title: Determining Cutoff Point of Ensemble Trees Based on Sample Size in Predicting Clinical Dose with DNA Microarray Data.
abstract: 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.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.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).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 ofn= 25 as a cutoff point for RT bagging to outperform a single RT.
authors.affiliation: Vocational School of Social Sciences, Hacettepe University, Ankara, Turkey; Department of Biostatistics, Faculty of Medicine, Hacettepe University, Ankara, Turkey.
authors.forename: Selen
authors.identifier: 0000-0002-3725-2987
authors.initials: S
authors.lastname: Yılmaz Isıkhan
authors.affiliation: Department of Biostatistics, Faculty of Medicine, Hacettepe University, Ankara, Turkey.
authors.forename: Erdem
authors.initials: E
authors.lastname: Karabulut
authors.affiliation: Department of Biostatistics, Faculty of Medicine, Hacettepe University, Ankara, Turkey.
authors.forename: Celal Reha
authors.initials: CR
authors.lastname: Alpar
mesh_terms: D000465:Algorithms; D000818:Animals; D001185:Artificial Intelligence; D003198:Computer Simulation; D057225:Data Mining / Q000379:methods; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D023281:Genomics; D006801:Humans; D015233:Models, Statistical; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D004364:Pharmaceutical Preparations; D010597:Pharmacogenetics / Q000379:methods*; D011336:Probability; D051381:Rats; D012044:Regression Analysis; D015203:Reproducibility of Results; D018401:Sample Size; D013045:Species Specificity; D060388:Support Vector Machine; D015003:Yeasts / Q000235:genetics / Q000378:metabolism
chemical_list: D004364:Pharmaceutical Preparations