Statistical Methodology
Scalable Dirichlet Process Mixture Models with Unknown Concentration and Adaptive Covariance for High-Dimensional Clustering Applied to Leukemia Transcriptomics
Annesh Pal, Aguirre Mimoun, Rodolphe Thiébaut et al. (+1 more)
We propose a novel method that performs adaptive clustering with DPMM using collapsed VI, while incorporating weakly-informative priors for DP concentration parameter alpha and base distribution G0. We illustrate the importance of G0 covariance structure and prior choice by considering different parameterisations of the data covariance
matrix. On high-dimensional Gaussian simulations, our model demonstrates substantially faster convergence than a state-of-the-art MCMC splice sampler. We further evaluate performances on Negative Binomial simulations and conduct sensitivity analyses to assess robustness on realistic data conditions. Application to a publicly available leukemia transcriptomic data set comprising 72 samples and 2,194 gene expression successfully recovers every known sub-type, all while identifying additional gene expression-based sub-clusters with meaningful biological interpretation.
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All authors Annesh Pal, Aguirre Mimoun, Rodolphe Thiébaut, Boris P. Hejblum
Machine Learning (Statistics)
Multilevel and Sequential Monte Carlo for Training-Free Diffusion Guidance
Aidan Gleich and Scott C. Schmidler
We address the problem of accurate, training-free guidance for conditional generation in trained
diffusion models. Existing methods typically rely on point-estimates to approximate the posterior score, often resulting in biased approximations that fail to capture multimodality inherent to the reverse process of
diffusion models. We propose a sequential Monte Carlo (SMC) framework that constructs an unbiased
estimator of $p_\theta(y|x_t)$ by integrating over the full denoising distribution via Monte Carlo approximation. To ensure computational tractability, we incorporate variance-reduction schemes based on Multi-Level Monte Carlo (MLMC). Our approach achieves new state-of-the-art results for training-free guidance on CIFAR-10 class-conditional generation, achieving $95.6\%$ accuracy with $3\times$ lower cost-per-success than baselines. On ImageNet, our
algorithm achieves $1.5\times$ cost-per-success advantage over existing methods.
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Machine Learning (Statistics)
High-dimensional learning dynamics of multi-pass Stochastic Gradient Descent in multi-index models
Zhou Fan and Leda Wang
The learning dynamics of
Stochastic Gradient Descent (SGD) are believed to play an important role in influencing the generalization properties of trained models. While the precise dynamics of how online (one-pass) SGD optimizes the population risk are now understood in a broad range of high-dimensional problems, a comparable understanding of multi-pass SGD for empirical risk minimization is still largely lacking. In this work, we develop an asymptotically exact characterization of the dynamics of multi-pass SGD for a non-convex multi-index model, in the high-dimensional regime where sample size $n$ and data dimension $d$ increase proportionally. We consider any sub-linear batch size $\kappa \asymp n^\alpha$ with $\alpha \in [0,1)$ and a commensurate “critical” scaling of the learning rate, and show that the coordinate-wise dynamics of SGD admit a novel continuous-time scaling limit, given by a system of dynamical mean-field equations that are driven by a scalar Poisson jump process representing the asymptotic limit of SGD sampling noise. This scaling limit connects several previously disparate theories around SGD, namely (i) the classical interpretation of SGD as an approximation to gradient flow on the empirical risk, (ii) the characterization of online SGD via an autonomous ODE in its overlap statistics, and (iii) the coincidence between multi-pass SGD dynamics and
diffusion approximations in least-squares problems. We illustrate how these perspectives are recovered by specializing our result to small learning rates, large sample sizes, and linear models, respectively. Outside of these specializations, the scaling limit of SGD is distinct both from
diffusion approximations and gradient flow, and may enable SGD to converge to local optima of the non-convex empirical risk with different statistical properties.
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Machine Learning (Statistics)
An efficient, accurate, and interpretable machine learning method for computing probability of failure
Jacob Zhu and Donald Estep
We introduce a novel machine learning method called the Penalized Profile Support Vector Machine based on the Gabriel edited set for the computation of the probability of failure for a complex system as determined by a threshold condition on a computer model of system behavior. The method is designed to minimize the number of evaluations of the computer model while preserving the geometry of the decision boundary that determines the probability. It employs an adaptive sampling strategy designed to strategically allocate points near the boundary determining failure and builds a locally linear surrogate boundary that remains consistent with its geometry by strategic clustering of training points. We prove two convergence results and we compare the performance of the method against a number of state of the art classification methods on four test problems. We also apply the method to determine the probability of survival using the Lotka–Volterra model for competing species.
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Machine Learning (Statistics) · Cross-listed from cs.LG
Signal from Structure: Exploiting Submodular Upper Bounds in Generative Flow Networks
Alexandre Larouche and Audrey Durand
Generative Flow Networks (GFlowNets; GFNs) are a class of generative models that learn to sample compositional objects proportional to their a priori unknown value, their reward. We focus on the case where the reward has a specified, actionable structure, namely that it is submodular. We show submodularity can be harnessed to retrieve upper bounds on the reward of compositional objects that have not yet been observed. We provide in-depth analyses of the probability of such bounds occurring, as well as how many unobserved compositional objects can be covered by a bound. Following the Optimism in the Face of Uncertainty principle, we then introduce SUBo-GFN , which uses the submodular upper bounds to train a GFN. We show that SUBo-GFN generates orders of magnitude more learning signal than classical GFNs for the same number of queries to the reward function. We demonstrate the effectiveness of SUBo-GFN in terms of distribution matching and high-quality candidate generation on graph submodular tasks.
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Statistical Methodology
Experimental Design for Matching
Chonghuan Wang
Matching mechanisms play a central role in operations management across diverse fields including education, healthcare, and online platforms. However, experimentally comparing a new matching
algorithm against a status quo presents some fundamental challenges due to matching interference, where assigning a unit in one matching may preclude its assignment in the other. In this work, we take a design-based perspective to study the design of randomized experiments to compare two predetermined matching plans on a finite population, without imposing outcome or behavioral models. We introduce the notation of a disagreement set, which captures the difference between the two matching plans, and show that it admits a unique decomposition into disjoint alternating paths and cycles with useful structural properties. Based on these properties, we propose the Alternating Path Randomized Design, which sequentially randomizes along these paths and cycles to effectively manage interference. Within a minimax framework, we optimize the conditional randomization probability and show that, for long paths, the optimal choice converges to $\sqrt{2}-1$, minimizing worst-case variance. We establish the unbiasedness of the Horvitz-Thompson
estimator and derive a finite-population Central Limit
Theorem that accommodates complex and unstable path and cycle structures as the population grows. Furthermore, we extend the design to many-to-one matchings, where capacity constraints fundamentally alter the structure of the disagreement set. Using graph-theoretic tools, including finding augmenting paths and Euler-tour decomposition on an auxiliary unbalanced directed graph, we construct feasible alternating path and cycle decompositions that allow the design and inference results to carry over.
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Machine Learning (Statistics)
Diffusion-based Annealed Boltzmann Generators : benefits, pitfalls and hopes
Louis Grenioux and Maxence Noble
Sampling configurations at thermodynamic
equilibrium is a central challenge in statistical physics. Boltzmann Generators (BGs) tackle it by combining a generative model with a Monte Carlo (MC) correction step to obtain asymptotically unbiased samples from an unnormalized target. Most current BGs use classic MC mechanisms such as importance sampling, which both require tractable likelihoods from the backbone model and scale poorly in high-dimensional, multi-modal targets. We study BGs built on annealed Monte Carlo (aMC), which is designed to overcome these limitations by bridging a simple reference to the target through a sequence of intermediate densities.
Diffusion models (DMs) are powerful generative models and have already been incorporated into aMC-based recalibration schemes via the
diffusion-induced density path, making them appealing backbones for aMC-BGs. We provide an empirical meta-analysis of DM-based aMC-BGs on controlled multi-modal Gaussian mixtures (varying mode separation, number of modes, and dimension), explicitly disentangling inference effects from learning effects by comparing (i) a perfectly learned DM and (ii) a DM trained from data. Even with a perfect DM, standard integrations using only first-order
stochastic denoising kernels fail systematically, whereas second-order denoising kernels can substantially improve performance when covariance information is available. We further propose a deterministic aMC integration based on first-order transport maps derived from DMs, which outperforms the
stochastic first-order variant at higher computational cost. Finally, in the learned-DM setting, all DM-aMC variants struggle to produce accurate BGs; we trace the main bottleneck to inaccurate DM log-density estimation. Code available at https://github.com/h2o64/dabg.
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Machine Learning (Statistics)
A Diffusive Classification Loss for Learning Energy-based Generative Models
RuiKang OuYang, Louis Grenioux and José Miguel Hernández-Lobato
Score-based generative models have recently achieved remarkable success. While they are usually parameterized by the score, an alternative way is to use a series of time-dependent energy-based models (EBMs), where the score is obtained from the negative input-gradient of the energy. Crucially, EBMs can be leveraged not only for generation, but also for tasks such as compositional sampling or building Boltzmann Generators via Monte Carlo methods. However, training EBMs remains challenging. Direct maximum likelihood is computationally prohibitive due to the need for nested sampling, while score matching, though efficient, suffers from mode blindness. To address these issues, we introduce the Diffusive Classification (DiffCLF) objective, a simple method that avoids blindness while remaining computationally efficient. DiffCLF reframes EBM learning as a supervised classification problem across noise levels, and can be seamlessly combined with standard score-based objectives. We validate the effectiveness of DiffCLF by comparing the estimated energies against ground truth in analytical Gaussian mixture cases, and by applying the trained models to tasks such as model composition and Boltzmann Generator sampling. Our results show that DiffCLF enables EBMs with higher fidelity and broader applicability than existing approaches.
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Statistics Theory
Towards regularized learning from functional data with covariate shift
Markus Holzleitner, Sergiy Pereverzyev Jr., Sergei V. Pereverzyev et al. (+2 more)
This paper investigates a general regularization framework for unsupervised domain adaptation in vector-valued regression under the
covariate shift assumption, utilizing vector-valued reproducing kernel
Hilbert spaces (vRKHS).
Covariate shift occurs when the input distributions of the training and test data differ, introducing significant challenges for reliable learning. By restricting the hypothesis space, we develop a practical operator learning
algorithm capable of handling functional outputs. We establish optimal convergence rates for the proposed framework under a general source condition, providing a theoretical foundation for regularized learning in this setting. We also propose an aggregation-based approach that forms a linear combination of
estimators corresponding to different regularization parameters and different kernels. The proposed approach addresses the challenge of selecting appropriate tuning parameters, which is crucial for constructing a good
estimator, and we provide a theoretical justification for its effectiveness. Furthermore, we illustrate the proposed method on a real-world face image
dataset, demonstrating robustness and effectiveness in mitigating distributional discrepancies under
covariate shift.
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All authors Markus Holzleitner, Sergiy Pereverzyev Jr., Sergei V. Pereverzyev, Vaibhav Silmana, S. Sivananthan
Machine Learning (Statistics)
Efficient Causal Structure Learning via Modular Subgraph Integration
Haixiang Sun, Pengchao Tian, Zihan Zhou et al. (+3 more)
Learning causal structures from observational data remains a fundamental yet computationally intensive task, particularly in high-dimensional settings where existing methods face challenges such as the super-exponential growth of the search space and increasing computational demands. To address this, we introduce VISTA (Voting-based Integration of Subgraph
Topologies for Acyclicity), a modular framework that decomposes the global causal structure learning problem into local subgraphs based on Markov Blankets. The global integration is achieved through a weighted voting mechanism that penalizes low-support edges via exponential decay, filters unreliable ones with an adaptive threshold, and ensures acyclicity using a Feedback Arc Set (FAS)
algorithm. The framework is model-agnostic, imposing no assumptions on the inductive biases of base learners, is compatible with arbitrary data settings without requiring specific structural forms, and fully supports parallelization. We also theoretically establish finite-sample error bounds for VISTA, and prove its asymptotic consistency under mild conditions. Extensive experiments on both synthetic and real
datasets consistently demonstrate the effectiveness of VISTA, yielding notable improvements in both accuracy and efficiency over a wide range of base learners.
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All authors Haixiang Sun, Pengchao Tian, Zihan Zhou, Jielei Zhang, Peiyi Li, Andrew L. Liu
Statistics Theory · Cross-listed from cs.LG
A Theory of Universal Agnostic Learning
Steve Hanneke and Shay Moran
We provide a complete theory of optimal universal rates for binary classification in the agnostic setting. This extends the realizable-case theory of Bousquet, Hanneke, Moran, van Handel, and Yehudayoff (2021) by removing the realizability assumption on the distribution. We identify a fundamental tetrachotomy of optimal rates: for every concept class, the optimal universal rate of convergence of the excess error rate is one of $e^{-n}$, $e^{-o(n)}$, $o(n^{-1/2})$, or arbitrarily slow. We further identify simple combinatorial structures which determine which of these categories any given concept class falls into.
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Statistics Applications · Cross-listed from cs.LG
A generative machine learning model for designing metal hydrides applied to hydrogen storage
Xiyuan Liu, Christian Hacker, Shengnian Wang et al. (+1 more)
Developing new metal hydrides is a critical step toward efficient hydrogen storage in carbon-neutral energy systems. However, existing materials databases, such as the Materials Project, contain a limited number of well-characterized hydrides, which constrains the discovery of optimal candidates. This work presents a framework that integrates causal discovery with a lightweight generative machine learning model to generate novel metal hydride candidates that may not exist in current databases. Using a
dataset of 450 samples (270 training, 90 validation, and 90 testing), the model generates 1,000 candidates. After ranking and filtering, six previously unreported chemical formulas and
crystal structures are identified, four of which are validated by density functional theory simulations and show strong potential for future experimental investigation. Overall, the proposed framework provides a scalable and time-efficient approach for expanding hydrogen storage
datasets and accelerating materials discovery.
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All authors Xiyuan Liu, Christian Hacker, Shengnian Wang, Yuhua Duan
Machine Learning (Statistics)
Latent-IMH: Efficient Bayesian Inference for Inverse Problems with Approximate Operators
Youguang Chen and George Biros
We study sampling from posterior distributions in
Bayesian linear inverse problems where $A$, the parameters to observables operator, is computationally expensive. In many applications, $A$ can be factored in a manner that facilitates the construction of a cost-effective approximation $\tilde{A}$. In this framework, we introduce Latent-IMH, a sampling method based on the Metropolis-Hastings independence (IMH) sampler. Latent-IMH first generates intermediate latent variables using the approximate $\tilde{A}$, and then refines them using the exact $A$. Its primary benefit is that it shifts the computational cost to an offline phase. We theoretically analyze the performance of Latent-IMH using KL divergence and mixing time bounds. Using numerical experiments on several model problems, we show that, under reasonable assumptions, it outperforms state-of-the-art methods such as the No-U-Turn sampler (NUTS) in computational efficiency. In some cases, Latent-IMH can be orders of magnitude faster than existing schemes.
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Machine Learning (Statistics)
VSCOUT: A Hybrid Variational Autoencoder Approach to Outlier Detection in High-Dimensional Retrospective Monitoring
Waldyn G. Martinez
Modern industrial and service processes generate high-dimensional, non-Gaussian, and contamination-prone data that challenge the foundational assumptions of classical Statistical Process Control (SPC). Heavy tails, multimodality, nonlinear dependencies, and sparse special-cause observations can distort baseline estimation, mask true anomalies, and prevent reliable identification of an in-control (IC) reference set. To address these challenges, we introduce VSCOUT, a distribution-free framework designed specifically for retrospective (Phase I) monitoring in high-dimensional settings. VSCOUT combines an Automatic Relevance Determination Variational Autoencoder (ARD-VAE) architecture with ensemble-based latent outlier filtering and changepoint detection. The ARD prior isolates the most informative latent dimensions, while the ensemble and changepoint filters identify pointwise and structural contamination within the determined latent space. A second-stage retraining step removes flagged observations and re-estimates the latent structure using only the retained inliers, mitigating masking and stabilizing the IC latent
manifold. This two-stage refinement produces a clean and reliable IC baseline suitable for subsequent Phase II deployment. Extensive experiments across
benchmark datasets demonstrate that VSCOUT achieves superior sensitivity to special-cause structure while maintaining controlled false alarms, outperforming classical SPC procedures, robust
estimators, and modern machine-learning baselines. Its scalability, distributional flexibility, and resilience to complex contamination patterns position VSCOUT as a practical and effective method for retrospective modeling and anomaly detection in AI-enabled environments.
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Statistics Applications
A Survival Framework for Estimating Child Mortality Rates using Multiple Data Types
Katherine R Paulson, Taylor Okonek and Jon Wakefield
Child mortality is an important population health indicator. However, many countries lack high-quality vital registration to measure child mortality rates precisely and reliably over time. Research endeavors such as those by the United Nations Inter-agency Group for Child Mortality Estimation (UN IGME) and the Global Burden of Disease (GBD) study leverage statistical models and available data to estimate child survival summaries including neonatal, infant, and under-five mortality rates. UN IGME fits separate models for each age group and the GBD uses a multi-step modeling process. We propose a
Bayesian survival framework to estimate temporal trends in the probability of survival as a function of age, up to the fifth birthday, with a single model. Our framework integrates all data types that are used by UN IGME: household surveys, vital registration, and other pre-processed mortality rates. We demonstrate that our framework is applicable to any country using log-logistic and piecewise-exponential survival functions, and discuss findings for four example countries with diverse data profiles: Kenya, Brazil, Estonia, and Syrian Arab Republic. Our model produces estimates of the three survival summaries that are in broad agreement with both the data and the UN IGME estimates, but in addition gives the complete survival curve.
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Machine Learning (Statistics)
Demystifying Prediction Powered Inference
Yilin Song, Dan M. Kluger, Harsh Parikh et al. (+1 more)
Machine learning predictions are increasingly used to supplement incomplete or costly-to-measure outcomes in fields such as biomedical research, environmental science, and social science. However, treating predictions as ground truth introduces bias while ignoring them wastes valuable information. Prediction-Powered Inference (PPI) offers a principled framework that leverages predictions from large unlabeled
datasets to improve statistical efficiency while maintaining valid inference through explicit bias correction using a smaller labeled subset. Despite its potential, the growing PPI variants and the subtle distinctions between them have made it challenging for practitioners to determine when and how to apply these methods responsibly. This paper demystifies PPI by synthesizing its theoretical foundations, methodological extensions, connections to existing statistics literature, and diagnostic tools into a unified practical workflow. Using the MOSAIKS housing price data, we show that PPI variants produce tighter confidence intervals than complete-case analysis, but that double-dipping, i.e. reusing training data for inference, leads to anti-conservative confidence intervals and below-nominal coverage. Under missing-not-at-random mechanisms, all methods, including classical inference using only labeled data, yield biased estimates. We provide a decision flowchart linking assumption violations to appropriate PPI variants, a summary table of representative methods, and practical diagnostic strategies for evaluating core assumptions. By framing PPI as a general recipe rather than a single
estimator, this work bridges methodological innovation and applied practice, helping researchers responsibly integrate predictions into valid inference.
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All authors Yilin Song, Dan M. Kluger, Harsh Parikh, Tian Gu
Statistical Methodology
Effective Sample Size for Functional Spatial Data
Alfredo Alegría, John Gómez, Jorge Mateu et al. (+1 more)
The effective sample size quantifies the amount of independent information contained in a
dataset, accounting for redundancy due to correlation between observations. While widely used in geostatistics for scalar data, its extension to functional spatial data has remained largely unexplored. In this work, we introduce a novel definition of the effective sample size for functional geostatistical data, employing the trace-covariogram as a measure of correlation, and show that it retains the intuitive properties of the classical scalar ESS. We illustrate the behavior of this measure using a functional autoregressive process, demonstrating how serial dependence and the allocation of variability across eigen-directions influence the resulting functional ESS. Finally, the approach is applied to a real meteorological
dataset of
geometric vertical velocities over a portion of the Earth, showing how the method can quantify redundancy and determine the effective number of independent curves in functional spatial
datasets.
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All authors Alfredo Alegría, John Gómez, Jorge Mateu, Ronny Vallejos
Statistical Methodology
Joint estimation of the basic reproduction number and serial interval using Sequential Bayes
Tatiana Krikella, Jane M. Heffernan and Hanna Jankowski
Early in an infectious disease outbreak, timely and accurate estimation of the basic reproduction number ($R_0$) and the serial interval (SI) is critical for understanding transmission dynamics and informing public health responses. While many methods estimate these quantities separately, and a small number jointly estimate them from incidence data, existing joint approaches are largely likelihood-based and do not fully exploit prior information. We propose a novel
Bayesian framework for the joint estimation of $R_0$ and the serial interval using only case count data, implemented through a sequential Bayes approach. Our method assumes an SIR model and employs a mildly informative joint prior constructed by linking log-Gamma marginal distributions for $R_0$ and the SI via a Gaussian copula, explicitly accounting for their dependence. The prior is updated sequentially as new incidence data become available, allowing for real-time inference. We assess the performance of the proposed
estimator through extensive simulation studies under correct model specification as well as under model misspecification, including when the true data come from an SEIR or SEAIR model, and under varying degrees of prior misspecification. Comparisons with the widely used White and Pagano likelihood-based joint
estimator show that our approach yields substantially more precise and stable estimates of $R_0$, with comparable or improved bias, particularly in the early stages of an outbreak. Estimation of the SI is more sensitive to prior misspecification; however, when prior information is reasonably accurate, our method provides reliable SI estimates and remains more stable than the competing approach. We illustrate the practical utility of the proposed method using Canadian COVID-19 incidence data at both national and provincial levels.
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