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With the rapid advancement of deep learning, drug target interaction (DTI) prediction has seen substantial performance enhancements. However, existing methodologies face a critical, yet unaddressed challenge, i.e., the $\textbf{Modality Reliability Gap}$. Such a gap arises from the unpredictable variance in the informativeness and reliability of 1D sequence versus 3D structural data across different drug-target pairs, critically limiting model robustness and domain generalization capabilities. To overcome it, we introduce $\textbf{DrugCMF}$, a novel $\textbf{Drug}$-Target interaction prediction method via $\textbf{C}$onfidence-aware $\textbf{M}$ultimodal $\textbf{F}$usion framework designed specifically to bridge the Modality Reliability Gap. Specifically, the DrugCMF employs a four-stage approach: (1) it extracts rich features by utilizing four pre-trained models to obtain token-level embeddings from both 1D sequences and 3D structures. (2) it preserves modality informativeness by independently learning interaction patterns within each modality through a Token-level Interaction module. (3) it explicitly quantifies the reliability gap by employing a novel confidence estimation mechanism to dynamically learn weights for each modality. (4) it bridges the gap by using these confidence scores to guide a learnable cross-modal fusion module, adaptively fusing information from the most trustworthy source. By methodically addressing the Modality Reliability Gap, DrugCMF significantly outperforms SOTA methods. Extensive experiments demonstrate its superior performance and robustness (Our Code is available in the supplementary materials).
