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Fig. 9 | BMC Bioinformatics

Fig. 9

From: A new method for exploring gene–gene and gene–environment interactions in GWAS with tree ensemble methods and SHAP values

Fig. 9

The model fitting process based on top K features from both the ranking process (for different sets of XGBoost-hyperparameters indicated by the different colours and the legend) and from BOLT-LMM, for different values of K. In a hyperparameter sets 1–8 (all with \(\hbox {max}\_{\mathrm{depth}}=2\)) from Table 4 in the model fitting process are used. In b hyperparameter sets 9–16 (\(\hbox {max}\_{\mathrm{depth}}=3\)) are used. Both figures show that the use of the ranking process gives in general better model performance than for the BOLT-LMM ranking. There is also some gain in performance by increasing the hyperparameter max_depth from two to three

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