Nowadays, clinical decision support system (CDSS) is emerged broadly due to the growth of smart applications. Yet, labeling a massive amount of clinical data is expensive and needs domain expertise. Also, how to design a robust CDSS model in a healthcare platform with a minimal number of annotated clinical data was an essential problem. To tackle this issue, a generative adversarial network (GAN)-based semi-supervised training model was developed, which increases the quantity of annotated data and solves the unbalanced annotated labels. As well, support vector machine (SVM) and K-nearest neighbor (KNN) classifiers were applied as the base learners to predict the label for unannotated data. But, the result from both base learners was not often similar, which impacts the prediction efficiency. So, this article introduces a deep ensemble learner model (DELM) for predicting labels to the unannotated data by stacking multiple machine learning classifiers as base learners. In this model, two levels of prediction: the initial level and the second level. During the initial level, multiple base learners including SVM, KNN, naive bayes (NB) and random forest (RF) learn the dataset with both the annotated and unannotated samples independently to predict the class of the unannotated instances. Then, those prediction outcomes are merged during the second level, which applies the deep neural network (DNN) as an ensemble classifier to get the final predicted class of the unannotated instance. Finally, the experimental results exhibit that the DELM with GAN achieves 86.54 %, 84.83 % and 86.72 % accuracies on SPECT, WDBC and Hallmarks databases, correspondingly, compared to the Fuzzy-AHP+ANN, HTM+LSTM, DBSCAN+SMOTE-ENN+XGBoost and GAN-based semi-supervised models.