Statistical Methodology
Estimating the Shannon Entropy Using the Pitman–Yor Process
Takato Hashino and Koji Tsukuda
The Shannon
entropy is a fundamental measure for quantifying diversity and model complexity in fields such as information theory, ecology, and genetics. However, many existing studies assume that the number of species is known, an assumption that is often unrealistic in practice. In recent years, efforts have been made to relax this restriction. Motivated by these developments, this study proposes an
entropy estimation method based on the Pitman–Yor process, a representative approach in
Bayesian nonparametrics. By approximating the true distribution as an infinite-dimensional process, the proposed method enables stable estimation even when the number of observed species is smaller than the true number of species. This approach provides a principled way to deal with the uncertainty in species diversity and enhances the reliability and robustness of
entropy-based diversity assessment. In addition, we investigate the convergence property of the Shannon
entropy for regularly varying distributions and use this result to establish the consistency of the proposed
estimator. Finally, we demonstrate the effectiveness of the proposed method through numerical experiments.
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Machine Learning (Statistics)
Is Flow Matching Just Trajectory Replay for Sequential Data?
Soon Hoe Lim, Shizheng Lin, Michael W. Mahoney et al. (+1 more)
Flow matching (FM) is increasingly used in scientific domains for time series generation and
forecasting, where data often arise from underlying dynamical systems. However, it is not well-understood whether it learns transferable dynamical structure or simply performs an effective ”trajectory replay”. We study this question by deriving the optimal velocity field targeted by the empirical FM objective on sequential data. For the Gaussian conditional paths commonly used in practice, we show that the resulting sampler is an ODE whose dynamics describe a nonparametric,
memory-augmented continuous-time dynamical system. The driving velocity field admits a closed-form expression as a weighted mixture of instantaneous velocities determined by observed transitions. This characterization provides an interpretable view of neural FM models as parametric estimation of an underlying nonparametric target and naturally leads to FreeFM: a closed-form, training-free realization of this target. FreeFM provides a transparent reference for studying sequential FM while yielding effective probabilistic forecasts directly from historical transitions.
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All authors Soon Hoe Lim, Shizheng Lin, Michael W. Mahoney, N. Benjamin Erichson
Machine Learning (Statistics) · Cross-listed from cs.LG
Fast Flow Matching based Conditional Independence Tests for Causal Discovery
Shunyu Zhao, Yanfeng Yang, Shuai Li et al. (+1 more)
Constraint-based causal discovery methods require a large number of conditional independence (CI) tests, which severely limits their practical applicability due to high computational complexity. Therefore, it is crucial to design an
algorithm that accelerates each individual test. To this end, we propose the Flow Matching-based Conditional Independence Test (FMCIT). The proposed test leverages the high computational efficiency of flow matching and requires the model to be trained only once throughout the entire causal discovery procedure, substantially accelerating causal discovery. According to numerical experiments, FMCIT effectively controls type-I error and maintains high testing power under the alternative hypothesis, even in the presence of high-dimensional conditioning sets. In addition, we further integrate FMCIT into a two-stage guided PC skeleton learning framework, termed GPC-FMCIT, which combines fast screening with guided, budgeted refinement using FMCIT. This design yields explicit bounds on the number of CI queries while maintaining high statistical power. Experiments on synthetic and real-world causal discovery tasks demonstrate favorable accuracy-efficiency trade-offs over existing CI testing methods and PC variants.
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All authors Shunyu Zhao, Yanfeng Yang, Shuai Li, Kenji Fukumizu
Machine Learning (Statistics) · Cross-listed from cs.LG
Interaction-Grounded Learning for Contextual Markov Decision Processes with Personalized Feedback
Mengxiao Zhang, Yuheng Zhang, Haipeng Luo et al. (+1 more)
In this paper, we study Interaction-Grounded Learning (IGL) [Xie et al., 2021], a paradigm designed for realistic scenarios where the learner receives indirect feedback generated by an unknown mechanism, rather than explicit numerical rewards. While prior work on IGL provides efficient
algorithms with provable guarantees, those results are confined to single-step settings, restricting their applicability to modern sequential decision-making systems such as multi-turn Large
Language Model (LLM) deployments. To bridge this gap, we propose a computationally efficient
algorithm that achieves a sublinear regret guarantee for contextual episodic Markov Decision Processes (MDPs) with personalized feedback. Technically, we extend the reward-
estimator construction of Zhang et al. [2024a] from the single-step to the multi-step setting, addressing the unique challenges of decoding latent rewards under MDPs. Building on this
estimator, we design an Inverse-Gap-Weighting (IGW)
algorithm for policy optimization. Finally, we demonstrate the effectiveness of our method in learning personalized objectives from multi-turn interactions through experiments on both a synthetic episodic MDP and a real-world user booking
dataset.
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All authors Mengxiao Zhang, Yuheng Zhang, Haipeng Luo, Paul Mineiro
Machine Learning (Statistics) · Cross-listed from cs.LG
Noise Stability of Transformer Models
Themistoklis Haris, Zihan Zhang and Yuichi Yoshida
Understanding simplicity biases in deep learning offers a promising path toward developing reliable AI. A common metric for this, inspired by Boolean function analysis, is average sensitivity, which captures a model's robustness to single-
token perturbations. We argue that average sensitivity has two key limitations: it lacks a natural generalization to real-valued domains and fails to explain the "junta-like" input dependence we empirically observe in modern LLMs. To address these limitations, we propose noise stability as a more comprehensive simplicity metric. Noise stability expresses a model's robustness to correlated noise applied to all input coordinates simultaneously. We provide a theoretical analysis of noise stability for single-layer
attention and ReLU MLP layers and tackle the multi-layer propagation problem with a covariance interval propagation approach. Building on this theory, we develop a practical noise stability regularization method. Experiments on algorithmic and next-
token-prediction tasks show that our regularizer consistently catalyzes grokking and accelerates training by approximately $35\%$ and $75\%$ respectively. Our results sculpt a new connection between signal propagation in neural networks and interpretability, with noise stability emerging as a powerful tool for understanding and improving modern
Transformers.
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Machine Learning (Statistics)
A Statistical Framework for Alignment with Biased AI Feedback
Xintao Xia, Zhiqiu Xia, Linjun Zhang et al. (+1 more)
Modern
alignment pipelines are increasingly replacing expensive human preference labels with evaluations from large
language models (LLM-as-Judge). However, AI labels can be systematically biased compared to high-quality human feedback
datasets. In this paper, we develop two debiased
alignment methods within a general framework that accommodates heterogeneous
prompt-response distributions and external human feedback sources. Debiased Direct Preference Optimization (DDPO) augments standard DPO with a residual-based correction and density-ratio reweighting to mitigate systematic bias, while retaining DPO's computational efficiency. Debiased Identity Preference Optimization (DIPO) directly estimates human preference probabilities without imposing a parametric reward model. We provide theoretical guarantees for both methods: DDPO offers a practical and computationally efficient solution for large-scale
alignment, whereas DIPO serves as a robust, statistically optimal alternative that attains the semiparametric efficiency bound. Empirical studies on sentiment generation, summarization, and single-turn dialogue demonstrate that the proposed methods substantially improve
alignment efficiency and recover performance close to that of an oracle trained on fully human-labeled data.
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All authors Xintao Xia, Zhiqiu Xia, Linjun Zhang, Zhanrui Cai
Machine Learning (Statistics)
Discrete Adjoint Schrödinger Bridge Sampler
Wei Guo, Yuchen Zhu, Xiaochen Du et al. (+6 more)
Learning discrete neural samplers is challenging due to the lack of gradients and combinatorial complexity. While
stochastic optimal control (SOC) and Schrödinger bridge (SB) provide principled solutions, efficient SOC solvers like adjoint matching (AM), which excel in continuous domains, remain unexplored for discrete spaces. We bridge this gap by revealing that the core mechanism of AM is $\mathit{state}\text{-}\mathit{space~agnostic}$, and introduce $\mathbf{discrete~ASBS}$, a unified framework that extends AM and adjoint Schrödinger bridge sampler (ASBS) to discrete spaces. Theoretically, we analyze the optimality conditions of the discrete SB problem and its connection to SOC, identifying a necessary cyclic group structure on the state space to enable this extension. Empirically, discrete ASBS achieves competitive sample quality with significant advantages in training efficiency and scalability.
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All authors Wei Guo, Yuchen Zhu, Xiaochen Du, Juno Nam, Yongxin Chen, Rafael Gómez-Bombarelli, Guan-Horng Liu, Molei Tao, Jaemoo Choi
Machine Learning (Statistics) · Cross-listed from math.OC
Adaptive Matrix Online Learning through Smoothing with Guarantees for Nonsmooth Nonconvex Optimization
Ruichen Jiang, Zakaria Mhammedi, Mehryar Mohri et al. (+1 more)
We study online linear optimization with
matrix variables constrained by the operator norm, a setting where the geometry renders designing data-dependent and efficient adaptive
algorithms challenging. The best-known adaptive regret bounds are achieved by Shampoo-like methods, but they require solving a costly quadratic projection subproblem. To address this, we extend the gradient-based prediction scheme to adaptive
matrix online learning and cast
algorithm design as constructing a family of smoothed potentials for the
nuclear norm. We define a notion of admissibility for such smoothings and prove any admissible smoothing yields a regret bound matching the best-known guarantees of one-sided Shampoo. We instantiate this framework with two efficient methods that avoid quadratic projections. The first is an adaptive Follow-the-Perturbed-Leader (FTPL) method using Gaussian
stochastic smoothing. The second is Follow-the-Augmented-
Matrix-Leader (FAML), which uses a deterministic
hyperbolic smoothing in an augmented
matrix space. By analyzing the admissibility of these smoothings, we show both methods admit closed-form updates and match one-sided Shampoo's regret up to a constant factor, while significantly reducing computational cost. Lastly, using the online-to-nonconvex conversion, we derive two
matrix-based optimizers, Pion (from FTPL) and Leon (from FAML). We prove convergence guarantees for these methods in nonsmooth nonconvex settings, a guarantee that the popular
Muon optimizer lacks.
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All authors Ruichen Jiang, Zakaria Mhammedi, Mehryar Mohri, Aryan Mokhtari
Machine Learning (Statistics) · Cross-listed from cs.LG
Entropy-Generated Attention Beyond Softmax and Entmax: Kaniadakis and Reciprocal-Symmetric Abe Operators
Gunn Kim
We derive two
attention operators from generalized statistical
entropies. Kaniadakis
entropy yields an exact full-support normalization whose weights and low-score sensitivities decay algebraically, rather than exponentially as in Softmax or by exact truncation as in entmax. Classical Abe
entropy yields an implicit reciprocal-symmetric operator. With $q=e^\epsilon$, the involution $q\leftrightarrow q^{-1}$ removes every odd correction about Softmax; we obtain the normalized second- and fourth-order terms, including the deformation of the normalization multiplier. These stationary laws follow from a Fisher-metric Lagrangian on the probability simplex, whose Shannon sector recovers scaled dot-product Softmax. We also give a tangent-gradient test for deciding whether changing the
entropy changes the
attention profile or only its scale. Rényi and two-parameter Sharma–Mittal
entropies retain the Tsallis–entmax inverse-gradient shape, but their global moments make the effective temperature input dependent when the external temperature is fixed. Distinguishing profile-shape equivalence from fixed-parameter operator equivalence separates new normalization shapes from adaptive rescalings and organizes the operators by support, tail behavior, and realization complexity.
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Statistical Methodology · Cross-listed from cs.LG
Distribution-Free Robust Predict-Then-Optimize in Function Spaces
Yash Patel and Ambuj Tewari
The need to rapidly solve PDEs in engineering design workflows has spurred the rise of neural surrogate models. In particular, neural operator models provide a discretization-invariant surrogate by retaining the infinite-dimensional, functional form of their arguments. Despite improved throughput, such methods lack guarantees on accuracy, unlike classical numerical PDE solvers. Optimizing engineering designs under these potentially miscalibrated surrogates thus runs the risk of producing designs that perform poorly upon deployment. In a similar vein, there is growing interest in automated decision-making under black-box predictors in the finite-dimensional setting, where a similar risk of suboptimality exists under poorly calibrated models. For this reason, methods have emerged that produce adversarially robust decisions under uncertainty estimates of the upstream model. One such framework leverages conformal prediction, a distribution-free post-hoc uncertainty quantification method, to provide these estimates due to its natural pairing with black-box predictors. We herein extend this line of conformally robust decision-making to infinite-dimensional function spaces. We first extend the typical conformal prediction guarantees over finite-dimensional spaces to infinite-dimensional Sobolev spaces. We then demonstrate how such uncertainty can be leveraged to robustly formulate engineering design tasks and characterize the suboptimality of the resulting robust optimal designs. We then empirically demonstrate the generality of our functional conformal coverage method across a diverse collection of PDEs, including the Poisson and heat equations, and showcase the significant improvement of such robust design in a
quantum state discrimination task.
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Statistical Methodology
Improved Conditional Logistic Regression using Information in Concordant Pairs with Software
Jacob Tennenbaum and Adam Kapelner
We develop an improvement to conditional logistic regression (CLR) in the setting where the parameter of interest is the additive effect of binary treatment effect on log-odds of the positive level in the binary response. Our improvement is simply to use information learned above the nuisance control
covariates found in the concordant response pairs' observations (which is usually discarded) to create an informative prior on their coefficients. This prior is then used in the CLR which is run on the discordant pairs. Our power improvements over CLR are most notable in small sample sizes and in nonlinear log-odds-of-positive-response models. Our methods are released in an optimized R package called bclogit.
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Machine Learning (Statistics) · Cross-listed from cs.LG
CADO: From Imitation to Cost Minimization for Heatmap-based Solvers in Combinatorial Optimization
Hyungseok Song, Deunsol Yoon, Kanghoon Lee et al. (+3 more)
Heatmap-based solvers have emerged as a promising paradigm for Combinatorial Optimization (CO). However, we argue that the dominant Supervised Learning (SL) training paradigm suffers from a fundamental objective mismatch: minimizing imitation loss (e.g., cross-
entropy) does not guarantee solution cost minimization. We dissect this mismatch into two deficiencies: Decoder-Blindness (being oblivious to the non-differentiable decoding process) and Cost-Blindness (prioritizing structural imitation over solution quality). We empirically demonstrate that these intrinsic flaws impose a hard performance ceiling. To overcome this limitation, we propose CADO (Cost-Aware
Diffusion models for Optimization), a streamlined Reinforcement Learning fine-tuning framework that formulates the
diffusion denoising process as an MDP to directly optimize the post-decoded solution cost. We introduce Label-Centered Reward, which repurposes ground-truth labels as unbiased baselines rather than imitation targets, and Hybrid Fine-Tuning for parameter-efficient adaptation. CADO achieves state-of-the-art performance across diverse
benchmarks, validating that objective
alignment is essential for unlocking the full potential of heatmap-based solvers.
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All authors Hyungseok Song, Deunsol Yoon, Kanghoon Lee, Han-Seul Jeong, Soonyoung Lee, Woohyung Lim
Machine Learning (Statistics) · Cross-listed from cs.LG
Interpretable Dynamic Network Modeling of Tensor Time Series via Kronecker Time-Varying Graphical Lasso
Shingo Higashiguchi, Koki Kawabata, Yasuko Matsubara et al. (+1 more)
With the rapid development of web services, large amounts of time series data are generated and accumulated across various domains such as finance, healthcare, and online platforms. As such data often co-evolves with multiple variables interacting with each other, estimating the time-varying dependencies between variables (i.e., the dynamic network structure) has become crucial for accurate modeling. However, real-world data is often represented as tensor time series with multiple modes, resulting in large, entangled networks that are hard to interpret and computationally intensive to estimate. In this paper, we propose Kronecker Time-Varying Graphical Lasso (KTVGL), a method designed for modeling tensor time series. Our approach estimates mode-specific dynamic networks in a Kronecker product form, thereby avoiding overly complex entangled structures and producing interpretable modeling results. Moreover, the partitioned network structure prevents the exponential growth of computational time with data dimension. In addition, our method can be extended to stream
algorithms, making the computational time independent of the sequence length. Experiments on synthetic data show that the proposed method achieves higher edge estimation accuracy than existing methods while requiring less computation time. To further demonstrate its practical value, we also present a case study using real-world data. Our source code and
datasets are available at https://github.com/Higashiguchi-Shingo/KTVGL.
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All authors Shingo Higashiguchi, Koki Kawabata, Yasuko Matsubara, Yasushi Sakurai
Machine Learning (Statistics)
Information Geometry of Absorbing Markov-Chain and Discriminative Random Walks
Masanari Kimura
Discriminative Random Walks (DRWs) are a simple yet powerful tool for semi-supervised node classification, but their theoretical foundations remain fragmentary. We revisit DRWs through the lens of information geometry, treating the family of class-specific hitting-time laws on an absorbing Markov chain as a statistical
manifold. Starting from a log-linear edge-weight model, we derive closed-form expressions for the hitting-time probability mass function, its full moment hierarchy, and the observed Fisher information. The Fisher
matrix of each seed node turns out to be rank-one, taking the quotient by its null space yields a low-dimensional, globally flat
manifold that captures all identifiable directions of the model. Leveraging the geometry, we introduce a sensitivity score for unlabeled nodes that bounds, and in one-dimensional cases attains, the maximal first-order change in DRW betweenness under unit Fisher perturbations. The score can lead to principled strategies for active label acquisition, edge re-weighting, and explanation.
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Statistics Theory
Asymptotically Minimax Robust Likelihood Ratio Test
Gökhan Gül
This paper develops a unified framework for asymptotically minimax robust hypothesis testing under distributional uncertainty, applicable to both
Bayesian and Neyman–Pearson formulations (Type-I and Type-II). Uncertainty classes based on the KL-divergence, $\alpha$-divergence, and its symmetrized variant are considered. Using Sion's minimax
theorem and Karush-Kuhn-Tucker conditions, the existence and uniqueness of the resulting robust tests are established. The least favorable distributions and corresponding robust likelihood ratio functions are derived in closed parametric forms, enabling computation via systems of nonlinear equations. It is proven that Dabak's approach does not yield an asymptotically minimax robust test. The proposed theory generalizes earlier work by offering a more systematic and comprehensive derivation of robust tests. Numerical simulations confirm the theoretical results and illustrate the behavior of the derived robust tests.
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Statistics Theory
Fundamental Limits of Community Detection in Contextual Multi-Layer Stochastic Block Models
Shuyang Gong, Dong Huang and Zhangsong Li
We consider the problem of community detection from the joint observation of a high-dimensional
covariate matrix and $L$ sparse networks, all encoding noisy, partial information about the latent community labels of $n$ subjects. In the asymptotic regime where the networks have constant average degree and the number of features $p$ grows proportionally with $n$, we derive a sharp threshold under which detecting and estimating the subject labels is possible. Our results extend the work of \cite{MN23} to the constant-degree regime with noisy measurements, and also resolve a
conjecture in \cite{YLS24+} when the number of networks is a constant. Our information-theoretic lower bound is obtained via a novel comparison inequality between Bernoulli and Gaussian moments, as well as a statistical variant of the “recovery to chi-square divergence reduction” argument inspired by \cite{DHSS25}. On the algorithmic side, we design efficient
algorithms based on counting decorated cycles and decorated paths and prove that they achieve the sharp threshold for both detection and weak recovery. In particular, our results show that there is no statistical-computational gap in this setting.
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Statistics Applications
Learning from Literature: Integrating LLMs and Bayesian Hierarchical Modeling for Oncology Trial Design
Guannan Gong, Satrajit Roychoudhury, Allison Meisner et al. (+3 more)
Designing modern oncology trials requires synthesizing evidence from prior studies to inform hypothesis generation and sample size determination. Trial designs based on incomplete or imprecise summaries can lead to misspecified hypotheses and underpowered studies, resulting in false positive or negative conclusions. To address this challenge, we developed LEAD-ONC (Literature to Evidence for Analytics and Design in Oncology), an AI-assisted framework that transforms published clinical trial reports into quantitative, design-relevant evidence. Given expert-curated trial publications that meet prespecified eligibility criteria, LEAD-ONC uses large
language models to extract baseline characteristics and reconstruct individual patient data from Kaplan-Meier curves, followed by
Bayesian hierarchical modeling to generate predictive survival distributions for a prespecified target trial population. We demonstrate the framework using five phase III trials in first-line non-small-
cell lung cancer evaluating PD-1 or PD-L1 inhibitors with or without CTLA-4 blockade. Clustering based on baseline characteristics identified three clinically interpretable populations defined by histology. For a prospective randomized trial in the mixed-histology population comparing mono versus dual immune checkpoint inhibition, LEAD-ONC projected a modest median overall survival difference of 2.8 months (95 percent credible interval -2.0 to 7.6) and an estimated probability of at least a 3-month benefit of approximately 0.45. As LEAD-ONC remains under active development, these results are intended as preliminary demonstrations of the frameworks potential to support evidence-driven oncology trial design rather than definitive clinical conclusions.
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All authors Guannan Gong, Satrajit Roychoudhury, Allison Meisner, Lajos Pusztai, Sarah B Goldberg, Wei Wei
Statistics Applications · Cross-listed from cs.LG
A Causal Machine Learning Framework for Treatment Personalization in Clinical Trials: Application to Ulcerative Colitis
Cristian Minoccheri, Sophia Tesic, Kayvan Najarian et al. (+1 more)
Randomized controlled trials estimate average treatment effects, but treatment response heterogeneity motivates personalized approaches. A critical question is whether statistically detectable heterogeneity translates into improved treatment decisions – these are distinct questions that can yield contradictory answers. We present a modular causal machine learning framework that evaluates each question separately: permutation importance identifies which features predict heterogeneity, best linear predictor (BLP) testing assesses statistical significance, and doubly robust policy evaluation measures whether acting on the heterogeneity improves patient outcomes. We apply this framework to patient-level data from the UNIFI maintenance trial of ustekinumab in ulcerative colitis, comparing placebo, standard-dose ustekinumab every 12 weeks, and dose-intensified ustekinumab every 8 weeks, using cross-fitted X-learner models with baseline demographics, medication history, week-8 clinical scores, laboratory biomarkers, and
video-derived endoscopic features. BLP testing identified strong associations between endoscopic features and treatment effect heterogeneity for ustekinumab versus placebo, yet doubly robust policy evaluation showed no improvement in expected remission from incorporating endoscopic features, and out-of-fold multi-arm evaluation showed worse performance. Diagnostic comparison of prognostic contribution against policy value revealed that endoscopic scores behaved as disease severity markers – improving outcome prediction in untreated patients but adding noise to treatment selection – while clinical variables (fecal calprotectin, age, CRP) captured the decision-relevant variation. These results demonstrate that causal machine learning applications to clinical trials should include policy-level evaluation alongside heterogeneity testing.
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All authors Cristian Minoccheri, Sophia Tesic, Kayvan Najarian, Ryan Stidham