@inproceedings{meng-etal-2025-fusiondti,
    title = "{F}usion{DTI}: Fine-grained Binding Discovery with Token-level Fusion for Drug-Target Interaction",
    author = "Meng, Zhaohan  and
      Meng, Zaiqiao  and
      Yuan, Ke  and
      Ounis, Iadh",
    editor = "Christodoulopoulos, Christos  and
      Chakraborty, Tanmoy  and
      Rose, Carolyn  and
      Peng, Violet",
    booktitle = "Findings of the Association for Computational Linguistics: EMNLP 2025",
    month = nov,
    year = "2025",
    address = "Suzhou, China",
    publisher = "Association for Computational Linguistics",
    url = "https://preview.aclanthology.org/author-page-yu-wang-polytechnic/2025.findings-emnlp.237/",
    doi = "10.18653/v1/2025.findings-emnlp.237",
    pages = "4425--4444",
    ISBN = "979-8-89176-335-7",
    abstract = "Predicting drug-target interaction (DTI) is critical in the drug discovery process. Despite remarkable advances in recent DTI models through the integration of representations from diverse drug and target encoders, such models often struggle to capture the fine-grained interactions between drugs and protein, i.e. the binding of specific drug atoms (or substructures) and key amino acids of proteins, which is crucial for understanding the binding mechanisms and optimising drug design. To address this issue, this paper introduces a novel model, called FusionDTI, which uses a token-level **Fusion** module to effectively learn fine-grained information for **D**rug-**T**arget **I**nteraction. In particular, our FusionDTI model uses the SELFIES representation of drugs to mitigate sequence fragment invalidation and incorporates the structure-aware (SA) vocabulary of target proteins to address the limitation of amino acid sequences in structural information, additionally leveraging pre-trained language models extensively trained on large-scale biomedical datasets as encoders to capture the complex information of drugs and targets. Experiments on three well-known benchmark datasets show that our proposed FusionDTI model achieves the best performance in DTI prediction compared with eight existing state-of-the-art baselines. Furthermore, our case study indicates that FusionDTI could highlight the potential binding sites, enhancing the explainability of the DTI prediction."
}