BMC medical research methodology · 2026
A simulation-based comparison of Boruta, LASSO, and Elastic Net for variable selection in logistic regression, with an ovarian cancer miRNA application.
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Arabi Belaghi Reza, Yurekli Hulya, Hamidi Farzaneh, Gilani Neda
Аннотация
BACKGROUND: Variable selection is a central challenge in logistic regression, particularly in high-dimensional biomedical applications where correlated predictors and limited sample sizes complicate reliable identification of relevant variables. This study aims to systematically compare three widely used variable selection approaches - Boruta, LASSO, and Elastic Net - under a range of data-generating conditions and to illustrate their performance using an ovarian cancer miRNA dataset.
METHODS: We conducted a simulation study across 36 logistic regression scenarios varying in sample size, dimensionality, predictor correlation, and effect magnitude. Performance was evaluated using true-positive and false-positive selection rates. In addition, all three methods were applied to a real-world serum miRNA expression dataset, and discriminative performance was assessed using the area under the receiver operating characteristic curve (AUC).
RESULTS: Boruta, Elastic Net, and LASSO exhibited distinct variable selection behaviors across simulation scenarios. Boruta maintained strong true-positive recovery while controlling false positives in most settings, particularly when predictors were highly correlated. Elastic Net consistently achieved high sensitivity but produced comparatively large false-positive rates. LASSO showed the most conservative behavior, recovering fewer true predictors while maintaining low false-positive rates across nearly all scenarios. In the ovarian cancer miRNA application, all three methods achieved similarly strong test-set AUC performance, despite marked differences in the size of the selected biomarker panels.
CONCLUSIONS: The results demonstrate clear trade-offs among the three methods. Boruta offers a favorable balance between sensitivity and specificity in highly correlated settings. Elastic Net prioritizes sensitivity at the cost of increased false discoveries, whereas LASSO provides stricter false-positive control with reduced sensitivity. These findings offer practical guidance for selecting variable selection methods in logistic regression, particularly for high-dimensional biomedical applications.
METHODS: We conducted a simulation study across 36 logistic regression scenarios varying in sample size, dimensionality, predictor correlation, and effect magnitude. Performance was evaluated using true-positive and false-positive selection rates. In addition, all three methods were applied to a real-world serum miRNA expression dataset, and discriminative performance was assessed using the area under the receiver operating characteristic curve (AUC).
RESULTS: Boruta, Elastic Net, and LASSO exhibited distinct variable selection behaviors across simulation scenarios. Boruta maintained strong true-positive recovery while controlling false positives in most settings, particularly when predictors were highly correlated. Elastic Net consistently achieved high sensitivity but produced comparatively large false-positive rates. LASSO showed the most conservative behavior, recovering fewer true predictors while maintaining low false-positive rates across nearly all scenarios. In the ovarian cancer miRNA application, all three methods achieved similarly strong test-set AUC performance, despite marked differences in the size of the selected biomarker panels.
CONCLUSIONS: The results demonstrate clear trade-offs among the three methods. Boruta offers a favorable balance between sensitivity and specificity in highly correlated settings. Elastic Net prioritizes sensitivity at the cost of increased false discoveries, whereas LASSO provides stricter false-positive control with reduced sensitivity. These findings offer practical guidance for selecting variable selection methods in logistic regression, particularly for high-dimensional biomedical applications.