An Integrated TCN-CrossMHA Model for Predicting circRNA-RBP Binding Sites

Circular RNA (circRNA) has the capacity to bind with RNA binding protein (RBP), thereby exerting a substantial impact on diseases. Predicting binding sites aids in comprehending the interaction mechanism, thereby offering insights for disease treatment strategies. Here, we propose a novel approach based on temporal convolutional network (TCN) and cross multi-head attention mechanism to predict circRNA-RBP binding sites (circTCA). First, we employ two distinct encoding methodologies to obtain two raw matrices of circRNA sequences. Then, two parallel TCN blocks extract shallow and abstract features of the two matrices separately. The fusion of the two is achieved through cross multi-head attention mechanism and after this, global expectation pooling assigns weights to the concatenated feature. Finally, the task of classifying the input sequence is entrusted to a fully connected (FC) layer. We compare circTCA with other five methods and conduct ablation experiments to demonstrate its effectiveness. We also conduct feature visualization and assess the motifs extracted by circTCA with existing motifs. All in all, circTCA is effective for binding sites prediction of circRNA and RBP.