Popular Machine Learning Methods Tend to Over-Select Features

Abstract Background: Machine learning methods have been a standard approach to select features that are associated with an outcome and build a prediction model when the number of candidate features is large. Lasso has been one of the most popular approaches to this end. LASSO approach selects features with large regression estimates, rather than based on statistical significance, associating the outcome, while imposing L1-norm penalty to overcome the high dimensionality of the candidate features. As a result, LASSO may select insignificant features while possibly missing significant ones. Furthermore, from our experience, LASSO has been found to select too many features. By selecting features that are not associated with the outcome, we may have to spend more cost to collect and manage them in the future use of a fitted prediction model. Using the combination of L1- and L2-norm penalties, elastic net tends to select more features than LASSO. Results: The overly selected features that are not associated with the outcome play the role of white noise, so that the fitted prediction model loses the prediction accuracy. In this paper, we propose to use the standard regression methods (without any penalizing approach) with stepwise variable selection procedure to overcome these issues. Unlike the machine learning methods, this method selects features based on statistical significance. Through extensive simulations, we show that this maximum likelihood estimation based method selects very small number of features while maintaining a high prediction power, while the machine learning methods make a large number of false selections to result in loss of prediction accuracy. Conclusions: Contrary to the machine learning methods, the regression methods combined with a stepwise variable selection method is a standard statistical method, so that any biostatistician can use it to analyze high dimensional data even without advanced bioinformatics knowledge.