DL-TCNN: Deep Learning-based Temporal Convolutional Neural Network for prediction of conformational B-cell epitopes

Prediction of conformational B-cell epitopes (CBCE) is an essential phase for vaccine design, drug invention, and accurate disease diagnosis. Many laboratorial and computational approaches have been developed to predict CBCE. However, laboratorial experiments are costly and time consuming, leading to the popularity of Machine Learning (ML)-based computational methods. Although ML methods have succeeded in many domains, achieving higher accuracy in CBCE prediction remains a challenge. To overcome this drawback and consider the limitations of ML methods, this paper proposes a novel DL-based framework for CBCE prediction, leveraging the capabilities of deep learning in the medical domain. The proposed model is named Deep Learning-based Temporal Convolutional Neural Network (DL-TCNN), which hybridizes empirical hyper-tuned 1D-CNN and TCN. TCN is an architecture that employs causal convolutions and dilations, adapting well to sequential input with extensive receptive fields. To train the proposed model, physicochemical features are firstly extracted from antigen sequences. Next, the Synthetic Minority Oversampling Technique (SMOTE) is applied to address the class imbalance problem. Finally, the proposed DL-TCNN is employed for the prediction of CBCE. The model’s performance is evaluated and validated on a benchmark antigen–antibody dataset. The DL-TCNN achieves 94.44% accuracy, and 0.989 AUC score for the training dataset, 78.53% accuracy, and 0.661 AUC score for the validation dataset; and 85.10% accuracy, 0.855 AUC score for the testing dataset. The proposed model outperforms all the existing CBCE methods.