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通过选择后推断稳健发现微生物组成特征AI 解读

Identifying taxa associated with host phenotypes is crucial for understanding host-microbe interactions and their underlying molecular mechanisms. However, analyzing microbiome data presents unique challenges, as the observed abundances of taxa are high-dimensional, compositional, and subject to both sample-specific and taxon-specific biases. Many existing methods for differential abundance testing struggle to balance false discovery rate control with statistical power. In…

大规模低秩回归模型下的迁移学习AI 解读

In high-dimensional multiple response regression problems, the large dimensionality of the coefficient matrix poses a challenge to parameter estimation. To address this challenge, low-rank matrix estimation methods have been developed to facilitate parameter estimation in the high-dimensional regime, where the number of parameters increases with sample size. Despite these methodological advances, accurately predicting multiple responses with limited target data remains a…

泊松因子模型的数据稀释及其应用AI 解读

The Poisson factor model is a powerful tool for dimension reduction and visualization of large-scale count datasets across diverse domains. Despite the availability of efficient algorithms for estimating factors and loadings, existing methods either require prior knowledge of the number of factors, or resort to ad hoc criteria for its determination. This article proposes a novel data-driven criterion called Information Criterion via Data Thinning (ICDT), leveraging the…

混合表达数据中细胞类型比例估计的统计推断AI 解读

There is a growing interest in cell-type-specific analysis from bulk samples with a mixture of different cell types. A critical first step in such analyses is the accurate estimation of cell-type proportions in a bulk sample. Although many methods have been proposed recently, quantifying the uncertainties associated with the estimated cell-type proportions has not been well studied. Lack of consideration of these uncertainties can lead to missed or false findings in…

从整体基因表达数据估计细胞类型特异共表达网络AI 解读

Inferring and characterizing gene co-expression networks has led to important insights on the molecular mechanisms of complex diseases. Most co-expression analyses to date have been performed on gene expression data collected from bulk tissues with different cell type compositions across samples. As a result, the co-expression estimates only offer an aggregated view of the underlying gene regulations and can be confounded by heterogeneity in cell type compositions, failing…

多重二元响应的低秩回归及其癌症细胞系百科数据应用AI 解读

In this paper, we study high-dimensional multivariate logistic regression models in which a common set of covariates is used to predict multiple binary outcomes simultaneously. Our work is primarily motivated from many biomedical studies with correlated multiple responses such as the cancer cell-line encyclopedia project. We assume that the underlying regression coefficient matrix is simultaneously low-rank and row-wise sparse. We propose an intuitively appealing selection…

用于提取微生物组成的零膨胀逻辑正态多项模型AI 解读

High throughput sequencing data collected to study the microbiome provide information in the form of relative abundances and should be treated as compositions. Although many approaches including scaling and rarefaction have been proposed for converting raw count data into microbial compositions, most of these methods simply return zero values for zero counts. However, zeros can distort downstream analyses, and they can also pose problems for composition-aware methods. This…

因子增强逆回归及其微生物组数据分析应用AI 解读

We investigate the relationship between count data that inform the relative abundance of features of a composition, and factors that influence the composition. Our work is motivated from microbiome studies aiming to extract microbial signatures that are predictive of host phenotypes based on data collected from a group of individuals harboring radically different microbial communities. We introduce multinomial Factor Augmented Inverse Regression (FAIR) of the count vector…

基于函数型加性回归算子的非参数函数图模型AI 解读

In this article, we develop a nonparametric graphical model for multivariate random functions. Most existing graphical models are restricted by the assumptions of multivariate Gaussian or copula Gaussian distributions, which also imply linear relations among the random variables or functions on different nodes. We relax those assumptions by building our graphical model based on a new statistical object—the functional additive regression operator. By carrying out regression…

条件函数型图模型AI 解读

Graphical modeling of multivariate functional data is becoming increasingly important in a wide variety of applications. The changes of graph structure can often be attributed to external variables, such as the diagnosis status or time, the latter of which gives rise to the problem of dynamic graphical modeling. Most existing methods focus on estimating the graph by aggregating samples, but largely ignore the subject-level heterogeneity due to the external variables. In this…

基于加性条件独立的变量选择AI 解读

Summary We propose a non-parametric variable selection method which does not rely on any regression model or predictor distribution. The method is based on a new statistical relationship, called additive conditional independence, that has been introduced recently for graphical models. Unlike most existing variable selection methods, which target the mean of the response, the method proposed targets a set of attributes of the response, such as its mean, variance or entire…

全基因组关联研究中高维误设混合模型的分析AI 解读

We study behavior of the restricted maximum likelihood (REML) estimator under a misspecified linear mixed model (LMM) that has received much attention in recent genome-wide association studies. The asymptotic analysis establishes consistency of the REML estimator of the variance of the errors in the LMM, and convergence in probability of the REML estimator of the variance of the random effects in the LMM to a certain limit, which is equal to the true variance of the random…

加性偏相关算子与图模型的非参数估计AI 解读

We introduce an additive partial correlation operator as an extension of partial correlation to the nonlinear setting, and use it to develop a new estimator for nonparametric graphical models. Our graphical models are based on additive conditional independence, a statistical relation that captures the spirit of conditional independence without having to resort to high-dimensional kernels for its estimation. The additive partial correlation operator completely characterizes…

协变量调整高斯图模型的渐近正态与有效估计AI 解读

A tuning-free procedure is proposed to estimate the covariate-adjusted Gaussian graphical model. For each finite subgraph, this estimator is asymptotically normal and efficient. As a consequence, a confidence interval can be obtained for each edge. The procedure enjoys easy implementation and efficient computation through parallel estimation on subgraphs or edges. We further apply the asymptotic normality result to perform support recovery through edge-wise adaptive…

统计网络的加性半图模型及其通路分析应用AI 解读

We introduce a nonparametric method for estimating non-gaussian graphical models based on a new statistical relation called additive conditional independence, which is a three-way relation among random vectors that resembles the logical structure of conditional independence. Additive conditional independence allows us to use one-dimensional kernel regardless of the dimension of the graph, which not only avoids the curse of dimensionality but also simplifies computation. It…

条件图模型的稀疏估计及其基因网络应用AI 解读

In many applications the graph structure in a network arises from two sources: intrinsic connections and connections due to external effects. We introduce a sparse estimation procedure for graphical models that is capable of isolating the intrinsic connections by removing the external effects. Technically, this is formulated as a conditional graphical model, in which the external effects are modeled as predictors, and the graph is determined by the conditional precision…

利用分组结构控制错误发现率AI 解读

In the context of large-scale multiple hypothesis testing, the hypotheses often possess certain group structures based on additional information such as Gene Ontology in gene expression data and phenotypes in genome-wide association studies. It is hence desirable to incorporate such information when dealing with multiplicity problems to increase statistical power. In this article, we demonstrate the benefit of considering group structure by presenting a p-value weighting…

常微分方程参数广义剖面估计的渐近效率与有限样本性质AI 解读

Ordinary differential equations (ODEs) are commonly used to model dynamic behavior of a system. Because many parameters are unknown and have to be estimated from the observed data, there is growing interest in statistics to develop efficient estimation procedures for these parameters. Among the proposed methods in the literature, the generalized profiling estimation method developed by Ramsay and colleagues is particularly promising for its computational efficiency and good…

相关曲线：回归局部解释方差的度量AI 解读

We call (a model for) an experiment heterocorrelatious if the strength of the relationship between a response variable Y and a covariate X is different in different regions of the covariate space. For such experiments we introduce a correlation curve that measures heter-ocorrelaticity in terms of the variance explained by regression locally at each covariate value. More precisely, the squared correlation curve is obtained by first expressing the usual linear model “variance…

作为回归局部方差解释度量的相关曲线AI 解读

We call (a model for) an experiment heterocorrelatious if the strength of the relationship between a response variable Y and a covariate X is different in different regions of the covariate space. For such experiments we introduce a correlation curve that measures heter-ocorrelaticity in terms of the variance explained by regression locally at each covariate value. More precisely, the squared correlation curve is obtained by first expressing the usual linear model “variance…