Determining cutoff point of ensemble trees based on sample size in predicting clinical dose with DNA microarray data
Linear regression; mixed models (62J05) Generalized linear models (logistic models) (62J12) Applications of statistics to biology and medical sciences; meta analysis (62P10) Learning and adaptive systems in artificial intelligence (68T05) Pattern recognition, speech recognition (68T10) Medical applications (general) (92C50)
Summary: \textit{Background/Aim}. Evaluating the success of dose prediction based on genetic or clinical data has substantially advanced recently. The aim of this study is to predict various clinical dose values from DNA gene expression datasets using data mining techniques. \textit{Materials and Methods}. Eleven real gene expression datasets containing dose values were included. First, important genes for dose prediction were selected using iterative sure independence screening. Then, the performances of regression trees (RTs), support vector regression (SVR), RT bagging, SVR bagging, and RT boosting were examined. \textit{Results}. The results demonstrated that a regression-based feature selection method substantially reduced the number of irrelevant genes from raw datasets. Overall, the best prediction performance in nine of 11 datasets was achieved using SVR; the second most accurate performance was provided using a gradient-boosting machine (GBM). \textit{Conclusion}. Analysis of various dose values based on microarray gene expression data identified common genes found in our study and the referenced studies. According to our findings, SVR and GBM can be good predictors of dose-gene datasets. Another result of the study was to identify the sample size of \(n = 25\) as a cutoff point for RT bagging to outperform a single RT.
- Survival prediction using gene expression data: a review and comparison
- Empirical characterization of random forest variable importance measures
- Sample size planning for developing classifiers using high-dimensional DNA microarray data
- Trees garrote for regression analysis
- Boosting and microarray data
- Bagging predictors
- Boosting algorithms: regularization, prediction and model fitting
- Out-of-bag estimation of the optimal sample size in bagging
- Stochastic gradient boosting.
- Sure independence screening for ultrahigh dimensional feature space. With discussion and authors' reply
- The elements of statistical learning. Data mining, inference, and prediction
- Using iterated bagging to debias regressions
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