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autoRPA
A web server for constructing cancer staging models by recursive partitioning analysis
ID:18Uploader:周小帅
2021.12.12
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Abstract
Cancer staging provides a common language that is used to describe the severity of an individual's cancer, which plays a critical role in optimizing cancer treatment. Recursive partitioning analysis (RPA) is the most widely accepted method for cancer staging. Despite its widespread use, to date, only limited tools have been developed to implement the RPA algorithm for cancer staging. Moreover, most of the available tools can be accessed only from command lines and also lack visualization, making them difficult for clinical investigators without programing skills to use. Therefore, we developed a web server called autoRPA that is dedicated to supporting the construction of prognostic staging models and performance comparisons among different staging models. Based on the RPA algorithm and log-rank test statistics, autoRPA can establish a decision-making tree from survival data and provide clinicians an intuitive method to further prune the decision tree. Moreover, autoRPA can evaluate the contribution of each submitted covariate that is involved in the grouping process and help identify factors that significantly contribute to cancer staging. Four indicators, including hazard consistency, hazard discrimination, percentage of variation explained, and sample size balance, are introduced to validate the performance of the designed staging models. In addition, autoRPA can also be used to compare the performance of different prognostic staging models using a standard bootstrap evaluation method. The web server of autoRPA is freely available at http://rpa.renlab.org.
Keywords
Cancer staging; Clinical predictive ability; Performance comparison; Recursive partitioning analysis; Web services
Publication
autoRPA: A web server for constructing cancer staging models by recursive partitioning analysis
Yubin Xie,Xiaotong Luo,Huiqin Li,Qingxian Xu,Zhihao He,Qi Zhao,Zhixiang Zuo,Jian RenComputational and Structural Biotechnology Journal. 2019
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Documentation
Recursive Partitioning Analysis (RPA) is one of the most recognized methods for cancer prognosis staging. autoRPA combines RPA strategy and the log-rank test statistics to construct survival decision-making trees. According to their clinical knowledge and experience, users can further prune the survival trees generated by autoRPA in an interactive way.
Performances comparison for staging models
To evaluate and compare among different staging models, autoRPA establish a scoring system for evaluation. The evaluation of performance consists of four widely accepted criteria including hazard consistency, hazard discrimination, percent variance explained (outcome prediction), and sample size balance. To validate the rank of different models, autoRPA performed internal validation using bootstrap methods. To present the evaluation result in a more intuitive way, autoRPA will visualize the performance of all staging models in a radar map.
Statistics, analysis and visualization
The web server will conduct an automatic cancer staging by RPA algorithm and provide an adjustable survival decision-making tree with the help of D3 techniques. Besides, Kaplan-Meier survival curve, radar map, other statistical diagrams and tables are also provided for the evaluation and comparison of the prognosis staging models.
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