Effect of tissue-grouped regulatory variants associated to type 2 diabetes in related secondary outcomes

A novel interpretable deep transfer learning combining diverse learnable parameters for improved T2D prediction based on single-cell gene regulatory networks

Accurate deep learning (DL) models to predict type 2 diabetes (T2D) are concerned not only with targeting the discrimination task but also with learning useful feature representation. However, existing DL tools are far from perfect and do not provide appropriate interpretation as a guideline to explain and promote superior performance in the target task. Therefore, we provide an interpretable approach for our presented deep transfer learning (DTL) models to overcome such drawbacks, working as follows. We utilize several pre-trained models including SEResNet152, and SEResNeXT101. Then, we transfer knowledge from pre-trained models via keeping the weights in the convolutional base (i.e., feature extraction part) while modifying the classification part with the use of Adam optimizer to deal with classifying healthy controls and T2D based on single-cell gene regulatory network (SCGRN) images. Another DTL models work in a similar manner but just with keeping weights of the bottom layers in the feature extraction unaltered while updating weights of consecutive layers through training from scratch. Experimental results on the whole 224 SCGRN images using five-fold cross-validation show that our model (TFeSEResNeXT101) achieving the highest average balanced accuracy (BAC) of 0.97 and thereby significantly outperforming the baseline that resulted in an average BAC of 0.86. Moreover, the simulation study demonstrated that the superiority is attributed to the distributional conformance of model weight parameters obtained with Adam optimizer when coupled with weights from a pre-trained model.