection between
stochastic optimal transport geometry and statistical generalization theory, the proposed framework provides new insights into robust adaptation of modern foundation architectures operating in heterogeneous environments. These findings suggest that uncertainty-aware probabilistic
alignment constitutes a promising paradigm for reliable transfer learning in next-generation deep representation systems.
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Statistical Methodology
Age-Specific Logistic Regression with Complex Event Time Data
Haoxuan Zhou, X. Joan Hu, Yi Xiong et al. (+1 more)
In attempt to advance the current practice for assessing and predicting the primary ovarian insufficiency (POI) risk in female childhood cancer survivors, we propose two estimating function based approaches for age-specific logistic regression. Both approaches adapt the inverse probability of censoring weighting (IPCW) strategy and yield consistent
estimators with asymptotic normality. The first approach modifies the IPCW weights used by Im et al. (2023) to account for doubly censoring. The second approach extends the outcome weighted IPCW approach to use the information of the subjects censored before the analysis time. We consider variance estimation for the
estimators and explore by simulation the two approaches implemented in the situations where the conditional right-censoring time distribution required in the IPCW weighs is unknown and approximated using the survival random forest approaches, stratified empirical distribution functions, or the
estimator under the Cox proportional hazards model. The numerical studies indicate that the second approach is more efficient when right-censoring is relatively heavy, whereas the first approach is preferable when the right-censoring is light. We also observe that the performance of the two approaches heavily relies on the estimation of censoring distribution in our simulation settings. The POI data from a childhood cancer survivor study are employed throughout the paper for motivation and illustration. Our data analysis provides new insight into understanding the POI risk among cancer survivors.
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All authors Haoxuan Zhou, X. Joan Hu, Yi Xiong, Yan Yuan
Machine Learning (Statistics)
Wasserstein Parallel Transport for Predicting the Dynamics of Statistical Systems
Tristan Luca Saidi, Gonzalo Mena, Larry Wasserman et al. (+1 more)
Many scientific systems, such as cellular populations or economic cohorts, are naturally described by probability distributions that evolve over time. Predicting how such a system would have evolved under different forces or initial conditions is fundamental to causal inference, domain adaptation, and counterfactual prediction. However, the space of distributions often lacks the vector space structure on which classical methods rely. To address this, we introduce a general notion of parallel dynamics at a distributional level. We base this principle on parallel transport of tangent dynamics along optimal transport geodesics and call it “Wasserstein Parallel Trends”. By replacing the vector subtraction of classic methods with geodesic parallel transport, we can provide counterfactual comparisons of distributional dynamics in applications such as causal inference, domain adaptation, and batch-effect correction in experimental settings. The main mathematical contribution is a novel notion of fanning scheme on the Wasserstein
manifold that allows us to efficiently approximate parallel transport along geodesics while also providing the first theoretical guarantees for parallel transport in the Wasserstein space. We also show that Wasserstein Parallel Trends recovers the classic parallel trends assumption for averages as a special case and derive closed-form parallel transport for Gaussian measures. We deploy the method on synthetic data and two single-
cell RNA sequencing
datasets to impute gene-expression dynamics across biological systems.
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All authors Tristan Luca Saidi, Gonzalo Mena, Larry Wasserman, Florian Gunsilius
Statistical Methodology
Inverse Probability Weighting of Count Exposures in the Presence of Missing Data: A Simulation Study
Martin N. Danka, Jessica K. Bone, George B. Ploubidis et al. (+1 more)
Inverse probability of treatment weighting (IPTW) is widely used to estimate causal effects, but guidance is limited for count exposures. It is also unclear how IPTW performs when combined with multiple imputation in this context. In this study, we evaluated five IPTW methods applied to count exposures: multinomial binning, parametric and non-parametric
covariate balancing propensity scores (CBPS, npCBPS), generalised boosted models (GBM), and energy balancing. Our simulations were informed by an example using data from the 1970 British Cohort Study, aiming to estimate the effect of psychological distress, measured as a count of symptoms at age 34, on self-reported longstanding illness at age 42. We compared these approaches on bias, coverage, effective sample size, and other metrics under truncated negative binomial and Poisson exposure distributions. We also assessed the performance of Rubin's rules under different missingness mechanisms. Under complete data, multinomial, CBPS, GBM, and energy weights produced low bias and near-nominal coverage, whereas npCBPS resulted in bias and poor coverage due to extreme weights. When data were missing completely at random, similar performance patterns were observed for IPTW with multiple imputation. Under missing at random, bias increased with higher missingness, but this was present for both IPTW and
covariate-adjusted regression, possibly reflecting a limitation of the imputation model rather than a failure of IPTW. Overall, these findings support the use of multinomial, CBPS, GBMs, and energy weights for count exposures in similar settings while highlighting trade-offs between these methods and the need for imputation models accommodating right-truncated overdispersed counts.
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All authors Martin N. Danka, Jessica K. Bone, George B. Ploubidis, Richard J. Silverwood
Statistics Applications
The long shadow of pandemic: Understanding the lingering effects of cause-specific mortality shocks
Yanxin Liu and Kenneth Q. Zhou
In the aftermath of the COVID-19 pandemic, empirical data have revealed that large-scale health crises not only cause immediate disruptions in mortality dynamics but also have persistent effects that may last for several years. Existing mortality models largely assume that mortality shocks are transitory and overlook how their effects can be long-lasting and heterogeneous across age groups and causes of death. In response to this limitation, we propose a novel
stochastic mortality model that captures age- and cause-specific long-lasting effects of mortality jumps through a gamma-density-like decay function, estimated via a customized conditional maximum likelihood
algorithm. Applying the model to recent U.S. mortality data, we reveal divergent persistence patterns across demographic groups and provide key insights into the tail risk profiles of life insurance and annuity products. Our scenario-based analyses further show that neglecting persistent shock effects can lead to suboptimal hedging, while the proposed model enables what-if testing to analyze such effects under potential future health crises.
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Statistical Computation
Adaptive Gaussian Process Search for Simulation-Based Sample Size Estimation in Clinical Prediction Models: Validation of the pmsims R Package
Oyebayo Ridwan Olaniran, Diana Shamsutdinova, Sarah Markham et al. (+4 more)
Background: Determining an adequate sample size is essential for developing reliable and generalisable clinical prediction models, yet practical guidance on selecting appropriate methods remains limited. Existing analytical and simulation-based approaches often rely on restrictive assumptions and focus on mean-based criteria. We present and validate pmsims, an R package that uses Gaussian process surrogate modelling to provide a flexible and computationally efficient simulation-based framework for sample size determination across diverse prediction settings. Methods: We conducted a comprehensive simulation study with two aims. First, we compared three search engines implemented in pmsims: a Gaussian process-based adaptive method, a deterministic bisection method, and a hybrid approach, across binary, continuous, and survival outcomes. Second, we benchmarked the best-performing pmsims engine against existing analytical (pmsampsize) and simulation-based (samplesizedev) methods, evaluating recommended sample sizes, computational time, and achieved performance on large independent validation
datasets. Results: The Gaussian process-based method consistently produced the most stable sample size estimates, particularly in low-signal, high-dimensional settings. In benchmarking, pmsims achieved performance close to prespecified targets across all outcome types, matching simulation-based approaches and outperforming analytical methods in more challenging scenarios. Conclusions: pmsims provides an efficient and flexible framework for principled sample size planning in clinical prediction modelling, requiring fewer model evaluations than non-adaptive simulation approaches.
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All authors Oyebayo Ridwan Olaniran, Diana Shamsutdinova, Sarah Markham, Felix Zimmer, Daniel Stahl, Gordon Forbes, Ewan Carr
Statistics Applications
Dynamical behaviors of a stochastic SIS epidemic model with mean-reverting inhomogeneous geometric brownian motion
Lahcen Khammich and Driss Kiouach
The main purpose of this paper is to study the Dynamical behaviors of a
stochastic SIS epidemic model using mean-reverting inhomogeneous
geometric brownian motion process. First we demonstrate the existence of a global-in-time solution and establish that is unique and remains positive. Then we derive a sufficient condition for exponential extinction of infectious diseases and we show that our extinction threshold in the
stochastic case coincides with that of the deterministic case. Finaly, we define an appropriate theoretical framework to guarantee the existence of an ergodic stationary distribution.
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Statistics Theory
The Bernstein-von Mises theorem and efficiency for semiparametric inference in multivariate Hawkes processes
Mael Duverger and Judith Rousseau
In this paper, we study semiparametric inference for linear multivariate Hawkes processes, a class of point processes widely used to describe self and mutually exciting phenomena. We establish a convolution
theorem giving the best limiting distribution for a regular
estimator of smooth functional. Then, in the
Bayesian setting, we prove a semiparametric Bernstein-von Mises (BvM)
theorem for nonparametric random series priors. We apply this result to histogram and wavelet based priors. Taken together, the convolution and BvM
theorems show that, from a frequentist point of view, semiparametric
Bayesian procedures have asymptotically the optimal behavior. Deriving the BvM property for random series priors led us to prove L2 posterior contraction, complementing for these priors the results of Donnet, Rivoirard and Rousseau (2020).
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Machine Learning (Statistics)
The Mass Agreement Score: A Point-centric Measure of Cluster Size Consistency
Randolph Wiredu-Aidoo
In clustering, strong dominance in the size of a particular cluster is often undesirable, motivating a measure of cluster size uniformity that can be used to filter such partitions. A basic requirement of such a measure is stability: partitions that differ only slightly in their point assignments should receive similar uniformity scores. A difficulty arises because cluster labels are not fixed objects;
algorithms may produce different numbers of labels even when the underlying point distribution changes very little. Measures defined directly over labels can therefore become unstable under label-count perturbations. I introduce the Mass Agreement Score (MAS), a point-centric metric bounded in [0, 1] that evaluates the consistency of expected cluster size as measured from the perspective of points in each cluster. Its construction yields fragment robustness by design, assigning similar scores to partitions with similar bulk structure while remaining sensitive to genuine redistribution of cluster mass.
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Statistics Applications
Wafer-Level Etch Spatial Profiling for Process Monitoring from Time-Series with Time-LLM
Hyunwoo Kim, Munyoung Lee, Seung Hyub Jeon et al. (+1 more)
Understanding wafer-level spatial variations from in-situ process signals is essential for advanced
plasma etching process monitoring. While most data-driven approaches focus on scalar indicators such as average etch rate, actual process quality is determined by complex two-dimensional spatial distributions across the wafer. This paper presents a spatial regression model that predicts wafer-level etch depth distributions directly from multichannel in-situ process time series. We propose a Time-LLM-based spatial regression model that extends LLM reprogramming from conventional time-series
forecasting to wafer-level spatial estimation by redesigning the input
embedding and output projection. Using the BOSCH
plasma-etching
dataset, we demonstrate stable performance under data-limited conditions, supporting the feasibility of LLM-based reprogramming for wafer-level spatial monitoring.
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All authors Hyunwoo Kim, Munyoung Lee, Seung Hyub Jeon, Kyu Sung Lee
Machine Learning (Statistics) · Cross-listed from cs.LG
Causal Reconstruction of Sentiment Signals from Sparse News Data
Stefania Stan, Marzio Lunghi, Vito Vargetto et al. (+4 more)
Sentiment signals derived from sparse news are commonly used in financial analysis and technology monitoring, yet transforming raw article-level observations into reliable temporal series remains a largely unsolved engineering problem. Rather than treating this as a classification challenge, we propose to frame it as a causal signal reconstruction problem: given probabilistic sentiment outputs from a fixed classifier, recover a stable latent sentiment series that is robust to the structural pathologies of news data such as sparsity, redundancy, and classifier uncertainty. We present a modular three-stage pipeline that (i) aggregates article-level scores onto a regular temporal grid with uncertainty-aware and redundancy-aware weights, (ii) fills coverage gaps through strictly causal projection rules, and (iii) applies causal smoothing to reduce residual noise. Because ground-truth longitudinal sentiment labels are typically unavailable, we introduce a label-free evaluation framework based on signal stability diagnostics, information preservation lag proxies, and counterfactual tests for causality compliance and redundancy robustness. As a secondary external check, we evaluate the consistency of reconstructed signals against stock-price data for a multi-firm
dataset of AI-related news titles (November 2024 to February 2026). The key empirical finding is a three-week lead lag pattern between reconstructed sentiment and price that persists across all tested pipeline configurations and aggregation regimes, a structural regularity more informative than any single correlation coefficient. Overall, the results support the view that stable, deployable sentiment indicators require careful reconstruction, not only better classifiers.
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All authors Stefania Stan, Marzio Lunghi, Vito Vargetto, Claudio Ricci, Rolands Repetto, Brayden Leo, Shao-Hong Gan
Statistics Theory
Asymptotics of Nonparametric Estimation under general non-monotone MAR missingness: A Bayesian Approach
Badr-Eddine Chérief-Abdellatif and Jeffrey Näf
Missing values are ubiquitous in statistical practice, with potentially detrimental consequences for any statistical analysis. As such, a wealth of methods and theoretical results have been developed in the last decades. However, many questions remain open, in particular in the case of general non-monotone missing at random (MAR), where nonparametric results are still lacking. In this paper, we extend nonparametric
Bayesian theory to this MAR setting. We introduce a general
theorem of posterior contraction under MAR and an additional positivity condition and apply this result to density estimation as well as regression problems. In particular, we show that, despite the missing values, the complete-data density can be estimated with the minimax posterior contraction rate up to logarithmic factors. To the best of our knowledge, this is the first nonparametric result showing that the complete-data distribution can be consistently estimated under Rubin's MAR definition. As a consequence, we obtain an
algorithm that takes incomplete data and returns a sample from a consistent estimate of the complete-data distribution.
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Machine Learning (Statistics) · Cross-listed from cs.LG
Graph Energy Matching: Transport-Aligned Energy-Based Modeling for Graph Generation
Michal Balcerak, Suprosanna Shit, Chinmay Prabhakar et al. (+4 more)
Generative modeling of discrete data, such as graphs, underpins many scientific and industrial applications, including molecular discovery and materials design. In these domains, probabilistic inference is particularly valuable, as it enables composable generation and principled incorporation of desired constraints, such as structural or functional properties. Energy-based models naturally support this goal by capturing relative likelihoods and enabling composable inference by directly enforcing constraints during inference. However, discrete energy-based models typically struggle with efficient and high-quality sampling, as off-support regions often contain spurious local minima, trapping samplers and causing training instabilities, resulting in a fidelity gap compared to discrete
diffusion models. To address this gap, we introduce Graph Energy Matching (GEM), a discrete generative framework inspired by the Jordan-Kinderlehrer-Otto (JKO) transport-map optimization perspective. GEM learns a permutation-invariant potential energy that simultaneously guides discrete transport from noise toward high-likelihood graph regions and refines samples within these regions. We further introduce a sampling protocol leveraging an energy-based switching strategy, seamlessly bridging rapid, gradient-guided transport and a local mixing regime for effective exploration. On molecular graph
benchmarks, GEM matches or surpasses strong discrete
diffusion baselines on most reported metrics. Beyond improving generation quality, GEM's relative likelihood modeling enables targeted exploration, facilitating compositional generation, property-constrained sampling, and interpolation between graphs. Project page: https://michalbalcerak.ai/graph-energy-matching/.
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All authors Michal Balcerak, Suprosanna Shit, Chinmay Prabhakar, Sebastian Kaltenbach, Michael S. Albergo, Yilun Du, Bjoern Menze
Statistical Methodology
Kinetic Langevin Splitting Schemes for Constrained Sampling
Neil K. Chada and Lu Yu
Constrained sampling is an important and challenging task in computational statistics, concerned with generating samples from a distribution under certain constraints. There are numerous types of
algorithm aimed at this task, ranging from general Markov chain Monte Carlo, to unadjusted Langevin methods. In this article we propose a series of new sampling
algorithms based on the latter of these, specifically the kinetic Langevin dynamics. Our series of
algorithms are motivated on advanced numerical methods which are splitting order schemes, which include the BU and BAO families of splitting schemes.Their advantage lies in the fact that they have favorable strong order (bias) rates and computationally efficiency. In particular we provide a number of theoretical insights which include a Wasserstein contraction and convergence results. We are able to demonstrate favorable results, such as improved complexity bounds over existing non-splitting methodologies. Our results are verified through numerical experiments on a range of models with constraints, which include a toy example and
Bayesian linear regression.
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Statistical Methodology
Shape-Adaptive Conditional Calibration for Conformal Prediction via Minimax Optimization
Yajie Bao, Chuchen Zhang, Zhaojun Wang et al. (+2 more)
Achieving valid conditional coverage in conformal prediction is challenging due to the theoretical difficulty of satisfying pointwise constraints in finite samples. Building upon the characterization of conditional coverage through marginal moment restrictions, we introduce Minimax Optimization Predictive Inference (MOPI), a framework that generalizes prior work by optimizing over a flexible class of set-valued mappings during the calibration phase, rather than simply calibrating a fixed sublevel set. This minimax formulation effectively circumvents the structural constraints of predefined score functions, achieving superior shape adaptivity while maintaining a principled connection to the minimization of mean squared coverage error. Theoretically, we provide non-asymptotic oracle inequalities and show that the convergence rate of the coverage error attains the optimal order under regular conditions. The MOPI also enables valid inference conditional on sensitive attributes that are available during calibration but unobserved at test time. Empirical results on complex, non-standard conditional distributions demonstrate that MOPI produces more efficient prediction sets than existing baselines.
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All authors Yajie Bao, Chuchen Zhang, Zhaojun Wang, Haojie Ren, Changliang Zou