LNMGAT: a laplacian regularized pseudo-negative mining graph attention network for robust drug-target interaction...

Computational drug-target interaction (DTI) prediction provides a scalable alternative to costly and time-consuming experimental screening, but its reliability is limited by the scarcity of experimentally verified negative interactions. In public DTI databases, most unobserved drug-target pairs are unlabeled rather than true non-interactions. Randomly treating these unlabeled pairs as negatives can introduce label noise and reduce model reliability, particularly in cold-start scenarios involving unseen drugs or targets. To address this issue, we propose LNMGAT, a LapRLS-guided reliable pseudo-negative mining framework coupled with dual graph attention encoders. Instead of relying on experimentally confirmed negative labels or randomly sampled negatives, LNMGAT first applies Laplacian regularized least squares to drug and target similarity graphs to identify low-confidence unlabeled pairs as reliable pseudo-negatives. Drug and target representations are then learned separately on similarity-based k-nearest-neighbor graphs using graph attention networks, and their embeddings are concatenated for MLP-based interaction prediction. Across Yamanishi, Davis, KIBA, and BindingDB benchmarks, LNMGAT achieved the best AUPR in 10 of 16 evaluation settings and ranked within the top two in 14 of 16 settings. In the 12 cold-start settings, LNMGAT obtained the best AUPR in 9 cases, with absolute AUPR gains over the strongest baseline of up to 0.016 in pair cold-start prediction. External evaluation on DrugBank positive interactions and SwissDock-based molecular docking further provided database-level and in silico support for the plausibility of high-ranked predictions. Nevertheless, the biological validation in this study remains computational and database-based; no wet-lab binding assay was performed. LNMGAT therefore provides a competitive and interpretable framework for DTI prediction under negative-label uncertainty, while further experimental validation is required for its top-ranked candidates.