arXiv subjects

Zhenyao Ye

Publications and source records attributed to Zhenyao Ye.

4 recordsLinked to original sources

arXiv2026

A Fast Screening Approach for High-dimensional Outcomes and High-dimensional Predictors

Modeling interactions among multimodal, high-dimensional data is intrinsically challenging due to ultra-high dimensionality and complex dependence structure with high level noise. Screening methods are effective for reducing dimensionality, but most existing approaches shrink only the predictor space while retaining all outcomes. In cross-modal analyses, different outcomes often select different predictor subsets, so the union remains large and the response dimension is unchanged, limiting the practical benefit of screening. This gives rise to heavy computational burdens and poor interpretability. To address these limitations, we propose a new screening framework, Graph Independence Dual Screening (GIDS), which simultaneously reduces the dimensionality of response variables and predictors. We design computationally efficient algorithms that facilitate downstream selection procedures, improving accuracy and scalability, and establish supporting theoretical results. Extensive simulation studies demonstrate that GIDS outperforms existing methods that screen only predictors. To illustrate its utility, we applied GIDS to the Alzheimer's Disease Neuroimaging Initiative (ADNI) dataset, analyzing interactions between genome-wide 865,353 DNA methylation and 49,386 transcriptomic variables. GIDS reduced the feature space to approximately 9,000 CpGs and 2,000 transcripts, uncovering blockwise interaction structures: clusters of CpG sites and gene transcripts with strong associations. These findings not only improve computational tractability but also yield interpretable biological insights, highlighting coordinated regulatory mechanisms underlying Alzheimer's disease.

stat.ME↗

arXiv2026

Trustworthy AI/ML Regression and Unbiased Causal Inference for Real-World Data

Real-World Data (RWD), with its large sample sizes and rich clinical detail, offers a compelling alternative to randomized controlled trials (RCTs) for studying treatment effects in diverse and complex patient populations. However, its observational nature introduces confounding that prevents straightforward comparative effectiveness research. Target trial emulation leverages RWD to estimate average treatment effects (ATE) at the population scale and diversity that RCTs cannot achieve, yet its validity depends critically on unbiased ATE estimation under high-dimensional confounding. Many causal inference pipelines address high-dimensional confounding through machine learning and artificial intelligence (ML/AI) outcome regression. However, commonly used ML/AI regression models exhibit systematic prediction bias, with predicted outcomes shrinking toward the marginal outcome mean. This structural bias propagates into ATE estimation and cannot be corrected by cross-fitting, ensemble methods, or any standard ML practice. In this work, we first quantitatively characterize how systematic prediction bias in ML/AI outcome regression leads to biased ATE estimates in causal inference models. We further propose an unbiased ML/AI regression-based causal inference framework to ensure unbiased ATE estimation for observational studies. We demonstrate our approach by studying the effects of opioids on cardiovascular health in patients with chronic pain using UK Biobank data.

stat.AP↗

arXiv2025

Graph Canonical Correlation Analysis

Canonical correlation analysis (CCA) is a widely used technique for estimating associations between two sets of multi-dimensional variables. Recent advancements in CCA methods have expanded their application to decipher the interactions of multiomics datasets, imaging-omics datasets, and more. However, conventional CCA methods are limited in their ability to incorporate structured patterns in the cross-correlation matrix, potentially leading to suboptimal estimations. To address this limitation, we propose the graph Canonical Correlation Analysis (gCCA) approach, which calculates canonical correlations based on the graph structure of the cross-correlation matrix between the two sets of variables. We develop computationally efficient algorithms for gCCA, and provide theoretical results for finite sample analysis of best subset selection and canonical correlation estimation by introducing concentration inequalities and stopping time rule based on martingale theories. Extensive simulations demonstrate that gCCA outperforms competing CCA methods. Additionally, we apply gCCA to a multiomics dataset of DNA methylation and RNA-seq transcriptomics, identifying both positively and negatively regulated gene expression pathways by DNA methylation pathways.

stat.ML↗

arXiv2023

The Effect of Alcohol intake on Brain White Matter Microstructural Integrity: A New Causal Inference Framework for Incomplete Phenomic Data

Although substance use, such as alcohol intake, is known to be associated with cognitive decline during aging, its direct influence on the central nervous system remains incompletely understood. In this study, we investigate the influence of alcohol intake frequency on reduction of brain white matter microstructural integrity in the fornix, a brain region considered a promising marker of age-related microstructural degeneration, using a large UK Biobank (UKB) cohort with extensive phenomic data reflecting a comprehensive lifestyle profile. Two major challenges arise: 1) potentially nonlinear confounding effects from phenomic variables and 2) a limited proportion of participants with complete phenomic data. To address these challenges, we develop a novel ensemble learning framework tailored for robust causal inference and introduce a data integration step to incorporate information from UKB participants with incomplete phenomic data, improving estimation efficiency. Our analysis reveals that daily alcohol intake may significantly reduce fractional anisotropy, a neuroimaging-derived measure of white matter structural integrity, in the fornix and increase systolic and diastolic blood pressure levels. Moreover, extensive numerical studies demonstrate the superiority of our method over competing approaches in terms of estimation bias, while outcome regression-based estimators may be preferred when minimizing mean squared error is prioritized.

stat.ME↗