Deep Features from Pretrained Networks Do Not Outperform Hand-Crafted Features in Radiomics

In radiomics, utilizing features extracted from pretrained deep networks could result in models with a higher predictive performance than those relying on hand-crafted features. This study compared the predictive performance of models trained with either deep features, hand-crafted features, or a combination of these features in terms of the area under the receiver-operating characteristic curve (AUC) and other metrics. We trained models on ten radiological datasets using five feature selection methods and three classifiers. Our results indicate that models based on deep features did not show an improved AUC compared to those utilizing hand-crafted features (deep: AUC 0.775, hand-crafted: AUC 0.789; p = 0.28). Including morphological features alongside deep features led to overall improvements in prediction performance for all models (+0.02 gain in AUC; p < 0.001); however, the best model did not benefit from this (+0.003 gain in AUC; p = 0.57). Using all hand-crafted features in addition to the deep features resulted in a further overall improvement (+0.034 in AUC; p < 0.001), but only a minor improvement could be observed for the best model (deep: AUC 0.798, hand-crafted: AUC 0.789; p = 0.92). Furthermore, our results show that models based on deep features extracted from networks pretrained on medical data have no advantage in predictive performance over models relying on features extracted from networks pretrained on ImageNet data. Our study contributes a benchmarking analysis of models trained on hand-crafted and deep features from pretrained networks across multiple datasets. It also provides a comprehensive understanding of their applicability and limitations in radiomics. Our study shows, in conclusion, that models based on features extracted from pretrained deep networks do not outperform models trained on hand-crafted ones.