Informatic tools for predicting an ordinal response for high-dimensional data

用于预测高维数据顺序响应的信息工具

• 批准号: 9273725
• 负责人: Kellie J. Archer
• 金额: $ 10.49万
• 依托单位: OHIO STATE UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2012
• 资助国家: 美国
• 起止时间: 2012-09-01 至 2017-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9273725
• 关键词: Informatic; tools; predicting; ordinal; response

DESCRIPTION (provided by applicant): Health status and outcomes are frequently measured on an ordinal scale. Examples include scoring methods for liver biopsy specimens from patients with chronic hepatitis, including the Knodell hepatic activity index, the Ishak score, and the METAVIR score. In addition, tumor-node-metasis stage for cancer patients is an ordinal scaled measure. Moreover, the more recently advocated method for evaluating response to treatment in target tumor lesions is the Response Evaluation Criteria In Solid Tumors method, with ordinal outcomes defined as complete response, partial response, stable disease, and progressive disease. Traditional ordinal response modeling methods assume independence among the predictor variables and require that the number of samples (n) exceed the number of covariates (p). These are both violated in the context of high-throughput genomic studies. Recently, penalized models have been successfully applied to high-throughput genomic datasets in fitting linear, logistic, and Cox proportional hazards models with excellent performance. However, extension of penalized models to the ordinal response setting has not been fully described nor has software been made generally available. Herein we propose to apply the L1 penalization method to ordinal response models to enable modeling of common ordinal response data when a high-dimensional genomic data comprise the predictor space. This study will expand the scope of our current research by providing additional model-based ordinal classification methodologies applicable for high-dimensional datasets to accompany the heuristic based classification tree and random forest ordinal methodologies we have previously described. The specific aims of this application are to: (1) Develop R functions for implementing the stereotype logit model as well as an L1 penalized stereotype logit model for modeling an ordinal response. (2) Empirically examine the performance of the L1 penalized stereotype logit model and competitor ordinal response models by performing a simulation study and applying the models to publicly available microarray datasets. (3) Develop an R package for fitting a random-effects ordinal regression model for clustered ordinal response data. (4) Extend the random-effects ordinal regression model to include an L1 penalty term to accomodate high-dimensional covariate spaces and empirically examine the performance of the L1random-effects ordinal regression model through application to microarray data. Studies involving protocol biopsies where both histopathological assessment and microarray studies are performed at the same time point are increasingly being performed, so that the methodology and software developed in this application will provide unique informatic methods for analyzing such data. Moreover, the ordinal response extensions proposed in this application, though initially conceived of by considering microarray applications, will be broadly applicable to a variety of health, social, and behavioral research fields, which commonly collect human preference data and other responses on an ordinal scale.

描述（由申请人提供）：

项目成果

Elastic Net Constrained Stereotype Logit Model for Ordered Categorical Data.

用于有序分类数据的弹性网络约束刻板印象 Logit 模型。

• DOI: 10.15406/bbij.2015.02.00049
• 发表时间: 2015
• 期刊: Biometrics & biostatistics international journal
• 作者: Williams,AndréAa;Archer,KellieJ
• 通讯作者: Archer,KellieJ

Generalized monotone incremental forward stagewise method for modeling count data: application predicting micronuclei frequency.

用于建模计数数据的广义单调增量前向阶段方法：预测微核频率的应用。

• DOI: 10.4137/cin.s17278
• 发表时间: 2015
• 期刊: Cancer informatics
• 影响因子: 2
• 作者: Makowski,Mateusz;Archer,KellieJ
• 通讯作者: Archer,KellieJ