OpenDDI: A Comprehensive Benchmark for DDI Prediction

Drug–Drug Interactions (DDIs) significantly influence therapeutic efficacy and patient safety. As experimental discovery is resource-intensive and time-consuming, efficient computational methodologies have become essential. The predominant paradigm formulates DDI prediction as a drug graph-based link prediction task. However, further progress is hindered by two fundamental challenges: (1) lack of high-quality data: most studies rely on small-scale DDI datasets and single-modal drug representations; (2) lack of standardized evaluation: inconsistent scenarios, varied metrics, and diverse baselines. To address the above issues, we propose OpenDDI, a comprehensive benchmark for DDI prediction. Specifically, (1) from the data perspective, OpenDDI unifies 6 widely used DDI datasets and 2 existing forms of drug representation, while additionally contributing 3 new large-scale LLM-augmented datasets and a new multimodal drug representation covering 5 modalities. (2) From the evaluation perspective, OpenDDI unifies 20 SOTA model baselines across 3 downstream tasks, with standardized protocols for data quality, effectiveness, generalization, robustness, and efficiency. Based on OpenDDI, we conduct a comprehensive evaluation and derive 11 valuable insights for DDI prediction while exposing current limitations to provide critical guidance for this rapidly evolving field. Our code is available at https://anonymous.4open.science/r/anonym1234