Effect of hyperparameters on variable selection in random forests

• URL: http://arxiv.org/abs/2309.06943v2
• Date: Sat, 25 Jan 2025 11:32:29 GMT
• Title: Effect of hyperparameters on variable selection in random forests
• Authors: Cesaire J. K. Fouodo, Lea L. Kronziel, Inke R. König, Silke Szymczak,
• Abstract summary: We evaluate the effects on the Vita and Boruta variable selection procedures based on two simulation studies utilizing theoretical distributions and empirical gene expression data. For weakly correlated predictor variables, the default value of the number of splitting variables is optimal, but smaller values of the sample fraction result in larger sensitivity.
• Score: 0.0
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• Abstract: Random forests (RFs) are well suited for prediction modeling and variable selection in high-dimensional omics studies. The effect of hyperparameters of the RF algorithm on prediction performance and variable importance estimation have previously been investigated. However, how hyperparameters impact RF-based variable selection remains unclear. We evaluate the effects on the Vita and the Boruta variable selection procedures based on two simulation studies utilizing theoretical distributions and empirical gene expression data. We assess the ability of the procedures to select important variables (sensitivity) while controlling the false discovery rate (FDR). Our results show that the proportion of splitting candidate variables and the sample fraction for the training dataset influence the selection procedures more than the drawing strategy of the training datasets and the minimal terminal node size. A suitable setting of the RF hyperparameters depends on the correlation structure in the data. For weakly correlated predictor variables, the default value of the number of splitting variables is optimal, but smaller values of the sample fraction result in larger sensitivity. In contrast, the difference in sensitivity of the optimal compared to the default value of sample fraction is negligible for strongly correlated predictor variables, whereas smaller values than the default are better in the other settings. In conclusion, the default values of the hyperparameters will not always be suitable for identifying important variables. Thus, adequate values differ depending on whether the aim of the study is optimizing prediction performance or variable selection.

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