A Balanced Accuracy Fitness Function Leads to Robust Analysis using Grammatical Evolution Neural Networks in the Case of Class Imbalance.

Grammatical Evolution Neural Networks (GENN) is a computational method designed to detect gene-gene interactions in genetic epidemiology, but has so far only been evaluated in situations with balanced numbers of cases and controls. Real data, however, rarely has such perfectly balanced classes. In the current study, we test the power of GENN to detect interactions in data with a range of class imbalance using two fitness functions (classification error and balanced error), as well as data re-sampling. We show that when using classification error, class imbalance greatly decreases the power of GENN. Re-sampling methods demonstrated improved power, but using balanced accuracy resulted in the highest power. Based on the results of this study, balanced error has replaced classification error in the GENN algorithm.