摘要Multifunctional therapeutic peptides (MFTP) hold immense potential in diverse therapeutic contexts, yet their prediction and identification remain challenging due to the limitations of traditional methodologies, such as extensive training durations, limited sample sizes, and inadequate generalization capabilities. To address these issues, we present AMHF-TP, an advanced method for MFTP recognition that utilizes attention mechanisms and multi-granularity hierarchical features to enhance performance. The AMHF-TP is composed of four key components: a migration learning module that leverages pretrained models to extract atomic compositional features of MFTP sequences; a convolutional neural network and self-attention module that refine feature extraction from amino acid sequences and their secondary structures; a hypergraph module that constructs a hypergraph for complex similarity representation between MFTP sequences; and a hierarchical feature extraction module that integrates multimodal peptide sequence features. Compared with leading methods, the proposed AMHF-TP demonstrates superior precision, accuracy, and coverage, underscoring its effectiveness and robustness in MFTP recognition. The comparative analysis of separate hierarchical models and the combined model, as well as with five contemporary models, reveals AMHF-TP’s exceptional performance and stability in recognition tasks.