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Interconnections in Clinical Treatment Measures at the Pan-Disease Level: A Deep Neural Network Analysis of SEER-Medicare

跨疾病临床治疗指标的关联:基于 SEER-Medicare 的深度神经网络分析

In outcomes research, clinical treatment measures are routinely analyzed. Most existing studies focus on individual diseases, and increasing recent evidence suggests that clinical treatment measures of different diseases can be “correlated” (or interconnected). Existing studies on such interconnections are usually limited to a small number of diseases. In this study, for U.S. older patients with common cancers, we complement the existing literature and conduct a pan-disease…

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Deep Transformation Model

深度变换模型

The increasing data complexity leads to the demand for more general and flexible modeling approaches. We consider a nonparametric transformation model with weak assumptions, which encompasses many popular models as special cases. A rank-based deep neural network (DNN) estimation approach is developed, with a loss function significantly different from the existing ones. It can accommodate outliers in response, which is a robustness property not broadly shared. For…

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A flexible Bayesian framework for detecting cross-sample spatial expression variability in heterogeneous tissues

检测异质组织跨样本空间表达变异的灵活贝叶斯框架

Spatial transcriptomics measures gene expression alongside the spatial coordinates of each capture spot or cell across tissue samples. The detection of spatially variable (SV) genes, whose expression exhibits systematic spatial variation, enables the delineation of functional tissue domains and the identification of region-specific transcriptional changes that underlie disease heterogeneity. However, empirical evidence from spatial transcriptomics data indicates that…

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Heterogeneous Gene Network Estimation for Single-Cell Transcriptomic Data via a Joint Regularized Deep Neural Network

通过联合正则化深度神经网络估计单细胞异质基因网络

Estimation of intracellular gene networks has been a critical component of single-cell transcriptomic data analysis, which can provide crucial insights into the complex interplay between genes, facilitating the discovery of the biological basis of human life at single-cell resolution. Despite notable achievements, existing methodologies often falter in their practicality, primarily due to their narrow focus on simplistic linear relationships and inadequate handling of…

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Survival Mixed Membership Blockmodel

生存混合成员区块模型

Whenever we send a message via a channel such as e-mail, Facebook, WhatsApp, WeChat, or LinkedIn, we care about the response rate—the probability that our message will receive a response—and the response time—how long it will take to receive a reply. Recent studies have made considerable efforts to model the sending behaviors of messages in social networks with point processes. However, statistical research on modeling response rates and response times on social networks is…

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Rank-Based Greedy Model Averaging for High-Dimensional Survival Data

高维生存数据的秩驱动贪心模型平均

Model averaging is an effective way to enhance prediction accuracy. However, most previous works focus on low-dimensional settings with completely observed responses. To attain an accurate prediction for the risk effect of survival data with high-dimensional predictors, we propose a novel method: rank-based greedy (RG) model averaging. Specifically, adopting the transformation model with splitting predictors as working models, we doubly use the smooth concordance index…

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Promoting Similarity of Sparsity Structures in Integrative Analysis With Penalization

通过惩罚促进整合分析中的稀疏结构相似性

For data with high-dimensional covariates but small sample sizes, the analysis of single datasets often generates unsatisfactory results. The integrative analysis of multiple independent datasets provides an effective way of pooling information and outperforms single-dataset and several alternative multi-datasets methods. Under many scenarios, multiple datasets are expected to share common important covariates, that is, the corresponding models have similarity in their…

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The sparse Laplacian shrinkage estimator for high-dimensional regression

高维回归的稀疏拉普拉斯收缩估计量

We propose a new penalized method for variable selection and estimation that explicitly incorporates the correlation patterns among predictors. This method is based on a combination of the minimax concave penalty and Laplacian quadratic associated with a graph as the penalty function. We call it the sparse Laplacian shrinkage (SLS) method. The SLS uses the minimax concave penalty for encouraging sparsity and Laplacian quadratic penalty for promoting smoothness among…

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Penalized variable selection procedure for Cox models with semiparametric relative risk

半参数相对风险Cox模型的惩罚变量选择

We study the Cox models with semiparametric relative risk, which can be partially linear with one nonparametric component, or multiple additive or nonadditive nonparametric components. A penalized partial likelihood procedure is proposed to simultaneously estimate the parameters and select variables for both the parametric and the nonparametric parts. Two penalties are applied sequentially. The first penalty, governing the smoothness of the multivariate nonlinear covariate…

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Asymptotic properties of bridge estimators in sparse high-dimensional regression models

稀疏高维回归模型中桥估计量的渐近性质

We study the asymptotic properties of bridge estimators in sparse, high-dimensional, linear regression models when the number of covariates may increase to infinity with the sample size. We are particularly interested in the use of bridge estimators to distinguish between covariates whose coefficients are zero and covariates whose coefficients are nonzero. We show that under appropriate conditions, bridge estimators correctly select covariates with nonzero coefficients with…

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Marginal asymptotics for the “large $p$, small $n$” paradigm: With applications to microarray data

“大维度、小样本”范式的边际渐近理论及微阵列应用

The “large $p$, small $n$” paradigm arises in microarray studies, image analysis, high throughput molecular screening, astronomy, and in many other high dimensional applications. False discovery rate (FDR) methods are useful for resolving the accompanying multiple testing problems. In cDNA microarray studies, for example, $p$-values may be computed for each of $p$ genes using data from $n$ arrays, where typically $p$ is in the thousands and $n$ is less than 30. For FDR…

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Penalized log-likelihood estimation for partly linear transformation models with current status data

现时状态数据下部分线性变换模型的惩罚对数似然估计

We consider partly linear transformation models applied to current status data. The unknown quantities are the transformation function, a linear regression parameter and a nonparametric regression effect. It is shown that the penalized MLE for the regression parameter is asymptotically normal and efficient and converges at the parametric rate, although the penalized MLE for the transformation function and nonparametric regression effect are only n1/3 consistent. Inference…

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