arXiv subjects

Quran Wu

Publications and source records attributed to Quran Wu.

4 recordsLinked to original sources

arXiv2026

A Zero-Inflated Beta Mixture Model for Marginal Mediation Analysis with Compositional Microbiome Mediators

The role of the microbiome in disease pathogenesis is an emerging field with strong evidence suggesting that dysbiosis is associated with precancerous and cancerous states. Microbiome data present substantial challenges for causal mediation analysis due to sparsity, compositional constraints, and latent heterogeneity. To address these issues, we propose a zero-inflated beta mixture (ZIBM) method for mediation analysis with compositional microbiome mediators. The proposed method accommodates excess zeros through a zero-inflation component and captures heterogeneity in non-zero relative abundances using a beta mixture distribution. Within the potential-outcomes framework, the ZIBM provides estimates of marginal microbiome-mediated causal effects, and model parameters are estimated using an expectation-maximization algorithm. Simulation studies demonstrate that the ZIBM yields more accurate estimation and reliable inference under conditions commonly observed in microbiome data, compared with existing approaches. An application to a real microbiome study further illustrates its practical utility. These results indicate that the proposed method provides a more flexible and robust statistical framework for mediation analysis involving compositional microbiome data.

stat.ME↗

arXiv2026

Quantifying the radiative response to surface temperature variability: A critical comparison of current methods

Over the past decade, it has become clear that the radiative response to surface temperature change depends on the spatially varying structure in the temperature field, a phenomenon known as the "pattern effect''. The pattern effect is commonly estimated from dedicated climate model simulations forced with local surface temperatures patches (Green's function experiments). Green's function experiments capture causal influences from temperature perturbations, but are computationally expensive to run. Recently, however, several methods have been proposed that estimate the pattern effect through statistical means. These methods can accurately predict the radiative response to temperature variations in climate model simulations. The goal of this paper is to compare methods used to quantify the pattern effect. We apply each method to the same prediction task and discuss its advantages and disadvantages. Most methods indicate large negative feedbacks over the western Pacific. Over other regions, the methods frequently disagree on feedback sign and spatial homogeneity. While all methods yield similar predictions of the global radiative response to surface temperature variations driven by internal variability, they produce very different predictions from the patterns of surface temperature change in simulations forced with increasing CO2 concentrations. We discuss reasons for the discrepancies between methods and recommend paths towards using them in the future to enhance physical understanding of the pattern effect.

physics.ao-ph↗

arXiv2022

MarZIC: A Marginal mediation model for Zero-Inflated Compositional mediators with applications to microbiome data

The human microbiome can contribute to pathogeneses of many complex diseases by mediating disease-leading causal pathways. However, standard mediation analysis methods are not adequate to analyze the microbiome as a mediator due to the excessive number of zero-valued sequencing reads in the data that is compounded by its compositional structure. The two main challenges raised by the zero-inflated data structure are: (a) disentangling the mediation effect induced by the point mass at zero; and (b) identifying the observed zero-valued data points that are actually not zero (i.e., false zeros). We develop a novel marginal mediation analysis method under the potential-outcomes framework to fill this gap and show the marginal model can also account for the compositional structure. The mediation effect can be decomposed into two components that are inherent to the two-part nature of zero-inflated distributions. With probabilistic models to account for observing zeros, we also address the challenge with false zeros. A comprehensive simulation study and the application in a real microbiome study showcase our approach in comparison with existing approaches.

stat.ME↗

arXiv2019

IFAA: Robust association identification and Inference For Absolute Abundance in microbiome analyses

The target of inference in microbiome analyses is usually relative abundance (RA) because RA in a sample (e.g., stool) can be considered as an approximation of RA in an entire ecosystem (e.g., gut). However, inference on RA suffers from the fact that RA are calculated by dividing absolute abundances (AA) over the common denominator (CD), the summation of all AA (i.e., library size). Because of that, perturbation in one taxon will result in a change in the CD and thus cause false changes in RA of all other taxa, and those false changes could lead to false positive/negative findings. We propose a novel analysis approach (IFAA) to make robust inference on AA of an ecosystem that can circumvent the issues induced by the CD problem and compositional structure of RA. IFAA can also address the confounding effect of library size and handle zero-inflated data structures. IFAA identifies microbial taxa associated with the covariates in Phase one and estimates the association parameters by employing an independent reference taxon in Phase two. Two real data applications are presented and extensive simulations show that IFAA outperforms other established existing approaches by a big margin in the presence of confounding effect of library size.

stat.AP↗