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Thursday 22 January

Statistics Theory

On the Nonasymptotic Scaling Guarantee of Hyperparameter Estimation in Inhomogeneous, Weakly-Dependent Complex Network Dynamical Systems

Hierarchical Bayesian models are increasingly used in large, inhomogeneous complex network dynamical systems by modeling parameters as draws from a hyperparameter-governed distribution. However, theoretical guarantees for these estimates as the network population size grows have been lacking. A critical concern is that hyperparameter estimation may diverge for larger networks, undermining the model's reliability. Formulating the system's evolution in a measure transport perspective, we propose a theoretical framework for estimating hyperparameters with mean-type observations, which are prevalent in many scientific applications. Our primary contribution is a nonasymptotic bound for the deviation of estimate of hyperparameters in inhomogeneous complex network dynamical systems with respect to network population size, which is established for a general family of optimization algorithms within a fixed observation duration. For systems with independent nodes, we first establish a fixed-accuracy probabilistic hyperparameter bound and then use it to derive an explicit nonasymptotic hyperparameter bound. We subsequently extend both bounds to the more challenging and practically relevant setting of systems with weakly-dependent nodes. We validate our theoretical findings with numerical experiments on two representative models: a Susceptible-Infected-Susceptible model and a Spiking Neuronal Network model. In both cases, the results confirm that the estimation error decreases as the network population size increases, aligning with our theoretical guarantees. This research proposes the foundational theory to ensure that hierarchical Bayesian methods are statistically consistent for large-scale inhomogeneous systems, filling a gap in this area of theoretical research and justifying their application in practice.
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All authors Yi Yu, Yubo Hou, Yinchong Wang, Nan Zhang, Jianfeng Feng, Wenlian Lu

Statistical Methodology

Model-Free Inference for Characterizing Protein Mutations through a Coevolutionary Lens

Multiple sequence alignment (MSA) data play a crucial role in the study of protein mutations, with contact prediction being a notable application. Existing methods are often model-based or algorithmic and typically do not incorporate statistical inference to quantify the uncertainty of the prediction outcomes. To address this, we propose a novel framework that transforms the task of contact prediction into a statistical testing problem. Our approach is motivated by the partial correlation for continuous random variables. With one-hot encoding of MSA data, we are able to construct a partial correlation graph for multivariate categorical variables. In this framework, two connected nodes in the graph indicate that the corresponding positions on the protein form a contact. A new spectrum-based test statistic is introduced to test whether two positions are partially correlated. Moreover, the new framework enables the identification of amino acid combinations that contribute to the correlation within the identified contacts, an important but largely unexplored aspect of protein mutations. Numerical experiments demonstrate that our proposed method is valid in terms of controlling Type I errors and powerful in general. Real data applications on various protein families further validate the practical utility of our approach in coevolution and mutation analysis.
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All authors Fan Yang, Zhao Ren, Wen Zhou, Kejue Jia, Robert Jernigan

Machine Learning (Statistics) · Cross-listed from cs.LG

BanditLP: Large-Scale Stochastic Optimization for Personalized Recommendations

We present BanditLP, a scalable multi-stakeholder contextual bandit framework that unifies neural Thompson Sampling for learning objective-specific outcomes with a large-scale linear program for constrained action selection at serving time. The methodology is application-agnostic, compatible with arbitrary neural architectures, and deployable at web scale, with an LP solver capable of handling billions of variables. Experiments on public benchmarks and synthetic data show consistent gains over strong baselines. We apply this approach in LinkedIn's email marketing system and demonstrate business win, illustrating the value of integrated exploration and constrained optimization in production.
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All authors Phuc Nguyen, Benjamin Zelditch, Joyce Chen, Rohit Patra, Changshuai Wei

Wednesday 21 January

Machine Learning (Statistics) · Cross-listed from math.NA

Large Language Models: A Mathematical Formulation

Large language models (LLMs) process and predict sequences containing text to answer questions, and address tasks including document summarization, providing recommendations, writing software and solving quantitative problems. We provide a mathematical framework for LLMs by describing the encoding of text sequences into sequences of tokens, defining the architecture for next-token prediction models, explaining how these models are learned from data, and demonstrating how they are deployed to address a variety of tasks. The mathematical sophistication required to understand this material is not high, and relies on straightforward ideas from information theory, probability and optimization. Nonetheless, the combination of ideas resting on these different components from the mathematical sciences yields a complex algorithmic structure; and this algorithmic structure has demonstrated remarkable empirical successes. The mathematical framework established here provides a platform from which it is possible to formulate and address questions concerning the accuracy, efficiency and robustness of the algorithms that constitute LLMs. The framework also suggests directions for development of modified and new methodologies.
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Statistics Applications

Assessing the informative value of macroeconomic indicators for public health forecasting

Macroeconomic conditions influence the environments in which health systems operate, yet their value as leading signals of health system capacity has not been systematically evaluated. In this study, we examine whether selected macroeconomic indicators contain predictive information for several capacity-related public health targets, including employment in the health and social assistance workforce, new business applications in the sector, and health care construction spending. Using monthly U.S. time series data, we evaluate multiple forecasting approaches, including neural network models with different optimization strategies, generalized additive models, random forests, and time series models with exogenous macroeconomic indicators, under alternative model fitting designs. Across evaluation settings, we find that macroeconomic indicators provide a consistent and reproducible predictive signal for some public health targets, particularly workforce and infrastructure measures, while other targets exhibit weaker or less stable predictability. Models emphasizing stability and implicit regularization tend to perform more reliably during periods of economic volatility. These findings suggest that macroeconomic indicators may serve as useful upstream signals for digital public health monitoring, while underscoring the need for careful model selection and validation when translating economic trends into health system forecasting tools.
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Machine Learning (Statistics)

Low-Dimensional Adaptation of Rectified Flow: A Diffusion and Stochastic Localization Perspective

In recent years, Rectified flow (RF) has gained considerable popularity largely due to its generation efficiency and state-of-the-art performance. In this paper, we investigate the degree to which RF automatically adapts to the intrinsic low dimensionality of the support of the target distribution to accelerate sampling. We show that, using a carefully designed choice of the time-discretization scheme and with sufficiently accurate drift estimates, the RF sampler enjoys an iteration complexity of order $O(k/\varepsilon)$ (up to log factors), where $\varepsilon$ is the precision in total variation distance and $k$ is the intrinsic dimension of the target distribution. In addition, we show that the denoising diffusion probabilistic model (DDPM) procedure is equivalent to a stochastic version of RF by establishing a novel connection between these processes and stochastic localization. Building on this connection, we further design a stochastic RF sampler that also adapts to the low-dimensionality of the target distribution under milder requirements on the accuracy of the drift estimates, and also with a specific time schedule. We illustrate with simulations on the synthetic data and text-to-image data experiments the improved performance of the proposed samplers implementing the newly designed time-discretization schedules.
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Statistics Applications

Geometric Morphometrics approach for classifying children's nutritional status on out of sample data

Current alignment-based methods for classification in geometric morphometrics do not generally address the classification of new individuals that were not part of the study sample. However, in the context of infant and child nutritional assessment from body shape images this is a relevant problem. In this setting, classification rules obtained on the shape space from a reference sample cannot be used on out-of-sample individuals in a straightforward way. Indeed, a series of sample dependent processing steps, such as alignment (Procrustes analysis, for instance) or allometric regression, need to be conducted before the classification rule can be applied. This work proposes ways of obtaining shape coordinates for a new individual and analyzes the effect of using different template configurations on the sample of study as target for registration of the out-of-sample raw coordinates. Understanding sample characteristics and collinearity among shape variables is crucial for optimal classification results when evaluating children's nutritional status using arm shape analysis from photos. The SAM Photo Diagnosis Appo̧pyright} Program's goal is to develop an offline smartphone tool, enabling updates of the training sample across different nutritional screening campaigns.
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All authors Laura Medialdea, Ana Arribas-Gil, Álvaro Pérez-Romero, Amador Gómez

Machine Learning (Statistics) · Cross-listed from cs.LG

Learning from Synthetic Data: Limitations of ERM

The prevalence and low cost of LLMs have led to a rise of synthetic content. From review sites to court documents, "natural" content has been contaminated by data points that appear similar to natural data, but are in fact LLM-generated. In this work we revisit fundamental learning theory questions in this, now ubiquitous, setting. We model this scenario as a sequence of learning tasks where the input is a mix of natural and synthetic data, and the learning algorithms are oblivious to the origin of any individual example. We study the possibilities and limitations of ERM in this setting. For the problem of estimating the mean of an arbitrary $d$-dimensional distribution, we find that while ERM converges to the true mean, it is outperformed by an algorithm that assigns non-uniform weights to examples from different generations of data. For the PAC learning setting, the disparity is even more stark. We find that ERM does not always converge to the true concept, echoing the model collapse literature. However, we show there are algorithms capable of learning the correct hypothesis for arbitrary VC classes and arbitrary amounts of contamination.
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All authors Kareem Amin, Alex Bie, Weiwei Kong, Umar Syed, Sergei Vassilvitskii

Other Statistics

Treatment effect: a critique

Two broad positions within statistics define a treatment effect, on the one hand, as a parameter of a statistical model, and on the other, as an appropriate population-level difference in outcomes or counterfactual outcomes under the different treatment regimes. This short expository paper presents some simple but consequential insights on the two formulations, contrasting the answers under the most favourable fictitious idealisation for the counterfactual framework. These observations clarify the relationship between Fisherian model-based inference and modern counterfactual formulations, and emphasise concerns, raised by Cox and others, regarding the suitability of model-free definitions as targets of inference when scientific conclusions are intended to generalise beyond the observed sample. Parts of the paper are necessarily controversial; we follow Cox (1958a) in not putting these forward in any dogmatic spirit.
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Statistical Methodology

Distributional Balancing for Causal Inference: A Unified Framework via Characteristic Function Distance

Weighting methods are essential tools for estimating causal effects in observational studies, with the goal of balancing pre-treatment covariates across treatment groups. Traditional approaches pursue this objective indirectly, for example, via inverse propensity score weighting or by matching a finite number of covariate moments, and therefore do not guarantee balance of the full joint covariate distributions. Recently, distributional balancing methods have emerged as robust, nonparametric alternatives that directly target alignment of entire covariate distributions, but they lack a unified framework, formal theoretical guarantees, and valid inferential procedures. We introduce a unified framework for nonparametric distributional balancing based on the characteristic function distance (CFD) and show that widely used discrepancy measures, including the maximum mean discrepancy and energy distance, arise as special cases. Our theoretical analysis establishes conditions under which the resulting CFD-based weighting estimator achieves $\sqrt{n}$-consistency. Since the standard bootstrap may fail for this estimator, we propose subsampling as a valid alternative for inference. We further extend our approach to an instrumental variable setting to address potential unmeasured confounding. Finally, we evaluate the performance of our method through simulation studies and a real-world application, where the proposed estimator performs well and exhibits results consistent with our theoretical predictions.
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Machine Learning (Statistics) · Cross-listed from cs.AI

A tensor network formalism for neuro-symbolic AI

The unification of neural and symbolic approaches to artificial intelligence remains a central open challenge. In this work, we introduce a tensor network formalism, which captures sparsity principles originating in the different approaches in tensor decompositions. In particular, we describe a basis encoding scheme for functions and model neural decompositions as tensor decompositions. The proposed formalism can be applied to represent logical formulas and probability distributions as structured tensor decompositions. This unified treatment identifies tensor network contractions as a fundamental inference class and formulates efficiently scaling reasoning algorithms, originating from probability theory and propositional logic, as contraction message passing schemes. The framework enables the definition and training of hybrid logical and probabilistic models, which we call Hybrid Logic Network. The theoretical concepts are accompanied by the python library tnreason, which enables the implementation and practical use of the proposed architectures.
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All authors Alex Goessmann, Janina Schütte, Maximilian Fröhlich, Martin Eigel

Machine Learning (Statistics) · Cross-listed from cs.LG

You Need Better Attention Priors

We generalize the attention mechanism by viewing it through the lens of Entropic Optimal Transport, revealing that standard attention corresponds to a transport problem regularized by an implicit uniform prior. We introduce Generalized Optimal transport Attention with Trainable priors (GOAT), a new attention mechanism that replaces this naive assumption with a learnable, continuous prior. This prior maintains full compatibility with optimized kernels such as FlashAttention. GOAT also provides an EOT-based explanation of attention sinks and materializes a solution for them, avoiding the representational trade-offs of standard attention. Finally, by absorbing spatial information into the core attention computation, GOAT learns an extrapolatable prior that combines the flexibility of learned positional embeddings with the length generalization of fixed encodings.
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Machine Learning (Statistics)

Non-Stationary Functional Bilevel Optimization

Functional bilevel optimization (FBO) provides a powerful framework for hierarchical learning in function spaces, yet current methods are limited to static offline settings and perform suboptimally in online, non-stationary scenarios. We propose SmoothFBO, the first algorithm for non-stationary FBO with both theoretical guarantees and practical scalability. SmoothFBO introduces a time-smoothed stochastic hypergradient estimator that reduces variance through a window parameter, enabling stable outer-loop updates with sublinear regret. Importantly, the classical parametric bilevel case is a special reduction of our framework, making SmoothFBO a natural extension to online, non-stationary settings. Empirically, SmoothFBO consistently outperforms existing FBO methods in non-stationary hyperparameter optimization and model-based reinforcement learning, demonstrating its practical effectiveness. Together, these results establish SmoothFBO as a general, theoretically grounded, and practically viable foundation for bilevel optimization in online, non-stationary scenarios.
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All authors Jason Bohne, Ieva Petrulionyte, Michael Arbel, Julien Mairal, Paweł Polak

Machine Learning (Statistics)

Robust X-Learner: Breaking the Curse of Imbalance and Heavy Tails via Robust Cross-Imputation

Estimating Heterogeneous Treatment Effects (HTE) in industrial applications such as AdTech and healthcare presents a dual challenge: extreme class imbalance and heavy-tailed outcome distributions. While the X-Learner framework effectively addresses imbalance through cross-imputation, we demonstrate that it is fundamentally vulnerable to "Outlier Smearing" when reliant on Mean Squared Error (MSE) minimization. In this failure mode, the bias from a few extreme observations ("whales") in the minority group is propagated to the entire majority group during the imputation step, corrupting the estimated treatment effect structure. To resolve this, we propose the Robust X-Learner (RX-Learner). This framework integrates a redescending {\gamma}-divergence objective – structurally equivalent to the Welsch loss under Gaussian assumptions – into the gradient boosting machinery. We further stabilize the non-convex optimization using a Proxy Hessian strategy grounded in Majorization-Minimization (MM) principles. Empirical evaluation on a semi-synthetic Criteo Uplift dataset demonstrates that the RX-Learner reduces the Precision in Estimation of Heterogeneous Effect (PEHE) metric by 98.6% compared to the standard X-Learner, effectively decoupling the stable "Core" population from the volatile "Periphery".
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Statistics Applications

Reinforcement Learning in the Real World: A Survey of Statistical Challenges and Future Directions

Reinforcement learning (RL) has achieved remarkable success in real-world decision-making across diverse domains, including gaming, robotics, online advertising, public health, and natural language processing. Despite these advances, a substantial gap remains between RL research and its deployment in many practical settings. Two recurring challenges often underlie this gap. First, many settings offer limited opportunity for the agent to interact extensively with the target environment due to practical constraints. Second, many target environments often undergo substantial changes, requiring redesign and redeployment of RL systems (e.g., advancements in science and technology that change the landscape of healthcare delivery). Addressing these challenges and bridging the gap between basic research and application requires theory and methodology that directly inform the design, implementation, and continual improvement of RL systems in real-world settings. In this paper, we frame the application of RL in practice as a three-component process: (i) online learning and optimization during deployment, (ii) post- or between-deployment offline analyses, and (iii) repeated cycles of deployment and redeployment to continually improve the RL system. We provide a narrative review of recent advances that address the statistical challenges arising across these three components, including methods for enhancing sample efficiency during online deployment, maximizing data utility for post- or between-deployment inference, and designing sequences of deployments for continual improvement. We also outline future research directions in RL that are use-inspired – aiming for impactful application of RL in practice.
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All authors Asim H. Gazi, Yongyi Guo, Daiqi Gao, Ziping Xu, Kelly W. Zhang, Susan A. Murphy

Machine Learning (Statistics)

Many Experiments, Few Repetitions, Unpaired Data, and Sparse Effects: Is Causal Inference Possible?

We study the problem of estimating causal effects under hidden confounding in the following unpaired data setting: we observe some covariates $X$ and an outcome $Y$ under different experimental conditions (environments) but do not observe them jointly; we either observe $X$ or $Y$. Under appropriate regularity conditions, the problem can be cast as an instrumental variable (IV) regression with the environment acting as a (possibly high-dimensional) instrument. When there are many environments but only a few observations per environment, standard two-sample IV estimators fail to be consistent. We propose a GMM-type estimator based on cross-fold sample splitting of the instrument-covariate sample and prove that it is consistent as the number of environments grows but the sample size per environment remains constant. We further extend the method to sparse causal effects via $\ell_1$-regularized estimation and post-selection refitting.
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All authors Felix Schur, Niklas Pfister, Peng Ding, Sach Mukherjee, Jonas Peters

Statistical Methodology · Cross-listed from cs.LG

Recommending Best Paper Awards for ML/AI Conferences via the Isotonic Mechanism

Machine learning and artificial intelligence conferences such as NeurIPS and ICML now regularly receive tens of thousands of submissions, posing significant challenges to maintaining the quality and consistency of the peer review process. This challenge is particularly acute for best paper awards, which are an important part of the peer review process, yet whose selection has increasingly become a subject of debate in recent years. In this paper, we introduce an author-assisted mechanism to facilitate the selection of best paper awards. Our method employs the Isotonic Mechanism for eliciting authors' assessments of their own submissions in the form of a ranking, which is subsequently utilized to adjust the raw review scores for optimal estimation of the submissions' ground-truth quality. We demonstrate that authors are incentivized to report truthfully when their utility is a convex additive function of the adjusted scores, and we validate this convexity assumption for best paper awards using publicly accessible review data of ICLR from 2019 to 2023 and NeurIPS from 2021 to 2023. Crucially, in the special case where an author has a single quota – that is, may nominate only one paper – we prove that truthfulness holds even when the utility function is merely nondecreasing and additive. This finding represents a substantial relaxation of the assumptions required in prior work. For practical implementation, we extend our mechanism to accommodate the common scenario of overlapping authorship. Finally, simulation results demonstrate that our mechanism significantly improves the quality of papers selected for awards.
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All authors Garrett G. Wen, Buxin Su, Natalie Collina, Zhun Deng, Weijie Su

Machine Learning (Statistics)

Multi-context principal component analysis

Principal component analysis (PCA) is a tool to capture factors that explain variation in data. Across domains, data are now collected across multiple contexts (for example, individuals with different diseases, cells of different types, or words across texts). While the factors explaining variation in data are undoubtedly shared across subsets of contexts, no tools currently exist to systematically recover such factors. We develop multi-context principal component analysis (MCPCA), a theoretical and algorithmic framework that decomposes data into factors shared across subsets of contexts. Applied to gene expression, MCPCA reveals axes of variation shared across subsets of cancer types and an axis whose variability in tumor cells, but not mean, is associated with lung cancer progression. Applied to contextualized word embeddings from language models, MCPCA maps stages of a debate on human nature, revealing a discussion between science and fiction over decades. These axes are not found by combining data across contexts or by restricting to individual contexts. MCPCA is a principled generalization of PCA to address the challenge of understanding factors underlying data across contexts.
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All authors Kexin Wang, Salil Bhate, João M. Pereira, Joe Kileel, Matylda Figlerowicz, Anna Seigal

Statistical Methodology

Efficient prior sensitivity analysis for Bayesian model comparison

Bayesian model comparison implements Occam's razor through its sensitivity to the prior. However, prior-dependence makes it important to assess the influence of plausible alternative priors. Such prior sensitivity analyses for the Bayesian evidence are expensive, either requiring repeated, costly model re-fits or specialised sampling schemes. By exploiting the learned harmonic mean estimator (LHME) for evidence calculation we decouple sampling and evidence calculation, allowing resampled posterior draws to be used directly to calculate the evidence without further likelihood evaluations. This provides an alternative approach to prior sensitivity analysis for Bayesian model comparison that dramatically alleviates the computational cost and is agnostic to the method used to generate posterior samples. We validate our method on toy problems and a cosmological case study, reproducing estimates obtained by full Markov chain Monte Carlo (MCMC) sampling and nested sampling re-fits. For the cosmological example considered our approach achieves up to $6000\times$ lower computational cost.
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Statistics Theory · Cross-listed from math.CO

Decomposing Determinantal Varieties from Statistics via Matroid Theory

We study determinantal varieties from conditional independence models with hidden variables, focusing on their irreducible decompositions, dimensions, degrees, and Gröbner bases. Each variety encodes a collection of matroids, whose flats capture algebraic dependencies among variables. Using this approach, we provide a systematic description of the components, their dimensions, and defining equations, and introduce a combinatorial framework for computing the degree of the determinantal variety. Our approach highlights the central role of matroidal structures in the study of determinantal varieties and extends beyond the reach of current computational techniques.
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All authors Per Alexandersson, Yulia Alexandr, Emiliano Liwski, Fatemeh Mohammadi, Pardis Semnani

Machine Learning (Statistics) · Cross-listed from cs.LG

Factorizable joint shift revisited

Factorizable joint shift (FJS) represents a type of distribution shift (or dataset shift) that comprises both covariate and label shift. Recently, it has been observed that FJS actually arises from consecutive label and covariate (or vice versa) shifts. Research into FJS so far has been confined mostly to the case of categorical labels. We propose a framework for analysing distribution shift in the case of a general label space, thus covering both classification and regression models. Based on the framework, we generalise existing results on FJS to general label spaces and present and analyse a related extension to label distribution estimation of the expectation maximisation (EM) algorithm for class prior probabilities. We also take a fresh look at generalized label shift (GLS) in the case of a general label space.
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Statistical Computation · Cross-listed from eess.SP

Physical Layer Security in Massive MIMO: Challenges and Open Research Directions Against Passive Eavesdroppers

Massive Multiple-Input Multiple-Output (MIMO) has become a crucial enabling technology for 5G and beyond, providing previously unheard-of increases in energy and spectrum efficiency. It is still difficult to guarantee secure communication in these systems, particularly when it comes to passive eavesdroppers whose base station is unaware of their channel state information. By taking advantage of the inherent randomness of wireless channels, Physical Layer Security (PLS) offers a promising paradigm; however, its efficacy in massive MIMO is heavily reliant on resource allocation and transmission strategies. In this work, the performance of secure transmission schemes, such as Maximum Ratio Transmission (MRT), Zero-Forcing (ZF), and Artificial Noise (AN)-aided beamforming, is examined when passive eavesdroppers are present. This work will use extensive Monte Carlo simulations to assess important performance metrics such as energy efficiency, secrecy outage probability, and secrecy sum rate under different system parameters (e.g., number of antennas, Signal-to-Noise Ratio (SNR), power allocation). The results aim to provide comparative insight into the strengths and limitations of different PLS strategies and to highlight open research directions to design scalable, energy-efficient, and robust secure transmission techniques in future 6G networks.
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Machine Learning (Statistics)

Efficient and Minimax Optimal In-context Nonparametric Regression with Transformers

We study in-context learning for nonparametric regression with $\alpha$-Hölder smooth regression functions, for some $\alpha>0$. We prove that, with $n$ in-context examples and $d$-dimensional regression covariates, a pretrained transformer with $\Theta(\log n)$ parameters and $\Omega\bigl(n^{2\alpha/(2\alpha+d)}\log^3 n\bigr)$ pretraining sequences can achieve the minimax optimal rate of convergence $O\bigl(n^{-2\alpha/(2\alpha+d)}\bigr)$ in mean squared error. Our result requires substantially fewer transformer parameters and pretraining sequences than previous results in the literature. This is achieved by showing that transformers are able to approximate local polynomial estimators efficiently by implementing a kernel-weighted polynomial basis and then running gradient descent.
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All authors Michelle Ching, Ioana Popescu, Nico Smith, Tianyi Ma, William G. Underwood, Richard J. Samworth

Statistical Methodology

Consistency of Honest Decision Trees and Random Forests

We study various types of consistency of honest decision trees and random forests in the regression setting. In contrast to related literature, our proofs are elementary and follow the classical arguments used for smoothing methods. Under mild regularity conditions on the regression function and data distribution, we establish weak and almost sure convergence of honest trees and honest forest averages to the true regression function, and moreover we obtain uniform convergence over compact covariate domains. The framework naturally accommodates ensemble variants based on subsampling and also a two-stage bootstrap sampling scheme. Our treatment synthesizes and simplifies existing analyses, in particular recovering several results as special cases. The elementary nature of the arguments clarifies the close relationship between data-adaptive partitioning and kernel-type methods, providing an accessible approach to understanding the asymptotic behavior of tree-based methods.
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Machine Learning (Statistics) · Cross-listed from q-bio.GN

Robust Machine Learning for Regulatory Sequence Modeling under Biological and Technical Distribution Shifts

Robust machine learning for regulatory genomics is studied under biologically and technically induced distribution shifts. Deep convolutional and attention based models achieve strong in distribution performance on DNA regulatory sequence prediction tasks but are usually evaluated under i.i.d. assumptions, even though real applications involve cell type specific programs, evolutionary turnover, assay protocol changes, and sequencing artifacts. We introduce a robustness framework that combines a mechanistic simulation benchmark with real data analysis on a massively parallel reporter assay (MPRA) dataset to quantify performance degradation, calibration failures, and uncertainty based reliability. In simulation, motif driven regulatory outputs are generated with cell type specific programs, PWM perturbations, GC bias, depth variation, batch effects, and heteroscedastic noise, and CNN, BiLSTM, and transformer models are evaluated. Models remain accurate and reasonably calibrated under mild GC content shifts but show higher error, severe variance miscalibration, and coverage collapse under motif effect rewiring and noise dominated regimes, revealing robustness gaps invisible to standard i.i.d. evaluation. Adding simple biological structural priors motif derived features in simulation and global GC content in MPRA improves in distribution error and yields consistent robustness gains under biologically meaningful genomic shifts, while providing only limited protection against strong assay noise. Uncertainty-aware selective prediction offers an additional safety layer that risk coverage analyses on simulated and MPRA data show that filtering low confidence inputs recovers low risk subsets, including under GC-based out-of-distribution conditions, although reliability gains diminish when noise dominates.
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Statistics Theory

Central subspace data depth

Statistical data depth plays an important role in the analysis of multivariate data sets. The main outcome is a center-outward ordering of the observations that can be used both to highlight features of the underlying distribution of the data and as input to further statistical analysis. An important property of data depth is related to symmetric distributions as the point with the highest depth value, the center, coincides with the point of symmetry. However, there are applications in which it is more natural to consider symmetry with respect to a subspace of a certain dimension rather than to a point, i.e. a subspace of dimension zero. We provide a general framework to construct statistical data depths which attain maximum value in a subspace, providing a center-outward ordering from that subspace. We refer to these data depths as central subspace data depths. Moreover, if the distribution is symmetric with respect to a subspace, then the depth is maximized at that subspace. We introduce general notions of symmetry about a subspace for distributions, study the properties of central subspace data depths and provide asymptotic convergence for the corresponding sample versions. Additionally, we discuss connections with projection pursuit and dimension reduction. An application based on custom data fraud detection shows the importance of the proposed approach and strengthens its potential.
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Statistical Methodology

Geostatistics from Elliptic Boundary-Value Problems: Green Operators, Transmission Conditions, and Schur Complements

Classical geostatistics encodes spatial dependence by prescribing variograms or covariance kernels on Euclidean domains, whereas the SPDE–GMRF paradigm specifies Gaussian fields through an elliptic precision operator whose inverse is the corresponding Green operator. We develop an operator-based formulation of Gaussian spatial random fields on bounded domains and manifolds with internal interfaces, treating boundary and transmission conditions as explicit components of the statistical model. Starting from coercive quadratic energy functionals, variational theory yields a precise precision–covariance correspondence and shows that variograms are derived quadratic functionals of the Green operator, hence depend on boundary conditions and domain geometry. Conditioning and kriging follow from standard Gaussian update identities in both covariance and precision form, with hard constraints represented equivalently by exact interpolation constraints or by distributional source terms. Interfaces are modelled via surface penalty terms; taking variations produces flux-jump transmission conditions and induces controlled attenuation of cross-interface covariance. Finally, boundary-driven prediction and domain reduction are formulated through Dirichlet-to-Neumann operators and Schur complements, providing an operator language for upscaling, change of support, and subdomain-to-boundary mappings. Throughout, we use tools standard in spatial statistics and elliptic PDE theory to keep boundary and interface effects explicit in covariance modeling and prediction.
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Statistics Applications · Cross-listed from cs.DL

Citation of scientific evidence from video description and its association with attention and impact

This study investigates how YouTube content creators utilize scientific evidence in videos. Log-linear regression examines the influence of alternative communication channels on video creators in Biotechnology, using data from 81,302 papers (2018-2023). This reveals a positive association with news articles and Wikipedia pages, but a negative association with scientific papers, policy documents, and patents. Despite the potential for enriching discussions, science video creators seem to favor materials with wider public attention over influential science, technology, and policy papers. These findings suggest a need for improved dissemination strategies for scientific research. Authors, universities, and journals should consider how their work can be made more accessible and engaging for science communicators on video.
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Statistics Theory

Finite-Sample Inference for Sparsely Permuted Linear Regression

We study a linear observation model with an unknown permutation called permuted/shuffled linear regression, where responses and covariates are mismatched and the permutation forms a discrete, factorial-size parameter. The permutation is a key component of the data-generating process, yet its statistical investigation remains challenging due to its discrete nature. We develop a general statistical inference framework on the permutation and regression coefficients. First, we introduce a localization step that reduces the permutation space to a small candidate set building on recent advances in the repro samples method, whose miscoverage decays polynomially with the number of Monte Carlo samples. Then, based on this localized set, we provide statistical inference procedures: a conditional Monte Carlo test of permutation structures with valid finite-sample Type-I error control. We also develop coefficient inference that remains valid under alignment uncertainty of permutations. For computational purposes, we develop a linear assignment problem computable in polynomial time and demonstrate that, with high probability, the solution is equivalent to that of the conventional least squares with large computational cost. Extensions to partially permuted designs and ridge regularization are further discussed. Extensive simulations and an application to air-quality data corroborate finite-sample validity, strong power to detect mismatches, and practical scalability.
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Statistical Methodology

Graphical model-based clustering of categorical data

Clustering multivariate data is a pervasive task in many applied problems, particularly in social studies and life science. Model-based approaches to clustering rely on mixture models, where each mixture component corresponds to the kernel of a distribution characterizing a latent sub-group. Current methods developed within this framework employ multivariate distributions built under the assumption of independence among variables given the cluster allocation. Accordingly, possible dependence structures characterizing differences across groups are not directly accounted for during the clustering process. In this paper we consider multivariate categorical data, and introduce a model-based clustering method which employs graphical models as a tool to encode dependencies between variables. Specifically, we consider a Dirichlet Process mixture of categorical graphical models, which clusters individuals into groups that are homogeneous in terms of dependence (graphical) structure and allied parameters. We provide full Bayesian inference for the model and develop a Markov chain Monte Carlo scheme for posterior analysis. Our method is evaluated through simulations and applied to real case studies, including the analysis of genomic data and voting records. Results reveal the merits of a graphical model-based clustering, in comparison with approaches that do not explicitly account for dependencies in the multivariate distribution of variables.
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