Hongzhe Li

Changxiao Cai, T. Tony Cai, Hongzhe Li

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.

Hanxuan Ye, Hongzhe Li

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.

Binghao Yan, Yunbi Nam, Lingyao Li et al.

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.

Hongzhe Zhang, Hongzhe Li

Ridge regression with random coefficients provides an important alternative to fixed coefficients regression in high dimensional setting when the effects are expected to be small but not zeros. This paper considers estimation and prediction of random coefficient ridge regression in the setting of transfer learning, where in addition to observations from the target model, source samples from different but possibly related regression models are available. The informativeness of the source model to the target model can be quantified by the correlation between the regression coefficients. This paper proposes two estimators of regression coefficients of the target model as the weighted sum of the ridge estimates of both target and source models, where the weights can be determined by minimizing the empirical estimation risk or prediction risk. Using random matrix theory, the limiting values of the optimal weights are derived under the setting when $p/n \rightarrow γ$, where $p$ is the number of the predictors and $n$ is the sample size, which leads to an explicit expression of the estimation or prediction risks. Simulations show that these limiting risks agree very well with the empirical risks. An application to predicting the polygenic risk scores for lipid traits shows such transfer learning methods lead to smaller prediction errors than the single sample ridge regression or Lasso-based transfer learning.

Zhiwei Yi, Xin Cheng, Jingyu Ma et al.

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.

Haoshu Xu, Hongzhe Li

We propose a novel test for assessing partial effects in Frechet regression on Bures Wasserstein manifolds. Our approach employs a sample splitting strategy: the first subsample is used to fit the Frechet regression model, yielding estimates of the covariance matrices and their associated optimal transport maps, while the second subsample is used to construct the test statistic. We prove that this statistic converges in distribution to a weighted mixture of chi squared components, where the weights correspond to the eigenvalues of an integral operator defined by an appropriate RKHS kernel. We establish that our procedure achieves the nominal asymptotic size and demonstrate that its worst-case power converges uniformly to one. Through extensive simulations and a real data application, we illustrate the test's finite-sample accuracy and practical utility.

Fei Xue, Rong Ma, Hongzhe Li

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.

Linjun Zhang, Rong Ma, T. Tony Cai et al.

This paper studies the high-dimensional mixed linear regression (MLR) where the output variable comes from one of the two linear regression models with an unknown mixing proportion and an unknown covariance structure of the random covariates. Building upon a high-dimensional EM algorithm, we propose an iterative procedure for estimating the two regression vectors and establish their rates of convergence. Based on the iterative estimators, we further construct debiased estimators and establish their asymptotic normality. For individual coordinates, confidence intervals centered at the debiased estimators are constructed. Furthermore, a large-scale multiple testing procedure is proposed for testing the regression coefficients and is shown to control the false discovery rate (FDR) asymptotically. Simulation studies are carried out to examine the numerical performance of the proposed methods and their superiority over existing methods. The proposed methods are further illustrated through an analysis of a dataset of multiplex image cytometry, which investigates the interaction networks among the cellular phenotypes that include the expression levels of 20 epitopes or combinations of markers.

Sai Li, T. Tony Cai, Hongzhe Li

Transfer learning for high-dimensional Gaussian graphical models (GGMs) is studied with the goal of estimating the target GGM by utilizing the data from similar and related auxiliary studies. The similarity between the target graph and each auxiliary graph is characterized by the sparsity of a divergence matrix. An estimation algorithm, Trans-CLIME, is proposed and shown to attain a faster convergence rate than the minimax rate in the single study setting. Furthermore, a debiased Trans-CLIME estimator is introduced and shown to be element-wise asymptotically normal. It is used to construct a multiple testing procedure for edge detection with false discovery rate control. The proposed estimation and multiple testing procedures demonstrate superior numerical performance in simulations and are applied to infer the gene networks in a target brain tissue by leveraging the gene expressions from multiple other brain tissues. A significant decrease in prediction errors and a significant increase in power for link detection are observed.

Sai Li, T. Tony Cai, Hongzhe Li

This paper considers the estimation and prediction of a high-dimensional linear regression in the setting of transfer learning, using samples from the target model as well as auxiliary samples from different but possibly related regression models. When the set of "informative" auxiliary samples is known, an estimator and a predictor are proposed and their optimality is established. The optimal rates of convergence for prediction and estimation are faster than the corresponding rates without using the auxiliary samples. This implies that knowledge from the informative auxiliary samples can be transferred to improve the learning performance of the target problem. In the case that the set of informative auxiliary samples is unknown, we propose a data-driven procedure for transfer learning, called Trans-Lasso, and reveal its robustness to non-informative auxiliary samples and its efficiency in knowledge transfer. The proposed procedures are demonstrated in numerical studies and are applied to a dataset concerning the associations among gene expressions. It is shown that Trans-Lasso leads to improved performance in gene expression prediction in a target tissue by incorporating the data from multiple different tissues as auxiliary samples.

T. Tony Cai, Hongzhe Li, Rong Ma

Driven by a wide range of applications, many principal subspace estimation problems have been studied individually under different structural constraints. This paper presents a unified framework for the statistical analysis of a general structured principal subspace estimation problem which includes as special cases non-negative PCA/SVD, sparse PCA/SVD, subspace constrained PCA/SVD, and spectral clustering. General minimax lower and upper bounds are established to characterize the interplay between the information-geometric complexity of the structural set for the principal subspaces, the signal-to-noise ratio (SNR), and the dimensionality. The results yield interesting phase transition phenomena concerning the rates of convergence as a function of the SNRs and the fundamental limit for consistent estimation. Applying the general results to the specific settings yields the minimax rates of convergence for those problems, including the previous unknown optimal rates for non-negative PCA/SVD, sparse SVD and subspace constrained PCA/SVD.

Abhishek Chakrabortty, Jiarui Lu, T. Tony Cai et al.

We consider high dimensional $M$-estimation in settings where the response $Y$ is possibly missing at random and the covariates $\mathbf{X} \in \mathbb{R}^p$ can be high dimensional compared to the sample size $n$. The parameter of interest $\boldsymbolθ_0 \in \mathbb{R}^d$ is defined as the minimizer of the risk of a convex loss, under a fully non-parametric model, and $\boldsymbolθ_0$ itself is high dimensional which is a key distinction from existing works. Standard high dimensional regression and series estimation with possibly misspecified models and missing $Y$ are included as special cases, as well as their counterparts in causal inference using 'potential outcomes'. Assuming $\boldsymbolθ_0$ is $s$-sparse ($s \ll n$), we propose an $L_1$-regularized debiased and doubly robust (DDR) estimator of $\boldsymbolθ_0$ based on a high dimensional adaptation of the traditional double robust (DR) estimator's construction. Under mild tail assumptions and arbitrarily chosen (working) models for the propensity score (PS) and the outcome regression (OR) estimators, satisfying only some high-level conditions, we establish finite sample performance bounds for the DDR estimator showing its (optimal) $L_2$ error rate to be $\sqrt{s (\log d)/ n}$ when both models are correct, and its consistency and DR properties when only one of them is correct. Further, when both the models are correct, we propose a desparsified version of our DDR estimator that satisfies an asymptotic linear expansion and facilitates inference on low dimensional components of $\boldsymbolθ_0$. Finally, we discuss various of choices of high dimensional parametric/semi-parametric working models for the PS and OR estimators. All results are validated via detailed simulations.

Abhishek Chakrabortty, Preetam Nandy, Hongzhe Li

We consider the problem of identifying intermediate variables (or mediators) that regulate the effect of a treatment on a response variable. While there has been significant research on this classical topic, little work has been done when the set of potential mediators is high-dimensional (HD). A further complication arises when these mediators are interrelated (with unknown dependencies). In particular, we assume that the causal structure of the treatment, the confounders, the potential mediators and the response is a (possibly unknown) directed acyclic graph (DAG). HD DAG models have previously been used for the estimation of causal effects from observational data. In particular, methods called IDA and joint-IDA have been developed for estimating the effects of single and multiple simultaneous interventions, respectively. In this paper, we propose an IDA-type method called MIDA for estimating so-called individual mediation effects from HD observational data. Although IDA and joint-IDA estimators have been shown to be consistent in certain sparse HD settings, their asymptotic properties such as convergence in distribution and inferential tools in such settings have remained unknown. In this paper, we prove HD consistency of MIDA for linear structural equation models with sub-Gaussian errors. More importantly, we derive distributional convergence results for MIDA in similar HD settings, which are applicable to IDA and joint-IDA estimators as well. To our knowledge, these are the first such distributional convergence results facilitating inference for IDA-type estimators. These are built on our novel theoretical results regarding uniform bounds for linear regression estimators over varying subsets of HD covariates which may be of independent interest. Finally, we empirically validate our asymptotic theory for MIDA and demonstrate its usefulness via simulations and a real data application.