Analysis of noisy survival data with graphical proportional hazards measurement error models

AFFECT: an R package for accelerated functional failure time model with error-contaminated survival times and applications to gene expression data

BACKGROUND

Survival analysis has been used to characterize the time-to-event data. In medical studies, a typical application is to analyze the survival time of specific cancers by using high-dimensional gene expressions. The main challenges include the involvement of non-informaive gene expressions and possibly nonlinear relationship between survival time and gene expressions. Moreover, due to possibly imprecise data collection or wrong record, measurement error might be ubiquitous in the survival time and its censoring status. Ignoring measurement error effects may incur biased estimator and wrong conclusion.

RESULTS

To tackle those challenges and derive a reliable estimation with efficiently computational implementation, we develop the R package AFFECT, which is referred to Accelerated Functional Failure time model with Error-Contaminated survival Times.

CONCLUSIONS

This package aims to correct for measurement error effects in survival times and implements a boosting algorithm under corrected data to determine informative gene expressions as well as derive the corresponding nonlinear functions.

Analysis of length-biased and partly interval-censored survival data with mismeasured covariates

In this paper, we analyze the length-biased and partly interval-censored data, whose challenges primarily come from biased sampling and interfere induced by interval censoring. Unlike existing methods that focus on low-dimensional data and assume the covariates to be precisely measured, sometimes researchers may encounter high-dimensional data subject to measurement error, which are ubiquitous in applications and make estimation unreliable. To address those challenges, we explore a valid inference method for handling high-dimensional length-biased and interval-censored survival data with measurement error in covariates under the accelerated failure time model. We primarily employ the SIMEX method to correct for measurement error effects and propose the boosting procedure to do variable selection and estimation. The proposed method is able to handle the case that the dimension of covariates is larger than the sample size and enjoys appealing features that the distributions of the covariates are left unspecified.

Estimation of the average treatment effect with variable selection and measurement error simultaneously addressed for potential confounders

In the framework of causal inference, the inverse probability weighting estimation method and its variants have been commonly employed to estimate the average treatment effect. Such methods, however, are challenged by the presence of irrelevant pre-treatment variables and measurement error. Ignoring these features and naively applying the usual inverse probability weighting estimation procedures may typically yield biased inference results. In this article, we develop an inference method for estimating the average treatment effect with those features taken into account. We establish theoretical properties for the resulting estimator and carry out numerical studies to assess the finite sample performance of the proposed estimator.

BOOME: A Python package for handling misclassified disease and ultrahigh-dimensional error-prone gene expression data

In gene expression data analysis framework, ultrahigh dimensionality and measurement error are ubiquitous features. Therefore, it is crucial to correct measurement error effects and make variable selection when fitting a regression model. In this paper, we introduce a python package BOOME, which refers to BOOsting algorithm for Measurement Error in binary responses and ultrahigh-dimensional predictors. We primarily focus on logistic regression and probit models with responses, predictors, or both contaminated with measurement error. The BOOME aims to address measurement error effects, and employ boosting procedure to make variable selection and estimation.

NetDA: An R Package for Network-Based Discriminant Analysis Subject to Multilabel Classes

In this paper, we introduce the R package NetDA, which aims to deal with multiclassification with network structures in predictors accommodated. To address the natural feature of network structures, we apply Gaussian graphical models to characterize dependence structures of the predictors and directly estimate the precision matrix. After that, the estimated precision matrix is employed to linear discriminant functions and quadratic discriminant functions. The R package NetDA is now available on CRAN, and the demonstration of functions is summarized as a vignette in the online documentation.

Classification and prediction for multi-cancer data with ultrahigh-dimensional gene expressions

Analysis of gene expression data is an attractive topic in the field of bioinformatics, and a typical application is to classify and predict individuals’ diseases or tumors by treating gene expression values as predictors. A primary challenge of this study comes from ultrahigh-dimensionality, which makes that (i) many predictors in the dataset might be non-informative, (ii) pairwise dependence structures possibly exist among high-dimensional predictors, yielding the network structure. While many supervised learning methods have been developed, it is expected that the prediction performance would be affected if impacts of ultrahigh-dimensionality were not carefully addressed. In this paper, we propose a new statistical learning algorithm to deal with multi-classification subject to ultrahigh-dimensional gene expressions. In the proposed algorithm, we employ the model-free feature screening method to retain informative gene expression values from ultrahigh-dimensional data, and then construct predictive models with network structures of selected gene expression accommodated. Different from existing supervised learning methods that build predictive models based on entire dataset, our approach is able to identify informative predictors and dependence structures for gene expression. Throughout analysis of a real dataset, we find that the proposed algorithm gives precise classification as well as accurate prediction, and outperforms some commonly used supervised learning methods.

Generalized network structured models with mixed responses subject to measurement error and misclassification

Research of complex associations between a gene network and multiple responses has attracted extensive attention. A great challenge in analyzing genetic data is posited by the presence of the genetic network that is typically unknown in applications. Moreover, mismeasurement of responses introduces additional complexity to distort usual inferential procedures. In this paper, we consider the problem with mixed binary and continuous responses which are subject to mismeasurement and associated with complex structured covariates. We first start with the case where data are precisely measured. We propose a generalized network structured model and develop a two-step inferential procedure. In the first step, we employ a Gaussian graphical model to facilitate the covariates network structure, and in the second step, we incorporate the estimated graphical structure of covariates and develop an estimating equation method. Furthermore, we extend the development to accommodating mismeasured responses. We consider two cases where the information on mismeasurement is either known or estimated from a validation sample. Theoretical results are established and numerical studies are conducted to evaluate the finite sample performance of the proposed methods. We apply the proposed method to analyze the outbred Carworth Farms White mice data arising from a genome-wide association study. This article is protected by copyright. All rights reserved.