Machine Learning (Statistics) · Cross-listed from cs.CV
Scalable spatial point process models for forensic footwear analysis
Alokesh Manna, Neil Spencer and Dipak K. Dey
Shoe print evidence recovered from crime scenes plays a key role in forensic investigations. By examining shoe prints, investigators can determine details of the footwear worn by suspects. However, establishing that a suspect's shoes match the make and model of a crime scene print may not be sufficient. Typically, thousands of shoes of the same size, make, and model are manufactured, any of which could be responsible for the print. Accordingly, a popular approach used by investigators is to examine the print for signs of “accidentals,” i.e., cuts, scrapes, and other features that accumulate on shoe soles after purchase due to wear. While some patterns of accidentals are common on certain types of shoes, others are highly distinctive, potentially distinguishing the suspect's shoe from all others. Quantifying the rarity of a pattern is thus essential to accurately measuring the strength of forensic evidence. In this study, we address this task by developing a hierarchical
Bayesian model. Our improvement over existing methods primarily stems from two advancements. First, we frame our approach in terms of a latent Gaussian model, thus enabling inference to be efficiently scaled to large collections of annotated shoe prints via integrated nested Laplace approximations. Second, we incorporate spatially varying coefficients to model the relationship between shoes' tread patterns and accidental locations. We demonstrate these improvements through superior performance on held-out data, which enhances accuracy and reliability in forensic shoe print analysis.
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Machine Learning (Statistics)
Reinforcement Learning for Control Systems with Time Delays: A Comprehensive Survey
Armando Alves Neto
In the last decade, Reinforcement Learning (RL) has achieved remarkable success in the control and decision-making of complex dynamical systems. However, most RL
algorithms rely on the Markov Decision Process assumption, which is violated in practical cyber-physical systems affected by sensing delays, actuation latencies, and communication constraints. Such time delays introduce
memory effects that can significantly degrade performance and compromise stability, particularly in networked and multi-
agent environments. This paper presents a comprehensive survey of RL methods designed to address time delays in control systems. We first formalize the main classes of delays and analyze their impact on the Markov property. We then systematically categorize existing approaches into five major families: state augmentation and history-based representations, recurrent policies with learned
memory, predictor-based and model-aware methods, robust and domain-randomized training strategies, and safe RL frameworks with explicit constraint handling. For each family, we discuss underlying principles, practical advantages, and inherent limitations. A comparative analysis highlights key trade-offs among these approaches and provides practical guidelines for selecting suitable methods under different delay characteristics and safety requirements. Finally, we identify open challenges and promising research directions, including stability certification, large-delay learning, multi-
agent communication co-design, and standardized benchmarking. This survey aims to serve as a unified reference for researchers and practitioners developing reliable RL-based controllers in delay-affected cyber-physical systems.
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Machine Learning (Statistics)
Singular Bayesian Neural Networks
Mame Diarra Toure and David A. Stephens
Bayesian neural networks promise calibrated uncertainty but require $O(mn)$ parameters for standard mean-field Gaussian posteriors. We argue this cost is often unnecessary, particularly when weight
matrices exhibit fast singular value decay. By parameterizing weights as $W = AB^{\top}$ with $A \in \mathbb{R}^{m \times r}$, $B \in \mathbb{R}^{n \times r}$, we induce a posterior that is singular with respect to the Lebesgue measure, concentrating on the rank-$r$
manifold. This singularity captures structured weight correlations through shared latent factors, geometrically distinct from mean-field's independence assumption. We derive PAC-Bayes generalization bounds whose complexity term scales as $\sqrt{r(m+n)}$ instead of $\sqrt{m n}$, and prove loss bounds that decompose the error into optimization and rank-induced bias using the Eckart-Young-Mirsky
theorem. We further adapt recent Gaussian complexity bounds for low-rank deterministic networks to
Bayesian predictive means. Empirically, across MLPs, LSTMs, and
Transformers on standard
benchmarks, our method achieves competitive predictive performance while using up to $33\times$ fewer parameters than 5-member Deep Ensembles. It substantially improves OOD detection and often improves calibration relative to mean-field and perturbation baselines, while Deep Ensembles can still be stronger on in-distribution likelihood-based metrics.
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Statistics Theory · Cross-listed from q-fin.ST
Null-Validated Topological Signatures of Financial Market Dynamics
Samuel W. Akingbade
Financial
markets exhibit temporal organization that is not fully captured by
volatility measures or linear correlation structure. We study a null-validated topological approach for quantifying financial
market complexity using Bitcoin daily log returns and the S&P 500 index as examples of cryptocurrency and broad U.S. equity
market dynamics. The analysis uses the $L^1$ norm of the persistence landscapes computed from sliding-window delay
embeddings. This quantity co-moves strongly with
stochastic volatility during periods of
market stress, but the strength and form of this relationship vary over time and differ between the two
markets. Surrogate-based null models provide statistical validation of these observations. Rejection of shuffle surrogates rules out explanations based on marginal distributions alone, while departures from phase randomized surrogates indicate sensitivity to nonlinear and phase-dependent temporal organization beyond linear correlations. These results demonstrate that persistence landscape norms provide complementary information about
market dynamics across
market conditions.
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Statistics Applications · Cross-listed from astro-ph.IM
Simulating Roman+Gaia Combined Astrometry, Parallaxes, and Proper Motions
Kevin A. McKinnon and Roeland P. van der Marel
The next generation of high-precision astrometry is rapidly approaching thanks to ongoing and upcoming missions like Euclid, LSST, and RST. We present a new tool (available at https://github.com/KevinMcK95/
gaia_roman_astrometry) to simulate the astrometric precision that will be achieved when combining
Gaia data with Roman images. The statistics that underpin this method generalize to combinations of astrometric
datasets from any
telescope. We construct realistic Roman position uncertainties as a function of filter, magnitude, and exposure time, which are combined with
Gaia precisions and user-defined Roman observing strategies to predict the expected uncertainty in position, parallax, and proper motion (PM). We also simulate the core Roman surveys to assess their end-of-mission astrometric capabilities, finding that the High Latitude and
Galactic Bulge Time Domain Surveys will deliver
Gaia-DR3-quality PMs down to G=26.5 mag and G=29.0 mag, respectively. Due to its modest number of repeat observations, we find that the astrometry of the High Latitude Wide Area Survey (HLWAS) is very sensitive to particular choices in observing strategies. We compare possible HLWAS strategies to highlight the impact of parallax effects and conclude that a multi-year Roman-only baseline is required for useful PM uncertainties (<100 mas/yr). This simulation tool is actively being used for ongoing Roman proposal writing to ensure astrometric requirements for science goals will be met. Subsequent work will expand this tool to include simulated observations from other
telescopes to plan for a future where all surveys and
datasets are harnessed together.
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Statistical Methodology
A Bayesian Prevalence Incidence Cure model for estimating survival using Electronic Health Records with incomplete baseline diagnoses
Matilda Pitt and Robert J. B. Goudie
Retrospective cohorts can be extracted from Electronic Health Records (EHR) to study prevalence, time until disease or event occurrence and cure proportion in real world scenarios. However, EHR are collected for patient care rather than research, so typically have complexities, such as patients with missing baseline disease status. Prevalence-Incidence (PI) models, which use a two-component mixture model to account for this missing data, have been proposed. However, PI models are biased in settings in which some individuals will never experience the endpoint (they are 'cured'). To address this, we propose a Prevalence Incidence Cure (PIC) model, a 3 component mixture model that combines the PI model framework with a cure model. Our PIC model enables estimation of the prevalence, time-to-incidence, and the cure proportion, and allows for
covariates to affect these. We adopt a
Bayesian inference approach, and focus on the interpretability of the prior. We show in a simulation study that the PIC model has smaller bias than a PI model for the survival probability; and compare inference under vague, informative and misspecified priors. We illustrate our model using a
dataset of 1964 patients undergoing treatment for Diabetic Macular Oedema, demonstrating improved fit under the PIC model.
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Machine Learning (Statistics) · Cross-listed from cs.LG
GRIP2: A Robust and Powerful Deep Knockoff Method for Feature Selection
Bob Junyi Zou and Lu Tian
Identifying truly predictive
covariates while strictly controlling false discoveries remains a fundamental challenge in nonlinear, highly correlated, and low signal-to-noise regimes, where deep learning based feature selection methods are most attractive. We propose Group Regularization Importance Persistence in 2 Dimensions (GRIP2), a deep knockoff feature importance statistic that integrates first-layer feature activity over a two-dimensional regularization surface controlling both sparsity strength and sparsification geometry. To approximate this surface integral in a single training run, we introduce efficient block-
stochastic sampling, which aggregates feature activity magnitudes across diverse regularization regimes along the optimization trajectory. The resulting statistics are antisymmetric by construction, ensuring finite-sample FDR control. In extensive experiments on synthetic and semi-real data, GRIP2 demonstrates improved robustness to feature correlation and noise level: in high correlation and low signal-to-noise ratio regimes where standard deep learning based feature selectors may struggle, our method retains high power and stability. Finally, on real-world HIV drug resistance data, GRIP2 recovers known resistance-associated mutations with power better than established linear baselines, confirming its reliability in practice.
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Statistics Theory · Cross-listed from cs.LG
Analyzing Shapley Additive Explanations to Understand Anomaly Detection Algorithm Behaviors and Their Complementarity
Jordan Levy, Paul Saves, Moncef Garouani et al. (+2 more)
Unsupervised anomaly detection is a challenging problem due to the diversity of data distributions and the lack of labels. Ensemble methods are often adopted to mitigate these challenges by combining multiple detectors, which can reduce individual biases and increase robustness. Yet building an ensemble that is genuinely complementary remains challenging, since many detectors rely on similar decision cues and end up producing redundant anomaly scores. As a result, the potential of ensemble learning is often limited by the difficulty of identifying models that truly capture different types of irregularities. To address this, we propose a methodology for characterizing anomaly detectors through their decision mechanisms. Using SHapley Additive exPlanations, we quantify how each model attributes importance to input features, and we use these attribution profiles to measure similarity between detectors. We show that detectors with similar explanations tend to produce correlated anomaly scores and identify largely overlapping anomalies. Conversely, explanation divergence reliably indicates complementary detection behavior. Our results demonstrate that explanation-driven metrics offer a different criterion than raw outputs for selecting models in an ensemble. However, we also demonstrate that diversity alone is insufficient; high individual model performance remains a prerequisite for effective ensembles. By explicitly targeting explanation diversity while maintaining model quality, we are able to construct ensembles that are more diverse, more complementary, and ultimately more effective for unsupervised anomaly detection.
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All authors Jordan Levy, Paul Saves, Moncef Garouani, Nicolas Verstaevel, Benoit Gaudou
Statistical Methodology
On the calibration of survival models with competing risks
Julie Alberge, Tristan Haugomat, Gaël Varoquaux et al. (+1 more)
Survival analysis deals with modeling the time until an event occurs, and accurate probability estimates are crucial for decision-making, particularly in the competing-risks setting where multiple events are possible. While recent work has addressed calibration in standard survival analysis, the competing-risks setting remains under-explored as it is harder (the calibration applies to both probabilities across classes and time horizon). We show that existing calibration measures are not suited to the competing-risk setting and that recent models do not give well-behaved probabilities. To address this, we introduce a dedicated framework with two novel calibration measures that are minimized for oracle
estimators (i.e., both measures are proper). We also introduce some methods to estimate, test, and correct the calibration. Our recalibration methods yield good probabilities while preserving discrimination.
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All authors Julie Alberge, Tristan Haugomat, Gaël Varoquaux, Judith Abécassis
Machine Learning (Statistics)
Neuron Block Dynamics for XOR Classification with Zero-Margin
Guillaume Braun and Masaaki Imaizumi
The ability of neural networks to learn useful features through
stochastic gradient descent (SGD) is a cornerstone of their success. Most theoretical analyses focus on regression or on classification tasks with a positive margin, where worst-case gradient bounds suffice. In contrast, we study zero-margin nonlinear classification by analyzing the Gaussian XOR problem, where inputs are Gaussian and the XOR decision boundary determines labels. In this setting, a non-negligible fraction of data lies arbitrarily close to the boundary, breaking standard margin-based arguments. Building on Glasgow's (2024) analysis, we extend the study of training dynamics from discrete to Gaussian inputs and develop a framework for the dynamics of
neuron blocks. We show that
neurons cluster into four directions and that block-level signals evolve coherently, a phenomenon essential in the Gaussian setting where individual
neuron signals vary significantly. Leveraging this block perspective, we analyze generalization without relying on margin assumptions, adopting an average-case view that distinguishes regions of reliable prediction from regions of persistent error. Numerical experiments confirm the predicted two-phase block dynamics and demonstrate their robustness beyond the Gaussian setting.
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Machine Learning (Statistics)
Uncertainty-Aware Multimodal Learning via Conformal Shapley Intervals
Mathew Chandy, Michael Johnson, Judong Shen et al. (+4 more)
Multimodal learning combines information from multiple data modalities to improve predictive performance. However, modalities often contribute unequally and in a data dependent way, making it unclear which data modalities are genuinely informative and to what extent their contributions can be trusted. Quantifying modality level importance together with uncertainty is therefore central to interpretable and reliable
multimodal learning. We introduce conformal Shapley intervals, a framework that combines Shapley values with conformal inference to construct uncertainty-aware importance intervals for each modality. Building on these intervals, we propose a modality selection procedure with a provable optimality guarantee: conditional on the observed features, the selected subset of modalities achieves performance close to that of the optimal subset. We demonstrate the effectiveness of our approach on multiple
datasets, showing that it provides meaningful uncertainty quantification and strong predictive performance while relying on only a small number of informative modalities.
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All authors Mathew Chandy, Michael Johnson, Judong Shen, Devan V. Mehrotra, Hua Zhou, Jin Zhou, Xiaowu Dai
Statistical Computation
Nested Slice Sampling: Vectorized Nested Sampling for GPU-Accelerated Inference
David Yallup, Namu Kroupa and Will Handley
Model comparison and calibrated uncertainty quantification often require integrating over parameters, but scalable inference can be challenging for complex,
multimodal targets. Nested Sampling is a robust alternative to standard MCMC, yet its typically sequential structure and hard constraints make efficient accelerator implementations difficult. This paper introduces Nested Slice Sampling (NSS), a GPU-friendly, vectorized formulation of Nested Sampling that uses Hit-and-Run Slice Sampling for constrained updates. A tuning analysis yields a simple near-optimal rule for setting the slice width, improving high-dimensional behavior and making per-step compute more predictable for parallel execution. Experiments on challenging synthetic targets, high dimensional
Bayesian inference, and Gaussian process hyperparameter marginalization show that NSS maintains accurate evidence estimates and high-quality posterior samples, and is particularly robust on difficult
multimodal problems where current state-of-the-art methods such as tempered SMC baselines can struggle. An open-source implementation is released to facilitate adoption and reproducibility.
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Machine Learning (Statistics)
Graph Attention Network for Node Regression on Random Geometric Graphs with Erdős–Rényi contamination
Somak Laha, Suqi Liu and Morgane Austern
Graph
attention networks (GATs) are widely used and often appear robust to noise in node
covariates and edges, yet rigorous statistical guarantees demonstrating a provable advantage of GATs over non-
attention graph neural networks~(GNNs) are scarce. We partially address this gap for node regression with graph-based errors-in-variables models under simultaneous
covariate and edge corruption: responses are generated from latent node-level
covariates, but only noise-perturbed versions of the latent
covariates are observed; and the sample graph is a random
geometric graph created from the node
covariates but contaminated by independent Erdős–Rényi edges. We propose and analyze a carefully designed, task-specific GAT that constructs denoised proxy features for regression. We prove that regressing the response variables on the proxies achieves lower error asymptotically in (a) estimating the regression coefficient compared to the ordinary least squares (OLS)
estimator on the noisy node
covariates, and (b) predicting the response for an unlabelled node compared to a vanilla graph convolutional network~(GCN) – under mild growth conditions. Our analysis leverages high-dimensional
geometric tail bounds and concentration for neighbourhood counts and sample covariances. We verify our theoretical findings through experiments on synthetically generated data. We also perform experiments on real-world graphs and demonstrate the effectiveness of the
attention mechanism in several node regression tasks.
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Machine Learning (Statistics) · Cross-listed from cs.LG
YuriiFormer: A Suite of Nesterov-Accelerated Transformers
Aleksandr Zimin, Yury Polyanskiy and Philippe Rigollet
We propose a variational framework that interprets
transformer layers as iterations of an optimization
algorithm acting on
token embeddings. In this view, self-
attention implements a gradient step of an interaction energy, while MLP layers correspond to gradient updates of a potential energy. Standard GPT-style
transformers emerge as vanilla gradient descent on the resulting composite objective, implemented via Lie–Trotter splitting between these two energy functionals. This perspective enables principled architectural design using classical optimization ideas. As a proof of concept, we introduce a Nesterov-style accelerated
transformer that preserves the same
attention and MLP oracles. The resulting architecture consistently outperforms a nanoGPT baseline on TinyStories and OpenWebText, demonstrating that optimization-theoretic insights can translate into practical gains.
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Machine Learning (Statistics)
A Random Matrix Theory of Masked Self-Supervised Regression
Arie Wortsman Zurich, Federica Gerace, Bruno Loureiro et al. (+1 more)
In the era of
transformer models, masked self-supervised learning (SSL) has become a foundational training paradigm. A defining feature of masked SSL is that training aggregates predictions across many masking patterns, giving rise to a joint,
matrix-valued predictor rather than a single vector-valued
estimator. This object encodes how coordinates condition on one another and poses new analytical challenges. We develop a precise high-dimensional analysis of masked modeling objectives in the proportional regime where the number of samples scales with the ambient dimension. Our results provide explicit expressions for the generalization error and characterize the spectral structure of the learned predictor, revealing how masked modeling extracts structure from data. For spiked covariance models, we show that the joint predictor undergoes a Baik–Ben Arous–Péché (BBP)-type phase transition, identifying when masked SSL begins to recover latent signals. Finally, we identify structured regimes in which masked self-supervised learning provably outperforms PCA, highlighting potential advantages of SSL objectives over classical unsupervised methods
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All authors Arie Wortsman Zurich, Federica Gerace, Bruno Loureiro, Yue M. Lu
Statistics Applications
Beyond the Null Effect: Unmasking the True Impact of Teacher-Child Interaction Quality on Child Outcomes in Early Head Start
JoonHo Lee and Alison Hooper
In Early Head Start (EHS), teacher-child interactions are widely believed to shape infant-toddler outcomes, yet large-scale studies often find only modest or null associations. This study addresses four methodological sources of attenuation – item-level measurement error, center-level confounding, teacher- and classroom-level
covariate imbalance, and overlooked nonlinearities – to clarify classroom process quality's true influence on child development. Using data from the 2018 wave of the Early Head Start Family and Child Experiences Survey (Baby FACES), we applied a three-level generalized additive latent and mixed model (GALAMM) to distinguish genuine classroom-level variability in process quality, as measured by the Classroom Assessment Scoring System (CLASS) and Quality of Caregiver-Child Interactions for Infants and Toddlers (QCIT), from item-level noise and center-level effects. We then estimated dose-response relationships with children's
language and socioemotional outcomes, employing
covariate balancing weights and generalized additive models. Results show that nearly half of each item's variance reflects classroom-level processes, with the remainder tied to measurement error or center-wide influences, masking true classroom effects. After correcting for these biases, domain-focused dose-response analyses reveal robust linear associations between cognitive/
language supports and children's English communicative skills, while emotional-behavioral supports better predict social-emotional competence. Some domains display plateaus when pushed to extremes, underscoring potential nonlinearities. These findings challenge the "null effect" narrative, demonstrating that rigorous methodology can uncover the critical, domain-specific impacts of teacher-child interaction quality, offering clearer guidance for targeted professional development and policy in EHS.
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Statistical Methodology
Robust, partially alive particle Metropolis-Hastings via the Frankenfilter
Chris Sherlock, Andrew Golightly and Anthony Lee
When a hidden Markov model permits the conditional likelihood of an observation given the hidden process to be zero, all particle simulations from one observation time to the next could produce zeros. If so, the filtering distribution cannot be estimated and the estimated parameter likelihood is zero. The alive particle filter addresses this by simulating a random number of particles for each inter-observation interval, stopping after a target number of non-zero conditional likelihoods. For outlying observations or poor parameter values, a non-zero result can be extremely unlikely, and computational costs prohibitive. We introduce the Frankenfilter, a principled, partially alive particle filter that targets a user-defined amount of success whilst fixing lower and upper bounds on the number of simulations. The Frankenfilter produces unbiased
estimators of the likelihood, suitable for pseudo-marginal Metropolis–Hastings (PMMH). We demonstrate that PMMH with the Frankenfilter is more robust to outliers and mis-specified initial parameter values than PMMH using standard particle filters, and is typically at least 2-3 times more efficient. We also provide advice for choosing the amount of success. In the case of n exact observations, this is particularly simple: target n successes.
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Statistics Applications · Cross-listed from q-fin.ST
A unified theory of order flow, market impact, and volatility
Johannes Muhle-Karbe, Youssef Ouazzani Chahdi, Mathieu Rosenbaum et al. (+1 more)
We propose a microstructural model for the order flow in financial
markets that distinguishes between core orders and reaction flow, both modeled as Hawkes processes. This model has a natural scaling limit that reconciles a number of salient empirical properties: persistent signed order flow, rough trading volume and
volatility, and power-law
market impact. In our framework, all these quantities are pinned down by a single statistic $H_0$, which measures the persistence of the core flow. Specifically, the signed flow converges to the sum of a fractional process with Hurst index $H_0$ and a martingale, while the limiting traded volume is a rough process with Hurst index $H_0-1/2$. No-arbitrage constraints imply that
volatility is rough, with Hurst parameter $2H_0-3/2$, and that the price impact of trades follows a power law with exponent $2-2H_0$. The analysis of signed order flow data yields an estimate $H_0 \approx 3/4$. This is not only consistent with the square-root law of
market impact, but also turns out to match estimates for the roughness of traded volumes and
volatilities remarkably well.
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All authors Johannes Muhle-Karbe, Youssef Ouazzani Chahdi, Mathieu Rosenbaum, Grégoire Szymanski
Other Statistics
Revisiting the Lost Submarine Problem: A Decision Theoretic Approach
Anthony Almudevar
This article includes a discussion of the “lost submarine problem", following Morey et al (2016). As the title of that paper suggests (The fallacy of placing confidence in confidence intervals), the example is intended to illustrate the futility of relying on the confidence interval as a formal inference statement. In the view of this author, the misgivings expressed in Morey et al (2016) can be resolved using a decision theoretic approach. While it is true that a variety of statistical methods lead to a variety of confidence intervals, once we precisely define their purpose, a single optimal choice emerges. Furthermore, distinct purposes lead to distinct optimal choices. Therefore, that a variety of procedures exist is an advantage rather than a liability.
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Statistics Theory
Semi-knockoffs: a model-agnostic conditional independence testing method with finite-sample guarantees
Angel Reyero-Lobo, Bertrand Thirion and Pierre Neuvial
Conditional independence testing (CIT) is essential for reliable scientific discovery. It prevents spurious findings and enables controlled feature selection. Recent CIT methods have used machine learning (ML) models as surrogates of the underlying distribution. However, model-agnostic approaches require a train-test split, which reduces statistical power. We introduce Semi-knockoffs, a CIT method that can accommodate any pre-trained model, avoids this split, and provides valid p-values and false discovery rate (FDR) control for high-dimensional settings. Unlike methods that rely on the model-$X$ assumption (known input distribution), Semi-knockoffs only require conditional expectations for continuous variables. This makes the procedure less restrictive and more practical for machine learning integration. To ensure validity when estimating these expectations, we present two new theoretical results of independent interest: (i) stability for regularized models trained with a null feature and (ii) the double-robustness property.
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Machine Learning (Statistics)
Asymptotic Theory of Iterated Empirical Risk Minimization, with Applications to Active Learning
Hugo Cui and Yue M. Lu
We study a class of iterated empirical risk minimization (ERM) procedures in which two successive ERMs are performed on the same
dataset, and the predictions of the first
estimator enter as an argument in the loss function of the second. This setting, which arises naturally in active learning and reweighting schemes, introduces intricate statistical dependencies across samples and fundamentally distinguishes the problem from classical single-stage ERM analyses. For linear models trained with a broad class of convex losses on Gaussian mixture data, we derive a sharp asymptotic characterization of the test error in the high-dimensional regime where the sample size and ambient dimension scale proportionally. Our results provide explicit, fully asymptotic predictions for the performance of the second-stage
estimator despite the reuse of data and the presence of prediction-dependent losses. We apply this theory to revisit a well-studied pool-based active learning problem, removing oracle and sample-splitting assumptions made in prior work. We uncover a fundamental tradeoff in how the labeling budget should be allocated across stages, and demonstrate a double-descent behavior of the test error driven purely by data selection, rather than model size or sample count.
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Machine Learning (Statistics)
Neural Backward Filtering Forward Guiding
Gefan Yang, Frank van der Meulen and Stefan Sommer
Inference in nonlinear continuous
stochastic processes on trees is challenging, particularly when observations are sparse and the
topology is complex. Exact smoothing via Doob's $h$-transform is intractable for general nonlinear dynamics. We propose Neural Backward Filtering Forward Guiding (NBFFG), a unified framework for both discrete transitions and continuous
diffusions. Our method constructs a variational posterior by leveraging a proxy linear-Gaussian process. This proxy process yields a closed-form backward filter that serves as a guide, steering the generative path toward high-likelihood regions. We then learn a neural residual to capture the non-linear discrepancies. This formulation allows for an unbiased pathwise subsampling scheme, reducing the training complexity from tree-size dependent to path-length dependent. Empirical results show that NBFFG outperforms baselines on synthetic
benchmarks, and we demonstrate the method on a high-dimensional inference task in phylogenetic analysis with reconstruction of ancestral butterfly wing shapes.
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Statistical Methodology
Comparing Bayesian Dynamic Borrowing and Synthetic Control Methods: Apples to Oranges?
Nicole Cizauskas, Foteini Strimenopoulou, Svetlana S. Cherlin et al. (+1 more)
Bayesian dynamic borrowing (BDB) and synthetic control methods (SCM) are strategies to incorporate historical data in clinical trial design when control recruitment is a challenge. While both methods aim to improve efficiency, they differ in conceptual approach: BDB adjusts borrowing based on prior-data conflict, whereas SCM synthesizes individual-level control outcomes. This study aims to conduct a comparison BDB (using meta-analytic predictive prior (MAP)) and SCM using a case study of Pediatric Atopic Dermatitis. Six historical randomised control trials were selected for use in both the creation of the MAP prior and synthetic control arm. BDB MAP prior produced a mean response rate (historical control response probability) of 0.22 (posterior 95% credible interval: 0.11-0.36) (0.22 and 0.11-0.37 robustified), a power of 0.58, a type 1 error rate of 0.03, bias of 0.0007 (0.0008 robustified), a coverage of 0.96 (0.94 robustified) and prior ESS of 8.9 (3.32 robustified). SCM produced a mean response rate of 0.26 (95% confidence interval: 0.17-0.36), a power of 0.75, type 1 error rate of 0.013, bias of -0.0002, and coverage of 0.97; when adjusted to match the BDB ESS, SCM reported a similar mean response rate (0.27 and 0.13-0.46). a lower power (0.54), type 1 error rate (0.002) and bias(-0.0006), and the same coverage rate (0.97) to the initial SCM results. For this case study, the sample size adjusted SCM model produced a relatively similar power and type 1 error rate to the BDB MAP prior method. However, direct comparisons between these two methods fail to capture the true relationship due to how the data is handled differently and the purpose of each method. Method selection should consider trial-specific constraints, prior-data heterogeneity, and the desired balance between efficiency and robustness.
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All authors Nicole Cizauskas, Foteini Strimenopoulou, Svetlana S. Cherlin, James M. S. Wason