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Hongzhe Li

Publications and source records attributed to Hongzhe Li.

At least 19 recordsLinked to original sources

Inference and Uncertainty Quantification for Streaming $r$-PCA

We address two open questions in streaming PCA via Oja's algorithm: sharp operator-norm convergence for general rank under sub-Gaussian data, and distributional inference for the resulting subspace estimator. Existing convergence analyses, even in the rank-one case, either assume bounded data or leave non-vanishing remainder terms that prevent adaptation to a polynomially vanishing tail spectrum, while existing distributional results are confined to the rank-one case. Our convergence theory removes these remainder terms and yields a sharp rate. In the dense-tail spiked covariance regime, this rate matches the minimax rate up to logarithmic factors. More generally, we prove a matching lower bound, up to logarithmic factors, across both dense-tail and sparse-tail regimes under a mild nondegeneracy condition. The analysis yields a linearization of Oja's iterates, which in turn enables a high-dimensional Gaussian approximation for the general-rank subspace estimation error with an explicit limiting covariance. We also establish a row-wise Gaussian approximation over convex sets for the aligned difference, recovering prior rank-one results as special cases. For practical inference, we develop an online multiplier bootstrap algorithm and prove its consistency. Beyond streaming PCA, our techniques contribute to Gaussian approximation and bootstrap inference for nonconvex stochastic approximation.

stat.ML

Generation-Powered Inference for Distribution-Valued Outcomes

Modern generative models increasingly produce distribution-valued outputs, such as predicted cellular responses to genetic perturbations in single-cell genomics. While these models provide valuable auxiliary information, they are inherently imperfect, creating a need for statistical methods that leverage their predictions without relying on their correctness. We propose generation-powered inference (GPI), a general framework for improving inference on distribution-valued parameters using auxiliary generative models. Focusing on Wasserstein barycenters and related distributional functionals, we introduce a function-valued bridge representation that transforms inference in the nonlinear Wasserstein space into estimation of a mean function in a Hilbert space, enabling an augmented estimation framework analogous to prediction-powered inference. We develop a family of GPI estimators with optimal information borrowing, establish consistency, asymptotic normality, and simultaneous confidence bands, and derive valid inference for linear functionals and Wasserstein distances. Simulation studies demonstrate efficiency gains over labeled-data-only methods and robust performance under generative model misspecification. We illustrate the proposed framework using a Perturb-seq study of K562 cells, where synthetic perturbation responses generated by the State foundation model are used to improve inference for pathway-level consensus gene expression distributions associated with perturbations of the 40S ribosome module.

stat.ME

Knowing the Self, Understanding the World: A Dual-Cognition Benchmark for UAV Spatio-temporal Reasoning with MLLMs

Multimodal large language models have achieved strong performance across diverse vision-language tasks, yet their capabilities in UAV scenarios remain insufficiently explored. Recent UAV-oriented benchmarks have begun to evaluate MLLMs in aerial scenarios, but they typically focus on scene understanding, event recognition, or navigation completion, rather than jointly assessing the dual-cognition capability required for UAV agents: reasoning about both the UAV's own state and the external environment in multiview spatio-temporal contexts. To address this gap, we present UAV-DualCog, a benchmark for aerial multiview spatio-temporal reasoning built on this dual-cognition perspective. UAV-DualCog includes both image and video tasks to jointly evaluate self-state and environment-state reasoning, while requiring spatial or temporal grounding beyond discrete answer prediction. We also develop an automated pipeline that constructs data from scene-level semantic point clouds, yielding a scalable benchmark with diverse scenes, hundreds of landmarks, and thousands of QA samples. Extensive evaluations show that current MLLMs remain far from reliable in UAV dual cognition. Self-state reasoning, viewpoint transformation, precise spatial grounding, and temporal interval localization are persistent bottlenecks, and additional validation with thinking/frontier models and a human baseline confirms that the benchmark is understandable to humans but challenging for existing models. We further construct UAV-DualCog-Train from disjoint scenes and show through a lightweight optimization probe that it provides useful structured supervision, suggesting its value not only as an evaluation benchmark but also as a data resource for advancing MLLM-based UAV agents. Project website and supplementary materials: https://uav-dualcog.lozumi.com

cs.CV

Bias-Aware External-Model-Assisted Inference in High-Dimensional Regression

In high-dimensional semi-supervised linear regression, prediction-powered inference (PPI) corrects an external predictor with a rectifier estimated from the labeled data. In a linear model, however, this rectifier cancels the predictor: PPI and PPI++ reduce to ordinary least squares and can inflate variance when the predictor is close to the oracle. We propose the Debiased External-model-Assisted Lasso (DEAL), which routes the external estimator and the unlabeled covariates into the variance of a debiased estimator, with a bias-aware, cross-fitted shrinkage step that adapts across target-only, near-oracle, and biased-but-informative regimes. We prove coordinate-wise asymptotic normality with an adaptive variance, extend validity to the projection parameter under misspecification and nonlinear labelers, and show that, at a common unlabeled budget, DEAL intervals are shorter than those of debiased Lasso, PPI, and PPI++; a shift-aware variant preserves coverage under covariate shift. In simulations, DEAL intervals are 0.49-0.87 of the debiased-Lasso length, and across six real-data applications spanning astronomy, chemistry, proteomics, and oncology, the last using a large-language-model oracle, they tighten in every case, with median length ratios of 0.23-0.53.

stat.ME

Confounder-robust causal discovery and inference in Perturb-seq using proxy and instrumental variables

Emerging single-cell technologies that combine CRISPR-based genetic perturbations with single-cell RNA sequencing, such as Perturb-seq, offer unprecedented opportunities to uncover cause-and-effect relationships among genes. Nonetheless, Perturb-seq experiments are subject to unobserved factors that, if not properly handled, can severely bias the inferred causal relationships between genes. These latent factors may arise not only from intrinsic molecular features of the regulatory elements, but also from unmeasured genes omitted due to cost-constrained experimental designs. Although methods for analyzing large-scale Perturb-seq data are rapidly maturing, approaches that explicitly account for such unobserved confounders when inferring causal gene networks are still lacking. Here, we propose a novel approach to accurately reconstruct causal gene networks from Perturb-seq data even when important confounders are missing. Our framework leverages proxy and instrumental variable strategies to exploit the rich information embedded in the perturbations, enabling unbiased estimation of the underlying directed acyclic graph (DAG) of gene expression. Applications to both comprehensive synthetic data and real CRISPR interference experiments in K562 cells demonstrate that our method outperforms baseline approaches that lack principled adjustments for unmeasured confounding, yielding more accurate and biologically relevant recovery of the true causal DAGs.

stat.ME

Multicalibration Boosting: Theory, Convergence, and Transferability

Multicalibration extends classical calibration by requiring predictions to be unbiased over a rich collection of functions, encompassing both prediction slices and subpopulations. It has emerged as a powerful framework for fairness, robustness, and reliable prediction, yet the theoretical understanding of multicalibration boosting (MCBoost) remains fragmented and often relies on restrictive assumptions. In this work, we develop a unified and refined perspective on MCBoost that subsumes existing variants, including multiaccuracy, BatchGCP, and BatchMVP. We uncover several phenomena that provide new insights into its practical behavior: even highly accurate and flexible predictors can remain substantially miscalibrated; enforcing multicalibration introduces a calibration-risk trade-off; and early stopping plays a central role in controlling this trade-off. On the theoretical side, we establish a general framework for MCBoost under weaker and more realistic conditions. We show that the boosting iterates converge to a Bregman projection of the population-optimal predictor onto the cumulative span generated by the audit class, thereby explicitly characterizing the function space on which multicalibration is achieved. We further derive convergence rates under different smoothness assumptions, finite-sample guarantees, and principled stopping rules that ensure multicalibration at termination. Finally, we extend the theory of universal adaptability under covariate shift, providing more general transfer guarantees and clarifying when multicalibrated predictors generalize across domains. These results provide a more complete theoretical foundation and practical guidance for multicalibration boosting, positioning it as both a unifying framework and a reliable post-processing approach for modern predictive models.

stat.ML

Causal Network Discovery from Interventional Count Data with Latent Linear DAGs

The increasing availability of interventional data offers new opportunities for causal discovery, with gene perturbation studies providing a prominent example. Such data are typically count-valued and subject to substantial measurement error arising from technical variability and latent state heterogeneity. Motivated by these challenges, we study identification and estimation in latent linear structural causal models for interventional count data. We propose a latent linear Gaussian directed acyclic graph (DAG) model with Poisson measurement error that explicitly separates the latent causal structure from the observed counts. Under a mean-shift intervention design, we establish population-level identifiability of the latent causal DAG. Building on these identification results, we develop an estimation procedure based on sparse inverse matrix estimation and provide theoretical guarantees on estimation error and finite-sample causal discovery. Simulation studies and applications to Perturb-seq data demonstrate the practical effectiveness of the proposed method.

stat.ME

Differential Density Analysis in Single-Cell Genomics Using Specially Designed Exponential Families

Recent advances in high-resolution sequencing have paved the way for population-scale analysis in single-cell RNA-sequencing (scRNA-seq) data. scRNA-seq data, in particular, have proven to be extremely powerful in profiling a variety of outcomes such as disease and aging. The abundance of scRNA-seq data makes it possible to model each individual's gene expression as a probability density across cells, offering a richer representation than summary statistics such as means or variances, and allowing for more nuanced group comparisons. To this end, we propose a model-agnostic framework for density estimation and inference based on specially designed exponential families~(SEF), which accommodates diverse underlying models without requiring prior specifications. The proposed method enables estimation and visualization for both individual-specific and group-level gene expression densities, as well as conducting formal hypothesis testing for expression density difference across groups of interest. It relies on relaxed assumptions with established asymptotic properties and a consistent covariance estimator for valid inference. Through simulation under various scenarios, the SEF-based approach demonstrates good error control and improved statistical power over competing methods,including pseudo-bulk tests and moment estimators. Application to a population-scale scRNA-seq dataset from patients with systemic lupus erythematosus identified genes and gene sets that are missed from pseudo-bulk based tests.

stat.ME

Multicalibration for Modeling Censored Survival Data with Universal Adaptability

Traditional statistical and machine learning methods typically assume that the training and test data follow the same distribution. However, this assumption is frequently violated in real-world applications, where the training data in the source domain may under-represent specific subpopulations in the test data of the target domain. This paper addresses target-independent learning under covariate shift, focusing on multicalibration for survival probability and restricted mean survival time. A black-box post-processing boosting algorithm specifically designed for censored survival data is introduced. By leveraging pseudo-observations, our method produces a multicalibrated predictor that is competitive with inverse propensity score weighting in predicting the survival outcome in an unlabeled target domain, ensuring not only overall accuracy but also fairness across diverse subpopulations. Our theoretical analysis of pseudo-observations builds upon the functional delta method and the $p$-variational norm. The algorithm's sample complexity, convergence properties, and multicalibration guarantees for post-processed predictors are provided. Our results establish a fundamental connection between multicalibration and universal adaptability, demonstrating that our calibrated function is comparable to, or outperforms, the inverse propensity score weighting estimator. Extensive numerical simulations and a real-world case study on cardiovascular disease risk prediction using two large prospective cohort studies validate the effectiveness of our approach.

stat.ME

CGEarthEye:A High-Resolution Remote Sensing Vision Foundation Model Based on the Jilin-1 Satellite Constellation

Deep learning methods have significantly advanced the development of intelligent rinterpretation in remote sensing (RS), with foundational model research based on large-scale pre-training paradigms rapidly reshaping various domains of Earth Observation (EO). However, compared to the open accessibility and high spatiotemporal coverage of medium-resolution data, the limited acquisition channels for ultra-high-resolution optical RS imagery have constrained the progress of high-resolution remote sensing vision foundation models (RSVFM). As the world's largest sub-meter-level commercial RS satellite constellation, the Jilin-1 constellation possesses abundant sub-meter-level image resources. This study proposes CGEarthEye, a RSVFM framework specifically designed for Jilin-1 satellite characteristics, comprising five backbones with different parameter scales with totaling 2.1 billion parameters. To enhance the representational capacity of the foundation model, we developed JLSSD, the first 15-million-scale multi-temporal self-supervised learning (SSL) dataset featuring global coverage with quarterly temporal sampling within a single year, constructed through multi-level representation clustering and sampling strategies. The framework integrates seasonal contrast, augmentation-based contrast, and masked patch token contrastive strategies for pre-training. Comprehensive evaluations across 10 benchmark datasets covering four typical RS tasks demonstrate that the CGEarthEye consistently achieves state-of-the-art (SOTA) performance. Further analysis reveals CGEarthEye's superior characteristics in feature visualization, model convergence, parameter efficiency, and practical mapping applications. This study anticipates that the exceptional representation capabilities of CGEarthEye will facilitate broader and more efficient applications of Jilin-1 data in traditional EO application.

cs.CV

Test of partial effects for Frechet regression on Bures-Wasserstein manifolds

We propose a novel test for assessing partial effects in Fr\'echet regression with responses lying on the Bures-Wasserstein manifold. Under the null hypothesis, we show that the statistic admits a degenerate V-statistic approximation whose limiting distribution is a weighted mixture of chi-squared random variables, with weights determined by the eigenvalues of an integral operator associated with a reproducing kernel Hilbert space (RKHS) kernel. We establish the asymptotic validity and consistency of the proposed test. Its finite-sample performance is examined through simulation studies. We apply the proposed test to study the effect of age, while controlling for other covariates, on gene co-expression structure in single-cell data.

stat.ML

A Robust Local Fréchet Regression Using Unbalanced Neural Optimal Transport with Applications to Dynamic Single-cell Genomics Data

Single-cell RNA sequencing (scRNA-seq) technologies have enabled the profiling of gene expression for a collection of cells across time during a dynamic biological process. Given that each time point provides only a static snapshot, modeling and understanding the underlying cellular dynamics remains a central yet challenging task in modern genomics. To associate biological time with single cell distributions, we develop a robust local Fréchet regression for interpolating the high-dimensional cellular distribution at any given time point using data observed over a finite time points. To allow for robustness in cell distributions, we propose to apply the unbalanced optimal transport-based Wasserstein distance in our local Fréchet regression analysis. We develop a computationally efficient algorithm to generate the cell distribution for a given time point using generative neural networks. The resulting single cell generated models and the corresponding transport plans can be use to interpolate the single cells at any unobserved time point and to track the cell trajectory during the cell differentiation process. We demonstrate the methods using three single cell differentiation data sets, including differentiation of human embryonic stem cells into embryoids, mouse hematopoietic and progenitor cell differentiation, and reprogramming of mouse embryonic fibroblasts. We show that the proposed methods lead to better single cell interpolations, reveal different cell differential trajectories, and identify early genes that regulate these cell trajectories.

stat.AP

Simultaneous Estimation of Many Sparse Networks via Hierarchical Poisson Log-Normal Model

The advancement of single-cell RNA-sequencing (scRNA-seq) technologies allow us to study the individual level cell-type-specific gene expression networks by direct inference of genes' conditional independence structures. scRNA-seq data facilitates the analysis of gene expression data across different conditions or samples, enabling simultaneous estimation of condition- or sample-specific gene networks. Since the scRNA-seq data are count data with many zeros, existing network inference methods based on Gaussian graphs cannot be applied to such single cell data directly. We propose a hierarchical Poisson Log-Normal model to simultaneously estimate many such networks to effectively incorporate the shared network structures. We develop an efficient simultaneous estimation method that uses the variational EM and alternating direction method of multipliers (ADMM) algorithms, optimized for parallel processing. Simulation studies show this method outperforms traditional methods in network structure recovery and parameter estimation across various network models. We apply the method to two single cell RNA-seq datasets, a yeast single-cell gene expression dataset measured under 11 different environmental conditions, and a single-cell gene expression data from 13 inflammatory bowel disease patients. We demonstrate that simultaneous estimation can uncover a wider range of conditional dependence networks among genes, offering deeper insights into gene expression mechanisms.

stat.ME

Wasserstein F-tests for Fréchet regression on Bures-Wasserstein manifolds

This paper considers the problem of regression analysis with random covariance matrix as outcome and Euclidean covariates in the framework of Fréchet regression on the Bures-Wasserstein manifold. Such regression problems have many applications in single cell genomics and neuroscience, where we have covariance matrix measured over a large set of samples. Fréchet regression on the Bures-Wasserstein manifold is formulated as estimating the conditional Fréchet mean given covariates $x$. A non-asymptotic $\sqrt{n}$-rate of convergence (up to $\log n$ factors) is obtained for our estimator $\hat{Q}_n(x)$ uniformly for $\left\|x\right\| \lesssim \sqrt{\log n}$, which is crucial for deriving the asymptotic null distribution and power of our proposed statistical test for the null hypothesis of no association. In addition, a central limit theorem for the point estimate $\hat{Q}_n(x)$ is obtained, giving insights to a test for covariate effects. The null distribution of the test statistic is shown to converge to a weighted sum of independent chi-squares, which implies that the proposed test has the desired significance level asymptotically. Also, the power performance of the test is demonstrated against a sequence of contiguous alternatives. Simulation results show the accuracy of the asymptotic distributions. The proposed methods are applied to a single cell gene expression data set that shows the change of gene co-expression network as people age.

stat.ME

Recent advances in deep learning and language models for studying the microbiome

Recent advancements in deep learning, particularly large language models (LLMs), made a significant impact on how researchers study microbiome and metagenomics data. Microbial protein and genomic sequences, like natural languages, form a language of life, enabling the adoption of LLMs to extract useful insights from complex microbial ecologies. In this paper, we review applications of deep learning and language models in analyzing microbiome and metagenomics data. We focus on problem formulations, necessary datasets, and the integration of language modeling techniques. We provide an extensive overview of protein/genomic language modeling and their contributions to microbiome studies. We also discuss applications such as novel viromics language modeling, biosynthetic gene cluster prediction, and knowledge integration for metagenomics studies.

q-bio.QM

Transfer Learning for Contextual Multi-armed Bandits

Motivated by a range of applications, we study in this paper the problem of transfer learning for nonparametric contextual multi-armed bandits under the covariate shift model, where we have data collected on source bandits before the start of the target bandit learning. The minimax rate of convergence for the cumulative regret is established and a novel transfer learning algorithm that attains the minimax regret is proposed. The results quantify the contribution of the data from the source domains for learning in the target domain in the context of nonparametric contextual multi-armed bandits. In view of the general impossibility of adaptation to unknown smoothness, we develop a data-driven algorithm that achieves near-optimal statistical guarantees (up to a logarithmic factor) while automatically adapting to the unknown parameters over a large collection of parameter spaces under an additional self-similarity assumption. A simulation study is carried out to illustrate the benefits of utilizing the data from the auxiliary source domains for learning in the target domain.

stat.ML

A Regression-based Approach to Robust Estimation and Inference for Genetic Covariance

Genome-wide association studies (GWAS) have identified thousands of genetic variants associated with complex traits, and some variants are shown to be associated with multiple complex traits. Genetic covariance between two traits is defined as the underlying covariance of genetic effects and can be used to measure the shared genetic architecture. The data used to estimate such a genetic covariance can be from the same group or different groups of individuals, and the traits can be of different types or collected based on different study designs. This paper proposes a unified regression-based approach to robust estimation and inference for genetic covariance of general traits that may be associated with genetic variants nonlinearly. The asymptotic properties of the proposed estimator are provided and are shown to be robust under certain model mis-specification. Our method under linear working models provides a robust inference for the narrow-sense genetic covariance, even when both linear models are mis-specified. Numerical experiments are performed to support the theoretical results. Our method is applied to an outbred mice GWAS data set to study the overlapping genetic effects between the behavioral and physiological phenotypes. The real data results reveal interesting genetic covariance among different mice developmental traits.

stat.ME

Statistical Inference for High-Dimensional Linear Regression with Blockwise Missing Data

Blockwise missing data occurs frequently when we integrate multisource or multimodality data where different sources or modalities contain complementary information. In this paper, we consider a high-dimensional linear regression model with blockwise missing covariates and a partially observed response variable. Under this framework, we propose a computationally efficient estimator for the regression coefficient vector based on carefully constructed unbiased estimating equations and a blockwise imputation procedure, and obtain its rate of convergence. Furthermore, building upon an innovative projected estimating equation technique that intrinsically achieves bias-correction of the initial estimator, we propose a nearly unbiased estimator for each individual regression coefficient, which is asymptotically normally distributed under mild conditions. Based on these debiased estimators, asymptotically valid confidence intervals and statistical tests about each regression coefficient are constructed. Numerical studies and application analysis of the Alzheimer's Disease Neuroimaging Initiative data show that the proposed method performs better and benefits more from unsupervised samples than existing methods.

stat.ME