arXiv subjects

Minhao Yao

Publications and source records attributed to Minhao Yao.

4 recordsLinked to original sources

arXiv2026

Gradient-Flow Optimization as Dynamic Random-Effects Inference: Testing and Early Stopping with Applications to Deep Learning

Gradient-flow optimization is usually viewed as an algorithmic procedure for minimizing empirical loss, with training duration selected by validation or heuristic early stopping rules. We develop a statistical inference framework for gradient-flow training. We show that whenever fitted values evolve through a time-invariant positive semidefinite training operator, the output at each time is equivalent to the best linear unbiased predictor under a corresponding random-effects model. Training time then becomes a variance-component parameter governing variance reallocation from residual noise to structured signal. This turns two training decisions into inferential problems: whether training is needed becomes a variance-component test for signal beyond initialization, and how long to train becomes restricted maximum likelihood (REML) estimation of the training-time variance component. We show that the REML-guided early stopping rule selects the time at which optimized spectral losses become decorrelated from the training-operator eigenvalues. The asymptotic prediction optimality of the REML-guided early stopping time is established for fixed-design in-sample risk and random-design out-of-sample risk. Deep learning models in fixed-kernel gradient regimes provide canonical instantiations for our results. Numerical experiments and a UK Biobank proteomics application show competitive accuracy of the REML-guided early stopping time with reduced reliance on validation splits and repeated checkpoint evaluation.

stat.ML↗

arXiv2025

Mendelian Randomization Methods for Causal Inference: Estimands, Identification and Inference

Mendelian randomization (MR) has become an essential tool for causal inference in biomedical and public health research. By using genetic variants as instrumental variables, MR helps address unmeasured confounding and reverse causation, offering a quasi-experimental framework to evaluate causal effects of modifiable exposures on health outcomes. Despite its promise, MR faces substantial methodological challenges, including invalid instruments, weak instrument bias, and design complexities across different data structures. In this tutorial review, we provide a comprehensive overview of MR methods for causal inference, emphasizing clarity of causal interpretation, study design comparisons, availability of software tools, and practical guidance for applied scientists. We organize the review around causal estimands, ensuring that analyses are anchored to well-defined causal questions. We discuss the problems of invalid and weak instruments, comparing available strategies for their detection and correction. We integrate discussions of population-based versus family-based MR designs, analyses based on individual-level versus summary-level data, and one-sample versus two-sample MR designs, highlighting their relative advantages and limitations. We also summarize recent methodological advances and software developments that extend MR to settings with many weak or invalid instruments and to modern high-dimensional omics data. Real-data applications, including UK Biobank and Alzheimer's disease proteomics studies, illustrate the use of these methods in practice. This review aims to serve as a tutorial-style reference for both methodologists and applied scientists.

stat.ME↗

arXiv2025

Constructive Instrumental Variable Identification and Inference with Many Weak Interaction Moments

Instrumental variable methods are widely used for causal inference, but identification becomes especially challenging when instruments are weak and potentially invalid. These challenges are particularly pronounced in Mendelian randomization, where genetic variants serve as instruments and violations of exclusion restriction or independence assumptions are common. We propose MAGIC, a constructive and assumption-lean framework that achieves identification even when all candidate instruments may be invalid. The method exploits pairwise and higher-order interactions among mutually independent instruments to construct moment conditions orthogonal to both unmeasured confounding and direct effects under a linear structural model. The resulting estimation problem involves many potentially weak interaction moments with unknown nuisance parameters. We develop a semiparametric generalized method of moments estimator and introduce a global Neyman orthogonality condition to ensure robustness of both the moment function and its derivative to nuisance estimation under many weak moment asymptotics. We establish consistency and asymptotic normality when the number of moments diverges with sample size and characterize the semiparametric efficiency bound under fixed dimension. Simulations and an application to UK Biobank data illustrate the method.

stat.ME↗

arXiv2024

An Introduction to Causal Inference Methods with Multi-omics Data

Omics biomarkers play a pivotal role in personalized medicine by providing molecular-level insights into the etiology of diseases, guiding precise diagnostics, and facilitating targeted therapeutic interventions. Recent advancements in omics technologies have resulted in an increasing abundance of multimodal omics data, providing unprecedented opportunities for identifying novel omics biomarkers for human diseases. Mendelian randomization (MR) is a practically useful causal inference method that uses genetic variants as instrumental variables (IVs) to infer causal relationships between omics biomarkers and complex traits/diseases by removing hidden confounding bias. In this article, we first present current challenges in performing MR analysis with omics data, and then describe four MR methods for analyzing multi-omics data including epigenomics, transcriptomics, proteomics, and metabolomics data, all executable within the R software environment.

stat.AP↗