Statistics Applications · Cross-listed from cs.CV
StomaD2: An All-in-One System for Intelligent Stomatal Phenotype Analysis via Diffusion-Based Restoration Detection Network
Quanling Zhao, Meng'en Qin, Yanfeng Sun et al. (+2 more)
Stomata play a crucial role in regulating plant physiological processes and reflecting environmental responses. However, accurate and high-throughput stomatal phenotyping remains challenging, as conventional approaches rely on destructive sampling and manual annotation, restricting large-scale and field deployment. To overcome these limitations, a noninvasive restoration-detection integrated framework, termed StomaD2, is developed to achieve accurate and fast stomatal phenotyping under complex imaging conditions. The framework incorporates a
diffusion-based restoration module to recover degraded images and a specialized rotated object detection network tailored to the small, dense, and cluttered characteristics of stomata. The proposed network enhances feature representation through three key innovations: a column-wise structure for global feature interaction, context-aware resampling and reweighting mechanism to improve multi-scale consistency, and a feature reassembly module to boost discrimination against complex backgrounds. In extensive comparisons, StomaD2 demonstrated state-of-the-art performance. On public Maize and Wheat
datasets, it achieved accuracies of 0.994 and 0.992, respectively, significantly outperforming existing
benchmarks. When benchmarked against ten other advanced models, including Oriented Former and YOLOv12, StomaD2 achieved a top-tier F1-score/mAP of 0.989. The framework is integrated into a user-friendly, field-operable system that supports the fast extraction of eight stomatal phenotypes, such as density and conductance. Validated on more than 130 plant species, StomaD2's results highlight its strong generalizability and potential for large-scale phenotyping, plant physiology analysis, and precision agriculture applications.
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All authors Quanling Zhao, Meng'en Qin, Yanfeng Sun, Yuan Miao, Xiaohui Yang
Statistics Theory
Bayesian analysis for a generalised Dirichlet process prior
Nils Lid Hjort
A family of random probabilities is defined and studied. This family contains the Dirichlet process as a special case, corresponding to an inner point in the appropriate parameter space. The extension makes it possible to have random means with larger or smaller skewnesses as compared to skewnesses under the Dirichlet prior, and also in other ways amounts to additional modelling flexibility. The usefulness of such random probabilities for nonparametric
Bayesian statistics is discussed. The posterior distribution is complicated, but inference can nevertheless be carried out via simulation, and some exact formulae are derived for the case of random means. The class of nonparametric priors provides an instructive example where the speed with which the posterior forgets its prior with increasing data sample size depends on special aspects of the prior, which is a different situation from that of parametric inference.
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Statistical Methodology
Model Selection and Parameter Inference through Constraints via Sequences of Surrogate Smoothing Functions
Mateen R Shaikh
Models with fewer parameters are often easier to interpret and more robust. Parsimony can be achieved through optimizing objectives like the AIC or BIC, which are functions of the the number of free parameters in the model. Optimizing this discrete objective is a challenge, often relying on discrete optimization. We construct smooth functions with optima that reach the same optima of these objectives but permit continuous rather than discrete optimization, relieving some selection burden. Proofs of convergence are provided and a novel method of clustering through explicit overparamterization shows promising results.
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Statistical Methodology
Statistical Validation of Computer Models: Global and Subdomain Hypothesis Testing
Chaoan Li, Xianyang Zhang and Rui Tuo
Computer simulations play an important role in scientific discovery and engineering innovation. Reliable computer models enable virtual experimentation that reduces the need for costly and time-consuming physical testing. However, the credibility of such models hinges on rigorous statistical validation against real-world data. This paper develops a formal frequentist framework for both global and subdomain validation of computer models. We propose the
Fourier Maximum Modulus Test (FMMT), which leverages kernel ridge regression (KRR) to estimate the discrepancy between the computer model and the physical process, followed by a frequency-domain test based on weighted generalized
Fourier coefficients. The theoretical analysis establishes the asymptotic normality of these coefficients, allowing for closed-form p-values. Simulation studies and a shear-layer experiment demonstrate that FMMT achieves high power, accurate Type I error control, and strong sensitivity to localized discrepancies.
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Statistics Theory · Cross-listed from math.NT
On the normality of the concatenated Fibonacci constant
José Ricardo G. Mendonça
We study the concatenated Fibonacci constant $\mathcal{F} := 0.F_{1}F_{2}F_{3}\cdots = 0.11235813\cdots$, obtained by concatenating the Fibonacci numbers in the fractional part, and ask whether it is normal. We show that several classical sufficient conditions for normality by concatenation do not apply to the Fibonacci sequence because of its exponential growth, while a criterion of Pollack and Vandehey implies that the normality of $\mathcal{F}$ in base $10$ would follow if almost all Fibonacci numbers were $(\varepsilon,k)$-normal in base $10$. The Benford bias of leading digits and the Pisano periodicity of trailing digits are shown to contribute asymptotically negligible fractions of the total digits, isolating the distribution of the deep digits of large Fibonacci numbers as the remaining obstruction. Large-scale numerical experiments on the first $500{,}000$ Fibonacci numbers in bases $10$ and $2$ indicate that global single-digit counts and $k$-block statistics for $k = 2, 3, 4$ are compatible with i.i.d.-like fluctuations at the scales tested, and that a positional decomposition concentrates the visible structured deviation at the boundaries between consecutive Fibonacci numbers, while pooled interior blocks remain close to uniform. Our computations suggest that any obstruction to normality lies in the asymptotic behavior of the deep digits of $F_{n}$.
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Statistical Methodology
A proposal for PU classification under Non-SCAR using clustering and logistic model
Konrad Furmanczyk and Kacper Paczutkowski
The present study aims to investigate a cluster cleaning
algorithm that is both computationally simple and capable of solving the PU classification when the SCAR condition is unsatisfied. A secondary objective of this study is to determine the robustness of the LassoJoint method to perturbations of the SCAR condition. In the first step of our
algorithm, we obtain cleaning labels from 2-means clustering. Subsequently, we perform logistic regression on the cleaned data, assigning positive labels from the cleaning
algorithm with additional true positive observations. The remaining observations are assigned the negative label. The proposed
algorithm is evaluated by comparing 11 real data sets from machine learning repositories and a synthetic set. The findings obtained from this study demonstrate the efficacy of the clustering
algorithm in scenarios where the SCAR condition is violated and further underscore the moderate robustness of the LassoJoint
algorithm in this context.
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Statistical Computation · Cross-listed from astro-ph.IM
Simple approximations of some statistical functions
Zinovy Malkin
Possibilities are considered to simplify the computation of several statistical functions used to test statistical hypotheses when processing observations: the inverse normal distribution, the Student's t-distribution, and the criterion for rejecting outliers. For these three cases, simple approximation expressions are proposed for the
quantiles of these statistical distributions, which are accurate enough for most practical applications.
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Statistics Theory · Cross-listed from math.OC
Trajectory-Restricted Optimization Conditions and Geometry-Aware Linear Convergence
Faris Chaudhry, Anthea Monod and Keisuke Yano
Linear convergence of first-order methods is typically characterized by global optimization conditions whose constants reflect worst-case geometry of the ambient space. In high-dimensional or structured problems, these global constants can be arbitrarily conservative and fail to capture the geometry actually encountered by optimization trajectories. In this paper, we develop a trajectory-restricted framework for linear convergence based on localized
geometric regularity. We introduce restricted variants of the Polyak–Łojasiewicz inequality, error bound, and quadratic growth conditions that are required to hold only on subsets of the domain. We show that classical convergence guarantees extend under these localized conditions, and in key cases, we develop new arguments that yield explicit relationships between the corresponding constants. The resulting rates are governed by
geometric quantities associated with the regions traversed by the
algorithm. For polyhedral composite problems, we prove that convergence is controlled by restricted Hoffman constants corresponding to the active polyhedral faces visited along the trajectory. Once the iterates enter a well-conditioned face, the effective condition number improves accordingly. Our work provides a
geometric quantification for fast local convergence after active-set or
manifold identification and more broadly suggests that linear convergence is fundamentally governed by the geometry of the subsets explored by the
algorithm, rather than by worst-case global conditioning.
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Machine Learning (Statistics) · Cross-listed from math.NA
Convergence theory for Hermite approximations under adaptive coordinate transformations
Yahya Saleh
Recent work has shown that parameterizing and optimizing coordinate transformations using normalizing flows, i.e., invertible neural networks, can significantly accelerate the convergence of spectral approximations. We present the first error estimates for approximating functions using Hermite expansions composed with adaptive coordinate transformations. Our analysis establishes an equivalence principle: approximating a function $f$ in the span of the transformed basis is equivalent to approximating the pullback of $f$ in the span of Hermite functions. This allows us to leverage the classical approximation theory of Hermite expansions to derive error estimates in transformed coordinates in terms of the regularity of the pullback. We present an example demonstrating how a nonlinear coordinate transformation can enhance the convergence of Hermite expansions. Focusing on smooth functions decaying along the real axis, we construct a monotone transport map that aligns the decay of the target function with the Hermite basis. This guarantees spectral convergence rates for the corresponding Hermite expansion. Our analysis provides theoretical insight into the convergence behavior of adaptive Hermite approximations based on normalizing flows, as recently explored in the computational
quantum physics literature.
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Statistical Methodology · Cross-listed from cs.LG
L1 Regularization Paths in Linear Models by Parametric Gaussian Message Passing
Yun-Peng Li and Hans-Andrea Loeliger
The paper proposes new
algorithms for computing the regularization path of linear-model fitting (i) with L1 costs for the independent variables and L2 costs for the dependent variables, and (ii) with L2 costs for the independent variables and L1 costs for the dependent variables. Unlike previously proposed
algorithms, the proposed
algorithms for (i) and (ii) are exact duals of each other. The heart of the proposed
algorithms is parametric Gaussian message passing (i.e., Kalman-type forward-backward recursions) in the pertinent factor graphs. We first develop such
algorithms for linear models with general (but preferably low-dimensional) state space representations. We then specialize to specific state space representations of generic linear models; in this case, the structure of the factor graph allows to refine the proposed
algorithms such that the computational complexity drops to linear scale.
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Machine Learning (Statistics)
Neighbor Embedding for High-Dimensional Sparse Poisson Data
Noga Mudrik and Adam S. Charles
Across many scientific fields, measurements often represent the number of times an event occurs. For example, a document can be represented by word occurrence counts, neural activity by spike counts per time window, or online communication by daily email counts. These measurements yield high-dimensional count data that often approximate a Poisson distribution, frequently with low rates that produce substantial sparsity and complicate downstream analysis. A useful approach is to embed the data into a low-dimensional space that preserves meaningful structure, commonly termed dimensionality reduction. Yet existing dimensionality reduction methods, including both linear (e.g., PCA) and nonlinear approaches (e.g., t-SNE), often assume continuous Euclidean geometry, thereby misaligning with the discrete, sparse nature of low-rate count data. Here, we propose p-SNE (Poisson
Stochastic Neighbor
Embedding), a nonlinear neighbor
embedding method designed around the Poisson structure of count data, using KL divergence between Poisson distributions to measure pairwise dissimilarity and Hellinger distance to optimize the
embedding. We test p-SNE on synthetic Poisson data and demonstrate its ability to recover meaningful structure in real-world count
datasets, including weekday patterns in email communication, research area clusters in OpenReview papers, and temporal drift and stimulus gradients in neural spike recordings.
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Statistics Applications
Analyzing Process Data from Computer-Based Assessments: A Tutorial on Preprocessing, Feature Extraction, and Model-Based Inference
Daeun Hwangbo, Junyeong Park, Minjeong Jeon et al. (+1 more)
Computer-based assessments routinely generate detailed interaction logs – commonly referred to as process data – that record every action a respondent performs during task completion, yet systematic preprocessing guidance, integrated analytical workflows, and cross-method consistency checks remain scarce in the literature. This paper provides a unified, end-to-end analytical framework for analyzing process data from large-scale assessments – covering the full pipeline from raw log preprocessing to model-based inference – using the Programme for the International Assessment of Adult Competencies (PIAAC) Problem Solving in Technology-Rich Environments (PS-TRE) domain as an illustrative example. We first present a systematic preprocessing pipeline – including timestamp correction, duplicate removal, action block consolidation, and LLM-assisted standardization – that transforms raw event-level logs into analysis-ready action sequences. We then review and demonstrate two complementary families of analytical methods. The first consists of feature-based methods and their downstream applications, including descriptive process indicators, n-gram analysis with TF–IDF weighting, multidimensional scaling, and process data-informed differential item functioning (DIF) analysis. The second consists of model-based approaches, namely hidden Markov models and the subtask identification procedure. Empirical illustrations using the United States sample illustrate that n-gram-based behavioral clusters carry differential diagnostic information primarily among incorrect respondents, that multidimentionsl scaling-derived features comprehensively reconstruct observed behavioral variables, and that process-informed DIF analyses can identify and mitigate construct-irrelevant sources of group differences. Reproducible R code implementations are provided for all major techniques.
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All authors Daeun Hwangbo, Junyeong Park, Minjeong Jeon, Ick Hoon Jin
Statistical Methodology · Cross-listed from cs.LG
Covariance-Based Structural Equation Modeling in Small-Sample Settings with $p>n$
Hiroki Hasegawa, Aoba Tamura and Yukihiko Okada
Factor-based Structural Equation Modeling (SEM) relies on likelihood-based estimation assuming a nonsingular sample covariance
matrix, which breaks down in small-sample settings with $p>n$. To address this, we propose a novel estimation principle that reformulates the covariance structure into self-covariance and cross-covariance components. The resulting framework defines a likelihood-based feasible set combined with a relative error constraint, enabling stable estimation in small-sample settings where $p>n$ for sign and direction. Experiments on synthetic and real-world data show improved stability, particularly in recovering the sign and direction of structural parameters. These results extend covariance-based SEM to small-sample settings and provide practically useful directional information for decision-making.
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Machine Learning (Statistics)
Extraction of informative statistical features in the problem of forecasting time series generated by Itô-type processes
Victor Korolev, Mikhail Ivanov, Tatiana Kukanova et al. (+4 more)
In this paper, we consider the problem of extraction of most informative features from time series that are regarded as observed values of
stochastic processes satisfying the Itô
stochastic differential equations with unknown random drift and
diffusion coefficients. We do not attract any additional information and use only the information contained in the time series as it is. Therefore, as additional features, we use the parameters of statistically adjusted mixture-type models of the observed regularities of the behavior of the time series. Several
algorithms of construction of these parameters are discussed. These
algorithms are based on statistical reconstruction of the coefficients which, in turn, is based on statistical separation of normal mixtures. We obtain two types of parameters by the techniques of the uniform and non-uniform statistical reconstruction of the coefficients of the underlying Itô process. The reconstructed coefficients obtained by uniform techniques do not depend on the current value of the process, while the non-uniform techniques reconstruct the coefficients with the account of their dependence on the value of the process. Actually, the non-uniform techniques used in this paper represent a
stochastic analog of the Taylor expansion for the time series. The efficiency of the obtained additional features is compared by using them in the autoregressive
algorithms of prediction of time series. In order to obtain pure conclusion that is not affected by unwanted factors, say, related to a special choice of the architecture of the neural network prediction methods, we used only simple autoregressive
algorithms. We show that the use of additional statistical features improves the prediction.
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All authors Victor Korolev, Mikhail Ivanov, Tatiana Kukanova, Artyom Rukavitsa, Alexander Vakshin, Peter Solomonov, Alexander Zeifman
Machine Learning (Statistics)
A Mechanism Study of Delayed Loss Spikes in Batch-Normalized Linear Models
Peifeng Gao, Wenyi Fang, Yang Zheng et al. (+1 more)
Delayed loss spikes have been reported in neural-network training, but existing theory mainly explains earlier non-monotone behavior caused by overly large fixed learning rates. We study one stylized hypothesis: normalization can postpone instability by gradually increasing the effective learning rate during otherwise stable descent. To test this hypothesis at
theorem level, we analyze batch-normalized linear models. Our flagship result concerns whitened square-loss linear regression, where we derive explicit no-rising-edge and delayed-onset conditions, bound the waiting time to directional onset, and show that the rising edge self-stabilizes within finitely many iterations. Combined with a square-loss decomposition, this yields a concrete delayed-spike mechanism in the whitened regime. For logistic regression, under highly restrictive active-margin assumptions, we prove only a supporting finite-horizon directional precursor in a knife-edge regime, with an optional appendix-only loss lower bound under an extra non-degeneracy condition. The paper should therefore be read as a stylized mechanism study rather than a general explanation of neural-network loss spikes. Within that scope, the results isolate one concrete delayed-instability pathway induced by batch normalization.
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All authors Peifeng Gao, Wenyi Fang, Yang Zheng, Difan Zou