Conformal risk control (CRC) provides distribution-free guarantees for controlling the expected loss at a user-specified level. Existing theory typically assumes that the loss decreases monotonically with a tuning parameter that governs the size of the prediction set. However, this assumption is often violated in practice, where losses may behave non-monotonically due to competing objectives such as coverage and efficiency. In this paper, we study CRC under non-monotone loss functions when the tuning parameter is selected from a finite grid, a setting commonly arising in thresholding and discretized decision rules. Revisiting a known counterexample, we show that the validity of CRC without monotonicity depends critically on the relationship between the calibration sample size and the grid resolution. In particular, reliable risk control can still be achieved when the calibration sample is sufficiently large relative to the grid size. We establish a finite-sample guarantee for bounded losses over a grid of size $m$, showing that the excess risk above the target level $α$ scales on the order of $\sqrt{\log(m)/n}$, where $n$ is the calibration sample size. A matching lower bound demonstrates that this rate is minimax optimal. We also derive refined guarantees under additional structural conditions, including Lipschitz continuity and monotonicity, and extend the analysis to settings with distribution shift via importance weighting. Numerical experiments on synthetic multilabel classification and real object detection data illustrate the practical implications of non-monotonicity. Methods that explicitly account for finite-sample uncertainty achieve more stable risk control than approaches based on monotonicity transformations, while maintaining competitive prediction set sizes.

Adaptive specification search generates statistically significant backtests even under martingale-difference nulls. We introduce a falsification audit testing complete predictive workflows against synthetic reference classes, including zero-predictability environments and microstructure placebos. Workflows generating significant walk-forward evidence in these environments are falsified. For passing workflows, we quantify selection-induced performance inflation using an absolute magnitude gap linking optimized in-sample evidence to disjoint walk-forward realizations, adjusted for effective multiplicity. Simulations validate extreme-value scaling under correlated searches and demonstrate detection power under genuine structure. Empirical case studies confirm that many apparent findings represent methodological artifacts rather than genuine predictability.

When considering a model selection or, more generally, an aggregation approach for adaptive statistical inference, it is often necessary to compute estimators over a wide range of model complexities including unnecessarily large models even when the true data-generating process is relatively simple, due to the lack of prior knowledge. This requirement can lead to substantial computational inefficiency. In this work, we propose a novel framework for efficient model aggregation called the early-stopped aggregation (ESA): instead of computing and aggregating estimators for all candidate models, we compute only a small number of simpler ones using an early-stopping criterion and aggregate only these for final inference. Our framework is versatile and applies to both Bayesian model selection, in particular, within the variational Bayes framework, and frequentist estimation, including a general penalized estimation setting. We investigate adaptive optimal property of the ESA approach across three learning paradigms. We first show that ESA achieves optimal adaptive contraction rates in the variational Bayes setting under mild conditions. We extend this result to variational empirical Bayes, where prior hyperparameters are chosen in a data-dependent manner. In addition, we apply the ESA approach to frequentist aggregation including both penalization-based and sample-splitting implementations, and establish corresponding theory. As we demonstrate, there is a clear unification between early-stopped Bayes and frequentist penalized aggregation, with a common "energy" functional comprising a data-fitting term and a complexity-control term that drives both procedures. We further present several applications and numerical studies that highlight the efficiency and strong performance of the proposed approach.

Clinical decision-making often involves selecting tests that are costly, invasive, or time-consuming, motivating individualized, sequential strategies for what to measure and when to stop ascertaining. We study the problem of learning cost-optimal sequential decision policies from retrospective data, where test availability depends on prior results, inducing informative missingness. Under a sequential missing-at-random mechanism, we develop a doubly robust Q-learning framework for estimating optimal policies. The method introduces path-specific inverse probability weights that account for heterogeneous test trajectories and satisfy a normalization property conditional on the observed history. By combining these weights with auxiliary contrast models, we construct orthogonal pseudo-outcomes that enable unbiased policy learning when either the acquisition model or the contrast model is correctly specified. We establish oracle inequalities for the stage-wise contrast estimators, along with convergence rates, regret bounds, and misclassification rates for the learned policy. Simulations demonstrate improved cost-adjusted performance over weighted and complete-case baselines, and an application to a prostate cancer cohort study illustrates how the method reduces testing cost without compromising predictive accuracy.

We study the problem of estimating the effect function for a continuous treatment, which maps each treatment value to a population-averaged outcome. A central challenge in this setting is confounding: treatment assignment often depends on covariates, creating selection bias that makes direct regression of the response on treatment unreliable. To address this issue, we propose a two-stage kernel ridge regression method. In the first stage, we learn a model for the response as a function of both treatment and covariates; in the second stage, we use this model to construct pseudo-outcomes that correct for distribution shift, and then fit a second model to estimate the treatment effect. Although the response varies with both treatment and covariates, the induced effect function obtained by averaging over covariates is typically much simpler, and our estimator adapts to this structure. Furthermore, we introduce a fully data-driven model selection procedure that achieves provable adaptivity to both the unknown degree of overlap and the regularity (eigenvalue decay) of the underlying kernel.

Background: Single-cell RNA sequencing (scRNA-seq) enables gene expression profiling at cellular resolution but is inherently affected by sparsity caused by dropout events, where expressed genes are recorded as zeros due to technical limitations. These artifacts distort gene expression distributions and compromise downstream analyses. Numerous imputation methods have been proposed to recover latent transcriptional signals. These methods range from traditional statistical models to deep learning (DL)-based methods. However, their comparative performance remains unclear, as existing benchmarks evaluate only a limited subset of methods, datasets, and downstream analyses. Results: We present a comprehensive benchmark of 15 scRNA-seq imputation methods spanning 7 methodological categories, including traditional and DL-based methods. Methods are evaluated across 30 datasets from 10 experimental protocols on 6 downstream analyses. Results show that traditional methods, such as model-based, smoothing-based, and low-rank matrix-based methods, generally outperform DL-based methods, including diffusion-based, GAN-based, GNN-based, and autoencoder-based methods. In addition, strong performance in numerical gene expression recovery does not necessarily translate into improved biological interpretability in downstream analyses, including cell clustering, differential expression analysis, marker gene analysis, trajectory analysis, and cell type annotation. Furthermore, method performance varies substantially across datasets, protocols, and downstream analyses, with no single method consistently outperforming others. Conclusions: Our findings provide practical guidance for selecting imputation methods tailored to specific analytical objectives and underscore the importance of task-specific evaluation when assessing imputation performance in scRNA-seq data analysis.

Data leakage remains a recurrent source of optimistic bias in biomedical machine learning studies. Standard row-wise cross-validation and globally estimated preprocessing steps are often inappropriate for data with repeated measurements, study-level heterogeneity, batch effects, or temporal dependencies. This paper describes bioLeak, an R package for constructing leakage-aware resampling workflows and for auditing fitted models for common leakage mechanisms. The package provides leakage-aware split construction, train-fold-only preprocessing, cross-validated model fitting, nested hyperparameter tuning, post hoc leakage audits, and HTML reporting. The implementation supports binary classification, multiclass classification, regression, and survival analysis, with task-specific metrics and S4 containers for splits, fits, audits, and inflation summaries. The simulation artifacts show how apparent performance changes under controlled leakage mechanisms, and the case study illustrates how guarded and leaky pipelines can yield materially different conclusions on multi-study transcriptomic data. The emphasis throughout is on software design, reproducible workflows, and interpretation of diagnostic output.

We develop a theoretical framework for generalization in the interpolating regime of statistical learning. The central question is why highly overparameterized estimators can attain zero empirical risk while still achieving nontrivial predictive accuracy, and how to characterize the boundary between benign and destructive overfitting. We introduce a spectral-transport stability framework in which excess risk is controlled jointly by the spectral geometry of the data distribution, the sensitivity of the learning rule under single-sample replacement, and the alignment structure of label noise. This leads to a scale-dependent Fredriksson index that combines effective dimension, transport stability, and noise alignment into a single complexity parameter for interpolating estimators. We prove finite-sample risk bounds, establish a sharp benign-overfitting criterion through the vanishing of the index along admissible spectral scales, and derive explicit phase-transition rates under polynomial spectral decay. For a model-specific specialization, we obtain an explicit theorem for polynomial-spectrum linear interpolation, together with a proof of the resulting rate. The framework also clarifies implicit regularization by showing how optimization dynamics can select interpolating solutions of minimal spectral-transport energy. These results connect algorithmic stability, double descent, benign overfitting, operator-theoretic learning theory, and implicit bias within a unified structural account of modern interpolation.

Causal discovery from observational data remains a fundamental challenge in machine learning and statistics, particularly when variables represent inherently positive quantities such as gene expression levels, asset prices, company revenues, or population counts, which often follow multiplicative rather than additive dynamics. We propose the Hybrid Moment-Ratio Scoring (H-MRS) algorithm, a novel method for learning directed acyclic graphs (DAGs) from positive-valued data by combining moment-based scoring with log-scale regression. The key idea is that for positive-valued variables, the moment ratio $\frac{\mathbb{E}[X_j^2]}{\mathbb{E}[(\mathbb{E}[X_j \mid S])^2]}$ provides an effective criterion for causal ordering, where $S$ denotes candidate parent sets. H-MRS integrates log-scale Ridge regression for moment-ratio estimation with a greedy ordering procedure based on raw-scale moment ratios, followed by Elastic Net-based parent selection to recover the final DAG structure. Experiments on synthetic log-linear data demonstrate competitive precision and recall. The proposed method is computationally efficient and naturally respects positivity constraints, making it suitable for applications in genomics and economics. These results suggest that combining log-scale modeling with raw-scale moment ratios provides a practical framework for causal discovery in positive-valued domains.

Accurate classification requires not only high predictive accuracy but also well-calibrated confidence estimates. Yet, modern deep neural networks (DNNs) are often overconfident, primarily due to overfitting on the negative log-likelihood (NLL). While focal loss variants alleviate this issue, they typically reduce accuracy, revealing a persistent trade-off between calibration and predictive performance. Motivated by the complementary strengths of generative and discriminative classifiers, we propose Generative Cross-Entropy (GCE), which maximizes $p(x|y)$ and is equivalent to cross-entropy augmented with a class-level confidence regularizer. Under mild conditions, GCE is strictly proper. Across CIFAR-10/100, Tiny-ImageNet, and a medical imaging benchmark, GCE improves both accuracy and calibration over cross-entropy, especially in the long-tailed scenario. Combined with adaptive piecewise temperature scaling (ATS), GCE attains calibration competitive with focal-loss variants without sacrificing accuracy.