Tensor-DTI: Enhancing Biomolecular Interaction Prediction with Contrastive Embedding Learning

Abstract

Accurate drug-target interaction (DTI) prediction is essential for computational drug discovery, yet existing models often rely on single-modality predefined molecular descriptors or sequence-based embeddings with limited representativeness. We propose Tensor-DTI, a contrastive learning framework that integrates multimodal embeddings from molecular graphs, protein language models, and binding-site predictions to improve interaction modeling. Tensor-DTI employs a siamese dual-encoder architecture, enabling it to capture both chemical and structural interaction features while distinguishing interacting from non-interacting pairs. Evaluations on multiple DTI benchmarks demonstrate that Tensor-DTI outperforms existing sequence-based and graph-based models. We also conduct large-scale inference experiments on CDK2 across billion-scale chemical libraries, where Tensor-DTI produces chemically plausible hit distributions even when CDK2 is withheld from training. In enrichment studies against Glide docking and Boltz-2 co-folder, Tensor-DTI remains competitive on CDK2 and improves the screening budget required to recover moderate fractions of high-affinity ligands on out-of-family targets under strict family-holdout splits. Additionally, we explore its applicability to protein-RNA and peptide-protein interactions. Our findings highlight the benefits of integrating multimodal information with contrastive objectives to enhance interaction-prediction accuracy and to provide more interpretable and reliability-aware models for virtual screening.

Accepted at the Generative and Experimental Perspectives for Biomolecular Design Workshop at ICLR 2025 and at the Learning Meaningful Representations of Life Workshop at ICLR 2025